Long considered a failure, second-order symmetry-adapted perturbation theory (SAPT) based on Kohn-Sham orbitals, or SAPT0(KS), can be resurrected for semiquantitative purposes using long-range corrected density functionals whose asymptotic behavior is adjusted separately for each monomer. As in other contexts, correct asymptotic behavior can be enforced via „optimal tuning” based on the ionization energy theorem of density functional theory, but the tuning procedure is tedious, expensive for large systems, and comes with a troubling dependence on system size. Here, we show that essentially identical results are obtained using a fast, convenient, and automated tuning procedure based on the size of the exchange hole. In conjunction with „extended” (X)SAPT methods that improve the description of dispersion, this procedure achieves benchmark-quality interaction energies, along with the usual SAPT energy decomposition, without the hassle of system-specific tuning.Gold is the most inert metal and does not form a bulk hydride. However, gold becomes chemically active in the nanometer scale and gold nanoparticles have been found to exhibit important catalytic properties. Here, we report the synthesis and characterization of a highly stable ligand-protected gold hydride nanocluster, [Au22H3(dppee)7]3+ [dppee = bis(2-diphenylphosphino) ethyl ether]. A synthetic method is developed to obtain high purity samples of the gold trihydride nanocluster with good yields. The properties of the new hydride cluster are characterized with different experimental techniques, as well as theoretical calculations. Solid samples of [Au22H3(dppee)7]3+ are found to be stable under ambient conditions. Both experimental evidence and theoretical evidence suggest that the Au22H3 core of the [Au22H3(dppee)7]3+ hydride nanocluster consists of two Au11 units bonded via two triangular faces, creating six uncoordinated Au sites at the interface. The three H atoms bridge the six uncoordinated Au atoms at the interface. The Au11 unit behaves as an eight-electron trivalent superatom, forming a superatom triple bond (Au11 ≡ Au11) in the [Au22H3(dppee)7]3+ trihydride nanocluster assisted by the three bridging H atoms.A synchrotron-based vacuum ultraviolet (VUV) absorption spectrum of norbornadiene (NBD) is reported, and the extensive vibrational structure obtained has been analyzed. The previously known 5b13s-Rydberg state has been reinterpreted by comparison with our recent high-resolution photoelectron spectral analysis of the X2B1 ionic state. Additional vibrational details in the region of this Rydberg state are observed in its VUV spectrum when compared with the photoelectron 2B1 ionic state; this is attributed to the underlying valence state structure in the VUV. Valence and Rydberg state energies have been obtained by configuration interaction and time-dependent density functional theoretical methods. Several low-lying singlet valence states, especially those that arise from ππ* excitations, conventionally termed NV1 to NV4, have been examined in detail. Their Franck-Condon (FC) and Herzberg-Teller (HT) profiles have been investigated and fitted to the VUV spectrum. Estimates of the experimental 00 band positions have been made from these fits. The anomaly of the observed UV absorption by the 1A2 state of NBD is attributed to HT effects. Generally, the HT components are less than 10% of the FC terms. The calculated 5b13s lowest Rydberg state also shows a low level of HT components. The observed electron impact spectra of NBD have been analyzed in detail in terms of triplet states.Macromolecular crowding is a feature of cellular and cell-free systems that, through depletion effects, can impact the interactions of semiflexible biopolymers with surfaces. In this work, we use computer simulations to study crowding-induced adsorption of semiflexible polymers on otherwise repulsive surfaces. Crowding particles are modeled explicitly, and we investigate the interplay between the bending stiffness of the polymer and the volume fraction and size of crowding particles. Adsorption to flat surfaces is promoted by stiffer polymers, smaller crowding particles, and larger volume fractions of crowders. We characterize transitions from non-adsorbed to partially and strongly adsorbed states as a function of bending stiffness. The crowding-induced transitions occur at smaller values of the bending stiffness as the volume fraction of crowders increases. Concomitant effects on the size and shape of the polymer are reflected by crowding- and stiffness-dependent changes to the radius of gyration. For various polymer lengths, we identify a critical crowding fraction for adsorption and analyze its scaling behavior in terms of polymer stiffness. We also consider crowding-induced adsorption in spherical confinement and identify a regime in which increasing the bending stiffness induces desorption. The results of our simulations shed light on the interplay of crowding and bending stiffness on the spatial organization of biopolymers in encapsulated cellular and cell-free systems.The templated assembly of nanoparticles has been limited so far to yield only discontinuous nanoparticle clusters confined within lithographically patterned cavities. Here, we explored the templated assembly of nanoparticles into continuous 2D structures, using lithographically patterned templates with topographical features sized as the assembled nanoparticles. We found that these features act as nucleation centers, whose exact arrangement determines four possible assembly regimes (i) rotated, (ii) disordered, (iii) closely packed, and (iv) unpacked. These regimes produce structures strikingly different from their geometry, orientation, long-range and short-range orders, and packing density. Interestingly, for templates with relatively distant nucleation centers, these four regimes are replaced with three new ones, which produce large monocrystalline domains that are either (i) uniformly rotated, (ii) uniformly aligned, or (iii) nonuniformly rotated relative to the nucleation lattice. We rationalized our experimental data using a mathematical model, which examines all the alignment possibilities between the nucleation centers and the ideal hexagonal assembly. Our finding provides a new approach for the à la carte obtainment of various nanoscale structures unachievable by natural self-assembly and opens a route for the fabrication of numerous functional nanodevices and nanosystems that could not be realized so far by the standard bottom-up approach.Full details on the design, development, and successful implementation of suitable synthetic strategies directed toward the total synthesis of iso-archazolids and archazologs are reported. Both a biomimetic and a multistep total synthesis of iso-archazolid B, the most potent and least abundant archazolid, are described. The bioinspired conversion from archazolid B was realized by a high-yielding 1,8-Diazabicyclo[5.4.0]undec-7-ene catalyzed one-step double-bond shift. A highly stereoselective total synthesis was accomplished in 25 steps, involving a sequence of highly stereoselective aldol reactions, an efficient aldol condensation to forge two elaborate fragments, and a challenging ring-closing metathesis macrocyclization with an unusual Stewart-Grubbs catalyst. These strategies proved to be generally useful and could be successfully implemented for the preparation of three novel iso-archazolids as well as five novel archazologs, lacking the thiazole side chain. A wide variety of further archazolids and archazologs may now be targeted for exploration of the promising anticancer potential of these polyketide macrolides.Cellular oxidative thymines, 5-hydroxymethyluracil (5hmU) and 5-formyluracil (5fU), are found in the genomes of a diverse range of organisms, the distribution of which profoundly influence biological processes and living systems. However, the distribution of cellular oxidative thymines has not been explored because of lacking both specific bioorthogonal labeling and sensitivity methods for single-cell analysis. Herein, we report a bioorthogonal chemical signature enabling amplified visualization of cellular oxidative thymines in single cells. The synthesized ATP-γ-alkyne, an ATP analogue with bioorthogonal tag modified on γ-phosphate can be specifically linked to cellular 5hmU by chemoenzymatic labeling. DNA with 5-alkynephosphomethyluracil were then clicked with azide (N3)-modified 5hmU-primer. Identification of 5fU is based on selective reduction from 5fU to 5hmU, subsequent chemoenzymatic labeling of the newly generated 5hmU, and cross-linking with N3-modified 5fU-primer via click chemistry. Then, all of the 5hmU and 5fU sites are encoded with respective circularized barcodes. These barcodes are simultaneously amplified for multiplexed single-molecule imaging. The above two kinds of barcodes can be simultaneously amplified for differentiated visualization of 5hmU and 5fU in single cells. We find these two kinds of cellular oxidative thymines are spatially organized in a cell-type-dependent style with cell-to-cell heterogeneity. We also investigate their multilevel subcellular information and explore their dynamic changes during cell cycles. Further, using DNA sequencing