gebhart/patrepeval huggingface dataset:
Driving HIV-1 specific responses in immune suppressed recipients: Listeria as a vaccine vector (53.20) (2011)

Abstract Malaria, TB and HIV-1 remain tremendous disease burdens in much of the world’s population and functional vaccines are desperately needed. Although Sub-Saharan populations are those that will benefit most from these vaccines, they are also coincident with areas of endemic helminth infection. Infection with one or more species of parasitic helminths suppresses the immune system and has been shown, by our lab and others, to suppress vaccine-specific responses. One goal of our research is to find vaccines that drive significant vaccine-specific immune responses in helminth infected recipients, without the need to eliminate helminth infection prior to vaccination. In the current study, we demonstrate that administration of a Listeria vector HIV-1 gag vaccine to mice chronically infected with the helminth parasite Schistosoma mansoni drives significant immune responses to HIV-1 gag CTL and helper epitopes. This observation suggests that Listeria vector vaccines are capable of driving vaccine-specific responses in helminth-infected populations. Kinetic studies show the antigen-specific responses are both durable and capable of inducing CD8+ central memory. In addition to HIV-1, Listeria vectors should be considered in the development of new generation malaria and TB vaccines to be administered to sub-Saharan Africa populations where helminth infection is endemic. Studies are underway to determine if other vectors are also capable of overcoming helminth-induced immune suppression.
Abstract 193: RNA-sequencing of Disease-specific iPSC as a New Filter to Identify Genes Associated With Hypoplastic Left Heart Syndrome (2015)

Hypoplastic Left Heart Syndrome (HLHS) is a complex multifactorial disease for which no definitive genetic causes have been found. Current genetic filtering strategies render lists of genes with unknown relevance in terms of pathogenesis. A complementary filter based on biological evidence would create a new approach to prioritize relevant candidate genes and mutations. In our study, 5 members of a nuclear family including a child with HLHS were evaluated using echocardiography and their genetic information was obtained through whole genome sequencing (WGS). Data filtering including rarity, functional impact and mode of inheritance was implemented, resulting in identification of 34 genes with recessive or de novo variants potentially involved in the pathogenesis of HLHS. Additionally, iPSC were derived from proband and parents and subjected to RNA-sequencing at the undifferentiated state and following spontaneous differentiation. Comparative transcriptional analyses identified genes differentially expressed in proband samples at each stage. These gene sets were used as an additional filter for the previously generated WGS data. This strategy revealed that out of 34 mutated genes originally identified, 10 displayed transcriptional differences in undifferentiated iPSC from the HLHS-affected individual while 16 out of 34 mutated genes showed significantly different expression levels in differentiated cells from proband. Furthermore, expression dynamics were studied during guided cardiac differentiation for the 9 genes fulfilling all applied criteria. Two genes not previously linked to HLHS, ELF4 and HSPG2 were found to behave significantly different in HLHS-iPSC when compared to control counterparts. In summary, filtering WGS data according to a new layer of transcriptional information that leverages iPSC plasticity allows prioritization of genes associated with HLHS in an in vitro model of disease.
New tools provide a second look at HDV ribozyme structure, dynamics and cleavage (2014)

The hepatitis delta virus (HDV) ribozyme is a self-cleaving RNA enzyme essential for processing viral transcripts during rolling circle viral replication. The first crystal structure of the cleaved ribozyme was solved in 1998, followed by structures of uncleaved, mutant-inhibited and ion-complexed forms. Recently, methods have been developed that make the task of modeling RNA structure and dynamics significantly easier and more reliable. We have used ERRASER and PHENIX to rebuild and re-refine the cleaved and cis-acting C75U-inhibited structures of the HDV ribozyme. The results correct local conformations and identify alternates for RNA residues, many in functionally important regions, leading to improved R values and model validation statistics for both structures. We compare the rebuilt structures to a higher resolution, trans-acting deoxy-inhibited structure of the ribozyme, and conclude that although both inhibited structures are consistent with the currently accepted hammerhead-like mechanism of cleavage, they do not add direct structural evidence to the biochemical and modeling data. However, the rebuilt structures (PDBs: 4PR6, 4PRF) provide a more robust starting point for research on the dynamics and catalytic mechanism of the HDV ribozyme and demonstrate the power of new techniques to make significant improvements in RNA structures that impact biologically relevant conclusions.
PatchmatchNet: Learned Multi-View Patchmatch Stereo (2020)

