gebhart/patrepeval huggingface dataset:
Enhancing Mitochondrial Calcium Buffering Capacity Reduces Aggregation of Misfolded SOD1 and Motor Neuron Cell Death without Extending Survival in Mouse Models of Inherited Amyotrophic Lateral Sclerosis (2013)

Mitochondria have been proposed as targets for toxicity in amyotrophic lateral sclerosis (ALS), a progressive, fatal adult-onset neurodegenerative disorder characterized by the selective loss of motor neurons. A decrease in the capacity of spinal cord mitochondria to buffer calcium (Ca(2+)) has been observed in mice expressing ALS-linked mutants of SOD1 that develop motor neuron disease with many of the key pathological hallmarks seen in ALS patients. In mice expressing three different ALS-causing SOD1 mutants, we now test the contribution of the loss of mitochondrial Ca(2+)-buffering capacity to disease mechanism(s) by eliminating ubiquitous expression of cyclophilin D, a critical regulator of Ca(2+)-mediated opening of the mitochondrial permeability transition pore that determines mitochondrial Ca(2+) content. A chronic increase in mitochondrial buffering of Ca(2+) in the absence of cyclophilin D was maintained throughout disease course and was associated with improved mitochondrial ATP synthesis, reduced mitochondrial swelling, and retention of normal morphology. This was accompanied by an attenuation of glial activation, reduction in levels of misfolded SOD1 aggregates in the spinal cord, and a significant suppression of motor neuron death throughout disease. Despite this, muscle denervation, motor axon degeneration, and disease progression and survival were unaffected, thereby eliminating mutant SOD1-mediated loss of mitochondrial Ca(2+) buffering capacity, altered mitochondrial morphology, motor neuron death, and misfolded SOD1 aggregates, as primary contributors to disease mechanism for fatal paralysis in these models of familial ALS.
A Heparin Binding Protein Whose Expression Increases during Differentiation of Embryonal Carcinoma Cells to Parietal Endoderm Cells: cDNA Cloning and Sequence Analysis1 (1990)

A cDNA clone isolated from a lambda gt11 expression library of teratocarcinoma OTT6050 specifies for a glycoprotein with a molecular weight of about 44,000. The new glycoprotein was termed heparin binding protein-44 (HBP-44), since it was absorbed to a heparin-agarose column and was eluted from it by a buffer containing 1.5 M NaCl. HBP-44 mRNA was intensely expressed in PYS-2 parietal endoderm cells and in the kidney, and the RNA level increased about 10-fold during differentiation of F9 embryonal carcinoma cells to parietal endoderm cells. From the cDNA sequence, HBP-44 was concluded to be rich in charged amino acids, and large segments of the protein appeared to form alpha-helixes. The protein was considered to be anchored to the membrane by a cluster of hydrophobic amino acids present in the N-terminal region. Indeed, the N-terminal sequence of HBP-44 was homologous to asialoglycoprotein receptor, which is anchored to the membrane by the N-terminal region. Furthermore, a portion of the N-terminal region of HBP-44 was homologous to the leucine zipper domain. Except for the N-terminal region, HBP-44 had over-all homology with structural proteins such as myosin heavy chain. We propose that HBP-44 is extruded from plasma membranes and interacts with heparin and related molecules and that it is involved in the interactions of plasma membranes with basement membranes.
The IBM 2015 English conversational telephone speech recognition system (2015)

We describe a collection of acoustic and language modeling techniques that lowered the word error rate of our English conversational telephone LVCSR system to a record 6.6% on the Switchboard subset of the Hub5 2000 evaluation testset. On the acoustic side, we use a score fusion of three strong models: recurrent nets with maxout activations, very deep convolutional nets with 3x3 kernels, and bidirectional long short-term memory nets which operate on FMLLR and i-vector features. On the language modeling side, we use an updated model "M" and hierarchical neural network LMs.
Interstitial cells of Cajal, the Maestro in health and disease (2010)

