gebhart/patrepeval huggingface dataset:
Efficient recognition of protein fold at low sequence identity by conservative application of Psi-BLAST: validation (2004)

A substantial fraction of protein sequences derived from genomic analyses is currently classified as representing 'hypothetical proteins of unknown function'. In part, this reflects the limitations of methods for comparison of sequences with very low identity. We evaluated the effectiveness of a Psi-BLAST search strategy to identify proteins of similar fold at low sequence identity. Psi-BLAST searches for structurally characterized low-sequence-identity matches were carried out on a set of over 300 proteins of known structure. Searches were conducted in NCBI's non-redundant database and were limited to three rounds. Some 614 potential homologs with 25% or lower sequence identity to 166 members of the search set were obtained. Disregarding the expect value, level of sequence identity and span of alignment, correspondence of fold between the target and potential homolog was found in more than 95% of the Psi-BLAST matches. Restrictions on expect value or span of alignment improved the false positive rate at the expense of eliminating many true homologs. Approximately three-quarters of the putative homologs obtained by three rounds of Psi-BLAST revealed no significant sequence similarity to the target protein upon direct sequence comparison by BLAST, and therefore could not be found by a conventional search. Although three rounds of Psi-BLAST identified many more homologs than a standard BLAST search, most homologs were undetected. It appears that more than 80% of all homologs to a target protein may be characterized by a lack of significant sequence similarity. We suggest that conservative use of Psi-BLAST has the potential to propose experimentally testable functions for the majority of proteins currently annotated as 'hypothetical proteins of unknown function'.
The relationship between workplace stress, coping strategies and health status in New Zealand nurses (2008)

This study was part of an international project examining workplace stress among nurses and their coping strategies, and the relationship between stress, coping and health in the Asia-Pacific region. The aim of the present study was to identify dominant workplace stressors for New Zealand nurses, their most used coping strategies, and variables that best predict their mental and physical health. Postal surveys were sent to 190 randomly selected New Zealand nurses employed in clinical areas. Workload was the most common stressor, while "planful" problem-solving, seeking social support, and self-controlling were the most frequently used ways of coping. The link between stressors such as workload and reduced mental health is concerning, especially as effective coping strategies such as problem-solving are already predominantly used by nurses. The findings suggest that nurses' mental health could benefit from a workload that minimises stress, and from increased support in the workplace and encouragement of planned problem-solving.
A simplified least squares identification of permanent magnet synchronous motor parameters at standstill (2013)

In the automotive application, electrical parameters of the permanent-magnet synchronous machine (PMSM) must be identified at standstill before the startup of the motor. The identification process should be fast and requiring a low computing power in order to be incorporated in an electric variator. This paper presents a simple method based on high frequency (HF) signal injection and exploiting the implementation of state variable filters to obtain a linear model with respect to the parameters. Thus, a simplified procedure of identification based on a least squares algorithm can be used.
ChemInform Abstract: The Chemistry of Enols. The Chemistry of Ionized Enols in the Gas Phase (1991)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Correction: TAZ Expression as a Prognostic Indicator in Colorectal Cancer (2021)

[This corrects the article DOI: 10.1371/journal.pone.0054211.].
Perfect Implementation of Normal-Form Mechanisms (2007)

Privacy and trust affect our strategic thinking, yet they have not been precisely modeled in mechanism design. In settings of incomplete information, traditional implementations of a normal-form mechanism —by disregarding the players’ privacy, or assuming trust in a mediator — may not be realistic and fail to reach the mechanism’s objectives. We thus investigate implementations of a new type. We put forward the notion of a perfect implementation of a normal-form mechanism M: in essence, an extensive-form mechanism exactly preserving all strategic properties of M, without relying on a trusted mediator or violating the privacy of the players. We prove that any normal-form mechanism can be perfectly implemented by a public mediator using envelopes and an envelope-randomizing device (i.e., the same tools used for running fair lotteries or tallying secret votes). Differently from a trusted mediator, a public one only performs prescribed public actions, so that everyone can verify that he is acting properly, and never learns any information that should remain private.
Production, management, and chemistry of coal gasification wastewaters. Tenth quarterly report (1979)