instead of fluorescence imaging, our proposed bioorthogonal chemical signature holds great potential to offer the sequence information of these oxidative thymines in cells and may provide a reliable chemical biology approach for studying the whole-genome oxidative thymines profiles and insights into their functional role and dynamics in biology.In this paper, we applied an innovative nuclear magnetic resonance (NMR)-guided screening and ligand design approach, named focused high-throughput screening by NMR (fHTS by NMR), to derive potent, low-molecular-weight ligands capable of mimicking interactions elicited by ephrin ligands on the receptor tyrosine kinase EphA4. The agents bind with nanomolar affinity, trigger receptor activation in cellular assays with motor neurons, and provide remarkable motor neuron protection from amyotrophic lateral sclerosis (ALS) patient-derived astrocytes. Structural studies on the complex between EphA4 ligand-binding domain and a most active agent provide insights into the mechanism of the agents at a molecular level. Together with preliminary in vivo pharmacology studies, the data form a strong foundation for the translation of these agents for the treatment of ALS and potentially other human diseases.Anthraquinone-fused enediynes (AQEs) are renowned for their distinctive molecular architecture, reactive enediyne warhead, and potent anticancer activity. Although the first members of AQEs, i.e., dynemicins, were discovered three decades ago, how their nitrogen-containing carbon skeleton is synthesized by microbial producers remains largely a mystery. In this study, we showed that the recently discovered sungeidine pathway is a „degenerative” AQE pathway that contains upstream enzymes for AQE biosynthesis. Retrofitting the sungeidine pathway with genes from the dynemicin pathway not only restored the biosynthesis of the AQE skeleton but also produced a series of novel compounds likely as the cycloaromatized derivatives of chemically unstable biosynthetic intermediates. The results suggest a cascade of highly surprising biosynthetic steps leading to the formation of the anthraquinone moiety, the hallmark C8-C9 linkage via alkyl-aryl cross-coupling, and the characteristic epoxide functionality. The findings provide unprecedented insights into the biosynthesis of AQEs and pave the way for examining these intriguing biosynthetic enzymes.Although liquid chromatography-tandem mass spectrometry (LC-MS/MS) equipped with electrospray ionization (ESI) is widely employed for metabolite analysis, substituted phenethylamines commonly undergo fragmentation during ESI in-source collision-induced dissociation (CID). Unexpected fragmentation hampers not only unambiguous identification but also accurate metabolite quantification. ESI in-source CID induces N-Cα bond dissociation in substituted phenethylamines lacking a β-hydroxy group to produce fragment ions with a spiro[2.5]octadienylium motif. In contrast, phenethylamines with a β-hydroxy group generate substituted 2-phenylaziridium through ESI in-source CID-induced H2O loss. The fragment ion yield produced by ESI in-source CID can be estimated by the dissociation rate constant and internal energy of the analyte ion, determined by employing density functional theory calculations and the survival yield method using a thermometer ion, respectively. Fragmentation is strongly enhanced by the presence of an β-hydroxy group, whereas N-methylation suppresses fragmentation. In particular, octopamine and noradrenaline, which contain an β-hydroxy and primary amine groups, produce more intense fragment ion signals than protonated molecules. Regarding the quantitative analysis of phenethylamines present in the mouse brain, the noradrenaline fragment ion used as the precursor in multiple reaction monitoring (MRM) provided a higher signal-to-noise ratio in the resulting spectra than protonated noradrenaline. The present method allows for the quantitative analysis of substituted phenethylamines with high sensitivity.Methiozolin is a novel herbicide used to control annual bluegrass. It has low vapor pressure and high hydrophobicity, which could result in persistence in water and bioaccumulation. We measured the bioconcentration factors (BCFs) of methiozolin in ricefish (Oryzias latipes). Two radiolabels were used to quantify the parent compound and identify its metabolites. Ricefish were exposed to 2.0 and 20.0 ng/L methiozolin for 28 days in the uptake phase with a 96-h LC50 of 2.2 mg/L(95% confidence limit 2.1-2.5 mg/L) and water solubility of 4.2 mg/L after 48 h was observed. On the basis of total radioactivity residues (TRRs), BCFss and BCFk values of 797.0-851.9 and 992.9-1077.4 were observed, respectively, while BCFss values for methiozolin were 251.9-257.5. Several minor metabolites with TRR less then 3.4% were detected. Among them, 4-(2,6-difluorobenzyloxy-methyl)-3-hydroxy-3-methyl-1-(3-methylthiophen-2-yl)butan-1-one, 2,6-difluorobenzyl alcohol, and 4,5-dihydro-5-methyl-3-(3-methylthiophen-2-yl)isoxazol-5-yl)methanol were identified. Methiozolin is metabolized into numerous minor metabolites with potentially low bioaccumulation capacity in ricefish. These findings can facilitate risk assessments regarding methiozolin use, particularly its movements and final stages in aquatic environments.Understanding the comparative oxidative abilities of high-valent metal-oxo/hydroxo/hydroperoxo species holds the key to robust biomimic catalysts that perform desired organic transformations with very high selectivity and efficiency. The comparative oxidative abilities of popular high-valent iron-oxo and manganese-oxo species are often counterintuitive, for example, oxygen atom transfer (OAT) reaction by [(Me2EBC)MnIV-OOH]3+, [(Me2EBC)MnIV-OH]3+, and [(Me2EBC)MnIV═O]2+ (Me2EBC = 4,11-dimethyl-1,4,8,11-tetraazabicyclo[6.6.2]hexadecane) shows extremely high reactivity for MnIV-OOH species and no reactivity for MnIV-OH and MnIV═O species toward alkyl/aromatic sulfides. Using a combination of density functional theory (DFT) and ab initio domain-based local pair natural orbital coupled-cluster with single, double, and perturbative triples excitation (DLPNO-CCSD(T)) and complete-active space self-consistent field/N-electron valence perturbation theory second order (CASSCF/NEVPT2) calculations, here, we have explored the electronic structures and sulfoxidation mechanism of these species. Our calculations unveil that MnIV-OOH reacts through distal oxygen atom with the substrate via electron transfer (ET) mechanism with a very small kinetic barrier (16.5 kJ/mol), placing this species at the top among the best-known catalysts for such transformations. The MnIV-OH and MnIV═O species have a much larger barrier. The mechanism has also been found to switch from ET in the former to concerted in the latter, rendering both unreactive under the tested experimental conditions. Intrinsic differences in the electronic structures, such as the presence and absence of the multiconfigurational character coupled with the steric effects, are responsible for such variations observed. This comparative oxidative ability that runs contrary to the popular iron-oxo/hydroperoxo reactivity will have larger mechanistic implications in understanding the reactivity of biomimic catalysts and the underlying mechanisms in PSII.Violent inflammation has impeded worry-free application of polypropylene (PP) hernia meshes. Efficient anti-inflammatory coatings are urgently needed to alter the situation. Here, we present a zipper-like, two-layer coating with an intermediate antioxidant layer (I) and an outer antifouling layer (II) to endow PP meshes with synergistic anti-inflammatory effects. The controllable antioxidant ability of layer I was obtained by modulating the assembly cycle of the metal-phenolic network (MPN) composed of tannic acid (TA) and Fe3+. Polyzwitterionic (PMAD) brush-based layer II was generated upon multiple interactions between the catechol side groups of PMAD and layer I. To consolidate the entire assembly architecture, aryloxy radical coupling was initiated through alkali-catalyzed oxidation. The reaction is similar to a „zipping up” process to construct covalent bonds in the I-II interface and layer I by coupling adjacent catechol groups, which facilely achieved grafting and cross-linking. The obtained coating (PMAD-TA/Fe) did not affect the original properties of the PP mesh and remained stable during cyclic tensile testing or degradation. Most importantly, the excellent antioxidant and antifouling capacities enabled PMAD-TA/Fe-PP to exhibit desirable anti-inflammatory effects and reduce collagen deposition when compared with the bare material. The synergistic anti-inflammatory coating eliminates a major hindrance in the design of biocompatible meshes, and its potential application in developing medical implants with low immunogenicity is promising.The development of inhibitors that can effectively mitigate the amyloidogenesis of human islet amyloid polypeptide (hIAPP), which is linked to type II diabetes, remains a great challenge. Oligotyrosines are intriguing candidates in that they can block the hIAPP aggregation through multiplex phenol-hIAPP interactions. However, oligotyrosines containing too many tyrosine units (larger