gebhart/patrepeval huggingface dataset:
Human B Cell Tolerance and Its Failure in Rheumatoid Arthritis (2005)

Random V(D)J gene assembly generates many autoreactive B cell receptors (BCRs). In healthy donors, most autoreactive developing B cells are removed either in the bone marrow or in the periphery, revealing two B cell tolerance checkpoints. The regulation and the mechanisms that ensure this human B cell tolerance are poorly characterized, but they require proper BCR signaling. Indeed, patients with X-linked agammaglobulinemia who carry mutations in the BTK gene, which encodes an essential BCR signaling component, fail to establish proper central B cell tolerance, as demonstrated by the release of self-reactive B cells in the periphery. In autoimmune diseases such as rheumatoid arthritis (RA), B cell tolerance is broken and autoantibodies are secreted. Our recent results show that RA patients suffer from defective central and peripheral B cell tolerance checkpoints, which may favor the development of autoimmunity. Also, about half of our RA patients display unusual immunoglobulin light chain repertoires showing impaired secondary recombination regulation, which indicates that receptor editing, one of the mechanisms that normally ensures B cell tolerance, may often be defective in RA.
Strain induced changes in gate leakage current and dielectric constant of nitrided Hf-silicate metal oxide semiconductor capacitors (2008)

Uniaxial-mechanical-stress altered gate leakage current and dielectric constant of silicon metal-oxide-semiconductor (MOS) devices with nitrided Hf-silicate (HfSiON) dielectric are measured as a function of uniaxial stress applied using four-point wafer bending along the [110] direction. The gate leakage current and dielectric constant are found to increase by ∼2% per 100MPa of tensile and compressive stresses. A decrease in hole trap activation energy in hafnium oxide-based dielectric is used to explain the mechanical stress altered gate leakage. It is proposed that the HfSiON dielectric constant increase results from band gap narrowing caused by strain induced N p band splitting.
Electroactive Smart Materials: Novel Tools for Tailoring Bacteria Behavior and Fight Antimicrobial Resistance (2019)

Despite being very simple organisms, bacteria possess an outstanding ability to adapt to different environments. Their long evolutionary history, being exposed to vastly different physicochemical surroundings, allowed them to detect and respond to a wide range of signals including biochemical, mechanical, electrical, and magnetic ones. Taking into consideration their adapting mechanisms, it is expected that novel materials able to provide bacteria with specific stimuli in a biomimetic context may tailor their behavior and make them suitable for specific applications in terms of anti-microbial and pro-microbial approaches. This review maintains that electroactive smart materials will be a future approach to be explored in microbiology to obtain novel strategies for fighting the emergence of live threatening antibiotic resistance.
Survival and Success Rates of Different Shoulder Designs: A Systematic Review of the Literature (2018)

There was sufficient evidence that different implant shoulder positions/orientations/designs (scalloped, sloped, and one piece) offer no benefit when compared to two-piece, conventional flat implants. Current evidence is limited due to the quality of available studies.
pH regulation in barnacle muscle fibers: dependence on extracellular sodium and bicarbonate (1981)

Intracellular pH (pHi) regulation was studied in barnacle muscle fibers with pH-sensitive microelectrodes. The cells were acid loaded, and the subsequent recovery of pHi was monitored. The rate of recovery was reduced by one-third when external Na+ ([Na+]o) was replaced by Li+, but recovery was completely abolished when Na+ was replaced by choline or N-methyl-D-glucamine. In other experiments, varying amounts of Na+ were replaced by choline, and the acid extrusion rate, derived from the recovery rate of pHi, was calculated at a single value of pHi, 6.80. The dependence of the acid extrusion rate on [Na+]o could be described by Michaelis-Menten kinetics; at pHo (extracellular) = 8.0 and [HCO3-]o (extracellular) = 10 mM, the apparent Km and Vmax were 59 mM and 1.3 mmol x l(-1) x min-1. When [HCO3-]o was reduced to 2.5 mM at the same pHo, Km did not change significantly, but Vmax was substantially reduced. On the other hand, when pHo was reduced to 7.4 at constant [HCO3-]o, Vmax changed only slightly, but Km increased substantially. In similar experiments, we examined the dependence of the acid extrusion rate on [HCO3-]o. At pHo = 8.0 and [Na+]o = 440 mM, the apparent Km and Vmax were 4.1 mM and 2.1 mmol x 1-1 x min-1. When pHo was reduced to 7.4, Vmax was not altered, but Km substantially increased. The kinetic data are discussed in terms of the role of pHo, [Na+]o, and [HCO3-]o in the pHi-regulating system.
Empirical Analysis of Machine Learning Configurations for Prediction of Multiple Organ Failure in Trauma Patients (2021)

