gebhart/patrepeval huggingface dataset:
Structural and functional studies of the Als1 adhesin from candida albicans (2014)

The dimorphic fungus Candida albicans, a harmless commensal in approximately 60% of healthy adults, is also an opportunistic pathogen in humans. Immuno-compromised individuals are mainly at risk, for example those under immunosuppressive therapies, HIV/AIDS patients, the elderly and early neonates. Diseases caused include invasive candidiasis, which has a 40-60% mortality rate. The majority of invasive candidiasis is caused by C. albicans forming biofilms on medical devices (e.g. catheters, heart valves) from which yeast cells disperse and enter the blood stream. The adherence properties of C. albicans are crucial for colonisation and biofilm formation. An important adhesive factor in the early stages of colonisation is Als1 (Agglutinin-like Sequence protein 1). Another crucial virulence factor is hyphal-expressed Als3, which contributes to adhesion and invasion of host cells. These proteins belong to the Als family of glycoproteins (Als1-7 and Als9), all of which share similar domain organisation: an N-terminal adhesion region comprised of two immunoglobulin-like domains, plus central and C-terminal regions, which are highly glycosylated. Previously, the N-terminus of Als9 had been shown to bind the flexible C-termini of host cell proteins as ligands. Due to their relevance in C. albicans adhesion, the N-terminal domains of Als1 and Als3 are ideal templates for ligand binding studies and the development of antifungal compounds. Shortened constructs Als1 and Als3 with improved solubility and structural properties (relative to the full length adhesins) were employed in this project. Here I describe the X-ray crystallographic structure of sNT-Als1 with a peptide ligand, the backbone resonance assignments by Nuclear Magnetic Resonance (NMR) of the ligand-free protein and ligand-binding experiments using Differential Scanning Fluorimetry (DSF). Comparison of the structure and ligand binding behavior of sNT-Als1 with other Als proteins will guide the design of therapeutic molecules that block the adhesive properties of these adhesins, and thus the formation of disease-causing biofilms by C. albicans.
Inhibition of Ribosome Recruitment Induces Stress Granule Formation Independently of Eukaryotic Initiation Factor 2α Phosphorylation (2006)

Cytoplasmic aggregates known as stress granules (SGs) arise as a consequence of cellular stress and contain stalled translation preinitiation complexes. These foci are thought to serve as sites of mRNA storage or triage during the cell stress response. SG formation has been shown to require induction of eukaryotic initiation factor (eIF)2alpha phosphorylation. Herein, we investigate the potential role of other initiation factors in this process and demonstrate that interfering with eIF4A activity, an RNA helicase required for the ribosome recruitment phase of translation initiation, induces SG formation and that this event is not dependent on eIF2alpha phosphorylation. We also show that inhibition of eIF4A activity does not impair the ability of eIF2alpha to be phosphorylated under stress conditions. Furthermore, we observed SG assembly upon inhibition of cap-dependent translation after poliovirus infection. We propose that SG modeling can occur via both eIF2alpha phosphorylation-dependent and -independent pathways that target translation initiation.
A method of BDS/SINS integrated navigation fusion based on CKF algorithm (2017)

For the sake of navigation precision enhancement of BDS/SINS(Beidou Satellite Navigation System/SINS) tightly coupled navigation system. under complex environment, seeing the defects that linearization error introduced in Extended Kalman Filter (EKF) tends to cause filtering effect decline, and that improper parameter adjustment lead to filtering effect decline as this adjustment is necessary for Unscented Kalman Filter (UKF), this article suggests Cubature Kalman Filter (CKF) algorithm be applied in nonlinear model of BDS/SINS tightly coupled navigation, and conducts a comparison study on information fusion performance with the EKF and UKF under the same condition. The experiment result reveals that the CKF algorithm outperforms the EKF or UKF in precision. This simulation result is significant for hoisting navigation precision of BDS/SINS tightly coupled navigation system.
Zin en onzin van het onderzoek van fecesstalen van honden met diarree op de aanwezigheid van Escherichia coli (2008)

