gebhart/patrepeval huggingface dataset:
Oat5 and NaDC1 Protein Abundance in Kidney and Urine After Renal Ischemic Reperfusion Injury (2008)

The aim of this study was to evaluate the abundance of the organic anion transporter 5 (Oat5) and the sodium-dicarboxylate cotransporter 1 (NaDC1) in kidney and urine after renal ischemic reperfusion injury. Renal injury was induced in male Wistar rats by occlusion of both renal pedicles for 0 (Group Sham), 5 (Group I5R60), or 60 (Group I60R60) min. The studies were performed after 60 min of reperfusion. The expression of Oat5 and NaDC1 was evaluated by IHC and Western blotting. Oat5 and NaDC1 abundance and alkaline phosphatase activity (AP) were assayed in urine. A decreased expression in renal homogenates and apical membranes and an increase in urinary excretion of Oat5 and NaDC1 were observed in I60R60 rats, as well as alterations of other widely used parameters for renal dysfunction and injury (plasma creatinine, urinary AP activity, kidney weight, histological lesions). In contrast, in the I5R60 group, only an increase in urinary excretion of Oat5 and mild histopathological damage was detected. This is the first study on Oat5 and NaDC1 detection in urine. These results suggest that urinary excretion of Oat5 might be an early indicator of renal dysfunction, which is useful for detection of even minor alterations in renal structural and functional integrity.
Improving Image Quality by Accounting for Changes in Water Temperature during a Photoacoustic Tomography Scan (2012)

The emerging field of photoacoustic tomography is rapidly evolving with many new system designs and reconstruction algorithms being published. Many systems use water as a coupling medium between the scanned object and the ultrasound transducers. Prior to a scan, the water is heated to body temperature to enable small animal imaging. During the scan, the water heating system of some systems is switched off to minimize the risk of bubble formation, which leads to a gradual decrease in water temperature and hence the speed of sound. In this work, we use a commercially available scanner that follows this procedure, and show that a failure to model intra-scan temperature decreases as small as 1.5°C leads to image artifacts that may be difficult to distinguish from true structures, particularly in complex scenes. We then improve image quality by continuously monitoring the water temperature during the scan and applying variable speed of sound corrections in the image reconstruction algorithm. While upgrading to an air bubble-free heating pump and keeping it running during the scan could also solve the changing temperature problem, we show that a software correction for the temperature changes provides a cost-effective alternative to a hardware upgrade. The efficacy of the software corrections was shown to be consistent across objects of widely varying appearances, namely physical phantoms, ex vivo tissue, and in vivo mouse imaging. To the best of our knowledge, this is the first study to demonstrate the efficacy of modeling temporal variations in the speed of sound during photoacoustic scans, as opposed to spatial variations as focused on by previous studies. Since air bubbles pose a common problem in ultrasonic and photoacoustic imaging systems, our results will be useful to future small animal imaging studies that use scanners with similarly limited heating units.
Accidental needlesticks: do anesthesiologists practice proper infection control precautions? (1995)

Anesthesiologists as well as patients are at risk for acquiring blood-borne infections such as hepatitis and AIDS. We surveyed 2,530 anesthesiologists, a 10% random sample of the members of the American Society of Anesthesiologists, with a response rate of 57.1%, to determine the incidence of accidental needlestick exposure among anesthesia personnel and whether anesthesiologists are adhering to infection control guidelines to protect themselves and their patients from exposure to infectious diseases. Eighty-eight percent of respondents reported at least 1 accidental needlestick in the past 10 years; 21% received a needlestick from a high-risk patient and 4.5% a needlestick from a known HIV-positive patients. Residents reported significantly more accidental needlesticks from known HIV-positive patients (8.5%). Mucous membrane, open cut, eye, or other significant exposure to HIV-contaminated blood or body fluids was sustained by 8.34% of respondents in the past 10 years. Sixty percent of respondents reported they almost never reuse common syringes now compared with a 40.8% non-reuse rate (P < 0.001) in a similar survey on infection control practices conducted in 1990. Sixty-three percent reported they almost never reuse a vasopressor syringe compared with the 1990 non-reuse rate of 52.5% (P < 0.001). In the current survey, 39% of anesthesiologists reported reusing syringes from one patient to another and 36% reported reusing the same vasopressor syringes for different patients.(ABSTRACT TRUNCATED AT 250 WORDS)
Enhanced Single-Photon Emission from Single Quantum Dots Interacting with a One-Dimensional Plasmonic Chip (2022)

