gebhart/patrepeval huggingface dataset:
Building the vertebrate vasculature: research is going swimmingly (2000)

The vertebrate vasculature develops in remarkably similar fashion in all vertebrates. A cohort of unspecified mesodermal cells differentiates into primitive endothelial cells, which migrate to and occupy positions within the stereotypical blueprint of the primitive vasculature. Once in position, these cells coalesce and form cords, which lumenize and become ensheathed by supporting pericytes and smooth muscle cells. This primitive vascular network is extensively remodeled in some places, and expanded by sprouting in others. Various studies using the mouse, quail/chick, and frog have uncovered a number of signals that guide these complex processes but many gaps still exist in our understanding of the mechanisms by which the embryonic vasculature is built. Because many questions will require in vivo studies to be properly addressed, the zebrafish, with its unique accessibility to analysis by combined embryological, molecular, and genetic methods, should prove invaluable in identifying new molecules involved in blood vessel development and integrating pathways that influence embryonic blood vessel formation.
Intracellular Compartment ation and Control of Alanine Metabolism in Rat Liver Parenchymal Cells (1982)

The catabolism of alanine in isolated rat liver cells was studied using a perifusion system in order to titrate the cells with different concentrations of alanine. The Concentrations of the components of the alanine aminotransferase reaction in the cytosolic and mitochondrial compartments were measured after digitonin fractionation of samples of the cell suspension taken during each steady state. Comparison of the mass‐action ratios with the equilibrium constant indicated that the cytosolic enzyme is poised towards pyruvate formation at all concentrations of alanine used, whereas the mitochondrial enzyme is always poised towards alanine formation. The calculated flux through cytosolic alanine aminotransferase, using literature data for the kinetic parameters of the enzyme and experimental data for the concentration of metabolites, was in close agreement with the measured carbon flux. It is concluded that the transamination step in alanine catabolism occurs in the cytosol. The concentration of the components of the glutamate dehydrogenase and 3‐hydroxybutyrate dehydrogenase reactions in the mitochondrial compartment during each steady state were also measured. The ΔG of the combined reactions did not change appreciably on increasing the extracellular alanine concentration to 0.6 mM. At higher alanine concentrations ΔG became slightly more negative. As the extracellular Concentration of alanine was increased, the concentration of glutamate in both the cytosolic and the mitochondrial compartments increased. However, the cytosolic alanine concentration was always lower than that in the extracellular compartment even at the highest concentration of alanine (6 mM) infused. When increasing concentrations of pyruvate were infused together with a fixed concentration of alanine (0.6 mM), the cytosolic concentration of alanine increased to levels even higher than that in the perifusate. However, there was no significant effect in the rate of formation of nitrogenous products. It is concluded that the transport of alanine across the plasma membrane is the only rate‐controlling step in alanine catabolism under the conditions used.
Involvement of endogenous tumor necrosis factor alpha and transforming growth factor beta during induction of collagen type II arthritis in mice. (1992)

Both tumor necrosis factor alpha (TNF-alpha) and transforming growth factor beta (TGF-beta) are found in synovial fluid from arthritic joints of humans and of rodents with experimental arthritis. The role of endogenously produced TGF-beta and TNF in the pathogenesis of collagen type II-induced arthritis (CIA) in DBA/1 mice was examined by determining the effect of neutralizing monoclonal antibodies to these factors on the course of the disease. Endogenously produced as well as systemically administered TGF-beta 1 and TNF-alpha had opposite effects, since TGF-beta 1 and anti-TNF protected against CIA, whereas anti-TGF-beta and TNF-alpha increased CIA incidence and/or severity. Intraperitoneally injected TGF-beta 1 at a dose of 2 micrograms per day for 14 days significantly ameliorated arthritis, even when started at the time of arthritis development, although it did not reverse established disease. The resistance to CIA induction caused by a prior intravenous injection of collagen type II was not significantly influenced by the simultaneous injection of TGF-beta 1, TNF-alpha, or interleukin 1 alpha. It is concluded that the endogenous production of TNF and TGF-beta is important in determining the course of CIA.
Diabetes: insulin resistance and derangements in lipid metabolism. Cure through intervention in fat transport and storage (2004)

