gebhart/patrepeval huggingface dataset:
Relationship between rate of carbon dioxide evolution, microbial biomass carbon, and amount of dissolved organic carbon as affected by temperature and water content of a forest and an arable soil (1999)

Abstract Using an Ochrept soil of a forest at climax stage or of an arable site at Kita‐Ibaraki, a city in central Japan, the rates of carbon dioxide (CO2)‐carbon (C) evolution, the amounts of microbial biomass carbon (MBC) and the amounts of dissolved organic carbon (DOC) were measured in a laboratory with special reference to the incubation temperature and the soil water content. The rates of CO2‐C evolution increased exponentially with increase in the incubation temperature in the range of 4–40°C. The temperature coefficients (Q10) were 2.0 for the forest and 1.9 for the arable soil. The amounts of MBC were almost constant of 980 μg g‐1 soil in the incubation temperature up to 25°C for the forest, and 340 μg g‐1 soil in the incubation temperature up to 31 °C for the arable soil. The amounts of DOC in soil solutions were almost constant at 3.1 μg g‐1 soil in the incubation temperature up to 25°C for the forest, and 3.8 μg g‐1 soil in the incubation temperature up to 31°C for the arable soil. The rates of CO2‐C evolution and the amounts of DOC increased with increase in soil water content (% of soil dry weight) up to 91% for the forest or up to 26% for the arable soil. However, the rates of CO2‐C evolution and the amounts of DOC were almost constant within soil water content in the range of 91–160% or 26–53%, respectively. The amounts of MBC of the forest or arable soil were almost constant over a wide range of soil water content in the range of 41–220% or 8–73%, respectively. The rates of CO2‐C evolution of both the forest and the arable soils were highly correlated with the amounts of DOC, but not with the amounts of MBC, under laboratory conditions in the case that the amounts of DOC were changed by various treatments. The regression equation,
Anti‐tumor effects and lack of side effects in mice of an immunotoxin directed against human and mouse prostate‐specific membrane antigen (2004)

We have generated and characterized a rat mAb (E6) that reacts specifically with both human and mouse PSMA and have demonstrated that an immunotoxin constructed from E6 is safe and effective against human prostatic carcinoma cells growing subcutaneously in nude mice.
D-Cycloserine in Neuropsychiatric Diseases: A Systematic Review (2015)

D-Cycloserine, known from tuberculosis therapy, has been widely introduced to neuropsychiatric studies, since its central active mechanism as a partial NMDA-agonist has been found. In this review, we evaluate its therapeutic potential in neuropsychological disorders and discuss its pitfalls in terms of dosing and application frequency as well as its safety in low-dose therapy. Therefore, we identified 91 clinical trials by performing a Medline search. We demonstrate in part preliminary but increasing evidence that D-cycloserine may be effective in various psychiatric diseases, including schizophrenia, anxiety disorders, addiction, eating disorders, major depression, and autism as well as in neurological diseases, including dementia, Alzheimer's disease, and spinocerebellar degeneration. D-Cycloserine in low-dose therapy is safe, but there is still a need for new drugs with higher specificity to the different N-methyl-D-aspartate-receptor subunits.
Novel Cholesterol-Based Cationic Lipids for Gene Delivery (2009)

Gene therapy based on gene delivery is a promising strategy for the treatment of human disease. Here we present data on structure/biological activity of new biodegradable cholesterol-based cationic lipids with various heterocyclic cationic head groups and linker types. Enhanced accumulation of nucleic acids in the cells mediated by the lipids was demonstrated by fluorescent microscopy and flow cytometry. Light scattering and atomic force microscopy were used to find structure/transfection activity correlations for the lipids. We found that the ability of the lipids to stimulate intracellular accumulation of the oligodeoxyribonucleotides and plasmid DNA correlates well with their ability to form in solution lipid/NA complexes of sizes that do not exceed 100 nm. Screening of the lipids revealed the most promising transfection agents both in terms of low toxicity and efficient delivery: cholesterol-based lipids with positively charged pyridine and methyl imidazole head groups and either the ester or carbamate linker.
Differential register allocation (2005)

