gebhart/patrepeval huggingface dataset:
Toll-Like Receptors, Associated Biological Roles, and Signaling Networks in Non-Mammals (2018)

The innate immune system is the first line of defense against pathogens, which is initiated by the recognition of pathogen-associated molecular patterns (PAMPs) and endogenous damage-associated molecular patterns (DAMPs) by pattern recognition receptors (PRRs). Among all the PRRs identified, the toll-like receptors (TLRs) are the most ancient class, with the most extensive spectrum of pathogen recognition. Since the first discovery of Toll in <i>Drosophila melanogaster</i>, numerous TLRs have been identified across a wide range of invertebrate and vertebrate species. It seems that TLRs, the signaling pathways that they initiate, or related adaptor proteins are essentially conserved in a wide variety of organisms, from Porifera to mammals. Molecular structure analysis indicates that most TLR homologs share similar domain patterns and that some vital participants of TLR signaling co-evolved with TLRs themselves. However, functional specification and emergence of new signaling pathways, as well as adaptors, did occur during evolution. In addition, ambiguities and gaps in knowledge still exist regarding the TLR network, especially in lower organisms. Hence, a systematic review from the comparative angle regarding this tremendous signaling system and the scenario of evolutionary pattern across Animalia is needed. In the current review, we present overview and possible evolutionary patterns of TLRs in non-mammals, hoping that this will provide clues for further investigations in this field.
A parallel Viterbi decoding algorithm (2001)

Abstract In this paper we express the Viterbi algorithm as a matrix–vector reduction in which multiplication is replaced by addition and addition by minimization. The resulting algorithm is then readily parallelized in a form suitable for implementation on a systolic processor array. We describe the algorithm for Bose–Chaudhuri–Hocquenghem (BCH) codes which have a task graph with its valence restricted to four inputs and four outputs. The method is also applicable to convolution codes, but the complexity of the task graph increases with the number of input bits for these codes. Results for BCH codes are given for two general purpose parallel machines, an IBM SP2 and a Meiko CS2. Copyright © 2001 John Wiley &amp; Sons, Ltd.
Evidence for a conformational change in deglycosylated glycoprotein hormones (1985)

Removal of long-chain asparagine-linked carbohydrates leads to loss of receptor-effector coupling in gonadotropin target tissue. This implies a direct interaction between carbohydrate and cell membrane components. To examine other mechanisms by which carbohydrate could activate post-receptor events, we have used sequence-specific and conformation-specific alpha-subunit radioimmunoassays as probes for conformational changes in deglycosylated choriogonadotropin and follitropin. Immunoreactivity of either hormone was enhanced 8-13-fold after removal of carbohydrate by anhydrous hydrogen fluoride. Removal of sialic acid alone had little effect on reactivity. Based on the specificity of the antisera, the effect could be localized to a region in the amino-terminus remote in the linear sequence from actual sites of carbohydrate attachment. The results suggest that a conformational change in the alpha-subunit could account, at least in part, for the observed effects of deglycosylation on glycoprotein hormone action.
A Concise and Efficient Synthesis of (−)-Allosamizoline (2007)

A regio- and stereocontrolled total synthesis of (-)-allosamizoline is described. The key steps for this synthesis are ring-closing metathesis to form the cyclopentene core, halocyclization to afford the oxazoline ring, and finally stereoselective alkene radical addition followed by an alkene isomerization reaction to install the hydroxymethyl group. (-)-Allosamizoline was prepared in a total of 13 steps and 22% overall yield.
The Repeatability of Tear Mucus Ferning Grading (1998)

Based on the high rate of agreement between intraobserver and interobserver trials, Rolando's grading system appears to be an easy and consistent method for the classification of tear ferning patterns.
Online Handwriting Recognition for Tamil (2004)

