gebhart/patrepeval huggingface dataset:
Existent T-cell and antibody immunity to HER-2/neu protein in patients with breast cancer. (1994)

The HER-2/neu protooncogene is amplified and overexpressed in 20-40% of invasive breast cancers. HER-2/neu protein overexpression is associated with aggressive disease and is an independent predictor of poor prognosis in several subsets of patients. The protein may also be related to cancer formation, with overexpression being detectable in 50-60% of ductal carcinomas in situ. It has been suggested that it might be possible to develop specific T-cell therapy directed against proteins involved in malignant transformation. One question is whether normal proteins that are overexpressed are appropriate targets for therapeutic immune attack. This report demonstrates that some patients with HER-2/neu-positive breast cancers have both existent CD4+ helper/inducer T-cell immunity and antibody-mediated immunity to HER-2/neu protein. Initial studies performed on 20 premenopausal breast cancer patients identified antibodies to HER-2/neu in 11 individuals. Similar antibody responses have been found in some normal individuals. The patient with the greatest antibody response was studied in detail. In addition to a humoral immune response this patient had evidence of a significant proliferative T-cell response to the HER-2/neu protein and peptides. Similar T-cell responses have been detected in additional patients. It has been assumed that patients would be immunologically tolerant to HER-2/neu as a self-protein and that immunity might be difficult to generate. If immunity could be generated, the result might be destructive autoimmunity. The current data support the notion that HER-2/neu-specific immunity might be used in therapy without destroying normal tissue but also raises questions as to the role of existent immunity in immune surveillance and cancer progression.
Bifidobacteria exhibit social behavior through carbohydrate resource sharing in the gut (2015)

Abstract Bifidobacteria are common and frequently dominant members of the gut microbiota of many animals, including mammals and insects. Carbohydrates are considered key carbon sources for the gut microbiota, imposing strong selective pressure on the complex microbial consortium of the gut. Despite its importance, the genetic traits that facilitate carbohydrate utilization by gut microbiota members are still poorly characterized. Here, genome analyses of 47 representative Bifidobacterium (sub)species revealed the genes predicted to be required for the degradation and internalization of a wide range of carbohydrates, outnumbering those found in many other gut microbiota members. The glycan-degrading abilities of bifidobacteria are believed to reflect available carbon sources in the mammalian gut. Furthermore, transcriptome profiling of bifidobacterial genomes supported the involvement of various chromosomal loci in glycan metabolism. The widespread occurrence of bifidobacterial saccharolytic features is in line with metagenomic and metatranscriptomic datasets obtained from human adult/infant faecal samples, thereby supporting the notion that bifidobacteria expand the human glycobiome. This study also underscores the hypothesis of saccharidic resource sharing among bifidobacteria through species-specific metabolic specialization and cross feeding, thereby forging trophic relationships between members of the gut microbiota.
Oxovanadium(IV) Silsesquioxane Complexes (2010)

In the context of a potential modeling of reduced oxovanadium species occurring on the surfaces of silica-supported vanadia catalysts in the course of its turnover, the incompletely condensed silsesquioxane H3c-pentylT7 was reacted with Cl4V(THF)2 (where THF = tetrahydrofuran) in the presence of triethylamine. Precipitation of 3 equiv of HNEt3Cl seemed to point to the clean formation of [(c-pentylT7)(VIVCl)] (1), which was supported by electron paramagnetic resonance studies performed for the resulting solutions, but further analytical and spectroscopic investigations showed that the processes occurring at that stage are more complex than that and even include the formation of [(c-pentylT7)(VVO)]2 as a side product. Storage of a red-brown hexane solution of this product mixture reproducibly led to the precipitation of blue crystals belonging to the chloride-free compound [(c-pentylT7)2(VIV═O)3(THF)2] (2), as revealed by single-crystal X-ray diffraction. Performing the same reaction in the presence of 2 equiv of pyridine leads to an analogous product, where the THF ligands are replaced by pyridine. Subsequent investigations showed that the terminal oxo ligands at the vanadium centers are, on the one hand, due to the presence of adventitious water; on the other hand, the [c-pentylT7]3− ligand also acted as a source of O2−. The results of SQUID measurements performed for 2 can be interpreted in terms of a ferromagnetic coupling between the vanadyl units. Exposing 2 to a dioxygen atmosphere resulted in its immediate oxidation to yield the VV complex [(c-pentylT7)(VVO)]2, which may model a fast reoxidation reaction of oxovanadium(IV) trimers on silica surfaces.
Calf Thymus Polymerase (1960)

