gebhart/patrepeval huggingface dataset:
Human Glutathione-Dependent Formaldehyde Dehydrogenase. Structures of Apo, Binary, and Inhibitory Ternary Complexes (2002)

The human glutathione-dependent formaldehyde dehydrogenase is unique among the structurally studied members of the alcohol dehydrogenase family in that it follows a random bi bi kinetic mechanism. The structures of an apo form of the enzyme, a binary complex with substrate 12-hydroxydodecanoic acid, and a ternary complex with NAD+ and the inhibitor dodecanoic acid were determined at 2.0, 2.3, and 2.3 A resolution by X-ray crystallography using the anomalous diffraction signal of zinc. The structures of the enzyme and its binary complex with the primary alcohol substrate, 12-hydroxydodecanoic acid, and the previously reported binary complex with the coenzyme show that the binding of the first substrate (alcohol or coenzyme) causes only minor changes to the overall structure of the enzyme. This is consistent with the random mechanism of the enzyme where either of the substrates binds to the free enzyme. The catalytic-domain position in these structures is intermediate to the "closed" and "open" conformations observed in class I alcohol dehydrogenases. More importantly, two different tetrahedral coordination environments of the active site zinc are observed in these structures. In the apoenzyme, the active site zinc is coordinated to Cys44, His66 and Cys173, and a water molecule. In the inhibitor complex, the coordination environment involves Glu67 instead of the solvent water molecule. The coordination environment involving Glu67 as the fourth ligand likely represents an intermediate step during ligand exchange at the active site zinc. These observations provide new insight into metal-assisted catalysis and substrate binding in glutathione-dependent formaldehyde dehydrogenase.
Nonlinear optical contrast enhancement in OCT (2004)

We report on a new interferometric technique for measuring Coherent Anti-Stokes Raman Scattering and Second Harmonic Generation signals. The exploitation of these optical nonlinearities for molecular contrast enhancement in Optical Coherence Tomography is presented.
Spark: cluster computing with working sets (2010)

MapReduce and its variants have been highly successful in implementing large-scale data-intensive applications on commodity clusters. However, most of these systems are built around an acyclic data flow model that is not suitable for other popular applications. This paper focuses on one such class of applications: those that reuse a working set of data across multiple parallel operations. This includes many iterative machine learning algorithms, as well as interactive data analysis tools. We propose a new framework called Spark that supports these applications while retaining the scalability and fault tolerance of MapReduce. To achieve these goals, Spark introduces an abstraction called resilient distributed datasets (RDDs). An RDD is a read-only collection of objects partitioned across a set of machines that can be rebuilt if a partition is lost. Spark can outperform Hadoop by 10x in iterative machine learning jobs, and can be used to interactively query a 39 GB dataset with sub-second response time. 1
Thermally Developable Photographic Materials (TDPM): A Review of the State-of-the-Art in Mechanistic Understanding (1998)

This article reviews recent studies that have revealed much new information about tructure and morphology of the interface formed between silver halide and silver carboxylate phases during fabrication of thermally developable photographic materials (TDPM). This information has proved relevant not only to understanding how latent images may form in TDPM, but has also revealed that morphological features of the interface may govern the course of the development reaction as well.
Beamforming: a versatile approach to spatial filtering (1988)

An overview of beamforming from a signal-processing perspective is provided, with an emphasis on recent research. Data-independent, statistically optimum, adaptive, and partially adaptive beamforming are discussed. Basic notation, terminology, and concepts are included. Several beamformer implementations are briefly described.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Distinguishing multiple smart-phone interactions on a multi-touch wall display using tilt correlation (2011)

While very large collaborative surfaces are already being widely employed to facilitate concurrent interactions with multiple users, they involve no personalization in the touch interactions. Augmenting them to identify the touch interactions with multiple smart-phones can enable interesting co-located communal applications with context-based personalized interactions and information exchange amongst users' portable devices and the shared wall display. This paper proposes a novel matching technique, called tilt correlation, which employs the built-in tilt sensor to identify smart-phones that make concurrent two-point contacts on a common multi-touch wall display. Experimental investigations suggest that the resultant error rate is relatively low; in addition, we also propose a quantitative measure, called the Bourne Identity Index to allow application designers to determine the reliability of each device identification.
312-nanometer Ultraviolet B Light (Narrow-Band UVB) Induces Apoptosis of  T Cells within Psoriatic Lesions (1999)

