gebhart/patrepeval huggingface dataset:
4,5-Diarylisoxazole Hsp90 Chaperone Inhibitors: Potential Therapeutic Agents for the Treatment of Cancer (2007)

Inhibitors of the Hsp90 molecular chaperone are showing considerable promise as potential chemotherapeutic agents for cancer. Here, we describe the structure-based design, synthesis, structure-activity relationships and pharmacokinetics of potent small-molecule inhibitors of Hsp90 based on the 4,5-diarylisoxazole scaffold. Analogues from this series have high affinity for Hsp90, as measured in a fluorescence polarization (FP) competitive binding assay, and are active in cancer cell lines where they inhibit proliferation and exhibit a characteristic profile of depletion of oncogenic proteins and concomitant elevation of Hsp72. Compound 40f (VER-52296/NVP-AUY922) is potent in the Hsp90 FP binding assay (IC50 = 21 nM) and inhibits proliferation of various human cancer cell lines in vitro, with GI50 averaging 9 nM. Compound 40f is retained in tumors in vivo when administered i.p., as evaluated by cassette dosing in tumor-bearing mice. In a human colon cancer xenograft model, 40f inhibits tumor growth by approximately 50%.
Design and characterization of an electrochemical peptide-based sensor fabricated via“click” chemistry (2011)

We report an electrochemical peptide-based sensor fabricated via'click' chemistry for detection of anti-p24 antibodies. Our results also allude to a signaling mechanism similar to that of the linear probe electrochemical DNA sensor.
Dissolution of noble metals in halogen–halide–polar organic solvent systems (1992)

Noble metals (Pd, Ag and Au) can be dissolved in a variety of halogen–halide–polar organic solvent systems.
Gene expression profiling of papillary thyroid carcinomas in Korean patients by oligonucleotide microarrays (2012)

A disease classification model showed excellent accuracy in diagnosing PTCs, thus showing the possibility of molecular diagnosis in the future. This GEP could serve as baseline data for further investigation in the management of PTCs based on molecular signatures.
Contamination of drinking-water by arsenic in Bangladesh: a public health emergency. (2000)

The contamination of groundwater by arsenic in Bangladesh is the largest poisoning of a population in history, with millions of people exposed. This paper describes the history of the discovery of arsenic in drinking-water in Bangladesh and recommends intervention strategies. Tube-wells were installed to provide "pure water" to prevent morbidity and mortality from gastrointestinal disease. The water from the millions of tube-wells that were installed was not tested for arsenic contamination. Studies in other countries where the population has had long-term exposure to arsenic in groundwater indicate that 1 in 10 people who drink water containing 500 micrograms of arsenic per litre may ultimately die from cancers caused by arsenic, including lung, bladder and skin cancers. The rapid allocation of funding and prompt expansion of current interventions to address this contamination should be facilitated. The fundamental intervention is the identification and provision of arsenic-free drinking water. Arsenic is rapidly excreted in urine, and for early or mild cases, no specific treatment is required. Community education and participation are essential to ensure that interventions are successful; these should be coupled with follow-up monitoring to confirm that exposure has ended. Taken together with the discovery of arsenic in groundwater in other countries, the experience in Bangladesh shows that groundwater sources throughout the world that are used for drinking-water should be tested for arsenic.
A Simple Method for Chloroplast Transformation in <I>Chlamydomonas reinhardtii</i> (2004)

Photosystem (PS)I is a multi-subunit pigment-protein complex that uses light energy to transfer electrons from plastocyanin to ferredoxin. Application of genetic engineering to photo-synthetic reaction center proteins has led to a significant advancement in our understanding of primary electron transfer events and the role of the protein environment in modulating these processes. Chlamydomonas reinhardtii provides a system particularly amenable to analyze the structure-function relationship of PSI. Chlamydomonas reinhardtii is also a favorable organism for chloroplast transformation because it contains a single chloroplast and grows heterotrophically when supplemented with acetate. Chlamydomonas has served as a model organism for the development of chloroplast transformation procedures and the study of photosynthetic mutants generated using this method. Exogenous cloned cpDNA can be introduced into the chloroplast by using this biolistic gene gun method. DNA-coated tungsten or gold particles are bombarded onto cells. Upon its entry into chloroplasts, the transforming DNA is released from the particles and integrated into the chloroplast genome through homologous recombination. The most versatile chloroplast selectable marker is aminoglycoside adenyl transferase (aadA), which can be expressed in the chloroplast to confer resistance to spectinomycin or streptomycin. This chapter describes the procedures for chloroplast transformation.
Novel Approaches to the Design of Phased Array Antennas (2012)

