nils-herrmann/clean_scirepeval huggingface dataset:
The development of an attenuated Salmonella typhimurium vaccine carrying plamids encoding Helicobacter pylori ureB and IL-2

To construct a recombinant live attenuated Salmonella typhimurium nucleic acid vaccine encoding H.pylori ureB gene and murine interleukin 2 and to identify the immunogenicity of the proteins expressed. Methods ureB gene fragment was amplified with polymerase chain reaction (PCR) from the genomic DNA of standard H.pylori strain 17874 and murine IL 2 gene was amplified from pCIneo IL 2. ureB and IL 2 were cloned into pUCmT vector respectively. Both the genes of ureB and IL 2 were cloned into the eukaryotic expression vector pIRES through a serials of enzyme digestion and ligation reactions, the recombinant plasmids were screened by PCR reaction and restriction enzyme digestion. Then, the recombinant pIRES ureB and pIRES ureB IL 2 were transformed into LB5000 and the recombinant plasmids from LB5000 were then transformed into final host SL7207. The strains were grown in LB medium repeatedly. Recombinant pIRES ureB IL 2 and pIRES ureB were transfected into Cos 7 cells using LipofectAMINE TM 2000, the immunogenicity of UreB and IL 2 protein expressed was detected with SDS PAGE and Western blot.  The 1700 base pair ureB gene fragment and 510 bp IL 2 were amplified and they consistent with the sequence of the H.pylori ureB and murine IL 2 respectively. It was confirmed with PCR and restriction enzyme digestion that H.pylori ureB gene and murine IL 2 were inserted into the eukaryotic expression vector pIRES and a stable recombinant live attenuated Salmonella typhimurium nucleic acid vaccine encoding H.pylori ureB and murine IL 2 was successfully constructed and specific strip of 66kD ureB and 14kD IL 2 was detected through Western blot.  The recombinant attenuated Salmonella typhimurium nucleic acid vaccine strain encoding H.pylori ureB and immune adjuvant IL 2 with immunogenicity in vitro was constructed, it may be helpful for further investigation about the immune function of the nucleic acid vaccine in vivo .

Field of study: Biology
The Generalized Marshall–Olkin Type Multivariate Pareto Distributions

In this paper, two generalized Marshall–Olkin type multivariate Pareto distributions are developed. They are generated by two different methods and are denoted respectively by the notations GMOP(I), (II), (III), (IV) and the reduction multivariate Pareto, RMP(I), (II), (III), (IV). All of them have univariate Pareto as marginals. Several distributional properties of these two alternative multivariate Pareto distributions are studied and two characterization properties of GMOP(I) distribution are thoroughly verified. One special subset of GMOP(IV) family can be generated by a fatal shock model of an m-component system. The multivariate Pareto RMP family is a subclass of GMOP.

Field of study: Mathematics
Effects of HIV infection on the disease progression of hepatitis C in patients with HIV/HCV coinfection

To analyze the differentiation status of CTL and to evaluate its clinical value in patients with HIV/HCV coinfection. 
 
 
 
Twenty-eight patients with HIV/HCV coinfection and twelve patients with single HCV infection were enrolled in this study. The technique of Fibro-Scan was used to evaluate liver fibrosis. The viral load of HCV was detected by real-time quantitative PCR. Flow cytometry analysis was performed to measure the differentiation status of CTL. 
 
 
 
Both of the levels of alanine transaminase (ALT) and alkaline phosphatase (ALP) in patients with HIV/HCV coinfection were significantly higher than those in patients with single HCV infection [(53.7464±48.1180) U/L vs (27.4750±13.9850) U/L, P=0.012; (24.5071±8.1940) g/L vs (16.9667±7.1890) g/L, P=0.009]. The liver stiffness of patients with HIV/HCV coinfection was higher than that of patients with single HIV infection [(5.9500, 5.8250) Kpa vs (5.1500, 1.0500) Kpa, P=0.117]. Compared with the patients with single HCV infection, the patients with HIV/HCV coinfection showed higher viral loads of HCV [(6.4768, 5.3434) lg copy/ml vs (2.6815, 1.6990) lg copy/ml, P=0.012], but lower clearance rate of HCV [32.14% vs 75%, P=0.032]. Compared with the patients with single HCV infection, the patients with HIV/HCV coinfection showed lower percentages of CD27+ CD28+ CTL [(28.265±15.095)% vs (18.068±10.263)%, P=0.017), but higher percentages of CD27+ /-CD28+ CTL [(62.449±14.561)% vs (71.111±12.681)%, P=0.066]. A trend toward negative correlation was observed between the percentage of CD27+ CD28+ CTL and the degree of liver stiffness (r=-0.310, P=0.058). 
 
