nils-herrmann/clean_scirepeval huggingface dataset:
Rapid temporal changes in the expression of a set of neuromodulatory genes during alcohol withdrawal in the dorsal vagal complex: molecular evidence of homeostatic disturbance.

Chronic alcohol exposure produces neuroadaptation, which increases the risk of cellular excitotoxicity and autonomic dysfunction during withdrawal. The temporal progression and regulation of the gene expression that contributes to this physiologic and behavioral phenotype is poorly understood early in the withdrawal period. Further, it is unexplored in the dorsal vagal complex (DVC), a brainstem autonomic regulatory structure.



We use a quantitative polymerase chain reaction platform to precisely and simultaneously measure the expression of 145 neuromodulatory genes in more than 100 rat DVC samples from control, chronically alcohol-exposed, and withdrawn rats. To gain insight into the dynamic progression and regulation of withdrawal, we focus on the expression of a subset of functionally relevant genes during the first 48 hours, when behavioral symptoms are most severe.



In the DVC, expression of this gene subset is essentially normal in chronically alcohol-exposed rats. However, withdrawal results in rapid, large-magnitude expression changes in this group. We observed differential regulation in 86 of the 145 genes measured (59%), some as early as 4 hours into withdrawal. Time series measurements (4, 8, 18, 32, and 48 hours after alcohol removal) revealed dynamic expression responses in immediate early genes, γ-aminobutyric acid type A, ionotropic glutamate, and G-protein coupled receptors and the Ras/Raf signaling pathway. Together, these changes elucidate a complex, temporally coordinated response that involves correlated expression of many functionally related groups. In particular, the expression patterns of Gabra1, Grin2a, Grin3a, and Grik3 were tightly correlated. These receptor subunits share overrepresented transcription factor binding sites for Pax-8 and other transcription factors, suggesting a common regulatory mechanism and a role for these transcription factors in the regulation of neurotransmission within the first 48 hours of alcohol withdrawal.



Expression in this gene set is essentially normal in the alcohol-adapted DVC, but withdrawal results in immediate, large-magnitude, and dynamic changes. These data support both increased research focus on the biological ramifications of alcohol withdrawal and enable novel insights into the dynamic withdrawal expression response in this understudied homeostatic control center.

Field of study: Medicine
In situ detection of protein-hydrolysing microorganisms in activated sludge.

Protein hydrolysis plays an important role in the transformation of organic matter in activated sludge wastewater treatment plants, but no information is currently available regarding the identity and ecophysiology of protein-hydrolysing organisms (PHOs). In this study, fluorescence in situ enzyme staining with casein and bovine serum albumin conjugated with BODIPY dye was applied and optimized to label PHOs in activated sludge plants. A strong fluorescent labeling of the surface of microorganisms expressing protease activity was achieved. Metabolic inhibitors were applied to inhibit the metabolic activity to prevent uptake of the fluorescent hydrolysates by oligopeptide-consuming bacteria. In five full-scale, nutrient-removing activated sludge plants examined, the dominant PHOs were always different morphotypes of filamentous bacteria and the epiflora attached to many of these. The PHOs were identified by FISH using a range of available oligonucleotide probes. The filamentous PHOs belonged to the candidate phylum TM7, the phylum Chloroflexi and the class Betaproteobacteria. In total they comprised 1-5% of the bacterial biovolume. Most of the epiflora-PHOs hybridized with probe SAP-309 targeting Saprospiraceae in the phylum Bacteroidetes and accounted for 8-12% of the total bacterial biovolume in most plants and were thus an important and dominant part of the microbial communities.