This dissertation presents three new approaches to the design of phased array antennas in order to reduce their complexity. The first approach is based on extended resonance technique which, unlike conventional phased array designs, achieves power dividing and phase shifting tasks within a single circuit. A new extended resonance circuit is developed here that increases the maximum achievable scan angle by three times compared to the extended resonance phased array demonstrated previously. In order to expand the size of phased array, a new modular approach is used enabling a scalable design of extended resonance phased array for the first time. By applying heterodyne-mixing concept, a modular 24 GHz phased array has been demonstrated. The second approach presented in this dissertation is based on a bi-directional feeding method. A new phased array is designed based on this approach which demands less phase shift from phase shifters compared to any of common phased arrays. The new bi-directional phased array allows for beam steering using only a single control voltage. A general design procedure for a bidirectional N-element phased array feed network is presented for the first time which allows applying this approach to phased arrays with any number of antenna elements. Furthermore, a new, compact phase shifter is designed and utilized in the phased array. A 2.4 GHz bi-directional phased array has been designed and fabricated. Finally, the third approach described in the dissertation allows the phase progression across the antenna elements to be controlled by using a single phase shifter. Therefore, the number of phase shifters required in the phased array is substantially reduced compared to conventional phased array designs which require a separate phase shifter per each antenna element. A variable phase shift is achieved in this approach by vector summation of signals. The amplitude ratios of these vectors are adjusted to provide a linear phase progression. This approach is much simpler than the traditional Cartesian phase shifting scheme. A 2 GHz phased array designed based on this approach has been fabricated and tested.
Improved production of Trichoderma harzianum endochitinase by expression in Trichoderma reesei (1996)

The chromosomal endochitinase gene (ThEn-42) of the mycoparasite fungus Trichoderma harzianum P1 was isolated and overexpressed in the filamentous fungus Trichoderma reesei under the promoter of the major cellulase gene cbhl1. The host strain RutC-30 did not produce any endogenous endochitinase activity. The prepro region of the T harzianum endochitinase was correctly processed in T. reesei. No differences in expression were observed when the prepro region was replaced with the CBHI signal sequence. Shake flask cultivation yielded 130 mg of active enzyme per liter, which in terms of activity represents about a 20-fold increase over the endochitinase activity produced by T. harzianum. The presence of multiple copies of the expression cassette in the transformant resulted in limitation in transcription and/or regulation factors needed for full activity of the cbh1 promoter, although this was not the major limiting factor for higher expression of endochitinase. The endochitinase was very sensitive to an acidic protease at the late stages of T. reesei cultivation. T. reesei RutC-30 appeared to be tolerant of the endochitinase and can be used as a production host for this enzyme, which has antifungal activity toward plant pathogens.
Piezoelectric actuation for microfluidic cell sorting (2013)

Since the field of microfluidics is vastly improving and developing, and piezoelectric actuators offer good control on a micrometer scale, this work was created as a combination of the two. A microfluidic chip with an embedded piezoelectric actuator was designed and constructed using polydimethylsiloxane as the main material. The chip was experimented on by varying both mechanical and electrical properties. Performance dependencies of volumetric flow rate and input waveform were described and analyzed. Moreover, beneficial phenomena were discovered and analyzed using high-speed microscopy and digital image analysis. A situation where control of microfluidic flow direction could potentially be available was achieved. Other promising results showed new potential applications for piezoelectric actuation in microfluidic systems.
Lymphotoxin-α-deficient mice. Effects on secondary lymphoid organ development and humoral immune responsiveness (1995)

Targeted mutagenesis in embryonic stem cells was used to generate mice deficient in lymphotoxin-alpha (LT-alpha). Mice lacking LT-alpha -/- (LT-alpha -/- mice) exhibit a phenotype dominated by defects in secondary lymphoid organ development. LT-alpha -/- mice lack lymph nodes and Peyer's patches, and possess spleens in which the usual architecture is disrupted. However, in a few of the mutants, abnormal lymph node-like structures were observed, mainly within the mesenteric fat. Abnormal clusters of lymphocytes were also found to accumulate in the periportal and perivascular regions of the liver and lung of LT-alpha -/- mice. Yet, lymphocytes from LT-alpha -/- mice appeared phenotypically normal, expressing the expected ratios of B and T cell surface markers as well as the lymphocyte homing marker, L-selectin. In addition, bone marrow cells from LT-alpha -/- mice were able to successfully reconstitute the lymphoid organs of severe combined immunodeficient mice. However, LT-alpha -/- mutant mice examined for humoral immune responsiveness were found to be impaired in their ability to respond to different Ag. These data illustrate the utility of this mouse model as a system for understanding lymphoid organ development and its effects on immune responsiveness.
Preparation of Polyvinylamine by the Hofmann Degradation of Polyacrylamide (1976)

