gebhart/patrepeval huggingface dataset:
Persistent Interactions between Biguanide-Based Compound NB325 and CXCR4 Result in Prolonged Inhibition of Human Immunodeficiency Virus Type 1 Infection (2010)

We previously demonstrated that the biguanide-based compound NB325 inhibits human immunodeficiency virus type 1 (HIV-1) infection by interacting with the CXCR4 viral coreceptor. This interaction also appeared to be persistent, since HIV-1 infection was inhibited even when the virus was introduced subsequent to the removal of NB325 from the cell culture medium. The present studies were conducted to determine the extent and mechanism of this prolonged antiviral activity. Persistent inhibition of HIV-1 infection by NB325 was concentration dependent and was apparent up to 8 h after removal of the compound. Flow cytometric analyses of stimulated CD4(+) T lymphocytes exposed to NB325 demonstrated concentration-dependent reductions in CXCR4 extracellular loop 2 epitope recognition that were maintained up to 24 h after removal of the compound. CXCL12-induced chemotaxis was also persistently inhibited following pre-exposure to NB325. These results demonstrate that persistent inhibition of X4 HIV-1 infection by NB325 involves extended perturbation of the viral coreceptor CXCR4.
A Coupled Peel and Shear Stress-Diffusion Model for Adhesively Bonded Single Lap Joints (2017)

In this study, the Fickian diffusion formulation is extended to the adhesive layer of a single lap joint (SLJ) model, in order to develop a coupled peel and shear stress-diffusion model. Constitutive equations are formulated for shear and peel stresses in terms of adhesive material properties that are time- and location-dependent. Numerical solution is provided for the effect of diffusion on shear and peel stresses distribution. Detailed discussion of the results is presented.
Study of the Subjective and Objective Quality of High Motion Live Streaming Videos (2021)

Video livestreaming is gaining prevalence among video streaming service s, especially for the delivery of live, high motion content such as sport ing events. The quality of the se livestreaming videos can be adversely affected by any of a wide variety of events, including capture artifacts, and distortions incurred during coding and transmission. High motion content can cause or exacerbate many kinds of distortion, such as motion blur and stutter. Because of this, the development of objective Video Quality Assessment (VQA) algorithms that can predict the perceptual quality of high motion, live streamed videos is greatly desired. Important resources for developing these algorithms are appropriate databases that exemplify the kinds of live streaming video distortions encountered in practice. Towards making progress in this direction, we built a video quality database specifically designed for live streaming VQA research. The new video database is called the Laboratory for Image and Video Engineering (LIVE) Livestream Database. The LIVE Livestream Database includes 315 videos of 45 source sequences from 33 original contents impaired by 6 types of distortions. We also performed a subjective quality study using the new database, whereby more than 12,000 human opinions were gathered from 40 subjects. We demonstrate the usefulness of the new resource by performing a holistic evaluation of the performance of current state-of-the-art (SOTA) VQA models. We envision that researchers will find the dataset to be useful for the development, testing, and comparison of future VQA models. The LIVE Livestream database is being made publicly available for these purposes at https://live.ece. utexas.edu/research/LIVE_APV_Study/apv_index.html.
The DISC1–Girdin complex – a missing link in signaling to the T cell cytoskeleton (2020)

In this study, using Jurkat cells, we show that DISC1 (disrupted in schizophrenia 1) and Girdin (girders of actin filament) are essential for typical actin accumulation at the immunological synapse. Furthermore, DISC1, Girdin and dynein are bound in a complex. Although this complex initially forms as a central patch at the synapse, it relocates to a peripheral ring corresponding to the peripheral supramolecular activation cluster (pSMAC). In the absence of DISC1, the classic actin ring does not form, cell spreading is blocked, and the dynein complex fails to relocate to the pSMAC. A similar effect is seen when Girdin is deleted. When cells are treated with inhibitors of actin polymerization, the dynein-NDE1 complex is lost from the synapse and the microtubule-organizing center fails to translocate, suggesting that actin and dynein might be linked. Upon stimulation of T cell receptors, DISC1 becomes associated with talin, which likely explains why the dynein complex colocalizes with the pSMAC. These results show that the DISC1-Girdin complex regulates actin accumulation, cell spreading and distribution of the dynein complex at the synapse.This article has an associated First Person interview with the first author of the paper.
Robustness Analysis of Speech Enhancement Using a Bone Conduction Microphone - Preliminary Results (2012)

