gebhart/patrepeval huggingface dataset:
Impact génétique des pHs suboptimaux (2019)

Les cassures bicaténaires sont les dommages les plus dangereux pour une cellule puisque ceux-ci peuvent conduire à la perte de matériel génétique, à la perte de phénotype et à la mort cellulaire. Ces lésions à l’ADN peuvent être la conséquence de l’action néfaste de produits de mécanismes biologiques naturels, comme les espèces réactives de l’oxygène par exemple. L’exposition à certains facteurs exogènes peuvent également être responsable de la formation de cassures bicaténaires, comme l’irradiation ionisante ou le rayonnement ultraviolet. La variation physiologique locale du pH extracellulaire peut être considéré comme un facteur exogène lorsqu’elle résulte d’un stress conduisant à une fluctuation des ions hydrogènes dans le microenvironnement cellulaire.&#13;\nAfin de caractériser l’effet de variations locales du pH extracellulaire (pHe) sur la l’intégrité génétique, nous avons débuté par étudier leurs effets sur la réponse aux dommages à l’ADN et sa réparation. À l’aide de la bléomycine, un agent radiomimétique, des cassures bicaténaires ont été induites dans une culture primaire de fibroblastes en culture. La récupération a été effectuée pendant 24 heures et 48 heures à différents pHe physiologiques, appelés pHe suboptimaux, soit de 7.2 à 6.9. L’apparition et le suivi des cassures bicaténaires induites ont été observés à l’aide d’immunofluorescences et d’immunobuvardages contre la phosphorylation de l’histone H2AFX, un marqueur de remodelage de la chromatine, et contre la protéine 53BP1, un régulateur de la réponse cellulaire lors de cassures bicaténaires. Accompagné de tests de proliférations cellulaires, nous avons déterminé que l’incubation à pHe suboptimal induisait une baisse d’efficacité de la réparation des cassures bicaténaires de l’ADN. L’utilisation de puces PCR nous a également permis de mettre en évidence des baisses d’expressions de différents gènes impliqués dans la phase présynaptique et synaptique de la recombinaison homologue. Nous avons également déterminé que cette baisse d’efficacité pouvait induire des aberrations chromosomiques par la détection de micronoyaux. Cette instabilité chromosomique induite par les pHe suboptimaux a été d’avantage caractérisée à l’aide d’une culture cellulaire immortalisée lymphoblastoïde humaine, les cellules TK6. Suite à trois semaines d’incubation à pHe 7.2 et 6.9, une perte d’hétérozygotie pour le gène TK1 a été détectée par séquençage d’amplicons et des défauts d’épissage ont été observés par ASPCR. Enfin, par séquençage à haut débit des ARNm, nous avons pu déterminer que l’acidification modérée du pHe induisait des modifications du transcriptome.&#13;\nL’ensemble de ces résultats ont permis de démontrer pour la première fois que la variation physiologique localisé du pHe peut induire de l’instabilité génétique avec un potentiel mutagène chez des cellules saines.
Prebiotics and the Human Gut Microbiota: From Breakdown Mechanisms to the Impact on Metabolic Health (2022)

The colon harbours a dynamic and complex community of microorganisms, collectively known as the gut microbiota, which constitutes the densest microbial ecosystem in the human body. These commensal gut microbes play a key role in human health and diseases, revealing the strong potential of fine-tuning the gut microbiota to confer health benefits. In this context, dietary strategies targeting gut microbes to modulate the composition and metabolic function of microbial communities are of increasing interest. One such dietary strategy is the use of prebiotics, which are defined as substrates that are selectively utilised by host microorganisms to confer a health benefit. A better understanding of the metabolic pathways involved in the breakdown of prebiotics is essential to improve these nutritional strategies. In this review, we will present the concept of prebiotics, and focus on the main sources and nature of these components, which are mainly non-digestible polysaccharides. We will review the breakdown mechanisms of complex carbohydrates by the intestinal microbiota and present short-chain fatty acids (SCFAs) as key molecules mediating the dialogue between the intestinal microbiota and the host. Finally, we will review human studies exploring the potential of prebiotics in metabolic diseases, revealing the personalised responses to prebiotic ingestion. In conclusion, we hope that this review will be of interest to identify mechanistic factors for the optimization of prebiotic-based strategies.
Path to a drop-in replacement for current technologies with the 33%, large area, IMM cell (2010)

