gebhart/patrepeval huggingface dataset:
Simultaneous use of solution, solid-state NMR and X-ray crystallography to study the conformational landscape of the Crh protein during oligomerization and crystallization (2010)

We explore, using the Crh protein dimer as a model, how information from solution NMR, solid-state NMR and X-ray crystallography can be combined using structural bioinformatics methods, in order to get insights into the transition from solution to crystal. Using solid-state NMR chemical shifts, we filtered intra-monomer NMR distance restraints in order to keep only the restraints valid in the solid state. These filtered restraints were added to solid-state NMR restraints recorded on the dimer state to sample the conformational landscape explored during the oligomerization process. The use of non-crystallographic symmetries then permitted the extraction of converged conformers subsets. Ensembles of NMR and crystallographic conformers calculated independently display similar variability in monomer orientation, which supports a funnel shape for the conformational space explored during the solution-crystal transition. Insights into alternative conformations possibly sampled during oligomerization were obtained by analyzing the relative orientation of the two monomers, according to the restraint precision. Molecular dynamics simulations of Crh confirmed the tendencies observed in NMR conformers, as a paradoxical increase of the distance between the two β1a strands, when the structure gets closer to the crystallographic structure, and the role of water bridges in this context.
Role of Marine Metabolites in Shrimp Growth, Production and Disease Prevention (2017)

This review consolidates the recent information about the global aquaculture production status of fish andshellfish. Research reports on common and emerging microbial diseases of cultivable species of shrimp arenarrated together with resultant reductions in productivity. The harmful effects antibiotics usage in shrimpaquaculture and consequent effects on the species as well as ecosystem are highlighted. The in vitro and invivo tests of extracts containing metabolites isolated from marine macroalgae, sea grasses and invertebrates inrestraining the proliferation of disease causing microbes are presented. The metabolite bearing marine speciesand methods of extraction of marine metabolites are concisely indicated. Studies on unique bacteriaassociated with the metabolite - bearing marine organisms, their identity and their significance in metaboliteproduction are essential for future research and developmental activities in aquaculture and pharmaceuticalapplications. The administration of marine metabolites in the post larval and juvenile shrimps as feed additivefor controlling the common microbial diseases such as vibriosis together with essential administrationprotocols are reported. Many of the tested marine metabolites are of immense use as they increased thesurvival of farm reared shrimps and their growth rates. The resultant specific growth rate attained togetherwith survival contributed to the significant increase in production. Perusal of literature indicated that marinesecondary metabolites isolated from marine macro algae and sponges exhibited immune enhancing activity inshrimps in a non specific manner when administered as a feed ingredient.
Factorization homology and applications (introductory lecture) (2019)

Factorization algebras, and factorization homology, began in the work of Beilinson-Drinfeld, as an algebro-geometric/coordinate-free approach to vertex algebras and conformal blocks, respectively. They were re-interpreted by Costello-Gwilliam as a framework for algebras of observables in quantum field theory. A special class, the so-called "locally constant" factorization algebras received special attention from Lurie, Ayala-Francis, and Scheimbauer in the context of fully extended topological field theories. In the first lecture I shall recall this history, define factorization homology in the mold of Ayala-Francis, and recall the key property of excision, which both uniquely determines factorization homology as a functor, and gives an effective mechanism for its computation. In the second lecture, I will turn to examples in geometry and representation theory, following Ben-Zvi-Francis-Nadler, and our works with Ben-Zvi-Brochier and Brochier-Snyder. Specializing the "coefficients" to lie in presentable k-linear categories (the natural home of algebraic geometry and representation theory), one recovers character varieties, and their canonical quantizations, as a computation in factorization homology.
Reduction of the memory requirements for the VLSI implementation of the 2D-inverse fast wavelet transform, using a space-filling curve (2002)

