nils-herrmann/clean_scirepeval huggingface dataset:
Establishment and optimization of a high throughput phenotypic test for the detection of drug resist-ance in human immunodeficiency virus（HIV）strains

To establish a high throughput phenotypic test for the detection of drug resistance in human immunodeficiency virus（HIV）strains.  The gene encoding luciferase was inactivated through restriction enzyme digestion and ligation. LacZ gene was used to replace the genes encoding original protease and reverse transcriptase. pol genes were amplified from pSG3△env plasmid and cloned into a new backbone plasmid through infusion. The factors that might affect the results of the test were optimized.  The parental backbone plasmid pNL4-3. Lac was constructed,of which the gene encoding luciferase was inactivated and bearing the LacZ gene instead of genes encoding protease and reverse transcriptase. Several influential factors including cell numbers（10 000 / well）,virus inoculation（200 TCID50 /well）and the concentration of DEAE-dextran（15 μg/ ml）were optimized. The reproducibility of this test was confirmed by testing 12 anti-HIV drugs against 2 pseudovirus strains 8 times,presenting the coefficient of variations（CVs）from 4. 32% to 28. 46% . Six types of pseudovirus were constructed and tested against the 12 anti-HIV drugs,the results of which were compared with those by using the pSG3△env-based pseudovirus test. The results of the two tests presented good consistency.  The high throughput phenotypic test based on pNL4-3. Lac plasmid,combining the advantages of pSG3△env and pNL4-3 systems, could be used to analyze the drug resistance patterns of HIV-1 infectors and screen new drugs for antiretroviral therapy in a rapid and effective way. 
 
 
Human immunodeficiency virus; Drug resistance; Phenotypic test

Field of study: Biology
Environmentally-Friendly Dense and Porous Geopolymers Using Fly Ash and Rice Husk Ash as Raw Materials

This paper assesses the feasibility of two industrial wastes, fly ash (FA) and rice husk ash (RHA), as raw materials for the production of geopolymeric pastes. Three typologies of samples were thus produced: (i) halloysite activated with potassium hydroxide and nanosilica, used as the reference sample (HL-S); (ii) halloysite activated with rice husk ash dissolved into KOH solution (HL-R); (iii) FA activated with the alkaline solution realized with the rice husk ash (FA-R). Dense and porous samples were produced and characterized in terms of mechanical properties and environmental impact. The flexural and compressive strength of HL-R reached about 9 and 43 MPa, respectively. On the contrary, the compressive strength of FA-R is significantly lower than the HL-R one, in spite of a comparable flexural strength being reached. However, when porous samples are concerned, FA-R shows comparable or even higher strength than HL-R. Thus, the current results show that RHA is a valuable alternative to silica nanopowder to prepare the activator solution, to be used either with calcined clay and fly ash feedstock materials. Finally, a preliminary evaluation of the global warming potential (GWP) was performed for the three investigated formulations. With the mix containing FA and RHA-based silica solution, a reduction of about 90% of GWP was achieved with respect to the values obtained for the reference formulation.

Field of study: Materials science
Kazhdan-Lusztig cells in planar hyperbolic Coxeter groups and automata

Let C be a one- or two-sided Kazhdan–Lusztig cell in a Coxeter group (W, S), and let Red(C) be the set of reduced expressions of all w ∈ C, regarded as a language over the alphabet S. Casselman has conjectured that Red(C) is regular. In this paper, we give a conjectural description of the cells when W is the group corresponding to a hyperbolic polygon, and show that our conjectures imply Casselman's.

Field of study: Mathematics
A short note on the security of Round-Robin Differential Phase-Shift QKD

Round-Robin Differential Phase-Shift (RRDPS) is a Quantum Key Distribution (QKD) scheme proposed by Sasaki, Yamamoto and Koashi in 2014. It works with high-dimensional quantum digits (qudits). Its main advantage is that it tolerates more noise than qubit-based schemes while being easy to implement.

Field of study: Computer science, Mathematics
Amplitudes and phases of electron scattering in polyatomic systems for the structural analysis of disordered, amorphous, and nanosized materials via EXAFS spectroscopy

The results from developing and testing a software package for calculating the amplitudes and phases of electron scattering in polyatomic systems are presented. The potential with which an excited electron moves in a medium is constructed using the muffin-tin approximation with Hartree–Fock exchange interaction. Tests of the package for metals, oxides, and iron-bearing water sulphate solutions show that structural parameters can be derived with high degrees of accuracy (the error for interatomic distances is ~0.01 Å; for coordination numbers, it is ~7%). Using the developed approach and software, analysis of the Ag K-EXAFS spectra of silver nanoparticles in silica glass allow us to determine the average structural parameters of Ag–O and Ag–Ag bonds.

