gebhart/patrepeval huggingface dataset:
PCR and single-strand conformational polymorphism for recognition of medically important opportunistic fungi (1995)

The application of PCR technology to molecular diagnostics holds great promise for the early identification of medically important pathogens. PCR has been shown to be useful for the detection of the presence of fungal DNA in both laboratory and clinical samples. Considerable interest has been focused on the utility of selecting universal primers, those that recognize constant regions among most, if not all, medically important fungi. Once an amplicon, or piece of amplified DNA determined by the unique pair of oligonucleotide primers, has been generated, several different methods may be used to distinguish between genera and between species. The two major approaches have utilized differences in restriction enzyme digestion patterns or hybridization with specific probe. We report the application of single-strand conformational polymorphism (SSCP) as a technique to delineate the differences between fungal species and/or genera. Minor sequence variations in small single-stranded DNA cause subtle changes in conformation, allowing these strands to be separated on polyacrylamide gels by SSCP. We used a 197-bp fragment amplified from the 18S rRNA gene, common to all medically important fungi. After amplification, the fragments were denatured and run on an acrylamide-glycerol gel at room temperature or 4 degrees C for 4.5 or 4 h, respectively. Under room temperature conditions, the SSCP patterns for Candida albicans, Candida tropicalis, and Candida parapsilosis were identical and all strains within each species demonstrated the same pattern. These patterns differed markedly from those of the genus Aspergillus. The SSCP patterns of major and minor bands at room temperature permitted distinction between strains of Aspergillus fumigatus and Aspergillus flavus. There also was consistency of the SSCP banding pattern among different strains of the same Aspergillus species. The SSCP patterns for other medically important opportunistic fungi, such as Cryptococcus neoformans, Pseudallescheria boydii, and Rhizopus arrhizus, were sufficiently unique to permit distinction from those of C. albicans and A. fumigatus. We conclude that the technique of PCR-SSCP provides a novel method by which to recognize and distinguish medically important opportunistic fungi and which has potential applications to molecular diagnosis, taxonomic classification, molecular epidemiology, and elucidation of mechanisms of antifungal drug resistance.
Human smooth muscle myosin heavy chain gene mapped to chromosomal region 16q12 (1993)

The partial nucleotide sequence encoding the rod portion of the entire amino acid sequence of human smooth muscle myosin heavy chain (MHC) which corresponds to MYH11, according to Human Gene Mapping nomenclature, has been determined by cloning a complementary DNA (cDNA) and sequencing the cDNA (UMYHSM). Northern blot analysis with the UMYHSM fragment (4.3 Kb) showed that the smooth muscle MHC of the human umbilical artery is expressed in the human umbilical artery, bladder, esophagus and trachea. Southern blot analysis of human genomic DNA from human-mouse or human-Chinese hamster somatic cell hybrids demonstrated that the human smooth muscle MHC was mapped to human chromosome 16. Regional mapping of UMYHSM was performed using human cell lines with partial deletion and trisomy of chromosome 16. As a result, the human smooth muscle MHC gene segregated with 16p11-q12. In situ hybridization of biotin-labeled human smooth muscle MHC probe (UMYHSM fragment) to normal human metaphase chromosome independently showed that the human smooth muscle MHC gene (MYH11) is assigned to chromosome region 16q12. Analysis of early metaphase chromosomes showed that hybridization signals were in 16q12.1. In the human, although skeletal, cardiac, smooth muscle, and nonmuscle MHC genes are mapped to chromosomes 17, 14, 16, and 22, respectively, structural similarities of these MHC genes strongly suggest the common origin of these genes.
Capillary electrophoresis for the study of affinity interactions (1998)

Molecular recognition may be characterized both qualitatively and quantitatively by electrophoretic methods if complexed molecules differ in electrophoretic mobility from unbound ones. The use of capillary zone electrophoresis (CE) for the characterization of affinity interactions is advantageous because of the high resolution, reproducibility and wide applicability of the technique and because of the mild conditions, i.e., physiological buffers without additions of organics or detergents, that are often sufficient for highly efficient separations. CE gives the ability to characterize binding between small amounts of unlabelled reactants in solution, has few requirements for special characteristics of the interacting molecules and is also applicable to the study of interactions of individual components in mixtures, as detection of binding and analytical separation are achieved in one step. This is unique compared with other techniques for the study of non-covalent interactions. The advantages and disadvantages of using CE to demonstrate molecular interactions, to screen for specific ligand binding in complex mixtures and to calculate binding constants will be discussed.
Nitric oxide attenuates leukocyte-endothelial interaction via P-selectin in splanchnic ischemia-reperfusion (1994)

