nils-herrmann/clean_scirepeval huggingface dataset:
Complete genome sequence of a bacterium Pseudomonas fragi P121, a strain with degradation of toxic compounds.

A newly isolated strain P121 was identified as Pseudomonas fragi. The complete genome sequence of P.fragi P121 was carried out using the PacBio RSⅡ platform. The genome contains a circular chromosome with 5,101,809bp. The genome sequence suggests that the P121 exhibited the ability of degradation of toxic compounds. Genome sequencing information provides the genetic basis for the analysis of toxic compounds and the mechanism of extreme environmental adaptation of the strain.

Field of study: Biology, Engineering
Stable isotopes in leaf water of terrestrial plants.

Leaf water contains naturally occurring stable isotopes of oxygen and hydrogen in abundances that vary spatially and temporally. When sufficiently understood, these can be harnessed for a wide range of applications. Here, we review the current state of knowledge of stable isotope enrichment of leaf water, and its relevance for isotopic signals incorporated into plant organic matter and atmospheric gases. Models describing evaporative enrichment of leaf water have become increasingly complex over time, reflecting enhanced spatial and temporal resolution. We recommend that practitioners choose a model with a level of complexity suited to their application, and provide guidance. At the same time, there exists some lingering uncertainty about the biophysical processes relevant to patterns of isotopic enrichment in leaf water. An important goal for future research is to link observed variations in isotopic composition to specific anatomical and physiological features of leaves that reflect differences in hydraulic design. New measurement techniques are developing rapidly, enabling determinations of both transpired and leaf water δ(18) O and δ(2) H to be made more easily and at higher temporal resolution than previously possible. We expect these technological advances to spur new developments in our understanding of patterns of stable isotope fractionation in leaf water.

Field of study: Environmental science
Survey of Prior Learning Assessment Practices in Pharmacy Education

Nontraditional Pharm.D (NTPD) program directors were surveyed to determine the use of prior learning assessment (PLA) in NTPD programs. Eighty-four percent of the respondents reported using PLA for one or more purposes, including the admissions process and the awarding of advanced standing for didactic and experiential courses. Transcript review, faculty-developed exams, and portfolios are the most commonly used methods of PLA in NTPD programs.

Field of study: Education, Medicine
Social Cultural Factors Influencing Pupils’ Participation in Primary Education in Ololulunga Division, Narok County Kenya

Access to primary education is crucial as noted by World Bank reports that demonstrate that primary education enhances citizen partition in governance, development activities, creates health awareness and makes citizens less gullible, more receptive to change than the case would be with a populace that has no access   to education. Reports from studies and government annual education reports have noted discrepancies in access to education between high economic potential areas and low economic potential areas. Participation rates have been an issue of concern to most educational stakeholders in Kenya over the past years. This is manifested by lower rates of completion. This study sought to establish the influence of socio-cultural factors (female genital mutilation; moranism), economic factors (family incomes-poverty levels and child labour) and teenage pregnancies on pupils’ participation in public primary schools as perceived by head teachers, members of school management committees and class right pupils in Ololulunga Division, Narok County, Kenya. The study adopted descriptive survey design whose intent is to obtain pertinent and precise data on status of the phenomena. The study had a target population of 64 public primary schools translating to 64 head teachers, 64 members of school management committees and 1260 standard eight pupils spanning over three educational zones; namely Ololunga, Lemek and Melelo zones. The sample size consisted of 12 head teachers, 12 members of School Management Committees and 252 class eight pupils. Questionnaires were used to obtain data from the pupils while interview guides were administered to the head teachers and members of school Management committees (SMC). Data was analysed by use frequencies and percentages captured through the Statistical Package for Social Sciences (SPSS). Female genital mutilation and the associated rites of passage were rated as the greatest impediment to girl-child participation in primary education by 33.3 percent of the respondents, while teenage pregnancies were the second challenge. The rite of passage of circumcision and being a moran (community defender) was equally a challenge for boy child participation in education. Poverty and employment (child labour) were the least rated impediments to pupils’ participation in primary education. The study concluded that socio-cultural factors had a negative influence on pupils’ participation than the economic factors Keywords : socio-cultural factors, pupil participation, rites of passage (365 words)

