gebhart/patrepeval huggingface dataset:
PneumocystisColonization in Immunocompetent and Simian Immunodeficiency Virus-infected Cynomolgus Macaques (2008)

Pneumocystis (Pc) colonization is common among human immunodeficiency virus (HIV)-infected subjects, although the clinical consequences of Pc carriage are not fully understood. We examined the frequency of asymptomatic carriage in healthy and simian immunodeficiency virus (SIV)-infected cynomolgus macaques by use of polymerase chain reaction (PCR) and assessment of changes in the serologic response to a recombinant fragment of the Pc protein kexin (KEX1). Anti-KEX1 antibodies were detected in 95% of healthy monkeys. To create a model of natural transmission of Pc, SIV-infected monkeys were cohoused with macaques coinfected with SIV and Pc. Pc colonization occurred when the CD4(+) T cell count decreased to <500 cells/microL, despite anti-Pc prophylaxis with trimethoprim-sulfamethoxazole. Increases in anti-KEX1 antibody titers preceded detection of Pc DNA in bronchoalveolar lavage (BAL) fluid samples by use of PCR. These results demonstrate the usefulness of recombinant KEX1 in serologic studies of Pc colonization and will improve the understanding of Pc transmission and clinical consequences of Pc colonization in HIV-infected patients.
Relationship Between Retinal Blood Flow and Serum Adiponectin Concentrations in Patients With Type 2 Diabetes Mellitus (2015)

Our results indicated that a high concentration of serum adiponectin may be associated with increased RBF, probably via the increased blood velocity and dilated vessel diameter in males with type 2 diabetes with early-phase diabetic retinopathy.
Periodontal regeneration in human Class II furcations using purified recombinant human platelet-derived growth factor-BB (rhPDGF-BB) with bone allograft. (2003)

This human clinical trial evaluated the clinical and histologic response to recombinant human platelet-derived growth factor-BB (rhPDGF-BB) delivered in bone allograft for the treatment of advanced Class II furcation defects. Three mandibular and one maxillary molar furcation defects were treated: Two received 0.5 mg/mL and two received 1.0 mg/mL rhPDGF-BB, in all cases mixed with DFDBA. Clinical probing depths and attachment levels were obtained presurgically and 9 months postsurgical, after which the teeth and surrounding tissues were removed en bloc. Both concentrations of rhPDGF-BB resulted in substantially improved horizontal (mean 3.5 mm) and vertical (mean 4.25 mm) probing depths and attachment levels (mean 3.75 mm). Histologic evaluation revealed periodontal regeneration, including new bone, cementum, and periodontal ligament coronal to the reference notch. Regeneration was also present coronal to the original osseous crest In one case where an enamel projection extended into the fornix of the furcation, new calcified tissue with new inserting connective tissue fibers was observed over the enamel. This study documented the favorable tissue response to rhPDGF-BB treatment at both the clinical and microscopic levels, provided the first human histologic evidence that new calcified tissue with inserting collagen fibers can occur over enamel projections within furcations, and demonstrated for the first time that complete periodontal regeneration can be achieved in advanced Class II furcation defects using a combination of purified recombinant growth factor and bone allograft.
Effect of Nitrate on Biogenic Sulfide Production (1986)

The addition of 59 mM nitrate inhibited biogenic sulfide production in dilute sewage sludge (10% [vol/vol]) amended with 20 mM sulfate and either acetate, glucose, or hydrogen as electron donors. Similar results were found when pond sediment or oil field brines served as the inoculum. Sulfide production was inhibited for periods of at least 6 months and was accompanied by the oxidation of resazurin from its colorless reduced state to its pink oxidized state. Lower amounts of nitrate (6 or 20 mM) and increased amounts of sewage sludge resulted in only transient inhibition of sulfide production. The addition of 156 mM sulfate to bottles with 59 mM nitrate and 10% (vol/vol) sewage sludge or pond sediment resulted in sulfide production. Nitrate, nitrite, and nitrous oxide were detected during periods where sulfide production was inhibited, whereas nitrate, nitrite, and nitrous oxide were below detectable levels at the time sulfide production began. The oxidation of resazurin was attributed to an increase in nitrous oxide which persisted in concentration of about 1.0 mM for up to 5 months. The numbers of sulfate-reducing organisms decreased from 10 CFU ml sludge to less than detectable levels after prolonged incubation of oxidized bottles. The addition of 10 mM glucose to oxidized bottles after 14.5 weeks of incubation resulted in rereduction of the resazurin and subsequent sulfide production. The prolonged inhibition of sulfide production was attributed to an increase in oxidation-reduction potential due to biogenic production of nitrous oxide, which appeared to have a cytotoxic effect on sulfate-reducing populations.
A Tcl/Tk-based video annotation engine (1997)

