jimnoneill/paper-to-field-training huggingface dataset:
Correlating membrane‐protein dynamics with function: Integrating bioinformatics, molecular dynamics, and single‐molecule FRET

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

Abstract We present a strategy that deploys structural bioinformatics, molecular simulation, and single‐molecule Förster Resonance Energy Transfer (FRET) microscopy for observing the ligand‐dependent conformational dynamics of integral membrane proteins in situ. We focus on representative members of the small monotopic phosphoglycosyl transferase (SmPGT) superfamily, which catalyze the transfer of a phosphosugar from a soluble nucleotide‐sugar donor to a membrane‐embedded polyprenol phosphate acceptor in the initiating step of glycoconjugate biosynthesis in prokaryotes. Substrate‐specific structural features were identified across the superfamily and correlated with ligand‐dependent conformational dynamics in all‐atom simulations. To experimentally validate the role of this motion in ligand binding, we developed a platform to monitor intramolecular protein dynamics in a native‐like lipid environment. The presented approach incorporates selective cysteine protein labeling and non‐canonical amino acid mutagenesis with bicyclononyne‐tetrazine click chemistry to assemble dual‐labeled variants of PglC, the initiating enzyme of the N‐linked protein glycosylation pathway from the Campylobacter genus. The modified proteins are solubilized in styrene‐maleic acid liponanoparticles (SMALPs), which provide a model membrane environment. The conformational changes of PglC upon inhibitor binding correlate with inhibitor potency. The single‐molecule FRET‐SMALP strategy can be adapted to investigate protein dynamics across the superfamily of SmPGTs with different substrate selectivity, where structure prediction and molecular dynamics support significant conformational changes upon ligand binding.
Smallpox and Other Orthopoxvirus Diseases

Field: Medicine (Health Sciences)

Smallpox was a severe disease causing substantial mortality among populations over several thousand years. It is caused by an orthopoxvirus, the variola (= smallpox) virus. Smallpox is a febrile disease with a maculo-, papulo-, vesicular and finally pustular rash, the typical pox lesions, numerous complications and a fatality rate of approximately 30%. Material from smallpox patients was used to inoculate healthy subjects (“variolation”) in medieval China, possibly offering some protection, but it was associated with high risk of complications and death. In 1796, the English physician Edward Jenner discovered that material from cowpox lesions inoculated into healthy subjects protected against smallpox in a comparatively safe way. This discovery was the invention of vaccination. Vaccination campaigns in the 19th and 20th century controlled smallpox, and following a global WHO-coordinated eradication campaign, it was finally declared eradicated by 1980. Other orthopoxviruses, such as the monkeypox virus, are still causing human disease in some geographies and may be emerging due to waning population immunity and population growth in previously rural or forested areas. Two antiviral compounds have been licensed for specific treatment. Various vaccines based on Jenner’s invention, using scarification with replicating live vaccinia strains, are still available globally for outbreaks. In the Western world, two smallpox vaccines are licensed and stockpiled today for emergency use: ACAM2000, a cell culture GMP-produced vaccinia strain; and a non-replicating, “Modified Vaccinia Ankara” (MVA) vaccine, GMP-produced on chicken embryo fibroblasts.
SH0903983.09FU

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

UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
Experience with Groin Flap As A Cover for Hand and Fore-Arm

Field: Medicine (Health Sciences)

Summary This paper described our experience with groin flap as a full thickness cover for hand and lower forearm and in the reconstruction of first web. Advantages of groin flap in comparision to direct flaps, tube pedicle and the deito-pectoral flap have been discussed. Steps of the operative technique and the stages of transfer have been described.
Microwave Dielectric Permeability and Relaxation of Aqueous Solutions of 2,2-Dimethyl-1,3-Dioxolane

Field: Chemistry (Physical Sciences)

