gebhart/patrepeval huggingface dataset:
TopPred II: an improved software for membrane protein structure predictions (1994)

Integral membrane proteins have parts of their polypeptide backbones embedded in a phospholipid bilayer. These hydrophobic, membrane-spanning domains are separated by hydrophilic segments exposed to the aqueous environment and seem to fall into two basic modalities: a-helix bundle and anti-parallel /3-barrel membrane domains. For the helix bundle proteins, two easily identifiable features appear to be the major structural determinants: the long apolar stretches that form the transmembrane a-helices, and the biased distribution of charged residues in the polar regions, known as the 'positive-inside' rule (von Heijne, 1986). Recently, attempts to predict topologies of eukaryotic and prokaryotic integral membrane proteins that form a-helical structures, have been reported (von Heijne, 1992; Sipos and von Heijne, 1993). This work has indeed shown that the topology of such proteins can be effectively deduced from the amino acid sequence. Thus, the aim of developing TopPred II is to compile all existing knowledge about topology in order to permit easy access to prediction of membrane protein topologies. TopPred II is an improved version of the preceding freeware TOP-PRED (von Heijne, 1992). It is now a stand-alone application written in Symantec THINK Pascal to allow its operation on any Macintosh computer with a 6.0.2 (or beyond) system, respecting the standard Apple file- and window-handling procedures, and making extensive use of the graphic abilities of Macintosh computers. The compiled program is very compact (~90 kbytes) and all the default parameters, scales and texts have been built into resources to allow easy access and ability for permanent modifications by the user. Input sequence files are limited to 2000 amino acids. Sequences can be handled one by one or in groups of up to 20. Parameters and scales can be easily modified through standard dialogs, which also enable one to re-establish the TopPred II default values. Calculation of the hydrophobicity profile, transmembrane segments and topologies (see below) can be requested. All the displayed results (texts as well as graphics) can be printed out or saved in files that can be imported by other programs.
Novel potential serological prostate cancer biomarkers using CT100+ cancer antigen microarray platform in a multi-cultural South African cohort (2016)

There is a growing need for high throughput diagnostic tools for early diagnosis and treatment monitoring of prostate cancer (PCa) in Africa. The role of cancer-testis antigens (CTAs) in PCa in men of African descent is poorly researched. Hence, we aimed to elucidate the role of 123 Tumour Associated Antigens (TAAs) using antigen microarray platform in blood samples (N = 67) from a South African PCa, Benign prostatic hyperplasia (BPH) and disease control (DC) cohort. Linear (fold-over-cutoff) and differential expression quantitation of autoantibody signal intensities were performed. Molecular signatures of candidate PCa antigen biomarkers were identified and analyzed for ethnic group variation. Potential cancer diagnostic and immunotherapeutic inferences were drawn. We identified a total of 41 potential diagnostic/therapeutic antigen biomarkers for PCa. By linear quantitation, four antigens, GAGE1, ROPN1, SPANXA1 and PRKCZ were found to have higher autoantibody titres in PCa serum as compared with BPH where MAGEB1 and PRKCZ were highly expressed. Also, p53 S15A and p53 S46A were found highly expressed in the disease control group. Statistical analysis by differential expression revealed twenty-four antigens as upregulated in PCa samples, while 11 were downregulated in comparison to BPH and DC (FDR = 0.01). FGFR2, COL6A1and CALM1 were verifiable biomarkers of PCa analysis using urinary shotgun proteomics. Functional pathway annotation of identified biomarkers revealed similar enrichment both at genomic and proteomic level and ethnic variations were observed. Cancer antigen arrays are emerging useful in potential diagnostic and immunotherapeutic antigen biomarker discovery.
Long-term follow-up after thoracic outlet decompression: An analysis of factors determining outcome (1991)

