gebhart/patrepeval huggingface dataset:
Metabolomics reveals increased isoleukotoxin diol (12,13-DHOME) in human plasma after acute Intralipid infusion (2012)

Intralipid is a fat emulsion that is regularly infused into humans and animals. Despite its routine use, Intralipid infusion can cause serious adverse reactions, including immunosuppression. Intralipid is a complex mix of proteins, lipids, and other small molecules, and the effect of its infusion on the human plasma metabolome is unknown. We hypothesized that untargeted metabolomics of human plasma after an Intralipid infusion would reveal novel insights into its effects. We infused Intralipid and saline into 10 healthy men in a double-blind, placebo-controlled experiment and used GC/MS, LC/MS, and NMR to profile the small-molecule composition of their plasma before and after infusion. Multivariate statistical analysis of the 40 resulting plasma samples revealed that after Intralipid infusion, a less-well-characterized pathway of linoleic acid metabolism had resulted in the appearance of (9Z)-12,13-dihydroxyoctadec-9-enoic acid (12,13-DHOME, P < 10(-3)), a leukotoxin that has powerful physiological effects and is known to inhibit the neutrophil respiratory burst. Intralipid infusion caused increased plasma 12,13-DHOME. Given that 12,13-DHOME is known to directly affect neutrophil function, we conclude that untargeted metabolomics may have revealed a hitherto-unknown mechanism of intralipid-induced immunosuppression.
Bioprospecting of plant growth promoting psychrotrophic Bacilli from the cold desert of north western Indian Himalayas. (2016)

The plant growth promoting psychrotrophic Bacilli were investigated from different sites in north western Indian Himalayas. A total of 247 morphotypes were obtained from different soil and water samples and were grouped into 43 clusters based on 16S rDNA-RFLP analysis with three restriction endonucleases. Sequencing of representative isolates has revealed that these 43 Bacilli belonged to different species of 11 genera viz., Desemzia, Exiguobacterium, Jeotgalicoccus, Lysinibacillus, Paenibacillus, Planococcus, Pontibacillus, Sinobaca, Sporosarcina, Staphylococcus and Virgibacillus. With an aim to develop microbial inoculants that can perform efficiently at low temperatures, all representative isolates were screened for different plant growth promoting traits at low temperatures (5-15 degrees C). Among the strains, variations were observed for production (%) of indole-3-acetic acid (20), ammonia (19), siderophores (11), gibberellic acid (4) and hydrogen cyanide (2); solubilisation (%) of zinc (14), phosphate (13) and potassium (7); 1-aminocyclopropane-1-carboxylate deaminase activity (6%) and biocontrol activity (4%) against Rhizoctonia solani and Macrophomina phaseolina. Among all the strains, Bacillus licheniformis, Bacillus muralis, Desemzia incerta, Paenibacillus tylopili and Sporosarcina globispora were found to be potent candidates to be developed as inoculants as they exhibited multiple PGP traits at low temperature.
Could the Ebola virus matrix protein VP40 be a drug target? (2013)

Filoviruses are filamentous lipid-enveloped viruses and include Ebola (EBOV) and Marburg, which are morphologically identical but antigenically distinct. These viruses can be very deadly with outbreaks of EBOV having clinical fatality as high as 90%. In 2012 there were two separate Ebola outbreaks in the Democratic Republic of Congo and Uganda that resulted in 25 and 4 fatalities, respectively. The lack of preventive vaccines and FDA-approved therapeutics has struck fear that the EBOV could become a pandemic threat. The Ebola genome encodes only seven genes, which mediate the entry, replication, and egress of the virus from the host cell. The EBOV matrix protein is VP40, which is found localized under the lipid envelope of the virus where it bridges the viral lipid envelope and nucleocapsid. VP40 is effectively a peripheral protein that mediates the plasma membrane binding and budding of the virus prior to egress. A number of studies have demonstrated specific deletions or mutations of VP40 to abrogate viral egress but to date pharmacological inhibition of VP40 has not been demonstrated. This editorial highlights VP40, which is the most abundantly expressed protein of the virus and discusses VP40 as a potential therapeutic target.
Efficient expansion of regulatory T cells in vitro and in vivo with a CD28 superagonist (2003)

