nils-herrmann/clean_scirepeval huggingface dataset:
PacBio Long Reads Improve Metagenomic Assemblies, Gene Catalogs, and Genome Binning

PacBio long reads sequencing presents several potential advantages for DNA assembly, including being able to provide more complete gene profiling of metagenomic samples. However, lower single-pass accuracy can make gene discovery and assembly for low-abundance organisms difficult. To evaluate the application and performance of PacBio long reads and Illumina HiSeq short reads in metagenomic analyses, we directly compared various assemblies involving PacBio and Illumina sequencing reads based on two anaerobic digestion microbiome samples from a biogas fermenter. Using a PacBio platform, 1.58 million long reads (19.6 Gb) were produced with an average length of 7,604 bp. Using an Illumina HiSeq platform, 151.2 million read pairs (45.4 Gb) were produced. Hybrid assemblies using PacBio long reads and HiSeq contigs produced improvements in assembly statistics, including an increase in the average contig length, contig N50 size, and number of large contigs. Interestingly, depth-based hybrid assemblies generated a higher percentage of complete genes (98.86%) compared to those based on HiSeq contigs only (40.29%), because the PacBio reads were long enough to cover many repeating short elements and capture multiple genes in a single read. Additionally, the incorporation of PacBio long reads led to considerable advantages regarding reducing contig numbers and increasing the completeness of the genome reconstruction, which was poorly assembled and binned when using HiSeq data alone. From this comparison of PacBio long reads with Illumina HiSeq short reads related to complex microbiome samples, we conclude that PacBio long reads can produce longer contigs, more complete genes, and better genome binning, thereby offering more information about metagenomic samples.

Field of study: Biology
Enantioselective Construction of Spiro[2H-pyran-3,4′-indoline] by a Systematic Michael/Reduction/Cyclization Sequence Triggered by the Asymmetric Conjugate Addition of Ketones to Isatylidenemalononitriles

Heterocyclic spirooxindoles that bear a multisubstitutedheterocyclic motif and quaternary stereocenter at the 3-position are prevalent in a large number of spirooxindole alkaloids, which are pharmaceutically relevant compounds with remarkable biological activities. In this paper, we report an efficient method for the construction of enantiomerically enriched spiro[2H-pyran-3,4′-indoline] derivatives by a systematic Michael/reduction/cyclization sequence. The initial Michael addition of isatylidenemalononitriles with ketones was catalyzed by a cinchona-based chiral primary amine and L-camphorsulfonic acid and furnished multifunctional, optically active Michael adducts in high yields (81–99 %) with excellent enantioselectivities (95 to >99 % ee). Subsequently, the Michael adducts were converted into spiro[2H-pyran-3,4′-indoline] derivatives in 52–93 % yields with 1.5:1 to 20:1 diastereomeric ratio and 90–99 % ee by utilizing NaBH4 as a cascade reduction/cyclization reagent.

Field of study: Chemistry
Cracking Analysis on Side Gear of Ditch Digger

A series of comprehensive analysis on macrostructure, microstructure, chemical composition and hardness of failure gear were carried out. It is found that the gear's original structure is worse, the flex cracking exists on the pitch circle and the gear's ditch hardened quenching. The composite factors reduce the gear's operational performance and lead to the early failure of the gear.

Field of study: Materials science
Robust ridge estimation methods for predicting u. s. coal mining fatalities

This paper compares alternative combinations of ridge regression and robust regression techniques in predicting fatalities in the U.S. coal mining industry. The combined robust ridge approach is needed because of the simultaneous occurrence of multicollinearity and outliers in the data. Not surprisingly, the relative effectiveness of different ridge estimators in predicting coal mining fatalities is found to be dependent upon the particular choice of the robust weighting scheme employed.

Field of study: Mathematics
The Interplay of TVET and Formal Education

TVET and formal education have no formal relationship till these days especially in developing countries. In this way, they can’t develop adequate and efficient manpower that are needed for them. We need to establish the relationship between these two methods of education; then only we can produce better manpower. We need to produce transferable manpower by providing both educations to a person. Mainly, traditional practices of TVET models need some improvement as it can’t allow learner to move further to admit in higher education. This article aims to promote both education systems by analyzing it using secondary sources.  TVET, formal education, transferable skill.