Modification of the photoluminescence (PL) behavior of a single colloidal quantum dot (QD) using plasmonic nanostructures has attracted considerable attention. Here, we attempted to control the PL behavior of a single CdSe/ZnS QD by using a one-dimensional plasmonic chip (1D-PC) with the simplest Ag grating pattern. By optimizing the distance between the single QD and 1D-PC, the PL intensity of the single QD was successfully enhanced 5 times with maintaining single-photon emission via enhancement of the excitation rate due to the electric field of the surface plasmon on the 1D-PC. On the other hand, control of the emission photon statistics, that is, single-photon emission and multiphoton emission, from the single QD was difficult because enhancement of the radiative rate of the single QD was not achieved by the 1D-PC. These results indicate that the 1D-PC is an attractive plasmonic nanostructure to obtain efficient single-photon emission which is indispensable for next-generation quantum information technologies.
Engineering of porous π-stacked solids using mechanochemistry (2001)

Charge-assisted π-stacking interactions result in the formation of large porous arrays formed from the inclusion of metal tris(phenanthroline) cations into p-sulfonatocalix[4]arene anions.
Construction of a pepO gene‐deficient mutant of Porphyromonas gingivalis: potential role of endopeptidase O in the invasion of host cells (2003)

Porphyromonas gingivalis has been isolated from lesions of advanced adult periodontitis, and implicated as a periodontal pathogen. We have previously cloned a novel endopeptidase, designated PepO, from P. gingivalis 381, which exhibited significant homology to human endothelin-converting enzyme (ECE)-1. In order to determine the nature and function of the PepO in the host, a pepO gene-deficient mutant strain was constructed by allelic exchange mutagenesis using the ermF-ermAM cassette. No endopeptidase activity was detected in the pepO-deficient mutant. In addition, adherent HeLa (HEp-2) cells were infected with the mutant and the two wild-type strains for assessment of bacterial invasion by an antibiotic protection assay. The invasion efficiency of the mutant strain was about a quarter of the wild type strains. These results suggest that PepO is involved in the first step, i.e. invasion/lysis of mammalian cell membrane, which affects the kinetics of rate of invasion.
Meeting report: 34th international conference on antiviral research (2022)

As a result of the multiple gathering and travels restrictions during the SARS-CoV-2 pandemic, the annual meeting of the International Society for Antiviral Research (ISAR), the International Conference on Antiviral Research (ICAR), could not be held in person in 2021. Nonetheless, ISAR successfully organized a remote conference, retaining the most critical aspects of all ICARs, a collegiate gathering of researchers in academia, industry, government and non-governmental institutions working to develop, identify, and evaluate effective antiviral therapy for the benefit of all human beings. This article highlights the 2021 remote meeting, which presented the advances and objectives of antiviral and vaccine discovery, research, and development. The meeting resulted in a dynamic and effective exchange of ideas and information, positively impacting the prompt progress towards new and effective prophylaxis and therapeutics.
The Conserved Core of a HumanSIR2Homologue Functions in Yeast Silencing (1999)

Silencing is a universal form of transcriptional regulation in which regions of the genome are reversibly inactivated by changes in chromatin structure. Sir2 (Silent Information Regulator) protein is unique among the silencing factors in Saccharomyces cerevisiae because it silences the rDNA as well as the silent mating-type loci and telomeres. Discovery of a gene family of Homologues of Sir Two (HSTs) in organisms from bacteria to humans suggests that SIR2's silencing mechanism might be conserved. The Sir2 and Hst proteins share a core domain, which includes two diagnostic sequence motifs of unknown function as well as four cysteines of a putative zinc finger. We demonstrate by mutational analyses that the conserved core and each of its motifs are essential for Sir2p silencing. Chimeras between Sir2p and a human Sir2 homologue (hSir2Ap) indicate that this human protein's core can substitute for that of Sir2p, implicating the core as a silencing domain. Immunofluorescence studies reveal partially disrupted localization, accounting for the yeast-human chimeras' ability to function at only a subset of Sir2p's target loci. Together, these results support a model for the involvement of distinct Sir2p-containing complexes in HM/telomeric and rDNA silencing and that HST family members, including the widely expressed hSir2A, may perform evolutionarily conserved functions.
Coordinated Pilot Design for Massive MIMO (2019)