Multiple organ failure (MOF) is a life-threatening condition. Due to its urgency and high mortality rate, early detection is critical for clinicians to provide appropriate treatment. In this paper, we perform quantitative analysis on early MOF prediction with comprehensive machine learning (ML) configurations, including data preprocessing (missing value treatment, label balancing, feature scaling), feature selection, classifier choice, and hyperparameter tuning. Results show that classifier choice impacts both the performance improvement and variation most among all the configurations. In general, complex classifiers including ensemble methods can provide better performance than simple classifiers. However, blindly pursuing complex classifiers is unwise as it also brings the risk of greater performance variation.
Accurately estimating neuronal correlation requires a new spike-sorting paradigm (2012)

Neurophysiology is increasingly focused on identifying coincident activity among neurons. Strong inferences about neural computation are made from the results of such studies, so it is important that these results be accurate. However, the preliminary step in the analysis of such data, the assignment of spike waveforms to individual neurons ("spike-sorting"), makes a critical assumption which undermines the analysis: that spikes, and hence neurons, are independent. We show that this assumption guarantees that coincident spiking estimates such as correlation coefficients are biased. We also show how to eliminate this bias. Our solution involves sorting spikes jointly, which contrasts with the current practice of sorting spikes independently of other spikes. This new "ensemble sorting" yields unbiased estimates of coincident spiking, and permits more data to be analyzed with confidence, improving the quality and quantity of neurophysiological inferences. These results should be of interest outside the context of neuronal correlations studies. Indeed, simultaneous recording of many neurons has become the rule rather than the exception in experiments, so it is essential to spike sort correctly if we are to make valid inferences about any properties of, and relationships between, neurons.
SUN-140 EFFECTS OF PARATHYROID HORMONE ON GLUCOSE METABOLISM IN RENAL PROXIMAL TUBULES (2019)

Gluconeogenesis in renal proximal tubules (PTs) is markedly enhanced in prolonged fasting and even in diabetic patients, which is comparable to the liver. However, its pathophysiological significance and hormonal regulation are not well known. We have recently found that cAMP increases mRNA expression levels of gluconeogenic enzyme, and insulin suppresses PT gluconeogenesis via insulin receptor substrate (IRS)1/Akt2 pathway (ASN Kidney Week 2017). On the other hand, parathyroid hormone (PTH) has also been reported to enhance PT gluconeogenesis along with the fact that the high level of PTH is associated with abnormal glucose metabolism.
Application of the Proper Generalized Decomposition to the Simulation of RTM Processes (2010)

Simulation of RTM processes in thin plate geometries is usually performed in 2D. Thus,only a mesh of the middle plane is needed with the associated degrees of freedomyielding significant savings with respect to a fully 3D modeling. However suchmodeling needs the definition of an equivalent in-plane permeability representing theignored dimension (the plate thickness). The definition of such permeability is not atrivial task because each ply in the thickness direction can be anisotropic, the principalanisotropy direction being different from one ply to the neighboring plies. In this workwe propose a novel fully 3D modeling whose computational cost of the same order as a2D solution. It allows addressing properly the equivalent in-plane permeability issue aswell as other issues induced when averaging over the thickness dimension.
In silico COSMO-RS predictive screening of ionic liquids for the dissolution of plastic (2022)

Herein we report the screening of 9405 ionic liquids for plastic dissolution using the continuum solvation model (COMSO-RS) and the results are validated with experiments.
<title>Wireless capsule endoscopy of the small bowel: development, testing, and first human trials</title> (2001)