 
 
HIV infection could accelerate the progression of liver disease in patients with HIV/HCV coinfection by affecting the differentiation of CTL. 
 
 
 
HIV; HCV; Coinfection; CTL differentiation

Field of study: Biology
Latin America in the 21st Century: Toward a New Sociopolitical Matrix (review)

Although it contains only 100 pages of text, this book covers a surprising amount of ground in its analysis of contemporary Latin American political life in the context of economic globalization. It constitutes the product of a decade of discussion among its five authors: three political scientists (Marcelo Cavarozzi of the Universidad Nacional de San Martin in Buenos Aires; Peter Cleaves from the Swiss foundation AVINA; and Jonathan Hartlyn of the University of North Carplina at Chapel Hill) and two sociologists (Manuel Antonio Garreton from the Universidad de Chile; and Gary Gereffi of Duke University). Its six chapters exhibit an unusually consistent focus for a work that resulted from so many pairs of hands at the keyboard.

Field of study: History
Electron Propagation in the Field of Colliding Nuclei at Ultrarelativistic Energies

We calculate the asymptotic high-energy amplitude for electrons scattering at one ion as well as at two colliding ions, respectively, by means of perturbation theory. We show that the interaction with one ion eikonalizes and that the interaction with two ions causally decouples. We are able to put previous results on perturbative grounds and propose further applications for the obtained rules for interactions on the light cone. The formalism will be of use for the calculation of Coulomb corrections to electron-positron pair creation in heavy ion collisions. Finally we discuss the results and inherent dangers of the employed approximations.

Field of study: Physics
An integrated rock-magnetic and geochemical approach to loess/paleosol sequences from Bohemia and Moravia (Czech Republic): Implications for the Upper Pleistocene paleoenvironment in central Europe

Two central European loess/paleosol sequences (MIS 6-2), from central Bohemia (Zeměchy) and southern Moravia (Dobsice), situated in the important climatic transition zone between the oceanic (Atlantic) and continental climate regimes, were investigated for rock magnetism, geochemistry, grain size and micromorphology. In both sites the magnetic profile shows good agreement with the standard model of magnetic enhancement in paleosols as established in the Chinese loess. The magnetic signal is dominated by the presence of fine-grained magnetite and maghemite, formed in-situ and controlled by the intensity of soil formation. Magnetic proxies corresponded to proxies of chemical weathering and leaching intensity such as the Chemical Index of Alteration (CIA), the Cation Exchange Capacity (CEC) and the Rb/Sr ratio (correlation coefficient r = ∼ 0.6–0.93) during the whole Lower Weichselian (MIS 5d–5a) and, in general, also during the Pleniglacial (MIS 4-2). Nevertheless, for the Eemian period (MIS 5e) this relationship was not always valid, either due to weak magnetic enhancement (at Dobsice) or even weak depletion of the magnetic minerals with soil formation (at Zeměchy). The presented data demonstrate that magnetic signals can be overprinted more easily than chemical proxies during later diagenetic events, and are hence not in all cases reliable for deciphering paleoclimate changes during all periods of the studied time interval. Rock-magnetic, geochemical and micromorphological results suggest drier conditions in southern Moravia compared to central Bohemia during the Weichselian Glacial, probably due to the more continental climate in southern Moravia.

Field of study: Environmental science, Geography
Loss of chlorpyrifos in pond water: examination of results using three simple mathematical models.