Field of study: Biology, Environmental science
Partial fraction decompositions and an algorithm for computing the vector partition function

This paper gives an exposition of well known results on vector partition functions. The exposition is based on works of M. Brion, A. Szenes and M. Vergne and is geared toward explicit computer realizations. In particular, the paper presents two algorithms for computing the vector partition function with respect to a finite set of vectors $I$ as a quasipolynomial over a finite set of pointed polyhedral cones. We use the developed techniques to relate a result of P. Tumarkin and A. Felikson (and present an independent proof in the particular case of finite-dimensional root systems) to give bounds for the periods of the Kostant partition functions of $E_6$, $E_7$, $E_8$, $F_4$, $G_2$ (the periods are divisors of respectively 6, 12, 60, 12, 6). 
The first of the described algorithms has been realized and is publicly available under the Library General Public License v3.0 at {this http URL}. We include (non-unique) partial fraction decompositions for the generating functions of the Kostant partition function for $A_2$, $A_3$, $A_4$, $B_2$, $B_3$, $C_2$, $C_3$, $G_2$ in the appendix.

Field of study: Mathematics
[Construction and identification of infectious molecular clone of foot-and-mouth disease virus strain O/CHINA/99].

Nine primers were designed for the full-length genome of O/CHINA/99 and each sequence fragment was obtained by RT-PCR, and cloned into pOK12 vecter, the full-length genome cDNA clone of O/CHINA/99 was identified by restriction enzymes digestion, PCR, and the whole genome sequencing. The results showed that the O/CHINA/99 whole genome was formed with the length of 8200 nt. The nucleotide sequence of the full-length cDNA shared 99.1% homology with its prototype. RNA synthesized in vitro by means of a bacteriophage T7 promter inserted in front of the cDNA led to the production of infectious particle upon transfection of BHK-21 cell using lipofectamine reagent, as shown by cytopathic effects. The rescued virus had high pathogenicity in mice by endermic infection too. All the results showed that an infectious molecular clone was successfully constructed and rescued virus could be obtained.

Field of study: Biology
Source—sink characteristics of carbon transport in Chara hispida

Rates of uptake of 14C-labelled inorganic carbon were measured for whole Chara hispida plants, detached parts of the shoot and isolated (split-chamber technique) apices, lateral branchlets and rhizoid—node complexes. 
 
The rates of inorganic carbon uptake by the rhizoid—node complex expressed per gram fresh weight whole plant were three to four orders of magnitude less than the uptake for the whole plant. Up to 70% of the carbon taken up by the rhizoid—node complex was translocated to the shoot. After 12 h exposure to 14C-labelled inorganic carbon the concentration of 14C was greater in apices than in uppermost or central internodal cells and in all lateral branchlets, regardless of whether label was supplied to the whole plant or isolated rhizoid—node complexes. Measurement of inorganic carbon uptake by detached internodal cells and detached and isolated apices and lateral branchlets showed that lateral branchlets had the greatest rates of inorganic carbon uptake. During 12 h exposure to 14C, isolated lateral branchlets translocated to the attached shoot 55% of the labelled carbon taken up; for isolated apices this value was only 13%. 
 
It is concluded that it is highly unlikely that the rhizoid of Chara hispida could acquire a significant fraction of the whole plant requirement for inorganic carbon and that apices are sink regions for photosynthate while lateral branchlets are source regions.

Field of study: Environmental science
Flemish versus Netherlandish: A Discourse of Nationalism

This essay shows how scholarship on fifteenth-century Flemish panel painting became intertwined with efforts at national identity-building in nineteenth and early twentieth-century Europe. Paintings such as Jan van Eyck's Ghent Altarpiece were not only dispersed across regional and national boundaries, but were intellectually appropriated for competing national programs. The paintings consequently became a site of conflict between the Latin and Germanic traditions. These conflicts are clearly visible through the shifting terminology of this art, variously claimed as ``Flemish'' and ``Netherlandish.'' Such nationalist discourses shaped future scholarship on Flemish painting and contributed to its perceived inferiority vis-a-vis the Southern artistic tradition.