Since wavelet based codecs seem to be a promising alternative to the classically used block-transform based codecs, it is important to take a look at the hardware implementation constraints that are imposed by such multiresolution architectures. We show that by reorganising the data order within the 2D-FWT and taking the causality relation between the 2D-FWT and 2D-IFWT into account, the memory requirements and latencies for practical 2D-FWT/2D-IFWT compression/decompression schemes are minimised by using specific 2D fractal space-filling image scan curves.
Single Molecule Trapping and Sensing Using Dual Nanopores Separated by a Zeptoliter Nanobridge (2017)

There is a growing realization, especially within the diagnostic and therapeutic community, that the amount of information enclosed in a single molecule can not only enable a better understanding of biophysical pathways, but also offer exceptional value for early stage biomarker detection of disease onset. To this end, numerous single molecule strategies have been proposed, and in terms of label-free routes, nanopore sensing has emerged as one of the most promising methods. However, being able to finely control molecular transport in terms of transport rate, resolution, and signal-to-noise ratio (SNR) is essential to take full advantage of the technology benefits. Here we propose a novel solution to these challenges based on a method that allows biomolecules to be individually confined into a zeptoliter nanoscale droplet bridging two adjacent nanopores (nanobridge) with a 20 nm separation. Molecules that undergo confinement in the nanobridge are slowed down by up to 3 orders of magnitude compared to conventional nanopores. This leads to a dramatic improvement in the SNR, resolution, sensitivity, and limit of detection. The strategy implemented is universal and as highlighted in this manuscript can be used for the detection of dsDNA, RNA, ssDNA, and proteins.
ChemInform Abstract: SYNTHESIS OF 12‐ALKYL ANALOGS OF PROSTAGLANDIN‐A2 (1979)

Abstract Durch eine regiospezifische Reduktion von (I) mit anschließender Acetylierung entsteht das Acetat (II), dessen Bromierung mit N‐Brom‐succinimid in 99%iger Ausbeute zu einem Gemisch der Dihalogenide (III) und (IV) führt.
Serum demyelinating factors in multiple sclerosis (1983)

Sera from 21 patients with multiple sclerosis were applied to myelinated spinal cord cultures and evaluated for demyelinating activity. Samples were collected at various times when patients were on or off therapy with myelin basic protein or prednisone or both, and at various stages of disease. Five of 31 serum samples from 17 patients exhibited demyelinating activity when tested in a 40% concentration in tissue culture nutrient medium. Four of the 10 serum samples taken from patients with active or remitting multiple sclerosis (2 samples from the same patient) were demyelinative; 1 of 21 sera collected during stationary periods of disease was positive. There was no correlation between serum demyelinating activity and the presence or absence of treatment. Sera positive for demyelinating activity failed to inhibit myelin formation in initially unmyelinated cerebellar cultures.
Coding unstable scalar markov processes into two streams (2004)

This paper describes the encoding of a scalar unstable Markov process into two parallel fixed-rate bit streams. Source coding theorems for stable Markov and Gaussian auto-regressive processes (ARMA process) under mean-squared-error distortion used in calculating a standard information-theoretic rate-distortion function.
WWW 2008 workshop (2008)

The amount of information available on the Web has increased rapidly, reaching levels that few would ever have imagined possible. We live in what could be called the "information-explosion era," and this situation poses new problems for computer scientists. Users demand useful and reliable information from the Web in the shortest time possible, but the obstacles to fulfilling this demand are many including language barriers and the so-called "long tail." Even worse, users may provide only vague specifications of the information that they actually want, so that a more concrete specification must somehow be inferred by Web access tools. Natural language processing (NLP) is one of the key technologies for solving the above Web usability problems. Almost all the Web page provide with the essential information in the form of natural language texts, and the amount of these text information is huge. In order to offer solutions to these problems we must perform searching and extracting information from the Web texts using NLP technologies. The aim of this workshop: NLP Challenges in the Information Explosion Era (NLPIX 2008) is to bring researchers and practitioners together in order to discuss our most pressing needs with respect to accessing information on the Web, and to discuss new ideas in NLP technologies that might offer viable solutions for those issues.
Curvature effects on electric double-layer forces. Part 1.—Comparisions with parallel geometry (1995)

