nils-herrmann/clean_scirepeval huggingface dataset:
QTL Mapping for Agronomic and Adaptive Traits Confirmed Pleiotropic Effect of mog Gene in Black Gram [Vigna mungo (L.) Hepper]

Organ size and architecture of plants are important traits affecting crop yield and agronomic practices. An induced mutant, multiple-organ gigantism (MOG), of black gram (Vigna mungo) has been obtained, which shows gigantic leaves, fruit, seed, and architecture (plant height) but lower number of pods per plant. These traits are a pleiotropic effect of a single recessive gene, mog. In this study, we investigated variation of 16 agronomic and adaptive traits in a recombinant inbred line (RIL) population derived from a cross between the MOG mutant (V. mungo var. mungo) and wild black gram (V. mungo var. silvestris) accession TC2210 and identified quantitative trait loci (QTLs) controlling those traits to gain a better understanding of the effect of the mog gene on breeding. The results showed that most of the traits (100-seed weight, leaf size, and plant height) showed moderate narrow-sense heritability (h2) (45–65%), while pod size and seed length (SDL) showed high h2 (>75%) and pod dehiscence (shattering), and seed width (SDW) and days to flowering showed low h2 (<35%). The QTLs for the traits were mapped onto a high-density linkage map developed for the RIL population. Inclusive composite interval mapping identified 42 QTLs in total for the 16 traits with number of QTLs per trait ranging from one to six. Major QTLs for the MOG phenotypes were clustered on linkage group (LG) 6, confirming the pleiotropic effect of the mog gene. Effect of the mog gene/QTL for the MOG phenotypic variations was not high, ranging from about 15% in plant height to 40% in leaf size. For 100-seed weight, which is the most interesting trait, the mog gene/QTL contributed about 30% of the total trait variation and showed an additive effect of only 0.51 g, which is only about 1.5-fold higher than that of the other five QTLs detected for this trait. These results indicated that mog gene expression is highly affected by environment and the effect of the gene toward organ size and plant height is not extraordinarily high. Implications of the findings of this study and exploiting of the MOG mutant in breeding were also discussed.

Field of study: Biology
Geology and Origin of the Pollucite-Bearing Montgary Pegmatite, Manitoba

The Montgary Pegmatite in southeastern Manitoba is a large, complexly zoned, spodumene-bearing body containing the world9s largest known reserves of pollucite. The pegmatite is near the margin of a granitic intrusive rock and forms an elongate, disc-shaped body lying more or less perpendicular to the near-vertical schistosity of the enclosing Precambrian plagioclase amphibolite. The amphibolite has no compositional or textural trends beyond a narrow alteration zone that can be correlated with distance from the pegmatite. The alteration zone, 4–6 feet in average width, contains small amounts of glaucophane, biotite, apatite, and tourmaline in addition to the normal mineral assemblage of the amphibolite. The pegmatite is subdivided into six zones, two replacement bodies, and a unit that may be a replacement body. The six zones are: (1) a quartz–albite border zone; (2) a perthite–quartz–plagioclase–muscovite wall zone; (3) a spodumene–perthite–plagioclase–quartz intermediate zone; (4) a spodumene–quartz intermediate zone with minor perthite; (5) a microcline-quartz intermediate zone, and (6) a quartz core. Neglecting the quartz core and considering the two spodumene–bearing zones as one, the internal structure is one of concentric shells. Aplitic albite replaces lower portions of the spodumene-bearing zones and upper portions of the footwall portion of the wall zone. Fine-grained lepidolite replaces parts of the microcline-quartz intermediate zone. Pollucite forms very fine-grained, monomineralic bodies cut by veins of quartz; these bodies are tentatively regarded as replacement bodies. Lithia has been concentrated toward the hanging wall and up the dip of the pegmatite. The attitude of the pegmatite and the shape of the hanging wall amphibolite–pegmatite contact exerted an important control over lithia distribution during crystallization. An igneous hypothesis of origin is the most acceptable. Pegmatitic fluids, probably related to the nearby granitic intrusive rock, were permissively introduced into a dilatant zone along a sinuous shear. The internal structure is consistent with fractional crystallization accompanied by resurgent boiling of the residual liquid in a restricted system. Deposition of crystals took place from the walls inward. The zonal structure has been influenced, but not caused, by the attitude of the pegmatite. Upward lithia concentration is consistent with the development of a second fluid phase by resurgent boiling following the deposition of wall-zone material. Alkali-replacement bodies were formed late in the history of the pegmatite. The fluids responsible for their formation were probably either vapors formed by resurgent boiling or residual fluids left over after the main pegmatite crystallization.

