gebhart/patrepeval huggingface dataset:
Absence of WAF1 mutations in a variety of human malignancies (1994)

A newly cloned gene named wild-type p53-activated fragment 1 (WAF1; also known as p21, Pic-1, Cip-1, or SDI1) is directly regulated by p53 and can itself suppress tumor cell growth in culture. Induction of expression of WAF1 may be an important means by which cells with DNA injury arrest their growth to repair DNA or undergo apoptosis. Based on the hypothesis that mutations of this gene may play a role in carcinogenesis, we have studied 351 DNAs from 14 kinds of malignancies, as well as 36 human transformed cell lines, for alterations of WAF1 gene by single-strand conformation polymorphism analysis of polymerase chain reaction amplification of the DNA coding region of the WAF1 gene. No abnormal band shifts of WAF1 were noted in any of the samples or cell lines, but three major variants in exons 2 and 3 of the gene were found that are consistent with the existence of two different DNA polymorphisms. Sequence analysis of the amplified products producing these three variants in each exon from normal DNAs confirmed the presence of the polymorphisms in the WAF1 gene. Of 290 selected tumor samples previously evaluated for p53 mutations by single-strand conformation polymorphism, 90% had no detectable p53 alterations. In summary, mutations within the coding portion of the WAF1 gene were undetectable in a large series of human tumors, many of which had a normal p53 gene. This suggests that WAF1 alterations are generally caused indirectly, through p53 mutations rather than through intragenic mutation of the WAF1 itself.
Integration of Spatial ALD Aluminum Oxide for Rear Side Passivation of p-Type PERC/PERL Solar Cells (2013)

In this paper we present an overview of the integration of amorphous aluminum oxide (Al2O3) as rear side passivation layer for large area industrial PERC solar cells (i-PERC). The technique used for the deposition of the Al2O3 layers is spatial Atomic Layer Deposition (ALD), for its industrial relevance due to the high deposition speed and low Trimethyl-Aluminum (TMA) consumption. After analyzing the surface passivation properties, we will describe how Al2O3 can be integrated in an i-PERC process flow in a simple and cost-effective way, while maintaining high levels of solar cell efficiency. In particular, a special effort is devoted in finding solutions for process simplification and in the reduction of the cost per wafer (€/W) of the spatial ALD process step. Top efficiencies of 20.1 % and 20.6 % have been reached (Cz-Si, 6 inch cells) when coupling a spatial ALD Al2O3 rear passivation to a standard i-PERC integration flow with front Ag-screen printed or Ni/Cu/Ag plated contacts, respectively. Besides passivation, ALD Al2O3 can also be used as doping source of aluminum to form localized p+ back surface field (BSF) regions at the rear contact by means of laser processing. In this way, dielectric opening and BSF are formed simultaneously and firing step is not needed anymore, leading both to a suppression of Al2O3 blistering and optical enhancement. This process is a suitable complement of front contact formation based on plating schemes. Ni/Cu/Ag-plated solar cells with rear laser doping from ALD Al2O3 layers have been fabricated with efficiencies topping 20.4 % (FF = 79.7 %) and outperforming the control group featuring local BSF formed via a firing step.
Nonplanar Electrode Architectures for Ultrahigh Areal Capacity Batteries (2018)

We report on the design of a battery electrode architecture in which ion and electronic transport pathways are contiguous and span the entire volume of a thick, nonplanar electrode. It is shown that for a range of active materials conductivities, the length scale for electronic transport in such an architecture can be tuned by simple manipulations of the electrode design to enable good access to the active material. The benefits of such electrodes for basic science research and practical lithium metal batteries are demonstrated in low-N:P ratio cells in which a conventional (300–800 μm) Li foil is successfully cycled with LiCoO2 cathodes with high areal capacities (10–28 mAh/cm2).
Learning to Reconstruct People in Clothing from a Single RGB Camera (2019)

This repository contains code corresponding to the paper Learning to Reconstruct People in Clothing from a Single RGB Camera.
Dissulfurirhabdus thermomarina gen. nov., sp. nov., a thermophilic, autotrophic, sulfite-reducing and disproportionating deltaproteobacterium isolated from a shallow-sea hydrothermal vent (2016)