Micro-architecture designers are very cautious about expanding the number of architected registers (also the register field), because increasing the register field adds to the code size, raises I-cache and memory pressure, complicates processor pipeline. Especially for low-end processors, encoding space could be extremely limited due to area and power considerations. On the other hand, the number of architected registers exposed to the compiler could directly affect the effectiveness of compiler analysis and optimization. For high performance computers, register pressure can be higher than the available registers in some regions, e.g. due to optimizations like aggressive function inlining, software pipelining etc. The compiler cannot effectively perform compilation and optimization if only a small number of registers are exposed through the ISA. Therefore, it is crucial that more architected registers are available at the compiler's disposal without expanding the code size significantly.In this paper, we look at a new register encoding scheme called differential encoding that allows more registers to be addressed in the operand field of instructions than the direct encoding currently being used. We show it can be implemented with very low overhead. Based upon differential encoding, we apply it in several ways such that the extra architected registers can benefit the performance. Three schemes are devised to integrate differential encoding with register allocation. We demonstrate that differential register allocation is helpful in improving the performance of both high-end and low-end processors. Moreover, We can combine it with software pipelining to provide more registers and reduce spills.Our results show that differential encoding significantly reduces the number of spills and speeds up program execution. For a low-end configuration, we achieve over 12% speedup while keeping code size almost unaffected. For optimization on loops, it significantly speeds up loops with high register pressure (over 70% speedup).
A Comparison of Publicly Available Tools for Dynamic Buffer Overflow Prevention (2003)

The size and complexity of software systems is growing, increasing the number of bugs. Many of these bugs constitute security vulnerabilities. Most common of these bugs is the buffer overflow vulnerability. In this paper we implement a testbed of 20 different buffer overflow attacks, and use it to compare four publicly available tools for dynamic intrusion prevention aiming to stop buffer overflows. The tools are compared empirically and theoretically. The best tool is effective against only 50% of the attacks and there are six attack forms which none of the tools can handle.
Nicotine Inhaler and Nicotine Patch as a Combination Therapy for Smoking Cessation (2000)

Treatment with the nicotine inhaler plus nicotine patch resulted in significantly higher cessation rates than inhaler plus placebo patch.
Processing of antibody-radioisotope conjugates after binding to the surface of tumor cells (1994)

Different radiolabels are processed by tumor cells differently, after catabolism of the antibody to which they originally were conjugated. The data suggest that the prolonged retention of 111In, relative to that of 125I, is due not to deiodination of iodine conjugates, but rather to intracellular retention of catabolic products containing 111In, perhaps within lysosomes. The use of radioisotopes that are retained within cells after antibody internalization and degradation may improve both radioimmunodetection and radioimmunotherapy of cancer.
Target signature-constrained mixed pixel classification for hyperspectral imagery (2002)

Linear spectral mixture analysis has been widely used for subpixel detection and mixed pixel classification. When it is implemented as constrained LSMA, the constraints are generally imposed on abundance fractions in the mixture. In this paper, we consider an alternative approach, which imposes constraints on target signature vectors rather than target abundance fractions. The idea is to constrain directions of target signature vectors of interest in two different ways. One, referred to as linearly constrained minimum variance approach develops a linear filter to constrain these target signature vectors along preassigned directions using a set of specific filter gains while minimizing the filter output variance. Another, referred to as the linearly constrained discriminant analysis (LCDA), is derived from Fisher's linear discriminant analysis, but constrains the Fisher's discriminant vectors along predetermined directions to improve classification performance. Recently, Bowles et al. introduced another target signature-constrained approach, referred to as filter-vectors method, which requires a linear mixture model to implement constraints on target signature vectors. Interestingly, it turns out that the filter-vectors method can be considered as a special version of both linearly constrained minimum variance and linearly constrained discriminant analysis approaches.
Twist1 and Y‐box‐binding protein‐1 promote malignant potential in bladder cancer cells (2010)