Field of study: Geology
MO-FG-202-06: Improving the Performance of Gamma Analysis QA with Radiomics- Based Image Analysis.

The use of gamma analysis for IMRT quality assurance has well-known limitations. Traditionally, a simple thresholding technique is used to evaluated passing criteria. However, like any image the gamma distribution is rich in information which thresholding mostly discards. We therefore propose a novel method of analyzing gamma images that uses quantitative image features borrowed from radiomics, with the goal of improving error detection.



368 gamma images were generated from 184 clinical IMRT beams. For each beam the dose to a phantom was measured with EPID dosimetry and compared to the TPS dose calculated with and without normally distributed (2mm sigma) errors in MLC positions. The magnitude of 17 intensity histogram and size-zone radiomic features were derived from each image. The features that differed most significantly between image sets were determined with ROC analysis. A linear machine-learning model was trained on these features to classify images as with or without errors on 180 gamma images.The model was then applied to an independent validation set of 188 additional gamma distributions, half with and half without errors.



The most significant features for detecting errors were histogram kurtosis (p=0.007) and three size-zone metrics (p<1e-6 for each). The sizezone metrics detected clusters of high gamma-value pixels under mispositioned MLCs. The model applied to the validation set had an AUC of 0.8, compared to 0.56 for traditional gamma analysis with the decision threshold restricted to 98% or less.



A radiomics-based image analysis method was developed that is more effective in detecting error than traditional gamma analysis. Though the pilot study here considers only MLC position errors, radiomics-based methods for other error types are being developed, which may provide better error detection and useful information on the source of detected errors. This work was partially supported by a grant from the Agency for Healthcare Research and Quality, grant number R18 HS022244-01.

Field of study: Medicine, Physics
Landscape features associated to wind farms increase mammalian predator abundance and ground-nest predation

Wind farm implementation is a rapidly growing source of landscape transformation that may alter ecological processes such as predator–prey interactions. We tested the hypothesis that wind farms increase the activity of nest predators and, ultimately, increment ground-nest predation rates. We placed 18 plots in Iberian shrub-steppes (11 at control and seven at wind farm sites), each one comprised nine artificial ground-nests (three quail eggs/nest). Artificial nests were placed during two events: at the beginning (April) and at the end (June) of the breeding season in 2016 (n = 324 artificial nests). We estimated the relative abundance of avian and large mammalian predators in the surroundings of each plot and recorded nest fate after 12 days exposure. We also measured variables at landscape and microhabitat scale that potentially affect predator abundance and nest predation. Wind farm sites contained higher cover of gravel roads and more large mammalian predators. Moreover, the abundance of large mammalian predators increased with surrounding cover of both trees and gravel-roads. Avian predator abundance and nest predation rates did not differ between control and wind farm sites, though nest predation did increase with the surrounding cover of crops and gravel roads. Lastly, nest predation was higher at the end of the breeding season and decreased with moss and lichen cover. Our results support previous evidence on the increase of mammalian predator abundance as the surface area of gravel-roads increases, pointing towards a potential mechanism for wind farms leading to rise ground-nest predation. Future wind energy projects should minimize the development of gravel-roads for wind turbine access or maintenance.

Field of study: Environmental science
ALDH1 Expression and Vasculogenic Mimicry Are Positively Associated with Poor Prognosis in Patients with Breast Cancer

This study aimed to explore the prognostic value of aldehyde dehydrogenase 1 (ALDH1) expression and vasculogenic mimicry (VM) in patients with breast cancer.  ALDH1 expression and the presence of VM were examined by immunohistochemistry and CD31/PAS double staining, respectively, using formalin-fixed paraffin-embedded tissues from 202 breast cancer patients. The mean follow-up period ranged from 15 to 115 months. The Kaplan-Meier method was used to plot survival curves. Prognostic values were assessed by multivariate analysis using the Cox regression model.  ALDH1 expression was strongly associated with VM (P = 0.005). ALDH1 expression was positively correlated with histological grade (P = 0.011). Both ALDH1 expression and VM were negatively related to the status of the estrogen receptor and progesterone receptor and were statistically increased in triple-negative breast cancer. Patients with ALDH1 expression or VM displayed poorer disease-free survival (DFS) and overall survival (OS) than ALDH1-negative or VM-negative patients, with the worst OS and DFS observed in ALDH1/VM-double-positive patients. ALDH1-positive and VM-positive were independent survival risk factors for DFS and OS.  ALDH1 expression and VM are correlated with the survival rate of patients with breast cancer. ALDH1 and VM, either alone or together, are prognostic factors in patients with breast cancer.

