gebhart/patrepeval huggingface dataset:
‘TB or not TB’: the conundrum of pre-European contact tuberculosis in the Pacific (2020)

Tuberculosis (TB) is a major global health threat, infecting one-third of the world's population. Despite this prominence, the age, origin and spread of the disease have been topics of contentious debate. Molecular studies suggest that <i>Mycobacterium tuberculosis 'sensu stricto'</i>, the most common strain of TB infecting humans today, originated in Africa and from there spread into Europe and Asia. The <i>M. tuberculosis</i> strains most commonly found across the Pacific and the Americas today are most closely related to European strains, supporting a hypothesis that the disease only reached these regions relatively recently via European sailors or settlers. However, this hypothesis is inconsistent with palaeopathological evidence of TB-like lesions in human remains from across the Pacific that predate European contact. Similarly, genetic evidence from pre-European South American mummies challenges the notion of a European introduction of the disease into the Pacific. Here, we review the complex evidence for the age and origin of TB in the Pacific, and discuss key gaps in our knowledge and how these may be addressed. This article is part of the theme issue 'Insights into health and disease from ancient biomolecules'.
Supplementary Figure 2 from Chromosomal Breakpoints in Primary Colon Cancer Cluster at Sites of Structural Variants in the Genome (2023)

Supplementary Figure 2 from Chromosomal Breakpoints in Primary Colon Cancer Cluster at Sites of Structural Variants in the Genome
4: 15 p.m.: FATIGUE PROPERTIES OF FUNCTIONALLY OVERLOADED RAT MUSCLE (1981)

Dept. of Kinesiology, UCLA, L.A., CA 90024 and Dept. of Physiology and Biophysics, DC Irvine, Irvine, CA 92717
Genetic analysis of the 9.5-kilobase virulence plasmid of Yersinia pestis (1988)

The 9.5-kilobase plasmid of Yersinia pestis determines plasminogen activator, coagulase, pesticin, and pesticin immunity activities. We have mapped and cloned the loci encoding these activities and demonstrated that both plasminogen activator and coagulase were determined by the same gene, designated pla. The primary translation product of this gene (38 kilodaltons [kDa]) was processed in two sequential steps to produce peptides of 37 and 35 kDa. The first step in this processing occurred rapidly and probably cotranslationally and was blocked when protein export was inhibited. The second step was much slower and resulted in the presence of both the 37- and 35-kDa species in significant quantities. We also showed that the plasmid had a polA-dependent replicon and identified the region that contained its origin of replication and incompatibility functions.
Structural and Biochemical Analyses of Swine Major Histocompatibility Complex Class I Complexes and Prediction of the Epitope Map of Important Influenza A Virus Strains (2016)

We crystalized and solved the first SLA-3 structure, SLA-3*hs0202, and found that it could present the same IAV peptide with two distinct conformations. Unlike previous findings showing that variable peptide conformations are caused only by the flexibility of the side chains in the groove, the skewing of the α1 and α2 helixes is important in the different peptide conformations in SLA-3*hs0202. We also determined the fundamental motif for SLA-3*hs0202 to be X-(M/A/R)-(N/Q/R/F)-X-X-X-X-X-(V/I) based on a series of structural and biochemical analyses, and 28 SLA-3*hs0202-restricted epitope candidates were identified from important IAV strains. We believe our structure and analyses of pSLA-3*hs0202 can benefit vaccine development to control IAV in swine.
Bone marrow transplantation for Sanfilippo disease type B (1992)

Allogeneic bone marrow transplantation was performed on twins with Sanfilippo B disease. They were the first two patients with this disorder to undergo the procedure. There was definite evidence of engraftment as shown by conversion to donor blood group antigen and tissue type, and increased leukocyte alpha-glucosaminidase activity. Nine years post transplant, neither twin is as handicapped as her untreated brothers were at the same age, although in one twin hyperactivity and behavioural problems, characteristic of the disorder, are present. Details of the twins' intellectual development and growth, their alpha-glucosaminidase activity and urinary glycosaminoglycan excretion are reported.
Topical henna ameliorated capecitabine-induced hand-foot syndrome (2013)