Small bowel endoscopy with existing endoscopes is limited by problems of discomfort and the technical difficulty of advancing far into the small-bowel. Our aim has been to develop and test wireless capsule endoscopy. Wireless endoscopes, in the form of capsules (11 x 33 mm), were constructed by Given Imaging. These were powered by silver oxide batteries and each contained a CMOS imaging chip and miniature processor, white light emitting diodes (LEDs), a short focal length lens, and a miniature transmitter and antenna. Two video frames per second were transmitted, using radio-frequency (approx. 410 MHz), to an array of aerials attached to the body. The array of aerials can also be used to calculate the position of the capsule in the body. The images were stored on a portable recorder carried on a belt and subsequently downloaded for analysis. The batteries allow more than 5 hours of recording, although the capsule generally passes through the whole small bowel in under two hours. Clear video images of the human bowel were recorded from the pylorus to the caecum. Wireless endoscopy, for the first time, allows painless optical imaging of the whole of the small bowel.
Cell-Specific, Multidrug Delivery System Using Streptavidin–Protein A Fusion Protein (1996)

Tissue-specific delivery of variety of molecules has been a valuable technique for biological and medical research and for the diagnosis and therapy of cancer. We have therefore examined the ability of streptavidin-protein A (ST-PA) fusion protein complexed with monoclonal antibodies (mAbs) to transfer biotinylated proteins into specific type of cells. ST-PA/mAbs complexes could efficiently deliver biotinylated beta-galactosidase into a variety of cancer cell lines through molecules expressed on their surface. In addition, ST-PA/mAb complexed with either biotinylated glucose oxidase or biotinylated ribonuclease A could be transferred to specific cell types and made to display cytotoxic activity against the transduced cell. The flexibility of the system was enhanced by the fact that the cell-targeting specificity could be altered by just changing the mAb used and the "payload" molecule could be replaced by substituting one biotinylated protein or enzyme with another. This flexibility was achieved without the need to generate a covalent chemical link or engineering new recombinant molecules. Results obtained to date suggest that the ST-PA fusion protein may be used as a nearly "universal carrier" to transfer a variety of effector molecules into target cells with a high degree of specificity. Essentially, the ST-PA fusion protein effectively serves as a high-efficiency, modular "molecular bridge" for the transfer into cells of a wide variety of effector molecules.
Scheduling Ocean Transportation of Crude Oil (1987)

A crude oil tanker scheduling problem faced by a major oil company is presented and solved using an elastic set partitioning model. The model takes into account all fleet cost components, including the opportunity cost of ship time, port and canal charges, and demurrage and bunker fuel. The model determines optimal speeds for the ships and the best routing of ballast (empty) legs, as well as which cargos to load on controlled ships and which to spot charter. All feasible schedules are generated, the cost of each is accurately determined and the best set of schedules is selected. For the problems encountered, optimal integer solutions to set partitioning problems with thousands of binary variables have been achieved in less than a minute.
Inactivation of cell-associated fructosyltransferase in Streptococcus salivarius (1981)

In stationary phase, 95% of the fructosyltransferase (FTase) activity of Streptococcus salivarius ATCC 25975 was found associated with the cells. Within the first 15 min after inoculation into fresh medium, the specific activity of cell-associated FTase decreased by 92% of its initial value. After this period of initial loss, the enzyme was synthesized during exponential growth until a maximum level equivalent to that present before inoculation was obtained. The inactivation of FTase was also demonstrated in a nongrowing system. Washed cell suspensions incubated at 37 degrees C in 200 mM potassium phosphate buffer (pH 6.5) containing 10 microM Cu2+ lost 80 to 95% of their FRase activity after 30 min. This loss could be prevented by the addition of histidine, cysteine, or Ca2+ to the suspension mixture. A factor(s) essential for the inactivation of cell-associated FTase could itself be preferentially inactivated by heating cells at 40 degrees C for periods of up to 3 h, or by storage of cells at 0 to 4 degrees C for several days in a low-ionic-strength, low-pH, potassium phosphate buffer. Treatment of cells with the N-acetylmuramidase enzyme M-1, in the presence of 0.5 M melezitose, resulted in the release of FTase from the cell. The released enzyme was recovered in the supernatant fraction after centrifugation at 160,000 x g for 90 min. Comparison of solubilized active and inactivated FTase preparations by polyacrylamide gel electrophoresis demonstrated that the inactivation of cell-associated FTase activity was associated with the loss of specific protein bands.
“Talk to me with left, right, and angles”: Lexical entrainment in spoken Hebrew dialogue (2021)

