nils-herrmann/clean_scirepeval huggingface dataset:
Presence of splice variant forms of cytochrome P4502D1 in rat brain but not in liver.

Cytochromes P450 (P450), a family of heme-containing proteins, is involved in the oxidative metabolism of both foreign and endogenous compounds. Although liver is quantitatively the major organ involved in the metabolism of most xenobiotics, there is increasing evidence that these enzymes are present in extrahepatic tissues, such as lung, kidney, brain, etc and they may contribute to the in situ metabolism of xenobiotics in these organs. The possible relationship between genetic polymorphism seen in P4502D6 and incidence of neurodegenerative diseases, such as Parkinson's disease, has prompted the characterization of P4502D enzymes in rat brain. In the present study, we demonstrate that P4502D1 (the rat homologue of human P4502D6) is constitutively expressed in rat brain and the mRNA and protein are localized predominantly in neuronal cell population in the olfactory bulb, cortex, cerebellum, and hippocampus. An alternate spliced transcript of CYP2D1 having exon 3 deletion was detected in rat brain but not in liver. Deletion of exon 3 causes frame shift and generates a stop codon at 391 bp relative to the start codon ATG leading to premature termination of translation. Thus, Northern blotting and in situ hybridization represent contributions from functional transcripts and alternate spliced variants that do not translate into functional protein. Further, the splice variant having partial inclusion of intron 6 detected in human brain was not detected in rat brain indicating that alternate spliced gene products of P450 enzymes are generated in species-specific and tissue-specific manner.

Field of study: Biology
Contralateral interhemispheric, transfalcine approach with asleep motor mapping for parasagittal lesions near the medial precentral gyrus.

The contralateral interhemispheric approach has several advantages for approaching parasagittal lesions, including lesions involving or approaching the medial precentral gyrus. Supplementing the interhemispheric approach with asleep motor mapping is useful for confirming the location of the corticospinal tracts from the contralateral transfalcine corridor and identifying subcortical motor fibers at the deep aspect of the resection cavity. The authors describe the contralateral interhemispheric, transfalcine approach with asleep motor mapping to resect a parasagittal metastatic lesion involving the medial precentral gyrus. The video can be found here: https://youtu.be/L-fJ6m5kOWs .

Field of study: Medicine
A new method of synthesizing mesoionic 1,2,4-triazole-3-thiones and their spectra

Mesoionic 1,2,4-triazole-3-thiones have been synthesized by the reaction of 1-acyl-1-arylhydrazines and 1-acyl-1-alkylhydrazines with isothiocyanates in the presence of triethylamine. The structure of the compounds obtained has been confirmed by a study of their UV, IR, PMR, and mass spectra.

Field of study: Chemistry
Using Social Cognitive Theory to Explain the Intention of Final-year Pharmacy Students to Undertake a Higher Degree in Pharmacy Practice Research

To develop and test a conceptual model that hypothesized student intention to undertake a higher degree in pharmacy practice research (PPR) would be increased by self-efficacy, outcome expectancy, and the social influence of faculty members.  Cross-sectional surveys were completed by 387 final-year pharmacy undergraduates enrolled in 2012 and 2013. Structural equation modeling was used to explore relationships between variables and intention.  Fit indices were good. The model explained 55% of the variation in intention. As hypothesized, faculty social influence increased self-efficacy and indirectly increased outcome expectancy and intention.  To increase pharmacy students’ orientation towards a career in PPR, faculty members could use their social influence by highlighting PPR in their teaching.

Field of study: Education, Medicine
Uptake by cucurbitaceae of soil-Bome contaminants depends upon plant genotype and pollutant properties.