Field of study: Education
Theoretical analysis of resonance states in $^{4}H$, $^{4}He$ and $^{4}Li$ above three-cluster threshold

The resonance states of $^{4}H$, $^{4}He$ and $^{4}Li$, embedded in the three-cluster $d+N+N$ continuum, are investigated within a three-cluster model. The model treats the Pauli principle exactly and incorporates the Faddeev components for proper description of the boundary conditions for the two- and three-body continua. The hyperspherical harmonics are used to distinguish and numerate channels of the three-cluster continuum. It is shown that the effective barrier, created by three-cluster configuration $d+N+N$, is strong enough to accommodate two resonance states.

Field of study: Physics
Establishment of real-time PCR method for detecting HSV-2

To develop a real-time PCR method for herpes simplex virus-2 (HSV-2).  The recombinant plasmid pMD18-T-gG was constructed as HSV-2 DNA standard for quantitative analysis. According to the principle of TaqMan MGB technique, the primers and probe targeted at HSV-2-gG gene fraction were designed and applied to detect HSV-2. Then the PCR reaction system was optimized and evaluated.  The recombinant plasmid was constructed successfully. The real-time PCR method for HSV-2 using TaqMan MGB technique was established and the assay showed good reproducibility (intra-assay coefficients of variation was 2.29% and inter-assay coefficients of variation was 4.76% ) , good specificity (it can distinguish HSV-2 from other pathogenic microorganism) ,good linear range (4.75×10~1-4.75×10~6 copies/μl, r = 0.998) and sensitivity reached 47.5 copies/μl. At the same time, this new established method had more advantages than the ELISA method.  A novel real-time PCR detecting method for HSV-2 has been developed, which can be used in clinical detection.

Field of study: Biology
No Clear Link between G Loadings and Heritability: A Twin Study from Korea

A fundamental theoretical question in intelligence research is to what extent the g factor and heritability coefficients of the subtests of an IQ battery are correlated. Five studies from Western countries showed modest to strong positive correlations (range = 43-.77), and six studies from a Japanese meta-analysis showed zero to modest correlations (range = −0.01–0.59). The Western and Japanese studies were compared with a Korean sample of 24 monozygotic and 20 dizygotic young adult twin pairs administered the Korean Wechsler Adult Intelligence Scale-Revised (WAIS-R). A univariate twin model was applied to all subscale scores leading to estimates of heritability for all scales, g loadings were also computed using principal-axis factor analysis. Finally, the correlation between the heritabilities and the g loadings of these scales were computed. The correlations of r = −.15 were not in line with previous studies. It could be that Spearman's hypothesis is less strongly confirmed for Northeast Asians, but it is also possible that the study will be an outlier in a future meta-analysis. More primary research and a meta-analysis of all studies are needed.

Field of study: Psychology
DISTILLATION INFLUENCE ON THE COMPOSITION AND SENSORIAL QUALITY OF SUGAR CANE DISTILLED BEVERAGE

The knowledge of substances related to sensorial quality of sugar cane distilled beverage is fundamental in the production monitoring, in its characteristical changes and/or beverage quality control. Separation, selection and concentration of these substances are performed during the distillation process. Physical-chemical and sensorial analyses of sixteen sugar cane distilled beverage samples were analized. Their relationships were established through the factor analysis by the principal component method. Afterwards the substance behaviour related to the beverage sensorial quality during the distillation was studied. A need of analysing a greater number of sugar cane distilled beverage components was detected in order to increase the correlation coefficient between analytical and sensorial data, optimizing the setting of parameters for the distillation process and for the other stages that take part in the sugar cane distilled beverage production. It was also noticed that the higher the propanol content and acidity levels the worst was the product sensorial quality. On the other hand, when the product distillation is fractioned, the acidity levels drop as well as the propanol contents in the sugar cane distilled beverage.

Field of study: Agricultural and Food sciences
Immunoreactivity and diagnostic value of Mycobacterium tuberculosis PstS1 and HspX

To evaluate the humoral and cellular immunoreactivity of recombinant Mycobacterium tuberculosis (M.tuberculosis) PstS1 and HspX protein antigens in order to provide reference for immunodiagnosis of tuberculosis and screening of candidates for vaccine antigens. 
 
