jimnoneill/paper-to-field-training huggingface dataset:
Prediction and Design of Protease Specificity Using a Structure-Aware Graph Convolutional Network

Field: Computer Science (Physical Sciences)

Specific molecular recognition of substrates by enzymes, e.g., proteases, is critical for maintaining the robustness of crucial life processes. The ability to predictably tailor protease specificity would enable targeted proteolytic cleavage of any chosen target protein. Current methods for predicting protease specificity rely on sequence pattern recognition in experimentally-derived cleavage data obtained for libraries of substrates. We reasoned that a more semantically rich and robust model of protease specificity could be developed by incorporating the three-dimensional structure and energetics of molecular interactions between protease and substrates. We present a Protein Graph Convolutional Network (PGCN), which uses a physically-grounded, structure-based molecular interaction graph representation that describes molecular topology and energetics to predict specificity. PGCN was shown to accurately predict the specificity landscapes of several variants of two model proteases: the NS3/4 protease from the Hepatitis C virus (HCV) and the Tobacco Etch Virus (TEV) proteases. Node and edge ablation tests identified key graph elements for specificity prediction, some of which are consistent with known biochemical constraints for protease:substrate recognition. We used a pre-trained PGCN model to guide the design of TEV protease libraries for cleaving two non-canonical substrates and found high correspondence between PGCN prediction and experimental cleavage results for 19 designed protease variants. The described methodology should be applicable to the construction of tailor-made proteases for site-selectively cleaving chosen substrate sequences, enabling broad applications in protein design. Here is a brief description of each file: protease-gcnn-pytorch.zip PGCN codes. See the latest version here: https://github.com/Nucleus2014/protease-gcnn-pytorch train_val_test_graph_datasets.zip Datasets for the training process of PGCN. Statistics of them are shown in Table 1. tev_design_for_validation_pdbstructures.zip Final selected designs for experimental testing tev_oydv_design_candidates_pdbstructures.zip Candidate designs made by Rosetta
Suppressive Activity of Fexofenadine Hydrochloride on the Production of Eosinophil Chemoattractants from Human Nasal Fibroblasts in vitro

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

The influence of fexofenadine hydrochloride (FEX; CAS 138452-21-8) on the production of eosinophil chemoattractants, RANTES and eotaxin, from nasal polyp fibroblasts (NPFs) was examined in vitro. Seventh to tenth generation NPFs were cultured with or without 1 microg/ml lipopolysaccharide (LPS) in the presence of various concentrations of FEX. After 24 h, the culture supernatants were obtained and assayed for eosinophil chemoattractants by enzyme-linked immunosorbent assay (ELISA). FEX at a dose of more than 250 ng/ml (but not 100 ng/ml) inhibited RANTES and eotaxin production in response to LPS stimulation, when the agent was added at starting of cell cultures. FEX also showed suppressive effect on RANTES and eotaxin production from NPFs after stimulation with tumor necrosis factor alpha (TNF-alpha). However, the addition of FEX at 12 h after culture could not inhibit factor production. The influence of FEX on messenger RNA (mRNA) expression in NPFs was then examined. The addition of FEX at 100 ng/ml scarcely affected the expression of RANTES and eotaxin mRNA. On the other hand, 250 ng/ ml of FEX significantly inhibited these mRNA expressions that were enhanced by LPS stimulation.
Treatment, assessment and typologies of intimate partner violence

Field: Psychology (Social Sciences)

