jimnoneill/paper-to-field-training huggingface dataset:
Caudoventral coxofemoral luxation in a mature Holstein dairy cow

Field: Veterinary (Health Sciences)

"Logic", a 3-1/2 year old lactating Holstein dairy cow, presented to the Cornell University Hospital for Animals in January 2008 with a history of being knocked down by another cow. Upon her arrival, she had already been recumbent for 4 days. There was marked swelling of the gluteal and caudal thigh muscles, crepitus on flexion and extension, and an abnormally abducted left hind limb. With this history and presentation, coxofemoral luxation should be high on a list of differential diagnoses. Caudoventral coxofemoral luxation was diagnosed based on a palpable head of the femur within the obturator foramen and confirmed by radiographs. Closed reduction was attempted and determined successful but reluxation was diagnosed several hours later. Due to the value of the animal, the owners elected to attempt open reduction, but pre-operative radiographs revealed a femoral neck fracture. She was euthanized due to the grave prognosis associated with femoral neck fractures in adult cattle. This case report was used as an example to review the diagnosis, incidence, treatments, prognosis and complications associated with coxofemoral luxations in cattle.
Towards understanding the regulation of rubber biosynthesis: Insights into the initiator and elongator enzymes

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

Natural rubber is an important polymer produced by plants and made up of isoprene units derived from isopentenyl diphosphate (IPP). Although more than 2000 plant species are known to produce natural rubber, currently there are two important commercial sources, Hevea brasiliensis (the Brazilian rubber tree) andParthenium argentatum Gray (guayule). Natural rubber biosynthesis requires three distinct biochemical processes such as (i) initiation, (ii) elongation and (iii) termination. Computational analyses of the enzymes farnesyl diphosphate (FPP) synthase in P. argentatum and cis-prenyl transferase (CPT) in H. brasiliensis thatplay a vital role in initiation and elongation stages for biosynthesis of cis-1,4-polyisoprene has been undertaken in this study. Amino acid sequence comparisons of FPP synthase and CPT to their identified similar sequences were carried out to understand the evolutionary relationship among different species. Homology modeling and binding pocket analysis aided in the understanding of structure-function relationship and enzyme-substrate interaction of FPP synthase and CPT. The structural templates farnesyl diphosphate synthase (Source: Gallus gallus) [PDB ID: 1UBX] for FPP synthase and undecaprenyl diphosphate synthase (Source: Micrococcus luteus B-P 26) [PDB ID: 1F75] for CPT were selected for homology modeling. The Ramachandran plots were developed for modeled structures of FPP synthase and CPT, which showed 95.9 and 92.6% of amino acid residues occurring in favored regions. These models were deposited into Protein Model Database [PMDB ID: PM0075218 and PM0075509]. The substrate and cofactor binding site residues of FPP synthase (R103, L149, A184, Y197, L211, H214, E223, T226, D332, K246, Y306, K313) and CPT (Y4, E7, R20, K21, G22, K154, K178, D193, E231, T232, R233) were identified by using binding pocket analysis, which is consistent with available X-ray crystal structure of both the templates. The computational analysis of initiation and elongation for cis-1,4-polyisoprene biosynthesis provided invaluable insights into the identification of putative initiation and elongation factors for FPP synthase and CPT.

Key words: Cis-prenyl transferase, deep view, errat, farnesyl diphosphate synthase, Hevea brasiliensis, MODELLER, Parthenium argentatum, protein model database.
Accelerated Weight Histogram Method for Rare Event Simulations

Field: Mathematics (Physical Sciences)

We describe an adaptive Markov chain Monte Carlo method suitable for the estimation of rare failure probabilities in complex probabilistic models. This method, the Accelerated Weight Histogram (AWH) method, has its origin in statistical physics (Lidmar, 2012) and has successfully been applied to molecular dynamics simulations in biophysics. Here we introduce it in the context of structural reliability and demonstrate its usefulness for calculation of failure probabilities in some selected problems of varying degrees of complexity and compare with other established techniques, e.g., subset simulations.
Impact of Milk Consumption and Resistance Training on Body Composition of Female Athletes

