gebhart/patrepeval huggingface dataset:
Boron Nitride and Its Precursors (1988)

Stepwise condensation of a series of borazines was investigated. The compounds studied were B-trichloro-N-triphenylborazine, B-triamino-N-triphenylborazine, B-trianilinoborazine, B-tris[di(trimethylsilyl) amino]- borazine, B-trichloro-N-tris(trimethylsilyl) borazine, and B-triamino-N-tris(trimethylsilyl) borazine. The formation of preceramic polymers occurs by ring opening mechanism which leads to singly and doubly joined borazine rings. This process requires the presence of a combined total of six protons on the ring and exocyclic nitrogens. Compounds where this arrangement is absent, B-trichloro-N-triphenylborazine, B-tris[di(trimethylsilyl) amino]borazine, and B-trichloro-N-tris(trimethylsilyl) borazine, failed to undergo condensation to any significant degree. Materials obtained from the phenyl substituted borazines gave essentially nonprocessible polymers on pyrolysis; from B-triamino-N-tris(trimethylsilyl)borazine, preceramic polymers amenable to fiber manufacture were obtained. Investigation of potential linear precursor to boron-nitrogen polymers resulted in the synthesis of μ-imido-bis[bis(trimethylsilyl)-aminotrimethylsilylamino]borane (I) and μ-oxo-bis-[bis(trimethylsilyl)aminotrimethylsilylamino]borane (II). The crystal structures of the two compounds were essentially identical with the exception of the bridging atoms and their immediate environments. The same applied to mass spectral breakdown patterns wherein the major fragments differed by one amu, with the exception of the ion 332+ which is characteristic to the oxygen-bridged compound.
Restoration of HIV-Specific Cell-Mediated Immune Responses by Interleukin-12 in Vitro (1993)

Peripheral blood mononuclear cells (PBMCs) from many asymptomatic individuals infected with human immunodeficiency virus-type 1 (HIV) are unresponsive as measured by in vitro T cell proliferation and interleukin-2 (IL-2) production to influenza virus and synthetic peptides of HIV envelope (Env). Strong influenza virus- and Env-stimulated IL-2 responses and T cell proliferation were restored when cultures were stimulated in the presence of IL-12. Interferon-gamma production by PBMCs from HIV seropositive (HIV+) patients was also restored with IL-12. Furthermore, in vitro antigen-specific production of IL-2 and proliferation of PBMCs from HIV- donors were suppressed by antibody to IL-12, but were not enhanced by addition of exogenous IL-12. Thus, IL-12 may be limiting in PBMCs from HIV+ but not HIV- individuals. These findings demonstrate that IL-12 can restore HIV-specific cell-mediated immunity in vitro in HIV-infected individuals and suggest a potential use of IL-12 in augmenting the diminished immunologic functions associated with HIV infection.
Monoclonal antibodies in immunosuppression. (1991)

Experimental and clinical studies have been carried out to investigate the application of a number of monoclonal antibodies which recognise human lymphocytes in clinical organ transplantation. Where possible, preliminary studies have been carried out using a primate renal allograft model before proceeding to clinical pilot studies. The Campath-1 antigen (CDW52) appears to be a good target for antilymphocytic therapy; a powerful immunosuppressive effect has been demonstrated using both IgM and IgG2b antibodies which recognise this antigen. An IgG2b antibody which recognises the IL-2 receptor was shown to be immunosuppressive in the primate model but clinical studies have, as yet not demonstrated a significant, beneficial effect in preventing rejection. Patients who receive antilymphocyte monoclonal antibodies require monitoring of the expression of the target antigen, the level of free antibody in serum and the development of an antiglobulin response. The current issues in the use of antilymphocyte monoclonal antibodies in clinical immunosuppression include identification of the optimum target, interaction of the antibody with recipient effector mechanisms and methods to avoid or suppress the antiglobulin response.
Effects of plant oils on oviposition preference and larval survivorship of Callosobruchus chinensis (Coleoptera : Bruchidae) on azuki bean (1999)