Four outdoor artificial pools were fortified with two formulations of chlorpyrifos (the active ingredient in Dursban insecticide), as emulsifiable concentrate, and a slow-release granular formulation. From concentration-time data collected during summer months, the half life of chlorpyrifos was found to be 5 +/- 3 h and 14 +/- 4 h for the emulsifiable concentrate and slow release formulations respectively. The concentration-time data was analyzed by three mathematical models; the power rate model, the hyperbolic rate model, and an empirical power function. Their average correlation coefficients, determined by linear regression, were respectively, 0.78 +/- 0.08, 84 +/- 0.07, 0.76 +/- 0.16.

Field of study: Agricultural and Food sciences
Binge alcohol consumption in emerging adults: anterior cingulate cortical "thinness" is associated with alcohol use patterns.

The brain undergoes dynamic and requisite changes into the early 20s that are associated with improved cognitive efficiency, particularly in prefrontal regions that are still undergoing neuromaturation. As alcohol consumption is typically initiated and progresses to binge drinking (BD) during this time, the objective of the present study was to investigate the impact of binge alcohol consumption on frontal lobe cortical thickness in emerging adults.



Twenty-three binge drinking (11 females, mean age 22.0 ± 1.2) and 31 light drinking (15 females, mean age 21.5 ± 1.6) emerging adults underwent high-resolution magnetic resonance imaging at 3 Tesla. Cortical surface reconstruction and thickness estimation were performed using FreeSurfer for 3 a priori brain regions of interest: bilateral anterior cingulate cortex (ACC), posterior cingulate cortex (PCC), and parieto-occipital sulcus (POS). Cortical thickness measurements were then compared between binge drinker (BD) and light drinker (LD) groups.



Cortical thickness was significantly lower in BD than LD in the right middle ACC (mid-ACC; p ≤ 0.05) and in the left dorsal PCC (dPCC; p ≤ 0.01). No significant differences in cortical thickness were observed in the POS. Cortical thickness in the mid-ACC correlated negatively with higher quantity and frequency of drinks consumed (p < 0.01) and positively with the number of days elapsed since most recent use (p < 0.05). Furthermore, less cortical thickness in the mid-ACC in the BD group alone correlated with reported patterns of high quantity and frequency of alcohol consumption (p ≤ 0.05).



Findings suggest that past and recent patterns of intermittent heavy alcohol consumption are associated with less frontal cortical thickness (i.e., "thinness") of the right mid-ACC and left dPCC in emerging adults, but not the POS. While cortical thinness could have predated binge drinking, this pattern of maladaptive consumption may have acute neurotoxic effects that interfere with the finalization of neuromaturational processes in the vulnerable frontal cortex, resulting in increased microarchitectural pruning.

Field of study: Medicine
Organ Donation and the Ars Moriendi

Organ donation is rightly understood as a gift that is a genuine act of love. Organ donation as an act of love requires it to be an act of freedom that honors the integrity of the human person who is in the process of dying. However, the process of organ donation, by necessity, inserts a third party of interest whose primary aim is to assist someone other than the dying person. Caregivers can become “organ focused” instead of “patient focused.” The procurement of organs potentially results in the commodification of the potential organ donor. Furthermore, death is not a momentary event but rather an ontological change in the person where the union of body and soul becomes divided. This Catholic understanding of death is important to assess the impact of organ donation on the process of dying. Family members of organ donors often have traumatic memories associated with the organ donation process, potentially overshadowing the ars moriendi—the art of dying.  While organ donation is an act of love, the donation process can be distraction from the care of the dying patient, who may be treated differently than other dying patients who are not organ donors. A Catholic understanding of death is helpful in assessing the impact of the organ donation process.

Field of study: Medicine, Philosophy
Heat transfer and pressure drop in microchannels with isotropically etched pillars at sub-ambient temperatures

Glass microfluidic devices are often manufactured using micromachining techniques that involve the use of wet etching. In applications where high-pressure fluids are used, the microchannels in the microchip are filled with pillar structures for mechanical strength. Owing to the isotropic nature of the wet etching process, the pillars resulting from this process are shaped as truncated cones. In this paper, we present the results of a numerical study for predicting the flow and the heat transfer characteristics in a microchannel with truncated cone-shaped pillar arrays at sub-ambient temperatures. In order to verify the developed correlations, we use Joule-Thomson microcoolers that contain a counter-flow heat exchanger (CFHX) as test platforms and operate these with nitrogen gas. The performance of the microcoolers predicted with the new correlations matches well with the experimental data. Using these correlations, the CFHX is optimized and the CFHX losses are reduced by more than 30%.