CD4(+)CD25(+) T cells play a central role in the suppression of autoimmunity and inflammation, making their in vivo expansion a highly attractive therapeutic target. By phenotyping with a novel rat CTL antigen-4 (CTLA-4)-specific monoclonal antibody (mAb) and functional in vitro assays, we here first establish that rat CD4(+)CD25(+) T cells correspond to the regulatory T cells (Treg cells) described in mice and humans: they constitutively express CTLA-4, produce IL-10 but not IL-2, and are able to suppress the proliferation of costimulated CD25-negative indicator cells. Furthermore, we show that rat Treg cells respond less well than CD25(-) T cells to conventional costimulation, but are readily expanded in vitro with "superagonistic" CD28-specific mAb which are potent mitogens for all T cells without the need for TCR engagement. In vivo, functional Treg cells are preferentially expanded by CD28 stimulation over other T cell subsets, leading to a 20-fold increase within 3 days in response to a single antibody dose. These data suggest that CD28-driven activation of Treg cells may be highly effective in the treatment of inflammatory and autoimmune diseases.
The Insulin-dependent Biosynthesis of GLUT1 and GLUT3 Glucose Transporters in L6 Muscle Cells Is Mediated by Distinct Pathways (1995)

Insulin binding results in rapid phosphorylation of insulin receptor substrate-1 to activate p21ras and mitogen-activated protein kinase. Insulin also activates the ribosomal protein S6 kinase (pp70 S6 kinase) independently of the Ras pathway. Chronic (18 h) treatment of L6 muscle cells with insulin increases glucose transport activity severalfold due to biosynthetic elevation of the GLUT1 and GLUT3 but not the GLUT4 glucose transporters. Here we investigate the roles of p21ras and pp70 S6 kinase in the insulin-mediated increases in GLUT1 and GLUT3 expression. L6 cells were transfected with the dominant negative Ras(S17N) under the control of a dexamethasone-inducible promoter. Induction of Ras(S17N) failed to block the insulin-mediated increase in GLUT1 glucose transporter protein and mRNA; however, it abrogated the insulin-mediated increase in GLUT3 glucose transporter protein and mRNA. Inhibition of pp70 S6 kinase by rapamycin, on the other hand, eliminated the insulin-mediated increase in GLUT1 but had no effect on that of GLUT3 in both parental and Ras(S17N) transfected L6 cells. These results suggest that the biosynthetic regulation of glucose transporters is differentially determined, with pp70 S6 kinase and p21ras playing active roles in the insulin-stimulated increases in GLUT1 and GLUT3, respectively.
Site-Specific Gene Expression in Vivo by Direct Gene Transfer into the Arterial Wall (1990)

A recombinant beta-galactosidase gene has been expressed in a specific arterial segment in vivo by direct infection with a murine amphotropic retroviral vector or by DNA transfection with the use of liposomes. Several cell types in the vessel wall were transduced, including endothelial and vascular smooth muscle cells. After retroviral infection, a recombinant reporter gene was expressed for at least 5 months, and no helper virus was detected. Recombinant gene expression achieved by direct retroviral infection or liposome-mediated DNA transfection was limited to the site of infection and was absent from liver, lung, kidney, and spleen. These results demonstrate that site-specific gene expression can be achieved by direct gene transfer in vivo and could be applied to the treatment of such human diseases as atherosclerosis or cancer.
Prognostic factors in breast carcinoma (1995)

With greater public awareness and use of mammography, more breast carcinomas are detected early, before the axillary lymph nodes contain metastases. About 60% of patients will be node-negative; yet 20-30% of node-negative breast carcinoma patients will develop recurrent tumors, and they are at risk of dying of disease. These patients should be considered for adjuvant therapies, whereas the remaining 70-80% appear to be cured by surgery. Thus, accurate assessment of risk factors for recurrence provides valuable therapeutic information. This review focuses on recent reports that help identify subsets of patients at variable risk for recurrent disease.
[Effect of a heat and humidity exchanger (Humid-Vent-Mini) on the carbon dioxide washout effect of a neonatal ventilation model]. (1990)