Field of study: Physics
Comparing communication in two languages employing buffered message-passing

Parallel programming languages are usually compared informally. Such informal comparisons have led to considerable disagreement and debate about the relationship between various parallel programming languages and features. This article presents a model that permits more precise comparisons for a particular class of parallel programming languages: those in which the communication between the parallel processes is via a first-in, first-out queue of messages. This model was developed to assist with the detailed comparisons between the communication aspect of various parallel programming languages, required as part of the design of a new parallel programming language. The model is illustrated by describing interprocess communication in two buffered message-passing languages: the language of Kahn and MacQueen, and the language Cospol.

Field of study: Computer science, Engineering
Campanian to Paleocene dinoflagellate assemblages from the Turtle Mountain core hole, Manitoba, western Canada

Dinoflagellate assemblages from the Turtle Mountain core hole provide evidence for the Paleocene age of the Turtle Mountain Formation and confirm that the Boissevain Formation and the Coulter Member of the Pierre Formation are Maastrichtian. Evidence from dinoflagellates suggests that the Odonah Member of the Pierre Formation is late Campanian. The dinoflagellate assemblages indicate that nearshore shallow marine conditions were present at times during deposition of all the formations.  Les assemblages de Dinoflagelles etudies dans une carotte de sondage attestent que la Formation de Turtle Mountain date du Paleocene, et confirment que la Formation de Boissevain et le Membre de Coulter doivent etre assignes au Maastrichtien. Les resultats de l'examen des dinoflagelles suggerent que le Membre d'Odonah de la Formation de Pierre date du Campanien tardif. Les assemblages de dinoflagelles indiquent que le depot de toutes ces formations a eu lieu dans des conditions de littoral peu profond. (Traduit par la Redaction) McIntyre 774

Field of study: Environmental science
The Productivity of Peasant Agriculture: Oakington, Cambridgeshire, 1360–99

Agriculture was the largest and most important sector of the medieval English economy. Yet although peasants comprised the majority of the population, and were responsible for the greater part of land use, surprisingly little is known about peasant cropping patterns and production strategies. Taking the Crowland Abbey manor of Oakington, Cambridgeshire as a case study, this article examines peasant land use and agricultural strategies. Using data collected from the Oakington tithe accounts and manor court rolls, this article demonstrates that peasants used their land more extensively than did the lord, raising their output per acre above that of the demesne. This was driven by peasant need for fodder crops, and the strain placed on agricultural systems that required peasants to use their land to produce grains and legumes for consumption, fodder, and sale.

Field of study: Economics, History
Pitfalls in intraoperative nerve monitoring during vestibular schwannoma surgery.

Despite the widespread acceptance of intraoperative neurophysiological monitoring in skull base surgery over the last 2 decades, surgeon training in the technical and interpretive aspects of nerve monitoring has been conspicuously lacking. Inadequate fundamental knowledge of neurophysiological monitoring may lead to misinterpretations and an inability to troubleshoot system errors. Some surgeons perform both the technical and interpretive aspects of monitoring themselves while others enjoin coworkers (surgical residents, nurses, anesthetists, or a separate monitoring service) to perform the technical portion. Regardless, the surgeon must have a thorough understanding to avoid potential medical and legal pitfalls because poor monitoring is worse than no monitoring. A structured curriculum and protocol in both the technical and interpretive aspects of monitoring is recommended for all personnel involved in the monitoring process. This paper details the technical, interpretive, and surgical correlates necessary for optimal intraoperative nerve monitoring during vestibular schwannoma surgery with an emphasis on electromyographic monitoring for facial and recurrent laryngeal nerves. Just as the American Society of Anesthesiologists' 1986 "Standards for Basic Anesthetic Monitoring" became a useful tool for both patients and anesthesiologists, impending guidelines in intraoperative neurophysiological monitoring should likewise become an important instrument for optimizing intraoperative neurophysiological monitoring.