Field of study: Engineering
A Note on Learning Algorithms for Quadratic Assignment with Graph Neural Networks

Inverse problems correspond to a certain type of optimization problems formulated over appropriate input distributions. Recently, there has been a growing interest in understanding the computational hardness of these optimization problems, not only in the worst case, but in an average-complexity sense under this same input distribution. 
In this revised note, we are interested in studying another aspect of hardness, related to the ability to learn how to solve a problem by simply observing a collection of previously solved instances. These 'planted solutions' are used to supervise the training of an appropriate predictive model that parametrizes a broad class of algorithms, with the hope that the resulting model will provide good accuracy-complexity tradeoffs in the average sense. 
We illustrate this setup on the Quadratic Assignment Problem, a fundamental problem in Network Science. We observe that data-driven models based on Graph Neural Networks offer intriguingly good performance, even in regimes where standard relaxation based techniques appear to suffer.

Field of study: Computer science
Reduction and standardization of surgical instruments in pediatric inguinal hernia repair.

To standardize and reduce surgical instrumentation by >25% within a 9-month period for pediatric inguinal hernia repair (PIHR), using "improvement science" methodology.



We prospectively evaluated instruments used for PIHR in 56 consecutive cases by individual surgeons across two separate subspecialties, pediatric surgery (S) and pediatric urology (U), to measure actual number of instruments used compared with existing practice based on preference cards. Based on this evaluation, a single preference card was developed using only instruments that had been used in >50% of all cases. A subsequent series of 52 cases was analyzed to assess whether the new tray contained the ideal instrumentation. Cycle time (CT), to sterilize and package the instruments, and weights of the trays were measured before and after the intervention. A survey of operating room (OR) nurses and U and S surgeons was conducted before and after the introduction of the standardized tray to assess the impact and perception of standardization.



Prior to creating the standardized tray, a U PIHR tray contained 96 instruments with a weight of 13.5 lbs, while the S set contained 51, weighing 11.2 lbs. The final standardized set comprised 28 instruments and weighed 7.8 lbs. Of 52 PIHRs performed after standardization, in three (6%) instances additional instruments were requested. CT was reduced from 11 to 8 min (U and S respectively) to <5 min for the single tray. Nurses and surgeons reported that quality, safety, and efficiency were improved, and that efforts should continue to standardize instrumentation for other common surgeries.



Standardization of surgical equipment can be employed across disciplines with the potential to reduce costs and positively impact quality, safety, and efficiencies.

Field of study: Medicine
The Dynamics of Group Differentiation in the Face of Defeat

This study examined the process of between-group differentiation in a disadvantaged group to see how its members achieved some form of positive in-group distinctiveness. The players on the last-place ice hockey team in a competitive league were tested at eight games. Before and after each game, they were asked to rate how they perceived their team, the opposing team, and themselves. One hypothesis was that players could not ignore their past and present performance and would rate their opponents as superior on attributes that were critical for success. A second hypothesis was that players would achieve a measure of positive distinctiveness by seeing their opponents as more "dirty" in their play. Results, which supported these hypotheses, are discussed within the context of Tajfel and Turner's social identity theory.

Field of study: Psychology
Losses in a BSCCO/Ag tape carrying AC transport currents in AC magnetic fields applied in different orientations

In most prospective electric power applications of high-temperature superconductors (HTSs), the conductor is wound in a coil configuration. For a coil of finite length, the magnetic field orientation is axial in the middle of the coil, while the field contains a substantial radial component at the coil ends. In a superconducting BSCCO/Ag tape, the AC losses depend strongly on the orientation of the magnetic field. In this study, we present experimental results of the AC losses in a multifilamentary silver-sheathed Bi-2223 HTSs tape, carrying alternating transport currents in externally applied alternating magnetic fields at different orientations, with respect to the face of the tape and perpendicular to the transport current. The AC losses were measured calorimetrically, at fixed temperature and frequency. The results are compared to semi-empirical models of the AC losses in HTSs tape. We present a more general model of the angular dependence of the AC losses.