The influence of the heat-und humidity-exchanger Humid-Vent-Mini on CO2-washout was examined in an neonate lung model varying leakage, pressure and flow. We compared the performance of Humid-Vent-Mini to an exchanger modified and simplified by us in which the filter has been attached directly to the connector of the tracheal tube and to a system without any exchanger. In order to examine the influence of dryness and humidity we examined the exchanger in both states. Under all conditions the heat- and humidity exchanger Humid-Vent-Mini exhibited a significant CO2-retention (p less than 0.01). The modified type also showed a CO2-retention which was markedly lower compared to Humid-Vent-Mini (p less than 0.01). The CO2-washout effect (when measured under conditions of small leakage, reduced pressure and flow) was slightly better in a moist state of the filter compared to complete dryness (p less than 0.01). These results show, that the use of heat- and humidity-exchanger is not advisable.
Adeno-associated Virus and AAV Vectors for Gene Delivery (2000)

I. INTRODUCTION In this chapter we summarize the state of development of adeno-associated virus (AAV) vectors and provide an overview of AAV as well as some historical comment on early seminal studies that are generally overlooked in current reviews. We do not attempt to provide an exhaustive collection of references on development of AAV vectors but do discuss the key advances in the last several years, including improvements in vector production and studies on the applications for persistent gene expression. Other references provide general reviews of AAV (1,2) and extensive summaries on earlier development of AAV vectors (3-7).
Bottom-Up Growth of Carbon Nanotube Multilayers:  Unprecedented Growth (2005)

An unusual growth phenomenon, with no precedent in vapor-phase thin film growth, is described here, for the case of the growth of stacked multiple layers of vertically aligned carbon nanotubes(1-6) on solid substrates. As multiple layers of ordered nanotubes are sequentially deposited from the vapor onto the substrate, each layer nucleates and grows from the original substrate surface at the bottom of the existing multiple stacks of nanotubes. In contrast to conventional understanding of thin film deposition,(7) the mechanism here has similarities to porous oxide film formation on surfaces.(8) The stacked layers of aligned nanotubes act as fully permeable membranes for the downward diffusion of growth precursor vapors, allowing growth to occur at the buried solid interface. The preexisting multiple nanotube stacks lift up to accommodate the vertical growth of fresh layers, allowing the formation of nanotube towers extending in millimeter lengths. Our results provide evidence for a new growth phenomenon, characterized by selective, interface-driven, bottom-up growth of self-assembled nanowires at buried interfaces, covered with weakly adhering thick porous membranes.
Flexible control of plant architecture and yield via switchable expression of Arabidopsis gai (2003)

The growth of plants is repressed by DELLA proteins, nuclear regulators whose activities are opposed by the growth-promoting phytohormone gibberellin (GA). Mutations affecting DELLA protein function were previously used by plant breeders to create the high-yielding semidwarf wheat varieties of the green revolution. gai is an Arabidopsis mutant DELLA protein-encoding orthologue of the wheat semidwarfing genes. Here we describe the development of a transgene that confers ethanol-inducible gai expression. Transient induction of gai causes transient growth repression: growth prior to and after treatment is unaffected. Appropriate ethanol treatments result in dwarf plants that produce the same numbers of seeds as untreated controls. This new technology represents a substantial advance in the applicability of genes encoding mutant DELLA proteins to agricultural and horticultural improvement, enhancing the flexibity with which these genes can be used for the sustainable achievement of increased crop plant yields.
Dormancy Phenotype Displayed by Extracellular Mycobacterium tuberculosis within Artificial Granulomas in Mice (2004)

Mycobacterium tuberculosis residing within pulmonary granulomas and cavities represents an important reservoir of persistent organisms during human latent tuberculosis infection. We present a novel in vivo model of tuberculosis involving the encapsulation of bacilli in semidiffusible hollow fibers that are implanted subcutaneously into mice. Granulomatous lesions develop around these hollow fibers, and in this microenvironment, the organisms demonstrate an altered physiologic state characterized by stationary-state colony-forming unit counts and decreased metabolic activity. Moreover, these organisms show an antimicrobial susceptibility pattern similar to persistent bacilli in current models of tuberculosis chemotherapy in that they are more susceptible to the sterilizing drug, rifampin, than to the bactericidal drug isoniazid. We used this model of extracellular persistence within host granulomas to study both gene expression patterns and mutant survival patterns. Our results demonstrate induction of dosR (Rv3133c) and 20 other members of the DosR regulon believed to mediate the transition into dormancy, and that rel(Mtb) is required for Mycobacterium tuberculosis survival during extracellular persistence within host granulomas. Interestingly, the dormancy phenotype of extracellular M. tuberculosis within host granulomas appears to be immune mediated and interferon-gamma dependent.
Interleukin 6. A potential autocrine/paracrine factor in Paget's disease of bone. (1992)