We present PatchmatchNet, a novel and learnable cascade formulation of Patchmatch for high-resolution multi-view stereo. With high computation speed and low memory requirement, PatchmatchNet can process higher resolution imagery and is more suited to run on resource limited devices than competitors that employ 3D cost volume regularization. For the first time we introduce an iterative multi-scale Patchmatch in an end-to-end trainable architecture and improve the Patchmatch core algorithm with a novel and learned adaptive propagation and evaluation scheme for each iteration. Extensive experiments show a very competitive performance and generalization for our method on DTU, Tanks &amp; Temples and ETH3D, but at a significantly higher efficiency than all existing top-performing models: at least two and a half times faster than state-of-the-art methods with twice less memory usage.
Effect of Smoking Status on the Long-Term Outcome after Successful Percutaneous Coronary Revascularization (1997)

Patients who continued to smoke after successful percutaneous coronary revascularization were at greater risk for Q-wave infarction and death than nonsmokers. The cessation of smoking either before or after percutaneous revascularization was beneficial. Patients undergoing percutaneous revascularization should be encouraged to stop smoking.
Growth hormone signaling is necessary for lifespan extension by dietary methionine (2014)

Growth hormone significantly impacts lifespan in mammals. Mouse longevity is extended when growth hormone (GH) signaling is interrupted but markedly shortened with high-plasma hormone levels. Methionine metabolism is enhanced in growth hormone deficiency, for example, in the Ames dwarf, but suppressed in GH transgenic mice. Methionine intake affects also lifespan, and thus, GH mutant mice and respective wild-type littermates were fed 0.16%, 0.43%, or 1.3% methionine to evaluate the interaction between hormone status and methionine. All wild-type and GH transgenic mice lived longer when fed 0.16% methionine but not when fed higher levels. In contrast, animals without growth hormone signaling due to hormone deficiency or resistance did not respond to altered levels of methionine in terms of lifespan, body weight, or food consumption. Taken together, our results suggest that the presence of growth hormone is necessary to sense dietary methionine changes, thus strongly linking growth and lifespan to amino acid availability.
LAPAROSCOPIC CYST MARSUPIALIZATION IN PATIENTS WITH AUTOSOMAL DOMINANT POLYCYSTIC KIDNEY DISEASE (2001)

Laparoscopic cyst marsupialization may effectively decrease cyst associated pain. In some cases hypertension may be improved. Renal function remained stable in all except 1 patient. At a mean followup of 2.2 years the benefits of aggressive laparoscopic cyst decortication appear to be relatively long lasting when bilateral decortication is indicated. The benefits of unilateral cyst decortication are less predictable and of shorter duration.
Selective improvement by rifaximin of changes in the immunophenotype in patients who improve minimal hepatic encephalopathy (2019)

Rifaximin normalizes changes in the immune system in patients who improve MHE but not in non-responders. Some alterations before treatment are different in responders and non-responders. Understanding these differences may identify predictors of the response of MHE to rifaximin.
Variability-Aware Modeling of Filamentary Oxide-Based Bipolar Resistive Switching Cells Using SPICE Level Compact Models (2020)

Bipolar resistive switching (BRS) cells based on the valence change mechanism show great potential to enable the design of future non-volatile memory, logic and neuromorphic circuits and architectures. To study these circuits and architectures, accurate compact models are needed, which showcase the most important physical characteristics and lead to their specific experimental behavior. If BRS cells are to be used for computation-in-memory or for neuromorphic computing, their dynamical behavior has to be modeled with special consideration of switching times in SET and RESET. For any realistic assessment, variability has to be considered additionally. This study shows that by extending an existing compact model, which by itself is able to reproduce many different experiments on device behavior critical for the anticipated device purposes, variability found in experimental measurements can be reproduced for important device characteristics such as I-V characteristics, endurance behavior and most significantly the SET and RESET kinetics. Furthermore, this enables the study of spatial and temporal variability and its impact on the circuit and system level.
Collision-Free Trajectory Planning for Two Manipulators. The Case of Using Virtual Coordination Space. (1992)

