gebhart/patrepeval huggingface dataset:
Purification and characterization of rho-crystallin from Japanese common bullfrog lens. (1990)

In a previous paper, we reported that the partial amino acid sequence (225 residues) from the COOH terminus of rho-crystallin from European common frog lens shows 77% similarity to that of prostaglandin (PG) F synthetase, an aldo-keto reductase, from bovine lung (Watanabe, K., Fujii, Y., Nakayama, K., Ohkubo, H., Kuramitsu, S., Kagamiyama, H., Nakanishi, S., and Hayaishi, O. (1988) Proc. Natl. Acad. Sci. U.S.A. 85, 11-15). Here rho-crystallin was purified to apparent homogeneity from the eye lens of the Japanese common bullfrog (Rana catesbeiana) by four sequential chromatographies using Sephadex G-100, Red Sepharose, and dual Mono S. Two types of rho-crystallin, RHO-I and RHO-II, named according to their elution order from a Mono S column, are essentially identical in terms of immunochemical properties, amino acid composition, and partial amino acid sequence. But the NH2-terminal Thr of RHO-I is blocked with an acyl group, while that of RHO-II is free. Both crystallins as well as PGF synthetase are monomeric proteins with a molecular weight of about 35,000 and they have the ability to bind NADPH with a stoichiometry of 0.75 mol of cofactor/mol of protein. Although rho-crystallin does not cross-react with antibody against PGF synthetase, the NH2-terminal amino acid sequence (107 residues) of rho-crystallin shows 77% similarity to that of the enzyme. However, PGD2, PGE2, 9,10-phenanthrenequinone, p-nitrobenzaldehyde, DL-glyceraldehyde, D-glucuronic acid, D-glucose, D-xylose, menadione, p-nitroacetophenone, dihydroxyacetone, succinic semialdehyde, phenylglyoxal, and testosterone were not substrates for these crystallins. PGH2 9,11-endoperoxide reductase activities of RHO-I and RHO-II were 1.3 and 1.0 milliunits/mg of protein, respectively, which are only about 2% of that of bovine lung PGF synthetase. These results indicate that the rho-crystallins RHO-I and RHO-II belong to a group of aldo-keto reductases based on primary structure, molecular properties, and NADPH-binding ability, but show only low PGH2 9,11-endoperoxide reductase activity.
Spurious mode suppression via apodization for 1 GHz AlN Contour-Mode Resonators (2012)

This paper reports, for the first time, on the application of apodization techniques to 1 GHz MEMS AlN Contour-Mode Resonators (CMRs [1]) to efficiently suppress spurious modes in close proximity of the main mechanical resonance. This concept has been applied with excellent results to a variety of one port resonators formed by patterned top electrodes made out of Aluminum, and a floating bottom electrode made out of Platinum sandwiching the AlN film. As also predicted by 3D COMSOL simulations, a complete elimination of spurious responses in the admittance plot of these resonators is attained without impacting their quality factor and electromechanical coupling coefficient.
Supplementary Figure Legends from DiSCoVERing Innovative Therapies for Rare Tumors: Combining Genetically Accurate Disease Models with <i>In Silico</i> Analysis to Identify Novel Therapeutic Targets (2023)

&lt;p&gt;Legends for the supplementary figures&lt;/p&gt;
Chromophore Quench-Labeling: An Approach to Quantifying Catalyst Speciation As Demonstrated for (EBI)ZrMe2/B(C6F5)3-Catalyzed Polymerization of 1-Hexene (2016)

Chromophore-containing quench agents 2 and 3 enable quantitative active site counting and determination of the mass distribution of active catalyst polymeryls by refractive index (RI) and UV detected gel permeation chromatography (GPC) for the polymerization of 1-hexene catalyzed by (EBI)ZrMe2/B(C6F5)3. Time evolution of catalyst speciation data and the time profiles of monomer consumption, end-group generation, and bulk molecular weight distribution data have been analyzed by kinetic modeling to determine rate constants for initiation by insertion of hexene into a Zr–Me bond (ki), propagation (kp), chain transfer to form vinylidene (k1,2) and vinylene (k2,1) end groups, and reinitiation from a Zr–H bond (kr). Unlike previous models that assumed fast catalyst reinitiation, this analysis reveals that kr is considerably slower than kp; catalyst speciation data are critical to making this distinction. This study demonstrates that chromophore quench-labeling with 2 and 3 enables rapid, quantitative analysis of detailed kinetic models for catalytic olefin polymerization reactions using GPC with UV and RI detectors.
Peptidoglycan pathways: there are still more! (2019)