Narrow-band (312 nm) ultraviolet B light (UVB) is a new form of therapy for psoriasis, but its mechanism of action is unknown. In a bilateral comparison clinical study, daily exposure of psoriatic plaques to broad-band UVB (290-320 nm) or 312-nm UVB depleted T cells from the epidermis and dermis of psoriatic lesions. However, 312-nm UVB was significantly more depleting in both tissue compartments. To characterize the mechanism of T cell depletion, assays for T cell apoptosis were performed on T cells derived from UVB-irradiated skin in vivo and on T cells irradiated in vitro with 312-nm UVB. Apoptosis was induced in T cells exposed to 50-100 mJ/cm2 of 312-nm UVB in vitro, as measured by increased binding of fluorescein isothiocyanate (FITC)-Annexin V to CD3(+) cells and by characteristic cell size/granularity changes measured by cytometry. In vivo exposure of psoriatic skin lesions to 312-nm UVB for 1-2 wk also induced apoptosis in T cells as assessed by the terminal deoxynucleotidyl transferase-mediated dUTP-biotin nick end labeling (TUNEL) reaction in tissue sections, by binding of FITC-Annexin V to CD3(+) T cells contained in epidermal cell suspensions, and by detection of apoptosis-related size shifts of CD3(+) cells. Induction of T cell apoptosis could be the main mechanism by which 312-nm UVB resolves psoriasis skin lesions.
Melanoma immunotherapy by targeted IL-2 depends on CD4+ T-cell help mediated by CD40/CD40L interaction (2000)

The induction of tumor-protective immunity against malignancies remains a major challenge in cancer immunotherapy. A novel, humanized anti-ganglioside-GD(2)-IL-2 immunocytokine (hu14.18-IL-2) induced CD8(+) T cells to eradicate established pulmonary metastases of B78-D14 murine melanoma, in a process that required help by CD4(+) T cells and was mediated by the CD40/CD40 ligand (CD40L) interaction. The anti-tumor effect was diminished in mice deficient in CD4(+) T-cells. Three lines of evidence show that CD4(+) T-cell help was mediated by CD40/CD40L interaction but not by endogenous IL-2 production. First, the hu14.18-IL-2-induced anti-tumor response is partially abrogated in C57BL/6J CD40L knockout (KO) mice in contrast to C57BL/6J IL-2 KO animals, in which the immunocytokine was completely effective. Second, partial abrogation of the anti-tumor effect is induced with anti-CD40L antibodies to the same extent as with CD4(+) T-cell depletion. Third, a complete anti-tumor response induced by hu14.18-IL-2 can be reconstituted in C57BL/6J CD40L KO mice by simultaneous stimulation with an anti-CD40 mAb. These results suggest that help provided by CD4(+) T cells via CD40/CD40L interactions in our tumor model is crucial for effective immunotherapy with an IL-2 immunocytokine.
A three pulse phase response curve to three milligrams of melatonin in humans (2007)

Exogenous melatonin is increasingly used for its phase shifting and soporific effects. We generated a three pulse phase response curve (PRC) to exogenous melatonin (3 mg) by administering it to free-running subjects. Young healthy subjects (n = 27) participated in two 5 day laboratory sessions, each preceded by at least a week of habitual, but fixed sleep. Each 5 day laboratory session started and ended with a phase assessment to measure the circadian rhythm of endogenous melatonin in dim light using 30 min saliva samples. In between were three days in an ultradian dim light (< 150 lux)-dark cycle (LD 2.5 : 1.5) during which each subject took one pill per day at the same clock time (3 mg melatonin or placebo, double blind, counterbalanced). Each individual's phase shift to exogenous melatonin was corrected by subtracting their phase shift to placebo (a free-run). The resulting PRC has a phase advance portion peaking about 5 h before the dim light melatonin onset, in the afternoon. The phase delay portion peaks about 11 h after the dim light melatonin onset, shortly after the usual time of morning awakening. A dead zone of minimal phase shifts occurred around the first half of habitual sleep. The fitted maximum advance and delay shifts were 1.8 h and 1.3 h, respectively. This new PRC will aid in determining the optimal time to administer exogenous melatonin to achieve desired phase shifts and demonstrates that using exogenous melatonin as a sleep aid at night has minimal phase shifting effects.
Characterization of a glucoamylase G2 from Aspergillus niger (1986)