We reviewed our 12-year experience with transaxillary first rib resection in 136 patients screened by neurologists and thought to have neurologic thoracic outlet syndrome to determine what factors affected outcome. These patients represented 85% of the operative experience in a referral area of 1.2 million people. Patients were recalled every 2 years for surveillance. The mean follow-up was 60 +/- 7 months. There were no brachial plexus or vascular injuries. Secondary operations in the neck were required in 20 patients. The quality of the operative result was determined by whether the patient was able to return to preillness activities and whether the patient would undergo operation again if the same result would be obtained. The most important determinant of result was a history of trauma precipitating the neurologic symptoms, particularly in women. Only 25 of the 53 patients (47%) with a history of trauma returned to preillness activities compared to 65 of the 83 patients (78%) without such a history. Overall patient satisfaction was not affected by trauma. Thirty-eight of the 53 patients with trauma (72%) and 69 of the 83 patients (83%) without trauma were satisfied. When the men and women were analyzed separately men were found to have better results after trauma than did women. Other factors with a negative impact on operative results were the need to return to an activity that required repetitive arm movements, coverage under a worker's compensation insurance policy, and fixed joint abnormalities or neurologic findings in the upper extremity. The presence of an anatomic abnormality had no effect on operative results.(ABSTRACT TRUNCATED AT 250 WORDS)
Bacillus thuringiensis Delta-Endotoxin Cry1 Hybrid Proteins with Increased Activity against the Colorado Potato Beetle (2001)

Cry1 delta-endotoxins of Bacillus thuringiensis are generally active against lepidopteran insects, but Cry1Ba and Cry1Ia have additional, though low, levels of activity against coleopterans such as the Colorado potato beetle. Here we report the construction of Cry1Ba/Cry1Ia hybrid toxins which have increased activities against this insect species.
AAEM minimonograph #42: Intraoperative monitoring of peripheral and cranial nerves (1994)

Intraoperative studies of focal neuropathies have become increasingly common both as an aid to the localization of the neuropathy and a means of monitoring the integrity of the nerve in the course of surgery. Success very often depends on careful attention to the technical problems presented by working in the operating theater. Despite these difficulties, assessment of conduction directly from the exposed nerve offers opportunities for better understanding the pathophysiology of these neuropathies and correlating these findings with conventional electrodiagnostic studies.
Nucleotide and deduced amino acid sequences of Torpedo californica acetylcholine receptor gamma subunit. (1983)

The nucleotide sequence has been determined of a cDNA clone that codes for the 60,000-dalton gamma subunit of Torpedo californica acetylcholine receptor. The length of the cDNA clone is 2,010 base pairs. The 5' and 3' untranslated regions have respective lengths of 31 and 461 base pairs. Data suggest that the putative polyadenylylation consensus sequence A-A-T-A-A-A may not be required for polyadenylylation of the mRNA corresponding to the cDNA clone described in this study. From the DNA sequence data, the amino acid sequence of the gamma subunit was deduced. The subunit is composed of 489 amino acids giving a molecular mass of 56,600 daltons. The deduced amino acid sequence data also indicate the presence of a 17-amino acid extension or signal peptide on this subunit. From these data, structural predictions for the gamma subunit are made such as potential membrane-spanning regions, possible asparagine-linked glycosylation sites, and the assignment of regions of the protein to the extracellular, internal, and cytoplasmic domains of the lipid bilayer.
Construction of a fluorescein‐responsive chimeric receptor with strict ligand dependency (2008)

Since many cell functions are regulated by members of the cytokine receptor superfamily, the artificial mimicry of the cytokine receptor system would be attractive for cellular engineering. We previously showed that an antibody/cytokine receptor chimera can transduce a growth signal in response to non-natural ligands, such as fluorescein-conjugated BSA. However, considerable background of cell proliferation was observed without antigen. Therefore, we redesigned chimeric receptor constructs with different combinations of domains containing anti-fluorescein single chain Fv (ScFv), extracellular D1/D2 as well as transmembrane domains of erythropoietin receptor (EpoR), and the intracellular domain of glycoprotein 130 (gp130), to obtain strictly fluorescein-dependent chimeric receptors. When interleukin-3-dependent Ba/F3 cells were transduced with retroviral vectors encoding individual chimeric receptors, the chimeras either with both D1 and D2 domains or without any EpoR extracellular domain attained a strict ligand-dependent ON/OFF regulation.
Constraint propagation algorithms for temporal reasoning (1986)

