gebhart/patrepeval huggingface dataset:
The Swap, Expansion and Exwap Moves - A Simple Derivation and Implementation (2008)

Abstract. In the context of multi-label energy function minimization, the swap and the expansion are two types of moves that were introduced by Boykov et al. [3]. They pro-posed efficient algorithms for finding local minima with respect to each of these two moves when each energy term depends on two variables at most. The minimization was carried out by a sequence of optimal moves that were calculated by seeking minimum cuts of specially constructed weighted graphs. In this paper these optimal swap and ex-pansion moves are obtained in a short and simple manner by incorporating the original algorithm by Greig et al. [5] as a “black box. ” Our alternative derivation has three ad-vantages over the original one: 1. Given Greig et al.’s original solution as a black box, it is shorter, purely algebraic (that is, no graphs are involved) and, we believe, simpler to understand and implement. 2. It is derived under more general conditions. 3. It contains a proof that the found local minima with respect to expansion moves are actually also local minima with respect to swap moves – a point that seems to have been overlooked in previous work. All the results are extended for energy terms that depend on three variables by using Kolmogorov et al.’s binary minimization algorithm [9] as a black box. In addition, the exwap move type, a generalization of the expansion and the swap move types, is introduced and an efficient algorithm for minimizing with respect to it is derived.
Neonatal pigs are susceptible to experimental Zika virus infection (2017)

Emerging Microbes & Infections (2017) 6, e6; doi:10.1038/emi.2016.133; published online 15 February 2017
A Monte Carlo Simulation Study on Detector Arrangement for a Small Bore DOI-PET Scanner: jPET-RD (2006)

We are developing a dedicated small-bore DOI-PET scanner for small animals (jPET-RD). In this paper, we performed Monte Carlo simulations using the GATE (Geant4 Application for Emission Tomography) and investigated the influence of detector arrangement on the imaging and count rate performance. The jPET-RD is based on a large-sized depth-of-interaction (DOI) block detector that consists of a 4-layered array of 32 times 32 LSO crystals (1.4 mm times 1.4 mm times 4.5 mm) and a 256-ch flat panel position-sensitive photomultiplier tube. In this work, three geometries were simulated: two rings of six detector blocks arranged in a hexagonal pattern (FOV 85 mm in diameter), four detector blocks arranged in a tetragonal pattern (FOV 49 mm in diameter) and four detector blocks arranged in an overlapped tetragonal pattern (FOV 38 mm in diameter). Reconstructed images show that the hexagonal scanner has better spatial resolution and resolution uniformity than the other scanners. The resolution performance of the tetragonal scanner declines due to the large inter-detector gaps; however the deterioration of the image quality can be minimized by overlapping each detector. Count rate simulation results show that smaller bore geometry provide higher sensitivity because of its larger solid angle. Although small bore geometry clearly affected the noise equivalent count rate (NECR) due to high detector dead-time, parallel readout with appropriate anode segmentation improved the NECR at 20 MBq by a factor of ~1.4 compared with the non-parallel read out.
An approach to DFT calculations using standard microprocessors (1985)

The use of the DFT as an everyday tool is now commonplace, principally due to advances in hardware technology. Special-purpose VLSI chips for signal processing are available. In this paper, we describe an approach which marries the Winograd Fourier Transform Algorithm (WFTA) with a state-of-the-art 16-bit general-purpose microprocessor for the purpose of DFT calculation. The heart of the approach is the real-input 240-point WFTA, which has been carefully optimized for time and space. In particular, an implementation for the 10-MHz M68000 executes in 10.8 ms. A simple hardware module is described which implements the optimized software. The use of the module for the inverse transform and for the complex case is also discussed. Advantages to the approach taken in this paper are the low cost/performance ratio and the general-purpose nature of the system that allows many non-signal-processing functions to be performed by the microprocessor.
Classificiation of Atrial Fibrillation Prone Patients Using Electrocardiographic Parameters in Neuro-Fuzzy Modeling, (2010)

