gebhart/patrepeval huggingface dataset:
Hedging Bets on Hard Problems (1997)

Solving certain problems in computer science is a gamble: There's no way to know in advance how long an algorithm will take to yield an answer. In this issue (see page 51 ), a group of researchers presents a technique for bettering the odds by imitating Wall Street: splitting the computer's investment among a “portfolio” of different programs in the hope that one of them will get lucky.
Evaluation of the drug-polymer interaction in calcium alginate beads containing diflunisal. (2010)

Calcium alginate gel beads have been developed in recent years as a unique vehicle for oral drug delivery due to their excellent biocompatibility, biodegradability, simple method of preparation, abundant sources, low cost and minimal processing requirements. The objective of this study was to evaluate the drug-polymer interaction in calcium alginate beads containing diflunisal. Diflunisal loaded calcium alginate beads were successfully prepared by ionotropic gelation from solution of sodium alginate and diflunisal into calcium chloride solution. The weight ratio of drug to polymer was selected as 1:1. The calcium alginate beads were characterized by size, Scanning Electron Microscopy (SEM), weight uniformity and drug entrapment efficiency. The existence of a possible interaction between diflunisal and the calcium alginate was investigated by Differential Scanning Calorimetry (DSC), Powder X-Ray Diffraction (PXRD) and Fourier Transform Infra-Red (FTIR) analysis. Drug loaded beads were spherical to oval in shape with low drug entrapment efficiency. The drug was found to be present inside the beads as crystalline to semicrystalline form with no significant physical or chemical interaction between drug and excipients. The results implied that calcium alginate beads can be used as a suitable controlled release carrier for diflunisal.
Using B cell receptor lineage structures to predict affinity (2020)

ABSTRACT We are frequently faced with a large collection of antibodies, and want to select those with highest affinity for their cognate antigen. When developing a first-line therapeutic for a novel pathogen, for instance, we might look for such antibodies in patients that have recovered. There exist effective experimental methods of accomplishing this, such as cell sorting and baiting; how-ever they are time consuming and expensive. Next generation sequencing of B cell receptor (BCR) repertoires offers an additional source of sequences that could be tapped if we had a reliable method of selecting those coding for the best antibodies. In this paper we introduce a method that uses evolutionary information from the family of related sequences that share a naive ancestor to predict the affinity of each resulting antibody for its antigen. When combined with information on the identity of the antigen, this method should provide a source of effective new antibodies. We also introduce a method for a related task: given an antibody of interest and its inferred ancestral lineage, which branches in the tree are likely to harbor key affinity-increasing mutations? These methods are implemented as part of continuing development of the partis BCR inference package, available at https://github.com/psathyrella/partis . Comments . Please post comments or questions on this paper as new issues at https://git.io/Jvxkn .
Powerful quasars with young jets in multi‐epoch radio surveys (2021)

Abstract Energetic feedback driven by the large‐scale (100's of kpc) lobes of classical radio galaxies is known to play an important role in shaping galaxy evolution. However, the prevalence of young and compact jets – and their impact on the interstellar medium – remains an open question. Multi‐epoch radio surveys with cadences of years to decades offer a promising means of identifying even faint (mJy‐level) jets that are compact and potentially young on the basis of variability. Recently, a comparison of images from the Very Large Array Sky Survey (VLASS) and the Faint Images of the Radio Sky at Twenty Centimeters (FIRST) survey has revealed a population of distant ( ) quasars that have brightened dramatically in the past 1–2 decades. These quasars appear to have transitioned from “radio‐quiet” nondetections in FIRST to “radio‐loud” detections in VLASS. Extensive multiband follow‐up observations with the VLA from 1 to 18 GHz have revealed compact (sub‐kpc) radio sources that are consistent with young jets that were recently triggered. Here, we summarize the status of our on‐going study of quasars with newborn jets identified in the radio time domain.
Minimization of viral contamination in human pharmaceuticals produced in the milk of transgenic goats. (1996)