Traditionally, sociological accounts of the causes of intimate partner violence (IPV) have been adhered to by researchers and practitioners who consider men’s violence against female partners. However, a wide array of methodologically sound empirical literature highlights the importance of adopting a multi-factorial perspective in understanding the nature and aetiology of IPV and in informing policy, intervention and assessment in this domain. This thesis adheres to the empirical literature and aims to explore issues of IPV from a multifactor and gender inclusive perspective, with specific focus on the contribution that psychology can lend to understanding this phenomenon. A systematic review is presented to examine the interplay of psychological factors on the aetiology of male perpetration of IPV. The review identified that the risk factors substance abuse, childhood abuse, psychopathology and anger are predictive of male IPV. Future research should consider causal factors for female IPV offenders. Next, a critique of the psychometric State-Trait Anger Expression Inventory-2 is discussed in relation to the validity and reliability of its measurement of anger. Overall this protocol is a well established measurement of anger in male IPV offenders. However, further research is required to specify its applicability to the female population of IPV offenders. Third, an individual case study of an IPV and generally violent offender evaluates the usefulness of adopting a treatment strategy that is individually selected to suit the client’s criminogenic need. The outcome supports the notion that individualised approaches should be utilised in the context of treatment and assessment of IPV offenders. Finally, an empirical study explores the heterogeneity of females convicted of IPV and provides support for the typologies theorised by Holtzworth-Munroe and Stuart (1994). It is concluded that future research should explore this phenomena in community samples and the context of the violence when investigating subtypes of female IPV offenders. Consistently, the findings from this thesis highlight the need to adopt a multi-factorial and gender inclusive perspective to understand the true nature and aetiology of IPV. Multifactor approaches should be considered in the context of assessment and treatment of IPV offenders.
Long-term Outcomes of Nephrectomy and Inferior Vena Cava Thrombectomy in Patients with Advanced Renal Cell Carcinoma

Field: Medicine (Health Sciences)

Background/Purpose: This study evaluated the long-term outcomes of nephrectomy and inferior vena cava (IVC) thrombectomy in patients with advanced renal cell carcinoma (RCC). Methods: From January 1996 to December 2013, we retrospectively collected the clinical data of 31 patients with pathologically confirmed RCC and IVC tumor thrombus. All patients received nephrectomy and IVC thrombectomy. We examined the clinical outcomes, including cancer-specific survival, progression-free survival, and postoperative complications, during a 90-day period. The associated prognostic factors were also analyzed. This study is registered with the National Taiwan University Hospital Research Ethics Committee (number 201305059RINC). Results: The median follow-up period was 24 months. Of 20 patients with nonmetastatic disease, 15 developed metastases during the study period. The overall 5-year cancer-specific survival rate was 30.8% in the nonmetastatic group versus 12.5% in the metastatic group. The level of IVC thrombus (Levels I–II vs. Levels III–IV) was not significantly associated with the 5-year cancer-specific survival ( P = 0.43). The Fuhrman grade and sarcomatoid type were statistically significant predictors of cancer-specific survival (Fuhrman Grades III–IV vs. Grades I–II: Hazard ratio [HR] = 0.11, P = 0.04; sarcomatoid type: HR = 0.136, P = 0.001). Fuhrman grade, capsular invasion, and positive surgical margins were associated with 1-year progression-free survival (Fuhrman Grades III–IV vs. Grades I–II: HR = 0.08, P = 0.04; capsular invasion: HR = 0.15, P = 0.04; positive surgical margins: HR = 0.16, P = 0.05). The most common perioperative complication was massive blood loss. The most common recurrence sites were bones, liver, and lungs. Conclusion: The pathologic Fuhrman grade, sarcomatoid type, positive surgical margins, and capsular invasion were significant predictors of oncological outcomes in patients with advanced RCC and IVC thrombus.
ESTIMATION METHOD OF ROCK MASSES IN TUNNEL CONSTRUCTION BY CONVERSION ANALYSIS USING SEISMIC VELOCITY AND ELECTRIC RESISTIVITY

Field: Earth and Planetary Sciences (Physical Sciences)

トンネル建設における地質調査では弾性波探査と電気探査が実施されている例が多いが,これらの調査結果に基づく設計は経験的で,度々実際と異なることがある.設計,施工段階においては,断層,破砕帯等の地質構造を事前に把握することは重要である.筆者らは,トンネルを計画・設計する際に事前調査として,よく利用される弾性波探査と電気探査に着目し,弾性波速度と比抵抗値を間隙率と体積含水率に変換する解析手法の構築を試みた.ここでは,本解析手法を変換解析と称する.そして,トンネル施工における各種の施工記録や原位置の岩盤状態と,変換解析結果である間隙率,体積含水率を比較することで,変換解析の有用性を検証し,さらには,トンネルの支保設計への適用性について検討を行った.
Fatty acid composition in postmortem brains of people who completed suicide

