gebhart/patrepeval huggingface dataset:
Protein secondary structural types are differentially coded on messenger RNA (1996)

Tricodon regions on messenger RNAs corresponding to a set of proteins from Escherichia coli were scrutinized for their translation speed. The fractional frequency values of the individual codons as they occur in mRNAs of highly expressed genes from Escherichia coli were taken as an indicative measure of the translation speed. The tricodons were classified by the sum of the frequency values of the constituent codons. Examination of the conformation of the encoded amino acid residues in the corresponding protein tertiary structures revealed a correlation between codon usage in mRNA and topological features of the encoded proteins. Alpha helices on proteins tend to be preferentially coded by translationally fast mRNA regions while the slow segments often code for beta strands and coil regions. Fast regions correspondingly avoid coding for beta strands and coil regions while the slow regions similarly move away from encoding alpha helices. Structural and mechanistic aspects of the ribosome peptide channel support the relevance of sequence fragment translation and subsequent conformation. A discussion is presented relating the observation to the reported kinetic data on the formation and stabilization of protein secondary structural types during protein folding. The observed absence of such strong positive selection for codons in non-highly expressed genes is compatible with existing theories that mutation pressure may well dominate codon selection in non-highly expressed genes.
Evidence for a role for the gumB and gumC gene products in the formation of xanthan from its pentasaccharide repeating unit by Xanthomonas campestris (1998)

The biosynthesis of the extracellular polysaccharide xanthan in Xanthomonas campestris pv. campestris is directed by a cluster of 12 genes, gumB-gumM. Several xanthan-deficient mutants of the wild-type strain 8004 have previously been described which carry Tn5 insertions in this region of the chromosome. Here it is shown that the transposon insertion in one of these mutants, strain 8397, is located 15 bp upstream of the translational start site of the gumB gene. EDTA-treated cells of strain 8397 were able to synthesize the lipid-linked pentasaccharide repeating unit of xanthan from the three nucleotide sugar donors (UDP-glucose, GDP-mannose and UDP-glucuronic acid) but were unable to polymerize the pentasaccharide into mature xanthan. A subclone of the gum gene cluster carrying gumB and gumC restored xanthan production to strain 8397 to levels approximately 28% of the wild-type. In contrast, subclones carrying gumB or gumC alone were not effective. These results are discussed with reference to previous speculations, based on computer analysis, that gumB and gumC are both involved in the translocation of xanthan across the bacterial membranes.
Bcl6 Mediates the Development of T Follicular Helper Cells (2009)

A fundamental function of CD4+ helper T (T(H)) cells is the regulation of B cell-mediated humoral immunity. Development of T follicular helper (T(FH)) cells that provide help to B cells is mediated by the cytokines interleukin-6 and interleukin-21 but is independent of TH1, TH2, and TH17 effector cell lineages. Here, we characterize the function of Bcl6, a transcription factor selectively expressed in T(FH) cells. Bcl6 expression is regulated by interleukin-6 and interleukin-21. Bcl6 overexpression induced T(FH)-related gene expression and inhibited other T(H) lineage cell differentiation in a DNA binding-dependent manner. Moreover, Bcl6 deficiency in T cells resulted in impaired T(FH) cell development and germinal center reactions, and altered production of other effector T cell subsets. Our data thus illustrate that Bcl6 is required for programming of T(FH) cell generation.
A monoclonal antibody against LAV gag precursor: use for viral protein analysis and antigenic expression in infected cells. (1986)

A murine monoclonal antibody (MAb), named C.V.K., was produced after immunization with highly purified and sonicated lymphadenopathy-associated virus (LAV). No monoclonal antibody was observed with intact virus used as immunogen. C.V.K. MAb recognizes an epitope present on the precursor gag protein of 55 kilodaltons. Western blot analysis and pulse-chase experiments support the interpretation that after p55 cleavage into p25, p18, and p13, only p18 expresses this epitope. C.V.K. MAb selectively stained only LAV-infected lymphocytes. This intracytoplasmic staining appears 3 days after the infection and is correlated with reverse transcriptase activity. Neither membrane immunofluorescence of infected lymphocytes nor neutralizing activity was observed with C.V.K. MAb. These facts suggest that p55 and p18 are not expressed at the cell membrane or on the viral envelope. C.V.K. MAb should prove useful not only in the purification of core proteins but also for detecting infected cells producing the virus in suspension or on histologic sections.
A study on the application of on-chip EOS/ESD full-protection device for TMR heads (2010)

