gebhart/patrepeval huggingface dataset:
γδ Lymphocyte Response to Porcine Reproductive and Respiratory Syndrome Virus (2005)

Porcine reproductive and respiratory syndrome virus (PRRSV) continues to be one of the most important diseases facing swine industry today. Following PRRSV infection pigs develop both humoral and cell-mediated responses following PRRSV exposure; however, the relative importance in protection and clearance of the virus is not yet completely understood. Swine contain a large percentage of gammadelta T-lymphocytes in peripheral circulation capable of responding to various pathogens in both an innate and specific immune response. The objectives of this study were to determine whether gammadelta lymphocytes functionally respond to PRRSV upon initial exposure and re-exposure. Four month old PRRSV free gilts were intranasally inoculated with a field isolate MN-30100 then assessed at various time points post infection. On day 120, pigs were re-exposed with MN-30100 PRRSV strain and subsequently were bled on days 0, 7, and 14 post re-exposure. Lymphocyte subpopulations, antigen specific proliferation, and IFN-gamma production were evaluated throughout the study. Circulating gammadelta lymphocytes in PRRSV exposed animals expanded between days 14 to 70 (d14-d70, p = 0.016); following antigen stimulation, gammadelta lymphocyte proliferated by day 14 (d0-d14, p = 0.001) continuing through day 60. gammadelta lymphocytes produced IFN-gamma by day 14 pi continuing through day 50 (d0-d50, p = 0.004). Following re-exposure both gammadelta+ and CD4+ lymphocytes increased in IFN-gamma production. These results are not fully conclusive on the role of gammadelta lymphocytes against PRRSV; the data indicate that gammadelta lymphocytes specifically respond to PRRSV.
ECgene: Genome-based EST clustering and gene modeling for alternative splicing (2005)

With the availability of the human genome map and fast algorithms for sequence alignment, genome-based EST clustering became a viable method for gene modeling. We developed a novel gene-modeling method, ECgene (Gene modeling by EST Clustering), which combines genome-based EST clustering and the transcript assembly procedure in a coherent and consistent fashion. Specifically, ECgene takes alternative splicing events into consideration. The position of splice sites (i.e., exon-intron boundaries) in the genome map is utilized as the critical information in the whole procedure. Sequences that share any splice sites are grouped together to define an EST cluster in a manner similar to that of the genome-based version of the UniGene algorithm. Transcript assembly is achieved using graph theory that represents the exon connectivity in each cluster as a directed acyclic graph (DAG). Distinct paths along exons correspond to possible gene models encompassing all alternative splicing events. EST sequences in each cluster are subclustered further according to the compatibility with gene structure of each splice variant, and they can be regarded as clone evidence for the corresponding isoform. The reliability of each isoform is assessed from the nature of cluster members and from the minimum number of clones required to reconstruct all exons in the transcript.
Deoxycytidine kinase-mediated toxicity of deoxyadenosine analogs toward malignant human lymphoblasts in vitro and toward murine L1210 leukemia in vivo. (1980)

An inherited deficiency of adenosine deaminase (adenosine aminohydrolase, EC 3.5.4.4) produces selective lymphopenia and immunodeficiency disease in humans. Previous experiments have suggested that lymphospecific toxicity in this condition might result from the selective accumulation of toxic deoxyadenosine nucleotides by lymphocytes with high deoxycytidine kinase, levels and low deoxynucleotide dephosphorylating activity. The present experiments were designed to determine if deoxyadenosine analogs which are not substrates for adenosine deaminase might similarly be toxic toward lymphocytes and lymphoid tumors. Two such compounds, 2-chlorodeoxyadenosine and 2-fluorodeoxyadenosine, at concentrations of 3 nM and 0.15 microM, respectively, inhibited by 50% the growth of human CCRF-CEM malignant lymphoblasts in vitro. Each was phosphorylated in intact cells by deoxycytidine kinase accumulated as the nucleoside triphosphate, and inhibited DNA synthesis more than RNA synthesis. Both deoxynucleosides had significant chemotherapeutic activity against lymphoid leukemia L1210 in mice.
An integrated CAD-robotics system for total knee replacement surgery (2003)

