gebhart/patrepeval huggingface dataset:
Identification of the Immediate-Early Transcripts of Kaposi’s Sarcoma-Associated Herpesvirus (1999)

In the immediate-early phase of reactivation or primary infection, herpesviruses express a small number of genes without requiring prior viral protein synthesis. Immediate-early genes usually encode regulatory proteins critical for the viral life cycle. Kaposi's sarcoma-associated herpesvirus (KSHV) gene transcription in the immediate-early stage of viral reactivation was examined by using a chemical induction combined with a gene expression screening method. RNA transcripts from at least four KSHV genomic loci accumulate when latently infected B-lymphoma cells are induced for reactivation in the presence of an inhibitor of protein synthesis (cycloheximide) and thus represent immediate-early class transcripts. Among them, a 3.6-kb mRNA encodes three putative open reading frames (ORFs), namely, ORF50, K8, and K8.2. ORF50 is a homologue of Rta, a transcription activator encoded by Epstein-Barr virus (EBV). The K8 gene codes for a 237-amino-acid protein with a basic-leucine zipper domain near its C terminus and an acidic domain near its N terminus and which closely resembles the ZEBRA protein of EBV and Jun/Fos family proteins. Other immediate-early mRNAs of KSHV include a 1. 7-kb mRNA encoding ORF45, a 2.0-kb mRNA encoding ORF K4.2, and a 4. 5-kb mRNA. Functional roles of products of these KSHV immediate-early transcripts remain to be studied.
Impact of percutaneous oestradiol gels in postmenopausal hormone replacement therapy on clinical symptoms and endometrium (1997)

This trial confirmed that, when the two oestradiol gels tested were administered cyclically with nomegestrol acetate to postmenopausal women, they were well tolerated, effective and suitable for the treatment of oestrogen deficiency syndrome.
Residential Framing: A Homebuilder's Construction Guide (1993)

Opens the subject to anyone...starts out with detailed coverage of standard building materials and up-to-date how-to information about modern power tools and safety requirements...explores all the standard framing methods for floors, walls, ceilings and roofs...demystifies some of the more obscure tasks, such as building gable dormers, multiple-pitched roofs, staircase construction and structural foundations. There's even a section devoted to post-and-beam construction. The book concludes with a discussion about door and window installation, exterior siding and interior finishing.-- Popular Mechanics. 320 pages, 654 b/w illus., 8 1/4 x 11.
Estimation of genetic parameters and genome scan for 15 semen characteristics traits of Holstein bulls (2009)

A QTL detection experiment was performed in French dairy cattle to search for QTL related to male fertility. Ten families, involving a total of 515 bulls, were phenotyped for ejaculated volume and sperm concentration, number of spermatozoa, motility, velocity, percentage of motile spermatozoa after thawing and abnormal spermatozoa. A set of 148 microsatellite markers were used to realize a genome scan. First, genetic parameters were estimated for all traits. Semen production traits were found to have moderate heritabilities (from 0.15 to 0.30) while some of the semen quality traits such as motility had high heritabilities (close to 0.60). Genetic correlations among traits showed negative relationships between volume and concentration and between volume and most quality traits such as motility or abnormal sperm while correlations between concentration and these traits were rather favourable. Percentages of abnormal sperm were negatively related to quality traits, especially with motility and velocity of spermatozoa. Three QTL related to abnormal sperm frequencies were significant at p < 0.01. In total, 11 QTL (p < 0.05) were detected. However, the number of QTL detected was within the range of expected false positives. Because of the lack of power to find QTL in this design further analyses are required to confirm these QTL.
Parasporin, a Human Leukemic Cell-Recognizing Parasporal Protein of <i>Bacillus thuringiensis</i> (2000)

An unusual property, human leukemic cell-recognizing activity, associated with parasporal inclusions of a noninsecticidal Bacillus thuringiensis soil isolate was investigated, and a protein (named parasporin in this study) responsible for the activity was cloned. The parasporin, encoded by a gene 2,169 bp long, was a polypeptide of 723 amino acid residues with a predicted molecular weight of 81, 045. The sequence of parasporin contained the five conserved blocks commonly found in B. thuringiensis Cry proteins; however, only very low homologies (<25%) between parasporin and the existing classes of Cry and Cyt proteins were detected. Parasporin exhibited cytocidal activity only when degraded by proteases into smaller molecules of 40 to 60 kDa. Trypsin and proteinase K activated parasporin, while chymotrypsin did not. The activated parasporin showed strong cytocidal activity against human leukemic T cells (MOLT-4) and human uterus cervix cancer cells (HeLa) but not against normal T cells.
Intact proinsulin and beta-cell function in lean and obese subjects with and without type 2 diabetes. (1999)