Abstract: This paper revises and expands upon a paper presented by two of the present authors at AAAI 1986 [Vilain &amp;amp; Kautz 1986]. As with the original, this revised document considers computational aspects of intervalbased and point-based temporal representations. Computing the consequences of temporal assertions is shown to be computationally intractable in the interval-based representation, but not in the point-based one. However, a fragment of the interval language can be expressed using the point language and benefits from the tractability of the latter. The present paper departs from the original primarily in correcting claims made there about the point algebra, and in presenting some closely related results of van Beek [1989]. The representation of time has been a recurring concern of Artificial Intelligence researchers. Many representation schemes have been proposed for temporal reasoning; of these, one of the most attractive is James Allen&amp;apos;s algebra of temporal intervals [Allen 1983]. This representation scheme is particularly appealing for its simplicity and for its ease of implementation with constraint propagation algorithms. Reasoners based on
OMEGA, a Randomized, Placebo-Controlled Trial to Test the Effect of Highly Purified Omega-3 Fatty Acids on Top of Modern Guideline-Adjusted Therapy After Myocardial Infarction (2010)

URL: http://www.clinicaltrials.gov. Unique identifier: NCT00251134.
Sequencing and High Expression of Aminopeptidase P Gene from Escherichia coli HB101 (1989)

A plasmid pAPP1 with a 4 kbp insert at the PstI site of pBR322, encoding aminopeptidase P gene of Escherichia coli HB101 (Yoshimoto et al. (1988) J. Biochem. 104, 730-734), was subcloned into pUC18 and pUC19. The transformant of E. coli JM83 harboring pAPP4 with a 1.9 kbp fragment showed more than 50-fold higher enzyme activity than that of the host, after cultivation at 37 degrees C for 40 h in LB-medium containing ampicillin. When the gene DNA was inserted reversely in pAPP4, the enzyme productivity decreased markedly. The whole nucleotide sequence of the inserted fragment of plasmid pAPP4 was clarified by the dideoxy chain-terminating method. Within this sequence, the mature enzyme protein-encoding sequence was found to start just after an ATG codon, as judged by comparison with amino-terminal protein sequencing. Eleven bases upstream from the proposed initiation codon was an AGGAGA sequence which seemed to be a ribosome binding site. Thirty-four bases upstream from the proposed start codon was the 6-base sequence TACAAA, the so-called -10 region or Pribnow box. Further, the 6-base sequence TTTACT around 77 bases upstream from the start codon was deduced to be a putative -35 region consensus sequence. The inverted repeat at 1334 was tentatively assumed to be a terminator. The molecular weight of the enzyme was estimated to be 49,650 from the nucleotide sequence. The purified enzyme contained 0.2 gram atom of zinc per subunit. The enzyme activity was inhibited by EDTA and activated 5-fold by Mn2+.
Tocilizumab in Hospitalized Patients With COVID-19 Pneumonia (2020)

ABSTRACT BACKGROUND COVID-19 is associated with immune dysregulation and hyperinflammation. Tocilizumab is an anti–interleukin-6 receptor antibody. METHODS Patients hospitalized with severe COVID-19 pneumonia receiving standard care were randomized (2:1) to double-blinded intravenous tocilizumab 8 mg/kg or placebo. The primary outcome measure was clinical status on a 7-category ordinal scale at day 28 (1, discharged/ready for discharge; 7, death). RESULTS Overall, 452 patients were randomized; the modified-intention-to-treat population included 294 tocilizumab-treated and 144 placebo-treated patients. Clinical status at day 28 was not statistically significantly improved for tocilizumab versus placebo (P=0.36). Median (95% CI) ordinal scale values at day 28: 1.0 (1.0 to 1.0) for tocilizumab and 2.0 (1.0 to 4.0) for placebo (odds ratio, 1.19 [0.81 to 1.76]). There was no difference in mortality at day 28 between tocilizumab (19.7%) and placebo (19.4%) (difference, 0.3% [95% CI, –7.6 to 8.2]; nominal P=0.94). Median time to hospital discharge was 8 days shorter with tocilizumab than placebo (20.0 and 28.0, respectively; nominal P=0.037; hazard ratio 1.35 [95% CI 1.02 to 1.79]). Median duration of ICU stay was 5.8 days shorter with tocilizumab than placebo (9.8 and 15.5, respectively; nominal P=0.045). In the safety population, serious adverse events occurred in 34.9% of 295 patients in the tocilizumab arm and 38.5% of 143 in the placebo arm. CONCLUSIONS In this randomized placebo-controlled trial in hospitalized COVID-19 pneumonia patients, tocilizumab did not improve clinical status or mortality. Potential benefits in time to hospital discharge and duration of ICU stay are being investigated in ongoing clinical trials. Trial registration ClinicalTrials.gov NCTG432G615
Chemistry of Antibody Binding to a Protein (1987)