We studied the effects of exogenous nitric oxide (NO) on leukocyte-endothelial interaction after 60 min of splanchnic artery ischemia and 120 min of reperfusion (SAO/R) in pentobarbital sodium-anesthetized rats via intravital microscopy. Treatment with the NO donor S-nitroso-N-acetylpenicillamine (SNAP, 20 micrograms/kg bolus followed by infusion at 20 micrograms.kg-1.h-1), beginning 10 min before reperfusion, resulted in significantly decreased leukocyte-endothelial interaction. This was manifested by a significant decrease in leukocyte rolling and adherence in the postcapillary venules. Tissue protection was demonstrated by a significantly lower plasma free amino-nitrogen concentration in the SNAP-treated SAO/R rats compared with those receiving NO-depleted SNAP (P < 0.05). Immunohistochemical localization of P-selectin showed significantly decreased P-selectin expression on the venular endothelium after SAO/R in rats given SNAP 10 min before reperfusion (23.0 +/- 3.2% vs. 54.9 +/- 12.1% positive staining, respectively, P < 0.01). From these data, we conclude that the effects of exogenous NO on leukocyte-endothelial interaction after ischemia-reperfusion appear to be at least partially mediated through the endothelial adhesion molecule P-selectin.
Centrally truncated and stabilized porcine neuropeptide Y analogs: design, synthesis, and mouse brain receptor binding. (1989)

Porcine neuropeptide Y (pNPY) has been proposed to form an intramolecularly stabilized structure characterized by N- and C-terminal helical regions arranged antiparallel due to a central turn region. Analogs based on this structural model that have the central turn region and various amounts of the helical regions removed, yet retain the N and C termini in a similar spatial orientation were designed. The gap formed by removal of the central residues (residues 8-17 or 7-20) was spanned with a single 8-aminooctanoic acid residue (Aoc) and the structure was further stabilized by the introduction of a disulfide bridge. [D-Cys7,Aoc8-17,Cys20]pNPY and [Cys5,Aoc7-20,D-Cys24]pNPY were synthesized and found to have receptor binding affinities of 2.3 nM and 150 nM, respectively, in mouse brain membranes (pNPY affinity is 3.6 nM in this assay). It is proposed that the central region (residues 7-17) of pNPY serves a structural role in the peptide and is not involved in direct receptor interaction.
Impact of lignin polymer backbone esters on ionic liquid pretreatment of poplar (2017)

Our findings clearly demonstrate that the introduction of ester linkages into the lignin polymer backbone decreases biomass recalcitrance in poplar has the potential to reduce the energy and/or amount of IL required for effective pretreatment, and could enable the development of an economically viable and sustainable biorefinery process.
Acute treatment of migraine attacks (1995)

Migraine is a chronic neurological disorder, characterized by attacks of severe, usually unilateral and throbbing headache accompanied by nausea, vomiting, and photophobia and photophobia. Sometimes transient neurological (aura) symptoms may precede or accompany the headaches. Acute drug therapy comprises nonspecific drugs, including simple analgesics and non-steroidal anti-inflammatory drugs, often in combination with antiemetics, and specific antimigraine drugs, such as ergotamine, dihydroergotamine and sumatriptan. Sumatriptan is a potent and selective serotonin1D receptor agonist, which can be administered orally and via the subcutaneous or intranasal route. The drug is well tolerated and is consistently highly effective in most patients. Significant limitations, however, include the occurrence of chest symptoms, suggestive of cardiac ischaemia; recurrence of the headache within 24 h after initial successful treatment; and in a minority of patients, abuse of sumatriptan with daily 'sumatriptan-dependent headaches'. Administration during the aura phase does not affect the aura itself, but is not recommended because the subsequent headache will not be prevented in that case. Preliminary data of new serotonin1D receptor agonists, such as 311C90 and MK-462 are promising in terms of increased efficacy after oral administration, but side-effect profile and incidence of headache recurrence are similar to those observed after the use of sumatriptan. Intranasal administration of dihydroergotamine may also be effective, but data are very limited.
Efficacy and pharmacokinetics of subcutaneous exendin (9‐39) in patients with post‐bariatric hypoglycaemia (2017)

