gebhart/patrepeval huggingface dataset:
Coexpression Network Analysis in Abdominal and Gluteal Adipose Tissue Reveals Regulatory Genetic Loci for Metabolic Syndrome and Related Phenotypes (2012)

Metabolic Syndrome (MetS) is highly prevalent and has considerable public health impact, but its underlying genetic factors remain elusive. To identify gene networks involved in MetS, we conducted whole-genome expression and genotype profiling on abdominal (ABD) and gluteal (GLU) adipose tissue, and whole blood (WB), from 29 MetS cases and 44 controls. Co-expression network analysis for each tissue independently identified nine, six, and zero MetS-associated modules of coexpressed genes in ABD, GLU, and WB, respectively. Of 8,992 probesets expressed in ABD or GLU, 685 (7.6%) were expressed in ABD and 51 (0.6%) in GLU only. Differential eigengene network analysis of 8,256 shared probesets detected 22 shared modules with high preservation across adipose depots (D(ABD-GLU) = 0.89), seven of which were associated with MetS (FDR P<0.01). The strongest associated module, significantly enriched for immune response-related processes, contained 94/620 (15%) genes with inter-depot differences. In an independent cohort of 145/141 twins with ABD and WB longitudinal expression data, median variability in ABD due to familiality was greater for MetS-associated versus un-associated modules (ABD: 0.48 versus 0.18, P = 0.08; GLU: 0.54 versus 0.20, P = 7.8×10(-4)). Cis-eQTL analysis of probesets associated with MetS (FDR P<0.01) and/or inter-depot differences (FDR P<0.01) provided evidence for 32 eQTLs. Corresponding eSNPs were tested for association with MetS-related phenotypes in two GWAS of >100,000 individuals; rs10282458, affecting expression of RARRES2 (encoding chemerin), was associated with body mass index (BMI) (P = 6.0×10(-4)); and rs2395185, affecting inter-depot differences of HLA-DRB1 expression, was associated with high-density lipoprotein (P = 8.7×10(-4)) and BMI-adjusted waist-to-hip ratio (P = 2.4×10(-4)). Since many genes and their interactions influence complex traits such as MetS, integrated analysis of genotypes and coexpression networks across multiple tissues relevant to clinical traits is an efficient strategy to identify novel associations.
4‐Nitramino‐3,5‐dinitropyrazole‐Based Energetic Salts (2011)

4-Nitramino-3,5-dinitropyrazole was prepared and stabilized through the formation of its ammonium salt. With selected cations, 14 nitrogen-rich energetic salts were synthesized in high yield by metathesis reactions. These salts were fully characterized by (1)H, (13)C NMR, and IR spectroscopy and elemental analysis. Additionally, the structures of the ammonium, 3,4,5-triaminotriazolium, and biguanidinium salts were confirmed by single-crystal X-ray diffraction. Based on experimental and calculated values, the 4-nitramino-3,5-dinitropyrazolate salts show properties, such as decomposition temperatures (115-229 °C), detonation pressures (23.27-37.42 GPa) and velocities (7713-9013 ms(-1)), and impact sensitivities (5-40 J) that place them with energetics such as RDX and TATB.
THE ROLE OF DIPHOSPHONATES IN OSTEOPOROSIS OF DISUSE (1973)

From the Department of Orthopaedic Surgery, University of Pennsylvania School of Medicine, Philadelphia Presented at the Thirty-second Annual Session of the American Association for the Surgery of Trauma, San Francisco, California, 28-30 September 1972. Supported by a grant from the Procter and Gamble Company, Cincinnati, Ohio. Address for reprints: Joseph M. Lane, M.D., Department of Orthopaedic Surgery, Hospital of the University of Pennsylvania, 3400 Spruce Street, Philadelphia, Pennsylvania 19104.
Recovery Rate of Vapor Extraction in Heavy Oil Reservoirs—Experimental, Statistical, and Modeling Studies (2014)