 
 
Purified recombinant M. tuberculosis PstS1 and HspX proteins were obtained using molecular cloning expression and Ni2+ affinity chromatography. Blood samples and epidemiological data of healthy individuals and patients with M. tuberculosis infection were collected. Specific IgG antibodies and IFN-γ-producing antigen-specific T cells were respectively detected by enzyme-linked immunosorbent assay (ELISA) and enzyme-linked immunospot assay (ELISPOT) with the recombinant proteins used as antigens. The humoral and cellular immunoreactivity of the recombinant PstS1 and HspX proteins were assessed with statistical analysis of data. 
 
 
 
Both the recombinant PstS1 and HspX proteins could induce the secretion of IFN-γ by more specific effector T cells in patient with M. tuberculosis infection, and the differences between the infection and healthy control groups were statistically significant (P<0.05). The specificity and sensitivity of the recombinant PstS1 and HspX as the diagnostic antigens of ELISPOT were 92.11% (35/38) and 65.96% (31/47), and 68.42% (26/38) and 91.49% (43/47), respectively. The two proteins also possessed some humoral immunoreactivity, but statistically significant difference was only observed in the HspX-specific antibody level between the two groups (P<0.05). 
 
 
 
Both the recombinant PstS1 and HspX proteins had good cellular immunoreactivity and were the immunodominant antigens of cellular immunity. They performed well in cellular immunodiagnosis and were good potential candidate antigens for anti-tuberculosis vaccines. 
 
 
 
Mycobacterium tuberculosis; PstS1; HspX; Immunodominant

Field of study: Biology
Skeletal Ni-P Amorphous Alloy(R-Ni-P)as a Hydrogenation Catalyst

Ni-P amorphous alloy with skeletal structure like Raney nickel was prepared by alkali leaching of a Ni-Al-P amorphous alloy obtained by the rapid quenching method, which exhibits high selectivity and activity for the hydrogenation of the organic compounds with various unsaturated functional groups.

Field of study: Chemistry
Did Commons Have Few Followers? Continuing my Conversation with Yngve Ramstad

Yngve Ramstad claimed that John R. Commons had few followers and that his ideas had relatively little influence on others, at least partly because of the difficulties of separating particular aspects of Commons' work from his whole system of thought. In contrast, the argument in this paper is that Commons' work did have important impacts in a number of areas such as industrial relations, macroeconomic stabilization, and organizational theory, and that in these cases specific ideas from Commons were utilized in a form that did not involve taking over other aspects on his thinking.

Field of study: Economics
Purpose Neutrality and Procedure Fairness

" Neutrality"is a value proposal arousing disputes.Its connotation is that the country remains neutral towards "good life notion",which leads to multivariate neutrality including world outlook neutrality,system neutrality and morality neutrality.Positively,"Purpose neutrality" is good for the protection of fair competition,cultivation of citizens' rationality,expansion of political identification;negatively,it fosters liberalization,individualism and morality lack.In fact,to discuss "neutrality" in an abstract way is of no practical significance.Within which range neutrality is to be remained rests on the practice process and its effect.

Field of study: Agricultural and Food sciences
Reply to the Comment of M. V. Cheremisin (cond-mat/0408050)

In the preprint cond-mat/0408050 M. V. Cheremisin noticed that some results (namely Fig. 4) of our recent work (cond-mat/0407364) have been taken from his paper cond-mat/0405176. As clear from the caption to Fig. 4 as well as from the text of our paper, we did not consider the curves shown in that Figure as our original results, but emphasized that they have been obtained in the well known paper Chiu and Quinn,  (1974) 30 years ago. It is a surprise, that M. V. Cheremisin presents the 30-years-old results of Chiu and Quinn as his own results, obtained for the first time in cond-mat/0405176.