The minimization of viral contamination in therapeutic proteins produced in transgenic goats' milk can be achieved by a combinatorial approach. It begins with reduction in the risk in the starting material followed by appropriate clearance/inactivation steps in the purification process. To minimize risk in the starting material, Genzyme Transgenics Corporation (GTC)'s closed goat herds are subjected to routine serological surveillance for known viral diseases, especially those transmitted through milk. Although scrapie is defined as a slow-acting virus of sheep and goats, its incidence in goats in the US is rare (only four cases) and all four were in goats co-mingled with scrapie-infected sheep. All GTC's domestic goats were selected for previous non-exposure to sheep, cows or scrapie. In addition, milk, which is the starting material for transgenic protein production, is categorized as non-infectious for prions. Standard operating procedures are in place at GTC Farm sites to minimize human, animal or vehicular vectoring of viral diseases and the transgenic production animals are milked according to high standard Good Agricultural Practices (GAP). The transgenic protein (ATIII) purification process contains steps that should provide a high level of viral reduction. Validation of viral and prion removal will also be undertaken.
A Genetic Algorithm for Optimizing the Label Ordering in Multi-label Classifier Chains (2013)

First proposed in 2009, the classifier chains model (CC) has become one of the most influential algorithms for multi-label classification. It is distinguished by its simple and effective approach to exploit label dependencies. The CC method involves the training of q single-label binary classifiers, where each one is solely responsible for classifying a specific label in l <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">l</sub> , ..., l <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">q</sub> . These q classifiers are linked in a chain, such that each binary classifier is able to consider the labels predicted by the previous ones as additional information at classification time. The label ordering has a strong effect on predictive accuracy, however it is decided at random and/or combining random orders via an ensemble. A disadvantage of the ensemble approach consists of the fact that it is not suitable when the goal is to generate interpretable classifiers. To tackle this problem, in this work we propose a genetic algorithm for optimizing the label ordering in classifier chains. Experiments on diverse benchmark datasets, followed by the Wilcoxon test for assessing statistical significance, indicate that the proposed strategy produces more accurate classifiers.
Distinct Plasma Bile Acid Profiles of Biliary Atresia and Neonatal Hepatitis Syndrome (2015)

Biliary atresia (BA) is a severe chronic cholestasis disorder of infants that leads to death if not treated on time. Neonatal hepatitis syndrome (NHS) is another leading cause of neonatal cholestasis confounding the diagnosis of BA. Recent studies indicate that altered bile acid metabolism is closely associated with liver injury and cholestasis. In this study, we systematically measured the bile acid metabolome in plasma of BA, NHS, and healthy controls. Liver bile acids were also measured using biopsy samples from 48 BA and 16 NHS infants undergoing operative cholangiography as well as 5 normal adjacent nontumor liver tissues taken from hepatoblastoma patients as controls. Both BA and NHS samples had significantly elevated bile acid levels in plasma compared to normal controls. BA patients showed a distinct bile acid profile characterized by the higher taurochenodeoxycholic acid (TCDCA) level and lower chenodeoxycholic acid (CDCA) level than those in NHS patients. The ratio of TCDCA to CDCA in plasma was significantly higher in BA compared to healthy infants (p < 0.001) or NHS (p < 0.001). The area under receiver operating characteristic curve for TCDCA/CDCA to differentiate BA from NHS was 0.923 (95% CI: 0.862-0.984). These findings were supported by significantly altered expression levels of bile acid transporters and nuclear receptors in liver including farnesoid X receptor (FXR), small heterodimer partner (SHP), bile salt export pump (BSEP), and multidrug resistant protein 3 (MDR3) in BA compared to NHS. Taken together, the plasma bile acid profiles are distinct in BA, NHS, and normal infants, as characterized by the ratio of TCDCA/CDCA differentially distributed among the three groups of infants.
Symbiosal® and lowering of blood pressure and reduced risk of hypertension: evaluation of a health claim pursuant to Article 14 of Regulation (EC) No 1924/2006 (2018)