The triple-junction inverted-metamorphic (IMM-3) air-mass-zero (AM0) solar cell is a high-efficiency photovoltaic device with nearly optimized band-gaps for the solar spectrum. We discuss the path forward for a drop-in replacement of the conventional, 3J lattice-matched germanium based solar cell with an IMM-3 space solar cell. The IMM space solar cell can support several form factors, from flexible to rigid carriers, but a configuration similar to standard space solar cells could be quickly adopted into current panel configurations. The goal of the IMM development team has been to provide a stable processing platform that is also compatible with current solar panel configurations. The superstrate configuration has been the platform used for much of the IMM development to date. We discuss this form factor, as well as other alternatives to achieve a robust cell replacement form factor capable of successfully completing the AIAA-S111 space qualification.
Major contribution of the beta chain to the antigen specificity of a T cell receptor. (1994)

T cell receptors (TCR) recognize peptides presented by major histocompatibility complex (MHC) molecules on the surface of cells. Sequence homology between the variable regions of the T cell receptor and of antibodies suggests that similarly-folded domains participate in ligand binding in both cases. However, most current models assume that both TCR chains (alpha and beta) are required for specific binding, whereas the heavy chain alone can confer specificity on many antibodies. We have therefore constructed chimeric molecules with alpha and beta from two different TCR, one restricted by the class II MHC protein, Ek, and the other by the class I MHC, Kd. The beta chain alone was sufficient for specific recognition of a peptide, Cw3, bound to Kd, but the alpha chain contributed to the overall avidity. These results suggest that other TCR may recognize their ligands primarily through the beta chain.
Synthesis and Purification of Ionic Liquids (2002)

This chapter contains sections titled: Synthesis of Ionic Liquids Introduction Quaternization Reactions Anion-exchange Reactions Purification of Ionic Liquids Conclusions Quality Aspects and Other Questions Related to Commercial Ionic Liquid Production Introduction Quality Aspects of Commercial Ionic Liquid Production Upgrading of Commercial Ionic Liquids Scaling-up of Ionic Liquid Synthesis HSE data Future Price of Ionic Liquids Intellectual Property Aspects Regarding Ionic Liquids Synthesis of Task-specific Ionic Liquids
A scheme for constructing evidence structures in Dempster-Shafer evidence theory for data fusion (2004)

This paper addresses the issue of evidence structure construction involved in the Dempster-Shafer evidence theory (DSET) based reasoning for data fusion. An in-depth study is carried out on the properties of the proposed Proportional Difference Evidence Structure Constructing Scheme (PDESCS). Some properties have been mathematically proved for the PDESCS associated DSET. If PDESCS is applied to probabilistic evidence, in terms of posterior probability distributions, the DSET based reasoning with the maximum commonality decision making scheme is equivalent to the Beyesian approach with the maximum a posteriori probability principle (MAP). If PDESCS is applied to fuzzy evidence, in terms of fuzzy sets, the DSET based reasoning is equivalent to applying the maximum fuzzy membership decision making scheme to the intersected fuzzy set by the product T-norm operator. If PDESCS is applied to both probabilistic evidence and fuzzy evidence, the DSET based reasoning is equivalent to applying the maximum fuzzy set probability decision making scheme. To show the effectiveness of the PDESCS associated DSET, experiments are carried out for classifying human brain MR (magnetic resonance) images. It is concluded that the proposed scheme works well, and provides not only a unified framework to accommodate probabilistic evidence and fuzzy evidence, but also an effective reasoning mechanism to deal with different uncertainty, in terms of randomness and fuzziness, as well as precision.
Supplementary Methods and Materials from A Human Breast Cell Model of Preinvasive to Invasive Transition (2023)

Supplementary Methods and Materials from A Human Breast Cell Model of Preinvasive to Invasive Transition
Meta-analysis of genome-wide association studies for panic disorder in the Japanese population (2012)