Peptide fragments were generated by enzymic or chemical degradation of the small form, G2, and the large form, G1, of Aspergillus niger glucoamylase (EC 3.1.2.3). The G2 form was either identical to residues Ala1-Pro512 or to Ala1-Ala514 of the G1 polypeptide chain containing 616 amino acid residues. Structural analysis of the O-linked carbohydrates from the 70-amino-acid-residues long extensively glycosylated segment of G2 revealed no significant differences in the contents of single mannose and oligosaccharide units in comparison to the corresponding region of G1. The results suggest that the present G2 form has been generated by limited proteolysis of the larger G1. In contradistinction to this, a recently reported splicing out of an intervening sequence from G1 mRNA leads to a smaller mRNA coding for a G2 protein product with a different COOH-terminal sequence than the G2 form described in the present work [Boel et al. (1984) EMBO J. 3, 1097-1102].
A potent neutralizing antibody with therapeutic potential against all four serotypes of dengue virus (2017)

A therapy for dengue is still elusive. We describe the neutralizing and protective capacity of a dengue serotype-cross-reactive antibody isolated from the plasmablasts of a patient. Antibody SIgN-3C neutralized all four dengue virus serotypes at nano to picomolar concentrations and significantly decreased viremia of all serotypes in adult mice when given 2 days after infection. Moreover, mice were protected from pathology and death from a lethal dengue virus-2 infection. To avoid potential Fc-mediated uptake of immune complexes and ensuing enhanced infection, we introduced a LALA mutation in the Fc part. SIgN-3C-LALA was as efficient as the non-modified antibody in neutralizing dengue virus and in protecting mice while antibody-dependent enhancement was completely abrogated. The epitope of the antibody includes conserved amino acids in all three domains of the glycoprotein, which can explain its cross-reactivity. SIgN-3C-LALA neutralizes dengue virus both pre and post-attachment to host cells. These attributes likely contribute to the remarkable protective capacity of SIgN-3C.
Fast Blood Coagulation of Capillary Vessels by Cold Plasma: A Rat Ear Bleeding Model (2011)

Cold atmospheric pressure plasmas previously have been shown to be effective in vitro in generating active species, radicals, and charges, which may aid in various processes of interest to medicine, including blood coagulation. Floating electrode dielectric barrier discharge microsecond-pulsed, high-voltage plasma was used in an animal model of hairless Sprague-Dawley rats to treat an incision on the ear. The results confirm cold plasma's ability to coagulate blood in a live animal model. A small incision in the rat ear, cutting the thin epidermis and slicing through the capillaries, creates a small and controllable wound from which bleeding is observed. Without plasma treatment, the animal bleeds for approximately 2 minutes, whereas a 10-second treatment is sufficient to coagulate blood. Cold plasma floating electrode dielectric barrier discharge was shown to effectively coagulate bleeding small vessels, which may prove beneficial in surgical intervention treatments of, for example, vocal cord surgery, eye surgery, or brain surgery, for which other means of coagulation may be prohibitive. Future animal trials will include larger animals and different bleeding sites, with the potential to move on to human trials.
Energy harvesting from low frequency applications using piezoelectric materials (2014)

In an effort to eliminate the replacement of the batteries of electronic devices that are difficult or impractical to service once deployed, harvesting energy from mechanical vibrations or impacts using piezoelectric materials has been researched over the last several decades. However, a majority of these applications have very low input frequencies. This presents a challenge for the researchers to optimize the energy output of piezoelectric energy harvesters, due to the relatively high elastic moduli of piezoelectric materials used to date. This paper reviews the current state of research on piezoelectric energy harvesting devices for low frequency (0–100 Hz) applications and the methods that have been developed to improve the power outputs of the piezoelectric energy harvesters. Various key aspects that contribute to the overall performance of a piezoelectric energy harvester are discussed, including geometries of the piezoelectric element, types of piezoelectric material used, techniques employed to match the resonance frequency of the piezoelectric element to input frequency of the host structure, and electronic circuits specifically designed for energy harvesters.
The Gene ncgl2918 Encodes a Novel Maleylpyruvate Isomerase That Needs Mycothiol as Cofactor and Links Mycothiol Biosynthesis and Gentisate Assimilation in Corynebacterium glutamicum (2006)

