gebhart/patrepeval huggingface dataset:
Challenges in the Therapeutic Use of a “So-Called” Universal Hemostatic Agent: Recombinant Factor VIIa (2006)

Recombinant factor VIIa (rFVIIa) was developed in the early 1990s to provide "bypassing" hemostatic therapy for hemophilia A and B patients with inhibitors. More recently, it has been licensed for use in patients with inherited deficiency of factor VII. Since it was licensed for use in hemophilia with inhibitors in the US, Europe, and other countries for these specific indications, it has been used selectively but in a wide array of clinical settings for uncontrolled hemorrhage in individuals without an inherited bleeding disorder. Many of these uses have been described in the medical literature as case reports or small, uncontrolled series. Several randomized clinical trials (RCT) for these "off-label" medical uses have been published in recent months and will serve as the focus of this review. In particular, a review of an RCT for spontaneous intracranial hemorrhage that has demonstrated clinical efficacy in reducing both mortality and volume of central nervous system hemorrhage will be offered. A brief discussion of hypothesized physiologic mechanisms of supraphysiologic doses of rFVIIa will introduce the clinical discussion of these broad off-label uses. Since rFVIIa is a very expensive therapy, possible strategies for optimizing its use in the these settings will be presented.
PROLONGED DETECTION OF HUMAN BOCAVIRUS DNA IN NASOPHARYNGEAL ASPIRATES OF CHILDREN WITH RESPIRATORY TRACT DISEASE (2009)

Increasing evidence suggests that the recently identified human bocavirus (hBoV) is a cause of acute respiratory illness. However, the duration of hBoV shedding from the respiratory tract as demonstrated by positive hBoV polymerase chain reaction is unclear. We describe the virologic and clinical characteristics of 6 immunocompetent children with hBoV persistence in the respiratory tract for up to 4.5 months.
Genome Sequence of Antibiotic-Producing Bacillus amyloliquefaciens Strain KCTC 13012 (2015)

We report the 4.0-Mb draft genome sequence of Bacillus amyloliquefaciens (syn. Bacillus velezensis) KCTC 13012, which exhibits a broad spectrum of antagonistic activity against bacteria and fungi and promotes plant growth as well. The genome contains an array of biosynthetic gene clusters for secondary metabolites that are comparable to those in Bacillus amyloliquefaciens subsp. plantarum FZB42(T).
Pixel-Adaptive Convolutional Neural Networks (2019)

Convolutions are the fundamental building block of CNNs. The fact that their weights are spatially shared is one of the main reasons for their widespread use, but it also is a major limitation, as it makes convolutions content agnostic. We propose a pixel-adaptive convolution (PAC) operation, a simple yet effective modification of standard convolutions, in which the filter weights are multiplied with a spatially-varying kernel that depends on learnable, local pixel features. PAC is a generalization of several popular filtering techniques and thus can be used for a wide range of use cases. Specifically, we demonstrate state-of-the-art performance when PAC is used for deep joint image upsampling. PAC also offers an effective alternative to fully-connected CRF (Full-CRF), called PAC-CRF, which performs competitively, while being considerably faster. In addition, we also demonstrate that PAC can be used as a drop-in replacement for convolution layers in pre-trained networks, resulting in consistent performance improvements.
Mouse Ly-49A Interrupts Early Signaling Events in Natural Killer Cell Cytotoxicity and Functionally Associates with the SHP-1 Tyrosine Phosphatase (1997)

The lytic activity of natural killer (NK) cells is inhibited by the expression of class I major histocompatibility complex (MHC) antigens on target cells. In murine NK cells, Ly-49A mediates inhibition of cytotoxicity in response to the class I MHC antigen H-2Dd. In this report, we studied the function of mouse Ly-49A in both the rat NK cell tumor line, RNK-16, transfected with Ly-49A cDNA, and in primary NK cells. We show that ligation of Ly-49A by H-2Dd inhibits early signaling events during target cell stimulation, including polyphosphoinositide turnover and tyrosine phosphorylation. We also show that Ly-49A directly associates with the cytoplasmic tyrosine phosphatase SHP-1, and that Ly-49A function is impaired in NK cells from SHP-1 mutant viable motheaten mice and from SHP-1-deficient motheaten mice. Finally, we demonstrate that mutational substitution of the tyrosine within the proposed SHP-1 binding motif in Ly-49A completely abrogates inhibition of NK cell cytotoxicity through this receptor. These results demonstrate that Ly-49A interrupts early activating signals in NK cells, and that SHP-1 is an important mediator of Ly-49A function.
BEHAB/brevican: a brain-specific lectican implicated in gliomas and glial cell motility (1998)