Henna has been used for histories as a medicine, preservative, and cosmetic. Our case underlines the basis to further evaluate the anti-inflammatory, antipyretic, and analgesic effects of henna. We encourage other investigators to publish any similar cases or any other herbal or non-drug therapies. HFS is a common side effect of many drugs, including capecitabine, sorafinib and regorafenib. HFS is bothersome for patients even in low grades and impacts quality of life of patients. HFS cannot be prevented and currently the treatments aimed at controlling syndrome are not very effective. Exploring other potential treatment or management options such as henna is of high value.
Polymerization of glycidol and its derivatives: A new rearrangement polymerization (1985)

Abstract Anionic (KOH) polymerization of glycidol, or its trimethylsilyl ether (TMSGE) followed by hydrolysis, gives a low molecular weight, largely amorphous polymer that is not the reported 1,3‐polyglycidol but, based on 13 C‐NMR, largely a 1,4‐poly(3‐hydroxyoxetane) with much branching. This result is achieved by a simple rearrangement of the usual, propagating secondary oxyanion to a primary one. Substantial amounts of four dimers (5–10%), four trimers, and some tetramers were also found. One dimer was isolated and shown to be glycidyl glycerin, the usual thermal dimer from glycidol. Possible structures of the other dimers are proposed. The polymerization appears to begin with the rapid formation of the glycidoxy anion , formed by base abstraction of a proton from glycidol and by nucleophilic displacement of the SiMe 3 group from TMSGE. Other bases such as KO tert ‐Bu give similar 1,4 polymer for glycidol but, with TMSGE, there is considerable 1,3 polymerization. Detailed mechanisms are proposed. The polymer perpared from R‐TMSGE with KOH was highly crystalline, high melting (166°C), H 2 O soluble, isotactic poly(3‐hydroxyoxetane). The cationic polymerization of tert ‐butyl glycidyl ether (TBGE) and TMSGE gave low molecular weight 1,3 polyethers. The TBGE polymer was all head‐to‐tail whereas the polyglycidol from TMSGE contained extensive head‐to‐head chain units with considerable branching. Mechanisms for these interesting differences are proposed.
Efficient resource selection in distributed visual information systems (1997)

made available at other locations for purposes ranting from diagnostics, distance learning, to electronic c;rnI merce. Accessing these repositories in a distributed setting over either a proprietary or a public network poses a number of challenges.
Parachute deployment experiment for a small capsule dropped from a balloon (1997)

In order to verify the entire functions of a parachute deployment system, applicable to a small space capsule, and to examine the transonic dynamics of the capsule with a blunt nose, a free fall capsule experiment was successfully conducted using a balloon with 30,000 m in volume in September, 1996. The capsule weighed approximately 26 kg, and its configuration was 40 cm in diameter and 20 cm in height. The capsule was released from the balloon gondola at 36 km in altitude, and the maximum descent speed was 1.1 in Mach number 45 seconds after the release. As the velocity increased to supersonic, the capsule pitching amplitude was enlarged due to the dynamic instability, and the angle-of-attach was approximately 30 degrees at maximum. On the other hand, the velocity decreased to subsonic, the oscillation was little damped. The single stage cross-type parachute was directly pulled out by the parachute cover, using newly developed pyrotechnical cover openers. The opening shock was 24 G, and it corresponded with the opening shock coefficient of 1.3. The flight results well met the estimation based on the ground test results, except for the less damping efficiency. This paper presents the outline and the flight results of the balloon-borne drop test. Comparison with wind tunnel tests is also described. Penetrator. In MUSES-C (Mu-rocket Space Engineering Spacecraft #C) mission, which will launch a spacecraft towards a small asteroid, Nereus, in the early 2002, a reentry capsule will be applied so as to bring the asteroid material back to the ground. The current capsule design is tentatively as such the weight of the capsule is 18 kg, and the diameter is 40 cm. Besides, the capsule is covered with the relatively thick ablator materials of 2 to 3 cm in thickness. Thus, inside volume for equipments is quite severe. The capsule is not so heavy that the parachute enables to be a single-stage without a drogue nor a pilot chute. This simplification can reduce both weight and volume. Furthermore, the parachute is rigged in the torus-shaped container, so as to keep the maximum space for measurement and transmission instruments at the center of the capsule. Thus, the parachute is equipped in looping around the instruments, and it is directly pulled out by the cover of the parachute container. Therefore, it should be carefully discussed whether the rigid cover can generate the enough aerodynamic force to pull stably the parachute out in the back stream of the forebody. The shape of the capsule is conventional, which has a spherical nose of 20 cm in radius and a conical body of 45 degrees in half-cone-angle. Therefore, the dynamic instability should be carefully investigated. Capsule Configuration
Fault diagnosis of transformer based on cluster analysis (2011)

