gebhart/patrepeval huggingface dataset:
Hypoxia causes connexin 43 internalization in neonatal rat ventricular myocytes (2010)

Gap junctions produce low resistance pathways between cardiomyocytes and are major determinants of electrical conduction in the heart. Altered distribution and function of connexin 43 (Cx43), the major gap junctional protein in the ventricles, can slow conduction, and thus contribute to arrhythmogenesis in experimental models such as ischemic rat heart and pacing-induced atrial fibrillation. The mechanisms underlying reduced gap junctional density and conductance during ischemia may involve decreased Cx43 synthesis, increased degradation and/or Cx43 migration into areas which do not contribute to intercellular communication. To test more rigorously the hypothesis that hypoxia resulting from ischemia causes Cx43 internalization, we infected neonatal rat ventricular myocytes (NRVM) with a Cx43-GFP chimera, which enabled us to investigate by means of confocal microscopy the effect of hypoxia (1% O2 for 5 h) on Cx43 distribution in live cardiomyocytes. Importantly, this protocol permitted each culture to serve as its own control. To this end we used life confocal microscopy analysis to determine in the same pair of myocytes the effects of hypoxia on Cx43-GFP distribution at the gap junctional (GJ) and non-GJ areas. In support of this hypothesis, we found that compared to normoxia, 5 h of hypoxia reduced the Cx43-GFP signal at the GJ areas (defined as the border area) and caused a corresponding increase in the Cx43-GFP signal at the non-border areas, thus providing an additional explanation for the intercellular uncoupling during ischemic conditions.
Polymerization of methyl methacrylate with achiral 4B group metallocene compounds (1995)

Abstract Methyl methacrylate (MMA) was polymerized with Cp 2 ZrCl 2 / methylalyminoxane or Cp 2 M(CH 3) 2 (M: Zr, Hf; Cp = cyclopentadienyl) combined with B(C 6 F 5 ) 3 ( 1 ) or Ph 3 CB(C 6 F 5 ) 4 ( 2 ), (Ph = phenyl). in the presence of a Lewis acid like Zn(C 2 H 5 ) 2 with slow inititation, which gave syndiotactic‐rich poly(methyl methacrylate) (PMMA) with high molecular weight. The polymer yield increases with polymerization time, which indicates that the propagation rate is zero order in concentration of monomer. The polymer yield increases also with concentration of Cp 2 Zr(CH 3 ) 2 . 2 , which indicates the zirconocene to be the real catalyst. The polymer yield and the initiation efficiency (N/ [Zr]) increase with the concentration of Zn(C 2 H 5 ) 2, which indicates Zn(C 2 H 5 ) 2 , to be involved in the initiation. It is also shown that the propagation reaction is independent of the concentration of Zn(C 2 H 5 ) 2 .
A Hybrid Approach to Arbitrate Tag Collisions in RFID systems (2007)

In this paper, we propose a new hybrid approach based on query tree protocol to arbitrate tag collisions in RFID systems. The hybrid query tree protocol that combines a tree based query protocol with a slotted backoff mechanism. The proposed protocol decreases the average identification delay by reducing collisions and idle time. To reduce collisions, we use a 4-ary query tree instead of a binary query tree. To reduce idle time, we introduce a slotted backoff mechanism to reduce the number of unnecessary Query commands. Simulation and numerical analysis reveal that the proposed protocol achieves lower identification delay than existing tag collision arbitration protocols.
Self-correction of nonlinear sweep of tunable laser source in OFDR (2019)