The present study showed that Twist1 regulates YB-1 expression and that both Twist1 and YB-1 promote malignant potentials, including tumour growth, invasion and anti-cancer-drug resistance, indicating that both Twist1 and YB-1 are novel molecular targets in BC.
Exploring Recombinant Flavonoid Biosynthesis in Metabolically Engineered Escherichia coli (2004)

Flavonoids are important plant-specific secondary metabolites synthesized from 4-coumaroyl coenzyme A (CoA), derived from the general phenylpropanoid pathway, and three malonyl-CoAs. The synthesis involves a plant type III polyketide synthase, chalcone synthase. We report the cloning and coexpression in Escherichia coli of phenylalanine ammonia lyase, cinnamate-4-hydroxylase, 4-coumarate:CoA ligase, and chalcone synthase from the model plant Arabidopsis thaliana. Simultaneous expression of all four genes resulted in a blockage after the first enzymatic step caused by the presence of nonfunctional cinnamate-4-hydroxylase. To overcome this problem we fed exogenous 4-coumaric acid to induced cultures. We observed high-level production of the flavanone naringenin as a result. We were also able to produce phloretin by feeding cultures with 3-(4-hydroxyphenyl)propionic acid. Feeding with ferulic or caffeic acid did not yield the corresponding flavanones. We have also cloned and partially characterized a new tyrosine ammonia lyase from Rhodobacter sphaeroides. Tyrosine ammonia lyase was substituted for phenylalanine ammonia lyase and cinnamate-4-hydroxylase in our E. coli clones and three different growth media were tested. After 48 h induction, high-level production (20.8 mg L(-1)) of naringenin in metabolically engineered E. coli was observed for the first time.
Subcellular localization and physiological role of α-methylacyl-CoA racemase (2000)

alpha-Methylacyl-CoA racemase plays an important role in the beta-oxidation of branched-chain fatty acids and fatty acid derivatives because it catalyzes the conversion of several (2R)-methyl-branched-chain fatty acyl-CoAs to their (S)-stereoisomers. Only stereoisomers with the 2-methyl group in the (S)-configuration can be degraded via beta-oxidation. Patients with a deficiency of alpha-methylacyl-CoA racemase accumulate in their plasma pristanic acid and the bile acid intermediates di- and trihydroxycholestanoic acid, which are all substrates of the peroxisomal beta-oxidation system. Subcellular fractionation experiments, however, revealed that both in humans and rats alpha-methylacyl-CoA racemase is bimodally distributed to both the peroxisome and the mitochondrion. Our findings show that the peroxisomal and mitochondrial enzymes are produced from the same gene and that, as a consequence, the bimodal distribution pattern must be the result of differential targeting of the same gene product. In addition, we investigated the physiological role of the enzyme in the mitochondrion. Both in vitro studies with purified heterologously expressed protein and in vivo studies in fibroblasts of patients with an alpha-methylacyl-CoA racemase deficiency revealed that the mitochondrial enzyme plays a crucial role in the mitochondrial beta-oxidation of the breakdown products of pristanic acid byconverting (2R,6)-dimethylheptanoyl-CoA to its (S)-stereoisomer.
Effects of Metals within Ambient Air Particulate Matter (PM) on Human Health (2008)

We review literature providing insights on health-related effects caused by inhalation of ambient air particulate matter (PM) containing metals, emphasizing effects associated with in vivo exposures at or near contemporary atmospheric concentrations. Inhalation of much higher concentrations, and high-level exposures via intratracheal (IT) instillation that inform mechanistic processes, are also reviewed. The most informative studies of effects at realistic exposure levels, in terms of identifying influential individual PM components or source-related mixtures, have been based on (1) human and laboratory animal exposures to concentrated ambient particles (CAPs), and (2) human population studies for which both health-related effects were observed and PM composition data were available for multipollutant regression analyses or source apportionment. Such studies have implicated residual oil fly ash (ROFA) as the most toxic source-related mixture, and Ni and V, which are characteristic tracers of ROFA, as particularly influential components in terms of acute cardiac function changes and excess short-term mortality. There is evidence that other metals within ambient air PM, such as Pb and Zn, also affect human health. Most evidence now available is based on the use of ambient air PM components concentration data, rather than actual exposures, to determine significant associations and/or effects coefficients. Therefore, considerable uncertainties about causality are associated with exposure misclassification and measurement errors. As more PM speciation data and more refined modeling techniques become available, and as more CAPs studies involving PM component analyses are performed, the roles of specific metals and other components within PM will become clearer.
The Hypocretin/Orexin System: An Increasingly Important Role in Neuropsychiatry (2014)