Injection s.c. of Ex-9 appears to represent a safe, effective and targeted therapeutic approach for treatment of PBH. Further investigation involving multiple doses with chronic dosing is warranted.
Antibiotic-leaching from polymethylmethacrylate beads. (1993)

Aminoglycoside-impregnated polymethylmethacrylate beads, which are used to deliver antibiotic directly to infected sites in the musculoskeletal system, are available as a manufactured product or they can be mold-made by a pharmacy or hand-rolled by the orthopaedist in the operating suite. We investigated the leaching of antibiotic from each of these types of beads. Our hypothesis was that the elutions of antibiotic from the three types of beads are similar. Three study groups (hand-made, mold-made, and manufactured beads), each composed of four five-bead subsets, were formed so that twenty beads of each type were tested. Each bead was leached daily in a two-milliliter aliquot of normal saline solution throughout a sixty-day period, and the aminoglycoside concentration in twenty of these aliquots was determined. Analysis of variance showed no statistically significant differences when the antibiotic elutions within each subset, between the different subsets, and between the three groups were compared. The clinically important finding of this investigation is that the leaching characteristics of the three types of aminoglycoside-impregnated beads are equivalent when the beads have been fabricated out of comparable materials.
Construction and activity of a novel GHRH analog, Pro-Pro-hGHRH(1-44)-Gly-Gly-Cys. (2004)

Pro-Pro-hGHRH (1-44)-Gly-Gly-Cys had a better activity than that of Pro-Pro-hGHRH(1-44)OH. Variation at C-terminus of GHRH could modulate its GH releasing activity.
Profiling resource usage for mobile applications (2011)

Despite the popularity of mobile applications, their performance and energy bottlenecks remain hidden due to a lack of visibility into the resource-constrained mobile execution environment with potentially complex interaction with the application behavior. We design and implement ARO, the mobile Application Resource Optimizer, the first tool that efficiently and accurately exposes the cross-layer interaction among various layers including radio resource channel state, transport layer, application layer, and the user interaction layer to enable the discovery of inefficient resource usage for smartphone applications. To realize this, ARO provides three key novel analyses: (i) accurate inference of lower-layer radio resource control states, (ii) quantification of the resource impact of application traffic patterns, and (iii) detection of energy and radio resource bottlenecks by jointly analyzing cross-layer information. We have implemented ARO and demonstrated its benefit on several essential categories of popular Android applications to detect radio resource and energy inefficiencies, such as unacceptably high (46%) energy overhead of periodic audience measurements and inefficient content prefetching behavior.
Production and characterization of thermostable xylanase from Talaromyces byssochlamydoides YH-50. (1981)

Strain YH-50 from a thermophilic fungus isolated from compost heaps produced the highest amount of thermostable xylanase among 180 isolates tested. This xylanase-producing strain YH-50 was identified as Talaromyces byssochlamydoides Stolk & Samson by taxonomical characteristics. When it was cultivated in solid wheat bran medium containing xylan as an additive carbon source, the maximal amount of thermostable xylanase was produced after 3 days at 50°C. This culture filtrate hydrolyzed 90 % of xylan as xylose, and the sugars formed were xylose, arabinose, glucose and galactose. The optimal pH and temperature were 5.5 and 70°C, respectively. The enzyme was quite stable after heating at 65°C for 5 min and retained 55 % of original activity after heating at 95°C for 5 min.
The Clinical Significance of Aurora-A/STK15/BTAK Expression in Human Esophageal Squamous Cell Carcinoma (2005)

The up-regulation of Aurora-A expression may reflect the malignant behavior of ESCC and may prove useful information as a prognostic factor for ESCC patients.
A novel bivalent single‐chain variable fragment (scFV) inhibits the action of tumour necrosis factor α (2008)