On-chip EOS/ESD full-protection for TMR heads can be achieved using shunt diodes that are mounted permanently in the TMR device. This consists of two semiconductor diodes connected in parallel and in reverse order across the reader pads of TMR heads. This method also increases the ESD threshold of the TMR heads.
CD4 is expressed on murine pluripotent hematopoietic stem cells (1992)

We show here for the first time that pluripotent hematopoietic stem cells express the CD4 antigen. CD4+ cells isolated from mouse marrow repopulated all hematopoietic lineages in both the long-term repopulation assay and the competitive repopulation assay. This finding indicates that the CD4+ population contains primitive stem cells with extensive repopulation capacity. Interestingly, the CD4- population had significant life-sparing activity, even though this population was depleted of long-term repopulating stem cells when compared with CD4+ cells. The majority of the cells that respond to the stroma in Whitlock-Witte cultures with B-cell differentiation were recovered in the CD4- population. Thus, this bone marrow (BM)-derived B-cell precursor lacks CD4, which is in contrast to myeloid precursors and thymus-derived lymphoid precursors that reportedly express CD4. We show further that the CD4 molecule expressed on BM cells is similar in molecular weight and epitope makeup to the CD4 antigen found on thymocytes. Detection of CD4 on BM cells is dependent on using high concentrations of antibodies. Thus, it is not surprising that expression of CD4 on pluripotent stem cells has been missed previously. Taken together, our data suggest that the CD4 molecule may play an important role in lineage definition in early hematopoietic differentiation.
Feedback Motion Planning (2006)

So far in Part II it has been assumed that a continuous path sufficiently solves a motion planning problem. In many applications, such as computer-generated animation and virtual prototyping, there is no need to challenge this assumption because models in a virtual environment usually behave as designed. In applications that involve interaction with the physical world, future configurations may not be predictable. A traditional way to account for this in robotics is to use the refinement scheme that was shown in Figure 1.19 to design a feedback control law that attempts to follow the computed path as closely as possible. Sometimes this is satisfactory, but it is important to recognize that this approach is highly decoupled. Feedback and dynamics are neglected in the construction of the original path; the computed path may therefore not even be usable.
Nodal Signaling Uses Activin and Transforming Growth Factor-β Receptor-regulated Smads (2001)

Nodal, a member of the transforming growth factor beta (TGF-beta) superfamily, is implicated in many events critical to the early vertebrate embryo, including mesoderm formation, anterior patterning, and left-right axis specification. Here we define the intracellular signaling pathway induced by recombinant nodal protein treatment of P19 embryonal carcinoma cells. Nodal signaling activates pAR3-Lux, a luciferase reporter previously shown to respond specifically to activin and TGF-beta. However, nodal is unable to induce pTlx2-Lux, a reporter specifically responsive to bone morphogenetic proteins. We also demonstrate that nodal induces p(CAGA)(12), a reporter previously shown to be specifically activated by Smad3. Expression of a dominant negative Smad2 significantly reduces the level of luciferase reporter activity induced by nodal treatment. Finally, we show that nodal signaling rapidly leads to the phosphorylation of Smad2. These results provide the first direct biochemical evidence that nodal signaling is mediated by both activin-TGF-beta pathway Smads, Smad2 and Smad3. We also show here that the extracellular cripto protein is required for nodal signaling, making it distinct from activin or TGF-beta signaling.
Effect of topical application of fibronectin in duodenal wound healing in rats (2003)