A system for online recognition of handwritten Tamil characters is presented. A handwritten character is constructed by executing a sequence of strokes. A structure- or shape-based representation of a stroke is used in which a stroke is represented as a string of shape features. Using this string representation, an unknown stroke is identified by comparing it with a database of strokes using a flexible string matching procedure. A full character is recognized by identifying all the component strokes. Character termination, is determined using a finite state automaton. Development of similar systems for other Indian scripts is outlined.
Synaptic Dysfunction in Neurodevelopmental Disorders Associated with Autism and Intellectual Disabilities (2012)

The discovery of the genetic causes of syndromic autism spectrum disorders and intellectual disabilities has greatly informed our understanding of the molecular pathways critical for normal synaptic function. The top-down approaches using human phenotypes and genetics helped identify causative genes and uncovered the broad spectrum of neuropsychiatric features that can result from various mutations in the same gene. Importantly, the human studies unveiled the exquisite sensitivity of cognitive function to precise levels of many diverse proteins. Bottom-up approaches applying molecular, biochemical, and neurophysiological studies to genetic models of these disorders revealed unsuspected pathogenic mechanisms and identified potential therapeutic targets. Moreover, studies in model organisms showed that symptoms of these devastating disorders can be reversed, which brings hope that affected individuals might benefit from interventions even after symptoms set in. Scientists predict that insights gained from studying these rare syndromic disorders will have an impact on the more common nonsyndromic autism and mild cognitive deficits.
A Trivalent System from Vancomycin· d -Ala- d -Ala with Higher Affinity Than Avidin·Biotin (1998)

Tris(vancomycin carboxamide) binds a trivalent ligand derived from D-Ala-D-Ala with very high affinity: dissociation constant (Kd) approximately 4 x 10(-17) +/- 1 x 10(-17) M. High-affinity trivalent binding and monovalent binding are fundamentally different. In trivalent (and more generally, polyvalent) binding, dissociation occurs in stages, and its rate can be accelerated by monovalent ligand at sufficiently high concentrations. In monovalent binding, dissociation is determined solely by the rate constant for dissociation and cannot be accelerated by added monomer. Calorimetric measurements for the trivalent system indicate an approximately additive gain in enthalpy relative to the corresponding monomers. This system is one of the most stable organic receptor-ligand pairs involving small molecules that is known. It illustrates the practicality of designing very high-affinity systems based on polyvalency.
Management of the painful and nodular breast (1991)

Mild breast pain and nodularity are common and may be considered normal. Only when symptoms are severe enough to affect the patient's lifestyle should drug treatment be considered. Using danazol, bromocriptine or evening primrose oil a clinically useful improvement in pain can be anticipated in 77% of patients with cyclical mastalgia and 44% with non-cyclical mastalgia. Benign nodularity should not be biopsied surgically as it is unnecessary and makes subsequent assessment of the breast difficult.
Fuzzy decision trees and numerical attributes (2002)

Classical crisp decision trees (DT) are widely applied to classification tasks. Nevertheless, there are also a lot of fuzzy decision tree (FDT) solutions. Sometimes fuzzy borders for discretisation of continuous-valued attributes are used. The induction of FDT in these solutions need some parameters from the expert or user. An automatically generated membership function for discretisation of continuous-valued attributes is described in this paper. An example with the decision tree construction and the unseen data classification is given. The results of crisp and fuzzy decision trees are compared at the end.
Present Trends in High-Speed and Broad-Band Communications Services in Japan (1986)

This paper describes present trends in high-speed and broad-band communications services in Japan. It gives an overview of video, high-speed digital leased circuit and satellite digital communications services, and gives examples of their applications. Recent trends in telecommunication services and technology are described, including video conferencing services presently available in more than ten cities throughout Japan, as well as a video response system which is about to be put into service. It also describes the present status of Japan's cable television (CATV) system and discusses its future development. Finally, NTT's plans for high-speed and broad-band communications service in the future are previewed.
Fast Lexically Constrained Decoding with Dynamic Beam Allocation for Neural Machine Translation (2018)