The VAPor EXtraction process (also known as VAPEX) is a solvent-based enhanced oil recovery (EOR) technology that has great potential for the recovery of heavy oil and bitumen through mass transfer and gravity drainage mechanisms. In this study, laboratory tests, the multivariable regression technique, and the connectionist model optimized by a Genetic Algorithm (GA) were used to determine the oil production rate during the VAPEX process in homogeneous and fractured porous media. The smart technique and statistical models describe the VAPEX production rate in terms of three dimensionless numbers, namely the Schmidt number (Sc), the Peclet number (Pe), and a dimensionless parameter (NS) referred to as the VAPEX number. The developed smart model was constructed based on a large number of experimental data conducted under various process conditions in both training and testing phases. A comparison of results obtained from connectionist modeling, the regressive model, and the experimental VAPEX data exhibits an average absolute error lower than 7% between the predicted and actual values. Using both experimental and modeling results, the statistical analysis suggests that the Peclet number is the most important parameter affecting the oil production rate in the VAPEX, and also the smart technique is superior to the regression model developed. This study shows the effectiveness of connectionist model in prediction of VAPEX production in the absence of sufficient laboratory and/or field data, which may lead to a proper design of heavy oil recovery schemes.
Dose-escalated simultaneous integrated boost radiotherapy in early breast cancer (IMPORT HIGH): a multicentre, phase 3, non-inferiority, open-label, randomised controlled trial (2023)

Cancer Research UK.
ChemInform Abstract: High‐Pressure Synthesis and Characterization of New Actinide Borates, AnB4O8 (An: Th, U). (2014)

Abstract ThB 4 O 8 and UB 4 O 8 are synthesized from the corresponding metal oxides and B 2 O 3 at 5.5 and 10.5 GPa, respectively (multianvil Walker‐type apparatus, 1100 °C, 10 min).
The β+ and EC decay of 69Se, possible shape-coexistence and superdeformation effects in 69As (1987)

The β+ and electron‐conversion decay of 69Se to 69As and the subsequent γ and proton emissions have been investigated by means of the 40Ca(32S,2pn)69Se reaction with a 100 MeV beam delivered by the Strasbourg MP tandem. Direct proton spectra and proton‐X rays coincidence have been registered in a closed geometry with a proton resolution of 20keV. (AIP)
Laparoscopic Donor Nephrectomy Gene Expression Profiling Reveals Upregulation of Stress and Ischemia Associated Genes Compared to Control Kidneys (2005)

We compared gene expression profiles from six donor kidneys prior to surgical manipulation to six kidneys removed after laparoscopic donor nephrectomy (LDN) and several hours of CO2 pneumoperitoneum. Biopsies were obtained from renal cortex and hybridized to Affymetrix HG-U133A GeneChips. For control kidneys, we identified 1380 genes present on all six samples that had a signal intensity >1,000. Functional classification of these revealed genes for cellular signaling (201; 15%), regulation of transcription (156; 11%), cellular transport (144; 10%) and cellular metabolism (111; 8%). A class comparison between the controls and LDN kidneys yielded 865 differentially expressed genes. Functional classification of the 502 genes differentially upregulated in LDN kidneys identified associations with apoptosis, cell adhesion, cell signaling, regulation of cell growth/proliferation, immune/inflammation, ischemia/stress response and proteolysis/peptidolysis. These data demonstrate an altered renal transcriptome induced by several hours of CO2 pneumoperitoneum and laparoscopic surgery characterized by upregulation of ischemia and injury associated genes.
Heparin-Induced Thrombocytopenia With Thrombosis After Endovascular Aneurysm Repair (2008)

Heparin-induced thrombocytopenia is an immune-mediated syndrome that results from unfractionated heparin or low molecular weight heparin exposure. It often remains unrecognized and undertreated and can cause limb and/or life-threatening thrombosis. The authors present 2 cases of thrombosis: one arterial and the other venous that occurred following endovascular abdominal aortic aneurysm repair. To the authors' knowledge, this is only the second report of arterial thrombosis and the first of deep vein thrombosis as a result of heparin-induced thrombocytopenia developing following endovascular abdominal aortic aneurysm repair. This underscores the importance of considering heparin-induced thrombocytopenia as a potential cause for postendovascular thrombotic complications in the patient who develops thrombocytopenia following this procedure.
Crosslingual Generalization through Multitask Finetuning (2023)

Niklas Muennighoff, Thomas Wang, Lintang Sutawika, Adam Roberts, Stella Biderman, Teven Le Scao, M Saiful Bari, Sheng Shen, Zheng Xin Yong, Hailey Schoelkopf, Xiangru Tang, Dragomir Radev, Alham Fikri Aji, Khalid Almubarak, Samuel Albanie, Zaid Alyafeai, Albert Webson, Edward Raff, Colin Raffel. Proceedings of the 61st Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers). 2023.
Structural Analysis of the Core Region of O-Lipopolysaccharide of Porphyromonas gingivalis from Mutants Defective in O-Antigen Ligase and O-Antigen Polymerase (2009)

