gebhart/patrepeval huggingface dataset:
Charge-buildup damage to gate oxide (1994)

`Antenna' structures over thick oxide were used to detect charge buildup damage to gate oxide, and gate leakage was measured to characterize the extent of damage. Polycide, metal 1, and metal 3 antennas with both area-intensive and edge-intensive configurations were included. After processing through a full triple-level metal, 135 angstroms gate oxide, 0.6 micrometers CMOS flow, individual 5 micrometers X 1 micrometers transistors (over gate oxide which had been stressed by the charge collected through an attached antenna during wafer fabrication) were measured and considered damaged if a current &gt; 1 nA leaked through the oxide when a 5.5 V stress was applied to the gate during testing.
Study of the inclusive production of charged pions, kaons, and protons in pp collisions at $\sqrt{s} = 0.9, 2.76,\mbox{ and }7~\mbox{TeV}$ (2012)

Spectra of identified charged hadrons are measured in pp collisions at the LHC for s = 0.9, 2.76, and 7 TeV. Charged pions, kaons, and protons in the transversemomentum range p T 0.1-1.7 GeV/c and for rapidities |y| < 1 are identified via their energy loss in the CMS silicon tracker. The average p T increases rapidly with the mass of the hadron and the event charged-particle multiplicity, independently of the center-of-mass energy. The fully corrected p T spectra and integrated yields are compared to various tunes of the PYTHIA 6 and PYTHIA 8 event generators.
Supplementary Figure S10 from Preclinical Antitumor Efficacy of BAY 1129980—a Novel Auristatin-Based Anti-C4.4A (LYPD3) Antibody–Drug Conjugate for the Treatment of Non–Small Cell Lung Cancer (2023)

&lt;p&gt;Anti-tumor efficacy of C4.4A-ADC in human nasopharyngeal carcinoma FaDu cancer xenograft mouse model.&lt;/p&gt;
Correction of the bleeding time in treated patients with severe von willebrand disease is not solely dependent on the normal multimeric structure of plasma von willebrand factor (1987)

Even though it is generally held that cryoprecipitate and fraction I-O correct the prolonged bleeding time (BT) in patients with von Willebrand disease (VWD), perusal of reported data indicates that the correction is usually short-lasting and often partial. We decided to do a controlled study of the relationship between the multimeric structure of von Willebrand factor (VWF) and the BT in five patients with severe (type III) VWD after infusion of three plasma concentrates ("wet" cryoprecipitate, lyophilized cryoprecipitate, and fraction I-O) given in random order. The dosage of concentrates was tailored from in vitro measurements to achieve post-infusion levels of ristocetin cofactor above the lower normal limit (50 U/dL) for at least 3 hours. The postinfusion BT became transiently normal in only two of five patients treated with wet cryoprecipitate, whereas it remained prolonged in all five patients treated with lyophilized cryoprecipitate or fraction I-O. For all the concentrates, the proportion of large VWF multimers calculated by scanning the electrophoretic gels were the same as those for normal standard plasmas. An intact multimeric structure was recovered in postinfusion plasmas of patients treated with wet cryoprecipitate, whereas there was a postinfusion loss of large multimers after lyophilized cryoprecipitate and fraction I-O. These findings indicate that the attainment of a normal BT is the exception rather than the rule after the infusion of three plasma fractions used in the treatment of severe VWD, and that an intact multimeric structure in concentrates and postinfusion plasmas is necessary but not sufficient to sustain a normal BT.
Phosphorylation of the large subunit of replication factor C is associated with adipocyte differentiation (2007)

