nils-herrmann/clean_scirepeval huggingface dataset:
Split-gate point-contact for channelizing electron transport on MoS2/h-BN hybrid structures

Electrostatically defined nanoscale devices on two-dimensional semiconductor heterostructures are the building blocks of various quantum electrical circuits. Owing to its atomically flat interfaces and the inherent two-dimensional nature, van der Waals heterostructures hold the advantage of large-scale uniformity, flexibility and portability over the conventional bulk semiconductor heterostructures. In this letter we show the operation of a split-gate defined point contact device on a MoS2/h-BN heterostructure, a first step towards realizing electrostatically gated quantum circuits on van der Waals semiconductors. Our devices show signatures of channelized electron flow and a complete shutdown of transport similar to the conventional point contacts defined on bulk semiconductor heterostructures. We explore the role of back-gate and the drain-source voltages on the pinch-off characteristics and, we are able to tune the pinch-off characteristics by varying the back-gate voltage at temperatures ranging from 4K to 300 K.

Field of study: Physics
Three-dimensional structure of the Gly121Tyr dimeric form of ornithine decarboxylase from Lactobacillus 30a.

Ornithine decarboxylases catalyze the conversion of ornithine to putrescine at the beginning of the polyamine pathway. Ornithine decarboxylase (ODC) from Lactobacillus 30a is a 990612 Da dodecamer composed of six homodimers. A single point mutation (Gly121Tyr) was found to prevent association of dimers into dodecamers. The dimeric protein has been crystallized at pH 7.0 in the presence of guanosine triphosphate (GTP). Crystals belong to space group P3(2)21, with unit-cell parameters a = 111.8, c = 135.9 A and one monomer in the asymmetric unit. The structure was determined by molecular replacement and refined using simulated annealing to R = 0.211 at 2. 7 A resolution. The GTP-binding site was analyzed in detail. The protein exhibits a novel binding mode for GTP which is different from that seen in most G-proteins or GTPases. Central to this binding scheme appear to be three lysines, Lys190, Lys374 and Lys382, which form salt bridges with the three phosphates, and Thr191, which hydrogen bonds with the guanine base. Furthermore, the structure suggests that there is some flexibility in the wing domain, which can change its orientation as the protein adapts to its environment. The active site is similar to that of the native enzyme, consistent with the observation that the enzyme activity does not depend on its dodecameric state.

Field of study: Chemistry
Outcome of influenza vaccination in combat‐related post‐traumatic stress disorder (PTSD) patients

Post‐traumatic stress disorder (PTSD) is an anxiety disorder that can occur after exposure to extreme traumatic experience such as war trauma, and is accompanied by fear, helplessness or horror. Exposure to trauma can result in immune dysregulation and influence susceptibility to infectious disease as well as vaccine efficacy. The aim of the study was to determine the relation of psychological stress and the immune response to influenza vaccination in combat‐related PTSD patients (n = 28). Detection of anti‐viral antibody titre was performed by inhibition of haemagglutination assay. Ex vivo tetramer staining of CD8+ T lymphocytes was used to monitor T cells specific for human leucocyte antigen (HLA)‐A*0201‐restricted influenza A haemagglutinin antigens before and after vaccination. Twenty patients showed a fourfold antibody titre increase to one or both influenza A viral strains, and 18 of them showed the same response for both influenza B viral strains. Ten of 15 healthy controls showed a fourfold rise in antibody titre to both influenza A viral strains and eight of them showed the same response for both influenza B viral strains. HLA‐A*0201+ PTSD patients (n = 10) showed a significant increase of influenza‐specific CD8 T cells after vaccination. Although those PTSD patients had a lower number of influenza‐specific CD8+ T cells before vaccination compared to HLA‐A*0201+ healthy controls (n = 6), there was no difference in influenza A antibody titre between PTSD patients and control subjects before vaccination. The generated humoral and cellular immune response in PTSD patients argues against the hypothesis that combat‐related PTSD in war veterans might affect protection following influenza vaccination.

Field of study: Biology, Medicine
Methods for field measurement of antibiotic concentrations: limitations and outlook.