Data mining of the Corynebacterium glutamicum genome identified 4 genes analogous to the mshA, mshB, mshC, and mshD genes that are involved in biosynthesis of mycothiol in Mycobacterium tuberculosis and Mycobacterium smegmatis. Individual deletion of these genes was carried out in this study. Mutants mshC and mshD lost the ability to produce mycothiol, but mutant mshB produced mycothiol as the wild type did. The phenotypes of mutants mshC and mshD were the same as the wild type when grown in LB or BHIS media, but mutants mshC and mshD were not able to grow in mineral medium with gentisate or 3-hydroxybenzoate as carbon sources. C. glutamicum assimilated gentisate and 3-hydroxybenzoate via a glutathione-independent gentisate pathway. In this study it was found that the maleylpyruvate isomerase, which catalyzes the conversion of maleylpyruvate into fumarylpyruvate in the glutathione-independent gentisate pathway, needed mycothiol as a cofactor. This mycothiol-dependent maleylpyruvate isomerase gene (ncgl2918) was cloned, actively expressed,andpurifiedfromEscherichiacoli.Thepurifiedmycothioldependent isomerase is a monomer of 34 kDa. The apparent K m and V max values for maleylpyruvate were determined to be 148.4 11.9 M and 1520 57.4 mol/min/mg, respectively (mycothiol concentration, 2.5 M). Previous studies had shown that mycothiol played roles in detoxification of oxidative chemicals and antibiotics in streptomycetes and mycobacteria. To our knowledge, this is the first demonstration that mycothiol is essential for growth of C. glutamicum with gentisate or 3-hydroxybenzoate as carbon sources and the first characterization of a mycothiol-dependent maleylpyruvate isomerase.
Zika Virus Infection with Prolonged Maternal Viremia and Fetal Brain Abnormalities (2016)

The current outbreak of Zika virus (ZIKV) infection has been associated with an apparent increased risk of congenital microcephaly. We describe a case of a pregnant woman and her fetus infected with ZIKV during the 11th gestational week. The fetal head circumference decreased from the 47th percentile to the 24th percentile between 16 and 20 weeks of gestation. ZIKV RNA was identified in maternal serum at 16 and 21 weeks of gestation. At 19 and 20 weeks of gestation, substantial brain abnormalities were detected on ultrasonography and magnetic resonance imaging (MRI) without the presence of microcephaly or intracranial calcifications. On postmortem analysis of the fetal brain, diffuse cerebral cortical thinning, high ZIKV RNA loads, and viral particles were detected, and ZIKV was subsequently isolated.
Applications of a microfabricated device for evaluating sperm function (1993)

Mesoscale structures (microns dimensions, nL-pL volumes) have been designed and fabricated in silicon for use in various analytical tasks. We studied sperm motility and performed sperm selection in channels (80 microns wide x 20 microns deep), branching structures (40 microns wide x 20 microns deep, eight bifurcations), and channels containing barriers (7 microns feature size). Sperm-cervical mucus and sperm-hyaluronic acid interactions were assessed by using appropriate microchannel-chamber structures filled with either cervical mucus or hyaluronic acid. Simultaneous assessment of the potency of different spermicides (e.g., nonoxynol-9, C13G) and spermicide concentrations was achieved with structures comprising chambers containing spermicide connected via channels to a central chamber into which semen was introduced. Semen was also tested for the presence of sperm-specific antibodies by using microchannels filled with human anti-IgG antibody-coated microbeads.
Highly Z-Selective and Enantioselective Ring-Opening/Cross-Metathesis Catalyzed by a Resolved Stereogenic-at-Ru Complex (2013)