Panic disorder (PD) is a moderately heritable anxiety disorder whose pathogenesis is not well understood. Due to the lack of power in previous association studies, genes that are truly associated with PD might not be detected. In this study, we conducted a genome-wide association study (GWAS) in two independent data sets using the Affymetrix Mapping 500K Array or Genome-Wide Human SNP Array 6.0. We obtained imputed genotypes for each GWAS and performed a meta-analysis of two GWAS data sets (718 cases and 1717 controls). For follow-up, 12 single-nucleotide polymorphisms (SNPs) were tested in 329 cases and 861 controls. Gene ontology enrichment and candidate gene analyses were conducted using the GWAS or meta-analysis results. We also applied the polygenic score analysis to our two GWAS samples to test the hypothesis of polygenic components contributing to PD. Although genome-wide significant SNPs were not detected in either of the GWAS nor the meta-analysis, suggestive associations were observed in several loci such as BDKRB2 (P=1.3 × 10(-5), odds ratio=1.31). Among previous candidate genes, supportive evidence for association of NPY5R with PD was obtained (gene-wise corrected P=6.4 × 10(-4)). Polygenic scores calculated from weakly associated SNPs (P<0.3 and 0.4) in the discovery sample were significantly associated with PD status in the target sample in both directions (sample I to sample II and vice versa) (P<0.05). Our findings suggest that large sets of common variants of small effects collectively account for risk of PD.
Production performance and constraints in fish farming in Manipur (2012)

The present study was conducted to examine the production performance, yield gaps and the constraints faced by the fish farmers in Manipur. In order to achieve the stipulated objectives, 100 fish farmers wereselected randomly from Thoubal district of Manipur. The farmers were divided into two categories on the basis of fish stocked area. The Category-I comprised of the farmers having stocked area less than one hectare and Category-II consist of the farmers having stocked area of one hectare and above. The results revealed that the Category-I fish producers were more efficient as compared to Category-II farmers as far as realized yield of fish was concerned. The index of realized potential yield was found to be 62.70 and 42.08 per cent for Category-I and II farms respectively. This shows that Category-I have scope to increase the actual farm yield by 37.3 per cent. Similarly, 57.92 per cent scope was there to increase the actual farm yield in Category-II farmsif the sample farmers adopt the package of practices followed by the research farm.The farmers faced problems on account of non-availability of seeds, manure, fertilizers, high cost of labour, marketing of fish, and inadequate credit. Keeping in view the constraints faced by the respondents it seems that the fish farming in the state is not conducive to the interest of the farmers.
Interactions between the Human RNA Polymerase II Subunits (1997)

As an initial approach to characterizing the molecular structure of the human RNA polymerase II (hRPB), we systematically investigated the protein-protein contacts that the subunits of this enzyme may establish with each other. To this end, we applied a glutathione S-transferase-pulldown assay to extracts from Sf9 insect cells, which were coinfected with all possible combinations of recombinant baculoviruses expressing hRPB subunits, either as untagged polypeptides or as glutathione S-transferase fusion proteins. This is the first comprehensive study of interactions between eukaryotic RNA polymerase subunits; among the 116 combinations of hRPB subunits tested, 56 showed significant to strong interactions, whereas 60 were negative. Within the intricate network of interactions, subunits hRPB3 and hRPB5 play a central role in polymerase organization. These subunits, which are able to homodimerize and to interact, may constitute the nucleation center for polymerase assembly, by providing a large interface to most of the other subunits.
Association of left atrial volume index and all-cause mortality in patients referred for routine cardiovascular magnetic resonance: a multicenter study (2019)

LAVi determined on routine cine-CMR is independently associated with all-cause mortality in patients undergoing a clinically indicated CMR.
Surgical Options for Middle-Aged Patients with Osteoarthritis of the Knee (2001)

Starr, Adam J. MD; Borer, Drake S. MD; Reinert, Charles M.; Einhorn, Thomas A. MD Author Information
Should Postoperative Pulmonary Function Be a Criterion That Affects Upper Instrumented Vertebra Selection in Adolescent Idiopathic Scoliosis Surgery? (2013)