Field of study: Education
Structural context of the 2015 pair of Nepal earthquakes (Mw 7.8 and Mw 7.3): an analysis based on slip distribution, aftershock growth, and static stress changes

The Great Himalayan earthquakes are believed to originate on the Main Himalayan Thrust, and their ruptures lead to deformation along the Main Frontal Thrust (MFT). The rupture of the April 25, 2015 (Mw 7.8), earthquake was east-directed, with no part relayed to the MFT. The aftershock distribution, coseismic elevation change of ~1 m inferred from the InSAR image, and the spatial correspondence of the subtle surface deformations with PT2, a previously mapped out-of-sequence thrust, lead us to explore the role of structural heterogeneities in constraining the rupture progression. We used teleseismic moment inversion of P- and SH-waves, and Coulomb static stress changes to map the slip distribution, and growth of aftershock area, to understand their relation to the thrust systems. Most of the aftershocks were sourced outside the stress shadows (slip >1.65 m) of the April 25 earthquake. The May 12 (Mw 7.3) earthquake that sourced on a contiguous patch coincides with regions of increased stress change and therefore is the first known post-instrumentation example of a late, distant, and large triggered aftershock associated with any large earthquake in the Nepal Himalaya. The present study relates the slip, aftershock productivity, and triggering of unbroken stress barriers, to potential out-of-sequence thrusts, and suggests the role of stress transfer in generating large/great earthquakes.

Field of study: Environmental science
Approach to the geostrategy of the oceans: The case of the mediterranean

It is known that by the general ‘geostrategy’ for the oceans we mean the behaviour of countries of the world in defending their own vital economic interests as projected on different oceans. The means for protecting national interests can be economic, political, diplomatic or military. This paper dwells in particular on these last aspects, offering in the first part some useful reflections on the analysis of regional seas. The second part gives elements for the understanding of the complex Mediterranean situation where the East-West confrontation is accentuated by widespread economic, political, ideological and ethnic contrasts between coastal states. For these reasons this sea can be defined as one of the most unstable and belligerent regions in the world.

Field of study: Environmental science
РИСКИ ДЛЯ РОССИИ ОТ ЭМБАРГО НА ПОСТАВКИ ПРОДОВОЛЬСТВИЯ ИЗ ТУРЦИИ

В результате введения эмбарго на ввоз продовольствия из Турции в Россию турецкий экспорт в нашу страну сократится примерно на 1 млрд долл., что составляет около 60% экспорта всей агропродовольственной продукции из нее в РФ. Снижение экспорта произойдет прежде всего по овощам и фруктам. Эмбарго может оказать наиболее существенное влияние на российские рынки томатов, винограда, мандаринов. В российском импорте этих продуктов поставки из Турции составляли 34–50%. По томатам поставки из Турции обеспечивали 11% среднегодового потребления россиян. В отдельные месяцы этот процент оказывался значительно больше.

Field of study: Economics
IL-18 induced IL-23/IL-17 expression impairs Aβ clearance in cultured THP-1 and BV2 cells.