A thermophilic, anaerobic, chemolithoautotrophic bacterium, strain SH388<sup>T</sup>, was isolated from a shallow, submarine hydrothermal vent (Kuril Islands, Russia). Cells of strain SH388<sup>T</sup> were Gram-stain-negative short rods, 0.2-0.4 µm in diameter and 1.0-2.5 µm in length, and motile with flagella. The temperature range for growth was 25-58 °C (optimum 50 °C), and the pH range for growth was pH 5.0-7.0 (optimum pH 6.0-6.5). Growth of strain SH388<sup>T</sup> was observed in the presence of NaCl concentrations ranging from 0.5 to 4.0 % (w/v) (optimum 2.0-2.5 %). The strain grew chemolithoautotrophically with molecular hydrogen as electron donor, sodium sulfite as electron acceptor and bicarbonate/CO2 as a carbon source. It was also able to grow by disproportionation of sulfite and elemental sulfur but not thiosulfate. Sulfate, Fe(III) and nitrate were not used as electron acceptors either with H2 or organic electron donors. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belonged to the class Deltaproteobacteria and was most closely related to Dissulfuribacter thermophilus and Dissulfurimicrobium hydrothermale (91.6 % and 90.4 % sequence similarity). On the basis of its physiological properties and results of phylogenetic analyses, strain SH388<sup>T</sup> is considered to represent a novel species of a new genus, for which the name Dissulfurirhabdus thermomarina gen. nov., sp. nov. is proposed. The type strain of the species is SH388<sup>T</sup> (=DSM 100025<sup>T</sup>=VKM B-2960<sup>T</sup>). It is the first thermophilic disproportionator of sulfur compounds isolated from a shallow-sea environment.
Optimizing directed self-assembled morphology (2013)

Directed assembly of block polymers is rapidly becoming a viable strategy for lithographic patterning of nanoscopic features. One of the key attributes of directed assembly is that an underlying chemical or topographic substrate pattern used to direct assembly need not exhibit a direct correspondence with the sought after block polymer morphology, and past work has largely relied on trial-and-error approaches to design appropriate patterns. In this work, a computational evolutionary strategy is proposed to solve this optimization problem. By combining the Cahn-Hilliard equation, which is used to find the equilibrium morphology, and the covariance-matrix evolutionary strategy, which is used to optimize the combined outcome of particular substrate-copolymer combinations, we arrive at an efficient method for design of substrates leading to non-trivial, desirable outcomes.
CITU: A Peptide and Decarboxylative Coupling Reagent (2017)

Tetrachloro-N-hydroxyphthalimide tetramethyluronium hexafluorophosphate (CITU) is disclosed as a convenient and economical reagent for both acylation and decarboxylative cross-coupling chemistries. Within the former set of reactions, CITU displays reactivity similar to that of common coupling reagents, but with increased safety and reduced cost. Within the latter, increased yields, more rapid conversion, and a simplified procedure are possible across a range of reported decarboxylative transformations.
The novel resveratrol analog HS-1793-induced polyploid LNCaP prostate cancer cells are vulnerable to downregulation of Bcl-xL (2011)

Since resveratrol is not a potent cytotoxic compound when compared with other chemotherapeutic agents, several previous studies have been performed to obtain synthetic analogs of resveratrol with potent activity. Our previous study demonstrated that the resveratrol analog HS-1793 showed stronger antitumor activity than resveratrol in various cancer cells. We examined the antitumor activity exerted by HS-1793 in prostate cancer cells, and we observed that HS-1793 acts as a polyploidy inducer. Noticeably, multinucleation and polyploidization were induced in most LNCaP cells treated with HS-1793 at the dose causing a slight decline in cell viability. However, the induction of multinucleation and polyploidization was much lower in PC-3 prostate cancer cells treated with the same dose of HS-1793. Western blot and RT-PCR analyses showed that the expression of Aurora B was almost undetectable in LNCaP cells, but it was highly expressed in PC-3 cells. Further, silencing of Aurora B sensitized PC-3 cells to HS-1793-induced multi-nucleation. These results indicate that expression of Aurora B determines multinucleation in prostate cancer cells treated with HS-1793. Additional assays using multiple cancer cell lines show that the population of multinucleated cells induced by HS-1793 treatment is inversely proportional to Aurora B expression. We further elicited that the HS-1793-induced polyploid LNCaP cells are vulnerable to downregulation of Bcl-xL. Since the polyploidization in LNCaP induced by HS-1793 does not appear to cause definite commitment to apoptosis, the termination of polyploid cells by inhibition of Bcl-xL could provide an advantageous means to improve chemotherapeutic efficacy of HS-1793.
Cross-Reactive Antibodies to SARS-CoV-2 and MERS-CoV in Pre-COVID-19 Blood Samples from Sierra Leoneans (2021)