Three Cucurbitaceae, Cucurbita pepo L. subsp. pepo (cv. Black Beauty, true zucchini), Cucurbita pepo L. intersubspecific cross (cv. Zephyr, summer squash), and Cucumis sativis (cv. Marketmore, cucumber), were grown in rhizotrons containing soil contaminated with three classes of highly weathered, hydrophobic organic contaminants: (1) technical chlordane, (2) dichlorodiphenylethanes (DDT and DDD) and -ethene (DDE), (3) polyaromatic hydrocarbons (PAHs), and heavy metal residues. Movement of the contaminants through the soil/plant system was studied by comparing contaminant concentration in the bulk soil, the rhizosphere soil pore water, the xylem sap, and aerial tissue. This permitted, for the first time, calculation of bioconcentration factors (BCFs) based on concentration in the xylem sap versus that in the rhizosphere soil pore water. The bioconcentration factors so determined for the sum of five chlordane residues (two enantiomers of trans-chlordane, TC; two enantiomers of cis-chlordane, CC; and achiral trans-nonachlor, TN) were 36, 40, and 23 for Black Beauty, Zephyr, and Marketmore, respectively. In addition, the xylem sap of each cultivar had a consistent enantioselective profile for some of the chiral chlordane components. For the sum of dichlorodiphenylethanes and -ethene, comparable BCF values were 19, 4, and 0.8, respectively. In the case of PAHs, different BCF patterns among the cultivars were noted for three- versus four-ring compounds. Similarly, movement of heavy metals was cultivar-dependent, with cadmium BCF values 9.5, 3.5, and 0.6for Black Beauty, Zephyr, and Marketmore, respectively; the analogous BCFs for zinc were 9, 11, and 2. Thus, passage from ex planta to in planta regions of the soil/plant system is dependent not only on properties of the plant, but also on those of the pollutant. Such data will provide insight into transport mechanisms of highly hydrophobic organic contaminants, as well as heavy metal contaminants, in the soil/plant system.

Field of study: Environmental science
Human Respiratory Monitoring Based on Schottky Resistance Humidity Sensors

Two types of Schottky structure sensors (silicon nanowire (SiNW)/ZnO/reduced graphene oxide (rGO) and SiNW/TiO2/rGO) were designed, their humidity resistance characteristics were studied, and the sensors were applied to detect sleep apnea through breath humidity monitoring. The results show that the resistance of the sensors exhibited significant changes with increasing humidity, the response times of the two sensors within the relative humidity range of 23–97% were 49 s and 67 s, and the recovery times were 24 s and 43 s, respectively. Meanwhile, continuous breathing monitoring results indicate that the sensitivity of the sensors remained basically unchanged during 10 min of normal breathing and simulated apnea. The response of the sensor is still good after 30 days of use. We believe that the Schottky structure composite sensor is a very promising technology for human breathing monitoring.

Field of study: Materials science
Cirrhosis: a new, but expected cause of biliary sludge.

Biliary sludge is increasingly recognized as a natural stage in gallstone formation. Logically, cirrhosis, a well-documented cause of black pigment cholelithiasis, should be another condition predisposing to the development of sludge. The aim of this study was to assess the prevalence of biliary sludge in an unselected population and to test the hypothesis that cirrhosis could be one of the causes of sludge.



We reviewed the clinical findings and ultrasonograms of 2138 patients, hospitalized or not, consecutively seen in our department between January 1993 and December 1994. Sonograms showing biliary sludge mixed with stones were excluded. Three hundred and eighty-eight of the 2138 were cirrhotic patients.



The overall prevalence of biliary sludge was 4%. Sludge was found in 44 of 388 (11%) of the cirrhotic patients (alcoholism, n = 39; chronic viral B hepatitis, n = 3; hemochromatosis, n = 1; and cryptogenic, n = 1), compared with 42 of 1750 (2%) noncirrhotic patients (p < 0.000001). Thirteen cirrhotic patients received intravenous alimentation for 2 to 17 days, 8 were given somatostatin for variceal bleeding, and 7 have previously had 1 to 5 sessions of endoscopic sclerotherapy of esophageal varices with polidocanol.



This study convincingly demonstrates that cirrhosis must be added to the growing list of conditions associated with biliary sludge.

Field of study: Medicine
GC-MS analysis of aroma components in fermented Coix seed wine

The aromatic components in Coix seed wines fermented with saccharomyces cerevisiae 1394 were analyzed by the method of headspace solid-phase microextraction(HS-SPME) coupled to GC-MS.The results showed that 50 aromatic compounds were identified totally.These compounds includes 17 kinds of esters(60.32%) ,3 kinds of acids(3.06%) ,4 kinds of alcohols(6.66%) and 2 kinds of phenols(10.39%) .The main aromatic compounds were octylic acid ethyl ester,decanoic acid ethyl ester,Hex-4-enoic acid ethyl ester,butylated hydroxytoluene and 1-Butanol-3-methyl,with relative contents of 29.54%,10.38%,9.25%,9.28% and 4.05% respectively.The butylated hydroxytoluene is a kind of anti-oxidation agent,which has the function of preventing cardiovascular disease,cancer and others.