In this paper, we propose a method of planning collision-free trajectory for two manipulators along specified joint paths.
Self-assembled surfactants on patterned surfaces: confinement and cooperative effects on aggregate morphology (2014)

The adsorption and self-assembly of surfactants are ubiquitous processes in several technological applications, including the manufacture of nano-structured materials using bottom-up strategies. Although much is known about the adsorption of surfactants on homogeneous flat surfaces from experiments, theory, and simulations, limited information is available, in quantifiable terms, regarding the adsorption of surfactants on surfaces with chemical and/or morphological heterogeneity. In an effort to fill this knowledge gap, we report here results obtained using equilibrium dissipative particle dynamics (DPD) simulations for the adsorption of model surfactants onto patterned flat surfaces (i.e., flat surfaces with chemical heterogeneity). The patterns consist of one or two stripes of variable width on which the surfactants could adsorb. The adsorbing stripes are surrounded by a surface that effectively repels the surfactants. This repelling surface, perhaps not realistic, allows us to quantify the effect of lateral confinement on the morphology of surfactant aggregates. When the stripe width is large (effectively providing a homogeneous flat surface), the surfactants yield a flat monolayer. Our simulations suggest that the flat monolayers become hemi-cylinders, hemi-spheres, and individual surfactants as the stripe width decreases, a consequence of lateral confinement. In some cases our simulations show evidence of cooperative effects when two adsorbing stripes are present on the surface. If the distance between the stripes and the widths of the stripes are both less than about one surfactant length, hemi-cylindrical shells and irregular structures are observed because of cooperativity; otherwise the results match those found for a single isolated stripe. Our predictions could be useful for the design of new nano-structured materials and coatings, for applications ranging from nano-fluidic devices to nano-reactors.
High power and high gain AlGaN/GaN MIS‐HEMTs with high‐k dielectric layer (2008)

Abstract High power n‐GaN/n‐AlGaN/GaN metal‐insulator‐semi‐conductor high electron mobility transistors (MIS‐HEMTs) with high‐k Ta 2 O 5 dielectric layer were fabricated on a 3‐inch S.I.‐SiC substrate, for the first time. An n‐GaN/n‐AlGaN/GaN MIS‐HEMTs with 400 V breakdown voltage were obtained by using Ta 2 O 5 insulating layer/n‐GaN capstructure. The single‐chip GaN MIS‐HEMTs amplifier with a Ta 2 O 5 layer operated at 50 V achieve a high output power of 113 W with a linear gain of 16.3 dB at 2.5 GHz. We also investigated the RF stress reliability under the P3dB condition. The fluctuation of output power and drain current was lower than 5% even after 150 h stress test. (© 2008 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Mindfulness for Busy People: Turning Frantic and Frazzled into Calm and Composed (2013)

About the authors Acknowledgements Introduction Part 1: MINDFULNESS AND ME Chapter 1: How can mindfulness change your life? Chapter 2: Busy much!? Chapter 3: Understanding how to be mindful Part 1 summary Part 2: MINDFULNESS AND OUR MENTAL LIVES Chapter 4: The 'perfect illusion'- chasing a stress-free existence Chapter 5: To be or not to be busy? Chapter 6: Busy doing nothing (at all helpful, anyway)! Part 2 summary Part 3: MINDFULNESS AND DIFFUCULT EMOTIONS Chapter 7: What lies beneath all the busyness? Chapter 8: Boredom and distraction Chapter 9: Sleepiness, fantasising and physical discomfort Chapter 10: Anger, frustration and impatience Chapter 11: Fear and anxiety Chapter 12: Grief, loss and sadness Part 3 summary Part 4: MINDFULNESS AND APPRECIATING LIFE Chapter 13: Allowing the good times to roll Chapter 14: Rose-tinted roses Part 4 summary Part 5: MINDFULNESS AND MOVING FORWARD Chapter 15: No full stop Chapter 16: Mindfulness in the real world Part 5 summary Recommended reading Further useful contacts and support Index
Reevaluation of the Mechanism of the Amination of Aryl Halides Catalyzed by BINAP-Ligated Palladium Complexes (2006)