Many countries in sub-Saharan Africa have experienced lower COVID-19 caseloads and fewer deaths than countries in other regions worldwide. Under-reporting of cases and a younger population could partly account for these differences, but pre-existing immunity to coronaviruses is another potential factor. Blood samples from Sierra Leonean Lassa fever and Ebola survivors and their contacts collected before the first reported COVID-19 cases were assessed using enzyme-linked immunosorbent assays for the presence of antibodies binding to proteins of coronaviruses that infect humans. Results were compared to COVID-19 subjects and healthy blood donors from the United States. Prior to the pandemic, Sierra Leoneans had more frequent exposures than Americans to coronaviruses with epitopes that cross-react with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), SARS-CoV, and Middle Eastern respiratory syndrome coronavirus (MERS-CoV). The percentage of Sierra Leoneans with antibodies reacting to seasonal coronaviruses was also higher than for American blood donors. Serological responses to coronaviruses by Sierra Leoneans did not differ by age or sex. Approximately a quarter of Sierra Leonian pre-pandemic blood samples had neutralizing antibodies against SARS-CoV-2 pseudovirus, while about a third neutralized MERS-CoV pseudovirus. Prior exposures to coronaviruses that induce cross-protective immunity may contribute to reduced COVID-19 cases and deaths in Sierra Leone.
Mobility of Lumbar Segments Instrumented With a ProDisc II Prosthesis (2006)

Disc replacement in the lumbar spine by a ProDisc II implant fails to restore normal segmental rotational motion in the sagittal plane, specifically at levels L4-L5 and L5-S1. As segmental motion of the untreated segments was lower than normal as well, though not quite as conspicuous as that of instrumented segments, adaptation of soft tissue taken place during the preoperative symptomatic time period is conjectured to cause the observed motion deficit. Postoperative physical therapy might be considered if restoration of a normal range of rotational motion is desired.
Irreversible Alkylation of Human Serum Albumin by Zileuton Metabolite 2-Acetylbenzothiophene-S-oxide: A Potential Model for Hepatotoxicity (2007)

2-acetylbenzothiophene-S-oxide (2-ABT-S-oxide or M1) is a reactive metabolite of zileuton, a drug used in the treatment of asthma and is capable of conjugating with glutathione in vitro. Human serum albumin (HSA) is the most abundant protein in plasma and plays a critical role in detoxifying reactive oxygen species. The current research is focused on understanding the interaction between M1 and HSA. The stability studies revealed the half-life of M1 to be about 0.85 h in HSA, 1.82 h in human plasma, and 4.48 h in phosphate-buffered saline (PBS) as determined by first-order approximation. The alkylation rate constant k for HSA was 20 M(-1) min(-1). After quenching with acetonitrile, the half-life of M1 did not change significantly, indicating that M1 is covalently bound to HSA. LC-MS and LC-MS/MS analysis of human plasma revealed the M1 alkylated peptide P (m/z 870) formed by HSA conjugation and concomitant water elimination. The specific amino acid on HSA bound to M1 was identified as Cys-34. This alkylation is observed to be concentration- and incubation-time-dependent in human plasma. HSA oxidized by N, N'-diacetyl-L-cystine exhibits a compromised ability of HSA to react with M1. The alkylated HSA diminished the binding affinity for warfarin. Furthermore, the alkylation was found to be irreversible in the dialysis experiment. In addition, M1 decomposes to 2-ABT in the presence of HSA, presumably acting as an oxidant. The formation of 2-ABT in the incubation and the self-condensation of M1 in PBS indicate that the alkylation of Cys-34 is only one of a number of reactions that occur in the presence of HSA. Irreversible protein modification may potentially lead to a loss of its function. HSA irreversible alkylation represents a model for other proteins to be potentially toxic and thus may help explain zileuton hepatotoxicity.
Tests of Lepton Universality Using B0→KS0ℓ+ℓ− and B+→K*+ℓ+ℓ− Decays (2022)

