nils-herrmann/clean_scirepeval huggingface dataset:
Probabilistic hypergraph grammars for efficient molecular optimization

We present an approach to make molecular optimization more efficient. We infer a hypergraph replacement grammar from the ChEMBL database, count the frequencies of particular rules being used to expand particular nonterminals in other rules, and use these as conditional priors for the policy model. Simulating random molecules from the resulting probabilistic grammar, we show that conditional priors result in a molecular distribution closer to the training set than using equal rule probabilities or unconditional priors. We then treat molecular optimization as a reinforcement learning problem, using a novel modification of the policy gradient algorithm - batch-advantage: using individual rewards minus the batch average reward to weight the log probability loss. The reinforcement learning agent is tasked with building molecules using this grammar, with the goal of maximizing benchmark scores available from the literature. To do so, the agent has policies both to choose the next node in the graph to expand and to select the next grammar rule to apply. The policies are implemented using the Transformer architecture with the partially expanded graph as the input at each step. We show that using the empirical priors as the starting point for a policy eliminates the need for pre-training, and allows us to reach optima faster. We achieve competitive performance on common benchmarks from the literature, such as penalized logP and QED, with only hundreds of training steps on a budget GPU instance.

Field of study: Computer science
Appropriateness of Pediatric Hospitalization in a General Hospital in Kuwait

To determine the rate of inappropriate pediatric admissions using the Pediatric Appropriateness Evaluation Protocol (PAEP) and to examine variables associated with inappropriateness of admissions.  A prospective study was conducted in the Department of Pediatrics, Farwania General Hospital, Kuwait, to examine successive admissions for appropriateness of admission as well as several sociodemographic characteristics over a 5-month period (August 2010 to December 2010). A total of 1,022 admissions were included.  Of the 1,022 admissions, 416 (40.7%) were considered inappropriate. Factors associated with a higher rate of inappropriate admission included older age of patients and self-referral.  The rate of inappropriate hospitalization of children was high in Farwania Hospital, Kuwait, probably due to the relatively free health care services, parental preference for hospital care, easy access to hospital services, and insufficient education about the child’s condition.

Field of study: Medicine
On the role of hippocampal connections in the performance of place and cue tasks: comparisons with damage to hippocampus.

Behavioral changes following interruption of the main connections of hippocampus and closely related areas (entorhinal cortex, mammillary bodies, dentate gyrus) were determined and compared with findings of previous research that involved direct damage to hippocampus. By a within-subjects design, rats were trained to run in a radial maze with a procedure that involved two kinds of learning (place and cue) and two memory functions (working and reference memory). Rats with fimbria-fornix and entorhinal cortex lesions were impaired on both the place and the cue task. Specifically, the animals suffered a general impairment in working memory on both tasks but were impaired in reference memory only on the place task. Animals with lesions of the dentate gyrus and mammillary bodies were able to perform the complex place and cue tasks with minimal problems. In previous research it was found that direct damage to hippocampus (including all cell fields, alveus, fimbria) resulted in impaired performance only on the place task (Jarrard, 1983). Taken together, these findings indicate that interruption of hippocampal input/output pathways and/or damaging some closely related structures has a greater effect on the behaviors studied than does direct damage to hippocampus.

Field of study: Biology, Psychology
Severe Methanol Poisoning with Supralethal Serum Formate Concentration: A Case Report

To present a case of survival without visual and central nervous system sequelae at a formate concentration of twice the reported lethal level.  This was a case of a 33-year-old man who ingested 1 liter of a toxic mixture of methanol and ethanol. Upon admission, he presented with anxiety, tachycardia and hypertension and had a serum formate level of 1,400 mg/l (normal range 0.9-2.1 mg/l), a methanol level of 806 mg/l (normal range 2-30 mg/l), an undetectable ethanol concentration and a normal lactate level. A 10% solution of ethanol and folinic acid was administered intravenously and two 8-hour sessions of intermittent hemodialysis were performed. The patient was discharged on the fifth day without sequelae of poisoning. The follow-up examinations 3 months and 2 years later revealed no damage to the basal ganglia. The patient had normal visual-evoked potential and findings on optical coherence tomography. The genetic analysis revealed a rare minor allele for the gene coding CYP2E1 enzyme of the microsomal ethanol oxidizing system.  The patient survived acute methanol poisoning without long-term sequelae despite a high serum level of formic acid upon admission.