Field of study: Biology, Chemistry
Silicon spintronics with ferromagnetic tunnel devices

In silicon spintronics, the unique qualities of ferromagnetic materials are combined with those of silicon, aiming at creating an alternative, energy-efficient information technology in which digital data are represented by the orientation of the electron spin. Here we review the cornerstones of silicon spintronics, namely the creation, detection and manipulation of spin polarization in silicon. Ferromagnetic tunnel contacts are the key elements and provide a robust and viable approach to induce and probe spins in silicon, at room temperature. We describe the basic physics of spin tunneling into silicon, the spin-transport devices, the materials aspects and engineering of the magnetic tunnel contacts, and discuss important quantities such as the magnitude of the spin accumulation and the spin lifetime in the silicon. We highlight key experimental achievements and recent progress in the development of a spin-based information technology.

Field of study: Materials science
TheBDKRB2 +9/-9 Polymorphisms Influence Pro-Inflammatory Cytokine Levels in Knee Osteoarthritis by Altering TLR-2 Expression: Clinical and in Vitro Studies

The bradykinin B2 receptor (BDKRB2) +9/-9 gene polymorphisms have been shown to be associated with the susceptibility and severity of osteoarthritis (OA); however, the underlying mechanisms are unclear. In this study, we investigated the correlation between the BDKRB2 +9/-9 polymorphisms and pro-inflammatory cytokine levels in OA and the molecular mechanisms involved.  A total of 156 patients with primary knee OA and 121 healthy controls were enrolled. The BDKRB2 +9/-9 polymorphisms were genotyped. The tumor necrosis factor (TNF)-α, interleukin (IL)-1β, IL-6, and IL-8 levels were determined using Enzyme-linked immunosorbent assay (ELISA). The toll-like receptor (TLR)-2 and TLR-4 mRNA levels were determined by quantitative real-time PCR. The basal and bradykinin-stimulated pro-inflammatory cytokine secretion in human OA synoviocytes and the involvement of TLR-2 and mitogen-activated protein kinases (MAPKs) were investigated.  The presence of -9 bp genotype is associated with higher TNF-α, IL-6, and IL-8 levels and higher TLR-2 expression in OA patients. The basal and bradykinin-induced TLR-2 expressions in human OA synoviocytes were significantly reduced by specific inhibitors of p38, JNK1/2, and ERK1/2. Both the B2 receptor antagonist MEN16132 and TLR-2 silencing inhibited IL-6 and IL-8 secretion in human OA synoviocytes.  The data suggested that the BDKRB2 +9/-9 polymorphisms influence pro-inflammatory cytokine levels in knee osteoarthritis by altering TLR-2 expression.

Field of study: Biology, Chemistry
Über das Verhalten eines Elektrons im homogenen elektrischen Feld nach der relativistischen Theorie Diracs

ZusammenfassungEs werden die Lösungen der Diracgleichung mit dem PotentialV=vx angegeben und ihr Verhalten diskutiert. Zu dem Funktionsverlauf, der auch bei nichtrelativistischer Rechnung auftritt, kommt in der Diracschen Theorie noch ein Gebiet hinzu, in dem Elektronenimpuls und -geschwindigkeit entgegengesetztes Vorzeichen besitzen. Im Anschlu\ daran wird für ein Elektron die Wahrscheinlichkeit berechnet, aus dem Gebiet „positiven Impulses“ in das mit „negativem Impuls“ überzugehen. Es ergibt sich, da\ die Durchgangswahrscheinlichkeit erst dann endliche Werte annimmt, wenn die Grö\e des Potentialanstieges auf einer Strecke gleich der ComptonwellenlÄnge vergleichbar wird mit der Ruheenergie des Elektrons. Die von O. Klein berechneten gro\en Werte für die Durchgangswahrscheinlichkeit durch einen Potentialsprung von der Grö\enordnung der doppelten Ruheenergie sind in dem Sinne als Grenzwerte im Falle unendlich steilen Potentialanstieges zu verstehen.