Field of study: Physics
Impact of the ozone monitoring instrument row anomaly on the long-term record of aerosol products

Since about three years after the launch the Ozone Monitoring Instrument (OMI) on the EOS-Aura satellite, the sensor's viewing capability has been affected by what is believed to be an internal obstruction that has reduced OMI's spatial coverage. It currently affects about half of the instrument's 60 viewing positions. In this work we carry out an analysis to assess the effect of the reduced spatial coverage on the monthly average values of retrieved aerosol optical depth (AOD), single scattering albedo (SSA) and the UV Aerosol Index (UVAI) using the 2005–2007 three-year period prior to the onset of the row anomaly. Regional monthly average values calculated using viewing positions 1 through 30 were compared to similarly obtained values using positions 31 through 60, with the expectation of finding close agreement between the two calculations. As expected, mean monthly values of AOD and SSA obtained with these two scattering-angle dependent subsets of OMI observations agreed over regions where carbonaceous or sulphate aerosol particles are the predominant aerosol type. However, over arid regions, where desert dust is the main aerosol type, significant differences between the two sets of calculated regional mean values of AOD were observed. As it turned out, the difference in retrieved desert dust AOD between the scattering-angle dependent observation subsets was due to the incorrect representation of desert dust scattering phase function. A sensitivity analysis using radiative transfer calculations demonstrated that the source of the observed AOD bias was the spherical shape assumption of desert dust particles. A similar analysis in terms of UVAI yielded large differences in the monthly mean values for the two sets of calculations over cloudy regions. On the contrary, in arid regions with minimum cloud presence, the resulting UVAI monthly average values for the two sets of observations were in very close agreement. The discrepancy under cloudy conditions was found to be caused by the parameterization of clouds as opaque Lambertian reflectors. When properly accounting for cloud scattering effects using Mie theory, the observed UVAI angular bias was significantly reduced. The analysis discussed here has uncovered important algorithmic deficiencies associated with the model representation of the angular dependence of scattering effects of desert dust aerosols and cloud droplets. The resulting improvements in the handling of desert dust and cloud scattering have been incorporated in an improved version of the OMAERUV algorithm.

Field of study: Environmental science
Increased neutrophil membrane expression and plasma level of proteinase 3 in systemic vasculitis are not a consequence of the − 564 A/G promotor polymorphism

Several findings link proteinase 3 (PR3) to small vessel vasculitis. Besides being a major target of anti‐neutrophil cytoplasm antibodies (ANCA), previous findings have shown increased circulating levels of PR3 in vasculitis patients, increased levels of neutrophil membrane‐PR3 (mPR3) expression and a skewed distribution of the − 564 A/G polymorphism in the promotor region of the PR3 gene. In this study we elucidate how these three findings relate to each other. The plasma concentration of PR3 was measured by enzyme‐linked immunosorbent assay (ELISA), mPR3 expression by fluorescence activated cell sorter (FACS) and the gene polymorphism by real‐time polymerase chain reaction (PCR). We compared results from 63 patients with ANCA‐associated systemic vasculitis (AASV) with 107 healthy blood donors. In accordance with previous reports, AASV patients had increased plasma concentrations of PR3 compared to healthy controls (mean 224 µg/l versus 155 µg/l, P < 0·0001). They also showed an increased number of mPR3‐positive neutrophils (60%versus 42%, P < 0·001). However, contrary to a previous report, we found no skewed distribution of the polymorphism in PR3 gene. There was a weak correlation between mPR3 mean fluorescence intensity (MFI) and plasma PR3 among healthy controls and myeloperoxidase–ANCA (MPO–ANCA)‐positive patients (r = 0·24, P = 0·015 and r = 0·52, P = 0·011, respectively). In conclusion, increased plasma PR3 and high expression of mPR3 are associated with small vessel vasculitis, but neither of them is a consequence of the − 564 A/G polymorphism of the PR3 gene promotor.

Field of study: Biology, Medicine
Malate exchange between the cytosol and mitochondria.

1. By comparing the relative isotopic yields in glucose and CO(2) from precursors of mitochondrial and cytosolic malate, it is evident that the rate of isotopic exchange between these compartments is rapid. 2. A variety of potential inhibitors of malate exchange were tested, but no specific and effective inhibitor of the isotopic exchange has been found. 3. Compounds such as n-butylmalonate and p-iodobenzylmalonate, which have been used as inhibitors of the malate-phosphate transport system in isolated mitochondria, do not appear to be sufficiently specific to be useful in studies with intact cells.