Atrial Fibrillation (AF) is a significant clinical problem and the complications of cardiovascular postoperative AF often lead to longer hospital stays and higher heath care costs. The literature showed that AF may be preceded by changes in electrocardiogram (ECG) characteristics such as premature atrial activity, heart rate variability (HRV), and P-wave morphology. We hypothesize that the limitations of statistics-based attempts to predict AF occurrence may be overcome using a hybrid neuro-fuzzy prediction model that is better capable of uncovering complex, non-linear interactions between ECG parameters. We created a neuro-fuzzy network that was able to classify the patients into the control and AF groups with the performances: 99.42% sensitivity, 99.89% specificity, and 99.74% accuracy for 30 minutes just before AF onset.
High harmonic plasmon generation by dressed electrons (2018)

We show that high harmonics of highly spatially confined plasmons can be generated via free electrons using light intensities 104–106 times smaller than is required for an equivalent multiphoton effect in free space.
Pharmacologic Inhibition of COX-1 and COX-2 in Influenza A Viral Infection in Mice (2010)

Treatment with a COX-1 inhibitor during influenza A viral infection is detrimental to the host whereas inhibition of COX-2 does not significantly modulate disease severity. COX-1 plays a critical role in controlling the thermoregulatory response to influenza A viral infection in mice.
The challenge of follow-on biologics for treatment of multiple sclerosis (2009)

Intellectual property protections for biologic medicinals for multiple sclerosis (MS) are beginning to expire, opening the possibility of development, regulatory approval, and marketing of so-called follow-on biologics, biosimilars, or subsequent entry biologics that might be offered at lower price to consumers and third-party payers, as has been the case for generic drugs. Determining the comparability of a follow-on biologic to its innovator product is more difficult than for small-molecule drugs because of the greater complexity of biologics and the possibility that manufacturing differences can introduce differences in biologic activity and immunogenicity that could result in unpredictable differences in safety or efficacy. We provide a perspective on issues surrounding development, regulatory approval, and potential use of follow-on biologics, with an emphasis on disease-modifying agents for MS.
Frequency‐Switched Single‐Transition Cross‐Polarization: A Tool for Selective Experiments in Biomolecular NMR (2004)

Frequency-switched single-transition cross-polarization (FS-ST-CP) provides a versatile tool for selective coherence transfer in heteronuclear NMR of biomolecules such as proteins and nucleic acids. This type of coherence transfer is spin-state-selective and can therefore benefit from the extension of the life-times of selected coherences due to partial cancellation of interfering relaxation mechanisms. The limits of the selectivity of the transfer are discussed by theory and illustrated by experiment. The methods are particularly efficient to obtain quantitative structural and dynamic information for selected residues in medium-sized nitrogen-15 or carbon-13 labeled macromolecules.
Allelic Variation of Bile Salt Hydrolase Genes in Lactobacillus salivarius Does Not Determine Bile Resistance Levels (2009)

Commensal lactobacilli frequently produce bile salt hydrolase (Bsh) enzymes whose roles in intestinal survival are unclear. Twenty-six Lactobacillus salivarius strains from different sources all harbored a bsh1 allele on their respective megaplasmids. This allele was related to the plasmid-borne bsh1 gene of the probiotic strain UCC118. A second locus (bsh2) was found in the chromosomes of two strains that had higher bile resistance levels. Four Bsh1-encoding allele groups were identified, defined by truncations or deletions involving a conserved residue. In vitro analyses showed that this allelic variation was correlated with widely varying bile deconjugation phenotypes. Despite very low activity of the UCC118 Bsh1 enzyme, a mutant lacking this protein had significantly lower bile resistance, both in vitro and during intestinal transit in mice. However, the overall bile resistance phenotype of this and other strains was independent of the bsh1 allele type. Analysis of the L. salivarius transcriptome upon exposure to bile and cholate identified a multiplicity of stress response proteins and putative efflux proteins that appear to broadly compensate for, or mask, the effects of allelic variation of bsh genes. Bsh enzymes with different bile-degrading kinetics, though apparently not the primary determinants of bile resistance in L. salivarius, may have additional biological importance because of varying effects upon bile as a signaling molecule in the host.
Transport properties of porous media from the microstructure (1995)