Tests of lepton universality in B^{0}→K_{S}^{0}ℓ^{+}ℓ^{-} and B^{+}→K^{*+}ℓ^{+}ℓ^{-} decays where ℓ is either an electron or a muon are presented. The differential branching fractions of B^{0}→K_{S}^{0}e^{+}e^{-} and B^{+}→K^{*+}e^{+}e^{-} decays are measured in intervals of the dilepton invariant mass squared. The measurements are performed using proton-proton collision data recorded by the LHCb experiment, corresponding to an integrated luminosity of 9 fb^{-1} . The results are consistent with the standard model and previous tests of lepton universality in related decay modes. The first observation of B^{0}→K_{S}^{0}e^{+}e^{-} and B^{+}→K^{*+}e^{+}e^{-} decays is reported.
Erreurs médicales : regarder le problème en face (2001)

Le premier pas pour tenter de faire diminuer les erreurs medicales serait de connaitre leur frequence. Mais celle-ci est difficile a apprecier car la reprobation qui entoure les erreurs medicales est si forte que leurs auteurs hesitent a les rapporter. Bien des erreurs sont sans consequences, mais elles sont aussi importantes que les autres en un sens, puisqu'elles temoignent d'une faille dans notre systeme de soins ou de decision medicale. Il existe peu d'etudes publiees jusqu'a present sur ce sujet. Une etude retrospective de quelques 1000 cas cliniques provenant de deux hopitaux londoniens montre que pres de 11% des patients ont ete victimes d'une erreur plus ou moins grave. Ces patients etaient plus âges que ceux qui n'ont pas souffert ce type d'evenement. La moitie des incidents aurait pu etre prevenue par des soins ordinaires, et un tiers des patients a laisse des sequelles plus ou moins lourdes ou qui ont conduit au deces. C'est une etude pilote, mais il n'y a pas de raison de penser que ses resultats ne sont pas representatifs puisqu'ils se situent dans la moyenne des resultats publies dans d'autres pays. Ils font bien sentir en tout cas le besoin d'etudes plus vastes, et peut-etre a terme, de la mise en place d'un registre a l'echelle nationale de toutes les erreurs medicales, la seule facon probablement d'en tirer lecon au benefice des patients.1. Vincent C., et al. 2001. Adverse events in British hospitals : preliminary retrospective record review. BMJ 322 : 517-519.
Convergent Peripheral Pathways Catalyze Initial Glucose Catabolism inPseudomonas putida: Genomic and Flux Analysis (2007)

In this study, we show that glucose catabolism in Pseudomonas putida occurs through the simultaneous operation of three pathways that converge at the level of 6-phosphogluconate, which is metabolized by the Edd and Eda Entner/Doudoroff enzymes to central metabolites. When glucose enters the periplasmic space through specific OprB porins, it can either be internalized into the cytoplasm or be oxidized to gluconate. Glucose is transported to the cytoplasm in a process mediated by an ABC uptake system encoded by open reading frames PP1015 to PP1018 and is then phosphorylated by glucokinase (encoded by the glk gene) and converted by glucose-6-phosphate dehydrogenase (encoded by the zwf genes) to 6-phosphogluconate. Gluconate in the periplasm can be transported into the cytoplasm and subsequently phosphorylated by gluconokinase to 6-phosphogluconate or oxidized to 2-ketogluconate, which is transported to the cytoplasm, and subsequently phosphorylated and reduced to 6-phosphogluconate. In the wild-type strain, glucose was consumed at a rate of around 6 mmol g(-1) h(-1), which allowed a growth rate of 0.58 h(-1) and a biomass yield of 0.44 g/g carbon used. Flux analysis of (13)C-labeled glucose revealed that, in the Krebs cycle, most of the oxalacetate fraction was produced by the pyruvate shunt rather than by the direct oxidation of malate by malate dehydrogenase. Enzymatic and microarray assays revealed that the enzymes, regulators, and transport systems of the three peripheral glucose pathways were induced in response to glucose in the outer medium. We generated a series of isogenic mutants in one or more of the steps of all three pathways and found that, although all three functioned simultaneously, the glucokinase pathway and the 2-ketogluconate loop were quantitatively more important than the direct phosphorylation of gluconate. In physical terms, glucose catabolism genes were organized in a series of clusters scattered along the chromosome. Within each of the clusters, genes encoding porins, transporters, enzymes, and regulators formed operons, suggesting that genes in each cluster coevolved. The glk gene encoding glucokinase was located in an operon with the edd gene, whereas the zwf-1 gene, encoding glucose-6-phosphate dehydrogenase, formed an operon with the eda gene. Therefore, the enzymes of the glucokinase pathway and those of the Entner-Doudoroff pathway are physically linked and induced simultaneously. It can therefore be concluded that the glucokinase pathway is a sine qua non condition for P. putida to grow with glucose.
Decarbonization Analysis for Thermal Generation and Regionally Integrated Large-Scale Renewables Based on Minutely Optimal Dispatch with a Kentucky Case Study (2023)