Pilot contamination is a main limiting factor in multi-cell massive multiple-input multiple-output (MIMO) systems due to the non-orthogonality of pilot sequences which can seriously impair the channel measurement. Recent work has suggested coordinating pilot sequence design across multiple cells by choosing the sequences to minimize the channel estimation error. This paper further investigates this approach using a new optimization framework. Specifically, we reformulate the weighted minimum mean-squared error (MMSE) measure as a sum-of-functions-of-matrix-ratio program that can be efficiently solved via a matrix fractional programming approach. The proposed algorithm provides fast convergence to a stationary-point solution of the MMSE problem. Simulations demonstrate the advantage of the proposed method over alternative approaches in enhancing channel estimation accuracy.
Humanin Binds and Nullifies Bid Activity by Blocking Its Activation of Bax and Bak (2005)

Recently, we discovered that Humanin (HN), a small endogenous peptide of 24 amino acids, binds to and inhibits the proapoptotic protein Bax. We show here that HN also interacts with the BH3-only Bcl-2/Bax family protein, Bid, as well as a truncated form of Bid (tBid) associated with protease-mediated activation of this proapoptotic protein. Synthetic HN peptide binds purified Bid and tBid in vitro and blocks tBid-induced release of cytochrome c and SMAC from isolated mitochondria, whereas mutant peptides that fail to bind Bid or tBid lack this activity. Moreover, HN peptide also retained protective activity on bax-/-mitochondria, indicating that HN can block tBid-induced release of apoptogenic proteins from these organelles in a Bax-independent manner. HN peptide inhibits tBid-induced oligomerization of Bax and Bak in mitochondrial membranes, as shown by experiments with chemical cross-linkers or gel filtration. Gene transfection experiments showed that HN (but not an inactive mutant of HN) also protects intact cells from apoptosis induced by overexpression of tBid. We conclude that Bid represents an additional cellular target of HN, and we propose that HN-mediated suppression of Bid contributes to the antiapoptotic activity of this endogenous peptide.
Improving the virtualization of rich applications by combining VNC and streaming protocols at the hypervisor layer (2015)

Summary Virtual desktop infrastructure (VDI) solutions seek to provide a satisfactory user experience at the client side when accessing remote desktop applications, even from mobile devices with limited capabilities. This paper presents a new approach, improving on previous work by the authors, in which a combination of Virtual Network Computing (VNC) and streaming protocols allowed efficient remote web access to virtualized applications within a cloud architecture. The new approach simplifies virtual machine templates, from which virtual machine instances are deployed, by centralizing software modules, greatly simplifying their management. Our new contribution consists of an integrated solution with specific WebM video encoding modules in charge of application visual output processing, an Hypertext Transfer Protocol (HTTP) streaming server, and a VNC server. The solution can be installed in the hypervisor of the host machines instead of replicating the servers and modules throughout the guest (virtual) machines that run the virtualized applications. Consequently, their implementations are unique and independent of the operating system of the virtual machines. In short, it is not necessary to provide different implementations for different operating systems, which reduces the complexity of virtual machine templates and greatly simplies platform management. To demonstrate our solution, we have modified the Quick Emulator (QEMU)‐Kernel‐based Virtual Machine (KVM) hypervisor source code accordingly. We also present qualitative and quantitative analyses that demonstrate that the new approach is advantageous in terms of software management and quality of experience, compared with our previous work and other well‐known thin clients, contributing to the enhancement of VDI systems. Copyright © 2015 John Wiley &amp; Sons, Ltd.
Initial Phases of Biofilm Formation in Shewanella oneidensis MR-1 (2004)