In order to solve the problem of the imbalance between the fault data and the normal ones in the fault diagnosis of transformer, we adopt k-means algorithm to cluster the data. The result of clustering shows the existence of the boundary class that is between fault and normal ones. The separation of boundary class from the fault data and the normal ones improves the reliability and early warning ability of fault diagnosis of transformer, as well as reduces the influence from the imbalance of the two kinds of data.
Advanced iteration for a magnetic equivalent circuit and modeling a 3-phase transformer (2010)

Considering the nonlinearities of magnetic circuits such as a 3-phase transformer results in an iterative approach. A model of the magnetic circuit for the 3-phase transformer is built up with a magnetic equivalent circuit (MEC); the electric circuit is described by an electric equivalent circuit (EEC). The requests on the iteration procedure are low number of iteration steps and low complexity in order to prevent high computational effort. Newton-Raphson is one possible iteration method, which is useful for high magnetic saturation. Normally, Newton-Raphson requires high computational effort. Hence, it is often easier to use other methods such as direct iteration. Here we show a straightforward setup for Newton-Raphson based on the network analysis of the MEC. This results in a lower number of iteration steps especially for high saturation while requiring a minimum of additional computation operations. A comparison between measurement and simulation for the transformer points out a time efficient solver, and shows the benefit of the application of a MEC.
A graphitic carbon nitride-coated quartz crystal microbalance gas sensor for H2 detection (2023)

The quartz crystal microbalance (QCM) technique based on graphitic carbon nitride (g-C 3 N 4 ) modified QCM electrodes has been successfully used to detect H 2 gas without the need for noble metal composite materials, and heating for operation.
Comparison of convolutional neural networks for detecting large vessel occlusion on computed tomography angiography (2021)

The number of learnable parameters in our five models and best-ablated PhiNet directly related to cross-validated test performance-the smaller the model the better. However, this pattern did not hold when looking at generalization on the withheld external validation set. DenseNet-121 generalized the best; we posit this was due to its heavy use of residual connections utilizing concatenation, which causes feature maps from earlier layers to be used deeper in the network, while aiding in gradient flow and regularization.
La sensibilité au spectacle (2010)

Ruby Christian. La sensibilité au spectacle. In: Raison présente, n°174, 2e trimestre 2010. Racisme, race et sciences sociales. pp. 133-134.
Live documents with contextual, data-driven information components (2002)

We introduce the notion of a live document and we describe our concept of live documents with contextual, data driven information components. The dynamic and interactive features of live documents provide a consistent data source for multimedia presentations targeted to various audiences and multiple platforms. Therefore, they contribute to the solution of key challenges in single sourcing and repurposing. We motivate the use of live documents with sample scenarios from the field of systems documentation. We further discuss how live documents can benefit from an interdisciplinary research approach across the fields of technical communications, systems documentation, and software engineering. Finally, cit_af ref_bf(Greenberg, Saul 2001 ref_num129)ref_we describe our experiences with prototype implementations of live documents based on Scalable Vector Graphics (SVG) and Microsoft Office Automation, respectively.
Medicinal Chemistry Projects Requiring Imaginative Structure-Based Drug Design Methods (2016)