The growing prevalence of antibiotic resistance poses an increasingly serious threat to human health. Although an important driver of antibiotic resistance is the continuous exposure of bacteria to sublethal concentrations of antibiotics in natural environments, antibiotic pollutants are not currently tracked globally or systematically. This limits the international capacity to address the rise of antibiotic resistance at its source. To address this lack of data, the development of methods to measure antibiotic concentrations on-site is essential. These methods, ideally, must be sensitive to sublethal concentrations of antibiotics and require minimal technical expertise. Furthermore, factors such as cost, selectivity, biosafety and the ability to multiplex must be evaluated in the context of field use. Based on these criteria, we provide a critical review of current methods in antibiotic detection and evaluate their adaptability for use on-site. We categorize these methods into microbiological assays, physical and chemical assays, immunoassays, aptasensors and whole-cell biosensors. We recommend continued development of a dipstick or microfluidics approach with a bacterial promoter-based mechanism and colorimetric output. This technique would incorporate the advantageous aspects of existing methods, maximize shelf-life and ease-of-use, and require minimal resources to implement in the field.

Field of study: Biology, Environmental science
SCCA, TSGF, and the Long Non-Coding RNA AC007271.3 are Effective Biomarkers for Diagnosing Oral Squamous Cell Carcinoma

Oral squamous cell carcinoma (OSCC) is one of the most lethal malignancies worldwide and the most common type of oral cancer, characterized by invasive growth, frequent regional metastases, high recurrence, and poor prognosis. In the current study, we investigated the use of long non-coding RNAs (lncRNAs), tumor-specific growth factor (TSGF), and squamous cell carcinoma antigen (SCCA) as potential biomarkers for OSCC screening.  LncRNA expression was measured by microarray analysis in three sets of OSCC and paired normal mucosal tissues. The potential lncRNAs involved in OSCC development were investigated by bioinformatics and verification experiments. We also determined the expression of these potential biomarkers in tissue and serum samples in a case–control study of 80 OSCC cases and 70 controls. Receiver operating characteristics, decision curve analysis, and the combined detection of lncRNA AC007271.3, TSGF, and SCCA were carried out to screen for OSCC biomarkers.  A total of 691 lncRNAs (433 upregulated and 258 downregulated) were differentially expressed in OSCC tissues compared with normal controls (p< 0.05). Based on Gene Ontology and pathway analysis, we selected four differentially expressed lncRNAs (AC007271.3, AC007182.6, LOC283481, and RP11-893F2.9), and showed that aberrant AC007271.3 levels in OSCC patients were significantly associated with clinical stage, especially in early-stage disease, in an expanded case–control study. The combination of AC007271.3 and SCCA (AUC=0.902, p< 0.001) showed significantly better ability to discriminate between OSCC and controls compared with SCCA or AC007271.3 alone. Serum AC007271.3, SCCA, and TSGF levels could also discriminate between OSCC and normal controls with sensitivities of 77.6%, 55.0%, and 63.3%, and specificities of 84.5%, 93.3%, and 66.7%, respectively.  These results suggest that AC007271.3, SCCA, and TSGF could be novel circulating biomarkers for the determination of OSCC. However, further validation in large-scale prospective studies is necessary.

Field of study: Biology, Chemistry
Exploring the Oxygen Order in Hg -1223 and Hg -1201 by 199Hg Mas Nmr

We demonstrate the use of a high-resolution solid-state fast (45 kHz) magic angle spinning (MAS) NMR for mapping the oxygen distribution in Hg-based cuprate superconductors. We identify observed three peaks in 199Hg spectrum as belonging to the different chemical environments in the HgOδ layer with no oxygen neighbors, single oxygen neighbor, and two oxygen neighbors. We discuss observed differences between Hg-1201 and Hg-1223 materials.