The efficacy of four kinds of oils, neem, castor, sunflower and sesame, was evaluated for the control of infestation of stored azuki bean with Callosobruchus chinensis. Neem and sesame oil-treated beans were less preferred and oviposition of adults on these beans decreased. After three days of release, 100% adults were found dead on neem oil-treated beans and very few eggs were laid. Effects on the survival rate of immature beetles and percentage of seed weight loss were also recorded. Neem and sesame oils completely inhibited adult emergence and appeared to be most promising as a seed protectant against C. chinensis. The oil-specific activity and delay in larval development in oil-treated beans suggest that the protective properties involved chemical rather than physical factors.
Innate Sensing of Chitin and Chitosan (2013)

Chitin is the second most common polysaccharide found in nature. It is present in crustacean shells, insect exoskeletons, parasitic nematode eggs and gut linings, and in the cell wall of fungi. The deacetylated derivative of chitin, chitosan, is less common but is particularly evident in certain species of fungi, such as Cryptococcus, and the cyst wall of Entamoeba. How mammals sense and respond to these polymers is not well understood, and conflicting reports on their immunological activity have led to some controversy. Despite this, promising translational applications that exploit the unique properties of chitin and chitosan are being developed.
THE STRUCTURAL BIOLOGY OF TYPE II FATTY ACID BIOSYNTHESIS (2005)

The type II fatty acid synthetic pathway is the principal route for the production of membrane phospholipid acyl chains in bacteria and plants. The reaction sequence is carried out by a series of individual soluble proteins that are each encoded by a discrete gene, and the pathway intermediates are shuttled between the enzymes as thioesters of an acyl carrier protein. The Escherichia coli system is the paradigm for the study of this system, and high-resolution X-ray and/or NMR structures of representative members of every enzyme in the type II pathway are now available. The structural biology of these proteins reveals the specific three-dimensional features of the enzymes that explain substrate recognition, chain length specificity, and the catalytic mechanisms that define their roles in producing the multitude of products generated by the type II system. These structures are also a valuable resource to guide antibacterial drug discovery.
SPINGO: a rapid species-classifier for microbial amplicon sequences (2015)

SPINGO is an accurate, flexible and fast method for low-level taxonomic assignment. This combination is becoming increasingly important for rapid and accurate processing of amplicon data generated by newer next generation sequencing technologies.
Herpes simplex virus (HSV) antibodies in child psychiatric patients and normal children (1982)

The prevalence of herpes simplex virus (HSV) antibodies has been investigated in 123 child psychiatric patients and 86 normal children. HSV antibodies were measured by ELISA technique. The prevalence of HSV antibodies in different diagnostic groups (conduct disorder, emotional disorder, hyperkinetic syndrome, anorexia nervosa, infantile autism and borderline schizophrenia in childhood) was compared with age-matched normal children, but no significant differences were found.
Erythropoietin and its receptor: signaling and clinical manifestations. (2002)

The proliferation of erythroid progenitor cells and their differentiation into mature erythrocytes are mediated by the glycoprotein hormone erythropoietin. EPO is synthesized predominantly in the kidney and is secreted by renal cortical interstitial cells and proximal tubule cells in response to tissue hypoxia. The EPO receptor spans the membrane of developing erythroid cells and binds circulating EPO. Treatment of anemic patients with EPO increases their hemoglobin level, decreases the need for transfusion, and improves their quality of life. These significant clinical manifestations, as well as the key role of EPO in development of the red blood cell lineage, have prompted extensive studies on the molecular mechanisms underlying the activation of its receptor. The EPO-R is a 476 amino acid protein containing a transmembrane segment that divides the molecule into extracellular and cytosolic domains of equal length. It belongs to the family of cytokine receptors, as indicated by the lack of endogenous kinase activity and by small regions of homology in its extracellular domain. These homologous regions include four conserved cysteines forming two disulfide bonds, as well as the WSXWS motif near the membrane-spanning segment. The first tyrosine kinase found to interact with the EPO-R was Janus kinase-2, a member of the Janus protein kinase family. These kinases phosphorylate ligand-activated cytokine receptors, generating recognition sites for a wide range of intracellular signaling molecules. This review focuses on the intracellular signaling pathways activated upon binding of EPO to its receptor, hematologic diseases associated with the EPO-R, and clinical treatment with EPO.
Water‐Stable Silk Films with Reduced β‐Sheet Content (2005)