3.
Error-free transmission of microring-modulated BPSK (2012)

We demonstrate the generation of error-free binary-phase-shift-keyed (BPSK) data at 5 Gb/s using a silicon microring modulator. The microring-modulated BPSK signal is propagated at fiber lengths up to 80 km, maintaining error-free performance, while demonstrating resilience to chromatic dispersion. Bit-error-rate measurements and eye diagrams show near equivalent performance of a microring-based BPSK modulator as compared to commercial LiNbO₃ phase modulators.
Ultra-compact synthesis of space-time wave packets (2022)

Space-time wave packets (STWPs) are pulsed fields in which a strictly prescribed association between the spatial and temporal frequencies yields surprising and useful behavior. However, STWPs to date have been synthesized using bulky free-space optical systems that require precise alignment. We describe a compact system that makes use of a novel optical component: a chirped volume Bragg grating that is rotated by 45 degrees with respect to the plane-parallel device facets. By virtue of this grating's unique structure, cascaded gratings resolve and recombine the spectrum without free-space propagation or collimation. We produce STWPs by placing a phase plate that spatially modulates the resolved spectrum between such cascaded gratings, with a device volume of 25x25x8 mm3, which is orders of magnitude smaller than previous arrangements.
Concatenated soliton fibre link (1991)

An easy and practical 'soliton fibre' link by concatenating uniform fibre sections is proposed. An ultrahigh bit rate losslimited fibre communication system can be achieved.
Mining specifications of malicious behavior (2007)

Malware detectors require a specification of malicious behavior. Typically, these specifications are manually constructed by investigating known malware. We present an automatic technique to overcome this laborious manual process. Our technique derives such a specification by comparing the execution behavior of a known malware against the execution behaviors of a set of benign programs. In other words, we mine the malicious behavior present in a known malware that is not present in a set of benign programs. The output of our algorithm can be used by malware detectors to detect malware variants. Since our algorithm provides a succinct description of malicious behavior present in a malware, it can also be used by security analysts for understanding the malware. We have implemented a prototype based on our algorithm and tested it on several malware programs. Experimental results obtained from our prototype indicate that our algorithm is effective in extracting malicious behaviors that can be used to detect malware variants.
Decreased Expression of Type 1 Fimbriae by apstMutant of Uropathogenic Escherichia coli Reduces Urinary Tract Infection (2012)

The pstSCAB-phoU operon encodes the phosphate-specific transport system (Pst). Loss of Pst constitutively activates the Pho regulon and decreases bacterial virulence. However, specific mechanisms underlying decreased bacterial virulence through inactivation of Pst are poorly understood. In uropathogenic Escherichia coli (UPEC) strain CFT073, inactivation of pst decreased urinary tract colonization in CBA/J mice. The pst mutant was deficient in production of type 1 fimbriae and showed decreased expression of the fimA structural gene which correlated with differential expression of the fimB, fimE, ipuA, and ipbA genes, encoding recombinases, mediating inversion of the fim promoter. The role of fim downregulation in attenuation of the pst mutant was confirmed using a fim phase-locked-on derivative, which demonstrated a significant gain in virulence. In addition, the pst mutant was less able to invade human bladder epithelial cells. Since type 1 fimbriae contribute to UPEC virulence by promoting colonization and invasion of bladder cells, the reduced bladder colonization by the pst mutant is predominantly attributed to downregulation of these fimbriae. Elucidation of mechanisms mediating the control of type 1 fimbriae through activation of the Pho regulon in UPEC may open new avenues for therapeutics or prophylactics against urinary tract infections.
Toward Ubiquitous Blood Pressure Monitoring via Pulse Transit Time: Predictions on Maximum Calibration Period and Acceptable Error Limits (2017)

The predictions may help guide the implementation, evaluation, and application of PTT-based BP monitoring systems in practice.
Search for tb Resonances in Proton-Proton Collisions at √s=7 TeV with the ATLAS Detector (2012)