Computational methods for docking small molecules to proteins are prominent in drug discovery. There are hundreds, if not thousands, of documented examples-and several pertinent cases within our research program. Fifteen years ago, our first docking-guided drug design project yielded nanomolar metalloproteinase inhibitors and illustrated the potential of structure-based drug design. Subsequent applications of docking programs to the design of integrin antagonists, BACE-1 inhibitors, and aminoglycosides binding to bacterial RNA demonstrated that available docking programs needed significant improvement. At that time, docking programs primarily considered flexible ligands and rigid proteins. We demonstrated that accounting for protein flexibility, employing displaceable water molecules, and using ligand-based pharmacophores improved the docking accuracy of existing methods-enabling the design of bioactive molecules. The success prompted the development of our own program, Fitted, implementing all of these aspects. The primary motivation has always been to respond to the needs of drug design studies; the majority of the concepts behind the evolution of Fitted are rooted in medicinal chemistry projects and collaborations. Several examples follow: (1) Searching for HDAC inhibitors led us to develop methods considering drug-zinc coordination and its effect on the pKa of surrounding residues. (2) Targeting covalent prolyl oligopeptidase (POP) inhibitors prompted an update to Fitted to identify reactive groups and form bonds with a given residue (e.g., a catalytic residue) when the geometry allows it. Fitted-the first fully automated covalent docking program-was successfully applied to the discovery of four new classes of covalent POP inhibitors. As a result, efficient stereoselective syntheses of a few screening hits were prioritized rather than synthesizing large chemical libraries-yielding nanomolar inhibitors. (3) In order to study the metabolism of POP inhibitors by cytochrome P450 enzymes (CYPs)-for toxicology studies-the program Impacts was derived from Fitted and helped us to reveal a complex metabolism with unforeseen stereocenter isomerizations. These efforts, combined with those of other docking software developers, have strengthened our understanding of the complex drug-protein binding process while providing the medicinal chemistry community with useful tools that have led to drug discoveries. In this Account, we describe our contributions over the past 15 years-within their historical context-to the design of drug candidates, including BACE-1 inhibitors, POP covalent inhibitors, G-quadruplex binders, and aminoglycosides binding to nucleic acids. We also remark the necessary developments of docking programs, specifically Fitted, that enabled structure-based design to flourish and yielded multiple fruitful, rational medicinal chemistry campaigns.
Onset of CT scan morphological changes in metastatic lesions and associated responses in gastric patients treated with telatinib. (2011)

81 Background: Response to the antiangiogenic agent, bevacizumab, by CT has been associated with a unique morphologic change in liver metastasis (mets) where heterogeneous attenuation, variable degree of enhancement and ill-defined borders before treatment transform into homogeneous, hypoattenuating lesions with well defined borders, mimicking a cyst. CT-based morphologic criteria in colorectal cancer (CRC) had a statistically significant association with pathologic response and overall survival, (Chun, JAMA 2009). The CT changes likely reflect the replacement of mets by fibroconnective tissue rather than tumor necrosis. Telatinib (tel) is a novel orally available kinase inhibitor that is highly selective for the VEGFR, PDGFR, and KIT tyrosine kinases at nanomolar concentrations with potent antiangiogenic activity. Methods: TEL0805, a Phase 2 study administered tel with capecitabine (X) and cisplatin (P) in previously untreated metastatic or unresectable gastric or GEJ adenocarcinoma pts. Response assessments were every 2 cycles (6 weeks). The ORR in response evaluable pts was 69% (1 CR, 21 PR in 32 pts). CT films from 16/32 response evaluable pts were analyzed and reviewed by a radiologist at a single institution, 10 pts had liver mets. Results: The median onset of response was 49 days. CT changes of mets at week 6 scans included: decreased attenuation and/or a sharp interface with rapid reduction of mets (n=6); mixed response, with decreased attenuation but persistent borders, and/or slight increase in mets followed by onset of response week 12 (n=3), and PD (n=1). CT changes correlate with durable responses. Conclusions: Telatinib + XP produces rapid onset of tumor response with morphologic CT changes in gastric cancer liver mets similar to those observed in CRC pts with bevacizumab, consistent with antiangiogenic activity. Further analyses in a randomized setting to correlate CT morphologic response with survival are planned. [Table: see text]
Concurrent Symbol Processing Capable VLSI Architecture for Bit Plane Coder of JPEG2000 (2005)