Fibronectin (FN), a large family of plasma and extracellular matrix glycoproteins, plays an important role in wound healing. PURPOSE: To evaluate the effect of fibronectin on the healing of sutured duodenal wounds, correlating with the serum and tissue level of the substance. METHODS: An experimental study was done in 30 adult Wistar rats divided into two group. In the control group (n=15) a duodenal suture was treated with saline solution 0,9% and in the test group the duodenal wounds were treated with 1% FN. The duodenal wound healing process was studied in the 5th, 7tn and 10th postoperative days, by histological sections stained by hematoxylin-eosin, Masson trichromic and immunohistochemical reaction for FN. A digital histological grading system was used to obtain a score for each group and to observe the healing process. RESULTS: the FN was present in the several layers of the duodenum and the cellular and plasmatic FN increased with the evolution of healing. In the test group the FN enhanced the wound healing within 5, 7 and 10 days after injury, when compared with the control group. CONCLUSION: The topical use of FN in duodenal sutured wounds in rats enhances healing by stimulating the appearence of fibroblasts into the wound site and development of granulation tissue. This acceleration of the repair process may have an important application in the healing of duodenal wounds.
Characterization and classification of virus particles associated with hepatitis A. I. Size, density, and sedimentation (1978)

Virus-like particles were purified from stools of patients in an epidemic of hepatitis A in Germany. When reference MS-1 chimpanzee pre-inoculation and convalescent sera were used, the close serological relationship of the purified particles to well-known isolates of hepatitis A could be established. On the other hand, the physicochemical characteristics of the particles were determined in parallel to the characteristics of a marker parvovirus (LuIII) and a marker picornavirus (poliovirus type 2). It could be shown that the majority of the hepatitis A-associated particles band at 1.34 g/ml in CsCl and, like poliovirus, sediment at about 160S. In addition, a distinct hepatitis A antigen was observed, which banded at 1.305 g/ml and sedimented between 50 and 90S. A further component accumulated in the density range of between 1.38 and 1.44 g/ml. However, it seemed to be rather labile. Upon reisolation from CsCl and sedimentation in sucrose, it resolved into a 160S, a 90 to 100S, and a 50S form. The size of the 160S particles (27 to 29 nm) could be readily distinguished from that of the parvovirus (22 to 24 nm). It is concluded, therefore, that hepatitis A-associated virus particles are more likely to be classified with the picornaviruses than with the parvoviruses.
Bacterial endotoxin as inhibitor of the enzymatic activity of human thrombin (2006)

Endotoxemia caused by bacterial lipopolysaccharides (LPS) deleteriously affects many aspects of hemostasis. Much of this effect is well characterized as being secondary to the LPS-mediated inflammatory response, but direct effects of LPS on coagulation factors may also contribute to disregulation of the hemostatic process. Spectrophotometric assays were used to investigate the effects of LPS from different bacteria on thrombin and plasmin activities. We found that enzymatic activity of purified thrombin, but not plasmin, decreases in the presence of endotoxin. LPS-mediated inhibition of thrombin activity can be reversed by plasma gelsolin and recombinant endotoxin-neutralizing protein. Preincubation of thrombin with LPS before platelet activation results in inhibition of aggregation and secretion. Additionally, a decrease of elastic shear moduli of fibrin gels was observed when their formation was induced with thrombin preincubated with LPS or when LPS was present in fibrinogen solutions during fibrin gel formation. When added to platelet-rich plasma, after activation with collagen, LPS-inhibited thrombin activity. LPS-mediated inhibition of thrombin activity may contribute to the hemostasis dysfunctions observed during endotoxemia.
Isolation of an avirulent mutant of Sendai virus with two amino acid mutations from a highly virulent field strain through adaptation to LLC-MK2 cells. (1997)

A field strain of Sendai virus (SeV) Ohita-M1 (M1) was isolated from an epidemic in an animal laboratory by passaging in mice. A mutant strain, Ohita-MVC11 (MVC11), was then obtained by passaging M1 in rhesus monkey (LLC-MK2) cells. MVC11 was adapted to LLC-MK2 cells and produced 20 times higher levels of infectious virus than M1. This increased production of infectious virus in LLC-MK2 cells was associated with enhanced viral gene expression. However, MVC11 could not replicate efficiently in mouse lung and was not lethal to mice even when inoculated at a titre of 8 x 10(5) cell-infecting units (CIU) per mouse. On the other hand, with an inoculum of only 4 x 10(1) CIU per mouse, corresponding to 1 LD50, M1 replicated well in mouse lung and was highly virulent to mice. Nucleotide and deduced amino acid sequence analyses of the entire genomes of M1 and MVC11 revealed that adaptation to LLC-MK2 cells and the attenuation of mouse pathogenicity of MVC11 were associated with only two amino acid substitutions; one on the C protein (Phe substituted by Ser at position 170) and the other on the RNA polymerase, the L protein (Glu substituted by Ala at position 2050).
Topiramate in Migraine Prevention (2005)