Suppression of TNFalpha (tumour necrosis factor alpha) activity is widely considered to be among the most efficient treatments available for chronic inflammatory diseases. Here, a bivalent scFv (single-chain variable fragment) fragment, named TNF-BAb, was engineered by fusing two anti-TNFalpha scFV fragments in tandem via a long and flexible linking peptide derived from human serum albumin and produced in functional form from Escherichia coli inclusion bodies. The bioactivity assays demonstrated that TNF-BAb gained enormously in avidity and showed a much stronger ability to inhibit the biological action of TNFalpha, indicating that TNF-BAb may become a good candidate for anti-TNFalpha therapy.
Thrombotic Microangiopathy with Targeted Cancer Agents (2011)

Thrombotic thrombocytopenic purpura (TTP) and hemolytic uremic syndrome (HUS) are clinically similar disorders characterized by microvascular thrombosis, hemolysis, thrombocytopenia, and end-organ damage. Although they may present with overlapping symptoms, multiple etiologies have been proposed for these thrombotic microangiopathies (TMA). Chemotherapy-induced TMA, which has been described with the use of mitomycin, gemcitabine, and other drugs, has a poor prognosis. Recently, reports of TMA associated with targeted cancer agents have surfaced in the literature. We discuss the clinical presentation, outcome, and etiology of TMA reported with the use of immunotoxins, monoclonal antibodies, and tyrosine kinase inhibitors. A search of PubMed and meeting abstracts was conducted for cases of TMA with the use of targeted cancer agents. The defining symptoms, laboratory values, time to onset, and patient outcomes were compiled. Consistent definitions of TMA and grading of severity in these cases are lacking. However, presentation of TMA in these cases revealed the importance of monitoring for renal toxicity, hemolysis, and thrombocytopenia. Patient outcomes seem to differ from those seen in cases of chemotherapy-induced TMA and may reflect a different underlying etiology. Little is known about the pathogenesis of TMA with targeted cancer agents. In contrast to chemotherapy-induced TMA, partial to full reversibility may be a common outcome. However, further research is warranted into optimal management of patients diagnosed with TMA following treatment with targeted agents.
Biodegradation of the gasoline oxygenates methyl tert-butyl ether, ethyl tert-butyl ether, and tert-amyl methyl ether by propane-oxidizing bacteria (1997)

Several propane-oxidizing bacteria were tested for their ability to degrade gasoline oxygenates, including methyl tert-butyl ether (MTBE), ethyl tert-butyl ether (ETBE), and tert-amyl methyl ether (TAME). Both a laboratory strain and natural isolates were able to degrade each compound after growth on propane. When propane-grown strain ENV425 was incubated with 20 mg of uniformly labeled [14C]MTBE per liter, the strain converted > 60% of the added MTBE to 14CO2 in < 30 h. The initial oxidation of MTBE and ETBE resulted in the production of nearly stoichiometric amounts of tert-butyl alcohol (TBA), while the initial oxidation of TAME resulted in the production of tert-amyl alcohol. The methoxy methyl group of MTBE was oxidized to formaldehyde and ultimately to CO2. TBA was further oxidized to 2-methyl-2-hydroxy-1-propanol and then 2-hydroxy isobutyric acid; however, neither of these degradation products was an effective growth substrate for the propane oxidizers. Analysis of cell extracts of ENV425 and experiments with enzyme inhibitors implicated a soluble P-450 enzyme in the oxidation of both MTBE and TBA. MTBE was oxidized to TBA by camphor-grown Pseudomonas putida CAM, which produces the well-characterized P-450cam, but not by Rhodococcus rhodochrous 116, which produces two P-450 enzymes. Rates of MTBE degradation by propane-oxidizing strains ranged from 3.9 to 9.2 nmol/min/mg of cell protein at 28 degrees C, whereas TBA was oxidized at a rate of only 1.8 to 2.4 nmol/min/mg of cell protein at the same temperature.
Overexpression of Pax5 is not sufficient for neoplastic transformation of mouse neuroectoderm (2001)