Electrostatic interactions of electric double layers bounded by curved surfaces are studied using a combination of analytical and computational methods. Unlike the case of two parallel plates, the electric double-layer force inside spherical cavities or cylindrical pores is predicted to diverge as the surface potential goes to infinity. For typical values of surface potential, the double-layer forces for curved surfaces are found to be significantly larger than the corresponding force between two parallel plates for most values of salt concentration and separation distance.
A graphical interval logic for specifying concurrent systems (1994)

This article describes a graphical interval logic that is the foundation of a tool set supporting formal specification and verification of concurrent software systems. Experience has shown that most software engineers find standard temporal logics difficult to understand and use. The objective of this article is to enable software engineers to specify and reason about temporal properties of concurrent systems more easily by providing them with a logic that has an intuitive graphical representation and with tools that support its use. To illustrate the use of the graphical logic, the article provides some specifications for an elevator system and proves several properties of the specifications. The article also describes the tool set and the implementation.
A Pilot Study of Mifepristone in Combat-Related PTSD (2012)

Background. We obtained pilot data to examine the clinical and neuroendocrine effects of short-term mifepristone treatment in male veterans with PTSD. Methods. Eight male veterans with military-related PTSD completed a randomized, double-blind trial of one week of treatment with mifepristone (600 mg/day) or placebo. The primary clinical outcome measures were improvement in PTSD symptoms and dichotomously defined clinical responder status as measured by the CAPS at one-month follow-up. Additional outcome measures included self-reported measures of PTSD symptom severity, CAPS-2 symptom subscale scores, and morning plasma cortisol and ACTH levels. Results. Mifepristone was associated with significant improvements in total CAPS-2 score. At one-month follow-up, all four veterans in the mifepristone group and one of four veterans in the placebo group achieved clinical response; three of four veterans in the mifepristone group and one of four veterans in the mifepristone group remitted. Mifepristone treatment was associated with acute increases in cortisol and ACTH levels and decreases in cytosolic glucocorticoid receptor number in lymphocytes. Conclusions. Further controlled trials of the effects of mifepristone and their durability are indicated in PTSD. If effective, a short-term pharmacological treatment in PTSD could have myriad uses.
Observations on the circadian activity and seasonal prevalence of Telmatoscopus albipunctatus Williston (Psychodidae : Diptera) (1976)

Larvae of the moth fly, Telmatoscopus albipunctatus, were most active at about midnight and moderately active during the light period in the laboratory. Adult flies in captivity showed similar activity rhythm to that of the larvae. An observation in the field revealed that catch size of adult flies escaping a septic tank was maximum around sunset; the percentage of female flies decreased and the gravid rate increased in phase with the active time of the escaping flies. Eight species of moth flies were collected in a hen-house in a residential area of Nagoya City, among which Psychoda alternata and T. albipunctatus were most abundant (99.3%). The prevailing periods of these two moth flies were fairly segregated from each other : T. albipunctatus prevailed in the warmer months of August and September, while P. alternata from May to July. Both the percentage of female and the gravid rate were higher in P. alternata during the studing period. The adult flies in the septic tank were observed to die out in the winter months and the aquatic population seemed to overwinter mainly as the fourth instar larvae.
Impact of a Prospective Review Program for Reference Laboratory Testing Requests (2015)

Formal prospective review of reference laboratory testing requests resulted in substantial cost containment and improved the efficiency of patient care.
De potentiële natuurwaarde van de EHS; natuurwaardering op basis van abiotische omstandigheden; het Natuur Technisch Model (1998)

Een standplaatsmodel voor natuurwaardering (NTM)
Gold‐Catalyzed Direct Oxidative Arylation with Boron Coupling Partners (2016)

Abstract An efficient synthesis of biaryls through a gold‐catalyzed oxidative cross‐coupling of arenes with strong electron‐deprived aryl boronates is presented herein. Regio‐ and chemocontrol are achieved by the selective activation of these coupling partners by gold at different oxidation states. Under reaction conditions devoid of basic additives or directing groups, the role of acetato ligand as an internal base has been revealed as a key parameter for expanding the reaction scope in these transformations.
Pulsatile Blood Flow in a Stenosed Artery (1997)