Adipocyte differentiation is an ordered multistep process requiring the sequential activation of several groups of adipogenic transcription factors, including CCAAT/enhancer-binding protein-alpha and peroxisome proliferator-activated receptor-gamma, and coactivators. Here we show that replication factor C 140, which was known to act as a coactivator for CCAAT/enhancer-binding protein-alpha in our previous study, was phosphorylated on the proliferating cell nuclear antigen-bindng domain during the adipocyte differentiation process. Calmodulin-dependent protein kinase II was responsible for phosphorylating replication factor C 140 in the process of adipocyte differentiation. Ser518 of replication factor C 140 was identified as a major target of calmodulin-dependent protein kinase II phosphorylation in vitro. Calmodulin-dependent protein kinase II inhibitor attenuated phosphorylation of replication factor C 140 by differentiation inducers and blocked replication factor C 140-derived transcriptional activation. Taken together, these findings demonstrate that calmodulin-dependent protein kinase II signaling leads the cooperative transactivation of CCAAT/enhancer-binding protein-alpha and replication factor C 140 through an increase in replication factor C 140 phosphorylation, and subsequently enhances the transcriptional activation of target genes involved in adipocyte differentiation.
The Testis-Specific High-Mobility-Group Protein, a Phosphorylation-Dependent DNA-Packaging Factor of Elongating and Condensing Spermatids (1996)

Mammalian spermiogenesis is characterized by a striking restructuring of the spermatid chromatin caused by the replacement of nucleohistones with transition proteins and their subsequent replacement with nucleoprotamines. The onset of nuclear elongation and chromatin condensation in spermatids is accompanied by a general decrease in the transcriptional activity of the DNA. A recently identified testis-specific high-mobility-group (tsHMG) protein, similar to the human mitochondrial transcription factor I and to the linker-associated protein delta of Tetrahymena thermophila micronuclei, is thought to play a structural role in this process. We confirm by immunoblot analysis of fractionated germ cells that the presence of tsHMG is restricted to transcriptionally quiescent elongating and condensing spermatids. Purified recombinant tsHMG protein displays preferential binding to supercoiled plasmid DNA, which reversibly protects the DNA against the DNA-relaxing activity of eukaryotic topoisomerase I and also impairs the transcriptional activity of this template when assayed in vitro. The tsHMG protein can also introduce negative supercoils into a relaxed plasmid substrate in a topoisomerase I-dependent manner. We also show that the tsHMG protein is the substrate of a Ca2+-phospholipid-dependent protein kinase (protein kinase C) present in testis extracts of adult mice and demonstrate that phosphorylation by protein kinase C is required for both the DNA-binding and the topoisomerase I-dependent supercoiling activities of tsHMG. Our results support the hypothesis that the spermatid tsHMG protein is a topological factor (transition protein) that can modulate the activity of topoisomerase I. This activity could contribute to the important transition in chromatin structure which leads to the decrease in DNA metabolism observed at the early stages of spermatid elongation.
Search for resonant production of second-generation sleptons with same-sign dimuon events in proton–proton collisions at $$\sqrt{s} = 13\,\text {TeV} $$ s = 13 TeV (2019)

A search is presented for resonant production of second-generation sleptons ( <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msub><mml:mover><mml:mi>μ</mml:mi> <mml:mo>~</mml:mo></mml:mover> <mml:mi>L</mml:mi></mml:msub> </mml:math> , <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msub><mml:mover><mml:mi>ν</mml:mi> <mml:mo>~</mml:mo></mml:mover> <mml:mi>μ</mml:mi></mml:msub> </mml:math> ) via the <i>R</i>-parity-violating coupling <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msubsup><mml:mi>λ</mml:mi> <mml:mn>211</mml:mn> <mml:mo>'</mml:mo></mml:msubsup> </mml:math> to quarks, in events with two same-sign muons and at least two jets in the final state. The smuon (muon sneutrino) is expected to decay into a muon and a neutralino (chargino), which will then decay into a second muon and at least two jets. The analysis is based on the 2016 data set of proton-proton collisions at <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:mspace> <mml:mtext>TeV</mml:mtext></mml:mrow> </mml:math> recorded with the CMS detector at the LHC, corresponding to an integrated luminosity of 35.9 <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mspace></mml:mspace> <mml:msup><mml:mtext>fb</mml:mtext> <mml:mrow><mml:mo>-</mml:mo> <mml:mn>1</mml:mn></mml:mrow> </mml:msup> </mml:mrow> </mml:math> . No significant deviation is observed with respect to standard model expectations. Upper limits on cross sections, ranging from 0.24 to 730 <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mspace></mml:mspace> <mml:mtext>fb</mml:mtext></mml:mrow> </mml:math> , are derived in the context of two simplified models representing the dominant signal contributions leading to a same-sign muon pair. The cross section limits are translated into coupling limits for a modified constrained minimal supersymmetric model with <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msubsup><mml:mi>λ</mml:mi> <mml:mn>211</mml:mn> <mml:mo>'</mml:mo></mml:msubsup> </mml:math> as the only nonzero <i>R</i>-parity violating coupling. The results significantly extend restrictions of the parameter space compared with previous searches for similar models.
Mechanically Triggered Carbon Monoxide Release with Turn-On Aggregation-Induced Emission (2022)