Increased secretory demand from obesity-associated insulin resistance cannot explain elevated intact proinsulin and disproportionate hyperproinsulinemia in type 2 diabetes. This abnormality may be an integrated part of pancreatic beta-cell dysfunction in this disease.
Pseudomonas syringae Infection Assays in Arabidopsis (2013)

Pseudomonas syringae pv. tomato DC30000 (Pst DC3000) infection of Arabidopsis thaliana has been widely used to elucidate many of the general principles underlying the plant immune response and bacterial pathogenesis. Study of Pst DC3000 virulence factors has also proven useful in the discovery and elucidation of fundamental mechanisms in plant biology. In particular, Pst DC3000 produces a phytotoxin, coronatine, that is a remarkable molecular mimic of the active form of the plant hormone jasmonate. Here we illustrate several common methods used for Pst DC3000-based assays, including preparation of Pst DC3000 inocula, inoculation of soil-grown Arabidopsis plants, and subsequent bacterial quantification in planta. We also describe how Pst DC3000 infection can be applied to study gene expression and protein degradation associated with jasmonate signaling.
Histamine H3 receptors: an overview. (1992)

Histamine H3 receptors represent a new class of prejunctional receptors, which, first described as modulators of histamine synthesis and release in the central nervous system, were subsequently found to occur also in peripheral tissues. They may behave both as autoreceptors located in histaminergic neurons and as heteroreceptors localized in adrenergic, cholinergic, serotoninergic and NANC nerve endings. As far as the gastrointestinal tract is concerned, H3 receptors seem to negatively control gastric acid secretion induced by endogenous cholinergic stimuli as well as gastrointestinal motility, as observed in different isolated preparations electrically stimulated. So far experimental evidence suggests that these receptors are absent in the effector organs. The most selective agonist and antagonist of H3 receptors are (R) alpha-methylhistamine and thioperamide, respectively; however, a lot of similar compounds are being synthesized in a few laboratories. It is easy to foresee that in the near future the availability of such substances will help the investigators in enlarging our knowledge in this interesting field.
Biomarker Evidence for a Major Preservation Pathway of Sedimentary Organic Carbon (2006)

Hydrogenation processes leading from biomolecules to fossil biomarkers in anoxic sediments are crucial for the preservation of organic matter. However, these processes are still poorly understood. The present identification of several reduced carotenoids in recent sediments attests that these processes operate at the earliest stages of diagenesis without structural or stereochemical specificity, implying a nonbiological reduction pathway. Sulfur species (e.g., H2S) are the hydrogen donors involved in such reduction, as demonstrated with laboratory experiments. These reactions allow the preservation of abundant organic carbon in the rock record.
Overcoming Forgetting in Federated Learning on Non-IID Data (2019)

We tackle the problem of Federated Learning in the non i.i.d. case, in which local models drift apart, inhibiting learning. Building on an analogy with Lifelong Learning, we adapt a solution for catastrophic forgetting to Federated Learning. We add a penalty term to the loss function, compelling all local models to converge to a shared optimum. We show that this can be done efficiently for communication (adding no further privacy risks), scaling with the number of nodes in the distributed setting. Our experiments show that this method is superior to competing ones for image recognition on the MNIST dataset.
How reliable are the results from functional magnetic resonance imaging? (2010)

Functional magnetic resonance imaging (fMRI) is one of the most important methods for in vivo investigation of cognitive processes in the human brain. Within the last two decades, an explosion of research has emerged using fMRI, revealing the underpinnings of everything from motor and sensory processes to the foundations of social cognition. While these results have revealed the potential of neuroimaging, important questions regarding the reliability of these results remain unanswered. In this paper, we take a close look at what is currently known about the reliability of fMRI findings. First, we examine the many factors that influence the quality of acquired fMRI data. We also conduct a review of the existing literature to determine if some measure of agreement has emerged regarding the reliability of fMRI. Finally, we provide commentary on ways to improve fMRI reliability and what questions remain unanswered. Reliability is the foundation on which scientific investigation is based. How reliable are the results from fMRI?
Rethinking Ramoplanin:  The Role of Substrate Binding in Inhibition of Peptidoglycan Biosynthesis (2002)