Pagetic osteoclasts are greatly increased in number and size and have increased numbers of nuclei per cell compared to normal osteoclasts. The mechanisms responsible for enhanced osteoclast formation in Paget's disease are unknown. We have used our recently described model system for pagetic osteoclast formation to evaluate culture media conditioned by these atypical multinucleated cells (MNC) to determine if pagetic osteoclasts produce an autocrine or paracrine factor that enhances osteoclast formation. Conditioned media from long-term bone marrow cultures from patients with Paget's disease stimulated osteoclast-like MNC formation in normal marrow cultures. At least part of this activity could be ascribed to interleukin 6 (IL-6). In contrast, conditioned media from normal marrow cultures contained lower levels of IL-6 and did not stimulate formation of osteoclast-like MNC. 7 of 8 bone marrow plasma samples taken from involved bones and 18 of 27 peripheral blood serum samples from Paget's patients had high levels of IL-6. Normal marrow plasma and peripheral blood serum had no or very low levels of IL-6. These results suggest that IL-6 produced by marrow and/or bone cells in patients with Paget's disease may be an autocrine/paracrine factor for pagetic osteoclasts.
Probiotic Bacteria: Selective Enumeration and Survival in Dairy Foods (2000)

A number of health benefits have been claimed for probiotic bacteria such as Lactobacillus acidophilus, Bifidobacterium spp., and Lactobacillus casei. Because of the potential health benefits, these organisms are increasingly incorporated into dairy foods. However, studies have shown low viability of probiotics in market preparations. In order to assess viability of probiotic bacteria, it is important to have a working method for selective enumeration of these probiotic bacteria. Viability of probiotic bacteria is important in order to provide health benefits. Viability of probiotic bacteria can be improved by appropriate selection of acid and bile resistant strains, use of oxygen impermeable containers, two-step fermentation, micro-encapsulation, stress adaptation, incorporation of micronutrients such as peptides and amino acids and by sonication of yogurt bacteria. This review will cover selective enumeration and survival of probiotic bacteria in dairy foods.
A Convolutional Neural Network for Modelling Sentences (2014)

The ability to accurately represent sentences is central to language understanding. We describe a convolutional architecture dubbed the Dynamic Convolutional Neural Network (DCNN) that we adopt for the semantic modelling of sentences. The network uses Dynamic k-Max Pooling, a global pooling operation over linear sequences. The network handles input sentences of varying length and induces a feature graph over the sentence that is capable of explicitly capturing short and long-range relations. The network does not rely on a parse tree and is easily applicable to any language. We test the DCNN in four experiments: small scale binary and multi-class sentiment prediction, six-way question classification and Twitter sentiment prediction by distant supervision. The network achieves excellent performance in the first three tasks and a greater than 25% error reduction in the last task with respect to the strongest baseline.
The neurogenic bladder (2000)

Many people with incontinence and bladder problems have an underlying neurogenic cause, with damage to the neurological pathways which regulate the function of the bladder. This article demonstrates how an understanding of the neurological control of the bladder can lead to more effective assessment and treatment of incontinence.
Targeting of the polyhydroxybutyrate biosynthetic pathway to the plastids of Arabidopsis thaliana results in high levels of polymer accumulation. (1994)

In the bacterium Alcaligenes eutrophus, three genes encode the enzymes necessary to catalyze the synthesis of poly[(R)-(-)-3-hydroxybutyrate] (PHB) from acetyl-CoA. In order to target these enzymes into the plastids of higher plants, the genes were modified by addition of DNA fragments encoding a pea chloroplast transit peptide, a constitutive plant promoter, and a poly(A) addition sequence. Each of the modified bacterial genes was introduced into Arabidopsis thaliana by Agrobacterium-mediated transformation, and plants containing all three genes were obtained by sexual crosses. These plants accumulated PHB up to 14% of the dry weight as 0.2- to 0.7-micron granules within plastids. In contrast to earlier experiments in which expression of the PHB biosynthetic pathway in the cytoplasm led to a deleterious effect on growth, expression of the PHB biosynthetic pathway in plastids had no obvious effect on the growth or fertility of the transgenic plants and resulted in a 100-fold increase in the amount of PHB that accumulated. We conclude that there does not appear to be any biological barrier to high-level production of PHB in higher plants. The high level of PHB accumulation also suggests that the synthesis of plastid acetyl-CoA is regulated by a mechanism which responds to metabolic demand.
The Association of Red Cell Distribution Width with Glycated Hemoglobin among Healthy Adults without Diabetes Mellitus (2012)