Abstract Polyvinylamine which contained 95.6 mol% amine units was obtained when the Hofmann degradation was applied to polyacrylamide by use of a very slight excess of sodium hypochlorite and a large excess of sodium hydroxide at 0 to −15 °C for about 15 h. Polyvinylamine hydrochloride (PVAm·HCl) was isolated almost quantitatively as a white powder. PVAm·HCl was freely soluble in water, but insoluble in organic solvents such as methanol, acetone, dioxane, N,N-dimethylformamide (DMF), and dimethyl sulfoxide (DMSO). The desalting of PVAm·HCl was performed by passing its aqueous solution through columns of ion exchange resins. The product containing 30.5% nitrogen was obtained in reasonable yield. Polyvinylamine was freely soluble in water, acetic acid, or lower alcohols, but insoluble in solvents such as acetone, dioxane, DMF, and DMSO.
A Model of Copper CMP (2005)

A model of copper chemical mechanical polishing (CMP) based on methods of chemical kinetics is presented which includes both chemical and mechanical processes. This CMP model explains observed patterns in removal rates for peroxide and nonperoxide-based slurries as a function of oxidizer concentration, polishing pressure and speed, etchant concentration, and pH.
On the Absorption Spectra of Complex Ions IV. The Effect of the Spin-orbit Interaction and the Field of Lower Symmetry on d electrons in Cubic Field (1958)

It is shown that the matrix elements of the crystalline field of lower symmetry than cubic and of the spin-orbit interaction for d -electrons in octahedral complex ions can be easily evaluated by the method of tensor operators, and the tables necessary to evaluate these elements by this method are given. It is also pointed out that the effective Hamiltonian which plays the same role as the spin Hamiltonian for the non-degenerate states can be constructed for the degenerate orbital states and will be useful for the analysis of line spectra of these complexes.
Production and upgrading of 5-hydroxymethylfurfural using heterogeneous catalysts and biomass-derived solvents (2012)

High yields of HMF from glucose can be achieved using biomass-derived solvents and a combination of solid Lewis and Brønsted catalysts in a salt-free reaction system. The HMF produced in this system can be oxidized to FDCA or hydrogenated to DMF, both being high-value chemicals.
Feedback-Directed Random Test Generation (2007)

We present a technique that improves random test generation by incorporating feedback obtained from executing test inputs as they are created. Our technique builds inputs incrementally by randomly selecting a method call to apply and finding arguments from among previously-constructed inputs. As soon as an input is built, it is executed and checked against a set of contracts and filters. The result of the execution determines whether the input is redundant, illegal, contract-violating, or useful for generating more inputs. The technique outputs a test suite consisting of unit tests for the classes under test. Passing tests can be used to ensure that code contracts are preserved across program changes; failing tests (that violate one or more contract) point to potential errors that should be corrected. Our experimental results indicate that feedback-directed random test generation can outperform systematic and undirected random test generation, in terms of coverage and error detection. On four small but nontrivial data structures (used previously in the literature), our technique achieves higher or equal block and predicate coverage than model checking (with and without abstraction) and undirected random generation. On 14 large, widely-used libraries (comprising 780KLOC), feedback-directed random test generation finds many previously-unknown errors, not found by either model checking or undirected random generation.
Characterizing the antioxidant activity of amla (Phyllanthus emblica) extract (2001)

Amla is well-known for its rich vitamin C (ascorbic acid) and polyphenol contents. To assess its antioxidant activity, we examined aqueous amla extract for its ability to inhibit γ-radiation-induced lipid peroxidation (LPO) in rat liver microsomes and superoxide dismutase (SOD) damage in rat liver mitochondria. For the LPO experiment, amla extract was added as its aqueous solution; and irradiation was carried out at different time intervals. The extent of LPO was measured in terms of thiobarbituric acid reactive substances. It was observed that the amla extract acts as a very good antioxidant against γ-radiationinduced LPO. Similarly, it was found to inhibit the damage to antioxidant enzyme SOD. The antioxidant activity of the amla extract was found to be both doseand concentration-dependent. The amount of ascorbic acid in amla was standardized by HPLC and titrimetric methods and was found to be 3.25 to 4.5% w/w. However in microsomes containing this composition of pure ascorbic acid alone, no inhibition in LPO was observed. Cyclic voltammetry of the amla extract was carried out to estimate the ascorbic acid equivalents, which was found to be 9.4% w/w of amla. This value was found to be in agreement when compared with the reactivity of both amla and ascorbic acid towards ABTS radical, a stable free-radical. Based on these results it is concluded that amla is a more potent antioxidant than vitamin C.
The Use of Groundwater Pumping to Increase Agricultural Production and Reduce Land Degradation on the Huang-Huai-Hai Plain, China (1994)