Ramoplanin is a cyclicdepsipeptide antibiotic that inhibits peptidoglycan biosynthesis. It was proposed in 1990 to block the MurG step of peptidoglycan synthesis by binding to the substrate of MurG, Lipid I. The proposed mechanism of MurG inhibition has become widely accepted even though it was never directly tested. In this paper, we disprove the accepted mechanism for how ramoplanin functions, and we present an alternative mechanism. This work has implications for the design of ramoplanin derivatives and may influence how other proposed substrate binding antibiotics are studied.
The Vibrio parahaemolyticus Type III Secretion Systems manipulate host cell MAPK for critical steps in pathogenesis (2010)

This study demonstrated that V. parahaemolyticus activates the three major MAPK signalling pathways in intestinal epithelial cells in a TTSS1-dependent manner that involves the TTSS1 effector VP1680. Furthermore VP1680 and JNK and ERK activation were needed for maximal cytotoxicity of the bacterium. It was shown that V. parahaemolyticus is a strong inducer of IL-8 secretion and that induction reflects a balance between the effects of TTSS1 and TTSS2. Increases in IL-8 secretion were mediated by TTSS1 and VP1680, and augmented by ERK activation. These results shed light on the mechanisms of bacterial pathogenesis mediated by TTSS and suggest significant roles for MAPK signalling during infection with V. parahaemolyticus.
Extent of Hypoattenuation on CT Angiography Source Images Predicts Functional Outcome in Patients With Basilar Artery Occlusion (2008)

The CTASI pc-ASPECTS score may identify BAO patients unlikely to have a favorable outcome despite recanalization.
Vibration energy harvester with low resonant frequency based on flexible coil and liquid spring (2016)

This paper reports an electromagnetic vibration-energy harvester with low resonant frequency based on liquid spring composed of ferrofluid. Cylinder magnet array formed by four disc NdFeB magnets is suspended by ferrofluid in a laser-machined acrylic tube which is wrapped by flexible planar coil fabricated with microfabrication process. The magnet array and coil are aligned automatically by the ferrofluid. Restoring force when the magnet array is deviated from the balance position is proportional to the deviated distance, which makes the ferrofluid work as a liquid spring obeying Hook's law. Experimental results show that the electromagnetic energy harvester occupying 1.8 cc and weighing 5 g has a resonant frequency of 16 Hz and generates an induced electromotive force of Vrms = 2.58 mV (delivering 79 nW power into matched load of 21 Ω) from 3 g acceleration at 16 Hz.
MMISH: Multicolor microRNA in situ hybridization for paraffin embedded samples (2018)

To understand and assess the roles of miRNAs, visualization of the expression patterns of specific miRNAs is needed at the cellular level in a wide variety of different tissue types. Although miRNA <i>in situ</i> hybridization techniques have been greatly improved in recent years, they remain difficult to routinely perform due to the complexity of the procedure. In addition, as it is crucial to define which tissues or cells are expressing a particular miRNA in order to elucidate the biological function of the miRNA, incorporation of additional stainings for different cellular markers is necessary. Here, we describe a robust and flexible multicolor miRNA <i>in situ</i> hybridization (MMISH) technique for paraffin embedded sections. We show that the miRNA <i>in situ</i> protocol is sensitive and highly specific and can successfully be combined with both immunohistochemical and immunofluorescent stainings.
Inhibition of Poly(ADP-Ribose) Polymerase Attenuates Acute Kidney Injury in Sodium Taurocholate-Induced Acute Pancreatitis in Rats (2012)

Our results suggest that PARP activation may contribute to kidney injury and that PARP inhibitors may be beneficial in renal disorders associated with severe acute pancreatitis.
Test generation for synchronous sequential circuits to reduce storage requirements (2002)