Following an application from Han-Biotech GmbH, submitted for authorisation of a health claim pursuant to Article 14 of Regulation (EC) No 1924/2006 via the Competent Authority of Germany, the EFSA Panel on Dietetic Products, Nutrition and Allergies (NDA) was asked to deliver an opinion on the scientific substantiation of a health claim related to Symbiosal<sup>®</sup>, lowering of blood pressure and reduced risk of hypertension. The Panel considers that the food, Symbiosal<sup>®</sup>, which is the subject of the health claim, and the food, table salt, which Symbiosal<sup>®</sup> should replace, are sufficiently characterised. Lowering of blood pressure is a beneficial physiological effect. Increased blood pressure is a risk factor for hypertension. In weighing the evidence, the Panel took into account that one human study with some methodological limitations showed an effect of Symbiosal<sup>®</sup> on blood pressure in the context of a self-selected diet with a maximum of 3 g/day added salt. The Panel also took into account that no other human studies in which these results have been replicated were provided, that the animal studies did not support the results of the human study, that no evidence was provided in support of a mechanism by which Symbiosal<sup>®</sup> could induce a decrease in blood pressure upon oral consumption as compared to table salt <i>in vivo</i> in humans, and the low biological plausibility of the effect observed in the human intervention study. The Panel concludes that a cause and effect relationship has not been established between the consumption of Symbiosal<sup>®</sup> and lowering of blood pressure.
Preterm labor: One syndrome, many causes (2014)

Preterm birth is associated with 5 to 18% of pregnancies and is a leading cause of infant morbidity and mortality. Spontaneous preterm labor, a syndrome caused by multiple pathologic processes, leads to 70% of preterm births. The prevention and the treatment of preterm labor have been long-standing challenges. We summarize the current understanding of the mechanisms of disease implicated in this condition and review advances relevant to intra-amniotic infection, decidual senescence, and breakdown of maternal-fetal tolerance. The success of progestogen treatment to prevent preterm birth in a subset of patients at risk is a cause for optimism. Solving the mystery of preterm labor, which compromises the health of future generations, is a formidable scientific challenge worthy of investment.
Quantitative investigation of dose accumulation errors from intra-fraction motion in MRgRT for prostate cancer (2021)

Accurate spatial dose delivery in radiotherapy is frequently complicated due to changes in the patient's internal anatomy during and in-between therapy segments. The recent introduction of hybrid MRI radiotherapy systems allows unequaled soft-tissue visualization during radiation delivery and can be used for dose reconstruction to quantify the impact of motion. To this end, knowledge of anatomical deformations obtained from continuous monitoring during treatment has to be combined with information on the spatio-temporal dose delivery to perform motion-compensated dose accumulation (MCDA). Here, the influence of the choice of deformable image registration algorithm, dose warping strategy, and magnetic resonance image resolution and signal-to-noise-ratio on the resulting MCDA is investigated. For a quantitative investigation, four 4D MRI-datasets representing typical patient observed motion patterns are generated using finite element modeling and serve as a gold standard. Energy delivery is simulated intra-fractionally in the deformed image space and, subsequently, MCDA-processed. Finally, the results are substantiated by comparing MCDA strategies on clinically acquired patient data. It is shown that MCDA is needed for correct quantitative dose reconstruction. For prostate treatments, using the energy per mass transfer dose warping strategy has the largest influence on decreasing dose estimation errors.
Simultaneous Robust State Estimation, Topology Error Processing, and Outage Detection for Unbalanced Distribution Systems (2021)

This paper proposes an efficient algorithmic approach that overcomes the critical challenges in the real-time unbalanced distribution system state estimation, topology error processing, and outage identification simultaneously: (1) Limited locations of measurement devices and unsynchronized measurement data as well as missing and bad data, (2) Complicated mixed-phase switch actions and mutual impedances, and (3) the nonlinear nature of unbalanced distribution system power flow and measurement data . A single snap-shot mixed-integer quadratic programming (MIQP) optimization framework is proposed to cope with these challenges. This MIQP framework presents a more accurate unbalanced distribution system model, linearizes the nonlinear relationship between bus voltage and current injections, formulates the complicated mixed-phase switch operations, and executes the outage detection function via analytic constraints. The proposed model can be effectively solved by a general commercial MIP solver. The effectiveness of the proposed approach is verified on an actual distribution feeder in Arizona.
Influence of a charged phospholipid on the release pattern of timolol maleate from cubic liquid crystalline phases (2008)

