gebhart/patrepeval huggingface dataset:
An Overview of Sequence Comparison: Time Warps, String Edits, and Macromolecules (1983)

A wide variety of different applications lead to problems in which sequences of different lengths must be compared, to see how different they are, and to see which elements in one sequence correspond to which elements in the other sequence. Successful methods for handling these problems been repeatedly reinvented which incorporate two basic ideas a systematic concept of distance between sequences, and elegant recursive algorithms for doing the necessary computations. The major application areas are speech processing and macromolecular biology. Computer science is another significant application area, and applications have also been made to bird song, handwriting analysis, gas chromatography, geological strata, and text collation. This paper surveys the applications, methods and theory of sequence comparison.
Cerebral Glioblastoma with Cerebrospinal Fluid Dissemination: A Clinicopathological Study of 14 Cases Examined by Complete Autopsy (1989)

During the last 17 years, complete autopsies were performed on 51 patients who died of cerebral glioblastoma, and 14 were found to have dissemination by cerebrospinal fluid (CSF). In these 14 cases of glioma, the extent of intraparenchymal invasion by the primary tumor and the degree of seeding were studied in connection with histological findings and immunohistochemical staining for glial fibrillary acidic protein (GFAP) as the most reliable marker of astrocytic differentiation. From the findings obtained, the cases were divided into two groups. In one group, consisting of 7 gliomas, autopsy revealed intense seeding, despite only slight invasion by the primary tumor. Among these 7 extensively disseminated gliomas, 4 expressed almost no GFAP, 2 contained only a few GFAP-positive cells, and only 1 displayed an immunohistochemically high degree of astrocytic differentiation. Clinically, 6 of the 7 affected patients developed symptoms attributable to CSF seeding. In the other group consisting of the remaining 7 gliomas, only slight dissemination was seen, despite extensive infiltration of the primary tumor. Each of these 7 gliomas contained many GFAP-positive cells. None of the affected patients developed symptomatic seeding. This study shows the existence of two clinicopathologically distinct groups of disseminated cerebral glioblastomas and suggests that, regardless of morphological features, glioblastomas showing immunohistochemically poor astrocytic differentiation tend to shed tumor cells more vigorously but are less invasive at the primary site than those with many GFAP-positive cells. It is also suggested that, as a consequence, the former glioma type produces symptomatic seeding more frequently than the latter type. (Neurosurgery 25:533-540, 1989)
Nuclear disconnection within the amygdala reveals a direct pathway to fear (2009)

It is widely believed that a descending serial circuit consisting of neural projections from the basolateral complex (BLA) to the central nucleus (CEA) of the amygdala mediates fear expression. Here we directly test this hypothesis and show that disconnecting the BLA and CEA with asymmetric neurotoxic lesions after Pavlovian fear conditioning in rats completely abolishes the expression of conditional freezing. These results demonstrate that neural projections from the BLA to CEA are essential for the expression of learned fear responses.
Treatment of Myasthenia Gravis by Preventing Acetylcholine Receptor Modulation (2008)

Myasthenia gravis (MG) is an autoimmune disease caused by antibodies mainly directed to the acetylcholine receptor (AChR) of the neuromuscular junction. Induction of antigenic modulation and complement activation by such autoantibodies leads to ultrastructural damage of the postsynaptic membrane and loss of AChR and associated proteins. Reduction of antigenic modulation by increasing the expression of the receptor-associated anchor protein, rapsyn, or by functionally monovalent competing IgG4 anti-AChR antibodies was shown to prevent MG disease activity. We propose that preventing antigenic modulation can be used as a treatment strategy for MG.
Dynamic T‐lymphocyte Chemokine Receptor Expression Induced by Interferon‐beta Therapy in Multiple Sclerosis (2006)