The discovery of 3<sup>rd</sup> and 4<sup>th</sup> generations of currently existing classes of antibiotics has not hindered bacterial resistance, which is escalating at an alarming global level. This review follows WHO recommendations through implementing new criteria for newly discovered antibiotics. These recommendations focus on abandoning old scaffolds and hitting new targets. In light of these recommendations, this review discusses seven bacterial proteins that no commercial antibiotics have targeted yet, alongside their reported chemical scaffolds.
Ali Ayten. Din ve Sağlık-Kavram, Kuram ve Araştırma (2019)

Ali Ayten. Din ve Sağlık-Kavram, Kuram ve Araştırma. İstanbul: Marmara Akademi Yayınları, 2018, 165 s.
Characterization of Genetic Loci That Affect Susceptibility to Inflammatory Bowel Diseases in African Americans (2020)

Inflammatory bowel disease (IBD) has familial aggregation in African Americans (AAs), but little is known about the molecular genetic susceptibility. Mapping studies using the Immunochip genotyping array expand the number of susceptibility loci for IBD in Caucasians to 163, but the contribution of the 163 loci and European admixture to IBD risk in AAs is unclear. We performed a genetic mapping study using the Immunochip to determine whether IBD susceptibility loci in Caucasians also affect risk in AAs and identify new associated loci.
Barcoding quarantine nematodes and their close relatives: an update on the status of the QBOL-project (2011)

BARCODING QUARANTINE NEMATODES AND THEIR CLOSE RELATIVES: AN UPDATE ON THE STATUS OF THE QBOL-PROJECT Martijn H.M. HOLTERMAN1, Jürg E. FREY1, Hans HELDER2, Paul J.W. MOOYMAN2 & Sebastion KIEWNICK1 1 Agroscope Changins-Wädenswil Schloss, CH-8820 Wädenswil, Switzerland 2 Laboratory of Nematology, Wageningen University Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands Identification of plant pests, in particular quarantine species, needs to be fast and accurate to enable timely plant protection measures. In addition, a false diagnosis can cause serious financial losses for trade and producers. It is now well established that genetically based diagnosis is a reliable alternative to the classical identification procedures generally based on morphological features, which usually require expert taxonomic skills. On the other hand, genetic diagnosis through the use of so-called DNA-barcodes, stretches of DNA that contain taxon-specific information, can be performed by any skilled lab-worker. The European Union 7th framework program QBOL aims to establish DNA-barcodes for all European quarantine organisms as well as their close relatives and disseminate the results and protocols in a publicly available and curated database. To enable genetically based identification requires knowledge of the genetic variation both within and between the species of interest as well as their close relatives. Several gene regions (the COI, COII, SSU, LSU and RNA polymerase subunit II) are being evaluated for their barcoding potential. An update on the current status of the nematode part of QBOL will be provided as well as an example case of the genus Meloidogyne.
Manipulation and dynamic mechanical testing of microscopic objects using a tele-micro-robot system (2003)

A microrobot having two high-performance parallel drive limbs has been developed for manipulation, surgery, and dynamic mechanical testing of very small objects such as single living cells. The end-points of each limb move in overlapping spherical workspaces of 1 mm diameter with minimum open- and closed-loop movements of 1 nm and 10 nm, respectively. With optimal nonlinear model-based controllers the limbs can move at up to 2 m/s relative to each other. A variety of end effectors, including ferroelectric polymer microgrippers, may be attached to the limbs to permit cell manipulation. A 3D laser vision system with resolution of 50 to 100 nm has been developed to provide the microrobot with volume images containing magnitude, phase, polarization, and special information. A macro version of the microrobot has been built to enable force-reflecting teleoperation of the microrobot. The telemicrorobot system permits both microscopic objects and continuum models to be felt. A high-performance parallel computer has been designed to meet the substantial computational and control requirements of the system.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
NS 1231, a novel compound with neurotrophic‐like effects in vitro and in vivo (2002)

