Miracle-dz/UniFAR-FTUs huggingface dataset:
SAbPred: a structure-based antibody prediction server

SAbPred is a server that makes predictions of the properties of antibodies focusing on their structures. Antibody informatics tools can help improve our understanding of immune responses to disease and aid in the design and engineering of therapeutic molecules. SAbPred is a single platform containing multiple applications which can: number and align sequences; automatically generate antibody variable fragment homology models; annotate such models with estimated accuracy alongside sequence and structural properties including potential developability issues; predict paratope residues; and predict epitope patches on protein antigens. The server is available at http://opig.stats. ox.ac. uk/webapps/sabpred.
Air Emissions from In-Vessel Rotating Drum and Open Static Pile Composting of Swine Carcasses , Whole and Ground

Swine carcasses (292 ± 7.3 kg per batch), whole or ground, were composted using rotating drum in-vessel (IV) or open static pile (OSP) composting systems, in the 2 × 2 factorial designed experiment. Dairy manure compost, horse stall bedding, and dry wood shavings were mixed together (analyzed % H2O, % N, and C:N of 48.7 ± 0.32%, 0.76 ± 0.075%, and 31.8 ± 2.51, respectively) and added amendment to each batch of mortality compost. Total mass per batch was 812 ± 7.3 kg. The 8 batches were placed in eight individual rooms (2 reps/trt), and air emissions including NH3, H2S, CH4, N2O, and CO2 were measured continuously for 20 d during the primary phase (d 1 to 20), and a 15 d period 1.5 months later (secondary phase), where all batches were further composted as open static piles (identity preserved). Oxygen consumption did not differ among treatments, being unaffected by compost system, carcass form and phase of composting. Carbon dioxide emission was greater (P < 0.05) in the primary phase than in the secondary phase. Mass of CO2 per day tended to be greater with use of the IV system of composting (P = 0.07). The IV system emitted more (P < 0.05) NMTHC, NH3, and SO2, and less (P < 0.05) CH4, NO, N2O than the OSP system. Composting system did not affect the daily mass of NO2 and H2S emitted. In the primary phase, the IV system generated about 95% less (P < 0.05) CH4 than did the OSP system (0.31 vs. 6.7 g/d, respectively). Other environmentally-interesting differences (P < 0.05) between the IV and OSP systems in the primary phase were NMTHC (4.13 vs. 0.19 g/d), NH3 (86.96 vs. 5.04 g/d), and N2O (-1.00 vs. 1.94 g/d) emissions for IV and OSP systems, respectively. The amount of CH4, NMTHC, NO, and SO2 gases emitted in the second phase did not differ among treatments. Nitrous oxide emissions were greater (P < 0.05) with the use of the OSP system than with the IV composting system in the secondary phase. Emissions were greater (P < 0.05) for CH4, NMTHC, NH3, NO, and SO2 gases in the primary phase as compared to the secondary phase, but not for N2O, which was greater (P < 0.05) in the secondary phase than it was in the primary phase. Carcass form did not affect amounts of emissions. For a 2000 head finishing swine farm with a 2% mortality rate, we estimate that CO2e emitted annually from the composting of mortality for 6 months, 1908 and 1596 kg depending on which method of composting was used (IV or OSP, respectively). In conclusion, whether carcasses were ground or left whole changed did not result in differences in gas emissions. In-vessel and OSP composting systems emitted different amounts of gases in the early, active phases of composting; including those gases considered greenhouse gases.
Molecular subtyping of tumors from patients with familial glioma