Field of study: Agricultural and Food sciences
Helicobacter pylori VacA up-regulates secretion of macrophages by activating nuclear factor kB

To study the effect of VacA on the secretion of THP-1 macrophages as an individual virulence determinant, and the effect of NF-kB on the secretion of THP-1 macrophages.  The recombinant plasmid pDsRed-Monomer-Cl/vacA was transfected into macrophages. The cytokine con-tent of TNF-α or IL-1β in the culture medium was tested quantitatively with ELISA kit, respectively. The content of NO or ROS in the culture medium was tested with Griess reagent or DCFH-DA fluorescent probe. The apoptosis rate of macrophages was tested by flow cytometry. The effect of PDTC, an inhibitor of NF-kB, on the secretion and apoptosis of macrophages transfected with the recombinant plasmids, was also studied. The activity of NF-kB was examined in THP-1 cells by electrophoretic mobility gel shift assay(EMSA). Re-suits At 6 h after transfection, the level of TNF-α and IL-1 β in macrophages transfected with the recombi-nant plasmids was significantly higher than that of the control group (P <0.05). At 6 h or 12 h after trans-fection, the level of NO and ROS in macrophages transfected with the recombinant plasmids was significantly higher than that of the control group (P <0.05). At 16 h after transfection, the apoptosis rate of macropha-ges transfected with the recombinant plasmids was significantly higher than that of the control group (P < 0.05). PDTC decreased the production of TNF-α, IL-1 β, NO, ROS and apoptosis rate induced by VacA. VacA was found to trigger NF-kB activation.  The over-expression of VacA fusion protein can up-regulate secretion and apoptosis of macrophages. Activation of NF-kB is probably involved in the produc-tion of TNF-α, IL-1β, NO, ROS and apoptosis induced by VacA. 
 
 
Helicobacterpylori;  VacA;  Macrophages;  Apoptosis;  NF-kB

Field of study: Biology
Stability of density-based clustering

High density clusters can be characterized by the connected components of a level set L(λ) = {x : p(x) > λ} of the underlying probability density function p generating the data, at some appropriate level λ ≥ 0. The complete hierarchical clustering can be characterized by a cluster tree T = ∪λ L(λ). In this paper, we study the behavior of a density level set estimate L(λ) and cluster tree estimate T based on a kernel density estimator with kernel bandwidth h. We define two notions of instability to measure the variability of L(λ) and T as a function of h, and investigate the theoretical properties of these instability measures.

Field of study: Computer science
Some Speculations Regarding the Lower Hidden Zone of the Dore Lake Complex and Its Potential Mineral Resources

Note: This paper is dedicated to Aaron and Elizabeth Waters on the occasion of Dr. Waters' retirement. 

The Dore Lake Complex is an Archean layered intrusion in the Chibougamau area, Quebec. The complex has been folded and metamorphosed to the greenschist facies. The sill-shaped Chibougamau Pluton intrudes the Dore Lake Complex at the level of the Anorthosite Zone, hiding from view the lower 4,000 ft of the complex. The Lower Hidden Zone could contain important deposits of chromite and platinum-group metals.

Field of study: Geology
The Lost Promise of Democratic Socialism in Russia

To explain the failure to create democratic socialism in Russia after the 1917 Bolshevik Revolution, I apply Thorstein Veblen’s vision of economic democracy as a cure for vested interests. In late imperial Russia, many socialist thinkers imagined socialism primarily in terms of workplace democracy, worker ownership, local governance, and economic decentralization. Their vision was destroyed, first, by Bolshevik policies and then by Stalin’s tyrannical command economy. Thereafter, vested interests reemerged in the Soviet Union as an underground economy, rife with theft of public resources, and then, with the beginning of transition, capitalism in its most neoliberal form was restored.

