gebhart/patrepeval huggingface dataset:
Running on empty? The compensatory reserve index (2013)

Machine modeling can quickly and accurately detect and trend central blood volume reduction in real time during the compensatory phase of hemorrhage as well as estimate when an individual is "running on empty" and will decompensate (CRI, 0), well in advance of meaningful changes in traditional vital signs.
Asymmetric Total Synthesis of (+)-7-Deoxypancratistatin (1995)

An asymmetric synthesis of 7-deoxypancratistatin 1 has been accomplished starting from diol 2 via two pathways in overall yields of 2.6 and 3.0%, respectively. The key step involved the regioselective ring opening of tosylaziridine 3 or the new carbomethoxyaziridine 15 with a higher-order cuprate and the cyclization of urethane 11.
Self-Assembled Hydrogel Nanoparticles for Drug Delivery Applications (2010)

Hydrogel nanoparticles—also referred to as polymeric nanogels or macromolecular micelles—are emerging as promising drug carriers for therapeutic applications. These nanostructures hold versatility and properties suitable for the delivery of bioactive molecules, namely of biopharmaceuticals. This article reviews the latest developments in the use of self-assembled polymeric nanogels for drug delivery applications, including small molecular weight drugs, proteins, peptides, oligosaccharides, vaccines and nucleic acids. The materials and techniques used in the development of self-assembling nanogels are also described.
Epstein-Barr Virus (EBV) in Endemic Burkitt's Lymphoma: Molecular Analysis of Primary Tumor Tissue (1998)

Many aspects of Epstein-Barr virus (EBV) and tumor biology have been studied in Burkitt's lymphoma (BL)-derived cell lines. However, in tissue culture, patterns of gene expression and CpG [corrected] methylation often change and viral strain selection may occur. In this report, 10 cases of snap-frozen endemic BL tumors are characterized in terms of viral gene expression, promoter usage, methylation, and viral strain. EBNA1 and BamHI-A rightward transcripts (BART) were detected in 7 of 7 and LMP2A transcripts in 5 of 7 tumors with well-preserved RNA. Transcripts for the other EBNAs and for LMP1 were not detected in any tumor. These tumors differ from BL cell lines in that they lack a variety of lytic cycle transcripts. This pattern of viral gene expression in endemic BL is similar to that reported in peripheral blood mononuclear cells (PBMCs) from healthy EBV-seropositive individuals. EBNA1 transcripts originated from the Q promoter (Qp) but not C, W, or F promoters that drive transcription of EBNA1 in other circumstances. Whereas Cp has been previously shown to be entirely CpG methylated in BL, bisulfite genomic sequencing showed virtually no methylation in Qp. Type-A EBV was detected in 6 of 10 and type B in 4 of 10 cases. A previously reported 30bp deletion variant in the carboxyl terminal of LMP1 gene was detected in 5 of 10 cases. The association with both A and B strains contrasts with EBV-associated Hodgkin's disease, nasopharyngeal carcinoma, and post-transplant lymphoproliferative disease, which are much more consistently associated with A strain virus.
Quantitative Measurement of Human Papillomavirus Type 16 E5 Oncoprotein Levels in Epithelial Cell Lines by Mass Spectrometry (2012)

The high-risk human papillomavirus type 16 (HPV-16) E5 protein (16E5) induces tumors in a transgenic mouse model and may contribute to early stages of cervical carcinogenesis. Although high-risk E5 expression is generally thought to be lost during the progression to cervical carcinoma following integration of HPV DNA into the host genome, episomal viral DNA has been documented in a subset of HPV-16-positive malignant lesions. Numerous studies have shown that transcripts that could potentially encode 16E5 are present in cervical biopsy specimens and cervical cancer cell lines, but the presence of E5 protein has been demonstrated in only two reports that have not been corroborated. In the present study, we show that trypsin cleavage of 16E5 generates a unique four-amino-acid C-terminal peptide (FLIT) that serves as a marker for E5 expression in transfected cells and epithelial cell lines containing integrated and episomal HPV-16 DNA. Following trypsin cleavage, reversed-phase chromatography and mass spectrometry (MS) were used to detect FLIT. Immunoprecipitation assays using a newly generated anti-16E5 antibody confirmed that 16E5 was solely responsible for the FLIT signal, and deuterated FLIT peptide provided an internal standard that enabled us to quantify the number of 16E5 molecules per cell. We show that 16E5 is expressed in the Caski but not in the SiHa cervical cancer cell line, suggesting that 16E5 may contribute to the malignant phenotype of some cervical cancers, even in cells exclusively containing an integrated HPV genome.
Double knockout of the ALL-1 gene blocks hematopoietic differentiation in vitro. (1996)