Abstract Silk fibers have outstanding mechanical properties. These fibers are insoluble in organic solvents and water, are biocompatible, and exhibit slow biodegradation in vitro and in vivo due to the hydrophobic nature of the protein and the presence of a high content of β‐sheet structure. Regenerated silk fibroin can be processed into a variety of materials normally stabilized by the induction of β‐sheet formation through the use of solvents or by physical stretching. To extend the biomaterial utility of silk proteins, options to form water‐stable silk‐based materials with reduced β‐sheet formation would be desirable. To address this need for more rapidly degradable silk biomaterials, we report the preparation of water‐stable films from regenerated silk fibroin solutions, with reduced β‐sheet content. The keys to this process are the preparation of concentrated (8 % by weight) aqueous solutions of fibroin and a subsequent water‐based annealing procedure. These new materials degrade more rapidly due to the reduced β‐sheet content, as determined in vitro via enzymatic hydrolysis, yet support human adult stem‐cell expansion in vitro in a similar or improved fashion to the crystallized proteins in film form. These new silk‐based materials extend the range of biomaterial properties that can be generated from this unique family of proteins.
A role for aquaporin-4 in fluid regulation in the inner retina (2009)

Many diverse retinal disorders are characterized by retinal edema; yet, little experimental attention has been given to understanding the fundamental mechanisms underlying and contributing to these fluid-based disorders. Water transport in and out of cells is achieved by specialized membrane channels, with most rapid water transport regulated by transmembrane water channels known as aquaporins (AQPs). The predominant AQP in the mammalian retina is AQP4, which is expressed on the Müller glial cells. Müller cells have previously been shown to modulate neuronal activity by modifying the concentrations of ions, neurotransmitters, and other neuroactive substances within the extracellular space between the inner and the outer limiting membrane. In doing so, Müller cells maintain extracellular homeostasis, especially with regard to the spatial buffering of extracellular potassium (K+) via inward rectifying K+ channels (Kir channels). Recent studies of water transport and the spatial buffering of K+ through glial cells have highlighted the involvement of both AQP4 and Kir channels in regulating the extracellular environment in the brain and retina. As both glial functions are associated with neuronal activation, controversy exists in the literature as to whether the relationship is functionally dependent. It is argued in this review that as AQP4 channels are likely to be the conduit for facilitating fluid homeostasis in the inner retina during light activation, AQP4 channels are also likely to play a consequent role in the regulation of ocular volume and growth. Recent research has already shown that the level of AQP4 expression is associated with environmentally driven manipulations of light activity on the retina and the development of myopia.
Anti-GITR antibodies--potential clinical applications for tumor immunotherapy. (2010)

Since the development of the first vaccines, modern medicine has been consistently aiming to improve the efficacy of immune responses. Traditionally, adjuvants have been used as non-specific immune modulators to enhance recognition and activation against a desired antigen. By providing 'danger' signals to the immune system, adjuvants activate innate immunity, which enhances the development of protective and therapeutic adaptive immune responses. The newest class of immune modulators bypasses the innate response and targets cells of the adaptive response directly. Targeted immunomodulatory therapy is focused primarily on the activation of costimulatory receptors (eg, 4-1BB, OX40 and GITR [glucocorticoid-induced TNF receptor-related gene]) or the blockade of co-inhibitory receptors (eg, CTLA-4, PD-1 and PD-L1) on T-cells during activation and/or effector responses. With promising clinical results obtained to date, immunomodulatory therapy is becoming an integral part of immunotherapeutic approaches. The modulation of GITR is listed as one of the top 25 most promising research areas by the NCI, and has demonstrated potential in both antitumor and vaccine settings. This review discusses the role of GITR as a potential target for immunomodulatory therapy, as well as the research involved in understanding the mechanisms of anti-GITR therapy and current progress in translation into the clinic.
PreSense (2003)