Field of study: Medicine
Shoot structure, canopy openness, and light interception in Norway spruce

We analysed changes in shoot structure with canopy openness in control (C) and irrigated–fertilized (IL) Picea abies trees. Canopy openness, which was used to characterize light availability, varied between 0·23 and 0·90 for C shoots and 0·07 to 0·75 for IL shoots. Needle width and thickness increased with canopy openness, but were similar for C and IL needles. The ratio of needle thickness to width remained fairly close to one throughout the canopy. This resulted in large values (3·0–4·0) of the ratio of total to projected needle area. The ratio of total to projected needle area did not correlate with canopy openness. Shoot silhouette to total needle area ratio (STAR) and specific needle area decreased with canopy openness. As a result, shoot silhouette area per unit needle mass was up to three times larger in shade shoots than in sun shoots. STAR and specific needle area were similar for C and IL shoots and needles. Needle nitrogen concentration varied between 0·7 and 1·1% (C), and between 1·0 and 1·6% (IL). On both plots, nitrogen content was linearly related to estimated relative light interceptance (RLI) (both expressed per needle area), but the ratio of nitrogen content to RLI increased with decreasing canopy openness.

Field of study: Environmental science
Dolomite and Quartz Lamellae Stress and Strain Analysis in a Multiply-Deformed Terrane, West-Central Vermont

The methods of dynamic analysis for inferring principal stress axes from quartz, calcite, and dolomite petrofabrics (Carter and Raleigh, 1969) have been well developed during the last four decades through the availability of experimental equipment for rock deformation under controlled temperatures and pressures (Griggs, 1936) and the modern universal microscope stage (Emmons, 1943). Magnitudes of the stresses cannot be predicted from the methods they describe, however. Although Jamison and Spang (1976) proposed a method to infer differential stress from twinned carbonate aggregates, strain is in reality the only parameter that can be properly measured in deformed rocks. Well-known procedures for measuring finite strain in racks can be applied only to highly deformed rocks and require speculation about the undeformed state of the rock fabric (Ramsay, 1967). Groshong (1972) has recently developed a least-squares fit strain-gage technique which can be used to calculate the orientations and magnitudes of principal strain axes for small strains in deformed rocks containing mechanically twinned minerals. Groshong (1974) experimentally checked his method using twinned calcite aggregates, but he suggested that it could be applied to other minerals.

Field of study: Geology
Guidelines on How to Read a Physics Textbook and the Assessment of the Readability of Recommended Physics Textbooks in Secondary Schools in Osun State of Nigeria

This study assessed the readability of the four recommended physics textbooks in senior secondary schools in Osun State of Nigeria. A total of 25 physics teachers and 300 senior secondary three (SS3) physics students were randomly selected in the 12 secondary schools used for the study. A survey design was used for the study. Results showed that the four physics textbooks were appropriate for secondary school students in Osun state of Nigeria in terms of age (Fry graph mean age = 17years, students’ mean age =15 years) .The books had the highest rating by students on illustrations and clarity of prints while the lowest ratings were on sentence structure and examples. Teachers considered the vocabulary as appropriate while the exercises were considered least appropriate. The study also showed that the four physics textbooks were adjudged readable in term of students’ ability to read and understand the contents. However, senior secondary school physics textbooks (69%) was found to be most readable, seconded by ordinary level physics (64%), followed by principle of physics while science teacher association of Nigeria (STAN) physics (15%) was found to be least readable by the students. It is recommended that the readability of textbooks and the reading ability of students should be part of the criteria for selecting textbooks.

Field of study: Education
Generation of chicken monoclonal antibodies against the a1, a2, and a3 subunit isoforms of vacuolar-type proton ATPase.