Field of study: Economics
Resistance of mound-building termites to anthropogenic land-use change

Humans pose a major threat to many species through land-use change in virtually every habitat. However, the extent of this threat is largely unknown for invertebrates due to challenges with investigating their distributions at large scales. This knowledge gap is particularly troublesome for soil macrofauna because of the critical roles many of these organisms perform as ecosystem engineers. We used a combination of high-resolution airborne Light Detection and Ranging and deep learning models to map the distribution of the ecologically important termite genus Macrotermes across a South African savanna land-use gradient, quantifying the effects of land-use change on patterns of mound densities, heights and spatial patterning. Despite significant anthropogenic alteration to landscapes, termite mounds persisted and shared a number of similarities to mounds in untransformed areas. Mean mound height was not substantially reduced in transformed landscapes, and over-dispersion of mounds at localized scales was conserved. However, mound densities were partially reduced, and height distributions in transformed areas differed to those in protected areas. Our findings suggest that mound-building termites persist even in areas of relatively high human disturbance, but also highlight important differences in termite distributions that could lead to reductions in ecosystem services provided by termites in human-modified landscapes. The persistence of at least half of mounds in human-modified landscapes could serve as starting points for savanna restoration.

Field of study: Environmental science
English Markets and Royal Administration before 1200

A REGULAR relationship between early markets and hundredal organization has sometimes been suggested, but has never been explored. Studies of hundredal administration3 have not illuminated the association between local trade and local government which students of Anglo-Saxon law were led to expect.4 The separate development of economic and legal studies has caused the original problem to recede from view, so that the relevant questions are no nearer an answer now than they were seventy years ago. Yet the extent to which private trade in the early Middle Ages was facilitated, obstructed, or regulated by the institutions of government has enough interest to merit investigation for its own sake as well as for its bearing on the development of marketing institutions in later and better-documented periods.

Field of study: Economics, History
Limites tolérables et limites sûres

On entend par concentrations tolerables des toxiques industriels la quantite a laquelle on peut generalement exposer les ouvriers, durant une periode de temps illimitee, sans qu'il on derive des alterations cliniquement relevables. Si cette exposition a lieu dans des conditions de travail ou ambiantales difficiles, et le sujet n'est pas parfaitement sain, ou si la concentration est apeine superieure, cela n'exclus pas la possibilite d'apparition de symptomes de maladies professionnelles. Les concentrations absolument privees d'effets nocifs, quelque soient les sujets exposes, quelque soient les modalites et la duree de l'exposition, sont designees sous le nom de "concentrations sures ", et elles sont toujours beaucoup plus basses que celles tolerables. Devant l'importance de la defense de la sante des ouvriers et les enormes progres techniques accomplis, qui permettent des mesures preventives de plus en plus aisees et efficaces, on doit demander si les hygienistes et les medecins du travail peuvent continuer a considerer comme admissibles des concentrations qui ne donnent pas la certitude absolue de leur innocuite sur l'ouvrier. II faut, en effet, considerer que souvent les conditions de sante individuelles ne sont pas parfaites, qu'il n'est pas rare que le travail, en raison de sa duree ou de son rythme, comportent une fatigue importante, et se deroule dans des conditions defavorables, etc. Il semblerait opportun actuellement de ne considerer comme admissibles que les concentrations qui soient parfaitement sures, Mais, meme si l'on veut differentier les deux entites d'exposition, il est important de separer nettement Ie sens de " tolerabilite " de celui d'" adrnissibilite " de la part des hygienistes, pour l'identifier avec celui de " supportabilite sans danger" de la part du travailleur. La periode de temps alaquelle se referer devrait etre egale ala vie moyenne du travailleur. En pratique, la necessite d'effectuer des releves, afin de delimiter les concentrations, rend peu commode une periode aussi longue et l'on peut considerer provisoirement des periodes plus breves. Les concentrations seraient de cette maniere celles qui peuvent etre supportees sans danger pour des expositions de longue duree, y compris la vie entiere du travailleur, dans les conditions limitatives suivantes: Integrite physique: c'est-a-dire absence de maladie de toute nature ou sequelles, absence de troubles des divers organes ou appareils, absence d'un arnoindrissement du pouvoir de defense par suite d'un age trop jeune ou trop avance ; Conditions de travail normales: c'est-a-dire un travail qui ne comporte pas de fatigue pour des raisons de position, quantite ou rythme;

Field of study: Chemistry
On the definition and the computation of the type-reproduction number T for structured populations in heterogeneous environments