The use of appropriate storage schemes for test patterns and test responses on a tester may result in reduced memory requirements, and thus reduced tester cost. Such storage schemes result in new test compaction objectives beyond the need to reduce the number of test patterns as much as possible. We propose test generation procedures that take such test compaction objectives into account. Experimental results are presented to demonstrate the effectiveness of the proposed procedures in reducing the storage requirements of the resulting test sequences.
Effect of electrical stimulation on blood flow velocity and vessel size (2017)

Interferential current electrical stimulation alters blood flow velocity and vessel size. We aimed to investigate the changes in the autonomic nervous system depending on electrical stimulation parameters. Forty-five healthy adult male and female subjects were studied. Bipolar adhesive pad electrodes were used to stimulate the autonomic nervous system at the thoracic vertebrae 1-4 levels for 20 min. Using Doppler ultrasonography, blood flow was measured to determine velocity and vessel size before, immediately after, and 30 min after electrical stimulation. Changes in blood flow velocity were significantly different immediately and 30 min after stimulation. The interaction between intervention periods and groups was significantly different between the exercise and pain stimulation groups immediately after stimulation (p<0.05). The vessel size was significantly different before and 30 min after stimulation (p<0.05). Imbalances in the sympathetic nervous system, which regulates balance throughout the body, may present with various symptoms. Therefore, in the clinical practice, the parameters of electrical stimulation should be selectively applied in accordance with various conditions and changes in form.
A study of growth and the relaxation of elastic strain in MgO on Fe(001) (1996)

The deposition of MgO on the Fe(001) surface at room temperature and at elevated temperatures has been carried out using molecular beam epitaxy (MBE). MgO is observed to grow epitaxially with a 45° rotation between the Fe(001) and MgO(001) unit cell axes. The growth mode has been studied as a function of temperature using reflection high-energy electron diffraction (RHEED), while the chemical and structural characteristics of the MgO film have been studied using Auger electron spectroscopy and high resolution electron microscopy. The relaxation of the in-plane lattice parameter during growth at room temperature has been measured in situ using RHEED and ex situ using glancing incidence x-ray diffraction and during growth at elevated temperatures by means of RHEED. Pseudomorphic growth is observed up to a thickness of 4–5 monolayers, after which the in-plane lattice parameter starts to evolve towards the MgO bulk parameter as 1/2〈011〉 misfit dislocations are introduced at the Fe/MgO interface. The degree of relaxation as a function of epilayer thickness is compared with that expected for an equilibrium dislocation spacing in an array of dislocations of alternating orientation, and with that predicted by Freund’s criterion for the blocking of a threading segment by an orthogonal misfit dislocation [J. Appl. Phys. 68, 2073 (1990)].
A point mutation in the murine <i>Hem1</i> gene reveals an essential role for Hematopoietic Protein 1 in lymphopoiesis and innate immunity (2008)

Hem1 (Hematopoietic protein 1) is a hematopoietic cell-specific member of the Hem family of cytoplasmic adaptor proteins. Orthologues of Hem1 in Dictyostelium discoideum, Drosophila melanogaster, and Caenorhabditis elegans are essential for cytoskeletal reorganization, embryonic cell migration, and morphogenesis. However, the in vivo functions of mammalian Hem1 are not known. Using a chemical mutagenesis strategy in mice to identify novel genes involved in immune cell functions, we positionally cloned a nonsense mutation in the Hem1 gene. Hem1 deficiency results in defective F-actin polymerization and actin capping in lymphocytes and neutrophils caused by loss of the Rac-controlled actin-regulatory WAVE protein complex. T cell development is disrupted in Hem1-deficient mice at the CD4(-)CD8(-) (double negative) to CD4(+)CD8(+) (double positive) cell stages, whereas T cell activation and adhesion are impaired. Hem1-deficient neutrophils fail to migrate in response to chemotactic agents and are deficient in their ability to phagocytose bacteria. Remarkably, some Rac-dependent functions, such as Th1 differentiation and nuclear factor kappaB (NF-kappaB)-dependent transcription of proinflammatory cytokines proceed normally in Hem1-deficient mice, whereas the production of Th17 cells are enhanced. These results demonstrate that Hem1 is essential for hematopoietic cell development, function, and homeostasis by controlling a distinct pathway leading to cytoskeletal reorganization, whereas NF-kappaB-dependent transcription proceeds independently of Hem1 and F-actin polymerization.
Intrinsic 2D/3D registration based on a hybrid approach: use in the radiosurgical imaging process. (2007)