Field of study: History
Community structure explains antibiotic resistance gene dynamics over a temperature gradient in soil

Soils are reservoirs of antibiotic resistance genes (ARGs), but environmental dynamics of ARGs are largely unknown. Long‐term disturbances offer opportunities to examine microbiome responses at scales relevant for both ecological and evolutionary processes and can be insightful for studying ARGs. We examined ARGs in soils overlying the underground coal seam fire in Centralia, PA, which has been burning since 1962. As the fire progresses, previously hot soils can recover to ambient temperatures, which creates a gradient of fire impact. We examined metagenomes from surface soils along this gradient to examine ARGs using a gene‐targeted assembler. We targeted 35 clinically relevant ARGs and two horizontal gene transfer‐related genes (intI and repA). We detected 17 ARGs in Centralia: AAC6‐Ia, adeB, bla_A, bla_B, bla_C, cmlA, dfra12, intI, sul2, tetA, tetW, tetX, tolC, vanA, vanH, vanX and vanZ. The diversity and abundance of bla_A, bla_B, dfra12 and tolC decreased with soil temperature, and changes in ARGs were largely explained by changes in community structure. We observed sequence‐specific biogeography along the temperature gradient and observed compositional shifts in bla_A, dfra12 and intI. These results suggest that increased temperatures can reduce soil ARGs but that this is largely due to a concomitant reduction in community‐level diversity.

Field of study: Biology, Environmental science
Application of Boiler Plasma Ignition Burner and Effect Analysis

This article gives a brief introduction of the working principles of plasma ignition.According to the successful application of this burner on No.5 and No.6 boilers of Datang thermal power plant in Luoyang,the paper analyzes the configuration,debugging,operation mode,operation control parameters,considerations and so on in the plasam ignition system,and summarizes the reliable running measures of the plasma burner in the boiler start-up and steady combustion at low load,and briefly explains the collocating position of plasma burner in boiler.It has great reference significance in guiding the practical operation of plasma ignition and promoting application of this technology,especially in the newly built thermal power project.

Field of study: Engineering, Physics
Magnetoplasmons in modulated two-dimensional electronic systems

By using an analytically derived dynamical density response function of a unidirectional periodically modulated two-dimensional electron gas under a perpendicular magnetic field, we study the magnetoplasmon modes in this system within the random-phase approximation. It is found that the modulation potential does not introduce an additional low frequency mode nor cause high frequency magnetic oscillations in the principal magnetoplasmon mode, as has been previously reported. However, there exists a shift in the principal mode due to the modulation, and this shift is a slow oscillatory function of the inverse magnetic field.

Field of study: Materials science
Microscopic analysis of p^{10}B scattering at the intermediate energies

The differential cross sections of the p^{10}B scattering at energies of 197, 600 and 1000 MeV have been calculated within the framework of the Glauber theory. The operator of multiple scattering takes into account the contributions of single and double collisions. The contributions from protons scattering on the nucleons of different shells have been estimated in the single-scattering cross-section. The comparison with the experiment at 197 MeV and with DWBA calculation showed the adequate description of cross-sections in the region of the front angles.

Field of study: Physics
Similarities and differences in adsorption mechanism of dichlorvos and pymetrozine insecticides with coconut fiber biowaste sorbent

In this study, the similarities and differences of the adsorption mechanisms between dichlorvos and pymetrozine and coconut fiber biowaste sorbent (CF-BWS) were investigated. CF-BWS was produced using the slow pyrolysis process at 600 °C for 4 h. HCl acid modification was used to improve the specific surface area. The properties of CF-BWS were analyzed by SEM, FT-IR, BET, and pHpzc. The adsorption kinetics of dichlorvos and pymetrozine on the CF-BWS were well explained by the pseudo-second-order model. The adsorption isotherms for both insecticides were followed the Langmuir isotherm. The difference in molecular structures and surface chemistry caused the difference in adsorption mechanisms of both insecticides. The pore-filling and the hydrophobic interactions were the key mechanisms for both insecticide adsorptions. However, the π–π electron donor–acceptor interaction played the major role in the pymetrozine adsorption but hardly impacted on the adsorption of dichlorvos. The hydrogen bonding mechanism was pronounced in the pymetrozine adsorption, but it had little influence on the dichlorvos adsorption. The CF-BWS is exhibited as an excellent material for the removal of both pollutants and has high potential to be used further as the adsorbent in water treatment process.