The end-to-end nature of neural machine translation (NMT) removes many ways of manually guiding the translation process that were available in older paradigms. Recent work, however, has introduced a new capability: lexically constrained or guided decoding, a modification to beam search that forces the inclusion of pre-specified words and phrases in the output. However, while theoretically sound, existing approaches have computational complexities that are either linear We present an algorithm for lexically constrained decoding with a complexity of O(1) in the number of constraints. We demonstrate the algorithm's remarkable ability to properly place these constraints, and use it to explore the shaky relationship between model and BLEU scores. Our implementation is available as part of SOCKEYE.
Biological Effects of Various Doses of Conjugated Equine Estrogens in Postmenopausal Women* (1980)

To determine which dosage of estrogen might provide physiological replacement and also avoid possible harmful side effects, 21 postmenopausal women were studied before and after the oral administration of conjugated equine estrogens. The dosages studied were 0.15, 0.30, 0.625, and 1.25 mg/day, with each being given for 6 weeks. Fifteen premenopausal women were also studied, and their values were presumed to reflect normal physiological function. Variable responses of the different biochemical and biological markers of the action of estrogen were observed. Both LH and FSH levels showed stepwise decreases with increasing amounts of estrogen, but even 1.25 mg/day did not suppress these hormones to the range found in premenopausal women, suggesting a subphysiological response. The lower dosages of conjugated estrogen had minimal effects on vaginal cytology, with only the 1.25-mg dose changing the maturation index to values similar to those found in premenopausal subjects. The 0.3-mg dose of conjugated estrogen was the lowest amount that resulted in a significant reduction (P < 0.05) of the urinary calcium to creatinine ratio (an index of bone resorption). Liver protein synthesis was the most sensitive parameter to the action of estrogen. Hepatic resoponses were variable depending on which protein was assessed. These data indicate that the oral administration of conjugated equine estrogens results in inconsistent effects. All doses exerted subphysiological, physiological, and pharmacological responses at the different sites of action.
Activation of BAD by Therapeutic Inhibition of Epidermal Growth Factor Receptor and Transactivation by Insulin-like Growth Factor Receptor (2002)

Novel cancer chemotherapeutics are required to induce apoptosis by activating pro-apoptotic proteins. Both epidermal growth factor (EGF) and insulin-like growth factor (IGF) provide potent survival stimuli in many epithelia, and activation of their receptors is commonly observed in solid human tumors. Here we demonstrate that blockade of the EGF receptor by a new drug in phase III clinical trails for cancer, ZD1839, potently induces apoptosis in mammary epithelial cell lines and primary cultures, as well as in a primary pleural effusion from a breast cancer patient. We identified the mechanism of apoptosis induction by ZD1839. We showed that it prevents cell survival by activating the pro-apoptotic protein BAD. Moreover, we demonstrate that IGF transactivates the EGF receptor and that ZD1839 blocks IGF-mediated phosphorylation of MAPK and BAD. Many cancer therapies kill tumor cells by inducing apoptosis as a consequence of targeting DNA; however, the threshold at which apoptosis can be triggered through DNA damage is often different from that in normal cells. Our results indicate that by targeting a growth factor-mediated survival signaling pathway, BAD phosphorylation can be manipulated therapeutically to induce apoptosis.
Self‐Assembling Polymer–Peptide Conjugates: Nanostructural Tailoring (2004)

The synthesis and solution behavior of a series of β‐sheet fibril‐forming peptide–polymers is described. Several block copolymer architectures are explored, with various lengths and arrangements of the peptide and polymer blocks. One peptide–polymer, an 11‐amino acid peptide conjugated to a polydisperse poly(ethylene glycol) chain, has the ability to form uncommonly regular, aligned, and minimally aggregated β‐sheet fibrils (see Figure).
Cell surface expression of yellow fever virus non-structural glycoprotein NS1: consequences of interaction with antibody (1990)