Interstitial cells of Cajal (ICC) are important players in the symphony of gut motility. They have a very significant physiological role orchestrating the normal peristaltic activity of the digestive system. They are the pacemaker cells in gastrointestinal (GI) muscles. Absence, reduction in number or altered integrity of the ICC network may have a dramatic effect on GI system motility. More understanding of ICC physiology will foster advances in physiology of gut motility which will help in a future breakthrough in the pharmacological interventions to restore normal motor function of GI tract. This mini review describes what is known about the physiologic function and role of ICCs in GI system motility and in a variety of GI system motility disorders.
Direct Identification ofVibrio vulnificusin Clinical Specimens by Nested PCR (1998)

This study was performed to establish optimal nested PCR conditions and a high-yield DNA extraction method for the direct identification of Vibrio vulnificus in clinical specimens. We designed two sets of primers targeting the V. vulnificus hemolysin/cytolysin gene. The target of the first primer set (P1-P2; sense, 5'-GAC-TAT-CGC-ATC-AAC-AAC-CG-3', and antisense, 5'-AGG-TAG-CGA-GTA-TTA-CTG-CC-3', respectively) is a 704-bp DNA fragment. The second set (P3-P4; sense, 5'-GCT-ATT-TCA-CCG-CCG-CTC-AC-3', and antisense, 5'-CCG-CAG-AGC-CGT-AAA-CCG-AA-3', respectively) amplifies an internal 222-bp DNA fragment. We developed a direct DNA extraction method that involved boiling the specimen pellet in a 1 mM EDTA-0.5% Triton X-100 solution. The new DNA extraction method was more sensitive and reproducible than other conventional methods. The DNA extraction method guaranteed sensitivity as well, even when V. vulnificus cells were mixed with other bacteria such as Escherichia coli or Staphylococcus aureus. The nested PCR method could detect as little as 1 fg of chromosomal DNA and single CFU of V. vulnificus. We applied the nested PCR protocol to a total of 39 serum specimens and bulla aspirates from septicemic patients. Seventeen (94.4%) of the 18 V. vulnificus culture-positive specimens were positive by the nested PCR. Eight (42.1%) of the 19 culture-negative samples gave positive nested PCR results.
Exploring targeted pulmonary delivery for treatment of lung cancer (2013)

Lung cancer is the most malignant cancer today. The treatment of lung cancer continues to be a challenge for oncologists. The direct delivery of chemotherapeutic agents to the lungs could represent a novel therapeutic approach for patients with pulmonary metastases. The large alveolar surface area, the low thickness of the epithelial barrier, and an extensive vascularization make the pulmonary route an ideal route for administration of oncolytics. This paper reviews the research performed over the last and current decades on the delivery of various oncolytics for pulmonary delivery for the treatment of lung cancer. Inhaled drug delivery devices in cancer therapy are also discussed in the present manuscript.
Quantitative reevaluation of telomerase activity in cancerous and noncancerous gastrointestinal tissues (1999)

Telomerase activity has been examined extensively in a variety of human cancerous and noncancerous tissues. However, it was sometimes difficult to measure telomerase activity quantitatively with the methods used and in the tissues examined. We examined telomerase activity quantitatively in gastrointestinal tissues by using the hybridization protection assay combined with the telomeric repeat amplification protocol (TRAP) to assess the diagnostic utility of measuring telomerase activity and to determine the relationship between telomerase activity and human telomerase reverse transcriptase (hTERT) expression. We report here that (i) polymerase chain reaction (PCR) inhibitors in the tissue extracts used for the telomerase assay were practically nullified by using tissue extract at 0.1 μg of protein/assay; (ii) RNase activity in tissue extracts should be blocked with 0.5 U of RNase inhibitor/μg tissue protein for the quantitative telomerase assay; (iii) no inhibitors of telomerase were found in tissue extracts other than RNase and PCR inhibitors (iv) higher telomerase activity in cancerous tissue than in noncancerous tissue from the same patients was observed in both gastric and colorectal tissues, but the telomerase activity varied from low to high levels in cancerous tissues, and it was not practical to set a general cut-off level for cancer diagnosis; (v) hTERT was expressed in both cancerous and noncancerous tissues, and (vi) the telomerase activity levels were generally lower than expected from the hTERT expression levels, suggesting posttranscriptional regulation of expression of telomerase activity. Mol. Carcinog. 26:312–320, 1999. © 1999 Wiley-Liss, Inc.
Adaptive immune regulation of glial homeostasis as an immunization strategy for neurodegenerative diseases (2010)

