gebhart/patrepeval huggingface dataset:
Mechanistic Studies of the Process of Amyloid Fibrils Formation by the Use of Peptide Fragments and Analogues: Implications for the Design of Fibrillization Inhibitors (2002)

The process of amyloid fibrils formation is a common mechanism of a large number of unrelated infectious, genetic and spontaneous diseases. A partial list includes the bovine spongiform encephalopathy (BSE), Alzheimer's diseases, Type II diabetes, Creutzfeldt-Jakob disease, and various unrelated amyloidosis diseases. In spite of its significant clinical importance, the mechanism of fibrillization is not fully understood. This review discusses the recent advancements in the mechanistic studies of amyloid formation by the use peptide fragments and analogues of amyloid-forming proteins and polypeptides. The use of short peptide shed much light of the mechanism of amyloid fibrillization. Recent studies clearly prove that very short peptide fragments (as short as pentapeptides) can form well-ordered amyloidal structures. Therefore, the molecular recognition and self-assembly process that lead to the formation of order structures is being mediated by small structural elements. Analysis of short amyloid-related fragment by the use of an alanine-scan and sequence analysis of a variety of unrelated peptide and protein fragments suggest that aromatic interaction may play a central role in the process of amyloid formation. Inhibitors that are based on the short aromatic elements already demonstrated clear potency in arresting the process of amyloid fibrils formation. Taken together, the recent advancement in the mechanistic understanding of the process of amyloid fibrils formation has a major importance in the development of inhibitors of fibrillization that may serve as future therapeutic means to treat amyloid diseases.
Mother rotors and fibrillatory conduction: a mechanism of atrial fibrillation (2002)

Atrial fibrillation (AF) is the most common sustained cardiac arrhythmia and the major cardiac cause of stroke. Recent studies in patients with paroxysmal AF have shown that the arrhythmia is triggered by focal sources localized usually in one of the cardiac veins. However, in chronic AF, the prevailing theory is that multiple random wavelets of activation coexist to create an unorganized atrial rhythm. Experiments in isolated hearts have demonstrated that stable, self-sustained rotors can exist in the atria and that high frequency activation by such rotors results in the complex patterns of activation that characterize AF. Studies in animals and patients support the view that at least some cases of paroxysmal and chronic AF are the result of the uninterrupted periodic activity of discrete reentrant sites. In this brief review article, we examine historical data and more recent experimental evidence behind the hypothesis that AF may be organized by one, or a small number of high-frequency reentrant sources localized in the left atrium. We then discuss the potential implications and evidence supporting such a hypothesis for human AF. Finally, we suggest future studies designed to unravel the detailed molecular, cellular and pathophysiological mechanisms responsible for AF initiation and maintenance. The work discussed may open potentially exciting new diagnostic and therapeutic possibilities.
Community Structures of Fecal Bacteria in Cattle from Different Animal Feeding Operations (2011)

The fecal microbiome of cattle plays a critical role not only in animal health and productivity but also in food safety, pathogen shedding, and the performance of fecal pollution detection methods. Unfortunately, most published molecular surveys fail to provide adequate detail about variability in the community structures of fecal bacteria within and across cattle populations. Using massively parallel pyrosequencing of a hypervariable region of the rRNA coding region, we profiled the fecal microbial communities of cattle from six different feeding operations where cattle were subjected to consistent management practices for a minimum of 90 days. We obtained a total of 633,877 high-quality sequences from the fecal samples of 30 adult beef cattle (5 individuals per operation). Sequence-based clustering and taxonomic analyses indicate less variability within a population than between populations. Overall, bacterial community composition correlated significantly with fecal starch concentrations, largely reflected in changes in the Bacteroidetes, Proteobacteria, and Firmicutes populations. In addition, network analysis demonstrated that annotated sequences clustered by management practice and fecal starch concentration, suggesting that the structures of bovine fecal bacterial communities can be dramatically different in different animal feeding operations, even at the phylum and family taxonomic levels, and that the feeding operation is a more important determinant of the cattle microbiome than is the geographic location of the feedlot.
Activators of Protein Kinase C Induce Dissociation of CD4, But Not CD8, from p56 lck (1989)