The chemistry of antibody recognition was studied by mapping the antigenicity of the protein myohemerythrin with peptide homologs of the protein sequence. The results suggest that the entire protein surface is antigenic, but the probability of there being antibodies to a given site is influenced by local stereochemistry. Although accessible to an antibody binding domain, the least reactive positions cluster in the most tightly packed and least mobile regions and are closely associated with narrow, concave grooves in the molecular surface containing bound water molecules. The most frequently recognized sites form three-dimensional superassemblies characterized by high local mobility, convex surface shape, and often by negative electrostatic potential.
Response of a simian immunodeficiency virus (SIVmac251) to raltegravir: a basis for a new treatment for simian AIDS and an animal model for studying lentiviral persistence during antiretroviral therapy (2010)

In line with the high conservation of the three main amino acids Y143, Q148 and N155 (responsible for raltegravir binding) and molecular docking simulations showing similar binding modes of raltegravir at the SIVmac251 and HIV-1 IN active sites, raltegravir is capable of inhibiting SIVmac251 replication both in tissue culture and in vivo. This finding may help to develop effective ART regimens for the simian AIDS model entirely based on drugs adopted for treatment in humans. This ART-treated AIDS nonhuman primate model could be employed to find possible strategies for virus eradication from the body.
Nanowire-Based All-Oxide Solar Cells (2009)

We present an all-oxide solar cell fabricated from vertically oriented zinc oxide nanowires and cuprous oxide nanoparticles. Our solar cell consists of vertically oriented n-type zinc oxide nanowires, surrounded by a film constructed from p-type cuprous oxide nanoparticles. Our solution-based synthesis of inexpensive and environmentally benign oxide materials in a solar cell would allow for the facile production of large-scale photovoltaic devices. We found that the solar cell performance is enhanced with the addition of an intermediate oxide insulating layer between the nanowires and the nanoparticles. This observation of the important dependence of the shunt resistance on the photovoltaic performance is widely applicable to any nanowire solar cell constructed with the nanowire array in direct contact with one electrode.
Comparison of C-Reactive Protein and Low-Density Lipoprotein Cholesterol Levels in the Prediction of First Cardiovascular Events (2002)

These data suggest that the C-reactive protein level is a stronger predictor of cardiovascular events than the LDL cholesterol level and that it adds prognostic information to that conveyed by the Framingham risk score.
Renal blood flow varies during normal activity in conscious unrestrained rats (1992)

The extent to which renal blood flow (RBF) varied during normal daily activity and its dependence on renal nerve activity were studied in unrestrained rats. RBF (measured with a pulsed Doppler flow probe) and behavior pattern (observed with a video camera) were recorded during both phases of the light-dark cycle (n = 11). RBF was highest (100%) when the rat was fully relaxed and apparently asleep (9% time) but was significantly lower (P less than 0.01) during the remainder of the time. When quiescent but not fully relaxed, RBF was 89.7 +/- 0.3% of the maximum; when alert and completely still, it was 74.1 +/- 0.8%; and when grooming, it was 63.7 +/- 0.9%. Mean daily RBF was 80% of maximum flow. During saline infusion into cuffs around the renal arteries, RBF was reduced to 38.4 +/- 0.7% of maximum flow by gentle handling. When the infusion was changed to Xylocaine (5%), which blocked transmission in the renal nerve, similar treatment reduced RBF to 80.2 +/- 0.7% with ipsilateral and to 94.7 +/- 0.7% with bilateral infusions. We conclude that RBF varies considerably in unrestrained animals under normal conditions and that the variations largely result from changes in renal nerve activity.
Mutations in the Elongation Factor 2 Gene Which Confer Resistance to Diphtheria Toxin and Pseudomonas Exotoxin A (1995)