SUMMARY Ionic strength inhibition of calf thymus polymerase Each tube contained the following concentrations: deoxyribo- nucleoside triphosphates, 40 pM in each (dGTP, 1060 c.p.m./ mpmole); Mg++, 8 mm; potassium phosphate, pH 7, 40 mM; mer- captoethanol, 1 InM; 82 rg of DNA (salmon sperm) ; and 120 pg of Fraction D protein. Final volume, 0.25 ml. All tubes were in- cubated 30 minutes at 35” and aliquots were assayed by the paper disk procedure (4). Molarities are the final concentration of added salt with the exception of the last entry, where molarity is total phosphate. The 0.04 M phosphate reaction, the control for all reactions in this series, incorporated 2.0 mpmoles of dGMPs2. Partial purification of a deoxyribonucleic acid (DNA)-synthe- sizing enzyme from calf thymus gland has been achieved. The purified enzyme preparation requires the deoxyribonucleoside triphosphates of adenine, guanine, cytosine, and thymine, Mg++, and primer DNA for activity. The synthetic reaction is in- hibited by pyrophosphate and, if radioactive pyrophosphate is used, it is incorporated into deoxyribonucleoside triphosphate. The over-all reaction may therefore be written: Deoxyribonucleoside triphosphates , DNA, Mg++
Time-varying lapped transforms and wavelet packets (1993)

The perfect reconstruction conditions for a time-varying lapped transform (paraunitary filter bank) are developed through the factorization of the transform matrix into sparse factors. A general formulation is presented allowing one to switch between two paraunitary filter banks. However, the extended lapped transform (ELT) is often used as an example. Furthermore, an adaptive wavelet packet is developed employing a time varying, tree association of ELTs. In all cases perfect reconstruction is inherently assured.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Regulation of growth hormone messenger RNA by thyroid and glucocorticoid hormones. (1977)

Thyroid and glucocorticoid hormones stimulate growth hormone synthesis in cultured rat pituitary cells (GC). We have compared changes in growth hormone production and mRNA in these cells. Triiodothyronine (10 nM) and dexamethasone (1 micron) stimulated increases in growth hormone production by 2.5- and 3.8-fold, respectively. There were corresponding increases in the capacity of RNA from hormone-treated cells to direct synthesis of pregrowth hormone in a wheat germ cell-free translation system, suggesting hormone-regulated increases in growth hormone mRNA. Hormone-induced changes in mRNA were also demonstrated by determining the kinetics of hybridization of a cDNA probe prepared from RNA enriched (about 70%) for growth hormone translational activity with RNA from control and hormone-treated cells. These results suggest that thyroid and glucocorticoid hormones can regulate growth hormone production by influencing the levels of its mRNA.
Aggrecan-Mimetic, Glycosaminoglycan-Containing Nanoparticles for Growth Factor Stabilization and Delivery (2014)

The direct delivery of growth factors to sites of tissue healing is complicated by their relative instability. In many tissues, the glycosaminoglycan (GAG) side chains of proteoglycans like aggrecan stabilize growth factors in the pericellular and extracellular space, creating a local reservoir that can be accessed during a wound healing response. GAGs also regulate growth factor-receptor interactions at the cell surface. Here we report the development of nanoparticles for growth factor delivery that mimic the size, GAG composition, and growth factor binding and stabilization of aggrecan. The aggrecan-mimetic nanoparticles are easy to assemble, and their structure and composition can be readily tuned to alter their physical and biological properties. We use basic fibroblast growth factor (FGF-2) as a model heparin-binding growth factor, demonstrating that aggrecan-mimetic nanoparticles can preserve its activity for more than three weeks. We evaluate FGF-2 activity by measuring both the proliferation and metabolic activity of bone marrow stromal cells to demonstrate that chondroitin sulfate-based aggrecan mimics are as effective as aggrecan, and heparin-based aggrecan mimics are superior to aggrecan as delivery vehicles for FGF-2.
Characterization of Rat Calvarial Nonunion Defects (1990)