Field of study: Agricultural and Food sciences
A new method of preparing 1, 2, 4-triazole carboxylic-3 acids

A new convenient method of preparing 1, 2, 4-triazole carboxylic acids-3 is worked out. Aminoguanidine bicarbonate and oxalic acid give 5-amino-1, 2, 4-triazole carboxylic acid-3, and this is converted, via the diazotriazole carboxylic acid and treatment of the latter with methanol, to 1, 2, 4-triazole carboxylic-acid-3.

Field of study: Chemistry
Effects of Understanding the Problem Statement on Students’ Mathematical Performance of Senior Secondary Schools in Borno

The study assessed the relative effectiveness of understanding the problem statement on students’ mathematical behaviours in Borno State Secondary Schools. The study was guided by an objective: to determine the Understanding the problem statement on student’s performance in senior secondary school and a null hypothesis: there was no effect of understanding of mathematical problem statement on students’ performance in Borno State senior secondary school. Quasi-experimental design was used for the study. Out of 468 senior secondary two (SSII) students, 160 students were selected for this study through random sampling technique. Ten mathematics achievement tests were developed in the area of algebraic process as a research instrument for the study. The experiment was conducted for eighty sessions spread across four weeks. Pre-test and post-test results were used as data. The analysis of the data was done by t-test of independent means. The study revealed that understanding the problem statement has significantly increased on students mathematical behaviours. Therefore, the study recommended that understanding the problem statement technique should be used in teaching mathematical problem solving in secondary education.  Understanding, Problem Solving, Mathematical Behaviours and Student Performance

Field of study: Education
Global change and the biogeochemistry of the North Sea: the possible role of phytoplankton and phytoplankton grazing

Phytoplankton plays a dominant role in shelf biogeochemistry by producing the major part of organic matter. Part of the organic matter will reach the sediment where diagenetic processes like denitrification, apatite formation or burial will remove nutrients from the biogeochemical cycle. In this article current knowledge on the decadal plankton variability in the North Sea is summarized and possible implications of these changes for the biogeochemistry of the North Sea are discussed. Most of the observed interdecadal dynamics seem to be linked to large-scale oceanographic and atmospheric processes. Prominent changes in the North Sea ecosystem have taken place around 1979 and 1988. In general, the phytoplankton color (CPRS indicator of phytoplankton biomass) reached minimum values during the end of the 1970s and has increased especially since the mid 1980s. Changes with a similar timing have been identified in many time series from the North Sea through the entire ecosystem and are sometimes referred to as regime shifts. It is suggested that the impact of global change on the local biogeochemistry is largely driven by the phyto- and zooplankton dynamics during spring and early summer. At that time the extent of zooplankton–phytoplankton interaction either allows that a large part of the new production is settling to the sediment, or that a significant part of the new production including the fixed nutrients is kept within the pelagic system. The origin of the extent of the phytoplankton–zooplankton interaction in spring is probably set in the previous autumn and winter. In coastal areas, both large-scale atmospheric and oceanographic changes as well as anthropogenic factors influence the long-term dynamics. Due to eutrophication, local primary production nowadays still is up to five times higher than during pre-industrial conditions, despite a decreasing trend. Recently, introduced species have strengthened the filter feeder component of coastal ecosystems. Especially in shallow coastal seas like the Wadden Sea, this will enhance particle retention, shift organic matter degradation to the benthic compartment and enhance nutrient removal from the biogeochemical cycle by denitrification or apatite formation.

Field of study: Environmental science
Quantitation of anti-RNP and anti-Sm antibodies in MCTD and SLE patients by immunoblotting.