Field: Neuroscience (Life Sciences)

Objective: Cholesterol levels have been reported to be lower in suicidal patients, and alterations in blood levels of polyunsaturated fatty acids have been found in people with depression. Given that the evidence for the link between lipid metabolism and psychopathology thus far has almost exclusively hinged on alterations of these variables in blood, this study aimed to address whether similar alterations in fatty acids would be evident in the brains of people who complete suicide. Methods: Using gas chromatography, we measured 49 different fatty acids in the orbitofrontal cortex and the ventral prefrontal cortex of people who had completed suicide with ( n = 16) and without ( n = 23) major depression and in control subjects ( n = 19) with no current psychopathology and whose cause of death was sudden. Results: Comparisons of fatty acids between the 3 groups did not reveal significant differences. Conclusion: Further research is required to better understand the link between fatty acids in the peripheral circulation and those in the central nervous system before determining whether fatty acids play a mediating role in suicidal behaviour.
Application of Coal-Water Sllury in 220t/h Oil-Fired Boiler

Field: Energy (Physical Sciences)

An oil fired boiler in Maoming Thermal Plant was changed to burn CWS from December 2000. It was operating smoothly burning CWS since the change was finished at 40%～100% original nominal output. Some tests were made on it. It has high combustion efficiencies over 99.7% and many adjustment methods. The boiler was the first 220t/h boiler which was changed to burn CWS while burnt oil before by national technology. Figs 3, tables 5 and refs 3.
A Wireless Under-Mattress Sensor System for Sleep Monitoring in People with Major Depression

Field: Health Professions (Health Sciences)

Monitoring people during sleep time is of particular interest to patients with sleep disorders and elderly people or
infants. We have developed a battery powered electronic system to monitor people in the bed, store the data and send
them through a wireless link to a PC. The resulting data will be subject to further analysis using pattern recognition
to evaluate the feasibility of using the system as an indicator of sleep quality. The system is able to detect presence
on the bed and movements and breathing of the patient. The changes in pressure distribution on the mattress cause
changes in pressure in the layers of the sensor and a voltage will appear on the electrodes. The detection ability depends
strongly on the shape of the mattress and the bedbase.
Demographic profile of facial fractures in the Punjab population: a pilot study

Field: Medicine (Health Sciences)

Background: Trauma units of tertiary care centers of the north Indian state of Punjab are occupied with young individuals with a passion for driving on full acceleration. There is therefore a high rate of road traffic accidents with and fractures of the facial skeleton are frequently noted .This is noted more so in the male gender.Methods: A retrospective study of the records of 61 subjects admitted under Otolaryngology and Maxillofacial trauma units, during a period of 2 years (August 2013-August 2015) at Dayanand Medical College and hospital were analysed.Results: Males outnumbered the females in the ratio of 5:1. Maximum, 54% were seen in the age group 21-30 years and minimum at the extremes of age. The commonest cause of fracture was road-side accidents which was observed in 72% of patients. In 15% these were due to assaults, in 8% due to falls and only in 3.2% due to sports injury.Conclusions: Facial fractures are recorded more in middle aged males with vehicular trauma being the main aetiology.
Differential Maize Yield Hybrid Responses to Stand Density Are Correlated to Their Response to Radiation Reductions Around Flowering

Field: Agricultural and Biological Sciences (Life Sciences)