The objective of this paper is to discuss the production, management and chemistry of coal conversion process wastewater. The importance of water chemistry is emphasized in relation to wastewater characterization and wastewater reuse in coal gasification processes. Water management and treatment play critical roles in the design of coal gasification facilities. Much of our nation's easily exploitable coal reserves lie in semi-arid regions where municipal, agricultural, and industrial water demands compete for a limited water supply. For these reasons it is necessary that gasification plants be designed to minimize water consumption. A second consideration is that these plants must be environmentally acceptable. This means that maximum attention must be given to treatment of wastewater for reuse in order to effectively eliminate wastewater discharges. Naturally, this goal serves to help minimize water consumption. The quantity of water consumed in a given gasification plant depends mainly on product quality and on the fraction of unrecovered heat disposed of by wet cooling. Water leaves the plant primarily as vapor from cooling towers, as hydrogen in the methane product, and as occluded water in solid residues. Foul process waters which are treated for reuse, rather than being discharged, do not contribute to this consumption. The extent to which these foul process waters must be treated is dependent on the quality of the effluent and the quality constraints governing reuse options.
1668: Insulin-Like Growth Factor Binding Protein 2 is an Independant Predictor of Prostate Cancer Survival (2004)

used for decision tree building. A blinded test set consisting of 20 controls and 320 CaP patients was used to challenge the algorithms. Additional control specimens are being collected for further analysis.
ChemInform Abstract: Unusual Ligand Formation in CS<sub>2</sub> Chemistry: Synthesis, Structure, and Reactivity of Mo<sub>2</sub>(S<sub>2</sub>CNEt<sub>2</sub>)<sub>3</sub>(μ‐CSC(S)S)(μ‐S<sub>3</sub>C<sub>2</sub>NEt<sub>2</sub>). (1986)

Abstract The complex reaction of CS 2 with the dithiocarbamato‐Mo?l) complex (I) in the presence of 2 equiv. of PPh3 yields the dinuclear title complex (II).
Comparison of Fabrication Processes for Thin-Film Monolithic Electrochromic Devices (1995)

Interest in the use of electrochromic (EC) technology has been steadily growing in recent years (1) . Applications include architectural and automotive glazings for glare and energy management and automated attenuators and filtering for instrumentaion.
High Rate Capacity through Redox Electrolytes Confined in Macroporous Electrodes (2014)

The capacitive characteristics of a model macroporous electrode, comprised of vertically aligned carbon nanotubes, with a relatively large volume /unit mass (of ∼40 cm3/g) are discussed. The faradaic characteristics of the capacity were evidenced through a voltage plateau in the galvanostatic discharge experiments. It is shown that the confinement of electrolyte within the spacing between the nanostructures with respect to an appropriate choice of the voltage scan rate yields a regime where both high capacity and rate capability may be realized. Additionally, the absence of diffusional processes allows for large capacitance retention even at discharge current densities of the order of 200 mA/cm2. For 1M K3Fe(CN)6, the maximum observed capacity was found to be ∼26 mAh/cm3 (normalized to the pore volume) or 0.28 mAh/cm2 (normalized to the projected area of the electrode) and it was noted that the capacity could be cycled at very high rates for 5000 cycles.
Thirteen-Week Oral Toxicity Study of Branched-Chain Amino Acids in Rats (2004)