Shewanella oneidensis MR-1 is a facultative Fe(III)- and Mn(IV)-reducing microorganism and serves as a model for studying microbially induced dissolution of Fe or Mn oxide minerals as well as biogeochemical cycles. In soil and sediment environments, S. oneidensis biofilms form on mineral surfaces and are critical for mediating the metabolic interaction between this microbe and insoluble metal oxide phases. In order to develop an understanding of the molecular basis of biofilm formation, we investigated S. oneidensis biofilms developing on glass surfaces in a hydrodynamic flow chamber system. After initial attachment, growth of microcolonies and lateral spreading of biofilm cells on the surface occurred simultaneously within the first 24 h. Once surface coverage was almost complete, biofilm development proceeded with extensive vertical growth, resulting in formation of towering structures giving rise to pronounced three-dimensional architecture. Biofilm development was found to be dependent on the nutrient conditions, suggesting a metabolic control. In global transposon mutagenesis, 173 insertion mutants out of 15,000 mutants screened were identified carrying defects in initial attachment and/or early stages in biofilm formation. Seventy-one of those mutants exhibited a nonswimming phenotype, suggesting a role of swimming motility or motility elements in biofilm formation. Disruption mutations in motility genes (flhB, fliK, and pomA), however, did not affect initial attachment but affected progression of biofilm development into pronounced three-dimensional architecture. In contrast, mutants defective in mannose-sensitive hemagglutinin type IV pilus biosynthesis and in pilus retraction (pilT) showed severe defects in adhesion to abiotic surfaces and biofilm formation, respectively. The results provide a basis for understanding microbe-mineral interactions in natural environments.
Hysterectomy route and readmissions – a reply (2018)

Sir, We thank the author for his thoughtful comments 1 and for pointing out some inherent flaws with retrospective studies. We made every attempt to present a balanced view 2, but there are data that are not captured in the database that we are using, including the ones that the author mentions. However, given the size of the sample, it seems likely that at least some of these variables were evenly distributed.
Semantic Navigation of Large Code Bases in Higher-Order, Dynamically Typed Languages (2006)

Chuck is a new code browser that allows navigation of a code base along semantic structures, such as data-flow and higher-order control-flow relationships. Employing the fast DDP type inferencer, it is effective on dynamically typed code bases an order of magnitude larger than the code bases supported by previous browsers. Chuck supports the full Smalltalk language, and is now shipped as a standard component of the Squeak open-source Smalltalk system, where it routinely works with code bases exceeding 300,000 lines of code. Chuck's implementation is tuned for interactive use, and is transparently integrated with the Squeak system's existing code-browsing tools. Thus, it provides semantic navigation of a live code base that is still being edited without requiring long pauses for reanalysis due to edits of the code.
Positron Emission Tomography (PET) with 18F-FGA for Diagnosis of Myocardial Infarction in a Coronary Artery Ligation Model (2022)

Location and extent of necrosis are valuable information in the management of myocardial infarction (MI). <i>Methods</i>. We investigated 2-deoxy-2-<sup>18</sup>F-fluoro glucaric acid (FGA), a novel infarct-avid agent, for positron emission tomography (PET) of MI. We synthesized FGA from commercially available <sup>18</sup>F-fluoro-2-deoxy-2-D-glucose (FDG). MI was induced in mice by permanently occluding the left anterior descending coronary artery. Biodistribution of FGA was assessed 1 h after FGA injection (11 MBq). PET/CT was conducted 1 h, 6 h, 1 d, 3 d, and 4 d after MI. Subcellular compartment of FGA accumulation in necrosis was studied by tracing the uptake of biotin-labeled glucaric acid with streptavidin-HRP in H<sub>2</sub>O<sub>2</sub>-treated H9c2 cardiomyoblasts. Streptavidin-reactive protein bands were identified by LC-MS/MS. <i>Results</i>. We obtained a quantitative yield of FGA from FDG within 7 min (radiochemical purity > 99%). Cardiac uptake of FGA was significantly higher in MI mice than that in control mice. Imaging after 1 h of FGA injection delineated MI for 3 days after MI induction, with negligible background signal from surrounding tissues. Myocardial injury was verified by tetrazolium staining and plasma troponin (47.63 pg/mL control versus 311.77 pg/mL MI). In necrotic H9c2 myoblasts, biotinylated glucaric acid accumulated in nuclear fraction. LC-MS/MS primarily identified fibronectin in necrotic cells as a putative high fidelity target of glucaric acid. <i>Conclusion</i>. FGA/PET detects infarct early after onset of MI and FGA accumulation in infarct persists for 3 days. Its retention in necrotic cells appears to be a result of interaction with fibronectin that is known to accumulate in injured cardiac tissue.
Proceedings of the ACE Challenge Workshop - a satellite event of IEEE-WASPAA (2015) (2015)