This study examined the healing of nonunions by describing the histology and ultrastructural appearance of craniotomy defects as a model. Bone defects (3, 4 and 8 mm) were created in the calvaria of adult rats. Central and peripheral specimens of 8-mm defects were retrieved at 1, 3, 7, 10, 14, 21, 28 and 42 days and examined using both light and transmission electron microscopy. Specimens from the 3- and 4-mm defects were retrieved at 28 days and examined using light microscopy. In all sizes of defects, bony repair was consistently localized to the dural side of the defect. The 3- and 4 mm defects demonstrated the greatest degree of osseous bridging and evidence of normal osseous repair throughout the defect. The 8-mm defects repaired in general with the formation of nonunions which contained a small amount of bone at the periphery and fibrous connective tissue. Bone formation was evident at 10 days in the peripheral regions of the 8-mm defects and exhibited bony peninsulas with normal primary calcification fronts. Matrix vesicles containing hydroxyapatite-like crystals were present. In contrast, the central regions of the 8-mm defects were characterized by several islands of cartilage-like cells which stained metachromatically with toluidine blue. Transmission electron microscopy of this region at 14 days demonstrated a dense, collagenous extracellular matrix with matrix vesicles infiltrating the collagen bundles. There was no evidence of crystal formation in the matrix vesicles nor of calcification in the collagenous matrix. At 21 days, both the central and peripheral regions of the 8-mm calvarial nonunions were characterized by dense fibrous connective tissue repair and inactive fibroblasts.(ABSTRACT TRUNCATED AT 250 WORDS)
Cytochalasin B inhibits polyamine biosynthesis in HeLa cells. (1981)

Cytochalasin B (CB), a potent inhibitor of cytokinesis in mammalian cells, has been shown to cause the rapid inhibition of ornithine decarboxylase and S-adenosyl methionine decarboxylase activities followed by a gradual but marked decline in intracellular levels of both putrescine and spermidine. Further, the multinucleation induced by CB could be reversed to some extent by exogenous addition of polyamines to the growth medium. The results of this study suggested that polyamines might have some indirect role in the CB-induced multinucleation of mammalian cells.
Adenosine, Lidocaine, and Mg2+ (ALM™) Increases Survival and Corrects Coagulopathy After Eight-Minute Asphyxial Cardiac Arrest in the Rat (2013)

Small bolus of 0.9% NaCl ALM improved survival and hemodynamics following nonhemorrhagic, asphyxial CA and corrected prolonged clot times and clot retraction compared with controls.
Cytotoxicity of microglia (1993)

The most characteristic property of microglia is their swift activation in response to neuronal stress and their capacity for site-directed phagocytosis. The transformation of microglia into intrinsic brain macrophages appears to be under strict control and takes place if neuronal and/or terminal degeneration occurs in response to nerve lesion. The differentiation of microglia into brain macrophages is accompanied by the release of several secretory products, e.g., proteinases, cytokines, reactive oxygen intermediates, and reactive nitrogen intermediates. Interference with the microglial activation or the productions of cytotoxic metabolites by microglia may thus offer new therapeutic opportunities for the prevention of neuronal cell death in CNS disease.
Pinpointing the sources and measuring the lengths of the principal rivers of the world (2009)

Cultures throughout the world are associating with the rivers. People depend upon the rivers and their tributaries for food, water, transport, and many other aspects of their daily lives. Unfortunately, human beings have not calculated the accurate lengths for the great rivers even today. The lengths of the rivers are very different in popular textbooks, magazines, atlases and encyclopedias, etc. To accurately determine the lengths of the principal rivers of the world, the combination of satellite image analysis and field investigations to the source regions is proposed in this paper. The lengths of the Nile, Amazon, Yangtze, Mississippi, Yellow, Ob, Yenisey, Amur, Congo and Mekong, with lengths over or close to 5000 km, were calculated using the proposed method. The results may represent the most reliable and accurate lengths of the principal rivers of the world that are currently achievable.
Zinc Promoted Convenient and General Synthesis of Thiol Esters (1998)

Synthesis of thiol esters from acyl chlorides and thiols in the presence of activated zinc is described. The recovery of zinc and its reuse makes the procedure more economic.
Ordered nanocrystal/silica particles self-assembled from nanocrystal micelles and silicate (2006)