The vacuolar-type proton pump ATPase (V-ATPase) plays several pivotal roles in the acidification of diverse intracellular compartments and the extracellular environment. The a subunit isoforms a1, a2, and a3, constituting the membrane-embedded section, are expressed in various tissues, and they are involved in the regulation of subcellular localization and activity of the holocomplex. Therefore, the characterization of their properties is indispensable for dissection of the physiological roles of the V-ATPase in highly differentiated cells. In this study, we report the production and characterization of chicken monoclonal antibodies (MAbs) against these mouse a1, a2 and a3 subunit isoforms. These MAbs are shown to be suitable for both immunoblotting and immunofluorescence analysis. The MAbs obtained in this study are useful in understanding the pathological basis of V-ATPase dysfunction.

Field of study: Biology
Modular Lagrange Interpolation of the Mod Function for Bootstrapping for Approximate HE

We introduce a novel variant of Lagrange interpolation called modular Lagrange interpolation that allows us to obtain and prove error bounds for explicit low-degree polynomial approximations of a function on a union of equally-spaced small intervals even if the function overall is not continuous. We apply our technique to the mod function and obtain explicit low-degree polynomial approximations with small error. In particular, for every k and N >> k, we construct low-degree polynomials that approximate f(x) = x mod N , for |f(x)| ≤ 1 and |x| ≤ kN , to within O(1/N) additive approximation. For k = O(logN), the result is generalized to give O(d)-degree polynomial approximations to within O(N−d) error for any d ≥ 1. Literature in approximation theory allows for arbitrary precision polynomial approximation of only smooth functions, whereas the mod function is only piecewise linear. These polynomials can be used in bootstrapping for approximate homomorphic encryption, which requires computing the mod function near multiples of the modulus. Our work bypasses the fundamental error of approximation in prior works caused by first approximating the mod function by a scaled sine function. We implement the bootstrapping of HEAAN using our polynomials and profile various parameter settings. For example, we demonstrate bootstrapping that can achieve 67 bit message precision, larger than the precision of a double variable, whereas the most advanced prior work was only capable of up to 40 bit message precision.

Field of study: Computer science, Mathematics
Strongly temperature dependent resistance of meander-patterned graphene

We have studied the electronic properties of epitaxial graphene devices patterned in a meander shape with the length up to a few centimeters and the width of few tens of microns. These samples show a pronounced dependence of the resistance on temperature. Accurate comparison with the theory shows that this temperature dependence originates from the weak localization effect observed over a broad temperature range from 1.5 K up to 77 K. The comparison allows us to estimate the characteristic times related to quantum interference. In addition, a large resistance enhancement with temperature is observed at the quantum Hall regime near the filling factor of 2. Record high resistance and its strong temperature dependence are favorable for the construction of bolometric photodetectors.

Field of study: Physics
Identification and Expression Analysis of Wheat TaGF14 Genes

The 14-3-3 gene family members play key roles in various cellular processes. However, little is known about the numbers and roles of 14-3-3 genes in wheat. The aims of this study were to identify TaGF14 numbers in wheat by searching its whole genome through blast, to study the phylogenetic relationships with other plant species and to discuss the functions of TaGF14s. The results showed that common wheat harbored 20 TaGF14 genes, located on wheat chromosome groups 2, 3, 4, and 7. Out of them, eighteen TaGF14s are non-ε proteins, and two wheat TaGF14 genes, TaGF14i and TaGF14f, are ε proteins. Phylogenetic analysis indicated that these genes were divided into six clusters: cluster 1 (TaGF14d, TaGF14g, TaGF14j, TaGF14h, TaGF14c, and TaGF14n); cluster 2 (TaGF14k); cluster 3 (TaGF14b, TaGF14l, TaGF14m, and TaGF14s); cluster 4 (TaGF14a, TaGF14e, and TaGF14r); cluster 5 (TaGF14i and TaGF14f); and cluster 6 (TaGF14o, TaGF14p, TaGF14q, and TaGF14t). Tissue-specific gene expressions suggested that all TaGF14s were likely constitutively expressed, except two genes, i.e., TaGF14p and TaGF14f. And the highest amount of TaGF14 transcripts were observed in developing grains at 20 days post anthesis (DPA), especially for TaGF14j and TaGF14l. After drought stress, five genes, i.e., TaGF14c, TaGF14d, TaGF14g, TaGF14h, and TaGF14j, were up-regulated expression under drought stress for both 1 and 6 h, suggesting these genes played vital role in combating against drought stress. However, all the TaGF14s were down-regulated expression under heat stress for both 1 and 6 h, indicating TaGF14s may be negatively associated with heat stress by reducing the expression to combat heat stress or through other pathways. These results suggested that cluster 1, e.g., TaGF14j, may participate in the whole wheat developing stages, e.g., grain-filling (starch biosynthesis) and may also participate in combating against drought stress. Subsequently, a homolog of TaGF14j, TaGF14-JM22, were cloned by RACE and used to validate its function. Immunoblotting results showed that TaGF14-JM22 protein, closely related to TaGF14d, TaGF14g, and TaGF14j, can interact with AGP-L, SSI, SSII, SBEIIa, and SBEIIb in developing grains, suggesting that TaGF14s located on group 4 may be involved in starch biosynthesis. Therefore, it is possible to develop starch-rich wheat cultivars by modifying TaGF14s.