Several recent findings have advanced our understanding of the composition and function of the brain extracellular matrix (ECM). BEHAB/brevican, a recently identified CNS-specific proteoglycan, is a component of the brain ECM and is upregulated during glial cell motility. It is expressed at high levels during development, in response to injury, and in primary brain tumors. Cleavage of the BEHAB/brevican protein may increase invasion of tumor cells.
ChemInform Abstract: SYNTHESIS AND STRUCTURE OF (THIOACYL)HYDRAZONES (1984)

Abstract Es werden einige Thioacylhydrazone dargestellt ‐ die Verbindungen (III), (VI) und (VII) ‐ darunter die bisher nicht beschriebenen Thioacetyl‐ (VI) und Thioformylhydrazone (VII).
Clinical Gene Therapy for Neurodegenerative Diseases: Past, Present, and Future (2017)

Clinical gene therapy has made important advances over the last decade. Among neurological diseases, severe genetic neurodegenerative conditions have been the focus of initial clinical applications. Gene therapy has also addressed complex neurodegenerative diseases, particularly Parkinson's disease, with encouraging results in human patients, demonstrating that specific targeting of central nervous system (CNS) cells is a relevant strategy for severe pathologies and that efficient access to the CNS with viral vectors is an achievable goal. The purpose of this review is to summarize the gene therapy clinical applications that have been conducted for neurodegenerative diseases. Limitations and hurdles to obtain and demonstrate benefit in patients, and the new developments that should allow new clinical applications with high beneficial potential are discussed.
(ω–2) Hydroxylation of Fatty Acids by a Soluble System from Bacillus megaterium (1974)

Abstract A cell-free hydroxylating system which acts on long chain fatty acids has been isolated from Bacillus megaterium. When palmitic acid is used as a substrate, the major product is 14-hydroxypalmitate (about 50% of the total) while 15-hydroxypalmitate (30%) and 13-hydroxypalmitate (20%) are also produced. No 16-hydroxypalmitate is formed in this system. The effect of substrate chain length on hydroxylation activity was tested with various saturated fatty acids. The relative activity of the hydroxylase with the substrates tested was as follows: C15 (1.00), C16 (0.89), C14 (0.72), C17 (0.34), C18 (0.17), and C12 (0.08). When the distributions of isomeric hydroxy acids formed from C18 and C14 were determined, it was found that the major product from C18 was the (ω - 2) derivative with the (ω - 1) and (ω - 3) components being present in about the same ratio as for palmitate. Myristic acid, however, gave approximately equal amounts of the three isomers, with the (ω - 1) derivative being slightly favored. In neither case was the ω-hydroxy acid detected among the products. Several monounsaturated fatty acids were also tested and were found to be more active as substrates than their saturated analogs of the same chain length. The hydroxylation system is soluble and, in crude form, appears to be quite stable and active. All of the hydroxylase activity remains in the supernatant when a cell-free preparation from B. megaterium is centrifuged at 100,000 x g for 2 hours. Free palmitic acid is a much better substrate than the CoA derivative. Both NADPH and O2 are required for hydroxylase activity but no other non-protein cofactor seems to be involved. The hydroxylation activity is stable to dialysis but decreases to about 20 to 25% of the original level when the 100,000 x g supernatant is passed through Sephadex G-25, presumably due to the loss of a small protein component. The activity can be restored completely by the addition of bacterial ferredoxin to the gel-filtered preparation, but the preparation is no longer stable to freezing and thawing or further chromatographic procedures. The endogenous component for which ferredoxin substitutes is not removed by (NH4)2SO4 fractionation of the 100,000 x g supernatant protein followed by Sephadex G-200 chromatography, and a 10- to 11-fold purification of the hydroxylase was achieved in this manner. However, the hydroxylating activity of this preparation was not stimulated by added ferredoxin and further chromatographic procedures designed to remove the endogenous ferredoxin-like component always resulted in irreversible loss of activity.
C9ORF72 expression and cellular localization over mouse development (2015)

