gebhart/patrepeval huggingface dataset:
The Gauss-Newton learning method for a generalized dynamic synapse neural network (2003)

A new architecture for dynamic synapse neural networks (DSNNs) has been introduced based on incorporating a continuous nonlinear mechanism to simulate synaptic neuro-transmitter release, adding a nonlinear output layer, and utilizing a Gauss-Newton learning method to train the network. We applied this network to simulate two nonlinear dynamical systems and then identify the dynamical systems by generating random noise observation data. The network estimation error per sample on the training phase was less than approximately 2% and on the test set was less than approximately 3%.
Prosthetic joint infection (2005)

Infection is the second most common cause of prosthetic joint failure. Signs and symptoms associated with prosthetic joint infection may develop weeks or even years following arthroplasty. While some patients with prosthetic joint infection present with findings consistent with acute septic arthritis, many present with pain alone. Morbidity and cost associated with repeat surgery, prolonged medical treatment and joint immobilization render importance to the accurate and timely diagnosis, and appropriate treatment of prosthetic joint infection. No consensus exists, however, in terms of the most cost-effective diagnostic methods or the ideal medical and/or surgical interventions. This review describes diagnostic tests and available treatment for prosthetic joint infection and gives a practical approach to this challenging clinical entity.
Conformation of a Tetradecapeptide Epitope of Myelin Basic Protein (1995)

The peptide AcAla-Ser-Gln-Lys-Arg-Pro-Ser-Gln-Arg-His-Gly-Ser-Lys-Tyr, which comprises the first 14 residues of the acetylated N-terminus of myelin basic protein, is an epitopic site for two monoclonal antibodies to the human protein. The conformations of the tetradecapeptide in aqueous solutions were investigated employing high-resolution 1H- and 13C-NMR spectroscopy. Two-dimensional techniques were used to assign the spectra observed from both nuclei. Nuclear-Overhauser-effect data, amide proton temperature coefficients, 13C spin-lattice relaxation times, distance geometry calculations and dynamic simulated annealing provided evidence that the solution conformations of the tetradecapeptide included a nascent alpha-helix in the N-terminal segment, and a loop extending from Ser7 to Ser12 that bring His10 and Tyr14 into close proximity.
Active damping of oscillations in a long compliant manipulator link (1993)

A flexible manipulator test bed consisting of a fifteen foot long fixed-free compliant beam (representing a compliant manipulator link) with a Shilling Titan II dextrous manipulator mounted on its free end has been constructed at Pacific Northwest Laboratory (PNL). A comprehensive dynamic model which includes flexible body effects has been developed at PNL using a commercially available multibody dynamics code. A linearized version of the model is used to develop control strategies which use inertial forces generated by movements of the dextrous manipulator to damp out induced oscillations in the beam. These control strategies are tested on the model and shown to be feasible, and then implemented in the flexible manipulator testbed. Results from the hardware experiments are analyzed and compared with the model results.
Water and thermal management in PEMFCs – influencing parameters and operational conditions: A Review (2017)

Despite of huge prospects and efforts from the scientists around the world, Proton exchange membrane fuel cell (PEMFC) is still struggling to be commercialized. Numbers of issues are present in PEMFC, having both positive and negative impact on the cell performance. Water content in the membrane as well as the presence of water in the different zones of the PEMFC for wide range of operating conditions plays major role of the cell performance. Situations like: the presence of water content in the membrane, the initial feed of water as humidified reactants, the accumulation of water in the different zones, conversion of water vapor to liquid water in the cell and water removal process can be designated as crucial aspects of water management of the cell. This review article emphasizes different issues which directly and indirectly influence water transportation and thermal management in the cells and their ultimate effects on the fuel cell performance. The dependence of different physical and geometrical properties on water and thermal management is highlighted. Moreover, different operating conditions for fuel cell are discussed based on the water and thermal management along with other aspects which are common in the present research trends of PEM fuel cells. Keywords : water management, thermal management, PEMFC, durability, cell performance.
Steroid receptor coactivator-1 modulates the function of Pomc neurons and energy homeostasis. (2019)