Treatment with interferon (IFN)-beta reduces clinical disease activity in multiple sclerosis (MS). Using flow cytometry, an enzyme-linked immunosorbent assay and a real-time polymerase chain reaction, we studied in vivo IFN-beta-induced effects on CD4(+) T-lymphocyte chemokine receptor expression as these influence central nervous system (CNS) transmigration and inflammation. At 'steady state' (>/=1 day after the most recent IFN-beta injection), IFN-beta treatment increased CD4(+) T-cell surface expression of CC chemokine receptor (CCR)4, CCR5 and CCR7 after 3 months of treatment, whereas that of CXC chemokine receptor (CXCR)3 was unaltered. Conversely, at 9-12 h after the most recent IFN-beta injection, CCR4, CCR5 and CCR7 expressions were unaltered, while CXCR3 expression was reduced. CD4(+) T-cell surface expression of CCR4 was significantly lower in untreated MS patients compared with healthy volunteers. Of the plasma chemokines, only CXCL10 was increased by IFN-beta treatment; CCL3, CCL4, CCL5 and CXCL9 were unaltered. CCR5 mRNA expression in blood mononuclear cells correlated with the expression of T-helper type 1 (Th1)-associated genes whereas CCR4 and CCR7 mRNA expression correlated with Th2 and immunoregulatory genes. In conclusion, IFN-beta treatment caused 'steady-state' increases of several chemokine receptors relevant for CD4(+) T-lymphocyte trafficking and function, possibly facilitating lymphocyte migration into the CNS. An important therapeutic effect of IFN-beta treatment may be the normalization of a decreased Th2-related CD4(+) T-cell CCR4 expression in MS patients. Surface chemokine receptor expression and CXCL10 varied according to the timing of blood sampling in relation to the most recent IFN-beta injection. Thus, it is imperative to distinguish acute effects of IFN-beta from steady-state effects.
Levels of complement regulatory proteins, CD35 (CR1), CD46 (MCP) and CD55 (DAF) in human haematological malignancies (1992)

S ummary . Levels of the membrane complement regulatory proteins. C3b/C4b receptor (CR1, CD35), membrane cofactor protein (MCP, CD46), and decay‐accelerating factor (DAF, CD55), expressed on cells from patients with haematological malignancies and normal subjects were assessed by flowcytometry using the respective monoclonal antibodies (mAbs). All myeloid and most lymphoid leukaemia samples tested were CR1‐negative: two of the 42 leukaemia samples expressed minute amounts of CR1. Lack of CR1 in leukaemia cells was confirmed with two mAbs raised against CR1, 31R, and 243R, which recognized different epitopes and induced different degrees of CR1‐mediated fluorescent shift on flow‐cytometry in granulocytes and erythrocytes. MCP was increased in most chronic myelogenous leukaemia (CML) and chronic lymphocytic leukaemia (CLL), and was also increased in majority of acute nonlymphocytic leukaemia (ANLL), acute lymphocytic leukaemia (ALL) and non‐Hodgkin's lymphoma (NHL). Levels of DAF were also high in CML and CLL, and were variable in other types of leukaemia: some were DAF‐negative while others expressed extremely high levels of DAF. In CML patients, the high level of MCP and the lack of CR1 were normalized after medical treatment. These results are in agreement with the data obtained with human leukaemia cell lines, and support the hypothesis that CR1 is essentially a differentiated cell antigen and that a high level of MCP reflects some malignant transformation or an immature stage in blood cells.
Generation and Evaluation of a Cortical Area Parcellation from Resting-State Correlations (2014)

The cortical surface is organized into a large number of cortical areas; however, these areas have not been comprehensively mapped in the human. Abrupt transitions in resting-state functional connectivity (RSFC) patterns can noninvasively identify locations of putative borders between cortical areas (RSFC-boundary mapping; Cohen et al. 2008). Here we describe a technique for using RSFC-boundary maps to define parcels that represent putative cortical areas. These parcels had highly homogenous RSFC patterns, indicating that they contained one unique RSFC signal; furthermore, the parcels were much more homogenous than a null model matched for parcel size when tested in two separate datasets. Several alternative parcellation schemes were tested this way, and no other parcellation was as homogenous as or had as large a difference compared with its null model. The boundary map-derived parcellation contained parcels that overlapped with architectonic mapping of areas 17, 2, 3, and 4. These parcels had a network structure similar to the known network structure of the brain, and their connectivity patterns were reliable across individual subjects. These observations suggest that RSFC-boundary map-derived parcels provide information about the location and extent of human cortical areas. A parcellation generated using this method is available at http://www.nil.wustl.edu/labs/petersen/Resources.html.
CCR5 Antagonists: Host-Targeted Antivirals for the Treatment of HIV Infection (2005)