Neurodegenerative diseases, notably Alzheimer's and Parkinson's diseases, are amongst the most devastating disorders afflicting the elderly. Currently, no curative treatments or treatments that interdict disease progression exist. Over the past decade, immunization strategies have been proposed to combat disease progression. Such strategies induce humoral immune responses against misfolded protein aggregates to facilitate their clearance. Robust adaptive immunity against misfolded proteins, however, accelerates disease progression, precipitated by induced effector T cell responses that lead to encephalitis and neuronal death. Since then, mechanisms that attenuate such adaptive neurotoxic immune responses have been sought. We propose that shifting the balance between effector and regulatory T cell activity can attenuate neurotoxic inflammatory events. This review summarizes advances in immune regulation to achieve a homeostatic glial response for therapeutic gain. Promising new ways to optimize immunization schemes and measure their clinical efficacy are also discussed.
Mechanical properties of the upper airway (1983)

The series and shunt components of the impedance of the upper airway (Zuaw) were evaluated from measurements obtained during a Valsalva maneuver by means of a modified forced oscillation technique. When the cheeks are supported, the upper airway can be represented by a single distributed transmission line. The homogeneity of this line was confirmed by measuring separately Zuaw and the impedance of the mouth. Correction of the impedance of the respiratory system, determined by means of the forced oscillations technique, for the shunt properties of Zuaw results in some modifications of the frequency dependence of resistance (Rrs) in healthy adults and in marked changes of the absolute values of Rrs in children and in patients with obstructive lung disease.
Receptor-like kinases from Arabidopsis form a monophyletic gene family related to animal receptor kinases (2001)

Plant receptor-like kinases (RLKs) are proteins with a predicted signal sequence, single transmembrane region, and cytoplasmic kinase domain. Receptor-like kinases belong to a large gene family with at least 610 members that represent nearly 2.5% of Arabidopsis protein coding genes. We have categorized members of this family into subfamilies based on both the identity of the extracellular domains and the phylogenetic relationships between the kinase domains of subfamily members. Surprisingly, this structurally defined group of genes is monophyletic with respect to kinase domains when compared with the other eukaryotic kinase families. In an extended analysis, animal receptor kinases, Raf kinases, plant RLKs, and animal receptor tyrosine kinases form a well supported group sharing a common origin within the superfamily of serine/threonine/tyrosine kinases. Among animal kinase sequences, Drosophila Pelle and related cytoplasmic kinases fall within the plant RLK clade, which we now define as the RLK/Pelle family. A survey of expressed sequence tag records for land plants reveals that mosses, ferns, conifers, and flowering plants have similar percentages of expressed sequence tags representing RLK/Pelle homologs, suggesting that the size of this gene family may have been close to the present-day level before the diversification of land plant lineages. The distribution pattern of four RLK subfamilies on Arabidopsis chromosomes indicates that the expansion of this gene family is partly a consequence of duplication and reshuffling of the Arabidopsis genome and of the generation of tandem repeats.
Resuscitation from clinical death (1988)

Modern cardiopulmonary-cerebral resuscitation (CPCR) for the reversal of clinical death (i.e., prolonged cardiac arrest) is a sequence of basic, advanced and prolonged life-support steps. This system was initiated by research that started in the 1950s. Present community-wide results are encouraging, but suboptimal. Maximal benefit from CPCR will be achievable: a) by minimizing response times; and b) by extending reversible arrest times--the topic of this symposium. For reperfusion, closed chest CPR is more readily available than, but physiologically inferior to, open chest CPR and emergency cardiopulmonary bypass. To optimize outcome, four components of the postresuscitation syndrome are being investigated: a) perfusion failure; b) reoxygenation injury cascades; c) self-intoxication; and d) blood derangements. Results from animal outcome studies so far suggest significant but still inconsistent benefit from several special postarrest treatments. The longest normothermic no-flow time yet reversed to good functional survival of heart, brain and the entire organism appears to be not 5 min, but between 10 and 20 min. The following is recommended and in part has been initiated: a) simultaneous investigation of pathophysiologic limits, therapeutic potentials, and prognosticating measurements; b) simultaneous basic research at cellular, organ, and organism levels; c) increased communication and consensus on research models between research centers; d) use of short-term and long-term animal models for systematic mechanism-oriented and empirical outcome-oriented studies; e) development of etiology-specific combination treatments; and f) community-wide case registries combined with epidemiologic studies and randomized clinical treatment trials.
Multiple Components Are Required for Sequence Recognition of the API Site in the Gibbon Ape Leukemia Virus Enhancer (1989)