The determination of the effective transport properties of a random porous medium remains a challenging area of research because the properties depend on the microstructure in a highly complex fashion. This paper reviews recent theoretical and experimental progress that we have made on various aspects of this problem. A unified approach is taken to characterize the microstructure and the seemingly disparate properties of the medium.
Whole Genome Sequencing in Psychiatric Disorders: the WGSPD Consortium (2017)

Abstract As technology advances, whole genome sequencing (WGS) is likely to supersede other genotyping technologies. The rate of this change depends on its relative cost and utility. Variants identified uniquely through WGS may reveal novel biological pathways underlying complex disorders and provide high-resolution insight into when, where, and in which cell type these pathways are affected. Alternatively, cheaper and less computationally intensive approaches may yield equivalent insights. Understanding the role of rare variants in the noncoding gene-regulating genome, through pilot WGS projects, will be critical to determine which of these two extremes best represents reality. With large cohorts, well-defined risk loci, and a compelling need to understand the underlying biology, psychiatric disorders have a role to play in this preliminary WGS assessment. The WGSPD consortium will integrate data for 18,000 individuals with psychiatric disorders, beginning with autism spectrum disorder, schizophrenia, bipolar disorder, and major depressive disorder, along with over 150,000 controls.
Reactive collisions of multiply charged ions derived from electrospray (1991)

As part of our recent efforts to develop and apply quadrupole ion trap techniques to multiply charged ions derived from electrospray we have embarked on a study of the ion/molecule reaction chemistry of multiply charged ions. To date, these studies have been restricted primarily to gas-phase Bronsted acid-base reactions and, within this class, to reactions of multiply protonated molecules with small gaseous bases. We have, however, studied a limited number of reactions involving proton transfer from gaseous acids to multiply charged anions. The goals of this effort are to understand fundamental aspects underlying the phenomenology of these reactions and to identify, maximize, and exploit the information that they can provide. All experiments were carried out with a Finnigan-MAT ion trap mass spectrometer modified to allow ions formed by electrospray to be injected into the ion trap. The procedures necessary to form, inject, and analyze multiply charged ions have been described. For ion/molecule reaction studies a gas-phase base is admitted into the vacuum system to a pressure of roughly 1 {times} 10{sup {minus}7} torr. At this pressure, a mass spectrum can be obtained with minimal effect of the base provided the time between ion injection and mass analysis does not exceedmore » roughly 50 ms. However, with delay times on the order of a few hundred ms reactions with rate constants on the order of 10{sup {minus}9} cm{sup 3}-molecule{sup {minus}1}-s{sup {minus}1} can proceed largely to completion. Gas-phase bases used to date include in order of increasing basicity; ammonia dimethylamine, 1,6-hexanediamine, and N,N,N{prime},N{prime}-tetramethyl-1,8-naphthalenediamine. All of the results observed thus far can be rationalized as involving the formation of a proton-bound complex. The fate of the complex determines whether or not proton transfer takes place, adduct formation occurs, or no net reaction is observed. 5 refs., 2 figs.« less
Sleeve gastrectomy promotes colitis-associated colorectal cancer in a murine model via a modified gut microbiome (2022)

ABSTRACT Colorectal cancer (CRC) remains the third leading cause of cancer death in the United States with an alarming rise among young (&lt;50-years-old) patients. 1 Epidemiologically, obesity appears to be a risk factor for CRC. 1 Although bariatric surgery has been shown to be associated with decreased risk for most cancers, studies to date on bariatric surgery and CRC continue to yield conflicting results. 2 One possible explanation for this seeming irreconcilability is the inherent heterogeneity of CRC with its varied mechanisms. This is likely compounded by the differing bariatric operations currently employed. Here, we sharpen our focus and investigate how the most performed bariatric operation, sleeve gastrectomy (SG), affects colitis-associated CRC. Using a murine model, we found that SG significantly exacerbates both colitis and colitis-associated CRC. Using a germ-free (GF) microbiota transplant model, we found that the post-SG microbiota, when transplanted into GF mice, is capable of independently recapitulating the tumor-promoting phenotype of SG. Our results suggest that the postsurgical microbiome plays a key causal role in the increased risk for CRC after SG. This finding represents the first step in our understanding of this complex relationship that is at the intersection of two rising public health threats.
Clinical Implications of Negatively Adjudicated Heart Failure Events: Data From the VICTORIA Study (2023)

possible heart failure.
Application protocols and performance benchmarks (1989)