Altered stand density affects maize yields by producing changes in both numerical yield components, kernel number per plant (KNP), and kernel weight (KW). Kernel number is determined by the accumulation of ear biomass during the flowering period, whereas KW is determined by the sink potential established during flowering and the capacity of the plant to fulfill this potential during effective grain filling. Here, we tested if different short shading treatments during different stages around flowering can help discriminate genotypic differences in eco-physiological parameters relevant for maize stand density yield response and associated yield components. Our specific objectives were to: (i) identify hybrids with differential shading stress response, (ii) explore shading effects over eco-physiological parameters mechanistically related to KNP and KW, and (iii) test if shading stress can be used for detecting differential genotypic yield responses to stand density. The objectives were tested using four commercial maize hybrids. Results indicated that KNP was the yield component most related to yield changes across the different shading treatments, and that the specific shading imposed soon after anthesis generated the highest yield reductions. Hybrids less sensitive to shading stress were those that reduced their plant growth rate the least and the ones that accumulated more ear biomass during flowering. Genotype susceptibility to shading stress around flowering was correlated to stand density responses. This indicated that specific shading stress treatments are a useful tool to phenotype for differential stand density responses of commercial hybrids.
OCHRONOTIC ARTHROPATHY AND LYSOSOMES: A CLINICAL AND ELECTRON MICROSCOPIC STUDY

Field: Medicine (Health Sciences)

ABSTRACT: In order to understand better the time dependency of the arthritic manifestations of ochronosis, as well as its relationship with lysosomal activities, we sampled a small series of various arthropathies (11 joints). The joint fluid, serum, and urine lysosomal activity levels were measured. The lysosomal enzyme level was elevated in patients with acutely symptomatic, chronically involved ochronotic joints. The enzyme activity level in the other joints (chronically involved) was less. Postulated clinical manifestations of increased levels of intraarticular lysozymes seem to apply to ochronosis as well. Further studies with larger series of patients are warranted.
High-Provitamin A Carotenoid (Orange) Maize Increases Hepatic Vitamin A Reserves of Offspring in a Vitamin A-Depleted Sow-Piglet

Field: Agricultural and Biological Sciences (Life Sciences)

The relationship of dietary vitamin A transfer from mother to fetus is not well understood. The difference in swine offspring liver reserves was investigated between single-dose vitamin A provided to the mother post-conception compared with continuous provitamin A carotenoid dietary intake from biofortified (enhanced provitamin A) orange maize (OM) fed during gestation and lactation. Vitamin A-depleted sows were fed OM (n = 5) or white maize (WM) + 1.05 mmol retinyl palmitate administered at the beginning of gestation (n = 6). Piglets (n= 102) were killed at 0, 10, 20, and 28 d after birth. Piglets from sows fed OM had higher liver retinol reserves (P < 0.0001) and a combined mean concentration from d 10 to 28 of 0.11 6 0.030 mmol/g. Piglets from sows fed WM had higher serum retinol concentrations (0.56 6 0.25 mmol/L; P = 0.0098) despite lower liver retinol concentrations of 0.068 6 0.026 mmol/g from d 10 to 28. Milk was collected at 0, 5, 10, 20, and 28 d. Sows fed OM had a higher milk retinol concentration (1.36 6 1.30 mmol/L; P = 0.038), than those fed WM (0.93 61.03 mmol/L). Sow livers were collected at the end of the study (n = 3/group) and had identical retinol concentrations (0.22 6 0.05 mmol/g). Consumption of daily provitamin A carotenoids by sows during gestation and lactation increased liver retinol status in weanling piglets, illustrating the potential for provitamin A carotenoid consumption from biofortified staple foods to improve vitamin A reserves. Biofortified OM could have a measurable impact on vitamin A status in deficient populations if widely adopted. J. Nutr. doi: 10.3945/jn.113.175679.
Erratum to: “Rapid photometric and spectroscopic evolution of the young planetary nebula Hen 3-1357 and its central star SAO 244567”

Field: Physics and Astronomy (Physical Sciences)

Based on data from the IRAS point source catalogue (Beichmann et al. 1985), Parthasarathy and Pottasch (1989) suggested that SAO 244567 is a post-AGB star and also estimated the temperature, mass, and luminosity of the dust shell surrounding the star.
Development Of The Banking System Of The Russian Federation, Its Problems And Prospect

Field: Economics, Econometrics and Finance (Social Sciences)