Porphyromonas gingivalis synthesizes two lipopolysaccharides (LPSs), O-LPS and A-LPS. Here, we elucidate the structure of the core oligosaccharide (OS) of O-LPS from two mutants of P. gingivalis W50, Delta PG1051 (WaaL, O-antigen ligase) and Delta PG1142 (O-antigen polymerase), which synthesize R-type LPS (core devoid of O antigen) and SR-type LPS (core plus one repeating unit of O antigen), respectively. Structural analyses were performed using one-dimensional and two-dimensional nuclear magnetic resonance spectroscopy in combination with composition and methylation analysis. The outer core OS of O-LPS occurs in two glycoforms: an "uncapped core," which is devoid of O polysaccharide (O-PS), and a "capped core," which contains the site of O-PS attachment. The inner core region lacks L(D)-glycero-D(l)-manno-heptosyl residues and is linked to the outer core via 3-deoxy-D-manno-octulosonic acid, which is attached to a glycerol residue in the outer core via a monophosphodiester bridge. The outer region of the "uncapped core" is attached to the glycerol and is composed of a linear alpha-(1-->3)-linked d-Man OS containing four or five mannopyranosyl residues, one-half of which are modified by phosphoethanolamine at position 6. An amino sugar, alpha-D-allosamine, is attached to the glycerol at position 3. In the "capped core," there is a three- to five-residue extension of alpha-(1-->3)-linked Man residues glycosylating the outer core at the nonreducing terminal residue. beta-D-GalNAc from the O-PS repeating unit is attached to the nonreducing terminal Man at position 3. The core OS of P. gingivalis O-LPS is therefore a highly unusual structure, and it is the basis for further investigation of the mechanism of assembly of the outer membrane of this important periodontal bacterium.
The Uncomely Comedy: Celebrating the Divided Subject in Contemporary British Drama (2017)

Dans le théâtre britannique traditionnel, la comédie, qu’elle se donne comme comédie de mœurs ou plus tard comme pièce « bien faite », se caractérise par son aspect divertissant allié à une légèreté de ton. Péripéties et rires francs se succèdent pour culminer en un dénouement heureux et festif (bien souvent un mariage). Mais la Seconde Guerre mondiale a constitué un tournant décisif pour le genre comique, confrontant les dramaturges à un questionnement éthique autour de la possibilité même de rire dans ces nouvelles conditions. La comédie n’est pas sortie indemne de l’épisode de l’Holocauste, comme le révèlent les mises en scène de fêtes, devenues de pâles reflets spectraux voire lugubres de cette légèreté qui caractérisait jadis le genre. Les rassemblements festifs, désormais mornes voire inquiétants, n’ont plus vocation à célébrer le dénouement heureux de la pièce ni à faire valoir un quelconque retour à l’équilibre. En nous intéressant à un corpus de pièces contemporaines britanniques mettant en scène des fêtes de Noël ( Absurd Person Singular d’Alan Ayckbourn, Harry’s Christmas de Steven Berkoff et In the Republic of Happiness de Martin Crimp), nous analyserons le statut du comique dans ces festivités bien particulières où l’épuisement et la destruction ne sont jamais loin, où l’excès vient paradoxalement célébrer le rien. Nous nous attacherons à montrer que ces fêtes ( part-ies ) paradoxales s’efforcent de faire advenir sur scène un nouveau sujet contemporain, essentiellement divisé. L’exaltation et la célébration de cette division contribuent dès lors à un renouvellement de la forme dramatique et engendrent un nouveau type de comédies.
An Analysis of the Origins of a Cooperative Binding Energy of Dimerization (1998)

The cooperativity between binding of cell wall precursor analogs (ligands) to and antibiotic dimerization of the clinically important vancomycin group antibiotics was investigated by nuclear magnetic resonance. When dimerization was weak in the absence of a ligand, the increase in the dimerization constant in the presence of a ligand derived largely from changes associated with tightening of the dimer interface. When dimerization was strong in the absence of a ligand, the increase in the dimerization constant in the presence of a ligand derived largely from changes associated with tightening of the ligand-antibiotic interface. These results illustrate how, when a protein has a loose structure, the binding energy of another molecule to the protein can derive in part from changes occurring within the protein.
ARSyN: a method for the identification and removal of systematic noise in multifactorial time course microarray experiments (2011)