Results are presented from measuring the microwave dielectric properties of aqueous solutions of 2,2-dimethyl-1,3-dioxolane at seven frequencies in the range of 5–25 GHz at temperatures of 288, 298, 308 K. Static dielectric constants, activation parameters and relaxation times are calculated for the process of dielectric relaxation. The effect nonpolar groups of molecules have on water are considered.
Panax notoginseng saponins reduces damage and inhibits apoptosis in lung ischemia reperfusion injury of rabbits

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

Objective To explore potential relationship between apoptosis in the lung tissues and lung ischemia reperfusion injury,and to observe the effects of PNS by regulating apoptosis in lung ischemia reperfusion injury.Methods Eighty-four Japanese white rabbits were randomly divided into control group(control),ischemia reperfusion 1 h group(IR1h),IR3h,IR5h,panax notoginseng saponins 1 h group(PNS1h),PNS3h and PNS5h.The terminal deoxynucleotidyl transferase-mediate dUTP end labeling(TUNEL) and in situ hybridization were performed to observe apoptosis;Fas,FasL mRNA and caspase-3 mRNA expression in various phases of lung ischemia reperfusion;DNA fragmentation was observed by polyacrylamide gel electrophoresis(PAGE).Results Cell apoptosis(IR5h:22.08±1.93;control:2.04±0.67) in lung tissue of rabbits with lung ischemia reperfusion was significantly higher than in control group(P0.01),especially in pulmonary vascular endothelial cells and alveolar epithelial cells.Fas/FasL mRNA and caspase-3 mRNA(IR5h:0.241±0.029;control:0.121±0.015) were up-regulated in lung tissues of lung ischemia reperfusion injury than in those of control groups(P0.01).The PNS suppressed apoptosis as well as expression of Fas/FasL mRNA and caspase-3 mRNA(PNS5h:0.199±0.020,IR5h:0.241±0.029,P0.01).There was a significant correlation between expression of Fas/FasL mRNA,caspase-3 mRNA and cell apoptosis(P0.01).DNA ladder appeared in IR5h group,but not seen in PNS5h group.Conclusion The protective effects of PNS include suppressing the activation of Fas/FasL system and blocking apoptosis in lung tissues of lung ischemia reperfusion rabbits.
Derivation of the Optical Constants of Gold from Transmission Diffraction Measurements in the 280—640-eV Range

Field: Physics and Astronomy (Physical Sciences)

Eqs. (3) should be q.In the line following Eqs.(3), v. V should be replaced by v V.A phase error in the computer code affected de- tails of the results for P3a0 and cu )0.The nu- merical values of V, (m), and (j") that are quoted in the text are thus somewhat inaccurate.In the
TunGPR: Enhancing data-driven maintenance for tunnel linings through synthetic datasets, deep learning and BIM

Field: Engineering (Physical Sciences)

Non-destructive Testing (NDT) techniques and data-driven technologies are increasingly applied in underground infrastructure maintenance, which can facilitate predictive monitoring for informed decision-making. Ground Penetrating Radar (GPR) is extensively utilised in rapid condition assessment of tunnel linings, particularly for detecting defects that lead to unforeseen changes of dielectric properties of materials. In this paper, a prototyped framework is proposed, namely TunGPR, for GPR-based tunnel lining assessment by incorporating Building Information Modelling (BIM), synthetic database and deep learning-enabled interpretation. The first module integrates laser-scanned point clouds and GPR Scan-to-BIM of tunnel lining with geological model. Subsequently, interoperability is achieved between the geo-integrated BIM and GPR simulation software. From the dielectric model retrieved from the BIM model, a database is established, considering a variety of condition combinations (i.e., voids, cavities, delamination, and water intrusion) leveraging domain randomisation and Finite-Difference Time-Domain (FDTD) modelling, as well as monitored field data. The dataset is then fed into the diagnostic module underpinned by a dual-rotational Convolutional Neural Network (CNN) that is customised to enhance accuracy and automation of hyperbola detection. Lastly, a preliminary risk assessment matrix is implemented into the BIM model for data management and action prioritisation. These efforts serve as an initial step to validate the feasibility and effectiveness of the GPR-enabled data-driven maintenance for tunnel linings in a BIM-centred framework.
Pathogenic Role of Cyclic AMP in the Impairment of Urinary Concentrating Ability in Acute Hypercalcemia