Among antibodies to flaviviral proteins only those directed at the virion envelope protein (E) or the non-structural glycoprotein NS1 are known to confer protection. To investigate the possible role of complement-mediated cytolysis (CMC) in protection we measured the capacity of anti-NS1, or E monospecific serum or monoclonal antibodies to bind to yellow fever virus (YFV)-infected cells and of anti-NS1 or E serum to sensitize them to CMC. Although both anti-NS1 and anti-E antibody bound to YFV-infected cells, CMC was observed only with anti-NS1 antibody. Greater binding by anti-NS1 antibody suggested the presence of larger amounts of NS1 than E associated with the cell membrane. Using the cell membrane-impermeable, cross-linking reagent BS3, cell surface NS1, but not E, was detected as a homopolymer, a form in which bound antibody might be expected to activate complement more efficiently. Peak titres of progeny virus were reduced 10- to 100-fold when infected cells were treated with complement-fixing, anti-NS1 monoclonal antibody or monospecific, anti-NS1 rabbit serum and complement. Taken together these results are consistent with the hypothesis that CMC subserved by anti-NS1 antibody provides an alternative to direct neutralization of virus in the protective immune response to flaviviral infection.
Clinical Usefulness of a Biomarker-Based Diagnostic Test for Acute Stroke (2008)

These results suggest that a biomarker panel may add valuable and time-sensitive diagnostic information in the early evaluation of stroke. Such an approach is feasible on a point-of-care platform. The rapid identification of patients with suspected stroke would expand the availability of time-limited treatment strategies. Although the diagnostic accuracy of the current panel is clearly imperfect, this study demonstrates the feasibility of incorporating a biomarker based point-of-care algorithm with readily available clinical data to aid in the early evaluation and management of patients at high risk for cerebral ischemia.
RNA splice junctions of different classes of eukaryotes: sequence statistics and functional implications in gene expression (1987)

A systematic analysis of the RNA splice junction sequences of eukaryotic protein coding genes was carried out using the GENBANK databank. Nucleotide frequencies obtained for the highly conserved regions around the splice sites for different categories of organisms closely agree with each other. A striking similarity among the rare splice junctions which do not contain AG at the 3' splice site or GT at the 5' splice site indicates the existence of special mechanisms to recognize them, and that these unique signals may be involved in crucial gene-regulation events and in differentiation. A method was developed to predict potential exons in a bare sequence, using a scoring and ranking scheme based on nucleotide weight tables. This method was used to find a majority of the exons in selected known genes, and also predicted potential new exons which may be used in alternative splicing situations.
Early antibody response against hypervariable region 1 is associated with acute self-limiting infections of hepatitis C virus (1997)

Antibodies directed to hypervariable region 1 (HVR1) of hepatitis C virus (HCV) have recently been shown to neutralize the corresponding HCV isolate in vitro. We analyzed the appearance of antibodies directed to HVR1 during the course of infection in a large group of patients who have been infected by the same isolate of a HCV contaminated anti-D immunoglobulin (HCV-AD78). An enzyme-linked immunosorbent assay (ELISA) was established using a synthetic peptide to detect antibodies against the main HVR1 variant of HCV-AD78. 207 sera obtained at different time points post infection (p.i.) of 51 patients having either acute self-limiting (n = 28) or chronic infection (n = 23) were studied. Antibodies directed to HVR1 were found at least at one time point during the infection course in 15 of 28 patients (53%) having acute self-limiting infections and in 17 of 23 patients (74%) with chronic disease. The time of appearance of anti-HVR1 was significantly different between these two patient groups (P < .025) although appearance and titers of other HCV-specific antibodies were found to be similar at early time points p.i. In acute self-limiting infections 9 of 21 sera (43%) of respective patients with sera available within the first 6 months p.i. were anti-HVR1 positive. The highest prevalence of anti-HVR1 in this group of patients was within month 6 to 12 p.i. (64%). None of the sera available after 24 months p.i. had such antibodies. In contrast, only 2 of 15 sera (13%) of chronically infected patients with respective time points of sera were anti-HVR1 positive within the first 6 months p.i. and only 5 of 18 sera (28%) were positive within month 7 to 12 p.i. Seven patients with chronic HCV infections showed at least two consecutive anti-HVR1 negative early time points up to month 18 p.i. Prevalence of anti-HVR1 after 24 months p.i. was high (84%) in this group of patients and most of the patients maintained high levels of anti-HVR1 for up to 17 years p.i. Our findings suggest clearance of virus by respective neutralizing antibodies resulting in a self-limiting infection and may have implications for prognosis of the disease and also for any future vaccine development.
Markers of cell lineage, differentiation and activation. (2001)