Field: Medicine (Health Sciences)

Resistance exercise (RE) preceding the provision of high-quality dairy protein supports muscle anabolism. Milk contains bioactive components, including two high-quality protein fractions, calcium and vitamin D, each of which has been shown modulate body composition (increasing lean mass and decreasing fat mass) under energy balance and hypoenergetic conditions. These dairy nutrients are also essential for skeletal health. Acutely, no study of RE and milk/whey consumption has been undertaken exclusively in female athletes, let alone women, nevertheless, studies with both men and women show increased lean mass accretion following milk/whey compared to soy/placebo. Currently, no longer-term RE studies with milk supplementation have been done in female athletes. However, trials in young recreationally active women demonstrated augmented increases in lean mass and decreases in fat mass with RE and milk or whey protein consumption. The amount of protein consumed post-exercise is also important; two trials using yogurt (5 g protein/6 oz) failed to demonstrate a positive change in body composition compared to placebo. For bone health, RE plus dairy improved bone mineral density at clinically important sites and reduced bone resorption. With energy restriction, in one study, higher dairy plus higher protein resulted in greater fat loss, lean mass gain and improved bone health in overweight women. In another study, milk and calcium supplementation showed no greater benefit. Neither trial exclusively utilized RE. Overall, RE and milk/dairy consumption positively impact body composition in women by promoting losses in fat, gains or maintenance of lean mass and preservation of bone. Future studies in female athletes and under energy restriction with RE alone are warranted.
Effect of rGO Addition Toward Photocatalyst Properties of ZnO/rGO/TiO<sub>2</sub> for Rhodamine B Degradation

Field: Chemistry (Physical Sciences)

The growth of the textile industry in Indonesia has resulted in increased textile dye waste production. Rhodamine B is one of the dyes that are often used in the textile industry. The use of these dyes will cause serious environmental and biological problems, even able to induce irritation of the skin and eyes. Thus, it is necessary to filter dyes from the textile industry waste in Indonesia. Some conventional methods for removing Rhodamine B are carried out by biochemical and physical-chemical methods, such as liquid membranes, ozonation and adsorption, but this method requires expensive and not very effective costs. One alternative method that can be applied in Indonesia is photocatalysts. Photocatalytics are processes where light and catalyst are simultaneously used to accelerate chemical reactions. In this study, the photocatalyst used was semiconductor material ZnO and TiO 2 with the addition of rGO. rGO synthesis was carried out using the Hummer method, for the synthesis of ZnO using Zinc powder as a precursor, and the synthesis of TiO 2 using precursor of TiCl 3 . This study was conducted to analyze the effect of adding 5%, 10%, and 15% rGO to the photocatalytic properties of ZnO / rGO / TiO 2 composites for degradation of Rhodamine B. The characterization process carried out in this study included XRD, SEM & EDX, FTIR, and photocatalytic testing. Photocatalyst materials ZnO / rGO / TiO 2 with variations in the amount of rGO were synthesized as evidenced by XRD testing, where there was a peak for all three component, SEM, shows the morphology of Zn in the form of hexagonal nano rod, rGO in the form of transparent sheets and TiO 2 in the form of agglomerated balls. From FTIR testing, rGO and TiO 2 functional groups were seen. The highest efficiency for degradation of Rhodamine-B was obtained for the addition of 15% rGO with a 5-hour irradiation time, ie its efficiency reached 96.92% in degradation of Rhodamine B.
Studying Pre-Columbian Interaction Networks

Field: Social Sciences (Social Sciences)

There is a single idea to which every Caribbean archaeologist has subscribed: The idea that the history of the indigenous Caribbean is best described from a network perspective, which is most successfully achieved by studying the mobility of its people and their exchange of material and immaterial cultures. This article examines the concepts of mobility and exchange as they have been used in Caribbean archaeology and how they could be used to an even greater effect in the future. First, it discusses the history of research and recent conceptual trends in the regional archaeology of mobility and exchange. Second, the article describes how the distinct materialities of the networks that created this highly interrelated pre-Columbian past could be studied through a single theoretical and analytical network approach. It regards “mobility” as a concept encompassing the range of motivations and types of movement of people at multiple scales.
Vortigern and Aetius—a re-appraisal