Polymers that release functional small molecules under mechanical stress potentially serve as next-generation materials for catalysis, sensing, and mechanochemical dynamic therapy. To further expand the function of mechanoresponsive materials, the discovery of chemistries capable of small molecule release are highly desirable. In this report, we detail a nonscissile bifunctional mechanophore (i.e., dual mechano-activated properties) based on a unique mechanochemical reaction involving norborn-2-en-7-one (NEO). One property is the release of carbon monoxide (CO) upon pulsed solution ultrasonication. A release efficiency of 58% is observed at high molecular weights (<i>M</i><sub>n</sub> = 158.8 kDa), equating to ∼154 molecules of CO released per chain. The second property is the bright cyan emission from the macromolecular product in its aggregated state, resulting in a turn-on fluorescence readout coincident with CO release. This report not only demonstrates a unique strategy for the release of small molecules in a nonscissile way but also guides future designs of force-responsive aggregation-induced emission (AIE) luminogens.
High Level of Circulating Human Tissue Kallikrein Induces Hypotension in a Transgenic Mouse Model (1996)

We established a unique transgenic mouse model in liver-targeted expression of human tissue kallikrein using a mouse albumin enhancer and promoter. Northern blot analysis and ELISA showed that human tissue kallikrein was predominantly expressed in the liver of transgenic mice and secreted into the circulation at a high level. The transcript was also detected in the kidney, pancreas, salivary gland and heart at a low level by reverse transcription-polymerase chain reaction followed by Southern blot analysis. Systolic blood pressures were measured by the tail-cuff method, all three independent transgenic mouse lines are hypotensive (84.6 +/- 1.0 mmHg, n = 17; 84.5 +/- 1.5 mmHg, n = 9; 83.1 +/- 0.8 mmHg, n = 13, P < 0.01) compared with the control mice (100.9 +/- 0.9 mmHg, n = 17). Administration of aprotinin, a potent tissue kallikrein inhibitor or Hoe 140, a bradykinin receptor antagonist, restored the blood pressure of transgenic mice but had no significant effect on control littermates. These studies show that over-production of tissue kallikrein in the circulation plays a role in blood pressure regulation.
Equivalent Circuit Programming for Estimating the State of a Power\n System (2019)

An Equivalent Circuit Programming (ECP) approach that expresses the\noptimality conditions of an optimization problem in terms of an equivalent\ncircuit model and uses circuit simulation techniques to solve for an optimal\nsolution, is applied to the state estimation problem for power systems. The\nbenefits of using an equivalent circuit formulation for incorporating both\nPhasor Measurement Units (PMU) and Remote Terminal Units (RTU), as well as for\nreducing the nonlinearities of the state estimation problem was previously\ndemonstrated. In this paper we further exploit the circuit nature of the state\nestimation problem to formulate not only the model but also the optimality\nconditions as an ECP problem. The efficiency and accuracy of our approach are\ndemonstrated by estimating the states of large-scale power grids (80k+ buses).\n
Inference of Genetic Regulatory Networks with Recurrent Neural Network Models Using Particle Swarm Optimization (2007)