Hypocretins, also named as orexins, are excitatory neuropeptides secreted by neurons specifically located in lateral hypothalamus and perifornical areas. Orexinergic fibers are extensively distributed in various brain regions and involved in a number of physiological functions, such as arousal, cognition, stress, appetite, and metabolism. Arousal is the most important function of orexin system as dysfunction of orexin signaling leads to narcolepsy. In addition to narcolepsy, orexin dysfunction is associated with serious neural disorders, including addiction, depression, and anxiety. However, some results linking orexin with these disorders are still contradictory, which may result from differences of detection methods or the precision of tools used in measurements; strategies targeted to orexin system (e.g., antagonists to orexin receptors, gene delivery, and cell transplantation) are promising new tools for treatment of neuropsychiatric disorders, though studies are still in a stage of preclinical or clinical research.
Alergia a los guantes de látex en la práctica clínica: presentación de casos (1997)

Con el aumento de la incidencia de utilizacion de guantes por parte de los trabajadores sanitarios de la odontologia, tambien han aumentado la presentacion de problemas dermatologicos asociados. Entre estos estan las reacciones alergicas de tipo IV, como la urticaria de contacto, y las reacciones graves de tipo I. Los pacientes tambien pueden verse afectados. Presentamos tres casos de pacientes con reacciones adversas al latex o a los productos quimicos relacionados con la fabricacion del latex. Las areas de afectacion principales son la piel de alrededor del labio y de la cara, asi como del labio superior. Se evito una reaccion adversa potencial en un tercer paciente con el seguimiento de la historia que identificaba una reaccion adversa a un gorro de natacion.
(Quintessence Int 1995; 26: 859-863)
Stability, Precision, and Near-24-Hour Period of the Human Circadian Pacemaker (1999)

Regulation of circadian period in humans was thought to differ from that of other species, with the period of the activity rhythm reported to range from 13 to 65 hours (median 25.2 hours) and the period of the body temperature rhythm reported to average 25 hours in adulthood, and to shorten with age. However, those observations were based on studies of humans exposed to light levels sufficient to confound circadian period estimation. Precise estimation of the periods of the endogenous circadian rhythms of melatonin, core body temperature, and cortisol in healthy young and older individuals living in carefully controlled lighting conditions has now revealed that the intrinsic period of the human circadian pacemaker averages 24.18 hours in both age groups, with a tight distribution consistent with other species. These findings have important implications for understanding the pathophysiology of disrupted sleep in older people.
Elastic Moduli of Breast and Prostate Tissues under Compression (1998)