Decarbonization of existing electricity generation portfolios with large-scale renewable resources, such as wind and solar photo-voltaic (PV) facilities, is important for a transition to a sustainable energy future. This paper proposes an ultra-fast optimization method for economic dispatch of firm thermal generation using high granularity, one minute resolution load, wind, and solar PV data to more accurately capture the effects of variable renewable energy (VRE). Load-generation imbalance and operational cost are minimized in a multi-objective clustered economic dispatch problem with various generation portfolios, realistic generator flexibility, and increasing levels of VRE integration. The economic feasibility of thermal dispatch scenarios is evaluated through a proposed method of levelized cost of energy (LCOE) for clustered generation portfolios. Effective renewable economics is applied to assess resource adequacy, annual carbon emissions, renewable capacity factor, over generation, and cost to build between thermal dispatch scenarios with incremental increases in VRE penetration. Solar PV and wind generation temporally complement one another in the region studied, and the combination of the two is beneficial to renewable energy integration. Furthermore, replacing older coal units with cleaner and agile natural gas units increases renewable hosting capacity and provides further pathways to decarbonization. Minute-based chronological simulations enable the assessment of renewable effectiveness related to weather-related variability and of complementary technologies, including energy storage for which a sizing procedure is proposed. The generally applicable methods are regionally exemplified for Kentucky, USA, including eight scenarios with four major year-long simulated case studies and 176 subcases using high performance computing (HPC) systems.
Measurement of the energy asymmetry in $$t{\bar{t}}j$$ production at $$13\,$$TeV with the ATLAS experiment and interpretation in the SMEFT framework (2022)

Abstract A measurement of the energy asymmetry in jet-associated top-quark pair production is presented using $$139\,{\mathrm {fb}}^{-1}$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:mn>139</mml:mn> <mml:mspace/> <mml:msup> <mml:mrow> <mml:mi>fb</mml:mi> </mml:mrow> <mml:mrow> <mml:mo>-</mml:mo> <mml:mn>1</mml:mn> </mml:mrow> </mml:msup> </mml:mrow> </mml:math> of data collected by the ATLAS detector at the Large Hadron Collider during pp collisions at $$\sqrt{s}=13\,\text {TeV}$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:msqrt> <mml:mi>s</mml:mi> </mml:msqrt> <mml:mo>=</mml:mo> <mml:mn>13</mml:mn> <mml:mspace/> <mml:mtext>TeV</mml:mtext> </mml:mrow> </mml:math> . The observable measures the different probability of top and antitop quarks to have the higher energy as a function of the jet scattering angle with respect to the beam axis. The energy asymmetry is measured in the semileptonic $$t{\bar{t}}$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:mi>t</mml:mi> <mml:mover> <mml:mrow> <mml:mi>t</mml:mi> </mml:mrow> <mml:mrow> <mml:mo>¯</mml:mo> </mml:mrow> </mml:mover> </mml:mrow> </mml:math> decay channel, and the hadronically decaying top quark must have transverse momentum above $$350\,\text {GeV}$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:mn>350</mml:mn> <mml:mspace/> <mml:mtext>GeV</mml:mtext> </mml:mrow> </mml:math> . The results are corrected for detector effects to particle level in three bins of the scattering angle of the associated jet. The measurement agrees with the SM prediction at next-to-leading-order accuracy in quantum chromodynamics in all three bins. In the bin with the largest expected asymmetry, where the jet is emitted perpendicular to the beam, the energy asymmetry is measured to be $$-0.043\pm 0.020$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:mo>-</mml:mo> <mml:mn>0.043</mml:mn> <mml:mo>±</mml:mo> <mml:mn>0.020</mml:mn> </mml:mrow> </mml:math> , in agreement with the SM prediction of $$-0.037\pm 0.003$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:mo>-</mml:mo> <mml:mn>0.037</mml:mn> <mml:mo>±</mml:mo> <mml:mn>0.003</mml:mn> </mml:mrow> </mml:math> . Interpreting this result in the framework of the Standard Model effective field theory (SMEFT), it is shown that the energy asymmetry is sensitive to the top-quark chirality in four-quark operators and is therefore a valuable new observable in global SMEFT fits.