The human chemokine receptors, CCR5 and CXCR4, are potential host targets for exogenous, small-molecule antagonists for the inhibition of HIV-1 infection. HIV-1 strains can be categorised by co-receptor tropism - their ability to utilise CCR5 (CCR5-tropic), CXCR4 (CXCR4-tropic) or both (dual-tropic) as a co-receptor for entry into susceptible cells. CCR5 may be the more suitable co-receptor target for small-molecule antagonists because a natural deletion in the CCR5 gene preventing its expression on the cell surface is not associated with any obvious phenotype, but can confer resistance to infection by CCR5-tropic strains - the most frequently sexually-transmitted strains. The current leading CCR5 antagonists in clinical development include maraviroc (UK-427,857, Pfizer), aplaviroc (873140, GlaxoSmithKline) and vicriviroc (SCH-D, Schering-Plough), which have demonstrated efficacy and tolerability in HIV-infected patients. Pharmacodynamic data also suggest that these compounds have a long plasma half-life and/or prolonged CCR5 occupancy, which may explain the delay in viral rebound observed following compound withdrawal in short-term monotherapy studies. A switch from CCR5 to CXCR4 tropism occurs spontaneously in approximately 50% of HIV-infected patients and has been associated with, but is not required for, disease progression. The possibility of a co-receptor tropism switch occurring under selection pressure by CCR5 antagonists is discussed. The completion of ongoing Phase lib/Ill studies of maraviroc, aplaviroc and vicriviroc will provide further insight into co-receptor tropism, HIV pathogenesis and the suitability of CCR5 antagonists as a potent new class of antiyirals for the treatment of HIV infection.
Evaluation of Reagent-Based and Product-Based Strategies in the Design of Combinatorial Library Subsets (1999)

With the current and ever-growing offering of reagents along with the vast palette of organic reactions, virtual libraries accessible to combinatorial chemists have dramatically increased in size. Yet, extracting representative subsets for experimentation is an essential step in the design of combinatorial libraries. There has been some controversy whether it is necessary to consider product properties, at some computational expense, or whether sufficiently representative sets can be identified from considerations of the reagent space alone. This study compares the efficiency of reagent-based selections and that of product-based combinatorial subsetting in the identification of representative library subsets. Quantitative estimates reported herein show that the advantage of working in product space is descriptor dependent. For some descriptors, product-based approaches provide a distinct advantage, whereas for others results from reactant pools offer comparable results. Hence the behavior of descriptors, in mapping diversity from reagent space to product space, should be investigated prior to embarking into lengthy product-based considerations. Several classes of descriptors are studied including two-dimensional fingerprints (ISIS and Daylight) and physicochemical descriptors.
CLINICAL IMPLICATIONS OF THE p53 GENE (1996)

The capacity for malignant growth is acquired by the stepwise accumulation of defects in specific genes regulating cell growth and tissue homeostasis. Although several hundred genes are known to control growth, molecular genetic studies in cancer show that few of these are consistently involved in the natural history of human cancer, and those typically in only certain types of malignancy. Prospects for development of molecular-based diagnostic and therapeutic strategies with widespread application did not look promising, until it was realized that the p53 tumor suppressor gene was defective in approximately half of all malignancies. This discovery generated research efforts of unparalleled intensity to determine how p53 functions at the molecular level, and how to apply this knowledge to clinical ends.
Effects of food restriction on lactate production from glucose by rat adipocytes (1987)