The efficacy of topiramate in migraine prevention (prophylaxis) was established in two multicenter, randomized, double-blind, placebo-controlled, pivotal trials. Topiramate has received regulatory approval for use in adults for migraine prophylaxis (prevention) in the US and numerous other countries, including France, Ireland, Switzerland, Brazil, Taiwan, Spain, and Australia. Treatment with 100 or 200 mg per day of topiramate was associated with significant reductions in the frequency of migraine headaches, number of migraine days, and use of acute medications. No increase in efficacy was observed between 100 and 200 mg per day of topiramate. Based on efficacy and tolerability, 100 mg per day of topiramate should be the initial target dose for most patients. The most common adverse events were paresthesia, fatigue, decreased appetite, nausea, diarrhea, weight decrease, and taste perversion. Topiramate is a first-line migraine preventive drug and should especially be considered as a preferred treatment for all patients who are concerned about gaining weight, who are currently overweight, or who have coexisting epilepsy.
Determination of triethylenetetramine in plasma of patients by high-performance liquid chromatography. (1990)

A sensitive and simple fluorometric method for the determination of N,N'-bis(2-aminoethyl)-1,2-ethanediamine dihydrochloride (triethylenetetramine) in human plasma by high-performance liquid chromatography is described. Free triethylenetetramine (TETA) obtained by passing the TETA-copper chelate compound through a solid-phase cation exchange resin was converted to its fluorescamine derivative in the presence of ethylenediaminetetraacetic acid to mask the interfering metal ions in the reaction solution, and the derivatives were separated on a nitrile high-performance liquid chromatograph column (Nucleosil 5-CN) using isocratic elution. The plasma levels of TETA were measured in eight patients receiving treatment for excess copper. Absorption rates of TETA were relatively slow and the peak levels were significantly different among patients. The bioavailability of TETA in the rat was also examined and the ratio of intestinal absorption was extremely low.
A Compression Algorithm for DNA Sequences and Its Applications in Genome Comparison. (1999)

We present a lossless compression algorithm, GenCompress, for genetic sequences, based on searching for approximate repeats. Our algorithm achieves the best compression ratios for benchmark DNA sequences. Significantly better compression results show that the approximate repeats are one of the main hidden regularities in DNA sequences. We then describe a theory of measuring the relatedness between two DNA sequences. Using our algorithm, we present strong experimental support for this theory, and demonstrate its application in comparing genomes and constructing evolutionary trees.
Biochemical investigation of protein export in Escherichia coli (1989)

Export of proteins from the bacterial cytoplasm to a final destination in the periplasm and outer membrane is one example of the fundamental process occurring in all cells whereby polypeptides are transferred across biological membranes. Investigations on a variety of different systems have indicated similarities in the mechanism of this process. In the cases of bacterial protein export and the transfer of polypeptides across the endoplasmic reticulum in eukaryotic cells the processes are so similar that understanding gleaned from studies of the one is usually directly applicable to the other. The study of protein export in E. coli has two advantages over that of eukaryotic secretion. Not only is there the possibility of doing sophisticated genetic experiments, but also one can carry out biochemical investigations in vivo, a facility not so readily available with eukaryotic organisms. Such studies have, for example, shown that membrane translocation can occur both cotranslationally and post-translationally, that export requires protonmotive force, that some component of the export apparatus prevents the exported protein from assuming its native structure in the cytosol, and that there are probably at least two functions for the leader sequence, one in targeting the protein to the export pathway and one in translocation across the membrane.
Role of IL-18 in Second-Hand Smoke–Induced Emphysema (2013)