Field of study: Physics
The Impact of Instructional Supervision on Academic Performance of Secondary School Students in Nasarawa State, Nigeria

This study examined the Impact of Instructional Supervision on Academic Performance of Secondary School Students in Nasarawa State with reference to Senior Secondary Certificate Examination (SSCE). Five research questions were used to guide the study to a rational conclusion. Descriptive Survey method was adopted in which Instructional Supervision and Students’ Academic Performance Questionnaire (ISSAPQ) were used to obtain relevant data from 92 teachers in 37 selected Senior Secondary schools using the simple random sampling techniques. Pearson product moment correlational statistics (Pearson r) and t-test at 0.05 level of significance was used to analyse the data generated and answer the research questions. The study show that regular instructional supervision using robust supervision strategies like checking of students’ notebooks, classroom visitation/inspection by school administrators, checking teachers’ lesson plan/notes and inspection of teachers record keeping have significant correlation with teachers’ performance and academic achievement of students in Secondary Schools. Recommendations like proper alignment of government policies with educational needs of the society, provision of adequate and relevant instructional materials for teaching, regular in-service training for teachers’ capacity development, depoliticization of the free education programmes and proper evaluation of school administrative procedures and educational outcomes were adduced for remediation.  Students Academic Performance, Instructional Supervision, Secondary School

Field of study: Education
Palynological evidence for vegetation development and climatic change in the Sub-Himalayan Zone (Neogene, Central Nepal)

A palynological study on Miocene–Pleistocene sediments exposed at Surai Khola in central Nepal yields new information on vegetation and climate change over the last ∼11.5 Ma. Our results show that during the late Middle Miocene to early Late Miocene (∼11.5–∼8 Ma, Lower Siwalik) the Himalayan foothills and the Gangetic floodplain of Nepal were mainly forested with subtropical to temperate broad-leafed (b.l.) taxa (e.g. Quercus , Lithocarpus / Castanopsis , Alnus ), and tropical forest taxa respectively. Grasses were present at the time but were not abundant. Between the early to late Late Miocene (∼8–∼6.5 Ma; lower Middle Siwalik) grassland replaced subtropical and temperate b.l. forest. This change may be related to disturbance of the vegetation on the slopes due to uplift, perhaps enhanced by intensification of the monsoon. Between late Late Miocene to Pliocene/Early Pleistocene? (∼6.5– Potamogeton and better preservation of all specimens. Enhanced seasonal flooding in the system during the Pliocene (∼5.5–∼3.5 Ma; top Middle Siwalik) may have produced local lacustrine conditions on the overbanks, evidenced by an abundance of algae ( Spirogyra ) and pteridophytes in the pollen assemblages. Evidence of climatic cooling between ∼6.5–∼5 Ma ago is indicated by the onset of steppe taxa, decrease of tropical forest taxa and disappearance of certain Dipterocarpaceae. Pollen assemblages from the Surai Khola section suggest complex vegetation changes, of which the shift to C 4 grass dominance was only one. Global climatic cooling, the intensification of the monsoon, and the Late Miocene uplift may all have contributed to the phytogeography in the Sub-Himalayan Zone.

Field of study: Environmental science, Geography
Molecular genetic analysis of AKR1C2-4 and HSD17B6 genes in subjects 46,XY with hypospadias.

The formation of the male urethra depends to enzyme-mediated testosterone (T) conversion into 5α-dihydrotestosterone (DHT). Two metabolic pathways could be operating in the fetal testis to synthesize androgens: 1) the "classic" route (T→DHT) mediated by SRD5A2 and 2) a "backdoor" pathway in which DHT is synthesized by aldo-keto reductase family 1, member C2 (AKR1C2), AKR1C3, and AKR1C4 enzymes without formation of a T intermediate.



We studied four genes of the "backdoor" pathway in karyotypic males with hypospadias to ascertain whether gene defects in AKRs impair urethral DHT formation that result in hypospadias.



The coding regions of the AKR1C2-4 and HSD17B6 genes were analyzed by PCR-SSCP and sequencing in a cohort of 25 Mexican patients (0.3-9 year-old-children) with 46,XY-hypospadias. Chi-squared tests was performed to evaluate the distribution of genotypes, alleles, and the Hardy-Weinberg (H-W) equilibrium. The effect of the genetic variants was investigated by in silico studies.