Bacteriologisch onderzoek van fecesstalen van honden met diarree resulteert steevast in de isolatie van Escherichia coli. Het verband met de waargenomen klinische symptomen is tot nu toe niet duidelijk. Daarom werd in deze studie nagegaan of de aanwezigheid van bepaalde E. coli virulentiegenen geassocieerd is met de aanwezigheid van diarree bij honden. Hiertoe werden E. coli-isolaten uit fecesstalen van 34 gezonde honden en 25 honden met diarree (leeftijd: 7,5 maanden tot 10 jaar) onderzocht op de aanwezigheid van 17 virulentiegenen. Er konden geen virulentiegenen aangetoond worden in 15 van de 34 E. coli-isolaten van gezonde dieren en in 15 van de 25 E. coli-isolaten van dieren met diarree. In de overige isolaten werden genen teruggevonden die coderen voor n of meerdere van de toxinen cytotoxisch necrotiserende factor (CNF)1, CNF2, verotoxine (VT)1 en VT2 en/of voor n of meerdere van de adhesinen intimine, F5 fimbriae en F41 fimbriae. Er werden evenwel geen significante verschillen aangetoond in het voorkomen van deze virulentiegenen tussen de isolaten afkomstig van de onderzochte volwassen honden met of zonder diarree. Zo lang geen diagnostische merkers worden gevonden voor E. coli stammen die geassocieerd zijn met diarree bij honden is het dus weinig zinvol om de aanwezigheid van deze bacterie in de mest te laten bepalen.
<title>High-speed IP packet forwarding over Internet using ATM technology</title> (1995)

Framework of IP packet delivery with high throughput and small latency using ATM technology in large scaled internets is proposed, while keeping the current subnet model. Router has the mapping functionality between flow-identifier (e.g. in IPv6 header) and VPI/VCI value to forward IP packets cell-by-cell, rather than the conventional packet-by- packet forwarding. By using this cut-thru IP packet forwarding, both resource reservation oriented IP packet flows (i.e. IP packet flow provided by RSVP) and nonresource reservation oriented IP packet flows (i.e. best effort service) experience less packet delivery latency and obtain higher throughput, compared to the conventional hop-by-hop packet forwarding does. In order to perform the cut-thru IP packet forwarding using cell relaying capability in the router, routers exchange the information how the IP packet flows are aggregated into ATM- VCC. This information exchanging is hop-by-hop base, and the cut-thru decision is a matter of every router's local decision. With the hop-by-hop cut-thru IP packet forwarding, soft-state oriented and scalable QoS-ed high speed communication platform can be provided.
Istradefylline for the treatment of Parkinson's disease (2011)

The studies outlined continue to suggest that istradefylline may be a promising non-dopaminergic therapy for the treatment of PD. It has not been proven to be more efficacious than other currently available dopaminergic drugs, nor has it been shown to be of significant benefit as monotherapy; however, it seems to be a safe and well-tolerated drug that may help with wearing-off fluctuations. Istradefylline is not yet an FDA-approved drug. At this time, the potential for approval in the US or through the European Medical Agency remains unknown.
A vector oriented control for a magnetically levitated shaft (1998)

Considering the nonlinear model of active magnetic bearings, a new means of nonlinear control is presented which treats variables as rotating vectors in the control plane, specially the unbalance. It becomes easy to cancel out the effect of this perturbation in a rotating reference. Therefore, the rotor can rotate around any desired point, particularly the geometric center or the center of gravity. Simulations illustrate the efficacy of this control law.
Tribocorrosion Behavior of Inconel 718 Fabricated by Laser Powder Bed Fusion-Based Additive Manufacturing (2021)