A quantitative immunoblotting assay (QIBA) for the determination of specific antibody titres in human autoimmune sera is described. In this assay, a total HeLa nuclear protein fraction, immobilized on nitrocellulose blot strips, was used as source of antigens and immunoreactive species of autoantibodies were quantitated by an enzyme linked second antibody procedure. Besides being more discriminative, QIBA appeared to be up to 500 times more sensitive than immunodiffusion or immunoelectrophoresis. In this study we used 21 sera from patients with SLE or MCTD for a quantitative analysis of their specific autoantibody content. Within this group, a very diverse spectrum of antibody populations was observed; anti-RNP sera appeared to contain, among others, high tired antibody versus 70K and 31K polypeptides while all (n = 6) anti-Sm sera recognized a 25kD protein doublet. In a follow-up study of two MCTD patients significant flares in specific antibody content could be observed.

Field of study: Biology, Medicine
Evaluating emission widths of giant dipole resonances in a Fermi liquid model

It is shown in the theory of finite Fermi systems that giant resonances can be considered as zero-sound excitations in concrete nuclei. Solutions to the zero-sound dispersion equation in symmetric nuclear matter, ωs(k), are obtained. Hydrodynamic models determine the wave vector kA corresponding to giant resonance in a nucleus with atomic number A. The real and imaginary parts of ωs(kA) compare to the energy and escape width of giant resonance. Calculations are performed for giant dipole resonances.

Field of study: Physics
Natural and synthetic substances related to human health (IUPAC Technical Report)

There is a widespread belief on the part of the general public that natural substances are inherently superior to synthetic substances with regard to efficacy and safety in matters related to human health. This question is examined by reviewing the therapeutic use of drugs and herbal medicine preparations, the role of vitamins and nutrients, and the effects of toxic substances. A comparison of the characteristics of natural and synthetic substances within these categories shows a similar range of favorable and unfavorable effects. It is apparent that molecular structure and dose determine the effect of substances on human health, not whether they are of natural or synthetic origin.

Field of study: Chemistry
Fast and scalable conflict detection for packet classifiers

Packet filters provide rules for classifying packets based on header fields. High speed packet classification has received much study. However, the twin problems of fast updates and fast conflict detection have not received much attention. A conflict occurs when two classifiers overlap, potentially creating ambiguity for packets that match both filters. For example, if Rule 1 specifies that all packets going to CNN be rate controlled and Rule 2 specifies that all packets coming from Walmart be given high priority, the rules conflict for traffic from Walmart tc CNN. There has been prior work on efficient conflict detection for two-dimensional classifiers. However, the best known algorithm for conflict detection for general classifiers is the naive O(N2) algorithm of comparing each pair of rules for a conflict. In this paper, we describe an efficient and scalable conflict detection algorithm for the general case that is significantly faster. For example, for a database of 20000 rules, our algorithm is 40 times faster than the naive implementation. Even without considering conflicts, our algorithm also provides a packet classifier with fast updates and fast lookups that can be used for stateful packet filtering.

Field of study: Computer science
Choice models for predicting divisional winners in major league baseball

Major league baseball in the United States is divided into two leagues and four divisions. Each team plays 162 games against teams in the same league. The winner in each division is the team winning the most games of the teams in that division. We wish to predict the division winners based on games played up to any specified time. We use a generalized choice model for the probability of a team winning a particular game that allows for different strengths for each team, different home advantages, and strengths varying randomly with time. Future strengths and the outcomes of future games are simulated using Markov chain sampling. The probability of a particular team winning the division is then estimated by counting the proportion of simulated seasons in which it wins the most games. The method is applied to the 1991 National League season.

Field of study: Mathematics
RESEARCH STATUS AND PERSPECTIVE ON EXTERNALLY PRESTRESSED STEEL-CONCRETE COMPOSITE BEAMS

An externally prestressed steel-concrete composite beam is a new type of structural member combining a steel-concrete composite beam and prestressing technique.Compared with traditional steel-concrete composite beams,prestressed steel-concrete composite beams have six major advantages: 1) increasing the ultimate loading capacity;2) extending the elastic range of structural behavior;3) improving the fatigue and fracture behavior;4) fully utilizing the materials and reducing the structural height and weight;5) decreasing the deformation under service loading;6) being helpful to the crack-width control.Based on the review of available research work of externally prestressed steel-concrete composite beams,the research projects to be conducted are proposed.

Field of study: Engineering