RDW significantly predicts HbA1c independent of FBG in healthy nondiabetic adults, suggesting the possibility of chronic hyperglycemia mediating the association between RDW and CVD.
Crystal structures of RsbQ, a stress‐response regulator in Bacillus subtilis (2005)

Growth-limiting stresses in bacteria induce the general stress response to protect the cells against future stresses. Energy stress caused by starvation conditions in Bacillus subtilis is transmitted to the sigma(B) transcription factor by stress-response regulators. RsbP, a positive regulator, is a phosphatase containing a PAS (Per-ARNT-Sim) domain and requires catalytic function of a putative alpha/beta hydrolase, RsbQ, to be activated. These two proteins have been found to interact with each other. We determined the crystal structures of RsbQ in native and inhibitor-bound forms to investigate why RsbP requires RsbQ. These structures confirm that RsbQ belongs to the alpha/beta hydrolase superfamily. Since the catalytic triad is buried inside the molecule due to the closed conformation, the active site is constructed as a hydrophobic cavity that is nearly isolated from the solvent. This suggests that RsbQ has specificity for a hydrophobic small compound rather than a macromolecule such as RsbP. Moreover, structural comparison with other alpha/beta hydrolases demonstrates that a unique loop region of RsbQ is a likely candidate for the interaction site with RsbP, and the interaction might be responsible for product release by operating the hydrophobic gate equipped between the cavity and the solvent. Our results support the possibility that RsbQ provides a cofactor molecule for the mature functionality of RsbP.
A future for nuclear power (2006)

Exactly 20 years ago this month, on 21 April 1986, workers at the Chernobyl nuclear plant in the former Soviet Union carried out an experiment at very low power with one of the facility's two "RBMK" reactors. They were, however, unaware that their actions would make the reactor dangerously unstable. Its power rapidly increased, leading to the destruction of the core and a massive chemical explosion. The World Health Organisation estimates that between 40 and 50 staff and emergency workers died as a result of radiation released during the accident. It also resulted in widespread contamination and radiation exposure.
DNA microarrays and gene expression from experiments to data analysis and modeling (2002)

Preface 1. A brief history of genomics 2. DNA array formats 3. DNA array readout methods 4. Gene expression profiling experiments: problems, pitfalls and solutions 5. Statistical analysis of array data: inferring changes 6. Statistical analysis of array data: dimensionality reduction, clustering, and regulatory regions 7. Survey of current DNA array applications 8. Systems biology: overview of regulatory, metabolic and signaling networks.
Involvement of Claudin-1 in the β-Catenin/Tcf Signaling Pathway and its Frequent Upregulation in Human Colorectal Cancers (2001)

Accumulation of beta-catenin in cytoplasm and nuclei is frequently observed in a wide variety of tumors arising, for example, in the colon, liver, uterus, or brain. In association with Tcf/LEF transcription factors, beta-catenin regulates expression of genes involved in the Wnt/wingless signaling pathway, but the precise mechanisms are unclear. Here we report evidence that the claudin-1 (CLDNI) gene is one of the genes regulated by beta-catenin. Not only did expression of CLDN1 decrease significantly in response to reduction of intracellular beta-catenin by adenovirus-mediated transfer of wild-type APC into the APC-deficient colon cancer cells, but also two putative Tcf4 binding elements in the 5' flanking region of CLDN1 were confirmed to be responsible for activating its transcription. We documented increased expression of CLDN1 in all 16 primary colorectal cancers we examined, compared with adjacent noncancerous mucosae. Furthermore, immunohistochemical staining demonstrated that claudin-1 was weakly stained at apical boarder of lateral membrane of noncancerous epithelial cells and that it was strongly stained at all cell-cell boundaries and in the cytoplasms of cancer cells. Our results imply that claudin-1 is involved in the beta-catenin-Tcf/LEF signaling pathway, and that increased expression of claudin-1 may have some role in colorectal tumorigenesis.