Chronic second-hand smoke (SHS) exposure comprises the main risk factor for nonsmokers to develop chronic obstructive pulmonary disease (COPD). However, the mechanisms behind the chronic inflammation and lung destruction remain incompletely understood. In this study, we show that chronic exposure of Sprague-Dawley rats to SHS results in a significant increase of proinflammatory cytokine IL-18 and chemokine (C-C motif) ligand 5 in the bronchoalveolar lavage fluid (BALF) and a significant decrease of vascular endothelial growth factor (VEGF) in the lung tissue. SHS exposure resulted in progressive alveolar airspace enlargement, cell death, pulmonary vessel loss, vessel muscularization, collagen deposition, and right ventricular hypertrophy. Alveolar macrophages displayed a foamy phenotype and a decreased expression of the natural inhibitor of IL-18, namely, IL-18 binding protein (IL-18BP). Moreover, IL-18 down-regulated the expression of VEGF receptor-1 and VEGFR receptor-2, and induced apoptosis in pulmonary microvascular endothelial cells in vitro. We also observed a trend toward increased concentrations of IL-18 in the BALF of patients with COPD. Our findings suggest that IL-18-mediated endothelial cell death may contribute to vascular destruction and disappearance in SHS-induced COPD. Moreover, IL-18 and IL-18BP are potential new targets for therapeutics.
A Century of Alzheimer's Disease (2006)

One hundred years ago a small group of psychiatrists described the abnormal protein deposits in the brain that define the most common neurodegenerative diseases. Over the past 25 years, it has become clear that the proteins forming the deposits are central to the disease process. Amyloid-beta and tau make up the plaques and tangles of Alzheimer's disease, where these normally soluble proteins assemble into amyloid-like filaments. Tau inclusions are also found in a number of related disorders. Genetic studies have shown that dysfunction of amyloid-beta or tau is sufficient to cause dementia. The ongoing molecular dissection of the neurodegenerative pathways is expected to lead to a true understanding of disease pathogenesis.
cDNA cloning of porcine granulocyte‐macrophage colony‐stimulating factor (1995)

Porcine granulocyte-macrophage colony-stimulating factor (GM-CSF) cDNA was cloned by using polymerase chain reaction (PCR) and sequenced. A coding sequence of the porcine GM-CSF precursor protein, including the signal peptide sequence and stop codon, is 435 bp in length. The identities of the porcine GM-CSF coding sequence when compared to ovine, bovine, human and murine sequences were 89, 86, 83 and 70% at the nucleotide level, and 80, 74, 73, and 56% at the amino acid level. The hydrophobicity profiles, putative glycosylation sites and positions of cysteine residues were highly conserved in porcine, ovine, bovine and human GM-CSF but not murine. This is the first report of the porcine GM-CSF cDNA cloning and sequence.
Muscle Weakness and Foot Deformities in Diabetes (2004)

Important relationships have been shown between motor nerve conduction deficit and muscle weakness; however, it is still not clear whether abnormal nerve function, leading to a decrease in muscle strength, could be responsible for the development of foot deformities.
Utilization of Employment Tax Credits: An Analysis of the Empowerment Zone Wage Tax Credit (2011)

This paper provides estimates of utilization for the Empowerment Zone (EZ) wage tax credit, a subsidy claimed by employers who operate in and hire residents of federally designated areas experiencing economic distress. The EZ credit is currently the largest employer‐based wage tax credit in the federal tax code in terms of dollars claimed, with almost $250 million claimed in 2002. I show that about 6.4 percent (and at least 3.5 percent) of the working age population was claimed under the EZ wage credit in 1999. In addition, I estimate that 24.2 percent (and at least 13.1 percent) of those employed inside of the target area were claimed for the credit. I create these national estimates of use with information on credit dollars claimed from the Internal Revenue Service and population data on the eligible population from the census. These measures of tax credit use are an alternative to the use rate of firms that are presented in the existing literature, and reveal how effective the credit is at reaching residents of the target area.
Video Watermarking Combining with Hybrid Coding (2003)

A watermarking scheme combining with hybrid video coding is proposed. The intra-coded frame, which is called intra-frame, is blocked and discrete cosine transformed (DCT), watermark is embedded in the low-frequency coefficients in DCT domain. While for the inter-coded frame, the blocked motion compensation is discrete cosine transformed as in I frame, then the DC coefficient in the DCT matrix is watermarked. In this scheme, human perceptual model is considered. In the process of embedding, spread spectrum technology, which is originally used in communication, is cooperated with multidimensional watermarking technique. The watermark detection is based on the correlation and hypothesis testing and directly put on the video stream before decoding. For these reasons, computational complex can be greatly reduced to increase the usability of video watermarking.