Artículo escrito por un elevado número de autores, solo se referencian el que aparece en primer lugar, el nombre del grupo de colaboración, si le hubiere, y los autores pertenecientes a la UAM
Ultrafast electronic and vibrational dynamics in brominated aluminum corroles: Energy relaxation and triplet formation (2016)

We combined femtosecond (fs) VIS pump-IR probe spectroscopy with fs VIS pump-supercontinuum probe spectroscopy to characterize the photoreaction of the hexacoordinated Al(tpfc-Br8)(py)2 in a comprehensive way. Upon fs excitation at ∼400 nm in the Soret band, the excitation energy relaxes with a time constant of (250 ± 80) fs to the S2 and S1 electronic excited states. This is evident from the rise time of the stimulated emission signal in the visible spectral range. On the same time scale, narrowing of broad infrared signals in the C=C stretching region around 1500 cm(-1) is observed. Energy redistribution processes are visible in the vibrational and electronic dynamics with time constants between ∼2 ps and ∼20 ps. Triplet formation is detected with a time constant of (95 ± 3) ps. This is tracked by the complete loss of stimulated emission. Electronic transition of the emerging triplet absorption band overlaps considerably with the singlet excited state absorption. In contrast, two well separated vibrational marker bands for triplet formation were identified at 1477 cm(-1) and at 1508 cm(-1). These marker bands allow a precise identification of triplet dynamics in corrole systems.
Supplementary material from A Phase I Open-Label Study to Identify a Dosing Regimen of the Pan-AKT Inhibitor AZD5363 for Evaluation in Solid Tumors and in <i>PIK3CA</i>-Mutated Breast and Gynecologic Cancers (2023)

&lt;p&gt;Supplementary methods and results Supplementary Figure 1. Study 1 (NCT01226316) design Supplementary Figure 2. Dose escalation and DLTs in Part A, with MTDs of the continuous, 4/7, and 2/7 schedules being 320, 480, and 640 mg bid, respectively Supplementary Figure 3. Exploratory mutation analyses (ddPCR) in archival tissue and plasma (ctDNA) samples from a breast cancer patient who had progressive disease as best response (Cb cohort) Supplementary Figure 4. A) Tumour growth inhibition in preclinical tumor xenograft models (BT474c, HGC-27, HCC1954 and 786.0) treated with AZD5363 bid po at the indicated doses. B) AZD5363 PD in BT474c tumor xenografts. C) AZD5363 PD at steady state in BT474c xenograft tumors. D) Time course of pPRAS40 and pAkt S473 in BT474c tumor xenograft tissue following the final dose of AZD5363 after 3 weeks' continuous (100 mg/kg bid) or intermittent dosing (130 mg/kg bid 4/7 and 170 mg/kg bid 2/7) Supplementary Figure 5. Glucose (non-fasting/random) values over time after 480 mg single-dose AZD5363 (all dosing schedules) Supplementary Table 1. Percentage change from baseline for PoM biomarkers for 12 evaluable patients Supplementary Table 2. Antibodies and conditions for IHC analysis Supplementary Table 3. ddPCR primers and probes Supplementary Table 4. Tables with results of molecular analyses of Part C patients (PIK3CA and ESR1 mutation status in tissue and ctDNA, PTEN status in archival tissue) Supplementary Table 5. AEs of CTCAE grade {greater than or equal to}3 (irrespective of causality) in Parts A and B (frequency &gt;3% total) and Part C (frequency &gt;5% total)&lt;/p&gt;
A CAD tool for circuit extraction from VLSI layout cells (2003)

The authors present an approach to converting and displaying a VLSI layout definition file, such as one produced by the MAGIC layout editing system, into a circuit diagram. The ideas presented have been incorporated into a software tool written in C language for the Microvax GPX/II workstation; the routines in the graphic kernel system are used for the graphics component of the software. An example of a cell layout developed using MAGIC is shown along with the MAGIC layout definition file relative to this. It is also demonstrated that the circuit diagram developed by such a CAD (computer-aided design) tool can be useful in verification of layout. The terminal interconnectivity information generated from the layout definition file can also be used directly for circuit simulation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>