Additive manufacturing (AM) by laser powder bed fusion (LPBF) has gained significant research attention to fabricate complex 3D Inconel alloy components for jet engines. The strategic advantages of LPBF-based AM to fabricate jet components for aerospace applications are well reported. The jet components are exposed to a high degree of vibration during the jet operation in a variable aqueous environment. The combined vibration and the aqueous environment create a tribological condition that can accelerate the failure mechanism. Therefore, it is critical to understand the tribocorrosion behavior of the Inconel alloy. In the present work, tribocorrosion behavior of the LPBF fabricated standalone coating of Inconel 718 in the 3.5% NaCl aqueous solution is presented. The LPBF fabricated samples are analyzed to determine the impact of porosity, generated as a result of LPBF, on the triobocorrosion behavior of AM Inconel 718. The study includes potentiodynamic tests, cathodic polarization, along with OCP measurements. The corrosive environment is found to increase the wear by 29.24% and 49.5% without the initiation of corrosion in the case of AM and wrought Inconel 718, respectively. A corrosion accelerated wear form of tribocorrosion is observed for Inconel 718. Additionally, the corrosive environment has a significant effect on wear even when the Inconel 718 surface is in equilibrium potential with the corrosive environment and no corrosion potential scan is applied. This study provides an insight into a critical aspect of the AM Inconel components.
Y-Box-Binding Protein 1 Interacts with Hepatitis C Virus NS3/4A and Influences the Equilibrium between Viral RNA Replication and Infectious Particle Production (2011)

The hepatitis C virus (HCV) NS3/4A protein has several essential roles in the virus life cycle, most probably through dynamic interactions with host factors. To discover cellular cofactors that are co-opted by HCV for its replication, we elucidated the NS3/4A interactome using mass spectrometry and identified Y-box-binding protein 1 (YB-1) as an interacting partner of NS3/4A protein and HCV genomic RNA. Importantly, silencing YB-1 expression decreased viral RNA replication and severely impaired the propagation of the infectious HCV molecular clone JFH-1. Immunofluorescence studies further revealed a drastic HCV-dependent redistribution of YB-1 to the surface of the lipid droplets, an important organelle for HCV assembly. Core and NS3 protein-dependent polyprotein maturation were shown to be required for YB-1 relocalization. Unexpectedly, YB-1 knockdown cells showed the increased production of viral infectious particles while HCV RNA replication was impaired. Our data support that HCV hijacks YB-1-containing ribonucleoparticles and that YB-1-NS3/4A-HCV RNA complexes regulate the equilibrium between HCV RNA replication and viral particle production.
Traumatic glaucoma due to paintball injuries: A case series (2017)

Traumatic glaucoma can be managed with surgical and medical interventions, while VA usually does not return to baseline levels prior to the injury. Prognostic predictors can be used to guide treatment and identify patients who should be closely followed. Because the presentation and onset is widely variable, follow-up and screening is crucial even years after the injury.
Influence of naturally occurring insertions in the fingers subdomain of human immunodeficiency virus type 1 reverse transcriptase on polymerase fidelity and mutation frequencies in vitro (2006)

The fingers subdomain of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) is a hotspot for nucleoside analogue resistance mutations. Some multi-nucleoside analogue-resistant variants contain a T69S substitution along with dipeptide insertions between residues 69 and 70. This set of mutations usually co-exists with classic zidovudine-resistance mutations (e.g. M41L and T215Y) or an A62V mutation and confers resistance to multiple nucleoside analogue inhibitors. As insertions lie in the vicinity of the dNTP-binding pocket, their influence on RT fidelity was investigated. Commonly occurring insertion mutations were selected, i.e. T69S-AG, T69S-SG and T69S-SS alone, in combination with 3′-azido-2′,3′-deoxythymidine-resistance mutations M41L, L210W, R211K, L214F, T215Y (LAG AZ and LSG AZ ) or with an alternate set where A62V substitution replaces M41L (VAG AZ , VSG AZ and VSS AZ ). Using a lacZα gapped duplex substrate, the forward mutation frequencies of recombinant wild-type and mutant RTs bearing each of the above sets of mutations were measured. All of the mutants displayed significant decreases in mutation frequencies. Whereas the dipeptide insertions alone showed the least decrease (4·0- to 7·5-fold), the VAG series showed an intermediate reduction (5·0- to 11·4-fold) and the LAG set showed the largest reduction in mutation frequencies (15·3- and 16·3-fold for LAG AZ and LSG AZ , respectively). Single dNTP exclusion assays for mutants LSG AZ and LAG AZ confirmed their large reduction in misincorporation efficiencies. The increased in vitro fidelity was not due to excision of the incorrect nucleotide via ATP-dependent removal. There was also no direct correlation between increased fidelity and template–primer affinity, suggesting a change in the active site that is conducive to better discrimination during dNTP insertion.
Fitting a naturally scaled point system to the ACMG/AMP variant classification guidelines (2020)