In the context of mathematical epidemiology, the type-reproduction number (TRN) for a specific host type is interpreted as the average number of secondary cases of that type produced by the primary cases of the same host type during the entire course of infection. Here, it must be noted that T takes into account not only the secondary cases directly transmitted from the specific host but also the cases indirectly transmitted by way of other types, who were infected from the primary cases of the specific host with no intermediate cases of the target host. Roberts and Heesterbeek (Proc R Soc Lond B 270:1359–1364, 2003) have shown that T is a useful measure when a particular single host type is targeted in the disease control effort in a community with various types of host, based on the fact that the sign relation sign(R0 − 1) = sign(T − 1) holds between the basic reproduction number R0 and T. In fact, T can be seen as an extension of R0 in a sense that the threshold condition of the total population growth can be formulated by the reproduction process of the target type only. However, the original formulation is limited to populations with discrete state space in constant environments. In this paper, based on a new perspective of R0 in heterogeneous environments (), we give a general definition of the TRN for continuously structured populations in heterogeneous environments and show some examples of its computation and applications.

Field of study: Biology, Mathematics
In vitro cytokine release by activated murine peritoneal macrophages: role of prostaglandins in the differential regulation of tumor necrosis factor alpha, interleukin 1, and interleukin 6.

Distinct subpopulations of macrophages or differently activated macrophages display various functions in immune reactions. Some of their activities depend on specific sets of factors (i.e., cytokines and eicosanoids) produced by activated macrophages. We have studied the ability of murine (CBA/ca) peritoneal macrophages to selectively release tumor necrosis factor alpha (TNF-alpha), interleukin 1 (IL-1), and IL-6. We have found that the priming of cells (Mo) with different stimulants (thioglycolate vs. LPS) induces the release of particular cytokines by reactivated macrophages. The increased release of TNF-alpha correlates with lower levels of IL-1 and IL-6. We have also found that prostaglandin E2 (PGE2) and prostacyclin (PGI2) have opposing effects on the production of two of these cytokines. The release of TNF-alpha is inhibited by prostaglandins, whereas increased levels of PGE2 and PGI2 correlate with higher levels of IL-6.

Field of study: Medicine
To Defend Our Water with the Blood of Our Veins: The Struggle for Resources in Colonial Puebla. By Sonya Lipsett-Rivera. (Albuquerque: University of New Mexico Press, 1999. Pp. xiv, 199. Notes. Bibliography. Index. $49.95.)

A reliable supply of water was necessary to sustain human and animal population and to grow crops in the semi-arid region of Puebla in highland Mexico. Lacking adequate rainfall for productive dry farming, indigenous farmers turned to communal supervision for distribution of water and development and maintenance of irrigation. Since Spanish settlement and the introduction of new crops, notably wheat, in the sixteenth century overlapped with native depopulation of the region, allocation of water long posed no major problem. Expanding native population as from the late seventeenth century, however, created growing conflict over irrigation systems. In the absence of effective centralized authority over the irrigation systems, by the early nineteenth century, large landowners had achieved domination over water in Puebla.

Field of study: History
Optimization of the Pole Shape for Corrector Quadrupole Magnet in the J-PARC 3-GeV RCS

The corrector quadrupole magnet of J-PARC 3-GeV rapid cycling synchrotron (RCS) was developed as a pulse magnet with two functions. One is to correct the effect of magnetic field caused by the edge focus of the injection bump magnet, and the other is to control the tune at high speed during the beginning acceleration process of the beam (16 ms). At the beginning, the magnet is used for the first function. As RCS operates at 1 MW, beam loss needs to be as small as possible. However, beam loss is seen at the injection straight section of RCS caused by the edge focus of the bump magnet. In order to lessen this effect, the first 1 ms of beam injection has to be corrected using a quadrupole magnet. Field measurement was implemented in order to confirm performance of the fabricated magnets. However, the magnet did not show enough performance. We investigated the cause and found out that there was improper input of boundary condition during the magnetic field calculation. Then, a study to restore the magnetic field performance was carried out, and as a result, a pole piece was installed at the minimum gap of the magnetic pole, and the pole shape was optimized. Satisfactory performance of the correction quadrupole magnet with the pole piece was confirmed. In this paper, the authors will report optimization of a pole shape of the correction quadrupole magnets with pole pieces and a result of the field measurement carried out afterward.

Field of study: Physics