JPEG2000 image compression standard is designed to cater the needs of a large span of applications including numerous consumer products. However, its use is restricted due to the high hardware cost involved in its implementation. Bit Plane Coder (BPC) is the main resource intensive component of JPEG2000. Its throughput plays a key role in deciding the overall throughput of a JPEG2000 encoder. In this paper we present the algorithm and parallel pipelined VLSI architecture for BPC which processes a complete stripe-column concurrently during every pass. The hardware requirements and the critical path delay of the proposed technique are compared with the existing solutions. The experimental results show that the proposed architecture has 2.6 times greater throughput than existing architectures, with a comparatively small increase in hardware cost.
Adenovirus-mediated Expression of the Catalytic Subunit of Glucose-6-phosphatase in INS-1 Cells (1997)

Glucose-6-phosphatase (Glu-6-Pase) catalyzes the terminal step of gluconeogenesis, the conversion of glucose 6-phosphate (Glu-6-P) to free glucose. This enzyme activity is thought to be conferred by a complex of proteins residing in the endoplasmic reticulum (ER), including a Glu-6-P translocase that transports Glu-6-P into the lumen of the ER, a phosphohydrolase catalytic subunit residing in the lumen, and putative glucose and inorganic phosphate transporters that allow exit of the products of the reaction. In this study, we have investigated the effect of adenovirus-mediated overexpression of the Glu-6-Pase catalytic subunit on glucose metabolism and insulin secretion, using a well differentiated insulinoma cell line, INS-1. We found that the overexpressed Glu-6-Pase catalytic subunit was normally glycosylated, correctly sorted to the ER, and caused a 10-fold increase in Glu-6-Pase enzymatic activity in in vitro assays. Consistent with these findings, a 4.2-fold increase in 3H2O incorporation into glucose was observed in INS-1 cells treated with the recombinant adenovirus containing the Glu-6-Pase catalytic subunit cDNA (AdCMV-Glu-6-Pase). 3-[3H]Glucose usage was decreased by 32% in AdCMV-Glu-6-Pase-treated cells relative to controls, resulting in a proportional 30% decrease in glucose-stimulated insulin secretion. Our findings indicate that overexpression of the Glu-6-Pase catalytic subunit significantly impacts glucose metabolism and insulin secretion in islet beta-cells. However, INS-1 cells treated with AdCMV-Glu-6-Pase do not exhibit the severe alterations of beta-cell function and metabolism associated with islets from rodent models of obesity and non-insulin-dependent diabetes mellitus, suggesting the involvement of genes in addition to the catalytic subunit of Glu-6-Pase in the etiology of such beta-cell dysfunction.
Biosynthesis, characterization and antibacterial activity of silver nanoparticles by the Arctic anti-oxidative bacterium Paracoccus sp. Arc7-R13 (2019)

Silver nanoparticles (AgNPs) have attracted wide interest due to its broad range of applications. This study aims to describe the biosynthesis of AgNPs using an Arctic anti-oxidative bacterium Arc7-R13 and to study its characteristics and antibacterial activity. The biosynthesis of AgNPs was verified using UV-Vis spectrum with the maximum absorption at 416 nm. The morphology of the silver nanoparticles was characterized by TEM and its characterization were investigated by EDX and FTIR. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain Arc7-R13 was affiliated with genus Paracoccus. TEM analysis revealed that the AgNPs synthesized by strain Arc7-R13 were spherical and ellipsoidal in shape with size ranging from 2 to 25 nm. The optimal concentration of AgNO3 and temperature for the biosynthesis were 4 mmol/L and 37 °C, respectively. EDX analysis verified the presence of the element silver in the biosynthesized AgNPs. FTIR analysis revealed that the specific functional groups, OH, CH<sub>3</sub> and C≡N, might be responsible for reduction and stabilization of AgNPs. Antimicrobial test showed that the AgNPs had strong antimicrobial activity against all kinds of strains investigated, including Gram-positive Bacillus subtilis, Staphylococcus aureus and Gram-negative Pseudomonas aeruginosa, Escherichia coli.