Nonlinear laser wavelength tuning effects appear as phase noise in wavelength swept interferometry. A new method is proposed to compensate tuning nonlinear effects in optical frequency domain reflectometry (OFDR). The proposed method is simpler in configuration, and unlike conventional nonlinear compensation methods, it does not require separate auxiliary interferometer detection, which eliminates the need for an extra photo detector and an acquisition channel for the auxiliary interferometer. In the proposed method, an intentional beating signal is introduced in the beginning of the OFDR spectrum which is treated as an auxiliary interferometer to acquire tunable laser phase information for post signal processing. The proposed method can reduce overall OFDR system cost, reduce the data acquisition time and computational load by half, and make system configuration simpler by eliminating the need for extra components. Feasibility of the proposed method was demonstrated by compensating for tuning nonlinearity effects in an optical fiber approximately 35 m long with a measured spatial resolution of ~30 &mu;m. To confirm performance of the proposed method, a comparison was carried out with a conventional nonlinear tuning compensation method, which requires the separate auxiliary interferometer. Moreover, distributed sensing using the proposed method was also demonstrated in an optical fiber approximately 35 m in length by performing strain sensing with 3 cm sensing resolution.
Comparison of Simulated and Experimental Order Parameters in FePt—II (2011)

Eight FePt thin film specimens of various thicknesses, compositions, and order parameters have been analyzed to determine the robustness and fidelity of multislice simulations in determining the chemical order parameter via electron diffraction (ED). The shape of the simulated curves depends significantly on the orientation and thickness of the specimen. The ED results are compared to kinematical scattering order parameters, from the same films, acquired from synchrotron X-ray diffraction (XRD). For the specimens analyzed with convergent beam electron diffraction conditions, the order parameter closely matched the order parameter as determined by the XRD methodology. However, the specimens analyzed by selected area electron diffraction conditions did not show good agreement. This has been attributed to substrate effects that hindered the ability to accurately quantify the intensity values of the superlattice and fundamental reflections.
Intestinal Bacteria Maintain Adult Enteric Nervous System and Nitrergic Neurons via Toll-like Receptor 2-induced Neurogenesis in Mice (2020)

Abstract Background &amp; Aims The enteric nervous system (ENS) exists in close proximity to luminal bacteria. Intestinal microbes regulate ENS development, but little is known about their effects on adult enteric neurons. We investigated whether intestinal bacteria or their products affect the adult ENS via toll like receptors (TLRs) in mice. Methods We performed studies with conventional C57/BL6, germ-free C57/BL6, Nestin -creER T2 :tdTomato, Nestin -GFP, and ChAT-cre:tdTomato. Mice were given drinking water with ampicillin or without (controls). Germ-free mice were given drinking water with TLR2 agonist or without (controls). Some mice were given a blocking antibody against TLR2 or a TLR4 inhibitor. We performed whole-gut transit, bead latency, and geometric center studies. Feces were collected and analyzed by 16S rRNA gene sequencing. Longitudinal muscle myenteric plexus (LMMP) tissues were collected, analyzed by immunohistochemistry, and levels of nitric oxide were measured. Cells were isolated from colonic LMMP of Nestin -creER T2 :tdTomato mice and incubated with agonists of TLR2 (receptor for Gram-positive bacteria), TLR4 (receptor for Gram-negative bacteria), or distilled water (control) andd analyzed by flow cytometry. Results Stool from mice given ampicillin had altered composition of gut microbiota with reduced abundance of Gram-positive bacteria and increased abundance of Gram-negative bacteria, compared with mice given only water. Mice given ampicillin had reduced colon motility compared with mice given only water, and their colonic LMMP had reduced numbers of nitrergic neurons, reduced nNOS production, and reduced colonic neurogenesis. Numbers of colonic myenteric neurons increased after mice were switched from ampicillin to plain water, with increased markers of neurogenesis. Nestin-positive ENPCs expressed TLR2 and TLR4. In cells isolated from the colonic LMMP, incubation with the TLR2 agonist increased the percentage of neurons originating from ENPCs to approximately 10%, compared to approximately 0.01% in cells incubated with the TLR4 agonist or distilled water. Mice given an antibody against TLR2 had prolonged whole-gut transit times; their colonic LMMP had reduced total neurons and a smaller proportion of nitrergic neurons per ganglion, and reduced markers of neurogenesis compared with mice given saline. Colonic LMMP of mice given the TLR4 inhibitor did not have reduced markers of neurogenesis. Colonic LMMP of germ-free mice given TLR2 agonist had increased neuronal numbers compared with control germ-free mice. Conclusions In the adult mouse colon, TLR2 promotes colonic neurogenesis, regulated by intestinal bacteria. Our findings indicate that colonic microbiota help maintain the adult ENS via a specific signaling pathway. Pharmacologic and probiotic approaches directed towards specific TLR2 signaling processes might be developed for treatment of colonic motility disorders related to use of antibiotics or other factors.
Serum leptin concentration, obesity, and insulin resistance in Western Samoans: cross sectional study (1996)