than three) may fail to inhibit amyloidogenesis due to their increased hydrophobicity and strong self-aggregation propensity. In this work, we developed a strategy to hierarchically vitalize oligotyrosines in mitigating hIAPP amyloidogenesis. Tetratyrosine YYYY (4Y) was grafted into the third complementary-determining region (CDR3) of a parent nanobody to construct a sequence-programmed nanobody N4Y, in which the conformation of the grafted 4Y fragment was constrained for a significantly enhanced binding affinity with hIAPP. We next conjugated N4Y to a polymer to approach a secondary vitalization of 4Y through a multivalent effect. The in vitro and in vivo experiments validated that the resulting PDN4Y could completely inhibit the hIAPP amyloidogenesis at low stoichiometric concentrations and effectively suppress the generation of toxic reactive oxygen species and alleviate amyloidogenesis-mediated damage to INS-1 cells and zebrafish (Danio rerio) embryos. The hierarchical vitalization of 4Y via a synergistic conformation restraint and multivalent effect represents a strategic prototype of boosting the efficacy of peptide-based amyloidogenesis inhibitors, especially those with a high hydrophobicity and strong aggregation tendency, which holds great promise for future translational studies.Optimizing the molecular structures of organic solar cell (OSC) materials and boosting the power conversion efficiencies are the eternal theme in the solar energy region. A series of fused benzotriazole (BTA)-based A-DA’D-A structures of nonfullerene acceptors (such as Y18) were developed for application in efficient OSCs, in which high quantum efficiencies and low voltage losses could be achieved because of the optimized electron-deficient core and specific molecular geometry. Here, based on the BTA core, the bulky alkyl chain on the BTA unit was further tailored to minimize the lateral alkyl chains and enhance the crystallinity while maintaining an adequate solubility. The resulting NFAs of BTA-C1, BTA-C5, and BTA-C6 are synthesized. Compared with the well-designed molecular Y18 (BTA-C8), we found that simply replacing the 2-ethylhexyl chain with a single methyl (BTA-C1) can easily improve the fill factor up to 77%, but its poor light absorption capacity and large domain size impeded further efficiency improvement. In particular, the BTA-C5, with a shortened branch alkyl chain of 2-methylbutyl, achieves suitable solubility and enhanced crystallinity. Significantly, owing to the balanced charge carrier mobility and suitable phase separation, the BTA-C5-based binary single-junction OSCs achieve a high efficiency of 17.11%, which is one of the top values in BTA-based OSCs.Long residence time enzyme inhibitors with a two-step binding mechanism are characterized by a high internal energy barrier for target association. This raises the question of whether optimizing residence time via further increasing this internal energy barrier would inevitably lead to insufficient target occupancy in vivo due to slow, time-dependent binding. We attempted to address this question during optimization of cyclooxygenase-2 (COX-2) inhibitors. Defining long residence time drugs with acceptable association and dissociation rate constants required for sufficient target occupancy and sustained efficacy, which we termed „balanced internal energetics”, provides an important criterion for successful progression during lead optimization. Despite the advancement of several COX-2 inhibitors to marketed drugs, their detailed inhibition kinetics have been surprisingly limiting especially during the structure-activity relationship process mainly due to the lack of robust kinetic assays. Herein, we describe a reoptimized COX enzymatic assay and a novel MS-based assay enabling detailed mechanistic studies for identifying long residence time COX-2 inhibitors with balanced internal energetics. These efforts led to the discovery of promising leads possessing dissociation half-lives of ≤40 h, much greater than the values of 6 and 0.71 h for two marketed drugs, etoricoxib and celecoxib, respectively. Importantly, the inhibition rate constants remain comparable to those of the marketed drugs and above the lower limits set by the criteria of balanced internal energetics, predicting sufficient target occupancy required for efficacy. Taken together, this study demonstrates the feasibility of increasing the internal energy barrier as a viable approach for lead optimization toward discovering long residence time drug candidates.The electrode drying process is a crucial step in the manufacturing of lithium-ion batteries and can significantly affect the performance of an electrode once stacked in a cell. High drying rates may induce binder migration, which is largely governed by the temperature. Additionally, elevated drying rates will result in a heterogeneous distribution of the soluble and dispersed binder throughout the electrode, potentially accumulating at the surface. The optimized drying rate during the electrode manufacturing process will promote balanced homogeneous binder distribution throughout the electrode film; however, there is a need to develop more informative in situ metrologies to better understand the dynamics of the drying process. Here, ultrasound acoustic-based techniques were developed as an in situ tool to study the electrode drying process using NMC622-based cathodes and graphite-based anodes. The drying dynamic evolution for cathodes dried at 40 and 60 °C and anodes dried at 60 °C were investigated, with the attenuation of the reflective acoustic signals used to indicate the evolution of the physical properties of the electrode-coating film. The drying-induced acoustic signal shifts were discussed critically and correlated to the reported three-stage drying mechanism, offering a new mode for investigating the dynamic drying process. Ultrasound acoustic-based measurements have been successfully shown to be a novel in situ metrology to acquire dynamic drying profiles of lithium-ion battery electrodes. The findings would potentially fulfil the research gaps between acquiring dynamic data continuously for a drying mechanism study and the existing research metrology, as most of the published drying mechanism research studies are based on simulated drying processes. It shows great potential for further development and understanding of the drying process to achieve a more controllable electrode manufacturing process.Direct-infusion nanoelectrospray ionization high-resolution mass spectrometry (DI-nESI-HRMS) is an alternative approach to chromatography-MS-based techniques for nontargeted metabolomics, offering a high sample throughout. However, its annotation accuracy of analytes is still full of challenges. In this study, we proposed a strategy for the annotation and quantitation of nontargeted metabolomic data using a spectral-stitching DI-nESI-HRMS with data-independent acquisition. The metabolite annotation strategy included the isotopic distribution, MS/MS spectrum similarity, and precursor and product ion correlation as well as matching of the extracted metabolite features along with the targeted metabolite precursors. Two groups of mixed standard solutions containing 40 and 79 metabolites were, respectively, used to establish the metabolite annotation strategy and validate its reliability. The results showed that the detected standards could be well annotated at top three explanations and total qualitative percentages were 100% (40 of 40) for the standard solution and 94.9% (74 of 78) for the standards spiked into the serum matrix. The intensity of the precursor ions was used for quantitation except for isomers, which were quantified by the intensities of the characteristic product ions if available. Finally, the strategy was applied to study serum metabolomics in diabetes, and the results demonstrated that it is promising for a large-scale cohort metabolomic study.Cylindrical microlens arrays (CMLAs) play a key role in many optoelectronic devices, and 100% fill-factor CMLAs also have the advantage of improving the signal-to-noise ratio and avoiding stray-light effects. However, the existing preparation technologies are complicated and costly, which are not suitable for mass production. Herein, we propose a simple, efficient, and low-cost manufacturing method for CMLAs with a high fill-factor via the electric-field-driven (EFD) microscale 3D printing of polydimethylsiloxane (PDMS). By adjusting the printing parameters, the profile and the fill-factor of the CMLAs can be controlled to improve their optical performance. The optical performance test results show that the printed PDMS CMLAs have good image-projecting and light-diffraction properties. Using the two printing modes of this EFD microscale 3D-printing technology, a cylindrical dual-microlens array with a double-focusing function is simply prepared. At the same time, we print a series of specially shaped microlenses, proving the flexible manufacturing capabilities of this technology. The results show that the prepared CMLAs have good morphology and optical properties. The proposed method may provide a viable route for manufacturing large-area CMLAs with 100% fill-factor in a very simple, efficient, and low-cost manner.