Hypothalamic neurons expressing the anorectic peptide Pro-opiomelanocortin (Pomc) regulate food intake and body weight. Here, we show that Steroid Receptor Coactivator-1 (SRC-1) interacts with a target of leptin receptor activation, phosphorylated STAT3, to potentiate Pomc transcription. Deletion of SRC-1 in Pomc neurons in mice attenuates their depolarization by leptin, decreases Pomc expression and increases food intake leading to high-fat diet-induced obesity. In humans, fifteen rare heterozygous variants in SRC-1 found in severely obese individuals impair leptin-mediated Pomc reporter activity in cells, whilst four variants found in non-obese controls do not. In a knock-in mouse model of a loss of function human variant (SRC-1L1376P), leptin-induced depolarization of Pomc neurons and Pomc expression are significantly reduced, and food intake and body weight are increased. In summary, we demonstrate that SRC-1 modulates the function of hypothalamic Pomc neurons, and suggest that targeting SRC-1 may represent a useful therapeutic strategy for weight loss.
Preclinical efficacy of humanized, non–FcγR-binding anti-CD3 antibodies in T-cell acute lymphoblastic leukemia (2020)

T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignancy that accounts for ∼20% of ALL cases. Intensive chemotherapy regimens result in cure rates >85% in children and <50% in adults, warranting a search of novel therapeutic strategies. Although immune-based therapies have tremendously improved the treatment of B-ALL and other B-cell malignancies, they are not yet available for T-ALL. We report here that humanized, non-Fcγ receptor (FcγR)-binding monoclonal antibodies (mAbs) to CD3 have antileukemic properties in xenograft (PDX) models of CD3+ T-ALL, resulting in prolonged host survival. We also report that these antibodies cooperate with chemotherapy to enhance antileukemic effects and host survival. Because these antibodies show only minor, manageable adverse effects in humans, they offer a new therapeutic option for the treatment of T-ALL. Our results also show that the antileukemic properties of anti-CD3 mAbs are largely independent of FcγR-mediated pathways in T-ALL PDXs.
Neutron diffraction study on CDP-DCDP mixed crystals (1995)

Abstract Deuteration rate (x) dependent behavior of transition temperatures (Tc ) and hydrogen bond distances in Cs(H1-x D x )2PO4 mixed crystals were examined through neutron diffraction analysis and dielectric constant measurements. The neutron analysis proved that a hydrogen atom, H(1), involved in a shorter hydrogen bond has slight difficulty in substitution than the other, H(2), in a longer hydrogen bond in the region of intermediate x. The experimental ΔTc vs. x relation was compared with a theoretical result which was derived taking one-dimensional character of CDP into account. The ferroelectric structure, disorder in the paraelectric phase, change of the hydrogen bond by deuteration and its relation to geometrical isotope effect are discussed.
The Role of Abcb5 Alleles in Susceptibility to Haloperidol-Induced Toxicity in Mice and Humans (2015)

ABCB5 alleles alter susceptibility to HIT in mouse and humans. This discovery leads to a new model that (at least in part) explains inter-individual differences in susceptibility to a drug-induced CNS toxicity.
Probing the Binding Site of Bile Acids in TGR5 (2013)

TGR5 is a G-protein-coupled receptor (GPCR) mediating cellular responses to bile acids (BAs). Although some efforts have been devoted to generate homology models of TGR5 and draw structure-activity relationships of BAs, none of these studies has hitherto described how BAs bind to TGR5. Here, we present an integrated computational, chemical, and biological approach that has been instrumental to determine the binding mode of BAs to TGR5. As a result, key residues have been identified that are involved in mediating the binding of BAs to the receptor. Collectively, these results provide new hints to design potent and selective TGR5 agonists.
Potent Irreversible Inhibitors of LasR Quorum Sensing in Pseudomonas aeruginosa (2014)

Antagonism of quorum sensing represents a promising new antivirulence approach for the treatment of bacterial infection. The development of a novel series of non-natural irreversible antagonists of P. aeruginosa LasR is described. The lead compounds identified (25 and 28) display potent LasR antagonist activity and inhibit expression of the P. aeruginosa virulence factors pyocyanin and biofilm formation in PAO1 and PA14.
Programmable pH buffers (2023)

A programmable pH buffer comprises a copolymer that changes pK.sub.a at a lower critical solution temperature (LCST) in water. The copolymer comprises a thermally programmable polymer that undergoes a hydrophobic-to-hydrophilic phase change at the LCST and an electrolytic polymer that exhibits acid-base properties that are responsive to the phase change. The programmable pH buffer can be used to sequester CO.sub.2 into water.
Ricin Crosses Polarized Human Intestinal Cells and Intestines of Ricin-Gavaged Mice without Evident Damage and Then Disseminates to Mouse Kidneys (2013)