Andreas Weise, Vered Silber-Varod, Anat Lerner, Julia Hirschberg, Rivka Levitan. Proceedings of the 16th Conference of the European Chapter of the Association for Computational Linguistics: Main Volume. 2021.
Exhaust Gas Electrochemical Sensors with a Nb2O5 Sensing Electrode (2008)

Electrochemical planar sensors using Nb2O5 powders to fabricate sensing electrodes were tested both in laboratory and "in-situ", i.e. downstream a three-way catalytic converter of a FIAT fire 1242 c.c. spark ignition engine. Two cell configurations were compared, one with and the other without Pt paste under the metal oxide electrode. The best sensing performance both in laboratory and at the engine bench was obtained for the Pt | YSZ | Nb2O5 cell, without Pt below the oxide electrode. For this sensor configuration, very large EMF response values were obtained for hydrocarbon exposure, even at temperatures as high as 700{degree sign}C.
NOTCH inhibits osteoblast formation in inflammatory arthritis via noncanonical NF-κB (2014)

NOTCH-dependent signaling pathways are critical for normal bone remodeling; however, it is unclear if dysfunctional NOTCH activation contributes to inflammation-mediated bone loss, as observed in rheumatoid arthritis (RA) patients. We performed RNA sequencing and pathway analyses in mesenchymal stem cells (MSCs) isolated from transgenic TNF-expressing mice, a model of RA, to identify pathways responsible for decreased osteoblast differentiation. 53 pathways were dysregulated in MSCs from RA mice, among which expression of genes encoding NOTCH pathway members and members of the noncanonical NF-κB pathway were markedly elevated. Administration of NOTCH inhibitors to RA mice prevented bone loss and osteoblast inhibition, and CFU-fibroblasts from RA mice treated with NOTCH inhibitors formed more new bone in recipient mice with tibial defects. Overexpression of the noncanonical NF-κB subunit p52 and RELB in a murine pluripotent stem cell line increased NOTCH intracellular domain-dependent (NICD-dependent) activation of an RBPjκ reporter and levels of the transcription factor HES1. TNF promoted p52/RELB binding to NICD, which enhanced binding at the RBPjκ site within the Hes1 promoter. Furthermore, MSC-enriched cells from RA patients exhibited elevated levels of HES1, p52, and RELB. Together, these data indicate that persistent NOTCH activation in MSCs contributes to decreased osteoblast differentiation associated with RA and suggest that NOTCH inhibitors could prevent inflammation-mediated bone loss.
Modulation of Redox Signaling and Thiol Homeostasis in Red Blood Cells by Peroxiredoxin Mimetics (2020)

Red blood cell death or erythrocyte apoptosis (eryptosis) is generally mediated by oxidative stress, energy depletion, heavy metals exposure, or xenobiotics. As erythrocytes are a major target for oxidative stress due to their primary function as O<sub>2</sub>-carrying cells, they possess an efficient antioxidant defense system consisting of glutathione peroxidase (GPx), superoxide dismutase (SOD), catalase (CAT), and peroxiredoxin 2 (Prx2). The oxidative stress-mediated activation of the Ca<sup>2+</sup>-permeable cation channel results in Ca<sup>2+</sup> entry into the cells and subsequent cell death. Herein, we describe for the first time that selenium compounds having intramolecular diselenide or selenenyl sulfide moieties can prevent the oxidative stress-induced eryptosis by exhibiting an unusual Prx2-like redox activity under conditions when the cellular Prx2 and CAT enzymes are inhibited.
Characterization of a homolog of human bone morphogenetic protein 1 in the embryo of the sea urchin, Strongylocentrotus purpuratus (1994)

A cDNA clone encoding a protein homologous to human bone morphogenetic protein 1 (huBMP1) was isolated from a sea urchin embryo cDNA library. This sea urchin gene, named suBMP, encodes a protein of M(r) of 72 x 10(3). The deduced amino acid sequence of suBMP shares 72% sequence similarity (55% identity) with that of huBMP1. Like huBMP1 it also contains an N-terminal metalloendoprotease domain that shares sequence similarity with the astacin protease from crayfish, a C-terminal domain that is similar to the repeat domain found in C1r or C1s serine proteases, and an EGF-like segment. Although suBMP mRNA was detectable at a low level in the unfertilized egg, maximal expression of mRNA was observed at hatched blastula stage, with only a modest decrease in level at later stages of development. In situ hybridization studies revealed that suBMP mRNA is found in both ectodermal and primary mesenchyme cells in hatched blastula-stage embryos. Maximal expression of suBMP was observed at mesenchyme blastula, just before the onset of primitive skeleton (spicule) formation. SuBMP was found by immunoelectronmicroscopy in all cell types in late gastrula stage embryos. The antibody gold particles appeared in small clusters in the cytoplasm, on the surface of the cells and within the blastocoel. This distribution of suBMP, coupled with the finding that it was associated with membranes but was released by sodium carbonate treatment, suggests that the protein is secreted, and subsequently associates with a cell surface component. Two models for the possible function of suBMP in spiculogenesis in the sea urchin embryo are discussed.
Analytical and numerical solutions of thin lubricating films for differing shear-thinning viscosity models (2007)