At least two subunits contributed to the formation in vitro of a specific complex binding to the AP1 consensus sequence (TGAGTCA) in the gibbon ape leukemia virus (GALV) enhancer in MLA144 cells. This complex can be dissociated on a monomeric GALV oligonucleotide affinity column. One protein, termed the core protein, was retained on the oligonucleotide affinity column. The second protein flowed through the oligonucleotide affinity column and, when alone, did not bind to DNA; however, when present with the core protein, it bound strongly and very specifically to the GALV sequence. MLA144 cells contained only trace amounts of c-fos and c-jun by immunoblot analysis, suggesting that the proteins specifically binding to the GALV AP1 site were distinct from c-fos and c-jun. In addition to the major complex that recognized the GALV element, MLA144 cells contained a minor complex that is chromatographically different from and antigenically related to c-fos. The factor in the flowthrough complemented a human T-cell nuclear extract (Jurkat cell line), which, when alone, had no assayable complex that specifically bound to the GALV enhancer; this complementation gave rise to a specific complex similar to that seen in MLA144 cells. Together, these results suggest that the GALV enhancer can interact with multicomponent protein complexes in a cell-line-specific manner.
Isolation of a versatile Serratia marcescens mutant as a host and molecular cloning of the aspartase gene (1985)

An extracellular nuclease-deficient, antibiotic-sensitive, and restrictionless mutant was isolated from the wild-type strain of Serratia marcescens Sr41 by four rounds of mutagenesis. The mutant was transformed efficiently with plasmid DNAs prepared from Escherichia coli and S. marcescens, and was used as a host for the cloning of the aspartase gene (aspA+) of S. marcescens. Cells carrying the cloned aspA+ gene on a multicopy plasmid produced ca. 39-fold more aspartase than did control cells, and the level of enzyme overproduction was in proportion to the copy number of the aspA+ recombinant plasmid. Aspartase was identified as a polypeptide of molecular weight 52,000 on sodium dodecyl sulfate-polyacrylamide gel electrophoresis.
Optimality, sample size, and power calculations for the sequential parallel comparison design (2011)

The sequential parallel comparison design (SPCD) has been proposed to increase the likelihood of success of clinical trials in therapeutic areas where high-placebo response is a concern. The trial is run in two stages, and subjects are randomized into three groups: (i) placebo in both stages; (ii) placebo in the first stage and drug in the second stage; and (iii) drug in both stages. We consider the case of binary response data (response/no response). In the SPCD, all first-stage and second-stage data from placebo subjects who failed to respond in the first stage of the trial are utilized in the efficacy analysis. We develop 1 and 2 degree of freedom score tests for treatment effect in the SPCD. We give formulae for asymptotic power and for sample size computations and evaluate their accuracy via simulation studies. We compute the optimal allocation ratio between drug and placebo in stage 1 for the SPCD to determine from a theoretical viewpoint whether a single-stage design, a two-stage design with placebo only in the first stage, or a two-stage design is the best design for a given set of response rates. As response rates are not known before the trial, a two-stage approach with allocation to active drug in both stages is a robust design choice.
Constitutive production of IL-4 and IL-10 and stimulated production of IL-8 by normal peripheral blood eosinophils (1996)