Recent studies have provided overwhelming evidence of the involvement of microglia-related molecular networks in the pathogenesis of Alzheimer's diseases (AD). The potential involvement of pro-inflammatory cytokines interleukin (IL)-18, IL-23 and IL-17 on amyloid (Aβ) clearance is still unclear. In this study, we addressed that there might be a net relationship among IL-18, IL-23, and IL-17 and they can affect Aβ clearance in cultured macrophage/microglia cells. In human macrophage cell line THP-1, Aβ42 incubation could increase the expression of IL-18, IL-23 and IL-17 in a concentration dependent manner. THP-1 cell could clear Aβ42 in the culture medium time-dependently, but its capacity of Aβ clearance was impaired by IL-18, IL-23 or IL-17 treatment. Similarly, the capacity of the microglia cell line BV2 to clear Aβ42 was impaired by IL-18, IL-23 or IL-17 treatment. In co-cultures of BV2 with APP/PS1 neuron, Aβ was efficiently cleared by BV2 cell, but Aβ clearance was impaired by IL-18, IL-23 or IL-17 treatment. The effects of IL-18, IL-23 and IL-17 could be blocked by their corresponding neutralizing antibodies. In addition, the inhibitory effects of IL-18 were blocked by IL-23 or IL-17 neutralizing antibodies while the inhibitory effects of IL-23 were blocked by IL-17 neutralizing antibodies. Our study provides evidences showing that amyloid induced IL-18/IL-23/IL-17 axis could impair macrophage and microglia-mediated Aβ clearance. Thus, IL-18/IL-23/IL-17 axis might be a therapeutic target in AD.

Field of study: Medicine
Positive influence of ta addition on superconductive properties of high pressure synthesized MgB_2

Bulk MgB2 - based materials with the following critical current densities (jc) in 1 T field: 570 kA/cm^2 at 10 K, 350 kA/cm^2 at 20 K and 40 kA/cm^2 at 30 K and in 10 T field: 650 A/cm^2 at 10 K have been high-pressure (HP) synthesized from Mg and B with 2 - 10 wt.% addition of Ta. In synthesis and sintering process Ta plays the role of an absorbent of impurity gases (hydrogen, nitrogen, etc.) and forms Ta2H, TaH, TaN0.1, etc., thus promotes the reduction of MgH2 in Mg-B-O-matrix phase, as well as, the impurity nitrogen and oxygen in Mg-B grains (black MgB2 single crystals distributed over the matrix). Vickers microhardness of HP-synthesized material is Hv=12.54 (+/-)0.86 GPa (at 0.496-N load) The hardness (at 60-mN load) of MgB2 single crystals located in a sample matrix is 35.6 (+/-)0.9 GPa that is higher than the hardness of sapphire (31.1 (+/-)2.0 GPa).

Field of study: Physics
Half-life of short-lived neutron-excess nuclei that participate in the r-process

A quasi-classic model of a strength function based on finite Fermi systems is used to predict β-decay periods for neutron-excess nuclei. The results from calculations are compared to experimental data and other predictions. It is shown that the accuracy of the calculated half-life periods of short-lived neutronrich nuclei is sufficient for modeling the nucleosynthesis of heavy nuclei in the r-process.

Field of study: Physics
‘Militarized commerce’ in Sudan's oilfields: Lessons for Canadian foreign policy

H enry Kissinger once observed “no foreign policy – no matter how ingenious – has any chance of success if it is born in the minds of a few and carried in the hearts of none” (Simpson 1988). In the wake of controversy over Calgary-based Talisman Energy’s Sudanese operations, there is reason to question whether Kissinger’s assertion will prove true for Canada’s much-touted ‘human security’ foreign policy. The Talisman Energy case amounts to the first clear collision between a foreign policy of human security and the material self-interest of a powerful Canadian company. In conflict were the operations – and, in the minds of some, the survival – of Canada’s largest independent oil company and the ‘human security’ of southern Sudanese brutally displaced from Sudan’s oil fields. The controversy over the apparent role of Talisman’s operations in exacerbating the Sudanese conflict and the Government of Canada’s seeming inability to settle this matter has given Canada a black eye in the eyes of many critics, especially in the US and the human rights nongovernmental community. Yet, the Talisman situation is merely the tip of the iceberg. Rather than being a one-time aberration, the example of Talisman in Sudan reflects a potentially persistent dark-side to the globalization of Canadian business, one that presents new foreign policy concerns for the Government of Canada. This article focuses on the Talisman case to illustrate the emerging issue of ‘militarized commerce’ by Canadian companies and the challenge it presents to ‘human security’. For the purposes of this article, militarized commerce has several characteristics: first, reliance by business firms on state military forces for security; second, the provision by companies of financial, logistical, material or infrastructural assistance to human-rights abusing troops; third, the use of force by human rights abusing-regimes to supply resources to a company; and, fourth, the generation of revenues used by human rights abusing regimes to wage war against civilian populations. ‘Human security’, for its part, reflects “an effort to construct a global society in which the safety and well-being of the individual is an international priority” (Axworthy 1999). This article begins by arguing that militarized commerce is an increasingly common occurrence, one that challenges conventional wisdom about the positive role of business in supporting human security and political liberalization. It recounts the particulars of Talisman’s Sudanese operations and reviews evidence that the company’s presence in Sudan’s oilfields was fuelling civil conflict in 1999. It describes in detail the controversy relating to the company’s project and the Canadian government reaction prompted by this public scrutiny. Relying on material obtained via the Access to Information Act, the article argues that the government’s response in the Talisman case was 37