The CD4 and CD8 T cell receptor accessory molecules can both be isolated from T lymphocytes in association with p56lck, a membrane-associated, cytoplasmic tyrosine protein kinase that is expressed exclusively in lymphoid cells. The enzymatic activity of p56lck may therefore be regulated by CD4 and CD8 and be important in antigen-induced T cell activation. Exposure of human T cells and some mouse T cells to the tumor promoter 12-O-tetradecanoyl phorbol-13-acetate (TPA), an activator of protein kinase C, caused the dissociation of p56lck and CD4. Activation of protein kinase C may therefore interrupt regulation of p56lck by CD4 and alter the ability of p56lck to interact with polypeptide substrates. In contrast, exposure of cells to TPA did not cause dissociation of p56lck and CD8. Regulation of p56lck by CD4 may therefore differ from regulation by CD8.
High performance mixed matrix membranes (MMMs) composed of ZIF-94 filler and 6FDA-DAM polymer (2017)

Carbon capture and storage (CCS) using membranes for the separation of CO 2 holds great promise for the reduction of atmospheric CO 2 emissions from fuel combustion and industrial processes. Among the different process outlines, post-combustion CO 2 capture could be easily implemented in existing power plants. However, for this technology to become viable, new membrane materials have to be developed. In this article we present the development of high performance mixed matrix membranes (MMMs) composed of ZIF-94 filler and 6FDA-DAM polymer matrix. The CO 2 /N 2 separation performance was evaluated by mixed gas tests (15CO 2 :85N 2 ) at 25 C and 1-4 bar transmembrane pressure difference. The CO 2 membrane permeability was increased by the addition of the ZIF-94 particles, maintaining a constant CO 2 /N 2 selectivity of ~22. The largest increase in CO 2 permeability of ~200% was observed for 40 wt% ZIF-94 loading, reaching the highest permeability (2310 Barrer) at similar selectivity among 6FDA-DAM MMMs reported in literature. For the first time, the ZIF-94 metal organic framework crystals with particle size smaller than 500 nm were synthesized using nonhazardous solvent (tetrahydrofuran and methanol) instead of dimethylformamide (DMF) in a scalable process. Membranes were characterized by three non-invasive image techniques, i.e. SEM, AFM and nanoscale infrared imaging by scattering-type scanning near-field optical microscopy (s-SNOM). The combination of these techniques demonstrates a very good dispersion and interaction of the filler in the polymer layer, even at very high loadings.
Market-based cluster resource management (2001)

Resource management in high-performance, cluster computer systems is a challenging problem. Resources must be allocated amongst competing applications of varying levels of importance, and aggregate resource demand needs to be controlled to keep the system in a comfortable regime of operation. Effectively performing these tasks requires knowledge of user valuations of the resources being allocated and having a feedback signal that causes users to back off the system when it is overloaded. Unfortunately, current approaches to cluster resource management provide little, if any, means for users to express resource valuations and to inuence their resource allocations. In addition, while feedback signals are provided, there are no associated incentives for users to pay attention to and respond to them. As a result, traditional systems are incapable of delivering the maximum possible value to users. The thesis of this work is that...
Linking multimedia presentations with their symbolic source documents (2003)

An algorithm is presented that automatically matches images of presentation slides to the symbolic source file (e.g., PowerPoint™ or Acrobat™) from which they were generated. The images are captured either by tapping the video output from a laptop connected to a projector or by taking a picture of what's displayed on the screen in a conference room. The matching algorithm extracts features from the image data, including OCR output, edges, projection profiles, and layout and determines the symbolic file that contains the most similar collection of features. This algorithm enables several unique applications for enhancing a meeting in real-time and accessing the audio and video that were recorded while a presentation was being given. These applications include the simultaneous translation of presentation slides during a meeting, linking video clips inside a PowerPoint file that show how each slide was described by the presenter, and retrieving presentation recordings using digital camera images as queries.
T-cell receptor antagonists induce Vav phosphorylation by selective activation of Fyn kinase (2000)