&lt;p&gt;Previously, the use of a bone-conducting sensor worn on the neck was shown to improve the performance of a codebook-based speech enhancement system for non-stationary noise suppression, while reducing computational complexity. This system relies on a mapping between bone-conducted and air-conducted signals that is learned during an offline training phase for a certain location of the sensors. Signal properties such as speech intensity, quality, and intelligibility are more location-dependent for a bone-conducting sensor. This paper studies aspects of robustness related to location-errors between the original training location and those used in practice. The two main regions considered for sensor placement are the neck and temple areas to understand the benefits and tradeoff between higher signal-to-noise ratio (neck) and higher speech intelligibility (temple) for such a system.&lt;/p&gt;
Thermodynamics of Ligand Binding (2012)

Ligand binding is a fundamental process in many biological phenomena. Restricting our discussion to drug discovery, ligand binding includes the interaction of small molecules with their target, which is typically a protein. Binding events contribute to further properties of small molecules, whose in...
Chapter 17 SERENITY in e-Business and Smart Items Scenarios (2009)

SERENITY Artefacts, like Class, Patterns, Implementations and Exe- cutable Components for Security & Dependability (S&D) in addition to Serenity Runtime Framework (SRF) are discussed in previous chapters. How to integrate these artefacts with applications in Serenity approach is discussed here with two sce- narios. The e-Business scenario is a standard loan origination process in a bank. The Smart Item scenario is an Ambient intelligence case study where we take advantage of Smart Items to provide an electronic healthcare infrastructure for remote health- care assistance. In both cases, we detail how the prototype implementations of the scenarios select proper executable components through Serenity Runtime Frame- work and then demonstrate how these executable components of the S&D Patterns are deployed.
Ebola Virus Stability Under Hospital and Environmental Conditions (2016)

The West African outbreak of Ebola virus (EBOV) is largely contained, but sporadic new cases continue to emerge. To assess the potential contribution of fomites to human infections with EBOV, we tested EBOV stability in human blood spotted onto Sierra Leonean banknotes and in syringe needles under hospital and environmental conditions. Under some of these conditions, EBOV remained infectious for >30 days, indicating that EBOV-contaminated items may pose a serious risk to humans.
In situ carbon mineralization in ultramafic rocks: Natural processes and possible engineered methods (2018)

In this invited review, we summarize the main results of ongoing research on “in situ” carbon mineralization in ultramafic rocks, including outcrop studies in Oman (e.g., [1, 2]), investigation of carbon mass transfer in subduction zones from the Oman Drilling Project (e.g., [3-7]), laboratory investigations (e.g., [8-12]) and numerical modeling (e.g., [13-17]) of the pressure of crystallization and reaction-driven cracking, and assessment of the rate, cost and capacity of various proposed methods for engineered carbon mineralization [18, 19].
Iminosugar antivirals: the therapeutic sweet spot (2017)

Many viruses require the host endoplasmic reticulum protein-folding machinery in order to correctly fold one or more of their glycoproteins. Iminosugars with glucose stereochemistry target the glucosidases which are key for entry into the glycoprotein folding cycle. Viral glycoproteins are thus prevented from interacting with the protein-folding machinery leading to misfolding and an antiviral effect against a wide range of different viral families. As iminosugars target host enzymes, they should be refractory to mutations in the virus. Iminosugars therefore have great potential for development as broad-spectrum antiviral therapeutics. We outline the mechanism giving rise to the antiviral activity of iminosugars, the current progress in the development of iminosugar antivirals and future prospects for this field.
Preventing heart failure: a position paper of the Heart Failure Association in collaboration with the European Association of Preventive Cardiology (2021)

The heart failure epidemic is growing and its prevention, in order to reduce associated hospital readmission rates and its clinical and economic burden, is a key issue in modern cardiovascular medicine. The present consensus document aims to provide practical evidence-based information to support the implementation of effective preventive measures. After reviewing the most common risk factors, an overview of the population attributable risks in different continents is presented, to identify potentially effective opportunities for prevention and to inform preventive strategies. Finally, potential interventions that have been proposed and have been shown to be effective in preventing HF are listed.
Improved outcomes for newly diagnosed AL amyloidosis between 2000 and 2014: cracking the glass ceiling of early death (2017)