Pirfenidone slows the progression of idiopathic pulmonary fibrosis (IPF). We investigated its efficacy and safety in terms of dose and disease severity in real-world patients with IPF.

This multicenter retrospective cohort study investigated 338 patients treated with pirfenidone between July 2012 and March 2018. Demographics, pulmonary function, mortality, and pirfenidone-related adverse events were also investigated. Efficacy was analyzed according to pirfenidone dose and disease severity using linear mixed-effects models to assess the annual decline rate of forced vital capacity (FVC) and diffusing capacity of the lungs for carbon monoxide (DLCO).

The mean %FVCpredicted and %DLCOpredicted values were 72.6% ± 13.1% and 61.4% ± 17.9%, respectively. The mean duration of pirfenidone treatment was 16.1 ± 9.0 months. In the standard dose (1,800 mg/day) group, the mean %FVCpredicted was -6.56% (95% confidence interval [CI], -9.26 to -3.87) per year before, but -4.43% (95% CI, -5.87 to -3.00) per year after treatment with pirfenidone. In the non-standard lower dose group, the mean %FVCpredicted was -4.96% (95% CI, -6.82 to -3.09) per year before, but -1.79% (95% CI, -2.75 to -0.83) per year after treatment with pirfenidone. The FVC decline rate was significantly reduced, regardless of the Gender-Age-Physiology (GAP) stage. Adverse events and mortality were similar across dose groups; however, they were more frequent in GAP stages II-III than in the stage I group.