Genetic regulatory network inference is critically important for revealing fundamental cellular processes, investigating gene functions, and understanding their relations. The availability of time series gene expression data makes it possible to investigate the gene activities of whole genomes, rather than those of only a pair of genes or among several genes. However, current computational methods do not sufficiently consider the temporal behavior of this type of data and lack the capability to capture the complex nonlinear system dynamics. We propose a recurrent neural network (RNN) and particle swarm optimization (PSO) approach to infer genetic regulatory networks from time series gene expression data. Under this framework, gene interaction is explained through a connection weight matrix. Based on the fact that the measured time points are limited and the assumption that the genetic networks are usually sparsely connected, we present a PSO-based search algorithm to unveil potential genetic network constructions that fit well with the time series data and explore possible gene interactions. Furthermore, PSO is used to train the RNN and determine the network parameters. Our approach has been applied to both synthetic and real data sets. The results demonstrate that the RNN/PSO can provide meaningful insights in understanding the nonlinear dynamics of the gene expression time series and revealing potential regulatory interactions between genes.
Speaker Recognition With Session Variability Normalization Based on MLLR Adaptation Transforms (2007)

We present a new modeling approach for speaker recognition that uses the maximum-likelihood linear regression (MLLR) adaptation transforms employed by a speech recognition system as features for support vector machine (SVM) speaker models. This approach is attractive because, unlike standard frame-based cepstral speaker recognition models, it normalizes for the choice of spoken words in text-independent speaker verification without data fragmentation. We discuss the basics of the MLLR-SVM approach, and show how it can be enhanced by combining transforms relative to multiple reference models, with excellent results on recent English NIST evaluation sets. We then show how the approach can be applied even if no full word-level recognition system is available, which allows its use on non-English data even without matching speech recognizers. Finally, we examine how two recently proposed algorithms for intersession variability compensation perform in conjunction with MLLR-SVM.
Symbioflor2® Escherichia coli Genotypes Enhance Ileal and Colonic Gene Expression Associated with Mucosal Defense in Gnotobiotic Mice (2020)

Symbioflor2<sup>®</sup> is a probiotic product composed of six <i>Escherichia coli</i> genotypes, which has a beneficial effect on irritable bowel syndrome. Our objective was to understand the individual impact of each of the six genotypes on the host, together with the combined impact of the six in the compound Symbioflor2<sup>®</sup>. Gnotobiotic mice were mono-associated with one of the six genotypes or associated with the compound product. Ileal and colonic gene expression profiling was carried out, and data were compared between the different groups of gnotobiotic mice, along with that obtained from conventional (CV) mice and mice colonized with the probiotic <i>E. coli</i> Nissle 1917. We show that Symbioflor2<sup>®</sup> genotypes induce intestinal transcriptional responses involved in defense and immune mechanisms. Using mice associated with Symbioflor2<sup>®</sup>, we reveal that the product elicits a balanced response from the host without any predominance of a single genotype. The Nissle strain and the six bacterial genotypes have different effects on the intestinal gene expression, suggesting that the impacts of these probiotics are not redundant. Our data show the effect of the Symbioflor2<sup>®</sup> genotypes at the molecular level in the digestive tract, which further highlights their beneficial action on several aspects of intestinal physiology.
Towards the Practical Application of Near-Term Quantum Computers in Quantum Chemistry Simulations: A Problem Decomposition Approach (2018)

With the aim of establishing a framework to efficiently perform the practical application of quantum chemistry simulation on near-term quantum devices, we envision a hybrid quantum--classical framework for leveraging problem decomposition (PD) techniques in quantum chemistry. Specifically, we use PD techniques to decompose a target molecular system into smaller subsystems requiring fewer computational resources. In our framework, there are two levels of hybridization. At the first level, we use a classical algorithm to decompose a target molecule into subsystems, and utilize a quantum algorithm to simulate the quantum nature of the subsystems. The second level is in the quantum algorithm. We consider the quantum--classical variational algorithm that iterates between an expectation estimation using a quantum device and a parameter optimization using a classical device. We investigate three popular PD techniques for our hybrid approach: the fragment molecular-orbital (FMO) method, the divide-and-conquer (DC) technique, and the density matrix embedding theory (DMET). We examine the efficacy of these techniques in correctly differentiating conformations of simple alkane molecules. In particular, we consider the ratio between the number of qubits for PD and that of the full system; the mean absolute deviation; and the Pearson correlation coefficient and Spearman's rank correlation coefficient. Sampling error is introduced when expectation values are measured on the quantum device. Therefore, we study how this error affects the predictive performance of PD techniques. The present study is our first step to opening up the possibility of using quantum chemistry simulations at a scale close to the size of molecules relevant to industry on near-term quantum hardware.
Le talc synthétique : avancées dans la compréhension des spectres de Résonance Magnétique Nucléaire (RMN) et Infrarouge (IR) (2018)