In summary, the presence of C9ORF72 as puncta and within synaptic-rich fractions may indicate involvement at the synapse and differential expression of isoforms in nuclei and cytoplasm may suggest distinct roles for the isoforms. Determining the physiological role of C9ORF72 protein may help to determine the role it plays in disease.
Characterization and Functional Implications of the RNA Binding Properties of Nuclear Factor TDP-43, a Novel Splicing Regulator ofCFTR Exon 9 (2001)

Variations in a polymorphic (TG)m sequence near exon 9 of the human CFTR gene have been associated with variable proportions of exon skipping and occurrence of disease. We have recently identified nuclear factor TDP-43 as a novel splicing regulator capable of binding to this element in the CFTR pre-mRNA and inhibiting recognition of the neighboring exon. In this study we report the dissection of the RNA binding properties of TDP-43 and their functional implications in relationship with the splicing process. Our results show that this protein contains two fully functional RNA recognition motif (RRM) domains with distinct RNA/DNA binding characteristics. Interestingly, TDP-43 can bind a minimum number of six UG (or TG) single-stranded dinucleotide stretches, and binding affinity increases with the number of repeats. In particular, the highly conserved Phe residues in the first RRM region play a key role in nucleic acid recognition.
<title>Synthesis and characterization of cyanine dye poly(ethylene glycol) conjugates as contrast agents for in-vivo fluorescence imaging</title> (1998)

Cyanine dyes are promising near-IR contrast agents because of their high molar absorption between 700 and 1000 nm, minimal phototoxicity and convenient synthetic availability. It is known that the derivatization of drugs or contrast agents with polyethylene glycol residues leads to enhanced retention in tumor tissue. The purpose of this study was to generate indotricarbocyanines with improved pharmacological properties enabling in vivo fluorescence detection of tumors. Several hydrophilic indotricarbocyanine- poly(ethylene glycol) conjugates of different molecular weight were synthesized and characterized physicochemically and photophysically in order to test their applicability as near IR contrast media.
Measuring the Efficiency of Organic Light‐Emitting Devices (2003)

As organic light‐emitting devices emerge from the stage of being a research curiosity to that of becoming a practical appliance with important commercial applications, the need for a coherent and accurate standard technique for measuring device efficiencies becomes increasingly important. By following the methods described in this contribution, measurements made in disparate laboratories testing a wide range of materials and device structures should agree, to within small experimental errors, on the properties of the subject devices.
One-step formation of multiple emulsions in microfluidics (2010)

We present a robust way to create multiple emulsions with controllable shell thicknesses that can vary over a wide range. We use a microfluidic device to create a coaxial jet of immiscible fluids; using a dripping instability, we break the jet into multiple emulsions. By controlling the thickness of each layer of the jet, we adjust the thicknesses of the shells of the multiple emulsions. The same method is also effective in creating monodisperse emulsions from fluids that cannot otherwise be controllably emulsified, such as, for example, viscoelastic fluids.
Mechanism of pathogen recognition by human dectin-2 (2017)

Dectin-2, a C-type lectin on macrophages and other cells of the innate immune system, functions in response to pathogens, particularly fungi. The carbohydrate-recognition domain (CRD) in dectin-2 is linked to a transmembrane sequence that interacts with the common Fc receptor γ subunit to initiate immune signaling. The molecular mechanism by which dectin-2 selectively binds to pathogens has been investigated by characterizing the CRD expressed in a bacterial system. Competition binding studies indicated that the CRD binds to monosaccharides with modest affinity and that affinity was greatly enhanced for mannose-linked α1-2 or α1-4 to a second mannose residue. Glycan array analysis confirmed selective binding of the CRD to glycans that contain Manα1-2Man epitopes. Crystals of the CRD in complex with a mammalian-type high-mannose Man<sub>9</sub>GlcNAc<sub>2</sub> oligosaccharide exhibited interaction with Manα1-2Man on two different termini of the glycan, with the reducing-end mannose residue ligated to Ca<sup>2+</sup> in a primary binding site and the nonreducing terminal mannose residue occupying an adjacent secondary site. Comparison of the binding sites in DC-SIGN and langerin, two other pathogen-binding receptors of the innate immune system, revealed why these two binding sites accommodate only terminal Manα1-2Man structures, whereas dectin-2 can bind Manα1-2Man in internal positions in mannans and other polysaccharides. The specificity and geometry of the dectin-2-binding site provide the molecular mechanism for binding of dectin-2 to fungal mannans and also to bacterial lipopolysaccharides, capsular polysaccharides, and lipoarabinomannans that contain the Manα1-2Man disaccharide unit.
Genetic analysis of myeloproliferative leukemia virus, a novel acute leukemogenic replication-defective retrovirus (1987)