Two previous mechanistic studies of the amination of aryl halides catalyzed by palladium complexes of 1,1'-binaphthalene-2,2'-diylbis(diphenylphosphine) (BINAP) are reexamined by the authors of both studies. This current work includes a detailed study of the identity of the BINAP-ligated palladium complexes present in reactions of amines with aryl halides and rate measurements of these catalytic reactions initiated with pure precatalysts and precatalysts generated in situ from [Pd2(dba)3] and BINAP. This work reveals errors in both previous studies, and we describe our current state of understanding of the mechanism of this synthetically important transformation. 31P NMR spectroscopy shows that several palladium(0) species are present in the catalytic system when the catalyst is generated in situ from [Pd2(dba)3] and BINAP, and that at least two of these complexes generate catalytic intermediates. Further, these spectroscopic studies and accompanying kinetic data demonstrate that an apparent positive order in the concentration of amine during reactions of secondary amines is best attributed to catalyst decomposition. Kinetic studies with isolated precatalysts show that the rates of the catalytic reactions are independent of the identity and the concentration of amine, and studies with catalysts generated in situ show that the rates of these reactions are independent of the concentration of amine. Further, reactions catalyzed by [Pd(BINAP)2] with added BINAP are found to be first-order in bromoarene and inverse first-order in ligand, in contrast to previous work indicating zero-order kinetics in both. These data, as well as a correlation between the decay of bromobenzene in the catalytic reaction and the predicted decay of bromobenzene from rate constants of studies on stoichiometric oxidative addition, are consistent with a catalytic process in which oxidative addition of the bromoarene occurs to [Pd(BINAP)] prior to coordination of amine and in which [Pd(BINAP)2], which generates [Pd(BINAP)] by dissociation of BINAP, lies off the cycle. By this mechanism, the amine and base react with [Pd(BINAP)(Ar)(Br)] to form an arylpalladium amido complex, and reductive elimination from this amido complex forms the arylamine.
Phosphatidylinositol 3-kinase-γ activates Bruton’s tyrosine kinase in concert with Src family kinases (1997)

Bruton's tyrosine kinase (Btk) is essential for normal B lymphocyte development and function. The activity of Btk is partially regulated by transphosphorylation within its kinase domain by Src family kinases at residue Tyr-551 and subsequent autophosphorylation at Tyr-223. Activation correlates with Btk association with cellular membranes. Based on specific loss of function mutations, the Btk pleckstrin homology (PH) domain plays an essential role in this activation process. The Btk PH domain can bind in vitro to several lipid end products of the phosphatidylinositol 3-kinase (PI 3-kinase) family including phosphatidylinositol 3,4,5-trisphosphate. Activation of Btk as monitored by elevation of phosphotyrosine content and a cellular transformation response was dramatically enhanced by coexpressing a weakly activated allele of Src (E378G) and the two subunits of PI 3-kinase-gamma. This activation correlates with new sites of phosphorylation on Btk identified by two-dimensional phosphopeptide mapping. Activation of Btk was dependent on the catalytic activity of all three enzymes and an intact Btk PH domain and Src transphosphorylation site. These combined data define Btk as a downstream target of PI 3-kinase-gamma and Src family kinases.
IL-28B is a Key Regulator of B- and T-Cell Vaccine Responses against Influenza (2014)