NS 1231 [5-(4-chlorophenyl)-6,7,8,9-tetrahydro-1H-pyrrolo-[3.2-h]naphthalene-2,3-dione-3-oxime] belongs to a chemical series of compounds, which exhibit neurotrophic-like activities. In vitro, NS 1231 rescued nerve growth factor (NGF)-differentiated PC12 cells from death induced by withdrawal of trophic factors. In addition, NS 1231 stimulated NGF-induced neurite outgrowth of undifferentiated PC12 cells. At the molecular level, NS 1231 enhanced NGF-induced signalling events, such as TrkA phosphorylation at the Shc-binding site Tyr490 as well as ERK activation in PC12 cells. Moreover, NS 1231 reduced NMDA-induced excitotoxicity in organotypic hippocampal slice cultures. In a gerbil model of transient global ischaemia, treatment with NS 1231 reduced the delayed loss of neurons in the hippocampal CA1 layer. Furthermore, NS 1231 treatment resulted in a 43% reduction in total infarct volume in the mouse middle cerebral artery occlusion (MCAO) model. The present data thus implicate a therapeutic potential of NS 1231 or structural analogues in treatment of cerebral ischaemia.
A General Method for Imine Formation Using B(OCH2CF3)3 (2015)

Tris(2,2,2-trifluoroethyl)borate [B(OCH2CF3)3] was found to be a mild and general reagent for the formation of a variety of imines by condensation of amides or amines with carbonyl compounds. N-Sulfinyl, N-toluenesulfonyl, N-(dimethylamino)sulfamoyl, N-diphenylphosphinoyl, N-(α-methylbenzyl), and N-(4-methoxyphenyl) aldimines are all accessible using this reagent at room temperature. The reactions are operationally simple, and the products are obtained without special workup or isolation procedures.
Withdrawal of Immunosuppression in Pediatric Liver Transplant Recipients in Korea (2009)

The favorable markers for successful withdrawal of immunosuppression were 1) long-term (> 3 years) stable graft function, 2) no rejection for longer than 1 year after withdrawal of immunosuppression, 3) non-immune mediated liver diseases, and 4) pediatric patients.
Cold-Hardiness in the Antarctic Tick, Ixodes uriae (1987)

Ixodes uriae White (Ixodidae, Acarina) is the predominant tick on the Antarctic peninsula. This species has a circumpolar distribution in both hemispheres and is associated with or known to parasitize 48 species of seabirds. Large colonies of 1,000 or more individuals of all life stages were found beneath rocks on the periphery of Adélie penguin rookeries near Palmer Station, Anvers Island. All life stages (egg, larva, nymph, and adult) were intolerant of freezing. Engorged nymphs and larvae had supercooling points between -18 and -20 C. Eggs had the lowest supercooling points (-28.7 C), while adults had the highest values (from -7 to -13 C). Acclimation to temperatures between -12 and +25 C for 2 wk had no effect on the supercooling point of engorged immobile nymphs. Desiccation of engorged nymphs to 80% of their initial weight resulted in no change in supercooling points or glycerol levels. In January, engorged nymphs enter a state of apolysis and lose mobility. Correlated with this change is an increase in cold tolerance as evidenced by a decrease in supercooling points from -11.5 to -19.5 C. This species exhibits the greatest range of thermal tolerance, from -30 to 40 C, reported for any Antarctic terrestrial arthropod. Except for a short period associated with feeding, I. uriae remains in a permanent state of cold-hardiness throughout the year.
The Effect of Scale, Climate and Environment on Species Richness and Spatial Distribution of Finnish Birds (2011)

We used 10-km grid data from the Finnish Bird Atlas data and high-resolution data on temperature and rainfall to estimate species richness from climate and environmental variables across spatial scales. We used an ordinary least-squares (OLS) linear-regression model with a quadratic error function to estimate the number of bird species that occur. As a baseline, we used a simple dummy model that estimated the number of species in each grid to be the average number of species over all grids. We found that the best estimator for avian species richness in Finland is the length of the growing season with R2 values from 0.5 to 0.8, depending on the scale. Our results support the energy-water hypothesis, and we suggest that the proximate control of species richness in the present case is productivity, which is in turn controlled by climate. Some of the effects conventionally attributed to scaling may have trivial causes associated with sampling, in particular the completion of missing data as primary units of observation are merged. For broad surveys of patterns, medium resolution may often be adequate and even superior to the highest nominal resolution available.
Cryopreservation of infectious Cryptosporidium parvum oocysts (2018)