In light of major advances in immunoglobulin light chain (AL) amyloidosis, we evaluated the trends in presentation, management, and outcome among 1551 newly diagnosed AL amyloidosis patients seen in our institution from 2000 to 2014. As compared with the 2 intervals 2000-2004 and 2005-2009, patients diagnosed in 2010-2014 were less likely to have >2 involved organs. Utilization of autologous stem cell transplant (ASCT) was similar across all periods, about one-third of patients, but there was an increase in the use of pre-ASCT bortezomib induction and of unattenuated melphalan conditioning in 2010-2014 compared with earlier periods. Non-ASCT first-line regimen changed with 65% of patients in 2010-2014 received bortezomib-based therapy, 79% of patients in 2005-2009 received melphalan-dexamethasone, and 64% of patients in 2000-2004 received melphalan-prednisone. The rate of better than very good partial response (VGPR) was higher in more recent periods (66% vs 58% vs 51%; <i>P</i> = .001), a change largely driven by improved VGPR rates in the non-ASCT population. Overall survival (OS) has improved, with inflection points for improvement differing for the ASCT and non-ASCT groups. In the ASCT population, the greatest gains were after 2010 (4-year OS, 91% compared with 73% and 65%). In the non-ASCT group, greatest gains were after 2005 (4-year OS, 38%, 32%, and 16%). Fewer patients died within 6 months of diagnosis in the 2 later periods (24% vs 25% vs 37%; <i>P</i> < .001). Overall, outcomes among patients with AL amyloidosis have improved with earlier diagnosis, higher rates of VGPR, lower early mortality, and improved OS.
Diurnal changes in perineuronal nets and parvalbumin neurons in the rat medial prefrontal cortex (2020)

ABSTRACT Perineuronal nets (PNNs) surrounding fast-spiking, parvalbumin (PV) inhibitory interneurons are vital for providing excitatory:inhibitory balance within cortical circuits, and this balance is impaired in disorders such as schizophrenia, autism spectrum disorder, and substance use disorders. These disorders are also associated with altered diurnal rhythms, yet few studies have examined the diurnal rhythms of PNNs or PV cells. We measured the intensity and number of PV cells and PNNs labeled with Wisteria floribunda agglutinin (WFA) in the rat prelimbic medial prefrontal cortex (mPFC) at Zeitgeber times (ZT) ZT0, 6, 12, and 18. We also measured the oxidative stress marker 8-oxo-deoxyguanosine (8-oxo-dG). Relative to ZT0, the intensities of PNN and PV staining were increased in the dark (active) phase compared with the light (inactive) phase. The intensity of 8-oxo-dG was decreased from ZT0 at all time points (ZT6,12,18), in both PV cells and non-PV cells. To examine corresponding changes in inhibitory and excitatory inputs, we measured GAD 65/67 and vGlut1 puncta apposed to PV cells with and without PNNs. Relative to ZT6, there were more excitatory puncta on PV cells surrounded by PNNs at ZT18, but no changes in PV cells devoid of PNNs. No changes in inhibitory puncta were observed. Whole-cell slice recordings in fast-spiking (PV) cells with PNNs showed an increased ratio of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor:N-methyl-D-aspartate receptor (AMPA:NMDA) at ZT18 vs . ZT6. The number of PV cells and co-labeled PV/PNN cells containing the transcription factor orthodenticle homeobox 2 (OTX2), which maintains PNNs, showed a strong trend toward an increase from ZT6 to ZT18. These diurnal fluctuations in PNNs and PV cells are expected to alter cortical excitatory:inhibitory balance and provide new insights into treatment approaches for diseases impacted by imbalances in sleep and circadian rhythms.
Scale model experimentation: using terahertz pulses to study light scattering (2002)

We describe a new class of experiments involving applications of terahertz radiation to problems in biomedical imaging and diagnosis. These involve scale model measurements, in which information can be gained about pulse propagation in scattering media. Because of the scale invariance of Maxwell's equations, these experiments can provide insight for researchers working on similar problems at shorter wavelengths. As a first demonstration, we measure the propagation constants for pulses in a dense collection of spherical scatterers, and compare with the predictions of the quasi-crystalline approximation. Even though the fractional volume in our measurements exceeds the limit of validity of this model, we find that it still predicts certain features of the propagation with reasonable accuracy.
Isolation of a Streptococcus mutans strain producing a novel bacteriocin (1984)