T cell receptor (TCR) antagonists inhibit antigen-induced T cell activation and by themselves fail to induce phenotypic changes associated with T cell activation. However, we have recently shown that TCR antagonists are inducers of antigen-presenting cell (APC)-T cell conjugates. The signaling pathway associated with this cytoskeleton-dependent event appears to involve tyrosine phosphorylation and activation of Vav. In this study, we investigated the role played by the protein tyrosine kinases Fyn, Lck, and ZAP-70 in antagonist-induced signaling pathway. Antagonist stimulation increased tyrosine phosphorylation and kinase activity of Fyn severalfold, whereas little or no increase in Lck and ZAP-70 activity was observed. Second, TCR stimulation of Lck(-), Fyn(hi) Jurkat cells induced strong tyrosine phosphorylation of Vav. In contrast, minimal increase in tyrosine phosphorylation of Vav was observed in Lck(hi), Fyn(lo) Jurkat cells. Finally, study of T cells from a Fyn-deficient TCR transgenic mouse also showed that Fyn was required for tyrosine phosphorylation and activation of Vav induced by both antagonist and agonist peptides. The deficiency in Vav phosphorylation in Fyn-deficient T cells was associated with a defect in the formation of APC-T cell conjugates when T cells were stimulated with either agonist or antagonist peptide. We conclude from these results that Vav is a selective substrate for Fyn, especially under conditions of low-affinity TCR-mediated signaling, and that this signaling pathway involving Fyn, Vav, and Rac-1 is required for the cytoskeletal reorganization that leads to T cell-APC conjugates and the formation of the immunologic synapse.
Recombinant Vaccinia/Venezuelan Equine Encephalitis (VEE) Virus Expresses VEE Structural Proteins (1988)

cDNA molecules encoding the structural proteins of the virulent Trinidad donkey and the TC-83 vaccine strains of Venezuelan equine encephalitis (VEE) virus were inserted under control of the vaccinia virus 7.5K promoter into the thymidine kinase gene of vaccinia virus. Synthesis of the capsid protein and glycoproteins E2 and E1 of VEE virus was demonstrated by immunoblotting of lysates of CV-1 cells infected with recombinant vaccinia/VEE viruses. VEE glycoproteins were detected in recombinant virus-infected cells by fluorescent antibody (FA) analysis performed with a panel of VEE-specific monoclonal antibodies. Seven E2-specific epitopes and two of four E1-specific epitopes were demonstrated by FA.
Preferential expression of an ammonium transporter and of two putative nitrate transporters in root hairs of tomato. (1996)

Root hairs as specialized epidermal cells represent part of the outermost interface between a plant and its soil environment. They make up to 70% of the root surface and, therefore, are likely to contribute significantly to nutrient uptake. To study uptake systems for mineral nitrogen, three genes homologous to Arabidopsis nitrate and ammonium transporters (AtNrt1 and AtAmt1) were isolated from a root hair-specific tomato cDNA library. Accumulation of LeNrt1-1, LeNrt1-2, and LeAmt1 transcripts was root-specific, with no detectable transcripts in stems or leaves. Expression was root cell type-specific and regulated by nitrogen availability. LeNrt1-2 mRNA accumulation was restricted to root hairs that had been exposed to nitrate. In contrast, LeNrt1-1 transcripts were detected in root hairs as well as other root tissues under all nitrogen treatments applied. Analogous to LeNrt1-1, the gene LeAmt1 was expressed under all nitrogen conditions tested, and root hair-specific mRNA accumulation was highest following exposure to ammonium. Expression of LeAMT1 in an ammonium uptake-deficient yeast strain restored growth on low ammonium medium, confirming its involvement in ammonium transport. Root hair specificity and characteristics of substrate regulation suggest an important role of the three genes in uptake of mineral nitrogen.
Experiments in Optimal Control of a Flexible Arm with Passive Damping (1985)

Presented at the Fifth VPI &amp;SU / AIAA Symposium on Dynamics and Control of Large Structures, Blacksburg, VA, June 12, 1985.
Chemokines, inflammation and the immune system. (1994)