Cryptosporidiosis in an enteric infection caused by Cryptosporidium parasites and is a major cause of acute infant diarrhea in the developing world. A major bottleneck to research progress is the lack of methods to cryopreserve Cryptosporidium oocysts, thus requiring routine propagation in laboratory animals. Here, we report a method to cryopreserve C. parvum oocysts by ultra-fast cooling. Cryopreserved oocysts exhibit high viability and robust in vitro excystation, and are infectious to interferon-γ knockout mice. The course of the infection is comparable to what we observe with unfrozen oocysts. Oocyst viability and infectivity is not visibly changed after several weeks of cryogenic storage. Cryopreservation will facilitate the sharing of oocysts from well-characterized isolates and transgenic strains among different laboratories.
H2O2-mediated permeability II: importance of tyrosine phosphatase and kinase activity (2001)

We previously reported that exposure of endothelial cells to H(2)O(2) results in a loss of cell-cell apposition and increased endothelial solute permeability. The purpose of this study was to determine how tyrosine phosphorylation and tyrosine phosphatases contribute to oxidant-mediated disorganization of endothelial cell junctions. We found that H(2)O(2) caused a rapid decrease in total cellular phosphatase activity that facilitates a compensatory increase in cellular phosphotyrosine residues. H(2)O(2) exposure also results in increased endothelial monolayer permeability, which was attenuated by pp60, an inhibitor of src kinase. Inhibition of protein tyrosine phosphatase activity by phenylarsine oxide (PAO) demonstrated a similar permeability profile compared with H(2)O(2), suggesting that tyrosine phosphatase activity is important in maintaining a normal endothelial solute barrier. Immunofluorescence shows that H(2)O(2) exposure caused a loss of pan-reactive cadherin and beta-catenin from cell junctions that was not blocked by the src kinase inhibitor PP1. H(2)O(2) also caused beta-catenin to dissociate from the endothelial cytoskeleton, which was not prevented by PP1. Finally, we determined that PP1 did not prevent cadherin internalization. These data suggest that oxidants like H(2)O(2) produce biological effects through protein phosphotyrosine modifications by decreasing total cellular phosphatase activity combined with increased src kinase activity, resulting in increased endothelial solute permeability.
Mitochondrial Targeting of a Catalase Transgene Product by Plasmid Liposomes Increases RadioresistanceIn VitroandIn Vivo (2009)

To determine whether increased mitochondrially localized catalase was radioprotective, a human catalase transgene was cloned into a small pSVZeo plasmid and localized to the mitochondria of 32D cl 3 cells by adding the mitochondrial localization sequence of MnSOD (mt-catalase). The cell lines 32D-Cat and 32D-mt-Cat had increased catalase biochemical activity as confirmed by Western blot analysis compared to the 32D cl 3 parent cells. The MnSOD-overexpressing 32D cl 3 cell line, 2C6, had decreased baseline catalase activity that was increased in 2C6-Cat and 2C6-mt-Cat subclonal cell lines. 32D-mt-Cat cells were more radioresistant than 32D-Cat cells, but both were radioresistant relative to 32D cl 3 cells. 2C6-mt-Cat cells but not 2C6-Cat cells were radioresistant compared to 2C6 cells. Intratracheal injection of the mt-catalase-plasmid liposome complex (mt-Cat-PL) but not the catalase-plasmid liposome complex (Cat-PL) increased the resistance of C57BL/6NHsd female mice to 20 Gy thoracic irradiation compared to MnSOD-plasmid liposomes. Thus mitochondrially targeted overexpression of the catalase transgene is radioprotective in vitro and in vivo.
From Sulfur−Amine Solutions to Metal Sulfide Nanocrystals: Peering into the Oleylamine−Sulfur Black Box (2011)