The myeloproliferative leukemia virus (MPLV) is a new acute leukemogenic, nonsarcomatogenic retroviral complex that is generated during the in vivo passage of a molecularly cloned Friend ecotropic helper virus. Examination of viral RNA expression in MPLV-producing cells revealed the presence of two distinct molecular species that hybridized with a long terminal repeat or an ecotropic env-specific probe but not with a xenotropic mink cell focus-forming virus env-specific probe derived from a spleen focus-forming virus: an 8.2-kilobase species corresponding to a full-length Friend murine leukemia virus (F-MuLV) and a deleted species with a genomic size of 7.4 kilobases. This deleted virus was biologically cloned by limiting dilutions and single cell cloning in Mus dunni fibroblasts. Three nonproducer clones with normal morphologies and containing one single integrated copy of the deleted virus were superinfected with F-MuLV, Moloney murine leukemia virus, Gross murine leukemia virus, mink cell focus-forming virus (HIX), or the amphotropic 1504 murine leukemia virus. All pseudotypes caused macroscopic and microscopic abnormalities in mice that were similar to those seen in the parental stock. A comparison of the physical maps of F-MuLV and MPLV, which was deduced from the restriction enzyme digests of unintegrated proviral DNAs, indicated that the MPLV-defective genome (i) is probably derived from F-MuLV, (ii) has conserved the F-MuLV gag and pol regions, and (iii) is deleted and rearranged in the env region in a manner that is clearly distinct from that of Friend or Rauscher spleen focus-forming viruses.
Clinical Features of Clostridial Bacteremia: A Review from a Rural Area (2001)

Blood samples, which were obtained from patients who lived in a rural area with approximately 500 acute-care hospital beds, were cultured from 1990 through 1997. We retrospectively reviewed the blood cultures that yielded Clostridium species (74 [0.12%] of 63,296 cultures). These were obtained from 46 different hospitalized patients (incidents per hospital, 0.03%). The source of the Clostridium species was a gastrointestinal site in 24 patients (52.2%). The most frequently identified Clostridium species was Clostridium perfringens (in 10 [21.7%] of patients), followed by Clostridium septicum (in 9 [19.6%]). Thirty-one patients (67.4%) were aged > or =65 years, 13 patients (28.3%) had diabetes mellitus, and underlying malignancy was present in 22 patients (47.8%). The mortality rate of patients whose condition had been managed surgically was 33%; for those patients whose conditions required medical management, the mortality rate was 58%. Clostridium bacteremia in these patients usually had a gastrointestinal source, it often occurred in patients with serious underlying medical conditions, and it rarely was the result of traumatic farm accidents.
Vesicle-related microRNAs in plasma of nonsmall cell lung cancer patients and correlation with survival (2010)