The strong relation of leptin with obesity is consistent with leptin production being proportional of mass to adipose tissue. The relation with insulin independent of body mass index suggests a possible role for leptin in insulin resistance or hyperinsulinaemia.
Effective exploration strategies for the construction of visual maps (2004)

We consider the effect of exploration policy in the context of the autonomous construction of a visual map of an unknown environment. Like other concurrent mapping and localization (CML) tasks, odometric uncertainty poses the problem of introducing distortions into the map which are difficult to correct without costly on-line or post-processing algorithms. Our problem is further compounded by the implicit nature of the visual map representation, which is designed to accommodate a wide variety of visual phenomena without assuming a particular imaging platform, thereby precluding the inference of scene geometry. Such a representation presents a requirement for a relatively dense sampling of observations of the environment in order to produce reliable models. Our goal is to develop an online policy for exploring an unknown environment which minimizes map distortion while maximizing coverage. We do not depend on costly post-hoc expectation maximization approaches to improve the output, but rather employ extended Kalman filter (EKF) methods to localize each observation once, and rely on the exploration policy to ensure that sufficient information is available to localize the successive observations. We present an experimental analysis of a variety of exploratory policies, in both simulated and real environments, and demonstrate that with an effective policy an accurate map can be constructed.
Carbon monoxide‐induced axial skeletal dysmorphogenesis in the chick embryo (2003)

We hypothesize that the somitic defects and the resulting axial skeletal dysmorphogenesis are caused by disrupted neural tube or ectoderm functions related to somite formation and maintenance. We also hypothesize that CO-induced dysmorphogenesis at this critical period of somitogenesis is caused by the overabundance of CO acting endogenously as a cellular signal, while coincidentally exerting its influence as a toxicant of oxygen delivery or utilization.
Multi-Pose Fusion for Sparse-View CT Reconstruction Using Consensus Equilibrium (2022)

CT imaging works by reconstructing an object of interest from a collection of projections. Traditional methods such as filtered-back projection (FBP) work on projection images acquired around a fixed rotation axis. However, for some CT problems, it is desirable to perform a joint reconstruction from projection data acquired from multiple rotation axes. In this paper, we present Multi-Pose Fusion, a novel algorithm that performs a joint tomographic reconstruction from CT scans acquired from multiple poses of a single object, where each pose has a distinct rotation axis. Our approach uses multi-agent consensus equilibrium (MACE), an extension of plug-and-play, as a framework for integrating projection data from different poses. We apply our method on simulated data and demonstrate that Multi-Pose Fusion can achieve a better reconstruction result than single pose reconstruction.
Materials for thermoelectric energy conversion (2023)

A thermoelectric power generation (TEG) unit configured to be integrated into the exhaust system of a vehicle includes a plurality of thermoelectric power generator modules, each comprising an electrically interconnected plurality of p-type and n-type thermoelectric material legs, each leg extending between a substrate on a hot side and a substrate on a cold side of the module, wherein the thermoelectric materials for the legs are half-Heusler compounds having a thermoelectric figure of merit (ZT) greater than 1.0.
Improving Web Search Ranking by Incorporating User Behavior (2006)

We show that incorporating user behavior data can significantly improve ordering of top results in real web search setting. We examine alternatives for incorporating feedback into the ranking process and explore the contributions of user feedback compared to other common web search features. We report results of a large scale evaluation over 3,000 queries and 12 million user interactions with a popular web search engine. We show that incorporating implicit feedback can augment other features, improving the accuracy of a competitive web search ranking algorithms by as much as 31% relative to the original performance.
Emerging From the Unknown: Structural and Functional Features of Agnoprotein of Polyomaviruses (2016)