Field of study: Political science
A land systems science approach to assessing forest governance and characterizing the emergence of social forestry in the Western Cascades of Oregon

National forests in theUnited States are undergoing a spatially and temporally uneven governance transition in response toCongressional policies, agencymandates, and social and economic pressures, withmanymoving from awholly state-led ‘dominant federal’model to amore collaborative networked governancemodel whichwe refer to as ‘social forestry’.While the broad contours of this transition have been observed and studied previously, there have been few attempts to characterize it using quantitative, qualitative, or geospatialmethods.Here, we combine a novel remote sensing-based methodwith qualitative social science research to understand the emergence of social forestry and its implications for land use/land cover change associatedwith implementation of theNorthwest Forest Plan (NWFP) in theWesternCascades ofOregon.We linked time-series satellite datawith forest inventory data to track patterns of timber harvest at scales commensurate with timbermanagement decision-making.We then compared these patterns to policy-based expectations.We found a significant disconnect betweenNWFPpolicy and actual timber harvest patterns, raising questions about the effectiveness of theNWFP land use allocation system and the ‘land sparing’ approach to managing tensions between conservation and production. Qualitative research, including semistructured interviewswith federal agency personnel and local stakeholders, shed light on the causal mechanisms and reciprocal relationships driving spatial patterns of timber harvesting, whichwe discuss in terms of the emergence of social forestry involving complex, place-based negotiations between the federal government and local veto actors advocating for conservation. Findings have implications forUS Forest Service public engagement strategies and efforts to establish zones of agreement regarding timber harvesting, as well as broader discussions about the agency’s future.

Field of study: Environmental science
Model of Tadzkiroh Based Character Formation in School

Character formation in school is an effort to assess education output that can be expected to have noble characters started from school. In this effort, model of Tadzkiroh is an innovation to implement character formation by developing character formation through T (Tunjukkan teladan), A (Arahkan), D (Dorong), Z (Zakiyah), K (kontinuitas), I (ingatkan), R (Repetisi), O (Organisasikan), serta H (Heart). Each part of the tadzkiroh acronym is a series of stages of tadzkiroh-based character formation that are interrelated with each other. These steps provide a framework for character formation which leads to the internalization of character values in students  Model of Tadzkiroh, Based Character Formation, School DOI : 10.7176/JEP/10-29-08 Publication date :October 31 st 2019

Field of study: Education
The Oppressive Present: Literature and Social Consciousness in India, and: The Lie of the Land: English Literary Studies in India (review)

It was not uncommon for parents to withdraw their children immediately from Duff's school whenever they sensed what they saw as the "tyranny of the Bible." Some parents negotiated their needs in a more sanguine manner. Duff's biographer and former student, LaI Behari Day, records the plan his father had worked out: he would wait for the moment when his son had learned enough English to obtain a decent situation outside but was not yet intellectually advanced to understand lectures on ChristianityÂ—as soon as that moment arrived, he would instantly be withdrawn from school and placed in an office. "Let Duff Saheb do what he can," was the father's defiant challenge to the threat of proselytism. But Duff Saheb was a little more devious than even Day's father imagined .... Â—Gauri Vishwanathan, Masks of Conquest: Literary Study and British Rule in India (58)