Field of study: Biology
The Georgia State Litigation: Literal Copying in Education

This case note examines the long&#8208;standing litigation against Georgia State University in relation to the posting, by faculty and library staff, of unauthorised copies of book extracts on the University's electronic reserves and virtual learning environment. The central question in this litigation has been whether these acts of copying fall within the fair use doctrine in US copyright law. In answering this, a key question for the US courts &#8211; and one relevant to other jurisdictions with free exceptions for education, such as the UK &#8211; has been whether existing and potential licensing activity is relevant to the question of whether an exception applies. This case note discusses how market effect has been analysed in Georgia State, including the recent rejection by the Court of Appeals for the Eleventh Circuit of a strongly empirical approach to market harm.

Field of study: Law
Tuff fingerprinting and correlations between OGCP cores and outcrops for Pre-Bed I and Beds I/II at Olduvai Gorge, Tanzania

Sediment cores retrieved from the Pleistocene Olduvai Basin by the Olduvai Gorge Coring Project (OGCP) provide a high resolution record of tuffs and other volcaniclastic deposits, together with a lacustrine sedimentary record full of paleoenvironmental indicators. Correlating tuffs between the cores and outcrops at Olduvai, where these tuffs are identified at paleoanthropologically important sites, is critical for applying the new paleoenvironmental data to the conditions under which hominins lived. Tuffs and other volcaniclastic deposits from three cores were analyzed for mineral assemblages and glass and mineral major element compositions (feldspar, augite, hornblende, titanomagnetite, and glass where possible) to compare to published geochemical fingerprint data, based on marker tuffs from outcrop equivalents at Olduvai Gorge. In combination with stratigraphic position, these mineralogical and geochemical data were used to correlate between the cores and outcrops, providing direct temporal tie-lines between the cores and sites of paleoanthropological interest. Direct correlations are most certain for Olduvai Bed I, where all major tuff markers from outcrop are identified for one or more of the three core sites, and for the upper part of the underlying Ngorongoro Formation, which includes the Coarse Feldspar Crystal Tuff (CFCT) and Naabi ignimbrites exposed in the oldest Pleistocene exposures of the Western Gorge. Also characterized were the mineral and glass compositions of tuffs and ignimbrites pre-dating the oldest exposed outcrop units, extending our record of explosive events from the Ngorongoro Volcano. While no specific correlations can be confirmed between individual Bed II tuffs in the cores and in outcrops, correlations are possible between the cores themselves (using newly identified tuff compositions), and some potential correlations (non-unique, based on individual mineral phases) between core and outcrop can be used in conjunction with other stratigraphic tools to help constrain the intervals in question.

Field of study: Environmental science, Geography
Mechanism of Low Frequency Oscillation with Multiple Disturbances Based on Stability Region Theory in Wide-area System

Because of the characteristics of disturbances and operations in system,low frequency oscillation in wide area power system always performs multiple disturbances phenomenon,which brings huge challenge to analysis and control.Based on this phenomenon,a model named section power flow analysis is proposed.Based on this model,a practical approach is given to present for getting the energy function and stability region of wide-area power system.Then,a flowchart is presented on how to use stability region theory to analyze the low frequency oscillation with multiple disturbances.This method can be carried out in wide-area power system for on-line real-time security assessment and warning,on this basis some control strategies can be brought out correspondingly.So the controllability,observability of the system will be promoted at a higher level.As a result,a safe,reliable,economic and efficient power system will be secured well.And blackouts incidents caused by power system stability failure can be controlled.Meanwhile,it can improve system reliability.IEEE 4 machines 11 nodes system and Central China Grid system are used for simulation and analysis.At the same time,many results are obtained with different multiple disturbances.And the results verify the correctness andeffectivenessoftheproposedmethod.Thismethodcanbeusedforanalyzing,monitoring,andemergency controlforlow-frequencyoscillationwithmultipledisturbancesinpracticalwide-areasystemwithguidingsignificance.