Agnoprotein is an important regulatory protein of polyomaviruses, including JCV, BKV, and SV40. In the absence of its expression, these viruses are unable to sustain their productive life cycle. It is a highly basic phosphoprotein that localizes mostly to the perinuclear area of infected cells, although a small amount of the protein is also found in nucleus. Much has been learned about the structure and function of this important regulatory protein in recent years. It forms highly stable dimers/oligomers in vitro and in vivo through its Leu/Ile/Phe-rich domain. Structural NMR studies revealed that this domain adopts an alpha-helix conformation and plays a critical role in the stability of the protein. It associates with cellular proteins, including YB-1, p53, Ku70, FEZ1, HP1α, PP2A, AP-3, PCNA, and α-SNAP; and viral proteins, including small t antigen, large T antigen, HIV-1 Tat, and JCV VP1; and significantly contributes the viral transcription and replication. This review summarizes the recent advances in the structural and functional properties of this important regulatory protein. J. Cell. Physiol. 231: 2115-2127, 2016. © 2016 Wiley Periodicals, Inc.
Artificial Intelligence for Drug Discovery: Are We There Yet? (2023)

Drug discovery is adapting to novel technologies such as data science, informatics, and artificial intelligence (AI) to accelerate effective treatment development while reducing costs and animal experiments. AI is transforming drug discovery, as indicated by increasing interest from investors, industrial and academic scientists, and legislators. Successful drug discovery requires optimizing properties related to pharmacodynamics, pharmacokinetics, and clinical outcomes. This review discusses the use of AI in the three pillars of drug discovery: diseases, targets, and therapeutic modalities, with a focus on small-molecule drugs. AI technologies, such as generative chemistry, machine learning, and multiproperty optimization, have enabled several compounds to enter clinical trials. The scientific community must carefully vet known information to address the reproducibility crisis. The full potential of AI in drug discovery can only be realized with sufficient ground truth and appropriate human intervention at later pipeline stages.
Trans-activation of the long terminal repeat of human immunodeficiency virus type 1 by the parvovirus B19 NS1 gene product (1993)

Persistent parvovirus B19 infections in human immunodeficiency virus type 1 (HIV-1)-infected patients have been reported. The two viruses could share common target cells. The NS1 protein of B19 regulates B19 expression and we have investigated its possible effect on the long terminal repeat (LTR) of HIV-1. In transient transfection experiments, NS1 trans-activated the expression of reporter genes under the control of the HIV-1 LTR. The effect of NS1 was apparent only in the presence of the HIV-1 Tat protein, and required intact TAR and TATA box sequences.
Effects of roe deer browsing and site preparation on performance of planted broadleaved and conifer seedlings when using temporary fences (2009)

Abstract The effects of fencing and site preparation on performance of birch (Betula pendula Roth), oak (Quercus robur L.), pine (Pinus sylvestris L.) and spruce [Picea abies (L.) Karst.] seedlings were studied over four growing seasons in southern Sweden. The experiment was composed of four browsing treatments, from which roe deer (Capreolus capreolus L.) were excluded for 0, 12, 24 or 42 months, and four soil treatments. Natural browsing was combined with artificial browsing (clipping). It was demonstrated that browsing by roe deer could be isolated from browsing by moose (Alces alces L.) by selective fencing. Except for birch, browsing had little effect on seedling survival. Browsing reduced height growth by more than 100% for oak and pine, and more than 60% of pine seedling developed multiple stems. Except for oak, site preparation increased seedling survival. Inverting site preparation, in combination with or without fertilization, produced positive growth responses in seedlings, whereas patch scarification did not. There was no interaction between browsing and soil treatments on seedling performance. It was concluded that long-term protection against browsing by roe deer is needed for oak and pine, whereas short-term fences might be used for birch, and that spruce is relatively unaffected by browsing.
A new wireless communication platform for medium-voltage protection and control (2005)