The ALL-1 gene is involved in translocations with many partner genes in different types of the acute leukemias, but it is not clear whether it acts as an oncogene or whether the fusion proteins resulting from the translocations have dominant negative effects. To distinguish between these two possibilities, we analyzed the ability of wild-type AB2.1 embryonal stem (ES) cells and of single or double ALL-1 gene knockout cells derived from them to differentiate along hematopoietic lineages after withdrawal of leukemia inhibitory factor, using in vitro colony formation assays. All-1 double knockout ES cells formed a significantly greater number of colonies with faster kinetics than wild-type and ALL-1 single knockout ES cells. Parental ES cells formed lineage-restricted colonies, whereas single and double knockout ES cells developed, at high frequency, immature and/or "biphenotypic" colonies, mimicking the aberrant hematopoiesis typical of leukemic patients. These data are consistent with the possibility that loss of function of the ALL-1 gene is important in leukemogenesis.
Intravesical ALT-803 for BCG-unresponsive Bladder Cancer – A Case Report (2017)

The administration of intravesical chemotherapy or BCG often can prolong the progression-free interval after initial transurethral resection in select bladder cancer (BCa) patients. However, 60% of these patients will recur and up to 30% of patients with recurrent BCa will progress and succumb to their disease over a 15 year period, while another 50% will cystectomy in an attempt to control their disease. Thus better therapeutic strategies are needed for patients who have failed intravesical therapy. In this article, we report the treatment of a 91-year-old man with NMIBC with high-risk features that had failed multiple intravesical therapies.
Lockdown: A Safe and Practical Environment for Security Applications (CMU-CyLab-09-011) (2018)

We describe, build, and evaluate Lockdown, a system that significantly increases the level of security for online transactions, even on a platform infested with malicious code. Lockdown provides the user with a highly-protected, yet also highly-constrained trusted environment for performing online transactions, as well as a high-performance, general-purpose environment for all other (non-security-sensitive) applications. A simple, user-friendly external interface allows the user to securely learn which environment is active and easily switch between them. We focus on making Lockdown deployable and usable today. Lockdown works with both Windows and Linux, and provides immediate improvements to security-sensitive tasks while imposing, on average, only 3% memory overhead and 2–7% storage overhead on non-security-related tasks.
Effect of chromium tripicolinate on growth, glucose tolerance, insulin sensitivity, plasma metabolites, and growth hormone in pigs2 (1995)

Two experiments were conducted to evaluate the effect of Cr as Cr tripicolinate (CrPic) on growth, glucose tolerance, insulin sensitivity, plasma metabolites, and growth hormone (GH) in pigs. Pigs were fed a control diet or a diet supplemented with 200 micrograms of Cr/kg of diet as CrPic. Thirty (15 per diet, initial BW was 21.3 kg) and 24 (12 per diet, initial BW was 24.9 kg) crossbred barrows were used in Exp. 1 and 2, respectively. The diets were formulated to provide 120% of the lysine requirement for 20- to 50-kg pigs. A glucose tolerance test (IVGTT; 500 mg of glucose/kg BW) and an insulin challenge test (IVICT; .1 IU of porcine insulin/kg BW) were conducted. In addition, during Exp. 1, a GH-releasing hormone (GHRH) challenge was conducted. All data were pooled across experiments, except where noted. Average daily gain, ADFI, gain/feed, and fasting (15 to 18 h) plasma glucose and total protein concentrations were not affected (P > .10) by dietary treatment. Fasting plasma cholesterol (P < .05) was increased and NEFA (Exp. 2 only, P < .02), urea N (P < .07), and insulin (P < .10) concentrations were decreased in pigs fed CrPic. During the IVGTT and IVICT, glucose disappearance rate (k, percentage/minute) was increased (P < .04) and glucose half-life (t1/2, minutes) was decreased (P < .04) in pigs fed CrPic; however, insulin kinetics were not altered (P > .10). During the GHRH challenge, pigs fed CrPic had decreased (P < .09) area under the response curve for GH.(ABSTRACT TRUNCATED AT 250 WORDS)
Software transactional memory (2006)