Field of study: Medicine
Adsorption Characteristics of 2,4-Dichlorophenoxyacetic Acid (2,4-D) from Aqueous Solution on Powdered Activated Carbon

The removal of 2,4-dichlorophenoxyacetic acid (2,4-D), one of the most commonly used phenoxy acid herbicides, from aqueous solution was studied by using acid-washed powdered activated carbon (PAC) as an adsorbent in a batch system. Adsorption equilibrium, kinetics, and thermodynamics were investigated as a function of initial pH, temperature, and initial 2,4-D concentration. Powdered activated carbon exhibited the highest 2,4-D uptake capacity of 333.3 mg g− 1 at 25°C and an initial pH value of 2.0. Freundlich, Langmuir, and Redlich-Peterson isotherm models were used to express the equilibrium data of 2,4-D depending on temperature. Equilibrium data fitted very well to the Freundlich equilibrium model in the studied concentration range of 2,4-D at all the temperatures studied. Three simplified models including pseudo-first-order, pseudo-second-order, and saturation-type kinetic models were used to test the adsorption kinetics. It was shown that the adsorption of 2,4-D on PAC at 25, 35, and 45°C could be best fitted by the saturation-type kinetic model with film and intraparticle diffusions being the essential rate-controlling steps. The activation energy of adsorption (EA) was determined as −1.69 kJ mole− 1. Using the thermodynamic equilibrium coefficients obtained at different temperatures, the thermodynamic constants of adsorption (Δ Go, Δ Ho, and Δ So) were also evaluated.

Field of study: Agricultural and Food sciences
The Virtues of Uncertainty. The Role of the University in Training for Social Welfare.

The search for an adequate definition of the role of higher education is being carried on today with fresh intensity. Committees and conferences, individual educators, and critics of our schools have produced a plethora of new formulations and of conference resolutions. Having myself given assent to some of these formulations at several conferences, I can testify that common acceptance of a resolution rarely signifies that unanimity of opinion has been achieved or even that the meaning of the resolution can be clearly elucidated. Let us say the conferees have come to the conclusion that the role of higher education is to transmit a heritage of culture and knowledge, to seek a factual (from a scientific viewpoint) and a spiritual (from the viewpoint of values) understanding of our present world and to prepare men and women for the most fruitful kind of lives both as individuals and

Field of study: Education
Situation-Specific Effects in Person Memory

Given that most person memory models have concentrated on trait expectancies, and have ignored situational ones, this article attempts to show that new predictions can arise from an explicit focus on the situation. Participants were led to believe that a target person was kind or unkind either at work or at home. They were subsequently presented with congruent and incongruent behavioral items ostensibly performed by the target person in each of these settings. Consistent with the notion that people form situation-specific expectancies, incongruent behaviors were better recalled than congruent ones, but only if they pertained to the situation specified in the expectancy manipulation; an incongruity effect was not obtained for behaviors performed in the unspecified situation. These data suggest that situation-specific expectancies should be addressed in future person memory models.

Field of study: Psychology
Labor Conditions on Haciendas in Porfirian Mexico: Some Trends and Tendencies

o F THE MANY PROFOUND TRANSFORMATIONS which took place in the Mexican countryside in the period between 1876 and 191o, two have been emphasized: the expropriation of the lands of communal villages, and the decrease in real wages paid to laborers on haciendas. By the end of the Porfiriato over 95 percent of the communal villages had lost their lands, according to available data.' The buying power of wages paid to agricultural laborers on haciendas sharply declined between 1876 and LgLO.2 These statistics give only a partial and limited view of the situation in the countryside. What happened to the expropriated peasants? Did they become peones acasillados on the haciendas, industrial workers or free agricultural laborers? To state that the value of real wages paid to laborers on haciendas

Field of study: History
Specific lytic activity against mycobacterial antigens is inversely correlated with the severity of tuberculosis