An integrated system has been developed that allows the surgeon to more accurately place implant components during total knee surgery. A graphic computer displaying 3-D CT (computed tomography) data of the patient's knee is used to perform more informed and accurate preoperative planning. In the operating room, a robot and specially designed fixturing aid the surgeon in performing the bone resections as determined in the preoperative plan. Crucial to the accuracy of this system is the rigid immobilization of the involved bones and the robot's ability to determine their exact locations in space. The rationale and an overview of this system are presented as well as a discussion of some of the technical issues that have arisen.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The effects of acute or chronic cadmium exposure on the adult mouse CNS: a freeze-fracture study. (1985)

The effect of acute Cd exposure (0.5-12 mg CdCl2/kg body wt. for six hours) or chronic Cd exposure (40 ppm in the drinking water for 3 weeks) on the CNS of adult mice was investigated quantitatively by the use of the freeze-fracture technique to examine the nuclear membrane of cells from the cerebral cortex. Intramembrane particle density and nuclear pore density was determined for both the P face of the inner membrane and the E face of the outer membrane from control and experimental animals. The changes observed for both groups of experimental animals were similar in that particle numbers for both P and E faces were significantly increased over control values while nuclear pore numbers were unaffected. For the acute doses the increases were dose-dependent.
Experimental and Theoretical Studies of Transport through Large Scale, Partially Aligned Arrays of Single-Walled Carbon Nanotubes in Thin Film Type Transistors (2007)

Gate-modulated transport through partially aligned films of single-walled carbon nanotubes (SWNTs) in thin film type transistor structures are studied experimentally and theoretically. Measurements are reported on SWNTs grown by chemical vapor deposition with systematically varying degrees of alignment and coverage in transistors with a range of channel lengths and orientations perpendicular and parallel to the direction of alignment. A first principles stick-percolation-based transport model provides a simple, yet quantitative framework to interpret the sometimes counterintuitive transport parameters measured in these devices. The results highlight, for example, the dramatic influence of small degrees of SWNT misalignment on transistor performance and imply that coverage and alignment are correlated phenomena and therefore should be simultaneously optimized. The transport characteristics reflect heterogeneity in the underlying anisotropic metal-semiconductor stick-percolating network and cannot be reproduced by classical transport models.
TIG1 Promotes the Development and Progression of Inflammatory Breast Cancer through Activation of Axl Kinase (2013)

Inflammatory breast cancer (IBC) is the most lethal form of breast cancer, but the basis for its aggressive properties are not fully understood. In this study, we report that high tumoral expression of TIG1 (RARRES1), a functionally undefined membrane protein, confers shorter survival in patients with IBC. TIG1 depletion decreased IBC cell proliferation, migration, and invasion in vitro and inhibited tumor growth of IBC cells in vivo. We identified the receptor tyrosine kinase, Axl, as a TIG1-binding protein. TIG1 interaction stablilized Axl by inhibiting its proteasome-dependent degradation. TIG1-depleted IBC cells exhibited reduced Axl expression, inactivation of NF-κB, and downregulation of matrix metalloproteinase-9, indicating that TIG1 regulates invasion of IBC cells by supporting the Axl signaling pathway in IBC cells. Consistent with these results, treatment of IBC cells with the Axl inhibitor SGI-7079 decreased their malignant properties in vitro. Finally, TIG1 expression correlated positively with Axl expression in primary human IBC specimens. Our findings establish that TIG1 positively modifies the malignant properties of IBC by supporting Axl function, advancing understanding of its development and rationalizing TIG1 and Axl as promising therapeutic targets in IBC treatment.
PHARMACOLOGY OF NEUROTROPHIC FACTORS (1997)

The field of neurotrophic factor pharmacology emerged during the past decade with the discovery that these proteins can counteract neuronal atrophy and death in the adult nervous system. These concepts are being tested in clinical trials. Therapeutic use of neurotrophic proteins seems practical for diseases of the peripheral nervous system (PNS), where they can be given by systemic administration. For diseases of the CNS, special administration strategies will have to be developed to deliver the neurotrophic factors into the brain. The development of small molecule mimetics represents an alternative approach that is actively pursued to provide brain-penetrant neurotrophics.
Butyramide and monobutyrin: growth inhibitory and differentiating agents. (1993)