Field: Medicine (Health Sciences)

A possible association between the impairment of urinary concentrating ability and an impairment of the vasopressin-dependent cyclic AMP system in hypercalcemia was investigated in rat kidneys both in vivo and in vitro. The increases of urinary osmolality and negative free water clearance and the increase of urinary cyclic AMP excretion by vasopressin injection were significantly less in the hypercalcemic rats than in the control rats. The increase of cyclic AMP concentration by vasopressin in renal medullary tissue was significantly less in the slices obtained from the hypercalcem'c rats than in those obtained from the control rats. The activation of adenylate cyclase by vasopressin was significantly less in the group with an increased concentration of calcium in media than the control group, but phosphodiesterase activity was not affected by calcium concentration in the media. These data suggest that the impaired urinary concentrating ability in hypercalcemic kidneys is due at least in part to the direct inhibitory effect of calcium on the vasopressin-dependent cyclic AMP system at the level of adenylate cyclase in renal medulla.
Unveiling the effect of polymer on pipeline corrosion

Field: Chemical Engineering (Physical Sciences)

This study unveiled the corrosion modification potential of an enhanced oil recovery polymer on flowline material in different saline environments. Polymers such as xanthan gum are usually used to control the mobility of the displacing fluid during flooding process to achieve better sweep efficiency. These polymers and brines are normally transported through flowlines into and from reservoirs, but their effect on flowline materials is not known. The weight loss method was used to study the corrosion rates of mild steel of known weights that were exposed to 0%, 10%, 50%, and 100% formation brine environments and varied concentrations (0.5%, 1%, 3%, and 5%) of xanthan gum for a total period of 432 hours. The results showed that the corrosion rate of mild steel increases with increase in exposure time, but the use of xanthan gum generally reduced the corrosion rates. Also, the corrosion rate of mild steel reduces with an increase in the concentrations of xanthan gum. Furthermore, higher corrosion inhibition efficiencies (>70%) were observed in 10% formation brine environment and the effective corrosion inhibition concentration of xanthan gum was found to be 1 wt.% in all saline environments investigated. Conclusively, from the results of this study, it is evident that the application of xanthan gum polymer commonly used in the enhanced oil recovery process has the potential to reduce the corrosion rate of mild steel in saline environments. The result of this study is significant for the design of polymer-enhanced oil recovery operations.
The Effects of Chest Constriction at Rest on Aerobic Capacity

Field: Medicine (Health Sciences)

PURPOSE: This was a pilot study investigating whether an externally applied thoracic constriction band at rest over a four-week period, can improve aerobic capacity without having to perform aerobic exercise. METHODS: 15 sedentary college age individuals (between 18–35 yrs) were studied over a period of 4 weeks during which they participated in their normal everyday activities. Participants completed an activity questionnaire, a Physical Activity Readiness Questionnaire (Par-Q) and an aerobic capacity (VO2max) test. VO2max was measured Pre and Post 4 weeks using the 1.5-mile run/walk field test. Participants were instructed to cover the specified distance in the fastest time possible. A VO prediction equation (VO2max (ml kg−1. min−1) = 3.5 + 483/ (time in minutes)) was used. Following pre testing, participants were randomly placed into one of two groups: (1) Chest Wall Restriction Group (CWR) (n = 10), or (2) Control (Non-Chest Wall Restriction Group (N-CWR)) (n=5). Each participant in the Chest Wall Restriction Group (CWR) had their chest wall restricted with the use of an elastic strap for 1.5 hours 5 days/week. Strap widths ranged from 10 to 15 cm adjusted to fit just beneath the axillae and around the chest to envelop the rib cage. It is worth noting that this apparatus does not prevent the chest wall from expanding like earlier studies, but offers elastic eccentric resistance for the inspiratory muscles to work against. RESULTS: A significant 11 ± .07% improvement in aerobic capacity was observed in the experimental group (P <0.05). Estimated VO2max values for CWR increased from 27.92 ±5.98 to 31.46 ± 6.42, while the N-CWR group showed no significant change (30.22 ± 5.67 to 30.51 ±5.61). Units for VO2max are shown in ml.min−1. kg−1 ± SD. CONCLUSION: This pilot study shows the potential benefit of wearing an externally applied thoracic constriction band at rest. Sedentary individuals with low exercise tolerance may be able to increase their aerobic capacity without performing aerobic exercise.
Human Chorionic Gonadotropin Pattern in Serum and Its Relation to the Sex of the Fetus