Abstract–The population of a video database requires tools for manipulation and annotation of raw video data. Characteristic of this requirement is the need to satisfy many disparate video-based application domains. In this paper we describe the design and development of a video annotation engine called Vane, intended to address the issue of domain-independent video annotation. Rather than relying on a single, general data model and application interface, we developed a dynamic interface and data model using the Tcl/Tk environment and SGML document type definitions (DTDs). This approach allowed us to implement an intuitive graphical user interface application that is easily portable to different systems. The tool is currently in use to annotate a video archive comprised of educational and news video content at Boston University.
Anti-KIT Monoclonal Antibody Treatment Enhances the Antitumor Activity of Immune Checkpoint Inhibitors by Reversing Tumor-Induced Immunosuppression (2017)

The receptor tyrosine kinase KIT is an established oncogenic driver of tumor growth in certain tumor types, including gastrointestinal stromal tumors, in which constitutively active mutant forms of KIT represent an actionable target for small-molecule tyrosine kinase inhibitors. There is also considerable potential for KIT to influence tumor growth indirectly based on its expression and function in cell types of the innate immune system, most notably mast cells. We have evaluated syngeneic mouse tumor models for antitumor effects of an inhibitory KIT mAb, dosed either alone or in combination with immune checkpoint inhibitors. Anti-KIT mAb treatment enhanced the antitumor activity of anti-CTLA-4 and anti-PD-1 mAbs, and promoted immune responses by selectively reducing the immunosuppressive monocytic myeloid-derived suppressor cell population and by restoring CD8<sup>+</sup> and CD4<sup>+</sup> T-cell populations to levels observed in naïve mice. These data provide a rationale for clinical investigation of the human KIT-specific mAb KTN0158 in novel immuno-oncology combinations with immune checkpoint inhibitors and other immunotherapeutic agents across a range of tumor types. <i>Mol Cancer Ther; 16(4); 671-80. ©2017 AACR</i>.
Adaptive noise estimation algorithm for speech enhancement (2003)

An efficient noise estimation algorithm for speech enhancement is proposed. The noisy speech is decomposed into subband signals and the subband noise estimate is updated by adaptively smoothing the noisy signal power. The smoothing parameter is chosen as a function of the estimated signal-to-noise ratio (SNR). This noise estimation technique gives reliable results even at very low SNRs.
The Development of a Dual Injection Hydrogen Fueled Engine With High Power and High Efficiency (2002)

To achieve high power and high efficiency in a hydrogen fueled engine for all load conditions, the dual injection hydrogen fueled engine that can derive the advantage of both high efficiency from external mixture hydrogen engine and high power from direct cylinder injection hydrogen engine was introduced. For verifying the feasibility of the above engine, the high pressure hydrogen injector of ball valve type actuated by a solenoid was developed. A systematic experimental study was conducted by using a modified single cylinder dual injection hydrogen fueled engine which was equipped with both an intake injector and a high pressure in-cylinder injector. The results showed that (1) the developed high pressure hydrogen injector with a solenoid actuator had good gas-tightness and fine control performance, (2) the transient injection region, in which injection methods are changed from external fuel injection to direct-cylinder injection, ranged from 59 to 74 percent of the load, and (3) the dual injection hydrogen fueled engine had the maximum torque of direct-cylinder fuel injection and the maximum efficiency of external fuel mixture hydrogen engines.
Surgical Stress, Bacteria, and Mucosal Immune Function (1999)