Butyramide and monobutyrin were chosen for study as neutral compounds that might exhibit some of the growth inhibitory and differentiating effects of butyrate. Inhibitory effects on DNA synthesis in hepatoma cells and on cellular proliferation in mouse erythroleukemia cells were observed. Induction of differentiation by butyramide and monobutyrin was seen in mouse erythroleukemia cells as monitored by increased synthesis of hemoglobin and H1 zero histone. Butyramide and monobutyrin were less effective inducers of hemoglobin synthesis than butyrate but their neutral character may offer an advantage in the induction of tumor cell differentiation.
Successful treatment of a patient with takayasu arteritis using a humanized anti–interleukin‐6 receptor antibody (2008)

Takayasu arteritis (TA) is a chronic inflammatory disease that involves the aorta and its major branches. Since overproduction of interleukin-6 (IL-6) seems to play a pathogenic role in TA, we used the anti-IL-6 receptor (IL-6R) antibody tocilizumab to treat a 20-year-old woman with refractory active TA complicated by ulcerative colitis (UC). Treatment with tocilizumab improved the clinical manifestations of TA and the abnormal laboratory findings in this patient and ameliorated the activity of UC. These results indicate that IL-6R inhibition with tocilizumab might be a future treatment option for TA.
Expression, purification and characterization of recombinant human proinsulin (1997)

We have recently developed a method to produce native human proinsulin using a bacterial expression system. A proinsulin fusion protein was recovered from inclusion bodies and cleaved using cyanogen bromide. The released proinsulin polypeptide was S-sulfonated and purified by anion exchange chromatography. Following refolding, proinsulin was purified by reversed-phase high-performance liquid chromatography. Combined peptide mapping and mass spectrometric analysis indicated that the proinsulin contained the correct disulfide bridging pattern. This proinsulin will be used to study the specificity of the furin/PC family of converting enzymes by using it as a substrate in a recently developed assay.
Effect of TAAR1/5-HT1A agonist SEP-363856 on REM sleep in humans (2021)

SEP-363856 is a trace amine-associated receptor 1 (TAAR1) and 5-hydroxytryptamine type 1A (5-HT<sub>1A</sub>) agonist, currently in Phase 3 clinical trials for the treatment of schizophrenia. Although SEP-363856 activates TAAR1 and 5-HT<sub>1A</sub> receptors in vitro, an accessible marker of time- and concentration-dependent effects of SEP-363856 in humans is lacking. In rodents, SEP-363856 has been shown to suppress rapid eye movement (REM) sleep. The aim of the current study was to translate the REM sleep effects to humans and determine pharmacokinetic/pharmacodynamic (PK/PD) relationships of SEP-363856 on a measure of brain activity. The effects of SEP-363856 were evaluated in a randomized, double-blind, placebo-controlled, 2-way crossover study of single oral doses (50 and 10 mg) on REM sleep in healthy male subjects (N = 12 at each dose level). Drug concentrations were sampled during sleep to interpolate individual subject's pharmacokinetic trajectories. SEP-363856 suppressed REM sleep parameters with very large effect sizes (>3) following single doses of 50 mg and plasma concentrations ≥100 ng/mL. Below that effective concentration, the 10 mg dose elicited much smaller effects, increasing only the latency to REM sleep (effect size = 1). The PK/PD relationships demonstrated that REM sleep probability increased as drug concentrations declined below 100 ng/mL over the course of the night. SEP-363856 was generally safe and well tolerated at both doses. The REM sleep-suppressing effects of SEP-363856 provide an accessible marker of brain activity, which can aid in dose selection and help elucidate its therapeutic potential in further clinical trials.
Development of Gasoline Direct Injection Engine (1997)