Field of study: Biology, Computer science
Learning Causal Biological Networks With the Principle of Mendelian Randomization

Although large amounts of genomic data are available, it remains a challenge to reliably infer causal (i. e., regulatory) relationships among molecular phenotypes (such as gene expression), especially when multiple phenotypes are involved. We extend the interpretation of the Principle of Mendelian randomization (PMR) and present MRPC, a novel machine learning algorithm that incorporates the PMR in the PC algorithm, a classical algorithm for learning causal graphs in computer science. MRPC learns a causal biological network efficiently and robustly from integrating individual-level genotype and molecular phenotype data, in which directed edges indicate causal directions. We demonstrate through simulation that MRPC outperforms several popular general-purpose network inference methods and PMR-based methods. We apply MRPC to distinguish direct and indirect targets among multiple genes associated with expression quantitative trait loci. Our method is implemented in the R package MRPC, available on CRAN (https://cran.r-project.org/web/packages/MRPC/index.html).

Field of study: Biology
Neutron scattering and protein dynamics.

Neutrons play an important role in the study of proteins. The best known example is the determination of protein structures using neutron diffraction. Less well known, but possibly even more important in the future, is the determination of protein fluctuations using neutron scattering. Here, the background is sketched and some recent measurements are described that show how a relevant and revealing range of relaxation rates can be explored.

Field of study: Chemistry
Ext-enhanced monoidal Koszul duality for $\mathrm{GL}_2$.

The Hecke category participates in an equivalence called monoidal Koszul duality, which exchanges it with the category of (Langlands-dual) "free-monodromic tilting sheaves." Motivated by a recent conjecture of Gorsky and the first-named author on HOMFLYPT link homology, we propose to enhance this duality with an additional grading. We provide evidence for this enhancement in the case of $\mathrm{GL}_2$, working in the language of the second-named author's joint work with Achar, Riche, and Williamson.

Field of study: Mathematics
Effect of Support on the Suppression of Hot Spot Formation in the Partial Oxidation of Methane

Ni-based catalysts supported on perovskite oxides and α-Al 2 O 3 were prepared to investigate catalytic performance and catalyst bed temperature profile in the partial oxidation of methane. Ni/LaAlO 3 showed high activity and remarkably suppressed hot spot formation in the catalyst bed even at high space velocity. The effect of support is discussed on the basis of the state of Ni.

Field of study: Chemistry
An ALMA survey of submillimeter galaxies in the COSMOS field: Multiwavelength counterparts and redshift

We carried out targeted ALMA observations of 129 fields in the COSMOS region at 1.25 mm, detecting 152 galaxies at S/N ≥ 5with an average continuum RMS of 150 μJy. These fields represent a S/N-limited sample of AzTEC/ASTE sources with 1.1 mm S/N≥ 4 over an area of 0.72 square degrees. Given ALMA’s fine resolution and the exceptional spectroscopic and multiwavelength photometric data available in COSMOS, this survey allows us unprecedented power in identifying submillimeter galaxy counterparts and determining their redshifts through spectroscopic or photometric means. In addition to 30 sources with prior spectroscopic redshifts, we identified redshifts for 113 galaxies through photometric methods and an additional nine sources with lower limits, which allowed a statistically robust determination of the redshift distribution. We have resolved 33 AzTEC sources into multi-component systems and our redshifts suggest that nine are likely to be physically associated. Our overall redshift distribution peaks at z ~ 2.0 with a high-redshift tail skewing the median redshift to z = 2.48 ± 0.05. We find that brighter millimeter sources are preferentially found at higher redshifts. Our faintestsources, with S_(1.25 mm) 1.8 mJy, have a median redshift of z = 3.08 ± 0.17. After accounting for spectral energy distribution shape and selection effects, these results are consistent with several previous submillimeter galaxy surveys, and moreover, support the conclusion that the submillimeter galaxy redshift distribution is sensitive to survey depth.

Field of study: Physics