Transcriptomic profiling experiments that aim to the identification of responsive genes in specific biological conditions are commonly set up under defined experimental designs that try to assess the effects of factors and their interactions on gene expression. Data from these controlled experiments, however, may also contain sources of unwanted noise that can distort the signal under study, affect the residuals of applied statistical models, and hamper data analysis. Commonly, normalization methods are applied to transcriptomics data to remove technical artifacts, but these are normally based on general assumptions of transcript distribution and greatly ignore both the characteristics of the experiment under consideration and the coordinative nature of gene expression. In this paper, we propose a novel methodology, ARSyN, for the preprocessing of microarray data that takes into account these 2 last aspects. By combining analysis of variance (ANOVA) modeling of gene expression values and multivariate analysis of estimated effects, the method identifies the nonstructured part of the signal associated to the experimental factors (the noise within the signal) and the structured variation of the ANOVA errors (the signal of the noise). By removing these noise fractions from the original data, we create a filtered data set that is rich in the information of interest and includes only the random noise required for inferential analysis. In this work, we focus on multifactorial time course microarray (MTCM) experiments with 2 factors: one quantitative such as time or dosage and the other qualitative, as tissue, strain, or treatment. However, the method can be used in other situations such as experiments with only one factor or more complex designs with more than 2 factors. The filtered data obtained after applying ARSyN can be further analyzed with the appropriate statistical technique to obtain the biological information required. To evaluate the performance of the filtering strategy, we have applied different statistical approaches for MTCM analysis to several real and simulated data sets, studying also the efficiency of these techniques. By comparing the results obtained with the original and ARSyN filtered data and also with other filtering techniques, we can conclude that the proposed method increases the statistical power to detect biological signals, especially in cases where there are high levels of structural noise. Software for ARSyN is freely available at http://www.ua.es/personal/mj.nueda.
Bilayered Antimicrobial Nanofiber Membranes for Wound Dressings via in Situ Cross-Linking Polymerization and Electrospinning (2018)

The aim of this study was to fabricate a novel bilayered wound dressing with excellent antibacterial performance through electrospinning and in situ cross-linking polymerization. Quaternary ammonium salts ([2-(methacryloyloxy)ethyl] trimethylammonium, MTA) were first polymerized and cross-linked in the presence of polycaprolactone (PCL) to form PCL/PMTA composites. Then, PCL was electrospun as the cytocompatible inner layer that directly contacts the wound, and the PCL/PMTA layer was placed as the outer layer as a defense against bacteria. The PCL/PMTA layer exhibited a hydrophilic surface and showed a strong antibacterial effect on E. coli and S. aureus. All bilayered antimicrobial nanofiber membranes did not release any toxic agents to cells, and the PCL layer exhibited better effects on cell growth. The electrospun bilayered nanofiber membranes are promising candidates for antimicrobial wound dressings.
Image transmission through incoherent optical fiber bundle: methods for optimization and image quality improvement (2008)

Artificial vision, in spite of all theoretical and practical progress accomplished during last thirty years, still cannot be employed technically in some hazardous and strong industrial areas, where conditions are such that cameras would not operate properly. Possible alternatives on such problem are the quite recent IP65 and IP67 industrial cameras, and associated connectors, protected by an anticorrosive, waterproof, and high temperatures resistive carcass employing a dedicated electronic, in addition robust to almost 3G accelerations. Nevertheless, such cameras are still very expensive compared to conventional industrial cameras and would still not be enough in hardest conditions (explosive gas or dust environment) or in electromagnetic interferences environments. A good alternative in extreme conditions is the use of optical fiber bundle. Since such cable only transmits light, they intrinsically have electromagnetic interferences immunity and, depending on the fiber material, could be exposed to very high temperature (over 1000°C for sapphire fibers for example), could be employed in almost all corrosive, environment, and totally submersible. Nevertheless, the coherent optical fiber bundles are very expensive, and for large distances could be non-competitive facing the other hardware solutions (armor plating, electromagnetic interferences isolation). Thus, the best suitable option to develop a competitive system in those particular cases is the use of incoherent optical fiber bundle (IOFB), nowadays just we discuss in this paper. Improvement of the noisy resulting quality image is also exposed here, achieved by experimental post calibration methods.