The effect of pirfenidone on reducing disease progression of IPF persisted even with a consistently lower dose of pirfenidone.

The effect of pirfenidone on reducing disease progression of IPF persisted even with a consistently lower dose of pirfenidone.Identifying relationships between genetic variations and their clinical presentations has been challenged by the heterogeneous causes of a disease. It is imperative to unveil the relationship between the high-dimensional genetic manifestations and the clinical presentations, while taking into account the possible heterogeneity of the study subjects.We proposed a novel supervised clustering algorithm using penalized mixture regression model, called component-wise sparse mixture regression (CSMR), to deal with the challenges in studying the heterogeneous relationships between high-dimensional genetic features and a phenotype. The algorithm was adapted from the classification expectation maximization algorithm, which offers a novel supervised solution to the clustering problem, with substantial improvement on both the computational efficiency and biological interpretability. Experimental evaluation on simulated benchmark datasets demonstrated that the CSMR can accurately identify the subspaces on which subset of features are explanatory to the response variables, and it outperformed the baseline methods. Application of CSMR on a drug sensitivity dataset again demonstrated the superior performance of CSMR over the others, where CSMR is powerful in recapitulating the distinct subgroups hidden in the pool of cell lines with regards to their coping mechanisms to different drugs. CSMR represents a big data analysis tool with the potential to resolve the complexity of translating the clinical representations of the disease to the real causes underpinning it. We believe that it will bring new understanding to the molecular basis of a disease and could be of special relevance in the growing field of personalized medicine.Emerging evidence indicates that the abnormal expression of miRNAs involves in the evolution and progression of various human complex diseases. Identifying disease-related miRNAs as new biomarkers can promote the development of disease pathology and clinical medicine. However, designing biological experiments to validate disease-related miRNAs is usually time-consuming and expensive. Therefore, it is urgent to design effective computational methods for predicting potential miRNA-disease associations. Inspired by the great progress of graph neural networks in link prediction, we propose a novel graph auto-encoder model, named GAEMDA, to identify the potential miRNA-disease associations in an end-to-end manner. More specifically, the GAEMDA model applies a graph neural networks-based encoder, which contains aggregator function and multi-layer perceptron for aggregating nodes’ neighborhood information, to generate the low-dimensional embeddings of miRNA and disease nodes and realize the effective fusion of heterogeneous information. Then, the embeddings of miRNA and disease nodes are fed into a bilinear decoder to identify the potential links between miRNA and disease nodes. The experimental results indicate that GAEMDA achieves the average area under the curve of $93.56\pm 0.44\%$ under 5-fold cross-validation. Besides, we further carried out case studies on colon neoplasms, esophageal neoplasms and kidney neoplasms. As a result, 48 of the top 50 predicted miRNAs associated with these diseases are confirmed by the database of differentially expressed miRNAs in human cancers and microRNA deregulation in human disease database, respectively. The satisfactory prediction performance suggests that GAEMDA model could serve as a reliable tool to guide the following researches on the regulatory role of miRNAs. Besides, the source codes are available at https//github.com/chimianbuhetang/GAEMDA.