The developmental control genes of the Pax family are essential for brain development. Several Pax genes are also involved in chromosomal translocations causing malignancies in humans, and Pax5 expression is deregulated in medulloblastomas. We have investigated whether Pax5 can induce tumors in the developing mouse brain. Primary mouse embryonic neuroectodermal cells were retrovirally transduced with mouse Pax5 and transplanted into the brain of syngeneic host mice. No tumors developed in 36 transplants after one year, and there were no alterations in the differentiation pattern of the neural transplants. We then generated transgenic mice expressing human Pax5 under control of the Engrailed-2 promoter, which is expressed in the cerebellar external granule cell layer and in medulloblastomas. Sustained expression was achieved in the cerebellum of transgenic animals throughout lifetime. Expression levels were similar to those observed in human medulloblastomas. Again, cerebellar morphogenesis was undisturbed, and no tumors arose. These results strongly argue against a dominant transforming activity of PAX5 in NEC and in cerebellar granule cell precursors of mice, and underline the restricted tissue-specificity of PAX5 related oncogenesis.
Shear Stress and von Willebrand Factor in Health and Disease (2003)

Blood flow in the circulation creates shear stress that affects cell functions and cell-cell interactions. Recent studies reveal that shear stress is also critical in the homeostasis of the plasma glycoprotein von Willebrand factor (vWF). Because of its large molecular size, vWF has a flexible conformation that is uniquely responsive to shear stress. Exposure to shear stress causes conformational unfolding of vWF, enhancing its susceptibility to cleavage by a plasma zinc metalloprotease (a disintegrin and metalloprotease with thrombospondin type 1 motif [ADAMTS13]). In the absence of ADAMTS13, shear stress increases the capacity of vWF to support platelet aggregation. In normal individuals, a balance between endothelial secretion of an ultralarge form of vWF and intravascular proteolysis determines the size distribution of vWF multimers that seems to be optimum for hemostasis without imposing the risk of unwarranted platelet aggregation. In type 2A (group 2) von Willebrand disease, the mutant vWF is excessively susceptible to cleavage by ADAMTS13, resulting in a decrease of large vWF multimers and bleeding diathesis. In patients with aortic stenosis or the hemolytic-uremic syndrome, abnormally high levels of shear stress across the stenotic valve or in the microcirculation inflicted with thrombosis may promote cleavage of vWF by ADAMTS13, contributing to the loss of large multimers commonly observed among these patients. Conversely, a deficiency in ADAMTS13 because of genetic mutations or autoimmune inhibitors causes vWF- and platelet-rich microvascular thrombosis characteristic of thrombotic thrombocytopenic purpura.
Concise Review: The Involvement ofSOX2in Direct Reprogramming of Induced Neural Stem/Precursor Cells (2013)

Since induced pluripotent stem cells were first generated from mouse embryonic fibroblasts in 2006, somatic cell reprogramming has become a powerful and valuable tool in many fields of biomedical research, with the potential to lead to the development of in vitro disease models, cell-based drug screening platforms, and ultimately novel cell therapies. Recent research has now demonstrated the direct conversion of fibroblasts into stem, precursor, or mature cell types that are committed in their fate within a specific lineage, such as hematopoietic precursors or mature neurons. This has been achieved by ectopic expression of defined, tissue-specific transcription factors. Several studies have demonstrated direct reprogramming of mouse and human fibroblasts into immature neural stem or precursor cells, either by transient expression of the four pluripotency genes OCT3/4, KLF4, SOX2, and C-MYC or by application of different combinations of up to 11 neural transcription factors. Interestingly, in all of these studies SOX2 was introduced alone or in combination with other transcription factors. In this review we discuss the different combinations of ectopic transcription factors used to generate neural stem/precursor cells from somatic cells, with particular emphasis on SOX2 and its potential to act as a master regulator for reprogramming to a neural precursor state.
Short-term wind power forecasting using advanced statistical methods (2006)

HAL is a multi-disciplinary open access archive for the deposit and dissemination of sci-entific research documents, whether they are pub-lished or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L’archive ouverte pluridisciplinaire HAL, est destinée au dépôt et a ̀ la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d’enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.
Defining ‘forced migration’ in Burma (2008)

Most Burmese people fleeing their homes do so for a combination of reasons. The root causes for leaving, however,determine which ‘category’ they belong to: ‘internally displaced persons’ (IDPs) or ‘economic migrants’. There issome discussion as to whether people leaving their homes due to exhaustion of livelihoods options are IDPsaccording to the Guiding Principles on Internal Displacement1 – or not. Ashley South and Andrew Bosson presenttheir views below.By analogy, this debate can be extended to Burmese people in exile. Are Burmese people outside refugee camps‘economic migrants’ or ‘self-settled refugees’? The article ‘Invisible in Thailand’ (pp31-33) sheds more light on this.