The authors present results from performance measurements of application services. They have chosen widely available implementations of the file transfer protocols File Transfer Access and Management (FTAM) and FTP, and the transaction protocols Remote Operations Service Element (ROSE) and Sun's Remote Procedure Call (SunRPC). The measurements have all been run on the same Sun 3/60 workstations over Ethernet, using protocol-independent benchmarks. A tool called SICS Protocol Implementation Measurement System (SPIMS) is used for the measurements. It is structured as a protocol, with two peer entities communicating with each other using the service of the measured protocol. The authors describe how SPIMS can be used to measure response time, throughput, and the time to open and close connections. They describe the protocols and their implementations, and draw some conclusions, and present and comment on the results.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Multi-Task Federated Learning for Traffic Prediction and Its Application to Route Planning (2021)

A novel multi-task federated learning (FL) framework is proposed in this paper to optimize the traffic prediction models without sharing the collected data among traffic stations. In particular, a divisive hierarchical clustering is first introduced to partition the collected traffic data at each station into different clusters. The FL is then implemented to collaboratively train the learning model for each cluster of local data distributed across the stations. Using the multi-task FL framework, the route planning is studied where the road map is modeled as a time-dependent graph and a modified A * algorithm is used to determine the route with the shortest traveling time. Simulation results showcase the prediction accuracy improvement of the proposed multi-task FL framework over two baseline schemes. The simulation results also show that, when using the multi-task FL framework in the route planning, an accurate traveling time can be estimated and an effective route can be selected.
Filter exchange imaging with crusher gradient modelling detects increased blood–brain barrier water permeability in response to mild lung infection (2023)

Blood-brain barrier (BBB) dysfunction occurs in many brain diseases, and there is increasing evidence to suggest that it is an early process in dementia which may be exacerbated by peripheral infection. Filter-exchange imaging (FEXI) is an MRI technique for measuring trans-membrane water exchange. FEXI data is typically analysed using the apparent exchange rate (AXR) model, yielding estimates of the AXR. Crusher gradients are commonly used to remove unwanted coherence pathways arising from longitudinal storage pulses during the mixing period. We first demonstrate that when using thin slices, as is needed for imaging the rodent brain, crusher gradients result in underestimation of the AXR. To address this, we propose an extended crusher-compensated exchange rate (CCXR) model to account for diffusion-weighting introduced by the crusher gradients, which is able to recover ground truth values of BBB water exchange (k<sub>in</sub>) in simulated data. When applied to the rat brain, k<sub>in</sub> estimates obtained using the CCXR model were 3.10 s<sup>-1</sup> and 3.49 s<sup>-1</sup> compared to AXR estimates of 1.24 s<sup>-1</sup> and 0.49 s<sup>-1</sup> for slice thicknesses of 4.0 mm and 2.5 mm respectively. We then validated our approach using a clinically relevant Streptococcus pneumoniae lung infection. We observed a significant 70 ± 10% increase in BBB water exchange in rats during active infection (k<sub>in</sub> = 3.78 ± 0.42 s<sup>-1</sup>) compared to before infection (k<sub>in</sub> = 2.72 ± 0.30 s<sup>-1</sup>; p = 0.02). The BBB water exchange rate during infection was associated with higher levels of plasma von Willebrand factor (VWF), a marker of acute vascular inflammation. We also observed 42% higher expression of perivascular aquaporin-4 (AQP4) in infected animals compared to non-infected controls, while levels of tight junction proteins remain consistent between groups. In summary, we propose a modelling approach for FEXI data which removes the bias in estimated water-exchange rates associated with the use of crusher gradients. Using this approach, we demonstrate the impact of peripheral infection on BBB water exchange, which appears to be mediated by endothelial dysfunction and associated with an increase in perivascular AQP4.
Nouveaux systèmes modèles à aimantation perpendiculaire pour l'étude des effets de transfert de spin (2011)