Although graphical user interfaces started as imitations of the physical world, many interaction techniques have since been invented that are not available in the real world. This paper focuses on one of these "previewing", and how a sensory enhanced input device called "PreSense Keypad" can provide a preview for users before they actually execute the commands. Preview important in the real world because it is often not possible to undo an action. This previewable feature helps users to see what will occur next. It is also helpful when the command assignment of the keypad dynamically changes, such as for universal commanders. We present several interaction techniques based on this input device, including menu and map browsing systems and a text input system. We also discuss finger gesture recognition for the PreSense Keypad.
Malicious circuitry detection using fast timing characterization via test points (2013)

We develop a region-based timing characterization approach to detect hardware Trojans (HTs) on integrated circuits (ICs). In order to ensure the scalability of the approach, we partition the target IC into well-formed and non-overlapping regions and detect hardware Trojans on all circuit locations by examining the timing properties of the transistor paths. Based on the circuit partition, we insert a minimal number of test points that provide additional observation interfaces for the delay measurements of all circuit locations. Our evaluations on ISCAS and ITC benchmarks show that the region-based Trojan detection via test points can detect hardware Trojans accurately with well controlled area overhead and test time.
NAD(P)H regeneration is the key for heterolactic fermentation of hexoses in Oenococcus oeni (2002)

Oenococcus oeni (formerly Leuconostoc oenos) can perform malolactic fermentation, converting L-malate to L-lactate and carbon dioxide, in wines. The energy and redox potential required to support the growth of the micro-organism are supplied mainly by the consumption of carbohydrates via the heterolactic pathway. In the first steps of hexose metabolism two molecules of NAD(P)(+) are consumed, which must be regenerated in later reactions. The aim of this work was to test if aerobic growth of O. oeni promotes higher cell yields than anaerobic conditions, as has been shown for other lactic acid bacteria. O. oeni M42 was found to grow poorly under aerobic conditions with glucose as the only carbohydrate in the medium. It was demonstrated that O(2) inactivates the enzymes of the ethanol-forming pathway, one of the two pathways which reoxidizes NAD(P)(+) cofactors in the heterolactic catabolism of glucose. These results suggest that the regeneration of cofactors is the limiting factor for the aerobic consumption of glucose. When external electron acceptors, such as fructose or pyruvate, were added to glucose-containing culture medium the growth of O. oeni was stimulated slightly; fructose was converted to mannitol, oxidizing two molecules of NAD(P)H, and pyruvate was transformed to lactate, enabling the regeneration of NAD(+). The addition of cysteine seemed to suppress the inactivation of the ethanol-forming pathway enzymes by O(2), enabling glucose consumption in aerobic conditions to reach similar rates to those found in anaerobic conditions.
Molecular Drivers of the Non–T-cell-Inflamed Tumor Microenvironment in Urothelial Bladder Cancer (2016)

Muscle-invasive urothelial bladder cancer is a common malignancy with poor outcomes for which immune checkpoint blockade is now showing promise. Despite clinical activity of PD-1/PD-L1-targeted therapy in this disease, most patients do not benefit and resistance mechanisms remain unknown. The non-T-cell-inflamed tumor microenvironment correlates with poor prognosis and resistance to immunotherapies. In this study, we determined tumor-oncogenic pathways correlating with T-cell exclusion. We first establish in this report that T-cell-inflamed bladder tumors can be identified by immune gene expression profiling with concordance with CD8(+) T-cell infiltration. Upregulation of genes encoding immune checkpoint proteins PD-L1, IDO, FOXP3, TIM3, and LAG3 was associated with T-cell-inflamed tumors, suggesting potential for sensitivity to checkpoint blockade. β-Catenin, PPAR-γ, and FGFR3 pathways were activated in non-T-cell-inflamed tumors. No difference was seen in overall somatic mutational density between groups. The three pathways identified represent targetable potential pathways of tumor-intrinsic immunotherapy resistance. Cancer Immunol Res; 4(7); 563-8. ©2016 AACR.
High-Quality InGaN Films Grown on GaN Films (1992)

InGaN films were grown on GaN films with a high indium source flow rate and high growth temperatures between 780°C and 830°C. Strong and sharp band-edge (BE) emissions between 400 nm and 445 nm were observed, while deep-level emissions were barely observed in photoluminescence (PL) measurements at room temperature. The full width at half-maximum (FWHM) of the BE emissions was about 70 meV. The FWHM of the double-crystal X-ray rocking curve (XRC) from the InGaN films was about 8 minutes. This value of FWHM was the smallest one ever reported for InGaN films, and was almost the same as that of the GaN films which were used as the substrate.
Biological response to intravenously administered endotoxin in patients with advanced cancer. (1990)