During the latest years, numerous methods of multimodal image matching have been developed. Associated with medical imaging, these developments make it possible to match images using intrinsic data, as anatomical data, instead of external referential, as stereotactic frames. Thus, the use of intrinsic registration considerably increases possibilities in medical image analysis. Unfortunately, these techniques mostly remain in the research field and are rarely used in clinical daily practice. In this paper, we present a method for matching projective imaging (2D, radiography, angiography...) and tomographic imaging (3D, Magnetic Resonance Imaging, Computed Tomography). Furthermore, we propose a radiosurgical application for Arteriovenous Malformation (AVM). Radiosurgery planning for the treatment of AVM requires multiple image acquisitions in multimodality to define the irradiation target and to compute the dosimetry. All the planning images are acquired with a stereotactic frame. We describe in this paper the image registration technique that we propose to include diagnostic images in the planning process and the different steps required to validate our approach. In the current state, the results obtained do not enable us to replace the conventional technique due to the accuracy expected, but the analysis of the results shows that improvements of the protocol would make this application finally operational.
Dentin‐specific proteins in MDPC‐23 cell line (1998)

Only four established odontoblast-like cell lines have been reported in the literature (1-6). Of the four, only two synthesize dentin-specific proteins. These studies report that the cell line MO6-G3 synthesizes phosphophoryn (DPP), dentin sialoprotein (DSP) and dentin matrix protein-1 (DMP-1) while MDPC-23 synthesizes DSP, but not DMP-1. The objective of the present study was to determine whether polyclonal antibodies to rat DSP and DPP would label odontoblasts on microscopic sections of day-19 fetal mouse incisor odontoblasts as well as cultured cells of the MDPC-23 cell line. The spontaneously immortalized MDPC-23 cell line was derived from fetal mouse molar papillae, made continuous by the 3T6 method and cloned by dilution. These cultures have been passaged 77 times after cloning, form multilayered nodules, and have high alkaline phosphatase activity. The data show positive reactivity in odontoblasts in 19-d mouse fetal incisors as well as in cultures of MDPC-23 cells by fluorescence and confocal microscopy. In addition, these cultures were characterized by phase microscopy and scanning and transmission electron microscopy. These findings suggest that MDPC-23 cells are of the odontoblast lineage.
Robust Modeling With Erratic Data (1973)

Abstract An attractive alternative to least-squares data modeling techniques is the use of absolute value error criteria. Unlike the least-squares techniques the inclusion of some infinite blunders along with the data will hardly affect the solution to an otherwise well-posed problem. An example of this great stability is seen when an average is, determined by using the median rather than the arithmetic mean. Algorithms for absolute error minimization are often approximately as costly as least-squares algorithms; however, unlike least-squares, they naturally lend themselves to inequality or bounding constraints on models.
Structural Basis of Biological NO Generation by Octaheme Oxidoreductases (2013)

Nitric oxide is an important molecule in all domains of life with significant biological functions in both pro- and eukaryotes. Anaerobic ammonium-oxidizing (anammox) bacteria that contribute substantially to the release of fixed nitrogen into the atmosphere use the oxidizing power of NO to activate inert ammonium into hydrazine (N2H4). Here, we describe an enzyme from the anammox bacterium Kuenenia stuttgartiensis that uses a novel pathway to make NO from hydroxylamine. This new enzyme is related to octaheme hydroxylamine oxidoreductase, a key protein in aerobic ammonium-oxidizing bacteria. By a multiphasic approach including the determination of the crystal structure of the K. stuttgartiensis enzyme at 1.8 Å resolution and refinement and reassessment of the hydroxylamine oxidoreductase structure from Nitrosomonas europaea, both in the presence and absence of their substrates, we propose a model for NO formation by the K. stuttgartiensis enzyme. Our results expand the understanding of the functions that the widespread family of octaheme proteins have.
HbA1c Measurement Improves the Detection of Type 2 Diabetes in High-Risk Individuals With Nondiagnostic Levels of Fasting Plasma Glucose (2001)

Diagnostic criteria based on FPG criteria are relatively insensitive in the detection of early type 2 diabetes in at-risk subjects. HbA1c measurement improves the sensitivity of screening in high-risk individuals.