Les effets de transfert de spin sont devenus un sujet de recherche majeur ces quinze dernières années. Cependant, un manque de vérifications expérimentales pour beaucoup de modèles décrivant les effets de transfert de spin peut être constaté. Ceci est surtout lié à un manque de systèmes magnétiques modèles permettant un contrôle précis des paramètres pertinents utilisés dans les modèles théoriques. Dans ce travail deux systèmes magnétiques à aimantation perpendiculaire ont été analysés : les alliages amorphes de Co1-xTbx élaborés par pulvérisation cathodique et les super-réseaux [Co/Ni](111) élaborés par épitaxie par jets moléculaires. L'anisotropie et l'aimantation, qui sont des paramètres pertinents dans beaucoup de modèles sur le transfert de spin, sont variables dans une large gamme. L'origine de cette anisotropie est discutée. La structure des domaines magnétiques est analysée et les résultats des mesures de transport sont interprétés. Pour les super-réseaux [Co/Ni](111) une forte polarisation en spin au niveau de Fermi est démontrée grâce à des expériences de photo émission résolue en spin et un coefficient d'amortissement intrinsèque [alpha] très faible est trouvé. Il est conclu que les alliages amorphes de Co1-xTbx et les super-réseaux [Co/Ni](111) sont des systèmes modèles pour le transfert de spin.
Effect of Glycosylation on an Immunodominant Region in the V1V2 Variable Domain of the HIV-1 Envelope gp120 Protein (2016)

Heavy glycosylation of the envelope (Env) surface subunit, gp120, is a key adaptation of HIV-1; however, the precise effects of glycosylation on the folding, conformation and dynamics of this protein are poorly understood. Here we explore the patterns of HIV-1 Env gp120 glycosylation, and particularly the enrichment in glycosylation sites proximal to the disulfide linkages at the base of the surface-exposed variable domains. To dissect the influence of glycans on the conformation these regions, we focused on an antigenic peptide fragment from a disulfide bridge-bounded region spanning the V1 and V2 hyper-variable domains of HIV-1 gp120. We used replica exchange molecular dynamics (MD) simulations to investigate how glycosylation influences its conformation and stability. Simulations were performed with and without N-linked glycosylation at two sites that are highly conserved across HIV-1 isolates (N156 and N160); both are contacts for recognition by V1V2-targeted broadly neutralizing antibodies against HIV-1. Glycosylation stabilized the pre-existing conformations of this peptide construct, reduced its propensity to adopt other secondary structures, and provided resistance against thermal unfolding. Simulations performed in the context of the Env trimer also indicated that glycosylation reduces flexibility of the V1V2 region, and provided insight into glycan-glycan interactions in this region. These stabilizing effects were influenced by a combination of factors, including the presence of a disulfide bond between the Cysteines at 131 and 157, which increased the formation of beta-strands. Together, these results provide a mechanism for conservation of disulfide linkage proximal glycosylation adjacent to the variable domains of gp120 and begin to explain how this could be exploited to enhance the immunogenicity of those regions. These studies suggest that glycopeptide immunogens can be designed to stabilize the most relevant Env conformations to focus the immune response on key neutralizing epitopes.
Stem cell metabolism in tissue development and aging (2013)

Recent advances in metabolomics and computational analysis have deepened our appreciation for the role of specific metabolic pathways in dictating cell fate. Once thought to be a mere consequence of the state of a cell, metabolism is now known to play a pivotal role in dictating whether a cell proliferates, differentiates or remains quiescent. Here, we review recent studies of metabolism in stem cells that have revealed a shift in the balance between glycolysis, mitochondrial oxidative phosphorylation and oxidative stress during the maturation of adult stem cells, and during the reprogramming of somatic cells to pluripotency. These insights promise to inform strategies for the directed differentiation of stem cells and to offer the potential for novel metabolic or pharmacological therapies to enhance regeneration and the treatment of degenerative disease.