A detailed assessment of thin film lubrication, for shear-thinning fluids, in two benchmark geometries - a classical linear slider-bearing and a converging-diverging gap arrangement - is provided in terms of the associated pressure distribution, flowrate, and variation in friction. Solutions, both analytical and purely numerical are obtained, with three different rheological constitutive relationships, the viscosity being represented via either a power-law or a Moore or an Ellis model. Finite-element simulations, with these rheological models fully integrated within the weak form of the momentum equation, show that the accuracy of the corresponding analytical solutions depends on whether the resulting pressure gradient-flux relationships are derived using either a full or average shear-dependence formulation. Indeed, the analytical results obtained via the latter form reveal significant discrepancies as the shear-thinning effects increase, in that the behaviour of the pressure field is not well captured.
Tracking particles in four dimensions with in-line holographic microscopy (2003)

We describe a simple holographic method that has enabled us to capture as a single data set the trajectories of micrometer-sized objects suspended in water. By subtracting consecutive holograms of a particle suspension and then adding these difference holograms, we constructed a final data set that contains the time evolution of the particle trajectories free from spurious background interference effects. The method is illustrated by a recording of the motion of 5-10-microm diameter algae in water.
Generation of a pair of independently binding DNA aptamers in a single round of selection using proximity ligation (2015)

The ability to rapidly generate a pair of aptamers that bind independently to a protein target would greatly extend their use as reagents for two site ('sandwich') assays. We describe here a method to achieve this through proximity ligation. Using lysozyme as a target we demonstrate that under optimal conditions such a pair of aptamers, with nanomolar affinities, can be generated in a single round.
Synthesis and Antimycobacterial Activity of Capuramycin Analogues. Part 2. Acylated Derivatives of Capuramycin‐Related Compounds. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Ex vivo model of cranial suture fate (2007)

Slater, Bethany J. MD; Lenton, Kelly PhD; Longaker, Michael T. MD, MBA, FACS Author Information
Isolated Myocyte Contractile Function Is Normal in Postinfarct Remodeled Rat Heart With Systolic Dysfunction (1997)

Postinfarct LV remodeling occurs predominantly by myocyte lengthening rather than by myocyte slippage. However, contractile function of the unloaded myocytes from the remote noninfarcted LV myocardium of the remodeled heart is normal. Therefore, myocyte contractile abnormalities may not contribute to global dysfunction of the remodeled heart. Reduced myocyte mass and nonmyocyte factors like increased wall stress, altered LV geometry, and changes in the myocardial interstitium may be more important in the genesis of postinfarct LV dysfunction in this model.
Interpenetrating Cubes in the X-ray Crystallographic Structure of a Peptide Derived from Medin19–36 (2020)

Amyloidogenic peptides and proteins are rich sources of supramolecular assemblies. Sequences derived from well-known amyloids, including Aβ, human islet amyloid polypeptide, and tau have been found to assemble as fibrils, nanosheets, ribbons, and nanotubes. The supramolecular assembly of medin, a 50-amino acid peptide that forms fibrillary deposits in aging human vasculature, has not been heavily investigated. In this work, we present an X-ray crystallographic structure of a cyclic β-sheet peptide derived from the 19-36 region of medin that assembles to form interpenetrating cubes. The edge of each cube is composed of a single peptide, and each vertex is occupied by a divalent metal ion. This structure may be considered a metal-organic framework (MOF) containing a large peptide ligand. This work demonstrates that peptides containing Glu or Asp that are preorganized to adopt β-hairpin structures can serve as ligands and assemble with metal ions to form MOFs.