Branched-chain amino acids (L-isoleucine, L-valine, and L-leucine) are being increasingly used in sport supplements. This study evaluated toxicological and behavioral effects of L-isoleucine (Ile), L-valine (Val), and L-leucine (Leu) during a dosing study with male and female Sprague-Dawley rats. The amino acids were incorporated into a standard diet at doses equal to 1.25%, 2.5%, and 5.0% (w/w). A control group of rats received a standard diet. All diets were administered ad libitum for 13 consecutive weeks. To examine stability of any potential effects, the administration period was followed by a 5-week recovery period, during which only the standard diet was provided to all animals. No significant, dose-related effects on body weight were found in rats fed a Leu- and Ile-supplemented diet. Val mixed into a diet at 5.0% (w/w) decreased slightly, but significantly body weight gain in females, but not males. Ile (5.0% w/w) affected the urine electrolytes, protein, ketone bodies, urine glucose, and urobilinogen in both genders, yet the observed changes remained mostly within the range observed in controls. The random findings in hepatology and ophthalmology at the 13-week sacrifice were not considered toxicologically relevant to effects of the tested amino acids. No significant changes in organ weights were recorded. We estimate the no-observed-adverse-effect level (NOAEL) for Ile at 2.5% for both genders (male, 1.565 +/- 0.060 g/kg/day; females, 1.646 +/- 0.095 g/kg/day), Val at 5.0% for males (3.225 +/- 0.135 g/kg/day) and 2.5% for females (1.853 +/- 0.060 g/kg/day), and Leu at 5.0% for both genders (males, 3.333 +/- 0.101 g/kg/day: females, 3.835 +/- 0.257 g/kg/day).
Survey of Commercial Carnation Cultivars for Four Viruses in California by Indirect Enzyme-Linked Immunosorbent Assay (1983)

Application de la methode ELISA indirecte a la detection des CRSV, CERV, CaMoV, CNFV (virus des taches annulaires de l'œillet, virus de l'«etched ring» de l'œillet, virus de la marbrure de l'œillet, virus de la moucheture necrotique de l'œillet)
Simultaneously multiparametric spectroscopic monitoring of tissue viability in the brain and small intestine (2007)

Under body O<sub>2</sub> imbalance, the Autonomic Nervous System is responsible for redistribution of blood flow with preference to the most vital organs (brain, heart), while the less vital organs (intestine, GI tract) are hypoperfused. The aim of this study was to develop and use an animal model for real time monitoring of tissue viability in the brain, and the small intestine, under various levels of oxygen and blood supply. Male Wistar rats were anesthetized, the brain cortex and intestinal serosa were exposed and connected by optical fibers to the Multi-Site Multi-Parametric (MSMP) monitoring system. Tissue blood flow (TBF) and mitochondrial NADH redox state were monitored simultaneously in the two organs. The rats were subjected to short anoxia, 20 minutes hypoxia or epinephrine (2& 8&mgr;g/kg I.V.). Under oxygen deficiency, cerebral blood flow (CBF) was elevated, whereas intestinal TBF was reduced. Mitochondrial NADH was significantly elevated in both organs. Systemic injection of Adrenaline showed a dose-depended increase in systemic blood pressure and CBF response whereas, intestinal TBF similarly decreased in both doses. In addition, NADH was elevated (reduced form) in the intestine whereas oxidation was observed in the brain. In conclusion, our preliminary results may imply the ability of using of the MSMP for monitoring non-vital organs in order to detect early changes in the balance between oxygen supply and demand in the body.
Clinical studies on the use of radiation therapy as primary treatment of early breast cancer (1984)

The treatment of operable breast cancer by primary radiation therapy instead of mastectomy is undergoing evaluation in the United States and Europe. Retrospective studies of patients treated by primary radiation therapy show that local control and survival rates are comparable to those obtained by mastectomy. Detailed analysis of local failure following primary radiation therapy indicates the importance of excisional biopsy of the primary tumor, moderate doses of radiation to the breast and draining lymph node areas, and the use of a boost to the primary tumor area in maximizing local control. Further, the judicious use of local excision combined with meticulous radiotherapy technique yields highly satisfactory results for the majority of treated patients. Preliminary results from prospective trials also indicate that primary radiation therapy provides both local control and survival rates equivalent to mastectomy. Primary radiation therapy is becoming an increasingly important alternative to mastectomy where surgical and radiotherapeutic expertise are available to optimize both local tumor control and the final cosmetic outcome.
Induction therapy with paclitaxel and bevacizumab followed by switch maintenance therapy with eribulin in Japanese patients with HER2-negative metastatic breast cancer: a multicenter, collaborative, open-label, phase II clinical study for the SBCCSG 35 investigators (2018)