We present multiple findings on derangements in lipid metabolism in type 2 diabetes. The increase in the intracellular deposition of triglycerides (TG) in muscles, liver and pancreas in subjects prone to diabetes is well documented and demonstrated to attenuate glucose metabolism by interfering with insulin signaling and insulin secretion. The obesity often associated with type 2 diabetes is mainly central, resulting in the overload of abdominal adipocytes with TG and reducing fat depot capacity to protect other tissues from utilizing a large proportion of dietary fat. In contrast to subcutaneous adipocytes, the central adipocytes exhibit a high rate of basal lipolysis and are highly sensitive to fat mobilizing hormones, but respond poorly to lipolysis restraining insulin. The enlarged visceral adipocytes are flooding the portal circulation with free fatty acids (FFA) at metabolically inappropriate time, when FFA should be oxidized, thus exposing nonadipose tissues to fat excess. This leads to ectopic TG accumulation in muscles, liver and pancreatic beta-cells, resulting in insulin resistance and beta-cell dysfunction. This situation, based on a large number of observations in humans and experimental animals, confirms that peripheral adipose tissue is closely regulated, performing a vital role of buffering fluxes of FFA in the circulation. The central adipose tissues tend to upset this balance by releasing large amounts of FFA. To reduce the excessive fat outflow from the abdominal depots and prevent the ectopic fat deposition it is important to decrease the volume of central fat stores or increase the peripheral fat stores. One possibility is to downregulate the activity of lipoprotein lipase, which is overexpressed in abdominal relatively to subcutaneous fat stores. This can be achieved by gastrointestinal bypass or gastroplasty, which decrease dietary fat absorption, or by direct means that include surgical removal of mesenteric fat. Indirect treatment consists of the compliant application of drastic lifestyle change comprising both diet and exercise and pharmacotherapy that reduces mesenteric fat mass and activity. The first step should be an attempt to effectively induce a lifestyle change. Next comes pharmacotherapy including acarbose, metformin, PPARgamma, or PPARgammaalpha agonists, statins and orlistat, estrogens in postmenopausal women or testosterone in men. Among surgical procedures, gastric bypass has been proven to produce beneficial results in advance of other surgical techniques, the evidence basis of which still needs strengthening.
The role of thrombin and protease-activated receptors in pain mechanisms (2010)

As our knowledge of the mechanisms underlying the sensation of pain continues to expand, researchers are constantly searching for novel therapeutic targets. One such novel pain pathway involves thrombin and its associated protease-activated receptor (PAR). Besides its traditional role in haemostasis, thrombin has multiple roles in both the central and peripheral nervous system including activation of microglia, regulation of neuronal death and neurite outgrowth, and influencing the transmission of pain signals in the nociceptive circuitry. Eventually therapeutic modalities directed at these targets could provide novel therapeutic approaches for treating chronic pain. The thrombin-associated PARs also have roles in inflammation, neurodevelopment, and conducting pain, both in conjunction with thrombin and independently. Recent laboratory evidence suggests that the PARs can attenuate pain mediated by the enteric nervous system in animal models (for example in pancreatitis and colitis). This review highlights several pathways in the mediation of pain sensation that can be influenced by thrombin.
The Cross-national Epidemiology of Panic Disorder (1997)

Panic disorder is relatively consistent, with a few exceptions, in rates and patterns across different countries. It is unclear why the rates of panic and other psychiatric disorders are lower in Taiwan.
Cerebral hemorrhage after intra-arterial thrombolysis for ischemic stroke (2001)

Symptomatic ICH after IA thrombolysis with r-proUK for acute ischemic stroke occurs early after treatment and has high mortality. The risk of symptomatic ICH may be increased in patients with a blood glucose >200 mg/dL at stroke onset.
Designing prodrugs for the treatment of Parkinson's disease (2012)

In order to strengthen the pharmacological activity of antiparkinsonian drugs, enhancing their penetration of the blood-brain barrier (BBB), different approaches are possible. Among these, the prodrug approach appeared to be the most promising, and many prodrugs have been prepared in an effort to optimize physicochemical characteristics. In addition, novel therapeutic strategies based on formulations linking dopaminergic drugs with neuroprotective agents, increasing LD striatal levels and offering sustained release of the drug without any fluctuation of brain concentration, offer promising avenues for development of other effective new treatments for PD.
FOXP3+ Regulatory T Cells Affect the Development and Progression of Hepatocarcinogenesis (2007)