Background Single-gene mutation syndromes account for some familial glioma (FG); however, they make up only a small fraction of glioma families. Gliomas can be classified into 3 major molecular subtypes based on isocitrate dehydrogenase (IDH) mutation and 1p/19q codeletion. We hypothesized that the prevalence of molecular subtypes might differ in familial versus sporadic gliomas and that tumors in the same family should have the same molecular subtype. Methods Participants in the FG study (Gliogene) provided samples for germline DNA analysis. Formalin-fixed, paraffin-embedded tumors were obtained from a subset of FG cases, and DNA was extracted. We analyzed tissue from 75 families, including 10 families containing a second affected family member. Copy number variation data were obtained using a first-generation Affymetrix molecular inversion probe (MIP) array. Results Samples from 62 of 75 (83%) FG cases could be classified into the 3 subtypes. The prevalence of the molecular subtypes was: 30 (48%) IDH-wildtype, 21 (34%) IDH-mutant non-codeleted, and 11 (19%) IDH-mutant and 1p/19q codeleted. This distribution of molecular subtypes was not statistically different from that of sporadic gliomas (P = 0.54). Of 10 paired FG samples, molecular subtypes were concordant for 7 (κ = 0.59): 3 IDH-mutant non-codeleted, 2 IDH-wildtype, and 2 IDH-mutant and 1p/19q codeleted gliomas. Conclusions Our data suggest that within individual families, patients develop gliomas of the same molecular subtype. However, we did not observe differences in the prevalence of the molecular subtypes in FG compared with sporadic gliomas. These observations provide further insight into the distribution of molecular subtypes in FG.
Religious Heterogamy and Partnership Quality in Later Life.

Objectives Prior research points to the importance of couple-level religious similarity for multiple dimensions of partnership quality and stability but few studies have investigated whether this association holds for older couples. Method The current article uses dyadic data from the National Social Life, Health, and Aging Project (NSHAP), a representative sample of 953 individuals age 62-91 plus their marital or cohabiting partners. We use modified actor-partner interdependence models. Results Religious service heterogamy predicted lower relationship happiness and satisfaction. Both associations were partially explained by the fact that religiously dissimilar partners report relatively little free time in joint activity. Further, religiously heterogamous couples had less frequent sex and engaged in less nonsexual touch than their more similar counterparts. Conclusions Taken together, results attest to the ongoing importance of religious similarity-service attendance, in particular-for partnership quality in late life. Future research is needed to more fully examine which mechanisms account for these patterns.
A Plasmonic Coupling Substrate Based on Sandwich Structure of Ultrathin Silica‐Coated Silver Nanocubes and Flower‐Like Alumina‐Coated Etched Aluminum for Sensitive Detection of Biomarkers in Urine

Interactions between substrate and plasmonic nanostructures can give rise to unique optical properties and influence performance in plasmonic biosensing applications. In this study, a substrate with low refractive index and roughness based on flower‐like alumina‐coated etched aluminum foil (f‐Al2O3/e‐Al) has been fabricated. Silver@silica (Ag@SiO2) nanocubes (NCs) assemble in an edge–edge configuration when deposited on this substrate. The rough surface texture of f‐Al2O3/e‐Al provides a pathway for coupling of incident light to surface plasmons. The Ag@SiO2/f‐Al2O3/e‐Al substrate exhibits a coupling efficiency of laser light sources into surface plasmon hotspots for both surface‐enhanced Raman scattering (SERS) and metal‐enhanced photoluminescence (MEPL). Moreover, the shelf life of this substrate is significantly improved due to a reduction in oxygen diffusion rate mediated by the ultrathin silica spacer and the flower‐like Al2O3 dielectric layer. Creatinine and flavin adenine dinucleotide are biomolecules present in human blood and urine. With advanced label‐free SERS and MEPL techniques, it is possible to detect these biomarkers in urine, allowing cheap, noninvasive, yet sensitive analysis. The approach explored in this work can be developed into a powerful encoding tool for high‐throughput bioanalysis.
Phase response properties of a bursting neuron with spike adding structure

The phase response properties of the Hindmarsh-Rose model in different blocks are investigated in this paper. We find: (1) the location of the largest magnitude of the BPRCs can only be in the penultimate spike or the final spike which depends on the position of the system in the block. (2) the location of the largest magnitude of the BPRCs changes sharply when the system transits from one block to the neighbor one. Then we use bifurcation diagrams of fast subsystem with the slow variable as the bifurcation parameter to analyze the structure of the BPRCs, and draw the conclusions that the slow variable is critical in determining the properties of BPRCs, especially the location of the largest magnitude of the BPRCs, which depends on the difference between the values of slow variable for the spike maxima and for the homoclinic bifurcation.
Paradoxical enhancement of chemoreceptor detection sensitivity by a sensory adaptation enzyme