This study aimed to investigate whether everolimus (EVR) affects long-term survival after liver transplantation (LT) in patients with hepatocellular carcinoma (HCC).

The data from 303 consecutive patients with HCC who had undergone LT from January 2012 to July 2018 were retrospectively reviewed. The patients were divided into two groups 1) patients treated with EVR in combination with calcineurin inhibitors (CNIs) (EVR group; n=114) and 2) patients treated with CNI-based therapy without EVR (Non-EVR group; n=189). Time to recurrence (TTR) and overall survival (OS) after propensity score (PS) matching were compared between the groups, and prognostic factors for TTR and OS were evaluated.

The EVR group exhibited more aggressive tumor biology than the Non-EVR group, such as a higher number of tumors (P = 0.003), a higher prevalence of microscopic vascular invasion (P = 0.017) and exceeding Milan criteria (P = 0.029). Compared with the PS-matched Non-EVR group, the PS-matched EVR group had significantly better TTR (P < 0.001) and OS (P < 0.001). In multivariate analysis, EVR was identified as an independent prognostic factor for TTR (hazard ratio [HR]=0.248; P = 0.001) and OS (HR=0.145; P < 0.001).

Combined with CNIs, EVR has the potential to prolong long-term survival in patients undergoing LT for HCC. These findings warrant further investigation in a well-designed prospective study.

Combined with CNIs, EVR has the potential to prolong long-term survival in patients undergoing LT for HCC. These findings warrant further investigation in a well-designed prospective study.

The widely accepted treatment option of a traumatic carotid cavernous fistula (TCCF) has been detachable balloon or coils based fistula occlusion. Recently, covered stent implantation has been proving an excellent results. The purpose of this study is to investigate our experiences with first line choice of covered stent implantation for TCCF at level 1 regional trauma center.

From November 2004 to February 2020, 19 covered stents were used for treatment of 19 TCCF patients. Among them, 15 cases were first line treatment using covered stents. Clinical and angiographic data were retrospectively reviewed.

Procedures were technically successful in all 15 cases (100%). Immediate angiographic results after procedure were total occlusion in 12 patients (80%). All patients except two expired patients had image follow-up (mean 15 months). Recurred symptomatic three patients underwent additional treatments and achieved complete occlusion. Mean clinical follow-up duration was 32 months and results were modified Rankin Scale 1-2 in five, 3-4 in five, and 5 in three patients.

The covered stent could be considered as fist line treatment option for treating TCCF patients especially in unstable vital sign. Larger samples and expanded follow-up are required to further develop their specifications and indications.

The covered stent could be considered as fist line treatment option for treating TCCF patients especially in unstable vital sign. Larger samples and expanded follow-up are required to further develop their specifications and indications.Background Intravital microscopy is an emerging technique in life science with applications in kidney research. Longitudinal observation of (patho-)physiological processes in living mice is possible in the smallest functional unit of the kidney, a single nephron (sn). In particular, effects on glomerular filtration rate (GFR) – a key parameter of renal function – can be assessed. Methods After intravenous injection of a freely filtered, non-resorbable, fluorescent dye in C57BL/6 mice, a time series was captured by multiphoton microsopy. Filtration was observed from the glomerular capillaries to the proximal tubule (PT) and the tubular signal intensity shift was analyzed to calculate the snGFR. Results Previously described methods for snGFR analysis relied on two manually defined measurement points in the PT and the tubular volume was merely estimated in 2D images. We present an extended image processing workflow by adding continuous measurement of intensity along the PT in every frame of the time series using ImageJ. Automatic modelling of actual PT volume in a 3D dataset replaced 2D volume estimation. Subsequent data analysis in R, with a calculation of intensity shifts in every frame and normalization against tubular volume, allowed exact assessment of snGFR by linear regression. Repeated analysis of image data obtained in healthy mice showed a striking increase of reproducibility by reduction of user interaction. Conclusions These improvements in image processing and data analysis maximize the reliability of a sophisticated intravital microscopy technique for the precise assessment of snGFR, a highly relevant predictor of kidney function.

This study was conducted to evaluate the effects of the supplementation of diets of broiler chickens with hot-melt extruded CuSO4 (HME-Cu) on their growth performance, nutrient digestibility, gut microbiota, small intestinal morphology, meat quality, and copper (Cu) bioavailability.

A total of 225 broilers (Ross 308), one-day old and initial weight 39.14 g, were weighed and distributed between 15 cages (15 birds per cage) in a completely randomized experimental design with 3 treatments (diets) and 5 replicates per treatment. Cages were allotted to three treatments including control (without supplemental Cu), IN-Cu (16 mg/kg of CuSO4), and HME-Cu (16 mg/kg of HME processed CuSO4).

The HME-Cu treatment tended to increase the overall body weight gain (BWG) (p<0.10). The apparent digestibility of Cu was increased by supplementation of HME-Cu at phase 2 (p<0.05). The Escherichia coli (E. coli) count in cecum tended to decrease with the supplementation with Cu (p<0.10). In addition, the HME-Cu treatme and the physiological function of Cu in broilers. However, supplementation of Cu in HME form improved the meat quality and the bioavailability of Cu.