This article consists of a collection of slides from the author's conference presentation on software transactional memory (STM). Some of the specific topics discussed include: how to translate a language construct via STM, including runtime and compiler support; example of hybrid TM; and the outlook for the future development STM and the applications to be supported.
The contribution of intrinsically disordered regions to protein function, cellular complexity, and human disease (2016)

In the 1960s, Christian Anfinsen postulated that the unique three-dimensional structure of a protein is determined by its amino acid sequence. This work laid the foundation for the sequence-structure-function paradigm, which states that the sequence of a protein determines its structure, and structure determines function. However, a class of polypeptide segments called intrinsically disordered regions does not conform to this postulate. In this review, I will first describe established and emerging ideas about how disordered regions contribute to protein function. I will then discuss molecular principles by which regulatory mechanisms, such as alternative splicing and asymmetric localization of transcripts that encode disordered regions, can increase the functional versatility of proteins. Finally, I will discuss how disordered regions contribute to human disease and the emergence of cellular complexity during organismal evolution.
VLSI architectures for neural networks (1989)

An introduction to neural networks and neural information processing is provided. Neurocomputers are discussed, focusing on how their design exploits the architectural properties of VLSI circuits. General-purpose and special-purpose neurocomputer developments throughout the world are examined. As illustration, and to put European developments in perspective, some of the important projects in the United States and Japan are described. European research is then discussed in greater detail.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Mental State Recognition via Wearable EEG (2016)

The increasing quality and affordability of consumer electroencephalogram (EEG) headsets make them attractive for situations where medical grade devices are impractical. Predicting and tracking cognitive states is possible for tasks that were previously not conducive to EEG monitoring. For instance, monitoring operators for states inappropriate to the task (e.g. drowsy drivers), tracking mental health (e.g. anxiety) and productivity (e.g. tiredness) are among possible applications for the technology. Consumer grade EEG headsets are affordable and relatively easy to use, but they lack the resolution and quality of signal that can be achieved using medical grade EEG devices. Thus, the key questions remain: to what extent are wearable EEG devices capable of mental state recognition, and what kind of mental states can be accurately recognized with these devices? In this work, we examined responses to two different types of input: instructional (logical) versus recreational (emotional) videos, using a range of machine-learning methods. We tried SVMs, sparse logistic regression, and Deep Belief Networks, to discriminate between the states of mind induced by different types of video input, that can be roughly labeled as logical vs. emotional. Our results demonstrate a significant potential of wearable EEG devices in differentiating cognitive states between situations with large contextual but subtle apparent differences.
Cell‐cycle‐regulated transcription of A‐ and B‐type plant cyclin genes in synchronous cultures (1997)

Synchronously dividing cell cultures of Catharanthus roseus were used to isolate cDNAs for two mitotic cyclins, named CYS and CYM. The deduced protein sequence of CYS is similar to that of A-type cyclins, and CYM belongs to the group of B-type cyclins. In a fashion similar to the pattern of expression seen for A-type and B-type cyclins in mammalian cells, CYS is expressed before CYM in C. roseus cells during the cell cycle. CYS mRNA accumulated at the onset of S phase and disappeared early in the G2 phase, whereas CYM mRNA was detected in the G2 and M phases of the cell cycle. Tobacco homologs of the two genes showed similar cell-cycle dependent expression patterns in synchronous cultures of tobacco BY2 cells. In both systems, CYS was expressed much earlier in the cell cycle than most other plant A-type cyclins, and hence CYS along with the soybean cyc1GM can be classified into a distinct subclass. The activities of CYM and CYS promoters during the cell cycle were analyzed in stably transformed tobacco BY2 cells. Cyclin promoter sequences of 0.5 kb could confer the typical cell-cycle-dependent expression to the beta-glucuronidase (GUS) reporter gene: the CYS promoter directed S-phase-specific expression, whereas the CYM promoter drove M-phase-specific expression. These results indicate the important role of transcriptional regulation in the oscillations of cyclin mRNA levels during the cell cycle.
Expression of enzymatically active reverse transcriptase of simian immunodeficiency virus in bacteria: Sensitivity to nucleotide analogue inhibitors (1990)