Ricin is a potent toxin found in the beans of Ricinus communis and is often lethal for animals and humans when aerosolized or injected and causes significant morbidity and occasional death when ingested. Ricin has been proposed as a bioweapon because of its lethal properties, environmental stability, and accessibility. In oral intoxication, the process by which the toxin transits across intestinal mucosa is not completely understood. To address this question, we assessed the impact of ricin on the gastrointestinal tract and organs of mice after dissemination of toxin from the gut. We first showed that ricin adhered in a specific pattern to human small bowel intestinal sections, the site within the mouse gut in which a variable degree of damage has been reported by others. We then monitored the movement of ricin across polarized human HCT-8 intestinal monolayers grown in transwell inserts and in HCT-8 cell organoids. We observed that, in both systems, ricin trafficked through the cells without apparent damage until 24 hours post intoxication. We delivered a lethal dose of purified fluorescently-labeled ricin to mice by oral gavage and followed transit of the toxin from the gastrointestinal tracts to the internal organs by in vivo imaging of whole animals over time and ex vivo imaging of organs at various time points. In addition, we harvested organs from unlabeled ricin-gavaged mice and assessed them for the presence of ricin and for histological damage. Finally, we compared serum chemistry values from buffer-treated versus ricin-intoxicated animals. We conclude that ricin transverses human intestinal cells and mouse intestinal cells in situ prior to any indication of enterocyte damage and that ricin rapidly reaches the kidneys of intoxicated mice. We also propose that mice intoxicated orally with ricin likely die from distributive shock.
Optical matter: binding and crystallization in intense optical fields (1990)

It is now well known, mainly due to the pioneering work of Ashkin et al.,1 that intense laser beams can exert substantial forces on dielectric matter. Perhaps the greatest impact of this work to date has been in the field of biology, where impressive examples of the manipulation of biological material with laser beams have been demonstrated.2 We deal with the elaboration of these concepts in the wave optical region and their application to the problem of assembling complex structures such as crystals and quasicrystals in complex optical fields. We discuss not only order imposed on matter by externally imposed optical fields but also the order achieved as a result of self-organization, epitomized by the simplest examples of optical binding achieved to date.3
Structure and function of the murine chemokine receptor CXCR3 (1999)

The gene encoding the murine homologue of human CXCR3 exists in a single copy consisting of two exons with an intron interrupting the coding sequence between nucleotides 10 and 11. The deduced amino acid sequence is 86 % identical to the predicted human sequence. Murine CXCR3 mRNA is detectable in bone marrow cells cultured in the presence of IL-2 but not unstimulated cells. It is also detectable at low abundance in normal mouse spleen, lymph node, mammary gland, and thymus. Transfection of murine CXCR3 in murine pre-B lymphocyte line (CXCR3 / L1.2) conferred binding of the ligands IP10, ITAC and Mig with KD's of 1.35 ± 0.56, 1.41 ± 0.20, and 11.65 ± 0.90 nM, respectively. Lower affinity binding was observed for several beta or CC chemokines (eotaxin, MCP-3, MIP3α and SLC / 6Ckine / Exodus 2). ITAC, IP10 and Mig induced chemotaxis with an order of potency ITAC > IP10 = Mig. The chemokines also increased intracellular calcium concentration and were variably desensitized to repeated agonist stimulation. The hierarchy for cross- desensitization was ITAC > Mig > IP10. Thus, while Mig, ITAC and IP10 all act on the same receptor for binding and agonist stimulation, they may interact with different receptor conformational isoforms to produce divergent responses.
Correction: Corrigendum: The extracellular interactome of the human adenovirus family reveals diverse strategies for immunomodulation (2017)

Nature Communications 7: Article number: 11473 (2016); Published: 5 May 2016; Updated: 21 August 2017 In Supplementary Fig. 3 of this Article, the sequence given for CR1B_HAdV-D19a in the alignment shown is incorrect, and should have been identical to that listed for CR1B_HAdV-D37. A correct versionof Supplementary Fig.
Fundamental limits of image registration performance: effects of image noise and resolution in CT-guided interventions (2017)