A strain of Streptococcus mutans has been isolated that produces a bacteriocin with novel properties. Its antibiotic spectrum includes 123 of 124 strains of S. mutans tested and a variety of other gram-positive microorganisms. Experiments with dialysis membranes indicate that the molecular weight of the bacteriocin is less than 1,000. Mutants of the producer strain were obtained that are deficient in bacteriocin production or produce twofold elevated amounts. The ability of these strains to superinfect or preemptively colonize the oral cavities of rats correlated with the amount of bacteriocin they produced.
PD53-01 DEVELOPMENT OF A WHOLE-URINE, MULTIPLEXED, NEXT GENERATION RNA-SEQUENCING ASSAY FOR AGGRESSIVE PROSTATE CANCER EARLY DETECTION (2020)

INTRODUCTION AND OBJECTIVE: Despite advances in biomarker development, early detection of aggressive prostate cancer (PCa) remains challenging. We previously developed the Michigan Prostate Score (MiPS) for individualized risk prediction of aggressive prostate cancer. MiPS uses transcription-mediated amplification to quantify expression of TMPRSS2:ERG (T2:ERG) and PCA3 from whole urine obtained after a digital rectal exam (DRE), combined with serum PSA. To improve upon MiPS, herein we describe the pre-clinical development and validation of a targeted next generation RNA sequencing assay (NGS-MiPS). METHODS: We selected patients with available MiPS scores as well as representing a spectrum of disease grade on biopsy (Benign to Grade Group 5). We used 2.5 mL of post-DRE whole urine to asses ∼90 PCa transcriptomic biomarkers: including T2:ERG, PCA3, and additional isoforms of common PCa gene fusions, mRNAs, lncRNAs, and expressed mutations. RESULTS: NGS-MiPS showed a 98% informative sample rate, high technical reproducibility, robustness and concordance with orthogonal methods (TMA and RT-qPCR), and was able to detect an expressed HOXB13 p.G84E variant and SPOP mutations. NGS-MiPS accurately recapitulated clinical MiPS-measured risk scores for presence of PCa or high-grade PCa (Gleason Score >6) on biopsy as determined by clinical MiPS vs. the same model but with NGS-MiPS data. In an extreme design cohort (Benign or Gleason 6 vs. Gleason ≥ 4+3=7 cancer) NGS-MiPS showed expected differences in the levels of T2:ERG T1E4 (p<0.00001) and PCA3 (p=0.02), with additional T2:ERG splice isoforms and other biomarkers also showing significantly different expression between low vs. high grade cancer. We used a machine learning approach trained on a subset of the extreme design cohort (n=73) to generate a 29-transcript model that outperformed MiPS and serum PSA in two validation cohorts: 1. A held-out set from the extreme design cohort n=36, (AUC 0.82 vs. 0.73 and 0.69, respectively); and 2. A separate PCa active surveillance cohort n=45, (AUC 0.66 vs. 0.58 and 0.53, respectively). CONCLUSIONS: These results support the potential utility and continued development of our urine based targeted NGS assay to supplement serum PSA for improved early detection of aggressive prostate cancer. Source of Funding: University of Michigan Prostate Cancer S.P.O.R.E. Grant P50 CA186786-05. AKC was supported by the NIH Training Program in Translational Research T32-GM113900 and by the University of Michigan Precision Health, 2018 Scholars Awards.TMM and SAT have been supported by the A. Alfred Taubman Biomedical Research Institute.
Digital Word-Parallel Low-Power Recognition SoC for Mobile Equipment Based on Nearest Euclidean Distance Search and KNN Classification (2014)

2014 International Conference on Solid State Devices and Materials,Digital Word-Parallel Low-Power Recognition SoC for Mobile Equipment Based on Nearest Euclidean Distance Search and KNN Classification
ANTIOXIDATIVE FLAVONOID GLYCOSIDES FROM QUINOA SEEDS (CHENOPODIUM QUINOA WILLD) (2001)

ABSTRACT Six flavonol glycosides have been isolated from quinoa seeds ( Chenopodium quinoa Willd) via normal phase and reverse phase column chromatography. On the basis of spectral data, their structures were established as kaempferol 3‐O‐[β‐D‐apiofuranosyl(1′–2″)]‐β‐D‐galactopyranoside ( 1 ), kaempferol 3‐O‐[α‐L‐rhamnopyranosyl(1″–2″)]‐β‐D‐galactopyranoside ( 2 ), kaempferol 3‐O‐[β‐D‐apiofuranosyl(1′–2″)‐α‐L‐rhamnopyranosyl(1″–6″)]‐β‐D‐galactopyranoside ( 3 ), kaempferol 3‐O‐(2,6‐di‐α‐L‐rhamnopyranosyl)‐β‐D‐galactopyranoside ( 4 ), quercetin 3‐O‐[β‐D‐apiofuranosyl (1′–2″)‐α‐L‐rhamnopyranosyl(1″–6″)]‐β‐D‐galactopyranoside ( 5 ) and quercetin 3‐O‐(2,6‐di‐α‐L‐rhamnopyranosyl)‐β‐D‐galactopyranoside ( 6 ). Among them, compounds 1, 4 and 6 were the main flavonoid glycosides found in quinoa seeds and compounds 2, 5 , and 6 were isolated from this plant for the first time. All six compounds exhibited antioxidant
A Comparative Clinical Study of a Novel Pre-colonoscopy Bowel Capsule Preparation Against Two Commercially Available Liquid Preparations (2021)