The most widespread use of CD markers is in the determination of cell lineage and sublineage. For example, T cells are identified by the expression of CD3 (reviewed in this issue of CD corner). A mature T cell may belong to the T4 subset, in which case it will express CD4. Similarly, there are markers for other cell populations and sub-populations. Within the lineages, it is helpful to distinguish cells at different stages of differentiation and activation. Differentiation status is particularly useful in the diagnostic analysis of the lymphoid and myeloid malignancies, and in research on the haemopoietic system. Examples include markers for naïve or antigen-experienced cells (especially the CD45 isoforms) and molecules such as CALLA (CD9) found on B-lineage precursors, including B lineage acute lymphoblastic leukaemia. Activation status is especially interesting in studies of cell function. Activation markers include growth factor receptors such as CD25 (a component of the receptor for IL-2), and molecules who's cellular function is not fully understood, such as CD69 and CD98. These markers have revolutionised aspects of pathology and research, and the ease with which some cell populations can be identified has lead to some unrealised, and perhaps unrealistic, expectations. We expect to be able to identify T helper type 1 (TH1) and T helper type 2 (TH2) cells on the basis of a simple surface marker; we are frustrated by the lack of a single marker for all dendritic cells or for all NK cells; we are confused by the un-coordinated expression of different activation markers; we tend to over-interpret phenotype in some situations. To find solutions to these problems it is helpful to examine why the successful lineage markers work so well, and to reconsider our expectations. Lineage markers are the main focus in this commentary; the question of activation markers and markers of differentiation state will be considered in a separate paper.
Dissociation of the store‐operated calcium current ICRAC and the Mg‐nucleotide‐regulated metal ion current MagNuM (2002)

Rat basophilic leukaemia cells (RBL-2H3-M1) were used to study the characteristics of the store-operated Ca(2+) release-activated Ca(2+) current (I(CRAC)) and the magnesium-nucleotide-regulated metal cation current (MagNuM) (which is conducted by the LTRPC7 channel). Pipette solutions containing 10 mM BAPTA and no added ATP induced both currents in the same cell, but the time to half-maximal activation for MagNuM was about two to three times slower than that of I(CRAC). Differential suppression of I(CRAC) was achieved by buffering free [Ca(2+)](i) to 90 nM and selective inhibition of MagNuM was accomplished by intracellular solutions containing 6 mM Mg.ATP, 1.2 mM free [Mg(2+)](i) or 100 microM GTP-gamma-S, allowing investigations on these currents in relative isolation. Removal of extracellular Ca(2+) and Mg(2+) caused both currents to be carried significantly by monovalent ions. In the absence or presence of free [Mg(2+)](i), I(CRAC) carried by monovalent ions inactivated more rapidly and more completely than MagNuM carried by monovalent ions. Since several studies have used divalent-free solutions on either side of the membrane to study selectivity and single-channel behaviour of I(CRAC), these experimental conditions would have favoured the contribution of MagNuM to monovalent conductance and call for caution in interpreting results where both I(CRAC) and MagNuM are activated.
Algorithm 562: Shortest Path Lengths [H] (1980)

Key Words and Phrases CR Categor)es' 5 32 Language Fortran IV shortest path, shortest route problem DESCRIPTION This algorithm finds the shortest path lengths from a specific node to all other nodes in a network. It is a modification of Moore's algorithm [4], originally due to d'Esopo as reported by Pollack and Wiebenson [7] and refined by Pape The algorithm does not determine the shortest paths. If a shortest path is to be determined, this algorithm may be combined with any algorithm that traces the shortest path from the root node to any other node from the list of predecessors of nodes. As the calculation of the path lengths is the most rime-consuming part of the whole process, we confine our attention to this problem.