The aim of this study was to evaluate the effect of marinating turkey meat with buttermilk and acid whey on the technological traits and microbiological quality of the product.

Slices of turkey meat muscles were marinated for 12 hours in buttermilk (n=30), acid whey (n=30) and comparatively, in lemon juice (n=30). The control group (n=30) consisted of unmarinated slices of turkey breast muscles. Physical parameters (pH, WHC, colour L*a*b*, shear force, weight loss) were assessed and quantitative and qualitative microbiological evaluation of raw and roasted products was performed. The microbiological parameters were determined as the total viable counts of mesophilic aerobic bacteria, of the Enterobacteriaceae family, and Pseudomonas spp. Bacterial identification was performed by MALDI-TOF MS.

Marinating turkey meat in buttermilk and whey compared to marinating in lemon juice and the control sample resulted in a higher (p<0.05) degree of yellow color saturation (b*) and a reduction (p<0.05) in the number of mesophilic aerobic bacteria, Pseudomonas spp. and Enterobacteriaceae family as well as the number of identified mesophilic aerobic bacteria in both raw and roasted samples. The lowest (p<0.05) shear force values were found in products marinated in whey.

The use of buttermilk and acid whey as a marinade for meat increases the microbiological safety of the product compared to marinating in lemon juice, while maintaining good technological features of the product.

The use of buttermilk and acid whey as a marinade for meat increases the microbiological safety of the product compared to marinating in lemon juice, while maintaining good technological features of the product.

This study compared differentially expressed genes (DEGs) between groups with high and low numbers of fine marbling particles (NFMP) in the longissimus thoracis muscle (LT) of Korean cattle to understand the molecular events associated with fine marbling particle formation.

The size and distribution of marbling particles in the LT were assessed with a computer image analysis method. Based on the NFMP, 10 LT samples were selected and assigned to either high- (n = 5) or low- (n = 5) NFMP groups. Using RNA sequencing, LT transcriptomic profiles were compared between the high- and low-NFMP groups. DEGs were selected at P < 0.05 and |fold change| > 2 and subjected to functional annotation.

In total, 328 DEGs were identified, with 207 up-regulated and 121 down-regulated genes in the high-NFMP group. Pathway analysis of these DEGs revealed five significant (P < 0.05) Kyoto Encyclopedia of Genes and Genomes pathways; the significant terms included endocytosis (P = 0.023), protein processing in endoplasmic reticulum (P = 0.019), and adipocytokine signaling pathway (P = 0.024), which are thought to regulate adipocyte hypertrophy and hyperplasia. The expression of sirtuin4 (P < 0.001) and insulin receptor substrate 2 (P = 0.043), which are associated with glucose uptake and adipocyte differentiation, was higher in the high-NFMP group than in the low-NFMP group.

Transcriptome differences between the high- and low-NFMP groups suggest that pathways regulating adipocyte hyperplasia and hypertrophy are involved in the marbling fineness of the LT.

Transcriptome differences between the high- and low-NFMP groups suggest that pathways regulating adipocyte hyperplasia and hypertrophy are involved in the marbling fineness of the LT.

The study was conducted to investigate the impact of boron supplementation on nutrient digestibility, inflammatory responses, blood metabolites and diarrhea index, and their relevance to growth performance in weaned pigs housed in good and poor sanitary environments for 14 days after weaning.

A total of 108 male pigs [Duroc × (Yorkshire × Landrace)] weaned at 21 days of age were used in a randomized complete block design with 2 × 3 factorial arrangement. Pigs were assigned to three boron treatments (0, 5, and 10 mg/kg) under two environments (good and poor sanitary) to give six replicates per treatment (3 pigs per replicate). On 0, 7 and 14 days, one pig per replicate was euthanized to collect, ileum tissue samples, and rectal fecal samples.

Boron supplementation quadratically influenced (p<0.001) feed intake and weight gain in pigs housed in good sanitary conditions from 1 to 14 days post-weaning where pigs offered 5 mg/kg boron optimized weight gain and feed intake. There is a quadratic interactionrdless of the sanitary conditions.

Efficient gene editing technology is critical for successful knock-in in domestic animals. RAD51 gene plays an important role in strand invasion during homologous recombination (HR) in mammals, and is regulated by CHK1 and CHK2 genes, which are upstream elements of RAD51. In addition, mismatch repair (MMR) system is inextricably linked to HR-related pathways and regulates HR via heteroduplex rejection. Thus, the aim of this study was to investigate whether CRISPR/Cas9-mediated knock-in efficiency of human lactoferrin (hLF) knock-in vector in the bovine β-casein gene locus can be increased by suppressing DNA mismatch repair (MMR)-related genes (MSH2, MSH3, MSH6, MLH1 and PMS2) and overexpressing DNA double-strand break (DSB) repair-related genes (RAD51, CHK1, CHK2).

MAC-T cells were transfected with a knock-in vector, RAD51, CHK1 or CHK2 overexpression vector and CRISPR/sgRNA expression vector to target the bovine β-casein gene locus, followed by treatment of the cells with CdCl2 for 24 hours. After 3 days of CdCl2 treatment, the knock-in efficiency was confirmed by polymerase chain reaction (PCR). The mRNA expression levels of DNA MMR-related and DNA DSB repair-related genes were assessed by quantitative real-time PCR (RT-qPCR).