Analysis of the CRLB for image registration is an important step toward understanding and evaluating an intraoperative imaging system with respect to a registration task. While the CRLB is optimistic in absolute performance, it reveals a basis for relating the performance of registration estimators as a function of noise content and may be used to guide acquisition parameter selection (e.g., dose) for purposes of intraoperative registration.
Synthesis of human CCK26-33 and CCK-33 related analogs on 2,4-DMBHA and TMBHA (1993)

New analogues of human cholecystokinin in which the Tyr(SO3H) has been replaced by Phe(p-CH2SO3Na), methionines by norleucines, and tryptophan by 2-naphthylalanine([Phe(p-CH2- SO3Na)27,Nle28,31,Nal30]-CCK26-33 and [Phe(p-CH2SO3Na)27,Nle7,28,31,Nal30]-CCK-33) were synthesized by Fmoc solid phase methodology on two different resins (2,4- dimethoxybenzhydrylamine- and 4-(benzyloxy)-2',4'-dimethoxybenzhydrylamine resins, 2,4-DMBHA and TMBHA resins, respectively). While the syntheses on the TMBHA appeared to be more sluggish than those carried out on the 2,4-DMBHA, both final crude products were of equivalent relative purity and after purification gave approximately the same final yields of analogues estimated to have a purity greater than 93% using RPHPLC and CZE. The peptides were further characterized by amino acid analysis and LSIMS. Phe(p-CH2SO3Na)27,Nle7,28,31,Nal30]-CCK-33 was submitted to 33 Edman cycles and shown to be the desired product with less than 3% preview. Both analogues were tested for their ability to stimulate amylase release from isolated rat pancreatic acini. In this assay, [Phe(p-CH2SO3Na)27,Nle28,31,Nal30]-CCK26-33 and Phe(p-CH2SO3Na)27,Nle7,28,31,Nal30]-CCK-33 were 10 and 30 times less potent than CCK-8, respectively.
Dynamic models for musical rhythm perception and coordination (2023)

Rhythmicity permeates large parts of human experience. Humans generate various motor and brain rhythms spanning a range of frequencies. We also experience and synchronize to externally imposed rhythmicity, for example from music and song or from the 24-h light-dark cycles of the sun. In the context of music, humans have the ability to perceive, generate, and anticipate rhythmic structures, for example, "the beat." Experimental and behavioral studies offer clues about the biophysical and neural mechanisms that underlie our rhythmic abilities, and about different brain areas that are involved but many open questions remain. In this paper, we review several theoretical and computational approaches, each centered at different levels of description, that address specific aspects of musical rhythmic generation, perception, attention, perception-action coordination, and learning. We survey methods and results from applications of dynamical systems theory, neuro-mechanistic modeling, and Bayesian inference. Some frameworks rely on synchronization of intrinsic brain rhythms that span the relevant frequency range; some formulations involve real-time adaptation schemes for error-correction to align the phase and frequency of a dedicated circuit; others involve learning and dynamically adjusting expectations to make rhythm tracking predictions. Each of the approaches, while initially designed to answer specific questions, offers the possibility of being integrated into a larger framework that provides insights into our ability to perceive and generate rhythmic patterns.
Discovery and characterization of two new stem rust resistance genes in Aegilops sharonensis (2017)

We identified two novel wheat stem rust resistance genes, Sr-1644-1Sh and Sr-1644-5Sh in Aegilops sharonensis that are effective against widely virulent African races of the wheat stem rust pathogen. Stem rust is one of the most important diseases of wheat in the world. When single stem rust resistance (Sr) genes are deployed in wheat, they are often rapidly overcome by the pathogen. To this end, we initiated a search for novel sources of resistance in diverse wheat relatives and identified the wild goatgrass species Aegilops sharonesis (Sharon goatgrass) as a rich reservoir of resistance to wheat stem rust. The objectives of this study were to discover and map novel Sr genes in Ae. sharonensis and to explore the possibility of identifying new Sr genes by genome-wide association study (GWAS). We developed two biparental populations between resistant and susceptible accessions of Ae. sharonensis and performed QTL and linkage analysis. In an F<sub>6</sub> recombinant inbred line and an F<sub>2</sub> population, two genes were identified that mapped to the short arm of chromosome 1S<sup>sh</sup>, designated as Sr-1644-1Sh, and the long arm of chromosome 5S<sup>sh</sup>, designated as Sr-1644-5Sh. The gene Sr-1644-1Sh confers a high level of resistance to race TTKSK (a member of the Ug99 race group), while the gene Sr-1644-5Sh conditions strong resistance to TRTTF, another widely virulent race found in Yemen. Additionally, GWAS was conducted on 125 diverse Ae. sharonensis accessions for stem rust resistance. The gene Sr-1644-1Sh was detected by GWAS, while Sr-1644-5Sh was not detected, indicating that the effectiveness of GWAS might be affected by marker density, population structure, low allele frequency and other factors.
The role of diphenyl iodonium salt (DPI) in three‐component photoinitiator systems containing methylene blue (MB) and an electron donor (2004)