We investigated the effects of acute food deprivation on the rates of glucose metabolism and lactate production by epididymal fat cells isolated from 2- and 8-mo-old Wistar rats in one of three nutritional states: fed ad libitum, restricted to 50% of ad libitum, or fasted for 48 h. Food restriction did not affect total rates of basal glucose metabolism but significantly altered its pattern. In small fat cells from 2-mo-old rats, donor's food restriction led to decreased basal and insulin-stimulated glucose oxidation and fatty acid synthesis but led to increased lactate production, which increased from 4% of total glucose metabolized by cells from fed rats to 62% by cells from fasted rats. In large fat cells from 8-mo-old rats, donor's food restriction produced minimal changes in basal glucose metabolism and lactate production (already elevated at 37% of total) but caused insulin-stimulated lactate production to increase. These findings indicate that adipose tissue can produce significant amounts of lactate (with adipocyte enlargement and/or food deprivation) and may play an important role in extrahepatic generation of triose intermediates and in the Cori cycle.
Investigation of the Early Steps of Molybdopterin Biosynthesis in Escherichia coli through the Use of in Vivo Labeling Studies (1995)

The early steps in the biosynthesis of the molybdopterin portion of the molybdenum cofactor have been investigated through the use of radiolabeled precursors. Labeled guanosine was added to growing cultures of the molybdopterin-deficient Escherichia coli mutant, moeB, which accumulates large amounts of precursor Z, the final intermediate in molybdopterin biosynthesis (Wuebbens, M. M., and Rajagopalan, K. V. (1993) J. Biol. Chem. 268, 13493-13498). Precursor Z is readily oxidized to the stable, fluorescent pterin, compound Z, which contains all 10 of the carbon atoms present in molybdopterin. For these experiments, compound Z was isolated from both the cells and culture media and analyzed for the presence of label. The development of a method for sequential cleavage of the compound Z side chain carbons facilitated determination of the distribution of label between the ring and the side chain of compound Z. Addition of uniformly labeled [14C]guanosine to moeB cultures produced compound Z labeled in both the ring and the side chain. Growth on [8-14C]guanosine resulted in transfer of label to the C-1' position of compound Z. The label present in compound Z purified from cultures grown on [8,5'-3H]guanosine was lost by removal of the three terminal side chain carbons. These results indicate that although a guanosine compound serves as the initial precursor for molybdopterin biosynthesis, the early steps of this pathway in E. coli proceed via a pathway unlike that of any known pteridine biosynthetic pathway.
Activation and functionalization of alkanes (1989)

Historical evolution of homogeneous alkane activation systems electrophilic chemistry of alkanes some recent advances in alkane functionalization: metal phosphine catalysts and mercury photosensitization alkane activation processes by cyclopentadienyl complexes of rhodium, iridium, and related species the homogeneous activation of carbon-hydrogen bonds by high-valent early D-block, lanthanide and actinide metal systems alkane functionalization by cytochromes P-450 and by model systems shape-selective oxygenation of hydrocarbons catalytic oxygenation of unactivated C-H bonds: superior Oxo transfer catalysts and the inorganic metalloporphyrin selective functionalization of saturated hydrocarbons by the 'Gif' and 'Gif-Orsay' systems alkane oxidation studies in du Pont's central research department.
Differential expression and ligand binding properties of tumor necrosis factor receptor chimeric mutants (1993)

The receptors for tumor necrosis factor (TNF) are represented by two transmembrane proteins, p55TNFR and p75TNFR, which are members of a family of cell surface molecules, including the Fas antigen, CD30, CD40, OX40, a Shope fibroma virus protein, and the low affinity p75 nerve growth factor receptor. A common structural feature is a sequence of 40 amino acids that is found in adjacent repeated domains, with 6 cysteine residues in a conserved register. To assess the functional significance of this cysteine-rich domain (CRD), we have constructed chimeric receptors between each TNF receptor and the low affinity nerve growth factor receptor. The chimeric receptor cDNAs were expressed efficiently in COS-1 and 3T3 fibroblasts, as assessed by affinity cross-linking, cell surface biotinylation and immunoprecipitation, and equilibrium binding. Receptors with two CRD of either TNF receptor were incapable of binding TNF, whereas receptors with all four CRD retained the ability to bind TNF with wild type affinity. These results, in conjunction with previous deletion mutation studies, suggest that TNF binding to each receptor requires all four cysteine-rich repeats. Furthermore, analysis of chimeric receptors containing domains of p55TNFR suggests that cytoplasmic sequences directly influence the levels of receptor expression.
Ab initiomolecular-dynamics simulation of the liquid-metal–amorphous-semiconductor transition in germanium (1994)