Field: Medicine (Health Sciences)

The pattern of the human chorionic gonadotropin (HCG) level in serum throughout pregnancy has been established in longitudinal studies on 20 healthy women. Blood samples obtained at intervals of 3–4 weeks have been analyzed by means of a quantitative immunoassay procedure based on complement fixation. A biphasic course of the HCG level has been confirmed; a relatively sharp and acute peak in the first trimester and a comparatively small rise in the last 3 months are separated by an intervening low-level period in midpregnancy. A considerable individual scatter of the HCG levels is observed, particularly in the last trimester. A relation has been found between the sex of the fetus and the height of the HCG level during this period. In women with low HCG values there is a predominance of male fetuses, and in subjects with high levels a preponderance of female fetuses is observed. The statistical significance for a difference between male-fetus and female-fetus pregnancies is at the 0.5% level.
An Explainable Deep Model for Defect Prediction

Field: Computer Science (Physical Sciences)

Self attention transformer encoders represent an effective method for sequence to class prediction tasks as they can disentangle long distance dependencies and have many regularising effects. We achieve results substantially better than state of the art in one such task, namely, defect prediction and with many added benefits. Existing techniques do not normalise for correlations that are inversely proportional to the usefulness of the prediction but do, in fact, go further, specifically exploiting these features which is tantamount to data leakage. Our model is end-to-end trainable and has the potential capability to explain its prediction. This explainability provides insights and potential causes of a model's decisions, the absence of which has stopped defect prediction from gaining any traction in industry.
Analogies of the Sacrament in Sixteenth-Century French and Spanish Ethnography: Jean de Léry and José de Acosta.

Field: Arts and Humanities (Social Sciences)

This article uses the controversies surrounding the Eucharist in post-Reformation Europe to frame a comparison of two prominent ethnographic texts of the late sixteenth century. Calvinist Jean de Léry's Histoire d'un voyage fait en la terre du Brésil (1578) and Jesuit father José de Acosta's Historia natural y moral de las Indias (1590), both bestsellers in their time, served as important vehicles of knowledge about the New World for European readers. Despite being written from opposite sides of the denominational divide, the two works display notable similarities in their detailed examination of indigenous ritual practices and their insistent use of sacramental analogies to account for the most troubling and the most intriguing components of these practices: human sacrifice and cannibalism. In addition to showing how the analogies that structure ethnographic representation serve polemical and doctrinal ends, I examine how analogy itself functions as a contested site in which the radically divergent assumptions guiding Roman Catholic and Protestant hermeneutics come to the fore.
IDENTIFICATION OF TOURISM POTENTIALS IN CATUR VILLAGE KINTAMANI

Field: Social Sciences (Social Sciences)