The ability of peripheral blood mononuclear cells (PBMC) from patients with active tuberculosis to display cytotoxic responses against autologous Mycobacterium tuberculosis (Mtb)‐pulsed macrophages was evaluated. Non‐MHC restricted cell‐dependent lytic activity was observed in ex vivo effector cells from tuberculosis patients and was mediated mainly by CD3+γδ TCR+ T (γδ T) cells bearing CD56 and/or CD16 molecules. MHC‐restricted and non‐MHC restricted cytotoxic T cells (CTL) were differentially expanded upon stimulation with Mtb in tuberculosis patients and normal controls (N). Class‐I restricted CD8+ CTL and class‐II restricted CD4+ CTL were generated in PPD+N and to a lesser extent in PPD–N. Mtb‐stimulated effector cells from tuberculosis patients became progressively non‐MHC restricted CD4–CD8–γδ T cells, while lytic activity of CD4+ and CD8+CTL decreased gradually as the disease became more severe. On the other hand, target cells were lysed by ex vivo cells from tuberculosis patients through the Fas‐FasL and perforin pathways. Mtb‐induced CD4+ CTL from tuberculosis patients and N controls preferentially employed the Fas‐FasL mechanism. Mtb‐induced CD8+ CTL effector cells from patients used the perforin‐based mechanism while cells from N controls also used the Fas‐FasL pathway. While Mtb‐induced γδ CTL from patients and PPD–N employed the latter mechanism cells from PPD+N individuals also used the perforin pathway. It can be concluded that shifts in the CTL response and the cytolytic mechanisms take place as the pulmonary involvement becomes more severe.

Field of study: Biology, Medicine
Computed Tomography for Evaluation of Adrenal Dysfunction: A 10-Year Follow-Up

To evaluate the computed tomography (CT) morphology of the adrenal glands of patients with adrenal dysfunction.  CT examination of adrenal glands was performed in 331 consecutive patients with symptoms suggestive of adrenal dysfunction. CT was performed using 4-mm contiguous sections for the adrenal area. Intravenous contrast was injected in 78 cases of the adrenal mass lesions.  We analyzed 331 consecutive CT scans performed over a 10-year period. One hundred and twenty-seven patients had hypercortisolism, 23 had unilateral adrenal tumor, 18 had bilateral adrenal hyperplasia and 86 had normal adrenals. The CT diagnosis was confirmed at surgery in all 23 unilateral adrenal tumors except in 1 case (tuberculosis in a hyperplastic adrenal gland). Among the 91 cases of hypertension, 86 were being evaluated for pheochromocytoma and 5 for Conn’s syndrome. Forty-three had adrenal pheochromocytoma (1 bilateral) and 10 had extra-adrenal pheochromocytoma detectable on CT. Two of the 5 cases of hyperaldosteronism (Conn’s syndrome) had adrenal tumor. Adrenal enlargement was observed in 17 of the 33 cases of Addison’s disease. Four of them were cases of histoplasmosis.  CT scanning is a sensitive tool for the imaging of adrenal glands. Both neoplastic and inflammatory lesions can alter adrenal gland morphology. Our results highlight the importance of studying adrenal morphology. CT morphology is helpful to decide the modality of treatment.

Field of study: Medicine
Development of testing apparatus for 10 kA class AC superconductors

R&D on NbTi and Nb/sub 3/Sn superconductors has been carried out for application to AC power apparatus in the Super-GM project. 5 kA class NbTi stranded cables have already been tested and then the R&D aiming at the final target of 10 kA class conductors is in progress. However there is no testing apparatus which makes it possible to measure over 5 kArms AC quench current (Iq) and AC loss in AC magnetic field (50-60 Hz). The testing apparatus was developed under the specifications required for evaluating the AC characteristics of 10 kA class conductors. The AC magnet generating the maximum magnetic field of 1 Tpeak in the bore of 150 mm was manufactured. For the Iq measurement, the AC current is directly applied to the specimen in the field of 0.5 Tpeak (50-60 Hz), 10 kArms AC quench current was obtained for the developed large NbTi conductors. As regards the AC loss measurement, the magnetization method using pick-up coils was adopted and its sensitivity has been improved by reducing unnecessary output signal.

Field of study: Physics
Towards Efficient Connected and Automated Driving System via Multi-agent Graph Reinforcement Learning

Connected and automated vehicles (CAVs) have attracted more and more attention recently. The fast actuation time allows them having the potential to promote the efficiency and safety of the whole transportation system. Due to technical challenges, there will be a proportion of vehicles that can be equipped with automation while other vehicles are without automation. Instead of learning a reliable behavior for ego automated vehicle, we focus on how to improve the outcomes of the total transportation system by allowing each automated vehicle to learn cooperation with each other and regulate human-driven traffic flow. One of state of the art method is using reinforcement learning to learn intelligent decision making policy. However, direct reinforcement learning framework cannot improve the performance of the whole system. In this article, we demonstrate that considering the problem in multi-agent setting with shared policy can help achieve better system performance than non-shared policy in single-agent setting. Furthermore, we find that utilization of attention mechanism on interaction features can capture the interplay between each agent in order to boost cooperation. To the best of our knowledge, while previous automated driving studies mainly focus on enhancing individual's driving performance, this work serves as a starting point for research on system-level multi-agent cooperation performance using graph information sharing. We conduct extensive experiments in car-following and unsignalized intersection settings. The results demonstrate that CAVs controlled by our method can achieve the best performance against several state of the art baselines.