The release of timolol maleate, a drug for treatment of glaucoma, from cubic liquid crystals consisting of charged and uncharged lipids was investigated in vitro. It was shown that the release of drug was dependent on the ionic strength of the receptor medium and the relative amount of a charged phospholipid in the cubic phase. In the absence of charged lipids, the release of timolol was complete, irrespective of the medium used, i.e. distilled water or saline solution. In the presence of a negatively charged phospholipid, diacylphosphatidylglycerol, the release of drug from the cubic phase was incomplete when distilled water was the receptor medium. The residual drug was dependent on the amount of charged lipid in the cubic phase. In saline solution, on the other hand, all of the drug was released. The results are interpreted as an effect of electrostatic attraction between the positively charged drug with the negatively charged bilayer surface, which is screened in the presence of saline. The possible influence of the cubic geometry is discussed as well. This work shows that lipids offer many possibilities in the formulation of sustained drug release systems.
Flash memories: a review (1996)

Summary form only given. Many approaches are being used to manufacture or develop flash memory products to meet various market needs. These approaches can be classified broadly according to programming mechanism: channel hot electron (including source-side injection) and Fowler-Nordheim tunnelling. Some of the technologies in manufacturing or in development are: NOR stack gate, split gate, source-side injection NAND, DINOR, AND. In addition, a host of technologies for embedded flash applications are in different stages of development. Multi-level cell technologies are being developed to reduce cost/bit. 3-D structures are being investigated to realize small cell size. This paper reviews the different memory technologies, principles of operation, the status, the tradeoffs in cost, performance and reliability. It also discusses emerging flash technologies to serve industrial and next generation consumer electronic products including low voltage, low power portable and mobile devices.
Wild emmer genome architecture and diversity elucidate wheat evolution and domestication (2017)

Wheat (<i>Triticum</i> spp.) is one of the founder crops that likely drove the Neolithic transition to sedentary agrarian societies in the Fertile Crescent more than 10,000 years ago. Identifying genetic modifications underlying wheat's domestication requires knowledge about the genome of its allo-tetraploid progenitor, wild emmer (<i>T. turgidum</i> ssp. <i>dicoccoides</i>). We report a 10.1-gigabase assembly of the 14 chromosomes of wild tetraploid wheat, as well as analyses of gene content, genome architecture, and genetic diversity. With this fully assembled polyploid wheat genome, we identified the causal mutations in <i>Brittle Rachis 1</i> (<i>TtBtr1</i>) genes controlling shattering, a key domestication trait. A study of genomic diversity among wild and domesticated accessions revealed genomic regions bearing the signature of selection under domestication. This reference assembly will serve as a resource for accelerating the genome-assisted improvement of modern wheat varieties.
Deprotonation of Organic Compounds Bearing Acid Protons Promoted by Metal Amido Complexes with Chiral Diamine Ligands Leading to New Organometallic Compounds (2002)

Well-defined 16-electron metal amido complexes bearing chiral Ts-diamine ligands readily react with nitromethane, acetone, or phenylacetylene to give new organometallic compounds in almost quantitative yields. For example, an Ir amido complex, Cp*Ir[(R,R)-Tscydn], reacts with nitromethane at room temperature to give quantitatively a nitromethyl Ir complex, Cp*Ir(CH2NO2)[(R,R)-Tscydn], as a single diastereomer. The isolable organometallic compounds with chiral amine ligands are relevant to active catalysts for asymmetric C−C bond formation.
MR Perfusion Index as a Quantitative Method of Evaluating Epiphyseal Perfusion in Legg-Calve-Perthes Disease and Correlation With Short-term Radiographic Outcome (2013)

Prognostic level II.
Antidiuretic and pressor actions of vasopressin in age-dependent DOCA-salt hypertension (1989)