Recently, we demonstrated that the qualitative American College of Medical Genetics and Genomics/Association for Medical Pathology (ACMG/AMP) guidelines for evaluation of Mendelian disease gene variants are fundamentally compatible with a quantitative Bayesian formulation. Here, we show that the underlying ACMG/AMP "strength of evidence categories" can be abstracted into a point system. These points are proportional to Log(odds), are additive, and produce a system that recapitulates the Bayesian formulation of the ACMG/AMP guidelines. The strengths of this system are its simplicity and that the connection between point values and odds of pathogenicity allows empirical calibration of the strength of evidence for individual data types. Weaknesses include that a narrow range of prior probabilities is locked in and that the Bayesian nature of the system is inapparent. We conclude that a points-based system has the practical attribute of user-friendliness and can be useful so long as the underlying Bayesian principles are acknowledged.
Evaluating the Feasibility of Nondiffractive Bessel Beams for Shear Wave Elasticity Imaging: A Simulation Study (2020)

Shear wave elasticity imaging (SWEI) has been developed to characterize the elasticity of tissue that B-mode imaging cannot. However, focused push beam has its limitation of short focal zone due to the diffraction of the wave. To improve the depth of push beam, we proposed a non-diffractive Bessel push beam induced shear wave method and used it in SWEI. In this work, a simulation study presents the superiorities of Bessel push beam over focused push beam. From the results, Bessel beam shows a larger beam depth than focused beam. Also, Bessel push beam improves the accuracy and contrast of shear wave speed images of homogeneous digital phantom. In addition, this work presents scaling factor of Bessel beam is the main parameter affecting the beam depth.
Evaluation of pregnant rabbits as a laboratory model for bovid herpesvirus-4 infection (1990)

A field strain (87-8363) of bovid herpesvirus-4 (BHV-4) isolated from an aborted bovine fetus was used to inoculate pregnant rabbits. Eleven rabbits in midgestation were alloted to 4 groups consisting of 3 infected groups and 1 control group. Rabbits were inoculated with BHV-4 or mock-infected cell culture preparations via IV, intravaginal, and intrauterine routes. Mild vulvovaginitis and endometritis were observed after intravaginal and IV inoculation of BHV-4, whereas intrauterine inoculation of BHV-4 resulted in abortion of hemorrhagic fetuses and nonsuppurative endometritis. Virus was successfully isolated from organ explants of fetal tissues. Rabbits seroconverted 1 week after infection as detected by results of an indirect immunofluorescence assay.
Adaptive responses of Brachiaria grasses to hypoxia stress (2014)

It is likely that oxygen shortage in waterlogged soils is the most limiting factor for plant growth, restricting root aerobic respiration and ATP production (Vartapetian and Jackson 1997). When oxygen becomes limiting for oxidative phosphorylation, plant cells depend on alternative metabolic pathways to produce ATP (Rocha et al. 2010). The induction of fermentative metabolism is considered of adaptive value to maintain ATP production under oxygen-limited conditions. Ethanol is the main end product of fermentation metabolism in plants. Alcohol dehydrogenase (ADH) is a key enzyme in ethanolic fermentation. Roots can sustain aerobic respiration under oxygen deficiency if aerenchyma is present. Aerenchyma commonly refers to tissue containing air-filled spaces that provide oxygen un-der oxygen-limited conditions (Colmer and Voesenek 2009). The main objective of the present study was to determine morpho-physiological adaptive responses of seven Brachiaria genotypes to hypoxia stress.
The Legionella pneumophila GIG operon responds to gold and copper in planktonic and biofilm cultures (2017)