The chemokine superfamily comprise two families of small secreted proteins that, with the exception of RANTES, beta-TG, and PF-4, are not expressed in resting cells but are rapidly induced in response to various inflammatory and mitogenic stimuli. These proteins function as chemoattractants and activating agents for inflammatory cells. At present, it appears that each of the chemokines have some activities that are unique and many that are overlapping. Important areas that still need to be unravelled are the signal transduction pathways that lead to induction of these genes and the identification of the serpentine receptors and signal transduction pathways that are activated by these proteins. alpha and beta chemokines are implicated as major participants in acute as well as chronic inflammatory reactions, inhibition of haematopoeisis, modulation of angiogenesis, and fibroplasia. Chemokines that act on T lymphocytes presumably influence the recruitment of immunocompetent cells to inflammatory sites. Although there is no evidence that chemokines play a role in the induction of immune reactions, they undoubtedly promote the effector limb of immunity. The likely possibility that chemokines may also contribute to the normal homing and distribution of leukocytes also needs to be evaluated. Although chemokines obviously have major differentiative effects on the functions of target cells, the possibility that they act as costimulants of cell growth also needs more study. Finally, chemokines are attractive targets for the development of new therapeutic agents. Inhibition of their activities may be an effective anti-inflammatory strategy; promoting their activity might enhance wound healing and tissue repair.
Nerve growth factor receptor immunoreactivity in the new world monkey (Cebus apella) and human cerebellum (1991)

The present study used the NGFR-5 monoclonal antibody raised against human nerve growth factor receptor (NGFR) to determine the extent of NGFR immunoreactivity within the embryonic and young adult Cebus apella cerebellum as well as the human cerebellum. Immunohistochemically processed tissue revealed NGFR expressing Purkinje cell somata, axons, and dendrites, the latter being observed within the molecular layer of both adult species. Within all regions of the cerebellum we observed both darkly and lightly immunostained Purkinje cells. The proximal axons of these cells, which were visualized for short distances within the granular cell layer, appeared to contain bulbous aggregates of reaction product. In sagittal sections, the full extent of the Purkinje cell dendritic tree was observed in the more lightly stained portions of the cerebellum. In situ hybridization experiments revealed NGFR mRNA within Purkinje cells in a pattern similar to that seen with immunohistochemistry. The distribution of NGFR immunoreactivity within the cerebellum exhibits a general topographic organization with the heaviest and most consistent staining occurring within the archi- and neocerebellum and weaker staining within the paleocerebellum. In fetal Cebus monkey cerebellum obtained at gestational day 50 and 70, NGFR immunoreactivity was observed as a band composed of developing Purkinje cell neurites. These profiles were seen in the paleo- and neocerebellum, but not the archicerebellum. The present investigation is the first demonstration of NGFR immunoreactive profiles in the adult monkey and human cerebellum. These findings suggest that nerve growth factor may influence locomotor and vestibular behaviors that are mediated by cerebellar circuity. The precise mode of action for the NGF/NGFR system within the cerebellum remains to be determined.
The contributions of Ca2+, phospholipids and tissue-factor apoprotein to the activation of human blood-coagulation factor X by activated factor VII (1990)

In the extrinsic pathway of blood coagulation, Factor X is activated by a complex of tissue factor, factor VII(a) and Ca2+ ions. Using purified human coagulation factors and a sensitive spectrophotometric assay for Factor Xa, we could demonstrate activation of Factor X by Factor VIIa in the absence of tissue-factor apoprotein, phospholipids and Ca2+. This finding allowed a kinetic analysis of the contribution of each of the cofactors. Ca2+ stimulated the reaction rate 10-fold at an optimum of 6 mM (Vmax. of 1.1 x 10(-3) min-1) mainly by decreasing the Km of Factor X (to 11.4 microM). In the presence of Ca2+, 25 microM-phospholipid caused a 150-fold decrease of the apparent Km and a 2-fold increase of the apparent Vmax. of the reaction; however, both kinetic parameters increased with increasing phospholipid concentration. Tissue-factor apoprotein contributed to the reaction rate mainly by an increase of the Vmax., in both the presence (40,500-fold) and absence (4900-fold) of phospholipid. The formation of a ternary complex of Factor VIIa with tissue-factor apoprotein and phospholipid was responsible for a 15 million-fold increase in the catalytic efficiency of Factor X activation. The presence of Ca2+ was absolutely required for the stimulatory effects of phospholipid and apoprotein. The data fit a general model in which the Ca2(+)-dependent conformation allows Factor VIIa to bind tissue-factor apoprotein and/or a negatively charged phospholipid surface resulting into a decreased intrinsic Km and an increased Vmax. for the activation of fluid-phase Factor X.
Physicochemical properties of phospborothioate oligodeoxynucleotides (1988)