UMIN000015971 . Registration date: January 1, 2015.
Separation-encoded microparticles for single-cell western blotting (2019)

Direct measurement of proteins from single cells has been realized at the microscale using microfluidic channels, capillaries, and semi-enclosed microwell arrays. Although powerful, these formats are constrained, with the enclosed geometries proving cumbersome for multistage assays, including electrophoresis followed by immunoprobing. We introduce a hybrid microfluidic format that toggles between a planar microwell array and a suspension of microparticles. The planar array is stippled in a thin sheet of polyacrylamide gel, for efficient single-cell isolation and protein electrophoresis of hundreds-to-thousands of cells. Upon mechanical release, array elements become a suspension of separation-encoded microparticles for more efficient immunoprobing due to enhanced mass transfer. Dehydrating microparticles offer improved analytical sensitivity owing to in-gel concentration of fluorescence signal for high-throughput single-cell targeted proteomics.
Optimization of quantitative culture assay for human immunodeficiency virus from plasma. Plasma Viremia Group Laboratories of the AIDS Clinical Trials Group (National Institute of Allergy and Infectious Diseases) (1994)

Experimental conditions essential to a simple, reproducible, quantitative human immunodeficiency virus plasma assay were determined. Five parameters were evaluated: length of culture, reproducibility, assay dilution schema, washing procedures, and anticoagulant usage. The recommended quantitative plasma assay utilizes undiluted citrated plasma cultured with peripheral blood mononuclear cells for 14 days with fivefold dilutions and a medium change on day 1 with no washing.
Endocrine and genetic characterization of cousins with male pseudohermaphroditism: evidence that the Lubs pheno‐type can result from a mutation that alters the structure of the androgen receptor (1984)

Impaired virilization of genetic males with testes (male pseudohermaphroditism) can result either from deficiency in androgen production or defects in androgen action, the latter most commonly involving an abnormal androgen receptor. We report here two maternal cousins with male pseudohermaphroditism and clinical features characteristic of the Lubs phenotype, namely apparent females with sufficient fusion of the labioscrotal folds so that a single urogenital sinus orifice is present. Testosterone levels in these genetic males rose appropriately after administration of human chorionic gonadotropin. The amount (maximal binding capacity of 24 to 30 fmol/mg protein) and hormone binding affinity (half-maximal saturation of 0.2 nM) of the androgen receptor in cultured skin fibroblasts was normal, but the receptor was qualitatively abnormal as evidenced by instability on sucrose density gradient centrifugation. The pattern of inheritance in this family is compatible with X-linkage. These findings, together with previous studies, indicate that the spectrum of abnormalities that result from defects of the androgen receptor in genetic men can encompass the entire spectrum between male and female phenotypes.
3D PIC simulation study of the relativistic magnetron (2002)

Summary form only given. The magnetron is intrinsically a 3D problem. 3D simulation is required to obtain the correct electromagnetic fields and realistically model power extraction, for example. We have used the 3D PIC code QUICKSILVER to perform a simulation study of the Palevsky/Bekefi A6 magnetron experiments. The latter serve as somewhat of a benchmark for modeling this complicated tube. We discuss the results of this study, which are consistent with experimental observations. The simulations reveal details of phenomena that are not directly observable in experiments, such as efficiency loss due to current leakage along magnetic field lines and self insulation effects. Techniques for solving these problems are presented. Results of this study suggest that a different tube configuration may be necessary to obtain high efficiency from a relativistic magnetron.
[Effect of non-ionic surfactants on butanol production with Clostridium acetobutylicum ATCC 824]. (2014)

The low butanol concentration of acetone-butanol-ethanol fermentation causes uneconomical product recovery. In this work, the effect of small molecule non-ionic surfactants on butanol fermentation was evaluated, using laboratory stocks of Clostridium acetobutylicum ATCC 824. Non-ionic surfactants substantially increased butanol production when additive amount was higher than 1% (W/W). Butanol concentration reached 16.9 g/L with 5% (W/W) Tween 80 and 100 g/L glucose in a 5 L fermenter. It was found that surfactants micelle solubilization capacity to butanol was very limited, indicating that butanol could hardly enter the surfactants micelle. Butanol production improvement was probably caused by cell surface hydrophobicity change due to surfactants adsorption.
Facile and versatile synthesis of rod‐coil poly(3‐hexylthiophene)‐based block copolymers by nitroxide‐mediated radical polymerization (2012)