In this Article, we present our findings on the formation of metal sulfide nanocrystals from sulfur-alkylamine solutions. By pulsed field gradient diffusion NMR along with the standard toolbox of 1D and 2D NMR, we determined that sulfur-amine solutions used as a sulfur precursor exist as alkylammonium polysulfides at low temperatures. Upon heating to temperatures used in nanocrystal synthesis, the polysulfide ions react with excess amine to generate H(2)S, which combines with the metal precursor to form metal sulfide. Four different reaction pathways were found, each of which produced H(2)S and the byproducts identified in this Article. Thioamides were identified as an intermediate and were shown to exhibit much more rapid kinetics than sulfur-alkylamine solutions at low temperatures in the synthesis of metal sulfide nanocrystals.
Cenicriviroc Lacked Efficacy to Treat Liver Fibrosis in Nonalcoholic Steatohepatitis: AURORA Phase III Randomized Study (2023)

This study did not demonstrate the efficacy of CVC for treating liver fibrosis assessed by histology in adults with NASH; however, CVC was safe and well tolerated in patients with NASH and liver fibrosis. (ClinicalTrials.gov, Number: NCT03028740).
The computation of magnetic fields of permanent magnet cylinders used in the electrophotographic process (1993)

General analytic expressions for the magnetic field distributions created by permanent magnet cylinders are derived in this paper. These expressions take into account a finite slope of the B-H loop in the second quadrant, and they are valid for arbitrary magnetization patterns within the cylinders. They can be used for parametric studies of field strength and can also be used to test new and existing numerical techniques for computing the field due to permanent magnet materials. The theoretical discussion is illustrated by some sample calculations.
Arylphthalazines: Identification of a New Phthalazine Chemotype as Inhibitors of VEGFR Kinase. (2006)

Abstract For Abstract see ChemInform Abstract in Full Text.
Stream I/O (2016)

The C++ stream-based I/O library allows you to perform I/O operations without having to know details about the target to or source from which you are streaming. A stream’s target or source could be a string, a file, a memory buffer, and so on.
Frustratingly Easy Natural Question Answering (2019)

Existing literature on Question Answering (QA) mostly focuses on algorithmic novelty, data augmentation, or increasingly large pre-trained language models like XLNet and RoBERTa. Additionally, a lot of systems on the QA leaderboards do not have associated research documentation in order to successfully replicate their experiments. In this paper, we outline these algorithmic components such as Attention-over-Attention, coupled with data augmentation and ensembling strategies that have shown to yield state-of-the-art results on benchmark datasets like SQuAD, even achieving super-human performance. Contrary to these prior results, when we evaluate on the recently proposed Natural Questions benchmark dataset, we find that an incredibly simple approach of transfer learning from BERT outperforms the previous state-of-the-art system trained on 4 million more examples than ours by 1.9 F1 points. Adding ensembling strategies further improves that number by 2.3 F1 points.
Supplementary Figure 2 from A 12-Gene Set Predicts Survival Benefits from Adjuvant Chemotherapy in Non–Small Cell Lung Cancer Patients (2023)

&lt;p&gt;PDF file - 200K, Summary of the prognostic performance for the 12 hub-gene set.&lt;/p&gt;
Floatover Deck Installation on Spars (2007)

Deck installation is always a major installation challenge for floating structures, particularly deep draft floaters like the spar which must be installed in relatively deep water. Derrick barges have been used for spar deck installations until now. The 4000 mt deck for the Kikeh Spar was successfully installed using the floatover method in November 2006, off the coast of Sabah in the South China Sea. This demonstrates the feasibility of this concept and opens the door for more floatover decks on spars in the future. This paper will review the technical challenges associated with this type of installation. In particular, the authors will review past studies, which included analysis and model testing of similar deck floatovers for decks up to 30,000 t, and the analysis methods use to validate the procedures and equipment which was successfully used on the Kikeh project. The requirements for application of this technology in the Gulf of Mexico will be highlighted.
Changes in Internal Pressure of Composite Film Packages by Their Drop Impact. (1994)

The consumption of plastic containers used for packing foods was steadily increased in recent years, and so was the percentage in industrial waste. Attracting attention under these circumstances is the composite film with which the consumption of plastics can be reduced to 1/3-1/10 in weight of that required for hard plastic containers and which can be compressed to small volume after use. The subject focused up here relates to flexible packages which facilitate economical utilization of plastics made from limited resources of petroleum and effective reduction of plastic wastes. In particular, dynamic experiments were conducted to determine the causes of breakage during transportation of the packages containing liquid, for different viewparameters points including temperature and internal pressure of contents, and to clarify interrelationships among physical characteristics of film, types of contents and external force, in an effort to establish safe and economical transportation of products.