Field of study: Physics
ENZYMATIC ISOLATION AND ENRICHMENT OF ERUCIC ACID FROM HEA SEED OILS: CURRENT STATUS

Erucic acid (EA), a fatty acid of 22-carbon chain with one isolated double bond, has broad industrial applications. Currently, erucic acid is isolated from Crucifereae plant oils through steam splitting, namely the Colgate-Emery process, followed by fractional distillation. This two-step process involves drastic conditions, low energy efficiency, and extensive product degradation. Enzymatic approaches, on the other hand, have many advantages including mild operating conditions and high selectivities. To develop a more efficient alternative process, researchers have studied enzymatic approaches for EA isolation and enrichment for about two decades. Lipases have shown three types of specificities in catalyzing high-erucic-acid (HEA) oils, namely fatty-acid-specific, region-specific, and non-specific. With lipases of certain specificities, various processes of hydrolysis, esterification, interesterification, and transesterification have been studied. Research has also been conducted on investigating the effects of process parameters, including operating temperature, lipase content, and water content, on the process efficiency. The enzymatic approach has shown its potential in isolating and enriching EA from different Crucifereae seed oils. This article reviews the current status of the studies, especially the performance of different lipases and corresponding enzymatic reactions, for EA enrichment from Crucifereae plant oils.

Field of study: Agricultural and Food sciences
Schedule-induced ethanol self-administration in DBA/2J and C57BL/6J mice.

The purpose of these experiments was to provide an initial investigation into ethanol self-administration elicited in the schedule-induced polydipsia (SIP) paradigm.



Mature male mice were food deprived to between 80 and 85% of their baseline weight and received 20 daily 1 hr SIP test sessions in which a food pellet (20 mg) was delivered on a fixed-time 60 sec schedule. In different groups, the acquisition of drinking 5% (v/v) ethanol solution (experiment 1) or water (experiment 2) was recorded along with other behaviors that occurred in the test chambers.



Results indicated that C57BL/6J mice drank significantly more ethanol than DBA/2J mice and that C57 mice achieved blood alcohol concentrations as high as 300 mg/dl. Blood alcohol concentrations were consistently correlated with g/kg ethanol intake. The groups did not differ in consumption of water. SIP test sessions using higher concentrations of ethanol (10-20% v/v, experiment 1) or sucrose solutions (0.1-2% w/v, experiment 2) then were performed. Group differences in ethanol consumption were maintained at all ethanol concentrations. Although DBAs drank more of a low concentration of sucrose (0.1%), when expressed as g/kg, sucrose intake was equivalent in the two strains at all concentrations. Analysis of the time course of drinking clearly showed that this behavior was adjunctive in nature.



These results demonstrate the effectiveness of this procedure in inducing ethanol self-administration and its utility for investigating the genetic bases of vulnerability toward excessive ethanol consumption.

Field of study: Medicine
Classification of irreducible weight modules over higher rank Virasoro algebras

Let G be a rank n additive subgroup of C and Vir[G] the corresponding Virasoro algebra of rank n. In the present paper, irreducible weight modules with finite dimensional weight spaces over Vir[G] are completely determined. There are two different classes of them. One class consists of simple modules of intermediate series whose weight spaces are all 1-dimensional. The other is constructed by using intermediate series modules over a Virasoro subalgebra of rank n−1. The classification of such modules over the classical Virasoro algebra was obtained by O. Mathieu in 1992 using a completely different approach.

Field of study: Mathematics
LAW OF CRACK DEVELOPMENT AND CALCULATION OF CRACK WIDTH OF CONTINUOUS COMPOSITE BEAMS

Static model tests are conducted on three simply supported steel-concrete composite beams under negative moment and on three continuous two-span composite beams.The study focuses on the cracking mechanism and law of crack development,and test results show that transverse reinforcements space generate certain influence on cracking space.According to the test results as well as test data by others,the calculated formula is suggested with the consideration of the transverse reinforcements space and force ratio as two main parameters.At the same time,the formula of uneven coefficient of reinforcement strain in current code is modified,and the calculation formula of crack width for composite beam is suggested.The calculated crack widths are in good agreement with the test results.The results in this paper can provide reference for calculating crack width of composite beams.

Field of study: Engineering