Treatment with CdCl2 decreased the mRNA expression of RAD51 and MMR-related genes but did not increase the knock-in efficiency in MAC-T cells. Also, the overexpression of DNA DSB repair-related genes in MAC-T cells did not significantly affect the mRNA expression of MMR-related genes and failed to increase the knock-in efficiency.

Treatment with CdCl2 inhibited the mRNA levels of RAD51 and DNA MMR-related genes in MAC-T cells. However, the function of MMR pathway in relation to HR may differ in various cell types or species.

Treatment with CdCl2 inhibited the mRNA levels of RAD51 and DNA MMR-related genes in MAC-T cells. However, the function of MMR pathway in relation to HR may differ in various cell types or species.

The objective of this study was to investigate the of dietary pumpkin (Cucurbita moschata) seed meal (PSM) on laying performance, quality, fatty acids, cholesterol, antioxidant compounds and shelf life of eggs.

Eighty Tetra SL laying hens, 50-week-old, were randomly divided into two equal groups, having 10 replicates with 4 birds in each. The control (CON) treatment was fed with basal diet, while experimental treatment was fed a diet with 9% pumpkin seed meal (PSM), for a 6 week period.

Dietary PSM significantly decreased average daily feed intake (p<0.05), with no significant effect on other performance parameters. The PSM, enriched the eggs with polyunsaturated fatty acids, especially α linolenic acid (0.33 vs. 0.21g/100g) and linoleic acid (20.65 vs. 18.37 g/100g), whereas it reduced the amount of arachidonic acid with 3.91% and n-6/n-3 ratio in PSM eggs compared with CON. The inclusion of 9% PSM significantly (p<0.05) diminished the cholesterol concentration in yolk with 11.31% and in egg witho be effective improving shelf life of eggs for 28 days storage time.

The objective was to test additivity of digestible energy and nutrient concentrations in the hatchery byproduct mixture fed to nursery pigs.

In the previous studies, energy, phosphorus, calcium, and amino acid digestibility of infertile eggs, unhatched eggs, culled chicks, and a mixture of 3 hatchery byproduct ingredients was determined in nursery pigs (initial body weight = 9.4 to 14.2 kg). An additivity test was conducted using these determined values.

No difference was observed between determined and predicted metabolizable energy values in the mixture (4,224 and 4,203 kcal/kg as-is basis, respectively). Measured standardized total tract digestible phosphorus in the mixture was less than the predicted value (4.5 vs. 5.3 g/kg as-is basis, respectively; p<0.05). Measured standardized total tract digestible calcium in the mixture was greater compared with the predicted value (40.0 vs. 31.7 g/kg as-is basis, respectively; p<0.05). Measured standardized ileal digestible tryptophan in the mixture was greater than the predicted value (3.7 vs. 3.1 g/kg as-is basis, respectively; p<0.05) whereas other amino acid values were additive.

Energy and most of amino acid concentrations in hatchery byproducts are additive in the mixture fed to nursery pigs.

Energy and most of amino acid concentrations in hatchery byproducts are additive in the mixture fed to nursery pigs.

An experiment was conducted to evaluate the effect of different levels of crude protein (CP) and two rearing systems (cage and floor), on blood parameters and digestive and reproductive organ development of brown laying hens.

A total of 400 Hisex Brown laying hens between 30 and 45 weeks of age were distributed in a completely randomized design and a 2×4 factorial arrangement, with main effects including two rearing systems (cage and floor) and levels of CP (140, 150, 160, and 180 g/kg), in a total of eight treatments and five replicates of 10 birds each with initial body weight of 1,877 g (laying hen in cage) and 1,866 g (laying hens in floor). The parameters evaluated were plasma total protein, albumin, uric acid, total cholesterol, relative weights of oviduct, abdominal fat, liver, gizzard, crest and dewlap, length of small intestine and oviduct.

The blood parameters were similar in birds reared in cage and floor systems. The birds reared on the floor showed greater small intestine and oviduct weight (%) and lower liver and pancreas weight (%). A significant interaction was observed between factors for the relative gizzard, crest and dewlap weight, serum protein, uric acid, and total cholesterol (P<0.05). The diets with 140 g/kg CP resulted in lower serum protein and lower cholesterol in birds reared in floor system, while birds reared in cage system showed no effect of CP on both parameters. Birds reared in cage and fed with 140 and 150 g/kg CP presented lower uric acid. The group of birds reared in floor system fed 180 g/kg had greater uric acid.

The dietary protein level can be reduced up to 140 g/kg for Hisex Brown hens (30 to 45 weeks of age) without an important effect on metabolic profile and organ development in both rearing systems.

The dietary protein level can be reduced up to 140 g/kg for Hisex Brown hens (30 to 45 weeks of age) without an important effect on metabolic profile and organ development in both rearing systems.

The objective of this study was to determine the effects of different social ranking order (SRO) and the enrichments (perch and dust-bath) allocation (EA) on behavior of laying hens in furnished cages.

A total of 4 weeks in experiment period. 216 Hy-line brown layers beak-trimmed at 1 d of age were selected randomly at 14 weeks of age from a commercial farm, and randomly divided into 36 cages with 6 hens in each cage. High enrichments (perch and dust-bath) allocation (HEA) and low enrichments (perch and dust-bath) allocation (LEA) were provided. Video observations of behavior were obtained from the focal hens between 14 and 18 weeks of age and perching, dust-bathing and other general behaviors of the hens with different social orders were measured.

Perching behavior of high social ranking order hens (HSR) were significantly higher than that of medium social ranking order hens (MSR), and that of the MSR were significantly higher than that of low social ranking order hens (LSR) (P < 0.01), except for lying on perch (P > 0.