ABSTRACTThe community of Catur Village in Kintamani aims to initiate a community-based tourism program (CBT) based on the potential tourist attractions the village possesses, namely coffee plantations, unique culture, and captivating nature in the central mountains of Bali. This study seeks to identify the tourism potentials in Catur Village based on ‘4A’ (Attraction, Accessibility, Amenity and Ancillary Services), and identify the challenges in starting CBT by using PESTLE Analysis. This study utilizes descriptive analysis with qualitative approach. The findings of this study indicate several highly potential tourism attractions in Catur Village. The first is the potential for agro-tourism in the coffee, orange and marigold plantations. There is also potential for eco-tourism in Segeha Waterfall and the hills surrounding the village. Catur Village also has potential culture tourism attractions with the existence of the unique blend of Balinese and Chinese Peranakan cultures in Banjar Lampu and Pura Pebini that has intimate relation with the legend of Dewi Danu and Jaya Pangus. But those attractions are not yet supported with adequate aspects of accessibility, amenity and ancillary services, particularly in terms of accommodation and other supporting facilities.Keywords: tourism, tourist destination, development, village, community-based tourismABSTRAKMasyarakat Desa Catur, Kecamatan Kintamani mencanangkan program pariwisata berbasis masyarkat dalambentuk desa wisata berdasarkan potensi wisata yang ada di desa tersebut, terutama perkebunan kopi, budaya yang unik, dan pemandangan alam yang indah di wilayah pengunungan yang terletak di tengah-tengah pulau Bali. Artikel ini membahas potensi wisata di Desa Catur berdasarkan konsep ‘4A’ (Atraksi, Aksesibilitas, Amenitas, dan Ancillary Services), serta mengidentifikasi tantangan yang dihadapi dalam memulai program desa wisata dengan mengunakan alat analisis PESTLE, dengan melakukan analisis deskriptif dengan pendekatan kualitatif. Temuan dalam penelitian ini mengindentifikasikan beberapa potensi wisata yang menjanjikan di Desa Catur, antara lain wisata agro berupa perkebunan kopi, jeruk, dan bunga gumitir. Di samping itu, Desa Catur juga memiliki potensi ekowisata di Air Terjun Segeha dan perbukitan di sekitar desa, yang dilengkapi dengan penggabungan budaya Bali dan budaya Peranakan Tionghoa yang unik di Banjar lampu, serta wisata rohani di PuraPebini yang memiliki hubungan erat dengan legenda Dewi Danu dan Jaya Pangus.Namun potensi wisata tersebut belum didukung oleh aspek-aspek lain termasukakses, amenitas, dan ancillary services yang memadai, terutama dalam halakomodasi bagi pengunjung.Kata kunci: pariwisata, desa wisata, destinasi wisata, pariwisata berbasismasyarakat
Digital technologies in AIC management

Field: Agricultural and Biological Sciences (Life Sciences)

The article presents a study of the current state of the use of digital technologies in the agro-industrial complex. The development of the agro-industrial complex in the conditions of the digital economy involves the use of innovative, digital, cluster, information and computer technologies, as well as new managerial, economic, organizational methods, with fundamentally new properties, which are aimed at increasing the efficiency of production, management and implementation for all areas of the agro-industrial complex. Based on the analysis of foreign experience, the regulatory framework of the Russian Federation, digital standards, types of digital technologies, the paper considers the types of digital technologies in the agro-industrial complex and the possibility of their use for future development. The methodological basis of the study was the works of domestic scientists-economists on the development of innovations and digital technologies in the agro-industrial complex; general scientific research methods (abstract-logical, economic-statistical, etc.) were used, as well as open analytical materials on the development of digital technologies, the use of artificial intelligence and neural networks in the agro-industrial complex, etc. The article reveals that the range of digital technologies currently being created for the agro-industrial complex is diverse and it is aimed at solving a set of problems: growth of output and the efficiency of the agricultural enterprise, introduction of artificial intelligence; creation of insight based on images; determination of the optimal mixture for agronomic products; monitoring the state of crops; methods of automating irrigation and stimulating farmers, etc. As world best practices show, the use of digital technologies in agriculture makes it possible to achieve economic growth in the industry. However, the main problem of introducing digital technologies in agriculture is the high cost of their implementation.