Significance Escherichia coli cells track chemical gradients with high sensitivity over a wide dynamic range, using a feedback-controlled sensory adaptation system. CheR, a receptor methyltransferase, is a key component of the adaptation system. We discovered that CheR can enhance the response sensitivity of chemoreceptor molecules, a role that opposes the known signaling consequences of its catalytic activity. This enhancement effect requires CheR-receptor binding interactions, but is quantitatively inconsistent with a simple equilibrium binding mechanism. Rather, CheR binding appears to promote a long-lasting conformational or covalent change that enhances the affinity of chemoreceptor molecules for their attractant ligands. The CheR response enhancement effect opens a new window on the functional architecture of chemoreceptor molecules and their interactions with sensory adaptation enzymes. A sensory adaptation system that tunes chemoreceptor sensitivity enables motile Escherichia coli cells to track chemical gradients with high sensitivity over a wide dynamic range. Sensory adaptation involves feedback control of covalent receptor modifications by two enzymes: CheR, a methyltransferase, and CheB, a methylesterase. This study describes a CheR function that opposes the signaling consequences of its catalytic activity. In the presence of CheR, a variety of mutant serine chemoreceptors displayed up to 40-fold enhanced detection sensitivity to chemoeffector stimuli. This response enhancement effect did not require the known catalytic activity of CheR, but did involve a binding interaction between CheR and receptor molecules. Response enhancement was maximal at low CheR:receptor stoichiometry and quantitative analyses argued against a reversible binding interaction that simply shifts the ON–OFF equilibrium of receptor signaling complexes. Rather, a short-lived CheR binding interaction appears to promote a long-lasting change in receptor molecules, either a covalent modification or conformation that enhances their response to attractant ligands.
Event-based signaling for large-scale artificial robotic skin - realization and performance evaluation

In this paper we describe how we realized event-based signaling for large scale artificial robotic skin. We developed a new algorithm for the event generation on multi-modal skin cells. The skin cells have two modes, the conventional data sampling mode and the event mode. A comprehensive performance evaluation and comparison of these two modes is presented. We perform different experiments on our robot TOMM which has two UR5 robot arms, each covered with 260 multi-modal skin cells. Each skin cell samples 9 signals of 4 different modalities. Finally we derive models for extrapolating CPU usage and network traffic for larger numbers of skin cells and higher sample rates. The results show that the event-based system has superior performance and its performance edge increases with larger numbers of skin cells and higher sample rates. Experimental validation on our real robot system shows that in reactive control the event-based system reduces in comparison to the conventional system the packet rate by 48.2% and the CPU usage by 17.79%. We extrapolate the worst case for 5000 cells and show that the event-based system can at least reduce the packet rate by 21.2% and the CPU usage by 17.46%.
Usefulness of overnight pulse oximeter as the sleep assessment tool to assess the 6-year risk of road traffic collision: evidence from the Taiwan Bus Driver Cohort Study.

Background In order to support health service organizations in arranging a system for prevention of road traffic collisions (RTC), it is important to study the usefulness of sleep assessment tools. A cohort study was used to evaluate the effectiveness of subjective and objective sleep assessment tools to assess for the 6-year risk of both first RTC event only and recurrent RTC events. Methods The Taiwan Bus Driver Cohort Study (TBDCS) recruited 1650 professional drivers from a large bus company in Taiwan in 2005. The subjects were interviewed in person, completed the sleep assessment questionnaires and had an overnight pulse oximeter survey. Moreover, this cohort of drivers was linked to the National Traffic Accident Database (NTAD) and researchers found 139 new RTC events from 2005 to 2010. Primary outcomes were traffic collisions from NTAD, nocturnal oxygen desaturation index (ODI) from pulse oximeter, Pittsburg sleeping quality score, Epworth daytime sleepiness score, Snore Outcomes Survey score and working patterns from questionnaires. A Cox proportional hazards model and an extended Cox regression model for repeated events were performed to estimate the hazard ratio for RTC. Results The RTC drivers had increased ODI4 levels (5.77 ± 4.72 vs 4.99 ± 6.68 events/h; P = 0.008) and ODI3 levels (8.68 ± 6.79 vs 7.42 ± 7.94 events/h; P = 0.007) in comparison with non-RTC drivers. These results were consistent regardless of whether ODI was evaluated as a continuous or a categorical variable. ODI4 and ODI3 levels increased the 6-year RTC risks among professional drivers even after adjusting for age, education, history of cardiovascular disease, caffeine intake, sleeping pills used, bus driving experience and shift modes. Moreover, there was an increased trend for ODI between the stratification of the number of RTCs in comparison with the non-RTC group. In the extended Cox regression models for repeated RTC events with the Anderson and Gill intensity model and Prentice-Williams-Petersen model, measurement of ODI increased hazards of the subsequent RTC events. Conclusion This study showed that an increase in the 6-year risk of RTC was associated with objective measurement of ODI for a sign of sleep-disordered breathing (SDB), but was not associated with self-reported sleeping quality or daytime sleepiness. Therefore, the overnight pulse oximeter is an effective sleep assessment tool for assessing the risk of RTC. Further research should be conducted regarding measures to prevent against SDB among professional drivers.
Impaired Release of Vitamin D in Dysfunctional Adipose Tissue: New Cues on Vitamin D Supplementation in Obesity