Abstract Unsteady axisymmetric flow in a constricted tube is studied. A shear-thinning model for viscosity of the blood is proposed. The motion equation is written in vorticity-streamfunction formulation and is integrated numerically by a finite difference scheme. The dependence of the flow on the dimensionless parameters has been investigated and differences with the newtonian case are discussed.
Hydroxylamine as an oxygen nucleophile. Chemical evidence from its reaction with a phosphate triester (2008)

The reaction of hydroxylamine with 2,4-dinitrophenyl diethyl phosphate gives the O-phosphorylated product, which is rapidly converted to hydrazine and nitrogen gas in the presence of the excess of hydroxylamine.
Short-term pacing in the mouse alters cardiac expression of connexin43 (2008)

Our data suggest that short-term pacing is associated with incipient changes in the expression of the connexin43 gap junction, possibly including decreased production and a slowed rate of degradation. This murine model may facilitate the study of early molecular changes induced by pacing and may ultimately assist in the development of strategies to prevent gap junction remodeling and the associated arrhythmic complications of cardiac disease.
Bioremediation of crude oil contaminated soil by Pseudomonas aeruginosa strain-O2 and Micrococcus varians strain-X with different approaches (2013)

The efficiency of two bacterial candidates namely; Pseudomonas aeruginosa strain-O2 and Micrococcus varians strain-X, in degradation of crude oil extracted fromcontaminated sediment samples was evaluated. GC-analysis of the degradation products indicated that both strains were able to use crude oil as carbon and energy source.Aliphatic hydrocarbon fraction of the sediment extract, especially long chain alkanes (n-C22+), was degraded. For aromatic hydrocarbon fraction, namely methyl naphthalene compound, both strains were able to degrade 2,3,6- and 1,2,5- trimethyl naphthalenes to a comparable extent. Only P. aeruginosa strain- O2 was able to utilize 1,3,7- trimethyl naphthalene, whileM. varians strain- X was able to use 1,2,4- trimethyl naphthalene as a sole C-source. Application of different strategies in bioremediation of sea sand contaminated with 10%crude oil indicated that the bioaugmentation with mixed culture of both strains was the optimal treatment strategy (approximately 93.45%).While, treatment applying either one of the two strains indicated that M. varians strain-X is more efficient in crude oil degradation. Comparable to that of natural conditions, biostimulation resulted in limited crude oil removal (approximately 36.42%). Results collectively indicated that the bacterial strains used in this study were suitable candidates for practical field application and in situ bioremediation, namely by bioaugmentation.
An archive of high‐resolution temperature reconstructions over the past 2+ millennia (2010)

High‐resolution temperature reconstructions (typically annually to seasonally resolved) have played a key role in understanding paleoclimate immediately prior to the beginning of the instrumental record, especially when calibrated to form an extension of comparable instrumental data coverage (global, hemispheric, and regional). Such calibration allows the information in the instrumental record to be quantitatively extended backward in time in an objective way, enabling description of much longer term fluctuations in climate than possible with instrumental data alone, although with significantly increased uncertainties inherent in proxy‐based reconstructions. This data brief describes a newly integrated archive of nearly all the high‐resolution temperature reconstructions of the past 2+ millennia included in NOAA's National Climatic Data Center, from small‐regional to global scale, which also have been recalibrated to a standard set of instrumental data. Examination of the spectral structure of the data is additionally provided.
Significance of tumor biology compared to metastatic pattern (INSS 4 versus 4s) and age for prognosis of neuroblastoma less than 18 months of age (2009)