Bacteria share a benign coexistence with host mucosal surfaces in the gastrointestinal tract during periods of health. Both host epithelial defense function and bacterial virulence phenotypes are significantly affected by stress. Via discreet and specific sensory input signals to bacteria, the molecular machinery of otherwise commensal strains of bacteria can shift the phenotypes of residential colonizers to more virulent and invasive strains. This occurs at a time when the host may be relatively immunosuppressed by the injury. This adaptive response demonstrates the duplicitous nature of bacteria residing on mucosal surfaces whose ability to shift their virulence characteristics may play an important role in infectious-related morbidity following surgical stress.
COMPATIBILITY OF ENTOMOPATHOGENIC FUNGI, METARHIZIUM ANISOPLIAE AND PAECILOMYCES FUMOSOROSEUS WITH SELECTIVE INSECTICIDES (2010)

Investigations were carried out to evaluate influence of some selective insecticides on mycelial growth and conidial germination of Metarhizium anisopliae (Metsch.) Sorokin and Paecilomyces fumosoroseus (Wize) Brown & Smith. All insecticides significantly inhibited mycelial growth and conidial germination of the fungal pathogens. Lorsban was the most toxic insecticide to mycelial growth and conidial germination followed by Lannate, Larvin and Pirate. Cascade, Match, Steward and Proclaim were comparatively less toxic to mycelial growth (36.78-48.67% inhibition) and conidial germination (40.32-49.97% inhibition) of the fungal pathogens. Conversely, Runner, Capture, Abamectin and Curacron were compatible with significantly lesser inhibition in growth (25.19-36.47%) and conidial germination (27.78-43.66%) of the fungi. Tracer was found safe to conidial germination and growth of the fungi.
Bacterial infection as a cause of cancer. (1995)

Bacterial infections traditionally have not been considered major causes of cancer. Recently, however, bacteria have been linked to cancer by two mechanisms: induction of chronic inflammation and production of carcinogenic bacterial metabolites. The most specific example of the inflammatory mechanism of carcinogenesis is Helicobacter pylori infection. H. pylori has been epidemiologically linked to adenocarcinoma of the distal stomach by its propensity to cause lifelong inflammation. This inflammation is in turn thought to cause cancer by inducing cell proliferation and production of mutagenic free radicals and N-nitroso compounds. H. pylori is the first bacterium to be termed a definite cause of cancer in humans by the International Agency for Research on Cancer. Mutagenic bacterial metabolites are also suspected to increase risk for cancer. This model is best exemplified in colon cancer. Bile salt metabolites increase colonic cell proliferation. Exogenous compounds such as rutin may be metabolized into mutagens by resident colonic flora. Moreover, Bacteroides species can produce fecapentaenes, potent in vitro mutagens, in relatively high concentrations. In vivo data on human carcinogenesis by bacterial metabolites, however, are inconsistent. Local bacterial infections may also predispose to nonnodal lymphomas, although the mechanisms for this are unknown. Gastric lymphomas and immunoproliferative small intestinal disease have been most strongly linked to underlying bacterial infection. Because bacterial infections can be cured with antibiotics, identification of bacterial causes of malignancy could have important implications for cancer prevention.
Molecular genetics of muccpolysaccharidosis type I: Diagnostic, clinical, and biological implications (1995)

Mucopolysaccharidosis type I (MPS-I) is an autosomal recessive disease caused by mutations in the alpha-L-iduronidase (IDUA) gene. These mutations lead to a deficiency of the glycosidase alpha-L-iduronidase (IDUA), which is required for the degradation of heparan sulphate and dermatan sulphate and thus the storage of these glycosaminoglycans in the lysosome. There is a wide range of clinical phenotypes in MPS-I (eponyms: Hurler syndrome, severe; Hurler/Scheie syndrome, intermediate; Scheie syndrome, mild), which makes prediction of disease severity and genetic counselling difficult. However, since cloning of the IDUA gene, mutation analysis has provided some molecular explanations for the range of MPS-I phenotypes, in turn facilitating the selection and evaluation of patients undergoing experimental treatment protocols such as bone marrow transplantation. A total of 46 mutations now have been defined for MPS-I consisting of 8 nonsense mutations, 21 missense mutations, 3 splice site mutations, and 14 minor deletions and/or insertions. Furthermore, 30 polymorphisms or nonpathogenic sequence variants have been defined, including 7 amino acid substitutions. Among patients of European origin, there are two major MPS-I mutations and a number of less frequent mutations. It is possible to follow mutation analysis of 292 patients, which can be divided into eight main patient groups of different ethnic and/or geographic origin with significant variation in mutant allele frequencies. A complex picture of molecular heterogeneity is emerging, building a valuable database for genotype/phenotype correlation. Mutation analysis is also providing some of the first clues into the structure and function of IDUA.
Generating 3D Building Models from Architectural Drawings: A Survey (2009)