Several established parameters and metrics have been used to characterize the acoustics of a room. The most important are the Direct-To-Reverberant Ratio (DRR), the Reverberation Time (T60) and the reflection coefficient. The acoustic characteristics of a room based on such parameters can be used to predict the quality and intelligibility of speech signals in that room. Recently, several important methods in speech enhancement and speech recognition have been developed that show an increase in performance compared to the predecessors but do require knowledge of one or more fundamental acoustical parameters such as the T60. Traditionally, these parameters have been estimated using carefully measured Acoustic Impulse Responses (AIRs). However, in most applications it is not practical or even possible to measure the acoustic impulse response. Consequently, there is increasing research activity in the estimation of such parameters directly from speech and audio signals. The aim of this challenge was to evaluate state-of-the-art algorithms for blind acoustic parameter estimation from speech and to promote the emerging area of research in this field. Participants evaluated their algorithms for T60 and DRR estimation against the 'ground truth' values provided with the data-sets and presented the results in a paper describing the method used.
Integer-grid maps for reliable quad meshing (2013)

Quadrilateral remeshing approaches based on global parametrization enable many desirable mesh properties. Two of the most important ones are (1) high regularity due to explicit control over irregular vertices and (2) smooth distribution of distortion achieved by convex variational formulations. Apart from these strengths, state-of-the-art techniques suffer from limited reliability on real-world input data, i.e. the determined map might have degeneracies like (local) non-injectivities and consequently often cannot be used directly to generate a quadrilateral mesh. In this paper we propose a novel convex Mixed-Integer Quadratic Programming (MIQP) formulation which ensures by construction that the resulting map is within the class of so called Integer-Grid Maps that are guaranteed to imply a quad mesh. In order to overcome the NP-hardness of MIQP and to be able to remesh typical input geometries in acceptable time we propose two additional problem specific optimizations: a complexity reduction algorithm and singularity separating conditions. While the former decouples the dimension of the MIQP search space from the input complexity of the triangle mesh and thus is able to dramatically speed up the computation without inducing inaccuracies, the latter improves the continuous relaxation, which is crucial for the success of modern MIQP optimizers. Our experiments show that the reliability of the resulting algorithm does not only annihilate the main drawback of parametrization based quad-remeshing but moreover enables the global search for high-quality coarse quad layouts - a difficult task solely tackled by greedy methodologies before.
Electron-transfer processes: oxidation of naphthalene and p-cymene by peroxydisulfate (1979)

Evidence are provided for the f'ormation of aromatic radical cations in the interaction of the sulfate radical anion with naphthalene and p-cymene in the presence of metal cations.
Steady flow in models of abdominal aortic aneurysms. Part I: Investigation of the velocity patterns. (1996)

As an investigation into the mechanical factors that lead to rupture of abdominal aortic aneurysms, both color Doppler flow imaging and laser Doppler velocimetry measurements of steady flow through a series of aneurysm models are presented. The flow pattern in each model consisted of a core of relatively fast-moving fluid traveling through the center of the dilation, surrounded by an outer annulus of slowly recirculating fluid. At flow rates below a Reynolds number of 1750 +/- 150, the flow was smooth, steady, and laminar. At higher flow rates (Reynolds number above 2250 +/- 250), the flow was always irregular and turbulent. Between these fully laminar and fully turbulent regimes the flow was intermittently turbulent. Larger models showed a tendency to become turbulent at lower Reynolds numbers than smaller models. In addition, turbulence was amplified in the distal half of the model dilation, with the largest models producing velocity fluctuations as great as 35% of the time-average centerline velocities. These data suggest that larger aneurysms in vivo may be subject to more frequent and intense turbulence than smaller aneurysms. Concomitantly, increased turbulence may contribute significantly to risk of rupture, as is discussed in Part II.