&lt;div class="htmlview paragraph"&gt;The major problems of the various mixture formation concepts for direct injection gasoline engines that have been proposed up to the present were caused by the difficulties of preparing the mixture with adequate strength at spark plug in wide range of engine operating conditions. Novel combustion control technologies proposed by Mitsubishi is one of the solution for these problems. By adopting upright straight intake ports to generate air tumble, an electromagnetic swirl injector to realize optimized spray dispersion and atomization and a compact piston cavity to maintain charge stratification, it has become possible to achieve super-lean stratified combustion for higher thermal efficiency under partial loads as well as homogeneous combustion to realize higher performance at full loads.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;GDI™ (Gasoline Direct Injection) engine adopting these technologies is developed. At partial loads, fuel economy improvement exceeding 30 % is realized. At higher loads, since air cooling by the latent heat of vaporization increases volumetric efficiency and reduces the octane number requirement, a high compression ratio of 12 to 1 can be adopted. As a result, 10% increase in performance is realized. NOx emission had been considered as one of the most significant issues of lean burn engines. This problem is solved by using the inherent characteristics of stratified combustion of high EGR tolerance and by the newly developed lean-NOx catalyst.&lt;/div&gt;
Wnt-induced dephosphorylation of Axin releases beta -catenin from the Axin complex (1999)

The stabilization of beta-catenin is a key regulatory step during cell fate changes and transformations to tumor cells. Several interacting proteins, including Axin, APC, and the protein kinase GSK-3beta are implicated in regulating beta-catenin phosphorylation and its subsequent degradation. Wnt signaling stabilizes beta-catenin, but it was not clear whether and how Wnt signaling regulates the beta-catenin complex. Here we show that Axin is dephosphorylated in response to Wnt signaling. The dephosphorylated Axin binds beta-catenin less efficiently than the phosphorylated form. Thus, Wnt signaling lowers Axin's affinity for beta-catenin, thereby disengaging beta-catenin from the degradation machinery.
Complement activation in relation to development of preeclampsia. (1991)

Six hundred eighty-five primigravidas followed as a series had complement activation evaluated by the formation of anaphylatoxins (C3a and C5a) and terminal C5b-9 complement complexes in venous blood. Samples for complement determinations were obtained four times during pregnancy, in pregnancy weeks 12-16, 20-24, 28-32, and 34-36. Seven of the women developed preeclampsia and one of them the syndrome of hemolysis, elevated liver enzymes, and low platelet count (HELLP syndrome). Eleven others with uncomplicated pregnancies were selected as a control group. Plasma samples were taken from these 18 women at delivery and 1 and 7 days after delivery. At delivery, plasma C5a levels were significantly greater in the preeclamptics than in controls, and four of the seven preeclamptics had elevated plasma C3a values compared with controls. One week after delivery, these plasma anaphylatoxins had returned to normal. Elevations of the anaphylatoxins could not be detected before the women developed clinical signs of preeclampsia. No alterations in terminal C5b-9 complement complexes could be observed in the women with preeclampsia. However, the women who developed HELLP syndrome had elevated plasma concentrations of C3a, C5a, and terminal C5b-9 complement complex at delivery. These values returned to the normal range 1 week after delivery. We conclude that complement activation in the systemic circulation does not occur early in pregnancy and that plasma concentrations of C3a, C5a, or terminal C5b-9 complement complex cannot be used as predictors of preeclampsia.
Delay fault models and test generation for random logic sequential circuits (1992)

The authors study the problem of delay fault modeling and test generation for any random logic sequential circuit. The proposed test generation method, based on transition and hazard states of signals, is applicable to any sequential circuit of either non-scan, scan or scan-hold type of design. Three fault models based on different initial state assumptions during the propagation of the fault effect to a primary output are proposed and analyzed using the proposed delay fault test generation method. A novel thirteen-value algebra is considered to simplify the analysis of robust and nonrobust tests during fault simulation of path delay faults. >
Star PolyMOCs with Diverse Structures, Dynamics, and Functions by Three‐Component Assembly (2016)