Abstract A well‐defined and monofunctional poly(3‐hexylthiophene)‐based (P3HT) macroinitiator has been obtained through a clean, simple, and an efficient multistep synthesis process. The macroinitiator is obtained via intermolecular radical 1,2‐addition onto an ω‐acrylate‐terminated P3HT macromonomer. In a second step, well‐defined rod‐coil block copolymers were obtained by nitroxide‐mediated radical polymerization (NMRP) using the so‐called Blocbuilder ® . The polymerization was found to be controlled with various monomers such as styrene, isoprene, 4‐vinylpyridine, or methyl acrylate. This process constitutes a very promising way to obtain versatile and clean materials for organic electronics. © 2012 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012
A misleading example of a test function in space D from textbooks on Generalized Functions and Distributions (2012)

In many textbooks on Generalized Functions and Distributions, we can find an example of infinitely differentiable function of bounded support from space D, called a bump function. This example is incorrect since this function is not infinitely differentiable.
Photocatalytic Degradation of Methyl Orange by CeO2 and Fe–doped CeO2 Films under Visible Light Irradiation (2014)

Undoped CeO2 and 0.50-5.00 mol% Fe-doped CeO2 nanoparticles were prepared by a homogeneous precipitation combined with homogeneous/impreganation method, and applied as photocatalyst films prepared by a doctor blade technique. The superior photocatalytic performances of the Fe-doped CeO2 films, compared with undoped CeO2 films, was ascribed mainly to a decrease in band gap energy and an increase in specific surface area of the material. The presence of Fe(3+) as found from XPS analysis, may act as electron acceptor and/or hole donor, facilitating longer lived charge carrier separation in Fe-doped CeO2 films as confirmed by photoluminescence spectroscopy. The 1.50 mol% Fe-doped CeO2 film was found to be the optimal iron doping concentration for MO degradation in this study.
The Effect of Decreasing Reflection Coefficient of Ion Acoustic Waves Using an Altemative Electric Field (1982)

An effect has been found, allowing one to vary smoothly the reflection coefficient of the ion acoustic wave from a negatively charged grid.
TBAG (1994)

We present a paradigm and toolkit for rapid prototyping of interactive, animated 3D graphics programs. The paradigm has its roots in declarative programming, emphasizing immutable values, first class functions, and relations, applying these concepts to a broad range of types, including points, vectors, planes, colors, transforms, geometry, and sound. The narrow role of modifiable state in this paradigm allows applications to be run in a collaborative setting (multi-user and multi-computer) without modification.
Environmental constraints on sound transmission by humpback whales (1998)

Singing humpback whales in Hawaii produce a variety of sounds at high source levels (ca. 185 dB re: 1 μPa), in water 15–500 m deep. The utility of these sounds is limited by their detectability and discriminability (which is a function of their acoustic features and the channel through which they are transmitted). To investigate how shallow water propagation might constrain humpback whales use of sound, simulations were run to calculate optimum frequencies for environments frequented by singers [here optimum frequency is the f that maximizes maxzrI(zr,f), where I is intensity, and zr is receiver depth]. Simulations were performed using ORCA, an acoustic propagation model for multilayered acousto-elastic ocean environments based on normal mode theory [Westwood et al., J. Acoust. Soc. Am. 100, 3631–3645 (1996)]. The frequency band tested was 20–4000 Hz; the sub-bottom was taken to be a 50-m-thick sandy/silty layer with gradient, above a basalt half-space. Water depth, source depth and thermocline axis depth were varied across simulations. Source depth was found to be a major determinant of which frequencies propagated the farthest. Optimal frequencies decreased as source depth increased; they were typically above 500 Hz for source depths of 30 m or less. Humpbacks could affect transmission range (by factors of 2 to 3) by adjusting their position and sounds in response to environmental factors.