We have recently shown that phosphorothioate (PS) oligodeoxynucleotide (ODN) analogs, unlike their normal congeners, exhibit significant anti-HIV activity (Matsukura et al., (1987) Proc. Natl. Acad. Sci. USA 84, 7706-7710). We now report the syntheses, melting temperatures (Tm), and nuclease susceptibilities of a series of phosphorothioate ODN analogs. These include all-PS duplexes, duplexes with one normal chain and the other chain either all-PS, or end-capped with several PS groups at both 3' and 5' ends. The DNase susceptibilities of the S-ODNs are much less than the normal phosphodiesters, but by contrast duplexes of poly-rA with S-dT40 are much more susceptible to RNase H digestion. The Tm's for AT base pairs of S-ODNs are significantly depressed relative to normals, while GC base pairs show much less Tm depression. The Tm's of S-dT oligomers with poly-rA are reduced relative to the duplexes with normal dA oligomers. These results have significance for the biological properties of these analogs as anti-message inhibitors of gene expression, and provide a rational basis for the S-dC/G sequences as potential effective anti-AIDS agents.
Análisis comparativo del Libro de Alexandre (Estrofas 322-762) y la Ilíada de Homero (1998)

Comparacion de la obra medieval El libro de Alexandre (Estrofas 322-762) con la Iliada de Homero, con un estudio de las ediciones del texto castellano, y un breve analisis de la obra de Homero, confrontando las estrofas citadas con la obra griega.
Postanesthetic Vasoconstriction Slows Peripheral-to-Core Transfer of Cutaneous Heat, Thereby Isolating the Core Thermal Compartment (1997)

Forced-air warming during anesthesia increases core temperature comparably with and without thermoregulatory vasoconstriction. In contrast, postoperative forced-air warming may be no more effective than passive insulation. Nonthermoregulatory anesthesia-induced vasodilation may thus influence heat transfer. We compared postanesthetic core rewarming rates in volunteers given cotton blankets or forced air. Additionally, we compared increases in peripheral and core heat contents in the postanesthetic period with data previously acquired during anesthesia to determine how much vasomotion alters intercompartmental heat transfer. Six men were anesthetized and cooled passively until their core temperatures reached 34 [degree sign] C. Anesthesia was then discontinued, and shivering was prevented by giving meperidine. On one day, the volunteers were covered with warmed blankets for 2 h; on the other, volunteers were warmed with forced air. Peripheral tissue heat contents were determined from intramuscular and skin thermocouples. Predicted changes in core temperature were calculated assuming that increases in body heat content were evenly distributed. Predicted changes were thus those that would be expected if vasomotor activity did not impair peripheral-to-core transfer of applied heat. These results were compared with those obtained previously in a similar study of anesthetized volunteers. Body heat content increased 159 +/- 35 kcal (mean +/- SD) more during forced-air than during blanket warming (P < 0.001). Both peripheral and core temperatures increased significantly faster during active warming: 3.3 +/- 0.7[degree sign]C and 1.1 +/- 0.4[degree sign]C, respectively. Nonetheless, predicted core temperature increase during forced-air warming exceeded the actual temperature increase by 0.8 +/- 0.3[degree sign]C (P < 0.001). Vasoconstriction thus isolated core tissues from heat applied to the periphery, with the result that core heat content increased 32 +/- 12 kcal less than expected after 2 h of forced-air warming (P < 0.001). In contrast, predicted and actual core temperatures differed only slightly in the anesthetized volunteers previously studied. In contrast to four previous studies, our results indicate that forced-air warming increases core temperature faster than warm blankets. Postanesthetic vasoconstriction nonetheless impeded peripheral-to-core heat transfer, with the result that core temperatures in the two groups differed less than might be expected based on systemic heat balance estimates. Implications: Comparing intercompartmental heat flow in our previous and current studies suggests that anesthetic-induced vasodilation influences intercompartmental heat transfer and distribution of body heat more than thermoregulatory shunt vasomotion. (Anesth Analg 1997;85:899-906)