Context Vitamin D accumulates in adipose tissue (AT), and vitamin D deficiency is frequent in obesity. Objective We hypothesize that trafficking of vitamin D is altered in dysfunctional AT. Design, Patients, Settings Fifty-four normal-weight and 67 obese males were recruited in a prospective study and randomly assigned to supplementation with 50 µg/wk 25-hydroxyvitamin-D3 or 150 µg/wk vitamin D3 for 1 year, raising dosage by 50% if vitamin D sufficiency [serum 25-hydroxyvitamin-D3 >50 nmol/L], was not achieved at 6 months; 97 subjects completed the study. Methods Vitamin D3 and 25-hydroxyvitamin-D3 were quantified by HPLC-MS in control and insulin-resistant (IR) 3T3-L1 cells and subcutaneous AT (SAT) from lean and obese subjects, incubated with or without adrenaline; expression of 25-hydroxylase (Cyp27a1), 1α-hydroxylase (Cyp27b1), and vitamin D receptor (Vdr) was analyzed by real-time polymerase chain reaction. Results In IR adipocytes, uptake of D3 and 25-hydroxyvitamin-D3 was higher, but, after adrenaline stimulation, the decrement in D3 and 25-hydroxyvitamin-D3 was stronger in control cells, which also showed increased expression of Cyp27a1 and Cyp27b1 and higher levels of 25-hydroxyvitamin-D3. In SAT from obese subjects, adrenaline-induced release of D3 and 25-hydroxyvitamin-D3 was blunted; in both IR cells and obese SAT, protein expression of β2-adrenergic receptor was reduced. Supplementation with 25-hydroxyvitamin-D3 was more effective in achieving vitamin D sufficiency in obese, but not in normal weight subjects. Conclusion Dysfunctional AT shows a reduced catecholamine-induced release of D3 and 25-hydroxyvitamin-D3 and altered activity of vitamin D-metabolizing enzymes; for these reasons supplementation with 25-hydroxyvitamin-D3 is more effective in obese individuals.
Precise nanoinjection delivery of plasmid DNA into a single fibroblast for direct conversion of astrocyte

Abstract Direct conversion is a powerful approach to safely generate mature neural lineages with potential for treatment of neurological disorders. Astrocytes play a crucial role in neuronal homeostasis and their dysfunctions contribute to several neurodegenerative diseases. Using a single-cell approach for precision, we describe here a robust method using optimized DNA amounts for the direct conversion of mouse fibroblasts to astrocytes. Controlled amount of the reprogramming factors Oct4, Sox2, Klf4 and cMyc was directly delivered into a single fibroblast cell. Consequently, 2500 DNA molecules, no more or less, were found to be the optimal amount that dramatically increased the expression levels of the astrocyte-specific markers GFAP and S100b and the demethylation gene TET1, the expression of which was sustained to maintain astrocyte functionality. The converted astrocytes showed glutamate uptake ability and electrophysiological activity. Furthermore, we demonstrated a potential mechanism whereby fibroblast was directly converted into astrocyte at a single-cell level; this was achieved by activating BMP2 pathway through direct binding of Sox2 protein to BMP2 gene. This study suggests that nanotechnology for directly injecting plasmid DNAs into cell nuclei may help understand such a conversion at single-cell level.
Mesh Sequence Morphing