This article describes the development of the Russian banking system, modern problems, and prospects of its development. It shows the changes in the functioning of the financial sector, since the period of its functioning in the market economy and to the present. The illuminated impact of the crisis on the development of the banking system, as well as the problems faced by the banking system in 2015. The perspective directions of development of the banking sector, which will help it to emerge from the crisis until 2020. For writing the work was used common, (analysis, synthesis, classification, etc.) and practical (observation, comparison, etc.) methods. In the process, information was obtained about the development of the banking system, as well as the complexities of its functioning in the market economy. Analyzed the measures needed for the modernization of the banking sector and improving the competitiveness of the Russian banking sector.
Comparison of the SUMO1 and ubiquitin conjugation pathways during the inhibition of proteasome activity with evidence of SUMO1 recycling

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

To investigate potential interplay between the SUMO1 (small ubiquitin-related modifier-1) and ubiquitin pathways of post-translational protein modification, we examined aspects of their localization and conjugation status during proteasome inhibition. Our results indicate that these pathways converge upon the discrete sub-nuclear domains known as PML (promyelocytic leukaemia protein) NBs (nuclear bodies). Proteasome inhibition generated an increased number of PML bodies, without any obvious increase in size. Using a cell line that constitutively expresses an epitope-tagged version of SUMO1, which was incorporated into high-molecular-mass conjugates, we observed SUMO1 accumulating in clusters around a subset of the NBs. Nuclear ubiquitin was initially observed in numerous speckles and foci, which bore no relationship to PML NBs in the absence of proteasome inhibition. However, during proteasome inhibition, total ubiquitin-conjugated species increased in the cell, as judged by Western blotting. Concomitantly the number of nuclear ubiquitin clusters decreased, and were almost quantitatively associated with the PML NBs, co-localizing with the SUMO-conjugated pool. Proteasome inhibition depleted the pool of free SUMO1 in the cell. Reversal of proteasome inhibition in the presence or absence of protein synthesis demonstrated that free SUMO1 was regenerated from the conjugated pool. The results indicate that a significant fraction of the free SUMO1 pool could be accounted for by recycling from the conjugated pool and indeed it may be that, as for ubiquitin, SUMO1 needs to be removed from conjugated species prior to processing by the proteasome. Taken together with other recent reports on the proteasome and PML NBs, these results suggest that the PML NBs may play an important role in integrating these pathways.
Investigating the Mechanical Enhancement of Epoxy Composites with Human Hair

Field: Materials Science (Physical Sciences)

This study examines the utilization of human hair as a reinforcing material in epoxy-based composites. By conducting a series of experiments, the research investigates how various proportions of hair impact the properties of these composites. The results indicate that increasing the amount of hair significantly improves the strength of the materials. This research not only contributes to material engineering by repurposing a waste product but also holds potential for applications in industries such as automotive and aerospace where strong and lightweight materials are crucial.
Visual Complexity of Websites and its Effects on Users' Impressions, Psychophysiological Responses, Recognition Rate and Visual Search Time

Field: Psychology (Social Sciences)

Visual complexity is an apparent feature in website design yet its effects on cognitive and emotional processing are not well understood. The current study examined website complexity within the framework of aesthetic theory and psychophysiological research on cognition and emotion. We hypothesized that increasing the complexity of websites would have a detrimental cognitive and emotional impact on users. In a passive viewing task (PVT) 36 website screenshots differing in their degree of complexity (operationalized by JPEG file size; correlation with complexity ratings in a preliminary study r=.80) were presented to 48 participants in randomized order. Additionally, a standardized visual search task (VST) assessing reaction times, and a one-week-delayed recognition task on these websites were conducted and participants rated all websites for arousal and valence. Psychophysiological responses were assessed during the PVT and VST. Visual complexity was related to increased experienced arousal, more negative valence appraisal, decreased heart rate, and increased facial muscle tension (musculus corrugator). Visual complexity resulted in increased reaction times in the VST and decreased recognition rates. Reaction times in the VST were related to increases in heart rate and electrodermal activity. These findings demonstrate that visual complexity of websites has multiple effects on human cognition and emotion, including experienced pleasure and arousal, facial expression, autonomic nervous system activation, task performance, and memory. It should thus be considered an important factor in website design.