A combination of drought and shallow watertables has led to extensive areas of land salinization and low agricultural productivity on the alluvial Huang - Huai - Hai Plain. The lowering of groundwater levels by widespread pumping to a critical watertable depth has not only dramatically reduced land degradation problems but has increased agricultural production by tenfold at an experimental site, and fivefold over a whole district.
[Abnormality and significance of interleukin-9 and CD4(+)interleukin-9(+) T-cells in peripheral blood of patients with systemic lupus erythematosus]. (2013)

The abnormalities of IL-9 and CD4(+)IL-9(+)T-cells may play an important role in the pathogenesis of SLE. And the frequencies of CD4(+)IL-9(+)T-cells and the levels of IL-9 are evaluative parameters of SLE activity and severity.
Fast ambipolar carrier transport in smectic phases of phenylnaphthalene liquid crystal (1997)

The carrier transport of a new calamitic liquid crystal, i.e., 2-(4′-octylphenyl)6-dodecyloxynaphthalene (8-PNP-O12) was investigated by the time-of-flight technique. The fast ambipolar electronic conduction was observed in two smectic phases of 8-PNP-O12. The carrier mobilities were determined to be 1.6×10−3 cm2/V⋅s in the lower temperature smectic phase (Sm1) between 79 and 100 °C and to be 2.5×10−4 cm2/V⋅s in the higher temperature phase (Sm2) between 100 and 121 °C, regardless of carrier signs, i.e., electron and hole. The slower ambipolar transport was observed in isotropic phase as well, whose mobility was 8×10−5 cm2/V⋅s. These mobilities were independent of applied electric fields and temperature.
Nuclear DNA Sequences Present in Human Leukemic Cells and Absent in Normal Leukocytes (1972)

The central purpose of the present study was to test the proposition that the nuclear DNA of every human cell contains whatever information is necessary and sufficient for transformation to malignancy. The experiments were made possible by our earlier identification in human leukemic cells of particulate elements encapsulating 70S RNA and RNA-directed DNA polymerase. The [(3)H]DNA synthesized by these particles was used as a probe, through molecular hybridization, to normal and leukemic DNA. The results obtained establish that leukemic nuclear DNA contains particle-related sequences that cannot be detected in normal leukocytes. This outcome does not support the virogene-oncogene theory, which postulates the inclusion of at least one complete copy of oncogenic information in the genome of every normal cell. The data suggest that we may not be forced to cope with an omnipresent DNA segment coding for malignancy. Under the circumstances, we can perhaps entertain more hopeful pathways leading to the control and cure of cancer.
Myocardial vasoactive intestinal peptide and fibrosis induced by nitric oxide synthase inhibition in the rat (2003)

We conclude that depletion of VIP in the myocardium is associated with increasing myocardial fibrosis in l-NAME treated WKY. As VIP depletion occurs in other models of myocardial fibrosis, it appears to be a common mechanism. Myocardial VIP depletion may therefore be a new and important factor in the pathogenesis of cardiac fibrosis.
Swing Modulo Scheduling: A Lifetime-Sensitive Approach (1996)

This paper presents a novel software pipelining approach, which is called Swing Modulo Scheduling (SMS). It generates schedules that are near optimal in terms of initiation interval, register requirements and stage count. Swing Modulo Scheduling is an heuristic approach that has a low computational cost. The paper describes the technique and evaluates it for the Perfect Club benchmark suite. SMS is compared with other heuristic methods showing that it outperforms them in terms of the quality of the obtained schedules and compilation time. SMS is also compared with an integer linear programming approach that generates optimum schedules but with a huge computational cost, which makes it feasible only for very small loops. For a set of small loops, SMS obtained the optimum initiation interval in all the cases and its schedules required only 5% more registers and a 1% higher stage count than the optimum.
Phenotypes of Mouse diabetes and Rat fatty Due to Mutations in the OB (Leptin) Receptor (1996)

Mice harboring mutations in the obese (ob) and diabetes (db) genes display similar phenotypes, and it has been proposed that these genes encode the ligand and receptor, respectively, for a physiologic pathway that regulates body weight. The cloning of ob, and the demonstration that it encodes a secreted protein (leptin) that binds specifically to a receptor (OB-R) in the brain, have validated critical aspects of this hypothesis. Here it is shown by genetic mapping and genomic analysis that mouse db, rat fatty (a homolog of db), and the gene encoding the OB-R are the same gene.
Daclizumab Improves Asthma Control in Patients with Moderate to Severe Persistent Asthma (2008)

Daclizumab improved pulmonary function and asthma control in patients with moderate to severe chronic asthma inadequately controlled on ICS. The mechanism of action likely involves inhibition of proinflammatory cytokine generation by IL-2R blockade in activated T cells. Clinical trial registered with www.clinicaltrials.gov (NCT00028288).