Field: Arts and Humanities (Social Sciences)

Vortigern of Gloucester is perhaps the most maligned figure of British history. There can be little doubt that his reign ended in widespread disaster, but that very fact may have made him a traditional scapegoat. Some at least of the charges against him can readily be disproved—for instance, he certainly was not the father of the British-born Gallic Bishop, Faustus, by his daughter or anyone else. Faustus and Vortigern must have been born within a very few years of each other. Perhaps the Gildasian epithet of infuustus tyrunnus , applied to Vortigern, served as a starting-point.
Effects of positive end-expiratory pressure ventilation and extracorporeal ultrafiltration method in patients with refractory heart failure.

Field: Medicine (Health Sciences)

We studied the effects of positive end-expiratory pressure (PEEP) ventilation in ten patients with acute myocardial infarction (nine in Killip class III, one in Killip class IV; pulmonary capillary wedge pressure greater than 24 mmHg) and of extracorporeal ultrafiltration method (ECUM) in seven patients with refractory heart failure due to acute myocardial infarction and others. Application of PEEP resulted in significant increases in PaO2 and SaO2 and decrease in PaCO2. Significant reduction in mean pulmonary arterial and pulmonary capillary wedge pressures and heart rate was observed, while stroke work index increased significantly. There was a significant correlation between changes in stroke work index and PaO2 after the application of PEEP. The use of ECUM removed fluid of 1416 +/- 662 ml (680-2800 ml) with the ultrafiltration flux rate being 478 +/- 223 ml/hour. Significant decreases in mean pulmonary arterial, pulmonary capillary wedge and central venous pressures were observed, while PaO2 increased significantly. BUN and serum creatinine levels increased significantly, and total protein and serum albumin tended to increase. There was a significant correlation between fluid removed and change in PaO2 after the use of ECUM. Thus, PEEP and ECUM are beneficial for patients with refractory heart failure. The mechanism(s) are: reduction in preload due to an increased intrathoracic pressure and a decreased systemic venous return with PEEP, or due to removal of excess fluid with ECUM, and improvement of the oxygenation of the blood.
Trypsinogen mutations in hereditary pancreatitis: which nomenclature is convenient?

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

Viral vectors derived from different virus families, including poxvirus (canarypox virus vector ALVAC) and adenovirus (human Ad5 vector), have been widely used in vaccine development for a range of human diseases including HIV/AIDS. Less is known about the mechanisms underlying the host innate response to these vectors. Increasing evidence from clinical vaccine trials testing different viral vectors has suggested the importance of understanding basic elements of host–viral vector interactions. In this study, we investigated the innate interactions of APCs with two commonly used HIV vaccine vectors, ALVAC and Ad5, and identified AIM2 as an innate sensor for ALVAC, triggering strong inflammasome activation in both human and mouse APCs. Microarray and comprehensive gene-knockout analyses (CRISPR/Cas9) identified that ALVAC stimulated the cGAS/IFI16–STING–type I IFN pathway to prime AIM2, which was functionally required for ALVAC-induced inflammasome activation. We also provided evidence that, in contrast to ALVAC, the Ad5 vector itself was unable to induce inflammasome activation, which was related to its inability to stimulate the STING–type I IFN pathway and to provide inflammasome-priming signals. In preconditioned APCs, the Ad5 vector could stimulate inflammasome activation through an AIM2-independent mechanism. Therefore, our study identifies the AIM2 inflammasome and cGAS/IFI16–STING–type I IFN pathway as a novel mechanism for host innate immunity to the ALVAC vaccine vector.
A Framework for Pore‐Scale Simulation of Effective Electrical Conductivity and Permittivity of Porous Media in the Frequency Range From 1 mHz to 1 GHz

Field: Earth and Planetary Sciences (Physical Sciences)