Legionella pneumophila contaminates man-made water systems and creates numerous exposure risks for Legionnaires' Disease. Because copper/silver ionization is commonly used to control L. pneumophila, its mechanisms of metal response and detoxification are of significant interest. Here we describe an L. pneumophila operon with significant similarity to the GIG operon of Cupriavidus metallidurans. The Legionella GIG operon is present in a subset of strains and has been acquired as part of the ICE-βox 65-kB integrative conjugative element. We assessed GIG promoter activity following exposure of L. pneumophila to multiple concentrations of HAuCl4, CuSO4 and AgNO3. At 37°C, control stationary phase cultures exhibited GIG promoter activity. This activity increased significantly in response to 20 and 50uM HAuCl4 and CuSO4 but not in response to AgNO3. Conversely, at 26°C, cultures exhibited decreased promoter response to copper. GIG promoter activity was also induced by HAuCl4 or CuSO4 during early biofilm establishment at both temperatures. When an L. pneumophila GIG promoter construct was transformed into E. coli DH5α, cultures showed baseline expression levels that did not increase following metal addition. Analysis of L. pneumophila transcriptional regulatory mutants suggested that GIG up-regulation in the presence of metal ions may be influenced by the stationary phase sigma factor, RpoS.
Binarization based implementation for real-time human detection (2013)

Hardware implementation of human detection is a challenging task for embedded designs. This paper presents a real-time image-based field-programmable gate array (FPGA) implementation of human detection. Our implementation is based on the histograms of oriented gradients (HOG) feature and linear support vector machine (SVM) classifier. The novelty of this work is that we replace normalization process of HOG with a modified binarization process. Therefore, during classification process with SVM classifier, all multiplication operations are replaced by addition operations. All these modifications result in reduction of hardware resource. Experimental evaluation reveals that 293 fps can be achieved on a low-end Xilinx Spartan-3e FPGA. Moreover, a detection accuracy of 1.97% miss rate and 1% false positive rate is achieved. For further demonstration, a prototype system is developed with an OV7670 camera device. Restricted to the speed of camera, a detection rate of 30 fps is achieved.
Dynamic threshold-based keyframe detection and its application in rate control (2012)

This study proposes a new dynamic threshold model to detect keyframes for the coding of a video sequence. The proposed detection threshold is content adaptive which dynamically updates its value at each frame by taking into consideration both the statistical properties of the video sequence and the resolution as well as the quantisation parameters. The content variation metric used in the proposed detection method utilises the information that is already generated by the encoder during the encoding process and thus it makes the detection process fast. By applying the proposed scheme to rate control, the sizes of group of pictures are now adapted to the video content and it removes the temporal redundancy among different frames better, which transforms to the improvements on coding efficiency. The experimental results have shown that the proposed method achieves peak signal-to-noise ratio (PSNR) improvement.
The prevalence and clinical manifestation of hereditary thrombophilia in Korean patients with unprovoked venous thromboembolisms (2017)

About 15% of patients with unprovoked VTE had HT. A positive family history of VTE and age <45 years were independent predictors for unprovoked VTE caused by HT.
Time to Revisit Non-Pharmacological Research Approaches to Ameliorate Multiple Sclerosis Symptoms (2015)

Background: The current pharmacotherapies longest in use to treat multiple sclerosis (MS) do not slow progression to disability. The aim of this commentary is to stimulate interest in looking at MS from a new perspective. There is an abundance of evidence that MS is not primarily an autoimmune disease but is a disease where there is first damage to the blood-brain barrier as well as the oligodendrocyte-myelin unit; this damage then elicits an immune response in a subset of people that have an immune system predisposed to attacking myelin-associated antigens. A brief overview is given of the evidence for arterial compliance problems, intracranial compliance problems, venous return problems and hypoperfusion problems in MS. Conclusions: A rationale is given for the conduction of clinical trials examining the ability of dietary changes, hyperbaric oxygen treatment and approaches to improve venous return as means to ameliorate MS.
Adaptive lattice analysis of speech (1981)

The adaptive lattice has been shown to have fast convergence properties. In this paper we show experimentally that the convergence of the adaptive lattice is fast enough in that its performance cannot be distinguished from that of the optimal adaptive autocorrelation method for applications in speech analysis/synthesis. A generalized window filter is used in the adaptation process. We show that while the human listener prefers window filters with an effective length of about <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">20 ms</tex> , the shape of the window is especially important for better speech quality. The results have implications for other applications of adaptive filtering.