Tregs play a role in controlling the immune response to HCC during the progression of hepatocarcinogenesis. It has been suggested that primary hepatic cancers develop in liver that is immunosuppressed by a marked infiltration of Tregs. A high prevalence of Tregs infiltrating HCC is thought to be an unfavorable prognostic indicator.
Colonic expression of leukotriene-pathway enzymes in inflammatory bowel diseases (2007)

The 5-lipoxygenase data provide a cellular basis for increased tissue synthesis of the leukotriene B(4), as reflected in the colonic mucosa and rectal dialysates of patients with active inflammatory bowel disease, which contributes to neutrophil influx and colonic injury. The COX-1/COX-2 data highlight the ambiguous functional role of prostanoid pathways in inflammatory bowel diseases.
Rapid and Efficient Hybridization-Triggered Crosslinking Within a DNA Duplex by an Oligodeoxyribonucleotide Bearing a Conjugated Cyclopropapyrroloindole (1996)

The antitumor antibiotic CC-1065 binds in the minor groove of double-stranded DNA, and the cyclopropapyrroloindole (CPI) subunit of the drug alkylates adjacent adenines at their N-3 position. We have attached racemic CPI to oligodeoxyribonucleotides (ODNs) via a terminal phosphorothioate at either the 3'- or 5'-end of the ODNs. These conjugates were remarkably stable in aqueous solution at neutral pH even in the presence of strong nucleophiles. When a 3'-CPI-ODN conjugate was hybridized to a complementary DNA strand at 37 degrees C, the CPI moiety alkylated nearby adenine bases of the complement efficiently and rapidly, with a half-life of a few minutes. The 4'-CPR- ODN conjugate showed very little reactivity within the duplex. CPI-ODN conjugates should be highly effective sequence-specific inhibitors of single-stranded viral DNA replication or gene selective inhibitors of transcription initiation.
Experience with Speech Communication in Packet Networks (1983)

The integration of digital voice with data in a common packet-switched network system offers a number of potential benefits, including reduced systems cost through sharing of switching and transmission resources, flexible internetworking among systems utilizing different transmission media, and enhanced services for users requiring access to both voice and data communications. Issues which it has been necessary to address in order to realize these benefits include reconstitution of speech from packets arriving at nonuniform intervals, maximization of packet speech multiplexing efficiency, and determination of the implementation requirements for terminals and switching in a large-scale packet voice/data system. A series of packet speech systems experiments to address these issues has been conducted under the sponsorship of the Defense Advanced Research Projects Agency (DARPA). In the initial experiments on the ARPANET, the basic feasibility of speech communication on a store-and-forward packet network was demonstrated. Techniques were developed for reconstitution of speech from packets, and protocols were developed for call setup and for speech transport. Later speech experiments utilizing the Atlantic packet satellite network (SATNET) led to the development of techniques for efficient voice conferencing in a broadcast environment, and for internetting speech between a store-and-forward net (ARPANEI) and a broadcast net (SATNET). Large-scale packet speech multiplexing experiments could not be carried out on ARPANET or SATNET where the network link capacities severely restrict the number of speech users that can be accommodated. However, experiments are currently being carried out using a wide-band satellite-based packet system designed to accommodate a sufficient number of simultaneous users to support realistic experiments in efficient statistical multiplexing. Key developments to date associated with the wide-band experiments have been 1) techniques for internetting via voice/data gateways from a variety of local access networks (packet cable, packet radio, and circuit-switched) to a long-haul broadcast satellite network and 2) compact implementations of packet voice terminals with full protocol and voice capabilities. Basic concepts and issues associated with packet speech systems are described. Requirements and techniques for speech processing, voice protocols, packetization and reconstitution, conferencing, and multiplexing are discussed in the context of a generic packet speech system configuration. Specific experimental configurations and key packet speech results on the ARPANET, SATNET, and wide-band system are reviewed.
Eliminating the Issue of Skin Color in Assessment of the Blanch Response (2001)