We report star polymer metal-organic cage (polyMOC) materials whose structures, mechanical properties, functionalities, and dynamics can all be precisely tailored through a simple three-component assembly strategy. The star polyMOC network is composed of tetra-arm star polymers functionalized with ligands on the chain ends, small molecule ligands, and palladium ions; polyMOCs are formed via metal-ligand coordination and thermal annealing. The ratio of small molecule ligands to polymer-bound ligands determines the connectivity of the MOC junctions and the network structure. The use of large M<sub>12</sub> L<sub>24</sub> MOCs enables great flexibility in tuning this ratio, which provides access to a rich spectrum of material properties including tunable moduli and relaxation dynamics.
Effects of intra-mammary bacterial infection with coagulase negative staphylococci and stage of lactation on shedding of epithelial cells and infiltration of leukocytes into milk: Comparison among cows, goats and sheep (2012)

The effects of mammary gland bacterial infection and stage of lactation on leukocyte infiltration into the mammary gland were compared among cows, goats and sheep. Animals were at two stages of lactation: mid or late. In mid-lactation animals, bacterial-free glands and coagulase negative Staphylococcus (CNS)-infected glands were compared. In late lactation only uninfected glands were studied. Of mid-lactation bacteria-free animals, goats had the highest number of leukocytes and % polymorphonuclears (PMNs), whereas sheep had the lowest and leukocytes number in cows were intermediate between sheep and goats. Based on %PMN, two cell clusters were found in sheep, which overlapped with the parallel cell clusters of cows and goats, but with a slightly higher number of leukocytes in each cell cluster. At late lactation, goats had higher values for %PMN and leukocyte numbers in comparison to cows, which had a similar cellular profile to sheep. The cellular immune response to CNS infection was similar for the three animal species, although the number of cells was different, while the basal cell level at mid-lactation and especially at the end of lactation was species specific.
Single Polymer Dynamics in an Elongational Flow (1997)

The stretching of individual polymers in a spatially homogeneous velocity gradient was observed through use of fluorescently labeled DNA molecules. The probability distribution of molecular extension was determined as a function of time and strain rate. Although some molecules reached steady state, the average extension did not, even after a approximately 300-fold distortion of the underlying fluid element. At the highest strain rates, distinct conformational shapes with differing dynamics were observed. There was considerable variation in the onset of stretching, and chains with a dumbbell shape stretched more rapidly than folded ones. As the strain rate was increased, chains did not deform with the fluid element. The steady-state extension can be described by a model consisting of two beads connected by a spring representing the entropic elasticity of a worm-like chain, but the average dynamics cannot.
A new isoform of the laminin receptor integrin alpha 7 beta 1 is developmentally regulated in skeletal muscle. (1993)

Within the integrin family, there are two groups of receptors that bind laminin. One of these groups comprises the heterodimers alpha 3 beta 1, alpha 6 beta 1, and alpha 7 beta 1, all of which bind the E8 fragment of laminin, and whose alpha subunits show significant homology at the amino acid sequence level. alpha 3 and alpha 6 exist as isoforms with distinct cytoplasmic domains (termed A and B), suggesting that they may couple laminin adhesion to distinct cellular responses. We report the identification of a new alpha 7 mRNA which encodes an alpha 7 protein isoform with an alternative cytoplasmic domain. Based on homology with alpha 3 and alpha 6 isoforms, this new isoform is classified as alpha 7A and the previously published one as alpha 7B. This result extends the similarity between alpha 3, alpha 6, and alpha 7 laminin receptor subunits and suggests a common ancestral gene. The alpha 7 beta 1 laminin receptor was proposed to be involved in myogenic differentiation. However, alpha 7 isoforms were not investigated in that context. We detected the alpha 7B isoform mRNA in all tissues and cell types tested, including myocardial and skeletal muscle. In contrast, the alpha 7A isoform was detectable exclusively in skeletal muscle, not in myocardial muscle or cells or any other tissues or cell lines tested. Furthermore, the differentiating skeletal muscle cell line C2C12 expressed only alpha 7B at the replicating myoblast stage and acquired alpha 7A expression upon induction of differentiation and fusion. Splicing of alpha 7B mRNA in C2C12 occurred shortly after myogenin expression and could be an indicator of progression through the program of skeletal muscle differentiation.