Ordered gold nanocrystal/silica particles were synthesized through self-assembly of nanocrystal micelles and silicate. Depending on the use of surfactants, and the kinetic conditions of silica hydrolysis and condensation, well-shaped and irregularly-shaped silica particles were formed, inside which the nanocrystals self-organized in a face-centered cubic mesostructure.
The Good Block: Hardware/Software Design for Composable, Block-Atomic Processors (2011)

Power consumption, complexity, and on-chip latency are forcing computer systems to exploit more parallelism efficiently. Explicit Dataflow Graph Execution (EDGE) architectures seek to expose parallelism by dividing programs into blocks of efficient dataflow operations, exposing inter and intra-block concurrency. This paper studies the balance of complexity and capability between EDGE architectures and compilers. We address three main questions. (1) What are the appropriate block granularities for achieving high performance efficiently? (2) What are good block instruction selection policies? (3) What architecture and compiler support do these designs require? Our results show that the compiler requires multiple block sizes to adapt applications to block-atomic hardware and achieve high performance. Although the architecture for a single size is simpler, the additions for variable sizes are modest and ease hardware configuration. We propose hand-crafted and learned compiler policies for block formation. We find the best policies provide significant advantages of up to a factor of 3 in some configurations. Policies vary based on (1) the amount of parallelism inherent in the application, e.g., for integer and numerical applications, and (2) the available parallel resources. The resulting configurable architecture and compiler efficiently expose and exploit software and hardware parallelism.
Amino acid signatures in the detached cat retina. (1998)

Dramatic changes in Müller cell amino acid signatures triggered by retinal detachment are partially consistent with losses in glutamine synthetase activity. Taurine signal variations suggest that orthotopic RPE cells attempt to regulate abnormal taurine concentrations in the enlarged subretinal space. Surviving neurons possess characteristic neurotransmitter signals, but their metabolite regulation seems abnormal. On balance, microchemical and structural anomalies develop in the detached cat retina that represent serious barriers to recovery of normal visual function.
Poly‐3‐Hydroxyalkanoates containing unsaturated repeating units produced by pseudomonas oleovorans (1995)

Abstract Poly‐3‐hydroxyalkanoates (PHAs) containing repeating units with terminal alkene substituents at the 3‐position were produced by Pseudomonas oleovorans grown with either 7‐octeneoic acid [OA()] alone, or 10‐undeceneoic acid [UND()] alone, or mixtures of UND() and either nonanoic acid (NA) or octanoic acid (OA). For the latter, the biomass and PHA yields decreased as the fraction of UND() increased in the mixed carbon substrates. Essentially all of the repeating units in the PHA obtained from cells grown with UND() alone contained terminal alkene groups, including 3‐hydroxy‐10‐undeceneoate, 3‐hydroxy‐8‐noneneoate, and 3‐hydroxy‐6‐hepteneoate units, but less than half of the units in the PHA from OA() had alkene substituents. The PHAs obtained from cells grown with various mixtures of UND() and either OA or NA were random copolymers, and the fraction of units with alkene substituents in these polymers increased in proportion to the fraction of UND() in the mixed carbon substrates. © 1995 John Wiley &amp; Sons, Inc.
Capsaicin-Like Anti-Obese Activities of Evodiamine from Fruits of Evodia rutaecarpa, a Vanilloid Receptor Agonist (2001)