Abstract Geoelectrical methods are broadly used in earth sciences for various purposes. To correctly interpret field geoelectrical data, it is essential to have a mechanistic understanding of the effective electrical conductivity and permittivity of geological materials over a broad frequency range. Recently, the pore‐scale numerical simulation, which utilizes the digital microstructural images of the material, has become a powerful tool in studying the effective electrical properties of geological media. However, it is still difficult to incorporate surface‐related electrochemical processes in a pore‐scale simulation. In this study, we develop a general framework to consider these electrochemical processes in pore‐scale simulations, which enable the calculation of broadband effective electrical conductivity and permittivity of porous geological media. A Berea sandstone sample is utilized to demonstrate the use of the proposed framework. Laboratory experiments of the effective electrical conductivity and permittivity of the sample in the frequency range from 10 −3 to 10 9 Hz provided valuable measurement data for validating the simulation. The good agreement between our simulated spectra and the experimental data provides validation for the numerical simulation to reproduce the variations in the effective electrical conductivity and permittivity of porous geological materials induced by both the electrochemical polarizations and the interfacial polarization. This work thus provides a useful tool for studying the effective electrical properties of porous geological materials featuring complex microstructures.
VROA spectra in solvent.

Field: Chemistry (Physical Sciences)

This dataset includes the output files from Gaussian16 calculations including solvent effects through the usage of the C-PCM framework. Gas-phase geometries are labeled as GP+PCM, while the re-optimized geometries have been labeled as PCM. All calculations employed B3LYP-D3(BJ) with the aug-cc-pVDZ and def2-SVPD basis sets.
Semi-Automatic Ontology Engineering in Business Applications

Field: Computer Science (Physical Sciences)

Abstract: Search technology can be applied to many applications and is in the heart of always growing information society. A promising new development is the use of ontologies to enable semantic modeling of data and user queries. Generation and maintenance of ontologies are a costly thing though. We propose a framework to build and maintain ontologies in a semi-automatic way. The article motivates the development from application point of view, relates to work known from the literature and introduces the so-called ontology workbench. 1
Molecular Phylogeny of Polychaos annulatum (Amoebozoa, Tubulinea, Euamoebida) Shows that Genus Polychaos Belongs to the Family Hartmannellidae

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

Abstract We have obtained a sequence of the 18S rRNA gene of the species Polychaos annulatum (Penard 1902) Smirnov et Goodkov 1998 using the isolation of a single nucleus from an amoeba cell. Attempts to amplify the 18S rRNA gene from the DNA of this species by conventional PCR were not successful, so we applied the whole genome amplification of the nuclear DNA followed by NGS sequencing. The 18S rRNA gene was found among the resulting contigs. The analysis unexpectedly shows that P. annulatum robustly groups within the family Hartmannellidae, but not Amoebidae. This finding warrants revision of the basic morphological criteria used to classify Euamoebida families and show that “proteus‐type” amoebae may belong to other families rather than Amoebidae. This makes taxonomic assignments of such species more complex and the borders between Euamoebida families more nuanced. It is getting evident that molecular data are necessary to clarify the position of species even in this most “classical” order of naked lobose amoebae.
Azo-Coupling Reactions. I. The Couplin g Reaction of J Acid

Field: Chemistry (Physical Sciences)

J酸(6-アミノ-1-ナフトール-3-スルホン酸)の芳香族ジアゾ化合物に対する反応性を明らかにするために,P-ジアゾトルエン(I)またはp-ジアゾクロルベンゼン(II)をJ酸およびNW酸(1-ナフトール-4-スルホン酸)に種々のpHにおいて競争的カップリングを行なった。生成物中の各色素をペーパークロマトグラフィーにより分離し比色法によりそれらの生成量を定量した。生成色素のモル比から,みかけの速度定数比kOH/k'NWおよびk'NH2/k'NW(添字のOH,NH2およびNWはそれぞれJ酸の2-および5-およびNW酸の2-位置におけるカップリング反応を示す)を求めた。カップリング成分の反応種がナフトレートイオンおよび遊離アミンであるとした真の速度定数比kOH/kNWおよびkNH2/kNWをみかけの速度定数比およびJ酸とNW酸のPKa値より求めた。kOH/kNWはIのとき85.8,IIのとき212であった。kOH/kNWはpHに無関係であるべきであるが高pH域で減少し,またkNH2/kNWはpHとともに増加する。このkNH2/kNWの挙動はJ酸の5-位のカップリングにはナフトール型とナフトレート型の二つの反応種が関係していることから説明される。ナフトール型の速度定数比kNH2-1/kNWおよびナフトレート型の速度定数比kNH2-1/kNWはIのとき,それぞれ0.05, 0.3であり,IIのときは0.05, 0.25であった。
Napoléon et l’Empire de l’opinion : acteurs et enjeux du contrôle de l’opinion publique sous le Premier Empire