Automatically generating 3D building models from 2D architectural drawings has many useful applications in the architecture engineering and construction community. This survey of model generation from paper and CAD-based architectural drawings covers the common pipeline and compares various algorithms for each step of the process.
Choline-stabilised orthosilicic acid added for nutritional purposes to food supplements (2009)

Orthosilicic acid [Si(OH)4] is the major silicon species present in drinking water and other liquids, including beer, and is the most readily available source of silicon to man. The essentiality of silicon for man has not been established and a functional role for silicon in&#13;\nman has not yet been identified. The bioavailability of silicon under the form of orthosilicic acid has been proven for cholinestabilised orthosilicic acid. Acute oral toxicity studies in male and female rats as well as mice have been performed. The calculated mean LD50 value for ch-OSA exceeds (for both animal species) 5000 mg/kg bw.&#13;\nConcerning the acute oral toxicology of choline, an LD50 value of 6640 mg/kg bw as choline chloride was found. Subchronic toxicity studies on ch-OSA were conducted both in animals (rodents and mammals) and humans (supplementation studies). No adverse effects were observed.&#13;\nThe proposed dosage of ch-OSA in food supplements is 5 to 10 mg silicon/day (equivalent to 0.083-0.17 mg silicon/kg bw/day for a 60 kg person). The equivalent intake of choline amounts to 101-203 mg choline/day for the ch-OSA liquid, and to 117-234 mg choline/day for&#13;\nthe ch-OSA pellets. This results in an intake of 135-272 mg choline chloride/day for ch-OSA liquid and of 157-314 mg choline chloride/day for ch-OSA pellets. The European Food Safety Authority estimated the typical dietary intake of silicon to be 20-50 mg/day, corresponding to 0.3-0.8 mg silicon/kg bw/day for a 60 kg person, and concluded that&#13;\nthese intakes are unlikely to cause adverse effects. The Panel concludes that silicon is bioavailable from choline-stabilised orthosilicic acid and that its use in supplements, at the proposed use levels of the source, is of no safety concern provided that the upper level for choline is not exceeded.
Adsorption properties of U.I.C.C. Rhodesian chrysotile and crocidolite in aqueous solution—effects of cation depletion (1979)

Adsorption properties of U.I.C.C. Rhodesian chrysotile and crocidolite were tested in aqueous solution with acid and basic dyes (Eosine Y, Picric Acid, Acridine Orange and Methylene Blue). Rates of adsorption showed a diffusion of only basic dyes in micropores of fibers. The strong adsorption of basic dyes on the surface of the fibers led us to suppose that the active sites have a negative charge. Our hypothesis was supported by the verification of an increase in adsorption capacity which depends on depletion of Mg++ from chrysotile and of Fe++ from crocidolite.
Attenuation of arterial blood pressure fall in endotoxin shock in the rat using the competitive bradykinin antagonist Lys‐Lys‐[Hyp2, Thi5,8, DPhe7]‐Bk (B4148) (1988)

The selective competitive bradykinin (Bk) antagonist, B4148 (Lys-Lys-[Hyp2, Thi5,8, DPhe7]-Bk) infused at 100 micrograms kg-1 min-1 into rats produced a significant inhibition of the hypotensive effect of Bk and had no effect against acetylcholine-induced responses. In a rat model of endotoxin shock, the fall in mean arterial blood pressure in response to an intravenous injection of lipopolysaccharide from E. coli was significantly attenuated by the same infusion of B4148 compared to controls. These findings suggest that kinins are involved in the hypotensive response to endotoxin shock in rats. The development of potent Bk antagonists offers a new experimental approach for evaluating the role of kinins in this and other disease states and potential therapy in such disorders.
Progress toward the development of an implantable sensor for glucose. (1992)