Field of study: Art
Peace Corps Fantasies: How Development Shaped the Global Sixties by Molly Geidel (review)

It would be difficult to imagine a monograph that deftly weaves together analyses of the Black Panthers, frontier nostalgia, and the politics of birth control in Bolivia, but somehow Molly Geidel manages to pull it off. Geidel reexamines the histories of development and modernization theory in the 1960s through the lens of gender and cultural studies. Using one of the quintessential development initiatives of the United States, the Peace Corps, as a connecting thread, Geidel explores the relationships between domestic debates and anxieties and how Americans imagined their roles abroad. She argues that American social scientists and politicians “articulated and assuaged their own anxieties about the affluent, atomizing, repressive society of the 1950s by creating intimate yet hierarchical masculine fantasy spaces of development” (xv).

Field of study: History
Relativistic separable interaction kernel of the neutron-proton system with inelasticities

Within a covariant Bethe-Salpeter approach, the relativistic complex separable neutron-proton interaction kernel is proposed. The uncoupled partial-wave states with the total angular momentum $J$=0,1 are considered. The multirank separable potentials elaborated earlier are real-valued and, therefore, enable to describe the elastic part (phase shifts, low-energy parameters, etc.) of the scattering only. The description of the inelasticity parameter comes out of the imaginary part introduced into them. To obtain parameters of the complex potentials the elastic neutron-proton scattering experimental data up to 3 GeV are used. A signal of dybaryon resonances in the $^3P_0^+$ partial-wave state is discussed.

Field of study: Physics
Evaluating pediatric psychology consultation services in a medical setting: An example

We examined the nature of referrals to a health center-based pediatric psychology service from 1990 to 1993 and assessed the satisfaction of health professionals with these services. Archival evaluation of 1467 records showed that over half of the consultation requests came from general pediatrics, pediatric neurology, and surgical services and that 70% of the psychological services were delivered on an outpatient basis. The most frequent referrals were for cognitive/neuropsychological evaluation and externalizing behavior problems. Pediatric psychology trainees were involved in 94% of the consultations. Survey of health professionals (n = 143) indicated very high overall satisfaction with the quality of services delivered. Presenting problems yielding the greatest likelihood for future consultation requests were behavior problems, child abuse, coping with illness, and depression/suicide. Results are discussed in the context of previous evaluations of pediatric psychology services and recommendations for future evaluation research.

Field of study: Psychology
Biodegradation of α-Pinene in Model Biofilms in Biofilters

Treatment of air pollutants in a biofilter requires that the compound be effectively transported from the gas phase to the organisms that reside in a biofilm that forms upon a packing material. Models of biofiltration generally treat the biofilm like water by using a Henry's law constant to predict mass transfer rates into the biofilm where degradation occurs and, hence, predict low rates for hydrophobic compounds. However, some compounds that are virtually insoluble in water are also treated unusually well. The objective of this study was to develop a fundamental understanding of the apparent enhanced degradation of hydrophobic pollutants in biofilms. Specifically, the goals of this study were to experimentally determine transport and reaction rates of hydrophobic pollutants in artificial biofilms. We studied the transport and reaction rates of alpha-pinene (as a model hydrophobic pollutant) in a headspace in contact with a well-defined biofilm made up of biomass immobilized in low melting point agarose and found that reaction rates were similar in order of magnitude to biofilter rates. The transport rates through these films once deactivated were found to be the same as through agar (diffusion coefficient between 2.6 and 3.4 x 10(-6) cm2/s). The degradation rates through model biofilms ranged from 2 to 4 x 10(-7) (g/(cm2 min)). A new explanation of high degradation rates was put forth whereby a biologically mediated transformation is taking place in which alpha-pinene is oxidized into a more soluble, less volatile compound that can then penetrate deeper into the biofilm. The formation of this more soluble byproduct was confirmed with batch kinetics experiments using filtered samples, and its proposed identity is cis-2,8-p-menthadien-1-ol, a menthadienol, a novel metabolite of alpha-pinene degradation. A simple conceptual model based on these results is also presented.

Field of study: Environmental science