The purpose of the study was to evaluate the toxicity and biological activity of highly purified lipopolysaccharide (LPS) administered intravenously to cancer patients in order to establish an optimum dosage scheme. An initial subtoxic dose was increased in weekly increments in accordance with individual regimens that maintained patient reaction at a safe and acceptable level. Purified LPS from Salmonella abortus equi was administered to 11 patients with advanced solid tumors on a weekly schedule with intraindividually escalating dosage as determined by patient response. Biological response was monitored by complete blood count, C-reactive protein, and cytokine measurements at different time points after LPS injection. Tumor necrosis factor-alpha (TNF) and interleukin-1 beta serum levels were measured by enzyme-linked immunosorbent assay and interleukin-6 (IL-6) by bioassay. Dose-limiting toxicities including chills and fever (WHO grade III) were reached at 1.0 ng/kg of body weight (maximal tolerated dose-1, MTD-1). Pretreatment with ibuprofen (1,600 mg) abrogated these side effects, allowing further escalation of LPS doses up to 10 ng/kg of body weight. At dose levels greater than 8.0 ng/kg of body weight (MTD-2), the aforementioned side effects occurred again and, additionally, hepatic toxicity (WHO grade III) was observed. Hematological changes included neutropenia followed by a pronounced neutrophilia contributed to by up to 30% bands, marked monocytopenia for 3 h, and retarded lymphopenia. By 24 h, all hematological parameters returned to pretreatment values. TNF serum levels increased from 10 pg/ml before treatment to 7,000 pg/ml as a function of dosage. Maximum serum levels were reached at 60 to 90 min after LPS injection. Similarly, IL-6 serum concentrations increased from less than 4 to 2,500 U/ml; peak levels were obtained 30 min after TNF peak values. Prior administration of ibuprofen had no effect on the above-mentioned hematological changes nor on cytokine release. LPS can be administered intravenously in weekly intervals at escalating doses from 0.15-10.0 ng/kg of body weight, when patients are protected by pretreatment with ibuprofen at dose levels above 1.0 ng/kg of body weight. Cytokine release as measured by TNF and IL-6 increased in a dose-dependent manner although the constitutional symptoms are completely attenuated.
Site-Specific DNA Damage at the GGG Sequence by UVA Involves Acceleration of Telomere Shortening (2001)

Telomere shortening is associated with cellular senescence. We investigated whether UVA, which contributes to photoaging, accelerates telomere shortening in human cultured cells. The terminal restriction fragment (TRF) from WI-38 fibroblasts irradiated with UVA (365-nm light) decreased with increasing irradiation dose. Furthermore, UVA irradiation dose-dependently increased the formation of 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) in both WI-38 fibroblasts and HL-60 cells. To clarify the mechanism of the acceleration of telomere shortening, we investigated site-specific DNA damage induced by UVA irradiation in the presence of endogenous photosensitizers using (32)P 5'-end-labeled DNA fragments containing the telomeric oligonucleotide (TTAGGG)(4). UVA irradiation with riboflavin induced 8-oxodG formation in the DNA fragments containing telomeric sequence, and Fpg protein treatment led to chain cleavages at the central guanine of 5'-GGG-3' in telomere sequence. The amount of 8-oxodG formation in DNA fragment containing telomere sequence [5'-CGC(TTAGGG)(7)CGC-3'] was approximately 5 times more than that in DNA fragment containing nontelomere sequence [5'-CGC(TGTGAG)(7)CGC-3']. Catalase did not inhibit this oxidative DNA damage, indicating no or little participation of H(2)O(2) in DNA damage. These results indicate that the photoexcited endogenous photosensitizer specifically oxidizes the central guanine of 5'-GGG-3' in telomere sequence to produce 8-oxodG probably through an electron-transfer reaction. It is concluded that the site-specific damage in telomere sequence induced by UVA irradiation may participate in the increase of telomere shortening rate.