10010 Background: Neuroblastoma is a heterogeneous disease with variability in outcome among different risk groups. Historically, INSS stage 4s neuroblastoma (age less than 12 months, stage 1 or 2 primary tumor with metastases limited to liver, skin and bone marrow) has a more favorable outcome than infant stage 4 disease. The aim was to determine if metastatic pattern (4 vs 4s) predicted favorable prognosis in infants < 12 months or in toddlers aged 12–18 months when stratifying by biology. Methods: Outcome was analyzed by log rank tests and Cox models for 656 infants with stage 4s neuroblastoma and 1,019 stage 4 patients < 18 months of age in the International Neuroblastoma Risk Group database (n=8,800). Prognostic factors (tumor ploidy, histology, grade, MKI, LDH, MYCN, 11q, 1p, primary site) were tested for association with age/stage subgroups (Fisher's exact test) and in Cox models. Results: MYCNamplification, 1p aberration, diploidy, and high MKI and LDH were more frequent in infant stage 4 than infant 4s tumors. The incidence of unfavorable biology was higher in toddlers aged 12–18 months, but did not differ with stage 4 vs. 4s pattern. EFS was significantly better for infants <12 months with stage 4s than stage 4 (p=0.0004). EFS was similar for toddlers 12–18 months for stage 4 vs. 4s pattern (p=0.3893). Within the 717 patients with 4s pattern of metastases, age 12–18 months had worse EFS than <12 months (p<0.0001). After adjustment for age in 6 separate models, MYCN, 11q, 1p, MKI, and LDH were statistically significant prognostic factors. Although treatment regimens differed, EFS was similar for <12 months vs. 12–18 months for MYCN not amplified patients in both 4S pattern (p=0.8469) and stage 4 (p=0.3783). Conclusions: For patients with MYCN not amplified tumors, outcome for patients 12–18 months is similar to those <12 months regardless of the pattern of metastases. Tumor biology is more critical than metastatic pattern for prognosis of patients aged 12–18 months with stage 4 neuroblastoma. [Table: see text] No significant financial relationships to disclose.
A prospective evaluation of plain radiographic signs of chronic obstructive pulmonary disease (1991)

Plain film signs of COPD, spirometric evidence of airflow obstruction, and smoking history were correlated in a group of 182 men aged 32 to 85 years (average, 57.5 years) who presented for evaluation of possible pulmonary disability. There were 148 current or past smokers (range, 0.66 to 150 pack-years; average, 31.89 pack-years) and 34 lifetime nonsmokers. A single observer, who had no knowledge of the other parameters, prospectively evaluated posteroanterior chest radiographs for 11 signs of COPD. Airflow obstruction was defined as a reduction in FEV1/FVC% below the 95% confidence limit of normal. Obstruction was classified on the basis of the reduction in FEV1 as mild (FEV1 greater than 2.5L), moderate (FEV1 greater than 1.0 L and less than 2.5 L), or severe (FEV1 less than 1.0 L). Spirometric evidence of airflow obstruction was present in 67 patients; obstruction was mild in 26, moderate in 36, and severe in 5. We found a statistically significant association between smoking and airflow obstruction on spirometry (P less than 0.001) and an equally significant association between smoking and radiographic signs of COPD on plain chest films (P less than 0.001). Both airflow obstruction and radiologic signs of COPD were generally absent in lifetime nonsmokers. The plain film signs of COPD were only of moderate value in predicting spirometric evidence of airflow obstruction in smokers; spirometric evidence is not the gold standard for the presence of COPD, however, and the strong association between smoking and these radiologic signs may indicate that in smokers the presence of plain film signs of COPD reflects morphologic abnormality in the lungs indicative of disease.(ABSTRACT TRUNCATED AT 250 WORDS)
<i>Trichogramma ostriniae</i> (Hymenoptera: Trichogrammatidae) response to relative humidity with and without host cues (2017)

Trichogramma ostriniae is a parasitoid wasp species that is used as a biological control for several lepidopteran agricultural pests. Our study examined the effects of relative humidity (RH) on the behaviour of female T. ostriniae. In Y-tube RH choice assays, wasps generally chose higher RH over lower RH but the latency time taken to make a choice displayed no clear patterns that could be ascribed to the magnitude of the RH difference between arms of the Y-tube. In trials conducted in glass arenas with fixed humidities, the conditional probabilities of transition from searching to interacting with the leaf disk, and from interacting with leaf disks to antennal egg drumming and oviposition, were not significantly different among the RH levels, nor were there differences in latency times. These findings suggest that the level of RH may influence habitat choice but have little effect on search efficacy.