Field of study: Computer science
IL-4RA gene transfer by recombinant retroviral vector prevents the development of experimental asthma

目的 IL-4RA基因转染对哮喘模型过敏性炎症的干预性研究.方法 选择雌性BALB/c小鼠作为动物模型,随机分为5组(每组10只):空白对照组、哮喘模型组、空载体(104 CFU/ml pLNC-laz)干预组、激素治疗组、目的基因(104 CFU/ml pLNC-IL-4RA)干预组.各组在最后一次激发后24 h放血杀死小鼠,检测血中嗜酸性粒细胞(eosinophils,EOS)计数,用ELISA检测支气管肺泡灌洗液(broncho alveolar lavage fluid,BALF)中的各种细胞因子水平,并对BALF中各种炎症细胞计数,肺组织切片做HE染色.结果 哮喘模型鼠BALF中有大量嗜酸性粒细胞浸润,肺组织病理切片可见大量炎症细胞浸润、杯状细胞增生、黏膜壁破坏.哮喘模型的这些改变在激素和基因干预后明显减轻,差异有统计学意义(P＜0.01),而在空载体干预后则无明显的变化(P＞0.05).空白对照组的BALF中IL-5、IL-13低于检测水平,哮喘模型组BALF中IL-5、IL-13水平明显增高,而基因治疗组和激素治疗组IL-5、IL-13水平明显减少,差异有统计学意义(P＜0.01),空载体干预组BALF中细胞因子水平与哮喘模型组比较差异无统计学意义(P＞0.05).结论 通过逆转录病毒转染的IL-4RA的基因高表达成功地阻止在哮喘模型鼠气道由IL-4和IL-13诱发的气道嗜酸性粒细胞浸润,另外,逆转录病毒介导的IL-4RA在气道的表达明显地阻止了哮喘模型气道黏液的分泌,同时也减少了过敏性哮喘相关的TH2细胞因子水平,因此,基因治疗可能会成为治疗慢性哮喘气道炎症和哮喘症状的极有潜力的药物。

Field of study: Biology
Some 2-aryl-5-azaindandiones-1, 3

Condensation of cinchomeronic acid with p-nitrophenylacetic acid, of 2, 6-dimethylcinchomeronic acid with phenylacetic acid, and p-nitrophenylacetic acid in acetic anhydride solution in the presence of triethylamine followed by rearrangement of the condensation products with sodium methoxide gives 2-(p-nitrophenyl)-5-azaindandione-1, 3, 4, 6-dimethyl-2-phenyl-5-azaindandione-1, 3, and 4, 6-dimethyl-2-(p-nitrophenyl)-5-azaindandione-1, 3. Reaction of the alkali metal salts of these compounds with dimethyl sulfate leads to alkylation at the nitrogen atom, and formation of N-methyl betaines of the corresponding 5-azaindandiones. 2-Aryl-5-azaindandiones and their N-methyl betaines are dark in color (black to reddish brown), sparingly soluble, and decompose at 250-350°.

Field of study: Chemistry
Correlation between novel generalized correlative index and normal boiling point of organic compounds

Generalized correlative index (GCI) is a novel user-oriented descriptor for molecular structural representation.By defining generalized correlative function (GCF), property correlative parameters (PCPs) and distance-relational function (DRF), GCI is based on molecular topological pattern and mode of apex connection and is able to perform self-adaptation and regulation in actual problems, thus possessing more extensive applications and superior correlation with properties.Applying this index to normal boiling point (NBP) of three classes of organic compounds, the resultant QSPR models all have their correlative coefficients R_ cum above 0.99.It shows that GCI is superior in selecting molecular structures and correlating with molecular properties.

Field of study: Chemistry, Environmental science