The identification of tumour biomarkers that detect the presence of disease using noninvasive diagnostic procedures is a key part of cancer research. We determined in plasma the vesicle-related microRNA (miRNA) expression profile of nonsmall cell lung cancer (NSCLC) and evaluate whether plasma miRNAs can be both discriminating (between patients and healthy controls) and prognostic markers. 365 human miRNAs were analysed by Taqman® low-density arrays (Applied Biosystems, Foster City, CA, USA) in the plasma from 28 NSCLC patients and 20 controls. Five selected miRNAs (let-7f, miR-20b, miR-30e-3p, miR-223 and miR-301) were validated independently by real-time PCR in plasma from 78 NSCLC and 48 controls and correlated with pathologic parameters and survival. Levels of let-7f, miR-20b and miR-30e-3p were decreased in plasma vesicles of NSCLC patients. Moreover, levels of let-7f and miR-30e-3p distinguished between two groups of patients for stage of disease and therefore possibility of surgery. Plasma levels of miR-30e-3p and let-7f were associated with short disease-free survival and overall survival, respectively. NSCLC patients and healthy controls differ in vesicle-related miRNAs in plasma. Levels of let-7f and miR-30e-3p in NSCLC patients are associated with poor outcome. Thus, plasma vesicle-related miRNAs obtained by noninvasive methods could serve as circulating tumour biomarkers of discriminating and prognostic value.
SuperPoint: Self-Supervised Interest Point Detection and Description (2018)

This paper presents a self-supervised framework for training interest point detectors and descriptors suitable for a large number of multiple-view geometry problems in computer vision. As opposed to patch-based neural networks, our fully-convolutional model operates on full-sized images and jointly computes pixel-level interest point locations and associated descriptors in one forward pass. We introduce Homographic Adaptation, a multi-scale, multi-homography approach for boosting interest point detection repeatability and performing cross-domain adaptation (e.g., synthetic-to-real). Our model, when trained on the MS-COCO generic image dataset using Homographic Adaptation, is able to repeatedly detect a much richer set of interest points than the initial pre-adapted deep model and any other traditional corner detector. The final system gives rise to state-of-the-art homography estimation results on HPatches when compared to LIFT, SIFT and ORB.
Selective blockade of T lymphocyte K+channels ameliorates experimental autoimmune encephalomyelitis, a model for multiple sclerosis (2001)

Adoptive transfer experimental autoimmune encephalomyelitis (AT-EAE), a disease resembling multiple sclerosis, is induced in rats by myelin basic protein (MBP)-activated CD4(+) T lymphocytes. By patch-clamp analysis, encephalitogenic rat T cells stimulated repeatedly in vitro expressed a unique channel phenotype ("chronically activated") with large numbers of Kv1.3 voltage-gated channels (approximately 1500 per cell) and small numbers of IKCa1 Ca(2+)-activated K(+) channels (approximately 50-120 per cell). In contrast, resting T cells displayed 0-10 Kv1.3 and 10-20 IKCa1 channels per cell ("quiescent" phenotype), whereas T cells stimulated once or twice expressed approximately 200 Kv1.3 and approximately 350 IKCa1 channels per cell ("acutely activated" phenotype). Consistent with their channel phenotype, [(3)H]thymidine incorporation by MBP-stimulated chronically activated T cells was suppressed by the peptide ShK, a blocker of Kv1.3 and IKCa1, and by an analog (ShK-Dap(22)) engineered to be highly specific for Kv1.3, but not by a selective IKCa1 blocker (TRAM-34). The combination of ShK-Dap(22) and TRAM-34 enhanced the suppression of MBP-stimulated T cell proliferation. Based on these in vitro results, we assessed the efficacy of K(+) channel blockers in AT-EAE. Specific and simultaneous blockade of the T cell channels by ShK or by a combination of ShK-Dap(22) plus TRAM-34 prevented lethal AT-EAE. Blockade of Kv1.3 alone with ShK-Dap(22), but not of IKCa1 with TRAM-34, was also effective. When administered after the onset of symptoms, ShK or the combination of ShK-Dap(22) plus TRAM-34 greatly ameliorated the clinical course of both moderate and severe AT-EAE. We conclude that selective targeting of Kv1.3, alone or with IKCa1, may provide an effective new mode of therapy for multiple sclerosis.
The Reactive Keyboard: a predictive typing aid (1990)

The Reactive Keyboard, a device that accelerates typewritten communication with a computer system by predicting what the user is going to type next is described. The version described is designed for entering free text and runs on any Apple Macintosh computer with at least 1 MB of memory (though 2 MB is preferred). It makes full use of the Macintosh mouse-and-window environment to give users convenient control over display and acceptance of predictions, and it requires no physical keyboard. The interface increases the speed and ease of communicating with a computer, especially for physically disabled people.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>