Field of study: Engineering, Physics
Downregulation of microRNA-376a in Gastric Cancer and Association with Poor Prognosis

MicroRNAs have a significant role in the tumorigenesis and progression of cancers, including gastric cancer (GC). Our study aimed to identify a novel biomarker to predict the prognosis of patients with GC.  The GC microarray dataset, GSE28700, was downloaded from the Gene Expression Omnibus (GEO) database and screened for differentially expressed miRNAs (DEMs). The downregulation of miR-376a expression was verified in GC cell lines and 82 paired GC tissues by performing RT-qPCR and the correlation between its expression and clinicopathological characteristics was also explored. The target genes of miR-376a were predicted using TargetScan7.1, miRDB, and DIANA website tools. A functional enrichment analysis was performed to explore the biological role of the common target genes.  Bioinformatics analysis found that miR-376a was downregulated in GC tissues. Compared with the control group, RT-qPCR results showed that the expression of miR-376a in GC cell lines and tissues were also significantly decreased. The expression of miR-376a was statistically associated with T and N stage. Survival analysis with Kaplan–Meier showed that GC patients in the low expression group had a poorer prognosis than those in the high expression group (median survival of 26.4 and 46.9 months, respectively). Univariate and multivariate analysis demonstrated that low miR-376a expression was an independent prognostic marker for poor survival. Functional enrichment analysis indicated that the common targets genes were involved in cell–cell communication, VEGF and mTOR1-mediated signaling, and epithelial-to-mesenchymal transition (EMT).  The results suggest that miR-376a could play an important role in the tumorigenesis and progression of GC and act as a novel therapeutic target and prognostic indicator in patients with GC.

Field of study: Biology, Chemistry
박근혜 정부의 대북 인권정책 분석

박근혜 정부의 대북 인권정책은 한반도 신뢰프로세스와 평화통일 기반 구축과 연계되어있다. 본 연구는 현실주의, 자유주의, 구성주의 패러다임과 대외정책분석의 이론적 틀을 통해 박근혜 정부의 대북 인권정책을 분석,평가하고자 한다. 구체적으로 대북 인도적 지원, 재외 탈북민 보호, 북한인권법 논의를 중심으로 사안별로 분석했다. 분석한 결과, 대북 인도적 지원은 남북관계의 동학에 종속되었고, 재외 탈북민 보호는 국가 간 관계의 틀에서 벗어나지 못하였으며, 국내적 논의인 북한인권법 통과도 여전히 답보상태에 있어 대북 인권정책의 법적·제도적 일관성 및 효율성을 담보하지 못하고 있는 실정이다. 이는 박근혜 정부의 대북 인권정책이, 다양한 수사에도 불구하고, 국가이익 중심의 현실주의 패러다임에 머물러 있음을 보여준다. 통일한국의 가치 확립이라는 관점에서 대북 인권정책의 원칙을 확립하고, 자유주의 내지 구성주의적 요소를 가미하여 이를 구체적으로 실행하는 것이 향후의 정책적 과제가 될 것이다.

Field of study: Political science
Recontextualizing Clarence Ayres’s The Theory of Economic Progress through Archival Evidence

Our article seeks to recontextualize Clarence Ayres’s The Theory of Economic Progress through a reconsideration of the criticisms of the book and Ayres’s personal standpoint on it. We believe that the negative reception of the book conveys the mainstream perspective. Additionally, our article stresses some of Ayres’s thoughts on Western society that were not included in The Theory of Economic Progress but were introduced by him through correspondence around the same time his famous book was written and disseminated. We conclude that Ayres was more radical than his writings reveal.

Field of study: Economics