We propose in this work a new calibration method of incoherent optical fiber bundle (IOFB) for image transmission purpose. Firstly, we present the calibration method (an enhancement of previously published calibration methods), some resulting reconstructed image and a discussion on its quality improvement employing simple denoising methods assisted by low pass filters (smooth filter, resizing method,...). We finally depict the two post calibration method are: correction of the input plane optical aberrations and extraction of a unique pixel (almost centered) for each fibers. We finally present some resulting images that demonstrate how it efficiently refine the reconstruction Look Up Table (LUT) used for the output image reconstruction improving image quality, image contrast but also reconstruction processing time.
Delivery of DNA into Adipocytes within Adipose Tissue (2008)

Electroporation has been adapted for the transfer of macromolecules into various cells of tissues in vivo. Although mature adipocytes constitute less than 20% of cells residing in adipose tissue, we have found that fat cells are susceptible to selective electrotransfer of plasmid DNA owing to their large size relative to other cells in the tissue. The procedures detailed here permit electrotransfer of plasmid DNA into mature fat cells with greater than 99% selectivity over other cells in the tissue. This "adiporation" technique can be used to image the subcellular targeting of fluorescent bioreporter molecules and to manipulate the activity of specific pathways within adipocytes in situ.
In vitro T cell-mediated killing of Pseudomonas aeruginosa. IV. Nonresponsiveness in polysaccharide-immunized BALB/c mice is attributable to vinblastine-sensitive suppressor T cells. (1986)

We reported previously that BALB/c mice immunized with a polysaccharide (PS) antigen isolated from immunotype 1 Pseudomonas aeruginosa and vinblastine sulfate develop T cell-mediated protective immunity, despite their failure to produce specific antibody. In vitro, Lyt-1-,2+, I-J+ T cells from vinblastine- and PS-immunized mice kill P. aeruginosa by secretion of a bactericidal lymphokine. BALB/c mice immunized with PS alone generate neither protective antibodies nor a protective T cell response. The current studies indicate that T cells from mice immunized with PS alone significantly suppress the bactericidal activity of T cells from mice immunized with vinblastine and PS. The suppressor T cells are of the same Lyt-1-,2+, I-J+ phenotype as the bactericidal T cells. Suppression is mediated by a soluble product of these suppressor T cells which both inhibits T cell proliferation and interferes with the production or release of the bactericidal lymphokine. Cyclophosphamide, used in other systems to remove suppressor T cells, fails to enhance bacterial killing and does not inhibit suppressor cell activity. These studies indicate that immunization with PS elicits responses in two functionally distinct subgroups of Lyt-1-,2+, I-J+ T cells, and that these cells are distinguishable by their sensitivity to vinblastine sulfate.
Recognition of articulated roberts in the RoboCup domain (2006)

This paper presents a system for articulated object recognition. The system has been tested in the RoboCup domain (four-legged league), an international competition among autonomous doglike robots playing soccer. Nevertheless, the proposed method does not depend on any specific domain, but is thought to be applicable to generic objects composed of rigid subparts linked by rotational and/or translational joints.
A higher-dimensional analogue of Carlitz-Drinfeld theory (1995)

The purpose of this paper is to generalize the arguments of Carlitz and Drinfeld to the higher-dimensional case by giving some analogies of special functions like the Carlitz exponential, the zeta function, the gamma functions, and the modular forms. This is a resum of my master thesis at University of Tokyo, March 1994,
Clonetracker (2008)

Code clones are generally considered to be an obstacle to software maintenance. Research has provided evidence that it may not always be practical, feasible, or cost-effective to eliminate certain clone groups through refactoring. This paper describes CloneTracker, an Eclipse plug-in that provides support for tracking code clones in evolving software. With CloneTracker, developers can specify clone groups they wish to track, and the tool will automatically generate a clone model that is robust to changes to the source code, and can be shared with other collaborators of the project. When future modifications intersect with tracked clones, CloneTracker will notify the developer, provide support to consistently apply changes to a corresponding clone region, and provide support for updating the clone model. CloneTracker complements existing techniques by providing support for reusing knowledge about the location of clones in source code, and support for keeping track of clones when refactoring is not desirable.