Morphing is an important technique for the generation of special effects in computer animation. However, an analogous technique has not yet been applied to the increasingly prevalent animation representation, i.e. 3D mesh sequences. In this paper, a technique for morphing between two mesh sequences is proposed to simultaneously blend motions and interpolate shapes. Based on all possible combinations of the motions and geometries, a universal framework is proposed to recreate various plausible mesh sequences. To enable a universal framework, we design a skeleton‐driven cage‐based deformation transfer scheme which can account for motion blending and geometry interpolation. To establish one‐to‐one correspondence for interpolating between two mesh sequences, a hybrid cross‐parameterization scheme that fully utilizes the skeleton‐driven cage control structure and adapts user‐specified joint‐like markers, is introduced. The experimental results demonstrate that the framework, not only accomplishes mesh sequence morphing, but also is suitable for a wide range of applications such as deformation transfer, motion blending or transition and dynamic shape interpolation.
A SEQUENCE SCHEME TO REDUCE THE RESIDUAL STRESSES IN WELDING OF CIRCULAR ELEMENTS

Accurately predicting welding residual stresses and developing a convenient welding sequence for a weld system is an appropriate task since welding residual stress is inevitably produced in a welded structure. In this work, the effect of layered, block and cascade welding sequences on the thermo-mechanical response of shell weldments is studied by use of a 3-D thermo-viscoplastic model. An Anand model is used to simulate the rate dependent plastic deformation of welded materials. At the same time, modeling of the welded region in the present study has been done on the basis of the "isothermal melting pool" approach. The temperature dependency of the thermal and mechanical properties of materials is considered in the analysis and the effect of the welding speed and welding lag, and the inter-pass temperature is introduced into the model as well. Thus, the model presented here has provided a convenient welding sequence to enhance the fabrication process of a circular weld. Keywords– Welding sequence, thick shell, Anand model, cascade method, block method, layer method, 3D thermo viscoplastic model
In vitro microbicidal, anti‐biofilm and cytotoxic effects of different commercial antiseptics

Topical antiseptics are widely used for wound treatment, with the goal of disrupting biofilm capacity. We analysed the effectiveness of a variety of antiseptics to inhibit various stages of biofilm formation and to remove biofilms in vitro as well as the agents' cytotoxic effects on fibroblasts. We found that the chlorine‐releasing agents exhibited immediate anti‐biofilm effects in the short term, with lesser cytotoxicity than agents prepared from more stable compounds, such as biguanide or modified diallyl disulfide‐oxide, which, conversely, have better long‐term effectiveness. Among the examined organisms, Gram‐positive bacteria and Candida albicans were the most sensitive to the antiseptics, whereas Pseudomonas aeruginosa and Acinetobacter baumannii were relatively resistant to them. Formulations whose mechanisms of action involve the release of chemically active chlorine were more effective when administered in solution than the gel form, likely because of the stability of the active ingredients during or after preparation of the formula. Interestingly, hypochlorous acid and some superoxidation solutions were effective in preventing biofilm formation within a short time period and showed virtually no toxicity. Our study indicates that most antiseptics remain effective long enough to prevent biofilm formation; thus, even brief application of an antiseptic agent during initial wound treatment can lead to better wound management outcomes.
Spectrophotometric quantitation of antioxidant capacity through the formation of a phosphomolybdenum complex: specific application to the determination of vitamin E.

A spectrophotometric method has been developed for the quantitative determination of antioxidant capacity. The assay is based on the reduction of Mo(VI) to Mo(V) by the sample analyte and the subsequent formation of a green phosphate/Mo(V) complex at acidic pH. The method has been optimized and characterized with respect to linearity interval, repetitivity and reproducibility, and molar absorption coefficients for the quantitation of several antioxidants, including vitamin E. The phosphomolybdenum method, in combination with hexane monophasic extraction, has also been adapted for the specific determination of vitamin E in seeds. The results obtained with the proposed method were validated by comparison with a standard HPLC method. The phosphomolybdenum method is routinely applied in our laboratory to evaluate the total antioxidant capacity of plant extracts and to determine vitamin E in a variety of grains and seeds, including corn and soybean.