The observation of a significant difference in total hemoglobin at high and low pressure in both light- and dark-skinned groups in this study demonstrates the ability of visible and near-infrared spectroscopy to monitor blood volume changes associated with a blanch response. These findings support the potential use of this technology as the basis of a clinically useful blanch response tool that is insensitive to skin color.
Biological Activity of Lenalidomide and Its Underlying Therapeutic Effects in Multiple Myeloma (2012)

Lenalidomide is a synthetic compound derived by modifying the chemical structure of thalidomide. It belongs to the second generation of immunomodulatory drugs (IMiDs) and possesses pleiotropic properties. Even if lenalidomide has been shown to be active in the treatment of several hematologic malignancies, this review article is mostly focalized on its mode of action in multiple myeloma. The present paper is about the direct and indirect antitumor effects of lenalidomide on malignant plasmacells, bone marrow microenvironment, bone resorption and host's immune response. The molecular mechanisms and targets of lenalidomide remain largely unknown, but recent evidence shows cereblon (CRBN) as a possible mediator of its therapeutical effects.
Multi-Layer Resist Systems (1983)

6.1 Introduction The requirements on resist systems for modern IC fabrication are becoming more and more difficult to meet as the minimum feature size is reduced to the micrometer and submicrometer regime. As more exotic exposure sources are used, the available exposure intensity becomes limited, and the sensitivity of resist systems has to be improved to maintain a reasonable throughput. Furthermore, for smaller features, the vertical dimensions do not shrink as rapidly as the lateral dimensions, therefore, the height-to-width aspect ratio of resist images has to be higher. For example, a resist thickness of 1.5 - 2.0 μm is required for 1 - μm features. It reduces to 1-1.5 μm only when the feature size is reduced to 0.5 μm. Despite the aspect ratio requirement, maintaining linewidth control over high steps and at different parts of the wafer topography also becomes more difficult as the feature size becomes smaller. Many
A bacterial group II intron encoding reverse transcriptase, maturase, and DNA endonuclease activities: biochemical demonstration of maturase activity and insertion of new genetic information within the intron (1997)

The Lactococcus lactis group II intron Ll.ltrB is similar to mobile yeast mtDNA group II introns, which encode reverse transcriptase, RNA maturase, and DNA endonuclease activities for site-specific DNA insertion. Here, we show that the Lactococcal intron can be expressed and spliced efficiently in Escherichia coli. The intron-encoded protein LtrA has reverse transcriptase and RNA maturase activities, with the latter activity shown both in vivo and in vitro, a first for any group II intron-encoded protein. As for the yeast mtDNA introns, the DNA endonuclease activity of the Lactococcal intron is associated with RNP particles containing both the intron-encoded protein and the excised intron RNA. Also, the intron RNA cleaves the sense-strand of the recipient DNA by a reverse splicing reaction, whereas the intron-encoded protein cleaves the antisense strand. The Lactococcal intron endonuclease can be obtained in large quantities by coexpression of the LtrA protein with the intron RNA in E. coli or reconstituted in vitro by incubating the expressed LtrA protein with in vitro-synthesized intron RNA. Furthermore, the specificity of the endonuclease and reverse splicing reactions can be changed predictably by modifying the RNA component. Expression in E. coli facilitates the use of group II introns for the targeting of specific foreign sequences to a desired site in DNA.
Blockade of the OX40 ligand prolongs corneal allograft survival (2007)

Although corneal transplantation is one of the most common tissue transplantations and is known to have a high graft acceptance rate, occasional corneal graft rejection remains a cause of blindness. OX40, a member of the TNF receptor superfamily, is expressed on activated T cells, and transmits a costimulatory signal by binding to OX40 ligand (OX40L) expressed on several cells with antigen-presenting functions. Using a blocking monoclonal antibody (mAb) against murine OX40L, we investigated the role of OX40 in a murine model of corneal transplantation. C3H/He mouse corneas were transplanted to BALB/c mice orthotopically. Administration of anti-OX40L mAb significantly reduced allograft rejection, and increased graft survival rate to 40% at 8 weeks after transplantation, while all corneas were rejected within 5 weeks in control IgG-treated mice. Similar reduced rejection was observed when wild-type donor corneas were transplanted to OX40L-deficient recipients. In vitro study revealed that the anti-OX40L mAb treatment reduced proliferative response and IFN-gamma production of draining lymph node cells in response to stimulation with donor alloantigen. These results demonstrate that OX40L blockade is effective for prolongation of corneal allograft survival by inhibiting recipient T cell activation.
The diagnosis of Streptococcus pneumoniae infections (1994)