<b>Background and Aims:</b> Colonoscopy surveillance depends on effective bowel preparation. Inadequate bowel preparation can lead to inaccurate clinical diagnosis, insufficient visualization of the colon and increased risk of missed diagnosis. This study aimed to compare the efficacy and safety of a novel Capsule Bowel Preparation (RitePrep), high-volume (2L) polyethylene glycol electrolyte solution (MoviPrep®) and low-volume (1L) polyethylene glycol electrolyte solution (Plenvu™). <b>Methods:</b> Patients (<i>n</i> = 120) were divided into three groups and were administered either RitePrep, MoviPrep® or Plenvu™ as a pre-colonoscopy bowel preparation followed by a colonoscopy at a single center. Validated Boston Bowel Preparation Score (BBPS) and bubble score were used to evaluate bowel cleanliness. Blood tests were also evaluated. The scores and the blood results were analyzed using Kruskal-Wallis and Chi-squared tests. <b>Results:</b> A total of 120 patients (median age of 55; 57 males) [RitePrep (<i>n</i> = 40), MoviPrep® (<i>n</i> = 40) and Plenvu™ (<i>n</i> = 40)] were included in the study. RitePrep was the most effective method for cleansing the bowel, with a significantly higher median BBPS compared to MoviPrep® and Plenvu™ (<i>p</i> = 0.006 and 0.024, respectively). Nearly 50% of the patients in Plenvu™ group showed increased serum osmolality disturbance. Nausea and vomiting were higher in Plenvu™ and MoviPrep® groups than RitePrep group. <b>Conclusions:</b> RitePrep was demonstrated to be a more effective and safe preparation than the other two preparations. RitePrep was not only well-tolerated by all patients; the preparation sufficiently cleared the ascending, transverse, and descending colon, enabling optimal visualization for the clinician. RitePrep was also much safer than the comparators, with no alteration in electrolytes measured. For both the clinician and the patient, RitePrep was the preferred preparation.
Demystifying Low-Carbon Materials (2021)

Abstract Low-carbon materials (the ‘carbon’ is related to carbon dioxide emission potential and not elemental carbon) need to be developed and embraced ubiquitously for the sustainable development of human society and mitigate climate change. In the absence of clear consensus in the literature coupled with the presence of certain miss-information, this ‘discussion’ article seeks to define low-carbon materials as the materials that foster a healthy living environment and a circular economy via the elimination or reduction of associated greenhouse gas (GHG) emissions and resource depletion and wastage. Furthermore, the multidimensional facets of low-carbon products and services are described to promote widespread utilisation of low-carbon materials so as to transition to desired low-carbon or decarbonised economies. Several specific strategies for realising the aforementioned are illustrated, which include radical green chemistry and materials approach, efficient materials extraction and processing, utilising renewable feedstocks and energies, efficient product manufacturing, enhanced recycling rates, designing out wastes, circular flow of materials, and innovative business models. The information provided in this ‘discussion’ article strives to outline a variety of aspects and tools available and necessary to accelerate the growth of low-carbon materials and progress towards a sustainable future. Graphical abstract The integration of low-carbon materials, products and services with natural resource preservation, prosperity and a healthy living environment
Detection of clinically significant prostate cancer in biopsy‐naïve men: direct comparison of systematic biopsy, multiparametric MRI‐ and contrast‐ultrasound‐dispersion imaging‐targeted biopsy (2020)

In our study in biopsy-naïve men, the mpMRI- and CUDI-TBx strategies had comparable PCa detection rates, but the mpMRI-TBX strategy had the least false-positive findings. Both strategies were inferior to SBx for the detection of GG ≥2 PCa, despite reduced detection of insignificant GG = 1 PCa. Both strategies did not significantly differ from SBx for the detection of GG ≥2 PCa with CR/IDC and GG ≥3 PCa.