A fragment of the SIVmac251 pol gene was expressed in Escherichia coli as a trpE fusion protein. Analysis of extracts from bacteria containing this expression plasmid revealed the presence of a reverse transcriptase activity dependent on Mg2+ as divalent cation and active on both poly(rA).oligo(dT) and poly(rC.oligo(dG) templates. In comparative studies, the SIV and HIV-1 reverse transcriptases expressed in bacteria displayed very similar high sensitivities to the chain terminator inhibitors AZTTP and ddTTP. The reverse transcriptase of Moloney murine leukemia virus and the DNA polymerase of E. coli were both more resistant to ddTTP, and the E. coli enzyme was significantly more resistant to AZTTP.
Construction of Synthetic Immunogen: Use of New T-Helper Epitope on Malaria Circumsporozoite Protein (1987)

The circumsporozoite (CS) protein of Plasmodium falciparum is the focus of intense efforts to develop an antisporozoite malaria vaccine. Localization of sites for T-cell recognition on this molecule is critical for vaccine design. By using an algorithm designed to predict T-cell sites and a large panel of H-2 congenic mice, a major nonrepetitive T-cell site was located. When a synthetic peptide corresponding to this site was covalently linked to the major B-cell site on the molecule, an immunogen capable of eliciting a high-titer antibody response was formed. This peptide sequence could prime helper T cells for a secondary response to the intact CS protein. The new helper T-cell site is located outside the repetitive region of the CS protein and appears to be the immunodominant T site on the molecule. This approach should be useful in the rational design and construction of vaccines.
Affinity Purification and cDNA Cloning of Rat Neural Differentiation and Tumor Cell Surface Antigen gp130RB13-6 Reveals Relationship to Human and Murine PC-1 (1995)

Monoclonal antibody RB13-6 recognizes a subset of rat brain glial precursor cells that are highly susceptible to malignant conversion by the carcinogen N-ethyl-N-nitrosourea. The corresponding cell surface antigen was identified as a membrane glycoprotein (gp130RB13-6) and purified by immunoaffinity chromatography from the tumorigenic neuroectodermal rat cell line BT4Ca. Sequencing of 5 endoproteinase-generated peptides of the purified antigen permitted the specific amplification of a cDNA fragment by reverse transcription-polymerase chain reaction and subsequent isolation of the complete coding sequence from a fetal rat brain cDNA library. The derived amino acid sequence indicates that the RB13-6 antigen is related to the human and murine plasma cell membrane protein PC-1, a nucleotide pyrophosphatase/alkaline phosphodiesterase and ectoprotein kinase. Similarly, purified gp130RB13-6 possesses 5'-nucleotidase activity that can be inhibited with EDTA. Different from PC-1, gp130RB13-6 isolated from BT4Ca cells is not a disulfide-linked dimer and contains an RGD-tripeptide sequence which, together with other structural features, suggests a possible function in cell adhesion and its subversion in malignant phenotypes.
Optimization of Isothermal Growth of HgCdTe Layers (1982)

, n‐type, layers with low carrier concentration and high carrier mobilities were obtained, for the first time, in the "as‐grown state," i.e., without the standard postgrowth annealing in Hg‐rich atmosphere. This achievement was the result of the discovery that in isothermal growth, layers of a given composition and optimum electronic properties can be grown only from a source of a well‐defined composition and at well‐defined temperature. Such layers also exhibit mirror‐like surface morphology, and their composition is highly uniform radially and axially (to a depth up to about 15 μm).
A System for Specific, High-throughput Genotyping by Allele-specific Primer Extension on Microarrays (2000)

This study describes a practical system that allows high-throughput genotyping of single nucleotide polymorphisms (SNPs) and detection of mutations by allele-specific extension on primer arrays. The method relies on the sequence-specific extension of two immobilized allele-specific primers that differ at their 3'-nucleotide defining the alleles, by a reverse transcriptase (RT) enzyme at optimized reaction conditions. We show the potential of this simple one-step procedure performed on spotted primer arrays of low redundancy by generating over 8000 genotypes for 40 mutations or SNPs. The genotypes formed three easily identifiable clusters and all known genotypes were assigned correctly. Higher degrees of multiplexing will be possible with this system as the power of discrimination between genotypes remained unaltered in the presence of over 100 amplicons in a single reaction. The enzyme-assisted reaction provides highly specific allele distinction, evidenced by its ability to detect minority sequence variants present in 5% of a sample at multiple sites. The assay format based on miniaturized reaction chambers at standard 384-well spacing on microscope slides carrying arrays with two primers per SNP for 80 samples results in low consumption of reagents and makes parallel analysis of a large number of samples convenient. In the assay one or two fluorescent nucleotide analogs are used as labels, and thus the genotyping results can be interpreted with presently available array scanners and software. The general accessibility, simple set-up, and the robust procedure of the array-based genotyping system described here will offer an easy way to increase the throughput of SNP typing in any molecular biology laboratory.
T Cell Cross-Reactivity Among Viruses of the Paramyxoviridae (1987)