The role of antidiuretic and pressor effects of vasopressin (VP) in deoxycorticosterone acetate (DOCA)-salt hypertension was studied in young and adult Brattleboro rats. The antidiuretic VP action was a necessary prerequisite for the development of severe DOCA-salt hypertension. The insufficient expansion of extracellular fluid volume in DOCA-salt-treated VP-deficient (DI) rats was associated with the attenuation of their hypertensive response, although they had highly increased blood volume and extracellular sodium. Chronic [deamino]-D-arginine vasopressin supplementation that restored volume and distribution of body fluids in DI rats permitted the full development of DOCA-salt hypertension. Blood pressure response to DOCA-salt treatment was always greater in young than in adult Brattleboro rats (even in animals lacking pressor or both VP effects). In animals in which antidiuretic VP effects were present, the pattern of body fluid response to DOCA-salt treatment was also age dependent. There was a tendency to intravascular expansion in young hypertensive rats, whereas an increase of interstitial fluid volume was found in adult animals. The elimination of VP pressor action lowered systemic resistance much more in adult than in young hypertensive rats. We conclude that 1) in adult but not in young rats antidiuretic VP effects are essential for the occurrence of blood pressure response to DOCA-salt treatment, 2) the restoration of body fluids due to antidiuretic VP action enables the development of hypertension in both age groups of DI rats, and 3) pressor VP effects contribute to the maintenance of hypertension, especially in adult animals.
Performance characteristics of a dual‐energy detector for digital scan projection radiography (1987)

An energy discriminating x-ray detector has been developed for dual-energy, scan projection digital radiography. The detector is comprised of a pair of x-ray intensifying screen/linear photodiode arrays, aligned one behind the other. Energy discrimination is achieved by employing a low atomic number phosphor in the front screen and a high atomic number phosphor in the back screen. The x-ray response, modulation transfer function, and defective quantum efficiency of the detector are reported along with the experimental methodology utilized for the measurements. Also presented is an analysis which indicates that in a typical patient's lung field, the detector can resolve the projected density (g/cm2) of a 3-mm-thick, 1-cm2 area of bone to better than 1.5%.
A single amino acid substitution in hypervariable region 5 of the envelope protein of feline immunodeficiency virus allows escape from virus neutralization (1993)

We infected a specific-pathogen-free cat (cat 14) with molecularly cloned feline immunodeficiency virus clone 19k1 (FIV19k1 [K. H. J. Siebelink, I. Chu, G. F. Rimmelzwaan, K. Weijer, A. D. M. E. Osterhaus, and M. L. Bosch, J. Virol. 66:1091-1097, 1992]). Serum of this cat obtained 22 weeks postinfection (serum 1422) neutralized FIV19k1 but not FIV19k32, which is 99.3% identical to FIV19k1 in the envelope gene. Serum 1422 also neutralized virus isolated from cat 14 at weeks 2 and 32 postinfection. We then cultured FIV19k1 in the continuous presence of serum 1422, which resulted in a delay in virus replication of 6 weeks. The resulting virus population appeared to be resistant to virus neutralization by serum 1422. Nucleotide sequencing of the env open reading frame of this presumed escape mutant revealed the presence of one silent and two substitution mutations, both of the latter in hypervariable region 5. Through the construction of chimeric viruses and site-directed mutagenesis, we demonstrated that one of these mutations, the substitution of lysine to glutamine at amino acid position 560 in hypervariable region 5, was sufficient to allow the escape of FIV19k1 from neutralization by serum 1422.
Evaluation of potent odorants in Parsley leaves [Petroselinum crispum (Mill.) Nym. ssp. crispum] by aroma extract dilution analysis (1992)

Aroma extract dilution analysis of parsley leaf volatiles resulted in 14 odour compounds having high factors of dilution. Thirteen of these compounds were identified as methyl 2-methylbutanoate, myrcene, 1-octen-3-one, (Z)-1,5-actadien-3-one, 2-isopropyl-3-methoxypyrazine, p-mentha-1,3,8-triene, linalool, 2-sec-butyl-3-methoxyprazine, (E)-6-decenal, β-citronellol, (E,E)-2,4-decadienal, β-ionone and myristicin