International audience
The development of biomaterials from porcine skeletal muscle extracellular matrix (2009)

There is currently great interest in the development of biomaterials for use in the engineering and/or regeneration of skeletal muscle tissue. Here, we describe the development of an acellular scaffolding system from porcine skeletal muscle extracellular matrix (ECM) molecules. Acellular scaffolds were prepared through the decellularization, lyophilization, and sterilization of thin slices of porcine loin muscle tissue. Myogenic cells seeded onto these scaffolds exhibited the ability to fully penetrate and recellularize the scaffolds. This represents a significant advance over scaffolding systems in which seeded cells fail to penetrate and simply pile onto the scaffold's surface. We also demonstrate that decellularized skeletal muscle tissue can be processed into bioactive powder or gel forms that promote the growth of myogenic cells. Gels composed of skeletal muscle ECM embedded with myogenic cells supported cell growth and gel remodeling. Myogenic cells cultured on surfaces coated with skeletal muscle ECM extract underwent enhanced proliferation relative to uncoated surfaces and simple collagen I coated surfaces. These results demonstrate the feasibility of using bioactive materials comprised of porcine skeletal muscle ECM molecules to produce different classes of biomaterials for use in tissue engineering and regenerative medicine applications.
Evaluation of compression properties of human knee cartilage — In-vivo study at 7T MRI (2017)

Magnetic resonance (MR) transverse relaxation time (T2) mapping has frequently been used to evaluate collagen content and its organization. In this study, T2 mapping, using novel three-dimensional-triple-echo-steady-state technique was performed in volunteers in-vivo at 7 Tesla under the static load applied by MR compatible compression device. We observed that load of 250 N applied for 12 minutes was sufficient for in-vivo evaluation of reversible cartilage compression effect. MRI associated with in-vivo compression of cartilage could therefore provide more insight into the mechanical properties of cartilage tissue.
Joint Semantic Segmentation and Depth Estimation with Deep Convolutional Networks (2016)

Multi-scale deep CNNs have been used successfully for problems mapping each pixel to a label, such as depth estimation and semantic segmentation. It has also been shown that such architectures are reusable and can be used for multiple tasks. These networks are typically trained independently for each task by varying the output layer(s) and training objective. In this work we present a new model for simultaneous depth estimation and semantic segmentation from a single RGB image. Our approach demonstrates the feasibility of training parts of the model for each task and then fine tuning the full, combined model on both tasks simultaneously using a single loss function. Furthermore we couple the deep CNN with fully connected CRF, which captures the contextual relationships and interactions between the semantic and depth cues improving the accuracy of the final results. The proposed model is trained and evaluated on NYUDepth V2 dataset outperforming the state of the art methods on semantic segmentation and achieving comparable results on the task of depth estimation.
Integration of molecular profiles in a longitudinal wellness profiling cohort (2020)

An important aspect of precision medicine is to probe the stability in molecular profiles among healthy individuals over time. Here, we sample a longitudinal wellness cohort with 100 healthy individuals and analyze blood molecular profiles including proteomics, transcriptomics, lipidomics, metabolomics, autoantibodies and immune cell profiling, complemented with gut microbiota composition and routine clinical chemistry. Overall, our results show high variation between individuals across different molecular readouts, while the intra-individual baseline variation is low. The analyses show that each individual has a unique and stable plasma protein profile throughout the study period and that many individuals also show distinct profiles with regards to the other omics datasets, with strong underlying connections between the blood proteome and the clinical chemistry parameters. In conclusion, the results support an individual-based definition of health and show that comprehensive omics profiling in a longitudinal manner is a path forward for precision medicine.