Abstract Three‐component initiators generally include a light‐absorbing photosensitizer, an electron donor that is often an amine, and the third component, which is usually an iodonium salt. To characterize the role of diphenyl iodonium chloride (DPI) in three‐component photoinitiator systems containing methylene blue (MB) as the photosensitizer, a systematic series of electron donors was used. The Rhem–Weller equation was used to verify the thermodynamic feasibility for photo‐induced electron transfer from the electron donors to the MB. Comparison of the photopolymerization rates of each two‐component initiator system (containing the photosensitizer and amine) to those of the corresponding three‐component system (with the addition of (DPI) allowed fundamental information regarding the role of the DPI to be obtained. It was concluded that the DPI enhances the photopolymerization kinetics in two ways: (1) it consumes an inactive MB neutral radical and produces an active phenyl radical, thereby regenerating the original methylene blue, and (2) it reduces the recombination reaction of the MB neutral radical and amine radical/cation. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 5863–5871, 2004
Semiconductor and Nonsemiconductor Damage Study (1969)

Abstract : Contents: Determination of threshold failure levels of semiconductor diodes and transistors due to pulse voltages; Estimates of semiconductor failure due to multiple voltage pulses; Semiconductor damage test results; Nonsemiconductor damage test results.
BT-11 (omilancor), a first-in-class, topical therapeutic for psoriasis, ameliorates disease severity and inflammation through activation of LANCL2 pathway (2021)

Abstract BT-11 (omilancor) is a small molecule therapeutic that activates the LANCL2 pathway in immune and epithelial cells, resulting in regulatory effects at the intersection of immunity and metabolism. LANCL2 modulates the plasticity between Th17 and regulatory T cells (Tregs), favoring the stability and suppressive capacity of Tregs. Given the implication of the LANCL2 pathway in autoimmune disease and the demonstrated clinical efficacy and safety of BT-11 in a Phase 2 clinical trial of UC, we evaluated the therapeutic efficacy of BT-11 in psoriasis. In an imiquimod-induced mouse model of psoriasis, pharmacological activation of LANCL2 through topical BT-11 treatment ameliorates disease severity, resulting in over 60% reduction of PASI score. Indeed, BT-11 treatment decreased acanthosis and immune cell infiltration, with no signs of parakeratosis. The loss of LANCL2 in mice resulted in increased hyperkeratosis and parakeratosis. Local LANCL2 activation by BT-11 resulted in decreased TNF, IL17, IL6 and IL21-producing cells in the spleen. Additionally, LANCL2 activation regulated keratinocyte metabolism and function. Keratinocytes from BT-11-treated mice presented lower metabolic activation, reported as decreased ATP production, mitochondrial respiration and glucose metabolism. In translational studies with human PBMCs, BT-11 modulated the metabolic profile of CD4+ T cells at late state glycolysis, favoring oxidative pathways, and decreased expression of proinflammatory cytokines (IFNγ, TNFα), while upregulating IL-10. These results merit further exploration into the implication of LANCL2 signaling in human psoriasis and leverages the development of BT-11, as a first-in-class, topical therapeutic for psoriasis.
RF induced heating of pacemaker/ICD lead-tips during MRI Scans at 1.5T and 3T: evaluation in cadavers (2016)

Background Studies about the safety of MRI exams for patients with pacemakers/ICDs at 1.5T have been reported [Nazarian S., et al. Annals of internal medicine 155.7 (2011): 415-424.]. Of most concern is possible heating of the lead-tips in contact with the myocardium. Little is known about the relative safety of 3T MRI exams for these patients and in vivo lead-tip heating data is difficult, if not impossible, to obtain. Our objective was to measure lead-tip heating directly in human cadavers with pacemakers/ICDs at both 3.0T and 1.5T.