Blastogenesis and delayed-type hypersensitivity assays were used to examine mouse T cell responses to five viruses representing the three genera of the Paramyxoviridae. Cross-reactive T cell responses were observed in a lympho-proliferative assay for measles, mumps, respiratory syncytial, canine distemper and parainfluenza type 3 virus. Confirmation of T cell cross-reactivity among measles, mumps and respiratory syncytial virus was obtained with a delayed-type hypersensitivity test. These results show that T cell cross-reactivity is common for Paramyxoviridae viruses, even though these viruses show virtually no inter-genus antibody cross-reactivity. The cross-reactivity among respiratory syncytial, measles and mumps virus at the T cell level may have implications for usage of the attenuated measles/mumps/rubella (MMR) vaccine. Respiratory syncytial virus is contacted by many children before they receive the MMR vaccine and T cells induced by respiratory syncytial virus may influence subsequent development of immunity to measles and/or mumps virus.
Antirheumatic Agents. III. Novel Methotrexate Derivatives Bearing an Indoline Ring and a Modified Ornithine or Glutamic Acid. (1997)

The synthesis, biological profile and structure-activity relationship of various methotrexate (MTX) derivatives bearing an indoline ring are described. In particular, Nb-(3-carboxyphenyl)-N alpha-[1-[(2,4-diaminopteridin-6-yl)-methyl] indoline-5-ylcarbonyl]-L-glutamine (3d), compared to MTX, exhibited an enhanced anti-proliferative effect on human peripheral blood mononuclear cells obtained from healthy volunteers.
Large-scale expansion of human stem and progenitor cells from bone marrow mononuclear cells in continuous perfusion cultures (1993)

There is a growing consensus that clinical practice in the areas of bone marrow (BM) transplantation and gene therapy will rely on the ex vivo expansion of hematopoietic cells. We report here on the development of continuously perfused culture systems (bioreactor systems) that expand human stem and progenitor cells from BM mononuclear cell (MNC) populations obtained without cell enrichment. In three separate experiments, 10 bioreactors were each inoculated with 3 x 10(7) BM MNC from patients undergoing marrow harvest for autologous transplantation. At various times thereafter (between days 6 and 16), duplicate bioreactors were harvested and cells were analyzed. The bioreactors contained three cell populations that were analyzed separately: nonadherent cells; cells that were loosely adherent to the endogenously formed stromal layer; and an adherent cell layer that required trypsinization for removal. Total cell numbers increased continuously to give an overall 10-fold (range, 8- to 11-fold) expansion by day 14. The adherent stromal layer significantly expanded to more than 2 x 10(7) cells, but remained less than 6% of the total cell population. Colony-forming unit-granulocyte-macrophage (CFU-GM) numbers expanded 21-fold (range, 12- to 34-fold) by day 14 and, because this expansion was greater than that for total cells, CFU-GM were enriched by as much as fourfold by day 14. Burst-forming unit-erythroid (BFU-E) numbers peaked earlier than did CFU-GM numbers, with a 12-fold (range, 6- to 18-fold) expansion obtained on day 8. In contrast to CFU- GM, which were predominantly nonadherent, BFU-E were more evenly distributed between the three cell populations. Stem cell activity was measured by the long-term culture-initiating cell (LTC-IC) limiting dilution assay. The number of LTC-IC per reactor consistently increased with time in all cultures, resulting in a 7.5-fold (range, 3.4- to 9.8- fold) expansion. In summary, more than 3 billion cells, containing 12 million CFU-GM, were reproducibly generated from the equivalent of a 10 to 15 ml BM aspirate. These data indicate that small numbers of BM MNC can be readily expanded ex vivo in continuous perfusion cultures, and that such ex vivo expansion may have direct applications in clinical and experimental BM transplantation.