Screening studies revealed distinct genotypic patterns at different exons of AKR1C2-4 whereas HSD17B6 presented a wild-type sequence. The DNA analyses detected two synonymous variants (c.327C>T, c.666T>C/unreported) in AKR1C2. The AKR1C3 had two variants (c.15C>G, c.230A>G), two unreported variants (c.538T>C, c.596G>A), and one silent variant (c.312G>A). Two variants (c.434C>G, c.931C>G) were identified in AKR1C4. All variants were in H-W equilibrium without structural changes.



Hypospadias have been associated with defects that alter androgen biosynthesis in the human fetal testis, specifically 5α-DHT. We selected four candidate genes involved in the "backdoor" pathway for the formation of 5α-DHT. Molecular assays of the AKR1C2, AKR1C3, and AKR1C4 genes revealed a total of nine genetic single nucleotide variants. Several variants in the AKR1C genes have been associated with a variety of human pathologies. However, our studies suggest that active steroid biosynthesis via AKR1C might not be involved in hypospadias. Additionally, genetic research suggests a low involvement in the "backdoor" 5α-DHT pathway during human sexual development, specifically, the differentiation of male external genitalia.



These results indicate that substitutions in AKR1C2-4 are polymorphisms and all genetic variants lacks deleterious significant association with hypospadias. The data suggest that inactivating mutations in the AKR1C2-4 and HSD17B6 genes are an infrequent cause of hypospadias, which might weaken the contribution of the "backdoor" pathway to embryonic urethral masculinization.

Field of study: Medicine
On Optimum Regenerative Relaying With Imperfect Channel Knowledge

This correspondence is concerned with the performance of a regenerative relaying protocol on fading wireless channels with imperfect channel knowledge at the receivers. Assuming a single source and a single destination with multiple relay nodes, using binary modulation at the source, we present optimum receiver at the destination on frequency-flat Rayleigh fading channels by taking into account the effects of imperfect channel knowledge at the receivers. Since exact performance analysis of the optimal receiver is complicated due to the non-linear nature of the log-likelihood ratio contribution from the relay, upon using a standard technique in the literature, we present a simple approximate receiver and derive closed-form expression for the average bit error rate (BER) at the destination with a single relay node. We also present a simple analytical technique that allows us to numerically evaluate the average BER for an arbitrary number of relay nodes. Finally, with perfect channel estimation our proposed receiver subsumes the coherent receivers whereas with a minimum mean-square error channel estimation it reduces to the non-coherent receiver in the work of Chen and Laneman (2006).

Field of study: Engineering
Quaternary over-elevated torrential channels. Characteristics and depositional significance: the Maresme model (Catalonia, NE Spain)

Channel-levee deposits that occur in some large sand-dominated fluvial systems are commonly elevated above the surrounding floodplain. However, the over-elevation processes of small and isolated fluvial channels are poorly documented. The Maresme zone located NE of Barcelona (Spain) offers many examples of small over-elevated channels. This area is characterised by weathered granodiorites forming a thick coarse-grained sand-dominated regolith, which was initially covered by dense forests. In the XVIII and XIX centuries human activity led to the destruction of the vegetal cover, resulting in subsequent erosion and in the intense remobilisation of sediments during storms. Thus, large amounts of sand were transported during historical times. The intermittent discharges were confined to short (few km) and straight channels with high and uncommon gradients from 3.2 to 3.4%. These discharges flowed at high velocities towards the Mediterranean Sea, the regional base-level. High infiltration rates contributed to the accretion of sandy sediments along the channels coevally with levee development. This sandy lithosome, which is usually elevated above the surrounding floodplain, displays a characteristic convex-up cross section.

Field of study: Environmental science
Expression, purification, crystallization and preliminary X-ray diffraction data of methylmalonate-semialdehyde dehydrogenase from Bacillus subtilis.

Methylmalonate-semialdehyde dehydrogenase from Bacillus subtilis was cloned and overexpressed in Escherichia coli. Suitable crystals for X-ray diffraction experiments were obtained by the hanging-drop vapour-diffusion method using ammonium sulfate as precipitant. The crystals belong to space group P2(1)2(1)2(1), with unit-cell parameters a = 195.2, b = 192.5, c = 83.5 A, and contain one tetramer per asymmetric unit. X-ray diffraction data were collected to 2.5 A resolution using a synchrotron-radiation source. The crystal structure was solved by the molecular-replacement method.

Field of study: Chemistry