The synthesis of a ruthenium complex that catalyzes Z-selective (up to 98% Z) asymmetric ring-opening/cross-metathesis with high enantioselectivity (up to 95% ee) is reported. The synthesis of the catalyst features the resolution of a chelating N-heterocyclic carbene complex by ligand substitution with a chiral carboxylate.
Short term effects of dissolved oxygen concentration on the turbidity of the supernatant of activated sludge (1998)

Short term effects of dissolved oxygen (DO) concentration on the supernatant turbidity of activated sludge were studied in batch reactors, continuous reactors and in a full scale plant. Adsorption of colloidal material onto activated sludge was studied in batch reactors. The adsorption capacity of colloidal material, expressed as removal of turbidity, was larger in aerobic than in anaerobic conditions. The difference in adsorption capacity between high (≥5 mg/l) and low (&amp;lt;0.5 mg/l) DO concentrations was small. Experiments were made in pilot scale completely mixed reactors where the oxygen supply was turned off during different periods of length (1-4 hours). The turbidity increased directly when the anaerobic period started and decreased when the aerobic period started. Similar results were obtained when the influent was turned off. A few full scale experiments were carried out. The aerators were adjusted to change the DO concentration along the aeration tank (plug flow) for periods of 3-6 hours. Low DO concentrations by the end of the aeration tank produced a turbidity increase of the effluent, while low DO concentrations in the first half of the aeration tank did not affect the turbidity to a large extent.
Histamine and allergen induced changes in nasal airways resistance measured by anterior rhinomanometry: reproducibility of the technique and the effect of topically administered antihistaminic and anti‐ allergic drugs. (1987)

1. Changes in nasal airways resistance (NAR) following the topical application of histamine and allergen solutions were measured by passive anterior rhinomanometry. 2. The repeatability of five consecutive measurements of resting NAR prior to provocation with histamine or allergen (expressed as the coefficient of variation) was 32.8% and following instillation of saline control solution 37.2%. 3. The repeatability of five consecutive measurements of NAR during the nasal obstruction produced by histamine and allergen was similar to that recorded prior to provocation; the coefficients of variation (median values) being 39.6% and 33.1% respectively. The degree of variability was not related to the dose of agonist or the degree of nasal obstruction. 4. The reproducibility of histamine or allergen induced changes in NAR on four separate weekly occasions showed no significant intra-subject differences. 5. The effects of sodium cromoglycate (SCG), clemastine and ketotifen administered to the nasal mucosa 30 min before provocation with histamine and allergen were compared in a random order, double-blind, placebo controlled study. 6. Clemastine and SCG, but not ketotifen, significantly inhibited the nasal response to increasing concentrations of histamine. None of the drugs administered in the concentrations used in this study significantly inhibited the nasal response to allergen.
Simulating Cooperative Transportation Companies (1994)

In this paper we propose the use of methods from Distributed Artificial Intelligence for the simulation of complex economical and social Systems. Apart from [11], we stress the power that can be gained by applying mechanisms of coordination and cooperation among autonomous agents. As an example, the transportation domain is modeled as a multiagent scenario. Negotiation is used as a mechanism for achieving coordination among autonomous agents. We describe the different dimensions of cooperation and details of the simulation-system. Preliminary results are provided.
Monolithic FET structures for high-power control component applications (1989)

A monolithic FET switch is described that can be integrated with other monolithic functions or used as a discrete component in a microwave integrated circuit structure. This device increases the power-handling capability of the conventional single FET switch by an order of magnitude. It does this by overcoming the breakdown voltage limitation of the FET device. The design, fabrication and performance of two high-power control components using these circuits are described as examples of the implementation of this technology. They are an L-band terminated single-pole, single-throw (SPST) switch and an L-band limiter.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Asymmetric reduction of 7,8‐difluoro‐3‐methyl‐2H‐1,4‐benzoxazine. Synthesis of a key intermediate of (S)‐(‐)‐ofloxacin (DR‐3355) (1991)

Abstract An efficient, highly enantioselective synthesis of ( S )‐(‐)‐7,8‐difluoro‐2,3‐dihydro‐3‐methyl‐4 H ‐1,4‐benzoxazine, a key intermediate of ( S )‐(‐)‐ofloxacin, using various chiral sodium triacyloxyborohydrides as reducing agents is reported.