Influenza is a major cause of morbidity and mortality in immunosuppressed persons, and vaccination often confers insufficient protection. IL-28B, a member of the interferon (IFN)-λ family, has variable expression due to single nucleotide polymorphisms (SNPs). While type-I IFNs are well known to modulate adaptive immunity, the impact of IL-28B on B- and T-cell vaccine responses is unclear. Here we demonstrate that the presence of the IL-28B TG/GG genotype (rs8099917, minor-allele) was associated with increased seroconversion following influenza vaccination (OR 1.99 p = 0.038). Also, influenza A (H1N1)-stimulated T- and B-cells from minor-allele carriers showed increased IL-4 production (4-fold) and HLA-DR expression, respectively. In vitro, recombinant IL-28B increased Th1-cytokines (e.g. IFN-γ), and suppressed Th2-cytokines (e.g. IL-4, IL-5, and IL-13), H1N1-stimulated B-cell proliferation (reduced 70%), and IgG-production (reduced>70%). Since IL-28B inhibited B-cell responses, we designed antagonistic peptides to block the IL-28 receptor α-subunit (IL28RA). In vitro, these peptides significantly suppressed binding of IFN-λs to IL28RA, increased H1N1-stimulated B-cell activation and IgG-production in samples from healthy volunteers (2-fold) and from transplant patients previously unresponsive to vaccination (1.4-fold). Together, these findings identify IL-28B as a key regulator of the Th1/Th2 balance during influenza vaccination. Blockade of IL28RA offers a novel strategy to augment vaccine responses.
Probiotics to improve outcomes of colic in the community: Protocol for the Baby Biotics randomised controlled trial (2012)

Current Controlled Trials ISRCTN95287767.
DIagnosIs anD treatment of sarcoIDosIs. summary of feDeral concIlIatIve clInIcal recommenDatIons. Part I. classification, etiopathogenesis, clinic (2014)

Представлен сокращенный адаптированный вариант российских федеральных клинических рекомендаций по
Long-Term, Prospective, Multicenter Study of Poly-4-Hydroxybutyrate Mesh (Phasix Mesh) for Hernia Repair in Cohort at Risk for Complication: 60-Month Follow-Up (2022)

Five-year outcomes after VIHR with P4HB mesh were associated with infrequent complications and durable hernia repair outcomes. This study provides a framework for anticipated long-term hernia repair outcomes when using P4HB mesh.
Connection-Level Modeling of Network Traffic (2002)

Aggregate network traffic exhibits strong burstiness and non-Gaussian marginals, which popular models like fractional Gaussian noise (fGn) fail to capture. To better understand the cause of traffic burstiness, we look into connection-level information of traffic trace. A care- ful study reveals that traffic burstiness is directly related to the heterogeneity in connection bandwidths (and round-trip times), and that a small number of high-bandwidth connec- tions are solely responsible for burstiness. This leads to a new model for network traffic: the mixture of fGn and sta- ble Lnoise, which captures both long-range dependence and burstiness. This decomposition has far-reaching impli- cations on network control.
Automating performance bottleneck detection using search-based application profiling (2015)

Application profiling is an important performance analysis technique, when an application under test is analyzed dynamically to determine its space and time complexities and the usage of its instructions. A big and important challenge is to profile nontrivial web applications with large numbers of combinations of their input parameter values. Identifying and understanding particular subsets of inputs leading to performance bottlenecks is mostly manual, intellectually intensive and laborious procedure. We propose a novel approach for automating performance bottleneck detection using search-based input-sensitive application profiling. Our key idea is to use a genetic algorithm as a search heuristic for obtaining combinations of input parameter values that maximizes a fitness function that represents the elapsed execution time of the application. We implemented our approach, coined as Genetic Algorithm-driven Profiler (GA-Prof) that combines a search-based heuristic with contrast data mining of execution traces to accurately determine performance bottlenecks. We evaluated GA-Prof to determine how effectively and efficiently it can detect injected performance bottlenecks into three popular open source web applications. Our results demonstrate that GA-Prof efficiently explores a large space of input value combinations while automatically and accurately detecting performance bottlenecks, thus suggesting that it is effective for automatic profiling.
Tuning computer communications networks and protocols (2002)

The objective is to adjust the protocol parameters and network elements to achieve maximum data throughput over a certain circuit or set of circuits (a network path) subject to certain constraints, such as: delay-bandwidth product, error rate, and tuning parameter limits and accessibility. To provide optimal performance from the user's perspective, which is application to application, all peer layers of the protocol must be tuned. The key to tuning protocols is reducing idle time on the links caused by various protocol layers waiting for acknowledgements. Experiments have been conducted on test bed systems, and on live satellite and terrestrial circuits. Various aspects of network tuning and certain specific issues relating to the tuning of three protocols (DECnet, TCP/IP, NETEX) over various media types (point-to-point and broadcast) under several different conditions (terrestrial and satellite) are examined. Also described are the lessons learned about protocol and network tuning.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>