To evaluate the dynamic range of tissue imaged by elastography, the mechanical behavior of breast and prostate tissue samples subject to compression loading has been investigated. A model for the loading was validated and used to guide the experimental design for data collection. The model allowed the use of small samples that could be considered homogeneous; this assumption was confirmed by histological analysis. The samples were tested at three strain rates to evaluate the viscoelastic nature of the material and determine the validity of modeling the tissue as an elastic material for the strain rates of interest. For loading frequencies above 1 Hz, the storage modulus accounted for over 93 percent of the complex modulus. The data show that breast fat tissue has a constant modulus over the strain range tested while the other tissues have a modulus that is dependent on the strain level. The fibrous tissue samples from the breast were found to be 1 to 2 orders of magnitude stiffer than fat tissue. Normal glandular breast tissue was found to have an elastic modulus similar to that of fat at low strain levels, but the modulus of the glandular tissue increased by an order of magnitude above fat at high strain levels. Carcinomas from the breast were stiffer than the other tissues at the higher strain level; intraductal in situ carcinomas were like fat at the low strain level and much stiffer than glandular tissue at the high strain level. Infiltrating ductal carcinomas were much stiffer than any of the other breast tissues. Normal prostate tissue has a modulus that is lower than the modulus of the prostate cancers tested. Tissue from prostate with benign prostatic hyperplasia (BPH) had modulus values significantly lower than normal tissue. There was a constant but not significant difference in the modulus of tissues taken from the anterior and posterior portions of the gland.
WEE1 Kinase Targeting Combined with DNA-Damaging Cancer Therapy Catalyzes Mitotic Catastrophe (2011)

WEE1 kinase is a key molecule in maintaining G₂-cell-cycle checkpoint arrest for premitotic DNA repair. Whereas normal cells repair damaged DNA during G₁-arrest, cancer cells often have a deficient G₁-arrest and largely depend on G₂-arrest. The molecular switch for the G₂-M transition is held by WEE1 and is pushed forward by CDC25. WEE1 is overexpressed in various cancer types, including glioblastoma and breast cancer. Preclinical studies with cancer cell lines and animal models showed decreased cancer cell viability, reduced tumor burden, and improved survival after WEE1 inhibition by siRNA or small molecule inhibitors, which is enhanced by combination with conventional DNA-damaging therapy, such as radiotherapy and/or cytostatics. Mitotic catastrophe results from premature entry into mitosis with unrepaired lethal DNA damage. As such, cancer cells become sensitized to conventional therapy by WEE1 inhibition, in particular those with insufficient G₁-arrest due to deficient p53 signaling, like glioblastoma cells. One WEE1 inhibitor has now reached clinical phase I studies. Dose-limiting toxicity consisted of hematologic events, nausea and/or vomiting, and fatigue. The combination of DNA-damaging cancer therapy with WEE1 inhibition seems to be a rational approach to push cancer cells in mitotic catastrophe. Its safety and efficacy are being evaluated in clinical studies.
The stimulatory effects of interleukin (IL)-12 on hematopoiesis are antagonized by IL-12-induced interferon gamma in vivo. (1995)

Interleukin (IL)-12 synergizes with other cytokines to stimulate the proliferation and differentiation of early hematopoietic progenitors in vitro. However, in vivo administration of IL-12 decreases peripheral blood counts and bone marrow hematopoiesis. Here, we used interferon (IFN) gamma receptor-deficient (IFN gamma R-/-) mice to investigate whether the in vivo inhibition of hematopoiesis by IL-12 is indirectly mediated by IL-12-induced IFN-gamma. IL-12 administered for 4 d (1 microgram/mouse per day) resulted in lower peripheral blood counts and a 2-fold decrease in bone marrow cellularity in wild-type mice, but not in IFN gamma R-/- mice. Bone marrow hematopoietic progenitors were decreased after IL-12 treatment in wild-type mice, but rather increased in IFN gamma R-/- mice. Splenic cellularity was 2.3-fold higher after IL-12 administration in wild-type mice, largely due to natural killer (NK) cell and macrophage infiltration together with some extramedullary hematopoiesis. In IFN gamma R-/- mice, spleen cellularity was less increased, there were fewer infiltrating NK cells, but a strong extramedullary hematopoiesis. Thus, alterations mediated by IL-12-induced IFN-gamma include reduction in bone marrow cellularity and hematopoietic progenitors, as well as pronounced splenomegaly, largely caused by NK cell infiltration. In the absence of IFN-gamma signaling, IL-12 promotes hematopoiesis, consistent with its in vitro activities.
Use and Abuse of RNAi to Study Mammalian Gene Function (2012)

Realizing the full potential of si/shRNA technology requires more sophisticated approaches to address the pitfalls.