Evodiamine, a major alkaloidal principle of Evodia fruits (Evodia rutaecarpa, Rutaceae), showed vanilloid receptor agonistic activities comparable to capsaicin. The Chinese literature refers to Evodia fruits as a "hot nature" herb. In spite of the similarities in the actions of evodiamine and capsaicin in vitro, evodiamine has no perceptible taste, including a peppery hot taste. Therefore, the effectiveness of evodiamine and the extract of Evodia fruits in preventing obesity on male C3H mice, or male SD rats were examined. When evodiamine was supplemented at 0.03% of the diet and fed to mice for 12 days, the perirenal fat weight became significantly lower than in the control group. The epididymal fat mass was also decreased in the evodiamine diet group. When evodiamine was supplemented at 0.02% in the form of ethanol extract of Evodia fruits to the high-fat diet and fed to rats for 21 days, the body weight, the perirenal fat weight, epididymal fat weight, the levels of serum free fatty acid, total lipids in the liver, triglyceride in the liver, and cholesterol level in the liver were significantly reduced as compared with the control diet group. Furthermore, both lipolytic activity in the perirenal fat tissue and specific GDP binding in brown adipose tissue mitochondria, as the biological index of enhanced heat production, were significantly increased in the evodiamine fed rats. Fasting mice subcutaneously administered 1-3 mg/kg evodiamine showed decreased core body temperature by 1-2 degrees C. This hypothermic effect was prevented by the pretreatment of intraperitoneally administered 10 mg/kg capsazepine, a vanilloid receptor antagonist. On the other hand, food-sated mice subcutaneously administered 1-3 mg/kg evodiamine showed unchanged core body temperature and increased tail skin temperature by more than 5 degrees C, suggesting the increased energy expenditure by enhanced heat dissipation. In conclusion, we have demonstrated that a novel non-pungent vanilloid receptor agonist, evodiamine, mimics the characteristic anti-obese effects induced by capsaicin. Evodiamine would induce heat loss and heat production at the same time and dissipate food energy, preventing the accumulation of perivisceral fat and the body weight increase.
Murine retroviruses use at least six different receptors for entry into Mus dunni cells (1997)

Murine retroviruses have been divided into six interference groups that use different receptors for cell entry: the ecotropic, xenotropic, polytropic, amphotropic, 10A1, and Mus dunni endogenous virus groups. Some interference is observed between xenotropic and polytropic viruses and between amphotropic and 10A1 viruses, indicating some overlap in receptor specificity between these groups, but otherwise these interference groups appear completely independent. In contrast, one study found interference among many of these groups when Mus dunni wild mouse cells were examined with an immunofluorescence assay to detect infection by the challenge virus. Here we have used a more direct assay for cell entry by using pseudotyped retroviral vectors to measure interference in M. dunni cells, and we find no evidence for extensive interference between members of different murine retrovirus groups. Indeed, our results in M. dunni cells are consistent with interference results observed in other cell types and indicate that the anomalous interference results previously observed in M. dunni cells with the immunofluorescence assay were most likely due to factors other than those that affect receptor-mediated virus entry. In summary, our results show that murine retroviruses use at least six different receptors for entry into M. dunni cells.
Influence of the polymer architecture on morphology and device properties of polymer bulk heterojunction photovoltaic cells (2004)

Polymer bulk hetero junction solar cells were made from poly(2-methoxy-5-(3,7-dimethyloctyloxy)-1,4-phenylene-vinylene) (MDMO-PPV) as donor and poly(cyanoetherphenylenevinylene) (PCNEPV) derivatives as acceptor material. In this paper we start out with discussing the synthesis of the materials. Subsequently, the main issues concerning the devices are treated. Annealing the devices yielded devices with encouraging efficiencies of 0.5% (1 sun, 100mW/cm<sup>2</sup>), as calculated from the maximum power points (MPP). AFM studies revealed that this anneal step improves especially the interface of the active layer with the under laying PEDOT:PSS, although mobility and morphology changes can not be ruled out. Lowering the molecular weight (Mw) of the MDMO-PPV gave a slight improvement of the device performance. Decreasing the Mw of the acceptor material, MDMO-PCNEPV (PCNEPV derivative with the same side chains as MDMO-PPV) and optimizing the layer thickness led to a device with an efficiency of 0.65%. Finally we looked into the influence of the nature of the side chains on the acceptor polymer. The results suggest that the closer the resemblance between donor and acceptor is the better the device performance.
Simple Method to Calculate the Surgically Induced Refractive Change (1993)

Journal of Cataract & Refractive Surgery 19(2):p 319, March 1993. | DOI: 10.1016/S0886-3350(13)80968-6
Semantic clustering for adaptive language modeling (2002)

In this paper we present efficient clustering algorithms for two novel class-based approaches to adaptive language modeling. In contrast to bigram and trigram class models, the proposed classes are related to the distribution and co-occurrence of words within complete text units and are thus mostly of a semantic nature. We introduce adaptation techniques such as the adaptive linear interpolation and an approximation to the minimum discriminant estimation and show how to use the automatically derived semantic structure in order to allow a fast adaptation to some special topic or style. In experiments performed on the Wall-Street-Journal corpus, intuitively convincing semantic classes were obtained. The resulting adaptive language models were significantly better than a standard cache model. Compared to a static model a reduction in perplexity of up to 31% could be achieved.