Communication networks are becoming an increasingly important aspect of today's power transmission and distribution systems. Shrinking margins in power grid equipments call for new ways of reducing development and engineering costs while at the same time improving product performance and versatility. An innovative yet standard-compliant communication and control architecture supported by an integrated hardware solution is key to reach this target. As part of its R&D effort to provide better protection and control equipments, ABB is developing a new integrated communication platform-called e-breaker-for medium-voltage switchgears. Based on wireless technology and complying with the new international standard for substation communications, the e-breaker targets a 50% cut in engineering costs.
Comparison of ghosting effects for three commercial EPIDs (2006)

Many studies have reported dosimetric characteristics of amorphous silicon electronic portal imaging devices (EPIDs). Some studies ascribed a non-linear signal to gain ghosting and image lag. Other reports, however, state the effect is negligible. This study compares the signal-to-monitor unit (MU) ratio for three different brands of EPID systems. The signal was measured for a wide range of monitor units (5-1000), dose-rates, and beam energies. All EPIDs exhibited a relative under-response for beams of few MUs; giving 4 to 10% lower signal-to-MU ratios relative to that of 1000 MUs. This under-response is consistent with ghosting effects due to charge trapping.
Telotristat etiprate shows benefit in treating patients With carcinoid syndrome that is inadequately controlled by somatostatin analog therapy in the phase 3 TELESTAR clinical trial (2016)

Telotristat Etiprate Shows Benefit in Treating Patients With Carcinoid Syndrome That is Inadequately Controlled by Somatostatin Analog Therapy in the Phase 3 TELESTAR Clinical Trial
Isolation of Optically Targeted Single Bacteria by Application of Fluidic Force Microscopy to Aerobic Anoxygenic Phototrophs from the Phyllosphere (2013)

In their natural environment, bacteria often behave differently than they do under laboratory conditions. To gain insight into the physiology of bacteria in situ, dedicated approaches are required to monitor their adaptations and specific behaviors under environmental conditions. Optical microscopy is crucial for the observation of fundamental characteristics of bacteria, such as cell shape, size, and marker gene expression. Here, fluidic force microscopy (FluidFM) was exploited to isolate optically selected bacteria for subsequent identification and characterization. In this study, bacteriochlorophyll-producing bacteria, which can be visualized due to their characteristic fluorescence in the infrared range, were isolated from leaf washes. Bacterial communities from the phyllosphere were investigated because they harbor genes indicative of aerobic anoxygenic photosynthesis. Our data show that different species of Methylobacterium express their photosystem in planta, and they show a distinct pattern of bacteriochlorophyll production under laboratory conditions that is dependent on supplied carbon sources.
Mitosis detection of hematopoietic stem cell populations in time-lapse phase-contrast microscopy images (2012)

Understanding the heterogeneous behavior of hematopoietic stem cells (HSCs) is required for the expansion of the cells without loss of their regenerative capacity. As such, it is essential to establish their lineage relationships by tracking the history of individual cells in a cell population. However, the quality of lineage relationships is often degraded because of undetected or misdetected mitotic events, which lead to missed or inaccurate mother-daughter cell relationships. In this paper, we present an automated mitosis detection method for HSCs in time-lapse phase-contrast microscopy images. Since HSCs are nonadherent, i.e., free-floating in the culture medium, the method is distinguished from the recent mitosis detection methods developed for adherent cells that are attached to the surface of a petri dish. The proposed mitosis detection method detects individual cells in each image frame and subsequently tracks them over time and in so doing identifies newly appeared cells, each of which is considered as a candidate of a newborn cell. Each candidate is then examined to determine whether it is indeed a newborn cell based on temporal change of cell sizes of potential mother and daughter cells. Our method was quantitatively evaluated on 14 HSC populations, each of which is observed for four days, resulting in a precision of 97.4% and a recall of 96.6%.