Field: Arts and Humanities (Social Sciences)

This article outlines the history of the administration in charge of the regulation and control of public opinion during the French Empire. The context of this regulation is delineated by examining how Napoleon intended, as early as the Consulate, to merge the Ancien Regime traditions with the new values of the Revolution. This project acknowledges innovative developments in public opinion management, in the shaping of political legitimacy after 1789. I will examine three unpublished manuscripts produced by this administration in order to illustrate the administrative and political implications of the imperial control of public opinion. In addition, I will analyze the historical issues at stake determined by different figures who played a role in this administration.
A Free State for India With a Regional Plan for a New Constitution

Field: Social Sciences (Social Sciences)

Journal Article A Free State for India With a Regional Plan for a New Constitution Get access A Free State for India With a Regional Plan for a New Constitution. By A. S. N. Murti, Member, Indian Institute of International Affairs. 1946. (Berhampur, Gamjam, India. 8½″ × 5¼″. 108 pp. Not for sale.) N. F. N. F. Search for other works by this author on: Oxford Academic Google Scholar International Affairs, Volume 23, Issue 2, April 1947, Page 276, https://doi.org/10.2307/3018954 Published: 01 April 1947
Downregulation of HADH promotes gastric cancer progression via Akt signaling pathway

Field: Medicine (Health Sciences)

HADH is a key enzyme in fatty acid oxidation. The aim of this study was to identify the role of HADH in gastric cancer. We analyzed the expression of HADH in 102 pairs of gastric cancer samples. Western blot analysis revealed that HADH was decreased in stage I/II gastric cancer samples compared to matched adjacent normal gastric tissue, and its expression was further decreased in stage III/IV samples. Importantly, the reduced expression of HADH was associated with increased expression of p-Akt and reduced expression of PTEN in the gastric carcinoma tumor samples. To determine the significance of HADH downregulation in gastric cancer progression, we tested the impact of HADH knockdown or overexpression on the migration and invasion of the gastric cancer cells using a transwell assay. Knockdown of HADH significantly promoted gastric cancer cell migration and invasion, which was associated with increased expression of p-Akt. The PI3K inhibitor LY294002 inhibited HADH shRNA induced migration/invasion, and abolished the upregulation of p-Akt. By contrast, HADH overexpression inhibited the migration and invasion of MKN45 cells. Herein, for the first time, we demonstrate that downregulation of HADH promotes gastric cancer progression via activation of Akt signaling pathway.
Muscle relaxants: a clinical update.

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

The new nondepolarizing muscle relaxant rocuronium belongs to the chemical group of aminosteroidal muscle relaxants and is similar to vecuronium in its chemical structure and pharmacologic action. The principal clinical advantage of rocuronium over vecuronium is the short time to onset of the neuromuscular block. The two other new muscle relaxants, mivacurium and cis-atracurium, belong to the group of benzylisoquinoline muscle relaxants. Mivacurium is rapidly degraded in plasma and its principal characteristic is, hence, a short duration of action. Cis-atracurium is one of the 10 stereoisomers of atracurium. While its action is similar to that of atracurium, it does not release histamine and its administration is not accompanied by marked changes in blood pressure or heart rate. Even the simple tactile monitoring of the neuromuscular transmission enables the clinician to adjust the doses of these and other muscle relaxants to the needs of individual patients. Precise adjustment of the doses of muscle relaxants contributes to their safer clinical use by avoiding an excessively deep and unnecessarily prolonged neuromuscular block.