We present ab initio quantum-mechanical molecular-dynamics simulations of the liquid-metal--amorphous-semiconductor transition in Ge. Our simulations are based on (a) finite-temperature density-functional theory of the one-electron states, (b) exact energy minimization and hence calculation of the exact Hellmann-Feynman forces after each molecular-dynamics step using preconditioned conjugate-gradient techniques, (c) accurate nonlocal pseudopotentials, and (d) Nos\'e dynamics for generating a canonical ensemble. This method gives perfect control of the adiabaticity of the electron-ion ensemble and allows us to perform simulations over more than 30 ps. The computer-generated ensemble describes the structural, dynamic, and electronic properties of liquid and amorphous Ge in very good agreement with experiment. The simulation allows us to study in detail the changes in the structure-property relationship through the metal-semiconductor transition. We report a detailed analysis of the local structural properties and their changes induced by an annealing process. The geometrical, bonding, and spectral properties of defects in the disordered tetrahedral network are investigated and compared with experiment.
Hodgkin's lymphoma: the role of cell surface receptors in regulation of tumor cell fate. (2010)

The review presents the current views on the role of cell surface receptors in maintenance of HL microenvironment favorable for HRS cells survival.
Human T-cell mitogen-activated protein kinase kinases are related to yeast signal transduction kinases. (1992)

Mitogen-activated protein (MAP) kinase kinases, intermediates in a growth factor-stimulated protein kinase cascade, are dual specificity protein kinases that specifically phosphorylate and activate MAP kinases in response to extracellular signals. Here, we report the cloning of two forms of cDNA that encode this protein from human T-cells. MKK1a encodes a protein with predicted molecular size of 43,439 Da. Overexpression of this clone in COS cells led to elevated levels of protein and phorbol ester-stimulated MAP kinase kinase activity, confirming that MKK1a encodes the predicted protein. MKK1b, which appears to be an alternatively spliced form of the MKK1a gene, encodes a protein with predicted molecular size of 40,745 Da. Northern analysis revealed that the MKK1 cDNA hybridizes with a single 2.6-kilobase mRNA species in all human tissues examined. Sequence comparison shows homology to a group of yeast kinases that participate in signal transduction and to subdomain XI of other dual specificity kinase.
Conformational epitope matching and prediction based on protein surface spiral features (2021)

The proposed method significantly improves the performance of traditional epitope prediction. Matching followed by prediction is an efficient and effective approach compared to predicting directly on specific surfaces containing antigenic characteristics.
Biochemical characterization of the active heterodimer form of human heparanase (Hpa1) protein expressed in insect cells (2003)

The mammalian endoglycosidase heparanase (Hpa1) is primarily responsible for cleaving heparan sulphate proteoglycans (HSPGs) present on the basement membrane of cells and its potential for remodelling the extracellular matrix (ECM) could be important in embryonic development and tumour metastasis. Elevated expression of this enzyme has been implicated in various pathological processes including tumour cell proliferation, metastasis, inflammation and angiogenesis. The enzyme therefore represents a potential therapeutic target. Hpa1 protein is initially synthesized as an inactive 65 kDa proenzyme that is then believed to be subsequently activated by proteolytic cleavage to generate an active heterodimer of 8 and 50 kDa polypeptides. By analysis of a series of Hpa1 deletion proteins we confirm that the 8 kDa subunit is essential for enzyme activity. We present here for the first time an insect cell expression system used for the generation of large amounts of recombinant protein of high specific activity. Individual subunits were cloned into baculoviral secretory vectors and co-expressed in insect cells. Active secreted heterodimer protein was recovered from the medium and isolated by a one-step heparin-Sepharose chromatography procedure to give protein of >90% purity. The recombinant enzyme behaved similarly to the native protein with respect to the size of HS fragments liberated on digestion, substrate cleavage specificity and its preference for acidic pH. A significant amount of activity, however, was also detectable at physiological pH values, as measured both by an in vitro assay and by in vivo degradation of cell-bound heparan sulphate.