The development of an electrochemically based implantable sensor for glucose is described. The sensor is needle-shaped, about the size of a 28-gauge needle. It is flexible and must be implanted subcutaneously by using a 21-gauge catheter, which is then removed. When combined with a monitoring unit, this device, based on the glucose oxidase-catalyzed oxidation of glucose, reliably monitors glucose concentrations for as long as 10 days in rats. Various design considerations, including the decision to monitor the hydrogen peroxide produced in the enzymatic reaction, are discussed. Glucose constitutes the most important future target analyte for continuous monitoring, but the basic methodology developed for glucose could be applied to several other analytes such as lactate or ascorbate. The success in implementation of such a device depends on a reaction of the tissue surrounding the implant so as not to interfere with the proper functioning of the sensor. Histochemical evidence indicates that the tissue response leads to enhanced sensor performance.
Expression of the Xylulose 5-Phosphate Phosphoketolase Gene, xpkA , from Lactobacillus pentosus MD363 Is Induced by Sugars That Are Fermented via the Phosphoketolase Pathway and Is Repressed by Glucose Mediated by CcpA and the Mannose Phosphoenolpyruvate Phosphotransferase System (2002)

Purification of xylulose 5-phosphate phosphoketolase (XpkA), the central enzyme of the phosphoketolase pathway (PKP) in lactic acid bacteria, and cloning and sequence analysis of the encoding gene, xpkA, from Lactobacillus pentosus MD363 are described. xpkA encodes a 788-amino-acid protein with a calculated mass of 88,705 Da. Expression of xpkA in Escherichia coli led to an increase in XpkA activity, while an xpkA knockout mutant of L. pentosus lost XpkA activity and was not able to grow on energy sources that are fermented via the PKP, indicating that xpkA encodes an enzyme with phosphoketolase activity. A database search revealed that there are high levels of similarity between XpkA and a phosphoketolase from Bifidobacterium lactis and between XpkA and a (putative) protein present in a number of evolutionarily distantly related organisms (up to 54% identical residues). Expression of xpkA in L. pentosus was induced by sugars that are fermented via the PKP and was repressed by glucose mediated by carbon catabolite protein A (CcpA) and by the mannose phosphoenolpyruvate phosphotransferase system. Most of the residues involved in correct binding of the cofactor thiamine pyrophosphate (TPP) that are conserved in transketolase, pyruvate decarboxylase, and pyruvate oxidase were also conserved at a similar position in XpkA, implying that there is a similar TPP-binding fold in XpkA.
Crosslinking transfer RNA and messenger RNA at the ribosomal decoding region: identification of the site of reaction on the messenger RNA (1984)

Wybutine (Ywye), situated next to the 3'-side of the anticodon of tRNAPhe from Saccharomyces cerevisiae, can be photo-crosslinked to mRNA when bound to Escherichia coli ribosomes. Crosslinking can be obtained with poly(U) as well as with oligonucleotides such as pAUGUUU or p(U)6. In order to identify the site of reaction on the mRNA, 5'-[32P]-labelled pAUGUUU was crosslinked by irradiation at 320 nm with Phe-tRNAPhe from yeast bound to the acceptor-site. The photoproduct was subsequently digested with P1-nuclease and analyzed by electrophoresis followed by homochromatography in the second dimension. As a result of the photoreaction the wybutine was found to be crosslinked to the U at the 5'-position of the corresponding UUU-codon.
The origin of the 1918 pandemic influenza virus: a continuing enigma (2003)

Influenza A virus is a major public health threat, killing more than 30,000 per year in the USA alone, sickening millions and inflicting substantial economic costs. Novel influenza virus strains emerge periodically to which humans have little immunity, resulting in devastating pandemics. The 1918 pandemic killed nearly 700,000 Americans and 40 million people worldwide. Pandemics in 1957 and 1968, while much less devastating than 1918, also caused tens of thousands of deaths in the USA. The influenza A virus is capable of enormous genetic variability, both by continuous, gradual mutation and by reassortment of gene segments between viruses. Both the 1957 and 1968 pandemic strains are thought to have originated as reassortants, in which one or both human-adapted viral surface proteins were replaced by proteins from avian influenza virus strains. Analyses of the surface proteins of the 1918 pandemic strain, however, suggest that this strain may have had a different origin. The haemagglutinin gene segment of the virus may have come directly from an avian source different from those currently circulating. Alternatively, the virus, or some of its gene segments, may have evolved in an intermediate host before emerging as a human pathogen. Determining whether pandemic influenza virus strains can emerge via different pathways will affect the scope and focus of surveillance and prevention efforts.