Both diphtheria toxin and Pseudomonas exotoxin A inhibit eukaryotic protein synthesis by ADP-ribosylating diphthamide, a posttranslationally modified histidine residue present in the elongation factor 2 (EF-2) protein. Elongation factor 2 cannot be ADP-ribosylated by the toxins unless this histidine is modified. In this report we identify three new point mutations in toxin-resistant alleles of the Chinese hamster ovary cell elongation factor 2 gene. The mutations resulted in amino acid substitutions at positions 584 (serine to glycine), 714 (isoleucine to asparagine), and 719 (glycine to aspartic acid). All three amino acid substitutions prevented the biosynthesis of diphthamide. The amount by which the toxins reduced protein synthesis in each of these mutant cell strains suggested that all three mutations also either impaired the function of EF-2 or reduced its steady state level in the cytoplasm. Western blot analysis showed that equal amounts of EF-2 were present in each of the cell strains, indicating that the mutations impaired the catalytic function of EF-2.
Thermal Unfolding and Proteolytic Susceptibility of Ribonuclease A (1996)

With the aim to localize the structural region that becomes first accessible to proteolytic attack during thermal unfolding, the proteolysis of ribonuclease A was studied in the temperature range of 20-65 degrees C. Subtilisin, proteinase K, and elastase proved to be not appropriate as indicators of thermal unfolding, because even the native protein molecule was cleaved by these proteases. In contrast, chymotrypsin, trypsin, and thermolysin attacked ribonuclease A only after its thermal treatment. For thermolysin and trypsin, the first primary cleavage sites of ribonuclease A could be identified by blotting of the electrophoretic bands, partial N-terminal sequencing of the fragments and assignment according to their molecular masses. The results were confirmed by the separation of the proteolytic fragments by HPLC and subsequent matrix-assisted laser desorption ionization mass spectrometry. The first cleavage sites were determined to be Lys31-Ser32 and Arg33-Asn34 for trypsin and Asn34-Leu35 and Thr45-Phe46 for thermolysin. Hence the structural region from Lys31 to Leu35, together with the adjacent beta-structure containing Thr45-Phe46, is suggested to represent a labile region of the ribonuclease A molecule, which becomes exposed at thermal denaturation.
Advanced real-time classification methods for flow cytometry data analysis and cell sorting (2002)

While many flow cytometric data analysis and 'discovery' methods have been developed, few of these have been applied to the problem of separating out purified cell subpopulations by cell sorting. The fundamental problem is that the data analysis techniques have been performed using relatively slow computational methods that take far more time than is allowed by the sort decision on a cell sorter (typically less than a millisecond). Thus cell sorting, which is really a form of 'real-time data classification,' is usually done with few, if any, multivariate statistical tools used either in the sort decision or in the evaluation of the correctness of the classification. We have developed new multivariate data analysis and 'data discovery' methods that can be implemented for real-time data classification for cell sorting using linked lookup tables. One multivariate 'data discovery' method, 'subtractive clustering,' has been used to find which clusters of cells are different between two or more files (cell samples) and to help guide analysis or sort boundaries for these cell subpopulations. Multivariate statistical methods (e.g. principal component analysis or discriminant function analysis) were implemented in linked lookup tables to establish analysis/sort boundaries that include 'costs (or penalties) of misclassification. Costs of misclassification provided a measure of the quality of the analysis/sort boundary and were expressed in simple terms that describe the tradeoff between yield and purity.
Hierarchical binding of DNA fragments derived from scaffold-attached regions: correlation of properties in vitro and function in vivo (1990)

On its upstream side, the human interferon-beta gene is flanked by a 7-kb SAR (scaffold-attached region) DNA element. The core of this element is determined and subjected to in vitro reassociations with isolated scaffolds. Binding properties of SAR fragments with decreasing length are quantified and related to consensus sequences like the topoisomerase II box and an ATATTT motif. Characteristics as the stoichiometry, affinity, and cooperativity of the binding process are shown to depend on the length of SAR DNA and suggest a model involving a multiple-site attachment to protein scaffolds. We propose a rational approach for predicting the SAR mediated transcriptional enhancements in vivo from their binding properties in a standardized in vitro assay. The efficiency of this approach is demonstrated for a marker (huIFN-beta) and a selector gene (neor).