To study the capacity and regulation of cytokine production by normal peripheral blood eosinophils, we isolated eosinophils from healthy individuals and stimulated them with immobilized Ig or TNF-alpha, with or without exogenous IL-5. By reverse transcription-PCR, uncultured, freshly isolated eosinophils constitutively expressed mRNA for IL-4, IL-10, and TGF-beta1. Eosinophils stimulated by immobilized secretory IgA, immobilized IgA, immobilized IgG, or TNF-alpha for 3 h expressed mRNA encoding IL-3, IL-4, IL-8, IL-10, granulocyte-macrophage CSF, TNF-alpha, TGF-beta, and RANTES. The mRNA for IL-2, IL-5, or IFN-gamma was not detected. IL-4 and IL-10 protein, but not IL-8, were measurable in lysates of fresh eosinophils or eosinophils cultured with medium alone for 24 h. Eosinophils incubated with immobilized Ig or TNF-alpha released IL-8 protein into the supernatants. In contrast, IL-4 and IL-10 proteins were not detectable. Soluble secretory IgA immune complexes also induced degranulation, as measured by eosinophil-derived neurotoxin, and IL-8 release, but not IL-4 or IL-10 release, from eosinophils. Release of IL-8 protein and storage of IL-4 and IL-10 proteins were enhanced by exogenous IL-5 and inhibited by a transcription inhibitor, actinomycin D. Degranulation of stored granule proteins was not affected by actinomycin D. Therefore, normal peripheral blood eosinophils can transcribe and synthesize several cytokines, including IL-4, IL-8, and IL-10; some are stored, and some are released. These cytokines may play important roles in modulating immune responses in diseases associated with eosinophils.
Indoleamine 2,3-dioxygenase controls conversion of Foxp3+ Tregs to TH17-like cells in tumor-draining lymph nodes (2009)

The immunoregulatory enzyme indoleamine 2,3-dioxygenase (IDO) is expressed by a subset of murine plasmacytoid DCs (pDCs) in tumor-draining lymph nodes (TDLNs), where it can potently activate Foxp3+ regulatory T cells (Tregs). We now show that IDO functions as a molecular switch in TDLNs, maintaining Tregs in their normal suppressive phenotype when IDO was active, but allowing inflammation-induced conversion of Tregs to a polyfunctional T-helper phenotype similar to proinflammatory T-helper-17 (TH17) cells when IDO was blocked. In vitro, conversion of Tregs to the TH17-like phenotype was driven by antigen-activated effector T cells and required interleukin-6 (IL-6) produced by activated pDCs. IDO regulated this conversion by dominantly suppressing production of IL-6 in pDCs, in a GCN2-kinase dependent fashion. In vivo, using a model of established B16 melanoma, the combination of an IDO-inhibitor drug plus antitumor vaccine caused up-regulation of IL-6 in pDCs and in situ conversion of a majority of Tregs to the TH17 phenotype, with marked enhancement of CD8+ T-cell activation and antitumor efficacy. Thus, Tregs in TDLNs can be actively reprogrammed in situ into T-helper cells, without the need for physical depletion, and IDO serves as a key regulator of this critical conversion.
Lineage-Restricted Function of Nuclear Factor κB–Inducing Kinase (Nik) in Transducing Signals via Cd40 (2000)

CD40 signaling in B cells and dendritic cells (DCs) is critical for the development of humoral and cell-mediated immunity, respectively. Nuclear factor kappaB (NF-kappaB)-inducing kinase (NIK) has been implicated as a central transducing kinase in CD40-dependent activation. Here, we show that although NIK is essential for B cell activation, it is dispensable for activation of DCs. Such data provide compelling evidence that different intermediary kinases are used by different cellular lineages to trigger NF-kappaB activation via CD40.
Logic Trees: Fault, Success, Attack, Event, Probability, and Decision Trees (2008)

Abstract This article describes the fundamentals of logic trees used in decision and risk analysis. We include in the broad definition of logic trees any conceptual or mathematical model that describes scenarios of events and/or decisions in a treelike structure. Logic trees are important tools for analyzing uncertain events, defining accident scenarios, assessing risk, calculating joint probability distributions, and evaluating decision options. Six types of logic trees are described, compared, and illustrated in this article: fault trees, success trees, attack trees, event trees, probability trees, and decision trees. Fault trees deductively model the combination of system failures and human errors that could lead to an accident. Success trees are the complement of fault trees and model the combination of events that lead to success. Attack trees model the sequential actions of an intelligent adversary to defeat a defensive system. Event trees inductively model the sequences of events that lead to an accident. Probability trees model a sequence of uncertain events in order to calculate the probability of events in the outcome space. Decision trees are logic trees that include sequential decisions in addition to sequential uncertain events. Examples are provided in this article to illustrate the similarities and differences among the types of logic trees. We conclude with challenges for applying logic trees to homeland security applications.