The diagnosis of infection by Streptococcus pneumoniae is an important task for microbiology laboratories in view of its prevalence, high mortality and the recent spread of penicillin resistance. ELISA, CIE, LA and CoAG methods have been described for the detection of capsular polysaccharide (CPS) and C-polysaccharide (PnC) in sputum and all have similar sensitivity. Antigen detection in serum has a low diagnostic yield unless bacteraemia is present. Detection of antigen in urine is more sensitive but the need to concentrate the specimen has limited the application of this technique in routine practice. The polymerase chain reaction for an autolysin gene shows promise for diagnosis in blood and sputum.
Low power design for MPEG-2 video decoder (1996)

The I/O power consumption in an MPEG-2 decoder is significant because of the wide connection with large capacitances to the frame buffer. To reduce the power dissipation on the memory bus, the Gray code encoding scheme is proposed to increase the correlation of the image data transferred on the bus. The bit switching probability in the re-coded data will then decrease and in turn the bus power consumption will be reduced. Combined with the proposed bus arbitration and scheduling scheme proposed in this paper, 22% reduction of power dissipation may be achieved.
Kinetic and structural evidence for a sequential ordered Bi Bi mechanism of catalysis by Saccharomyces cerevisiae myristoyl-CoA:protein N-myristoyltransferase (1991)

The mechanism of catalysis of Escherichia coli-derived Saccharomyces cerevisiae myristoyl-CoA: protein N-myristoyltransferase (NMT) has been characterized. Previous studies indicated that a high affinity reaction intermediate forms between NMT and myristoyl-CoA in the absence of a peptide substrate. This complex has been further characterized using S-(2-oxo)pentadecyl-CoA, a nonhydrolyzable myristoyl-CoA analog. Binding studies involving this analog, as well as myristoylpeptide and CoA, have indicated that the CoA moiety of the acyl substrate is retained in the acyl-NMT complex prior to peptide addition. These structural data, along with kinetic studies of myristoylpeptide and CoA product inhibition, indicate that the mechanism of catalysis of NMT is ordered Bi Bi, with myristoyl-CoA binding to NMT occurring prior to peptide binding and CoA release taking place before release of acyl peptide. Further analyses of the interactions between NMT, acyl peptide, and CoA demonstrate that NMT is able to deacylate a myristoylpeptide in the presence of CoA.
Allergen Nomenclature (1994)

This is a revision of the allergen nomenclature system which was proposed in 1986. The nomenclature is for allergens which induce IgE-mediated allergy in humans. A table of allergens with known partial or complete sequences as of December 1993 is given.
Self-Terminated Artificial SEI Layer for Nickel-Rich Layered Cathode Material via Mixed Gas Chemical Vapor Deposition (2015)

Because of the higher specific capacity, nickel-rich layered cathode material has received much attention from the lithium-ion battery community. However, its cycle life is desired to improve further for practical applications, and unstable interface with electrolyte is one of the main capacity fading mechanisms. Here, we report a facile chemical vapor deposition process involving mixed gases of CO2 and CH4, which yields thin and conformal artificial solid-electrolyte-interphase (SEI) layer consisting of alkyl lithium carbonate (LiCO3R) and lithium carbonate (Li2CO3) on nickel-rich active cathode powder. The coating layer protects from side reactions and improves the cycle life and efficiency significantly. Remarkably, the coating process is self-terminated after the thickness reaches ∼10 nm, leading to the coating layer to account for only 0.48 wt %, because of the growing binding energy between the gas mixture and the surface products. The self-termination is characterized by various analytical tools and is well-explained by density functional theory calculations. The current gas phase coating process should be applicable to other battery materials that suffer from continuous side reactions with electrolyte.