Field of study: Physics
Detrital chrome spinels in the Cretaceous Sanchu sandstone, central Japan: indicator of serpentinite protrusion into a fore-arc region

The Sanchu Group is regarded as Lower Cretaceous fore-arc basin-fill sediments underlain unconformably by the Jurassic accretionary wedge. This group is accompanied with the Sanchu serpentinite which is probably correlated to the Kurosegawa Tectonic Zone or serpentinite melange of SW Japan. The Sanchu Group is divided into the newly defined Untis 1–3. Sandstones of Unit 1 contain numerous detrital chrome spinel grains which were probably derived from ultramafic and mafic rocks. These chrome spinels are classified into high-Ti and low-Ti groups based on microprobe analysis. The low-Ti group chrome spinels were supplied ultramafic rocks similar to the Sanchu serpentinite, while the high-Ti group ones seem to have been derived from volcanics which are geochemically different from the presently exposed greenstone (120±6 Ma) of the Otchizawa Formation. The spinel chemistry suggests that the source rocks of the low-Ti and the high-Ti groups were originated from the arc to fore-arc upper mantle and the intraplate basalt or E-type MORB, respectively. The serpentinite may have formed a complex together with the volcanics. The sedimentary environment of Unit 1 is presumed to have been the foreshore to nearshore shelf. The graded accumulation of chrome spinels in sandstone suggest that sediment gravity flow such as a storm-generated turbidity current was the transportation mode. The serpentinite-volcanics complex emerged subaerially as a ridge during the sedimentation of Unit 1 (late Hauterivian to early Aptian). This ridge referable to a tranch slope break was produced by the protrusion of serpentinized peridotite (the Sanchu serpentinite and its precursor) associated with E-type MORB or intraplate basalt along the plate boundary in teh fore-arc region. Left lateral slip-fault movements may facilitate the protrusion, which can be considered as phenomena in the “periphery” of the Kurosegawa Tectonic Zone or serpentinite melange.

Field of study: Environmental science, Geography
STRUCTURE OF THE NORTHERN MUDDY MOUNTAIN AREA, NEVADA

Instead of a single large thrust in the Muddy Mountain area, Nevada, as reported from earlier field study, the writer distinguishes two superposed thrusts which may represent distinct orogenic episodes separated by a considerable time interval. Both thrusts “root” to the west. The structurally lower thrust (for which the name Muddy Mountain thrust is retained) is the more extensive; as reported previously, it has brought Paleozoic carbonate formations over Jurassic sandstone, with the heave-component of slip at least 15 miles. The higher thrust (here called the Glendale thrust) has heave-displacement of at least 5 miles. Together with associated smaller thrusts, it involves formations of early Upper Cretaceous age, as well as thick piedmont deposits that may be considerably younger. “Orogenic deposits” several thousand feet thick were laid down in front of the Glendale thrust as it advanced. Accurate dating of these strata would give an exceptional record of structural events.

Conglomerate at the base of the Upper Cretaceous section, containing boulders and cobbles derived from resistant units in older systems as low as the Permian, indicates earlier strong deformation not far west of the Muddy Mountain area. This earlier orogenic episode may have included development of the Muddy Mountain and other large thrusts in the region which are not known to involve formations younger than Jurassic. Therefore the earlier orogeny can now be dated merely as post-Jurassic and pre-Upper Cretaceous.

Overturned and faulted folds associated with the Glendale thrust rival in complexity some structural features of the Swiss Alps. Important transverse faults with large strike-slip component pose problems of origin; the largest of these displaces the Muddy Mountain thrust plate as much as 2 miles vertically and may be genetically related to the Glendale thrust. Numerous normal faults, variously oriented, bear witness to movements ranging in date from the Glendale thrusting episode to late Cenozoic time.

Field of study: Geology
Some calibration estimators for finite population mean in two-stage stratified random sampling

In the present article, an effort has been made to develop calibration estimators of the population mean under two-stage stratified random sampling design when auxiliary information is available at primary stage unit (psu) level. The properties of the developed estimators are derived in-terms of design based approximate variance and approximate consistent design based estimator of the variance. Some simulation studies have been conducted to investigate the relative performance of calibration estimator over the usual estimator of the population mean without using auxiliary information in two-stage stratified random sampling. Proposed calibration estimators have outperformed the usual estimator without using auxiliary information.

Field of study: Mathematics
Die Berechnung der Schallgeschwindigkeit in Gasen und FlÜssigkeiten mittels einer neuen thermischen Zustandsgleichung

ZusammenfassungAus einer neuen thermischen Zustandsgleichung wird eine allgemein gÜltige Beziehung zur Berechnung der Schallgeschwindigkeit in Gasen und FlÜssigkeiten abgeleitet. Die gefundene Beziehung wird an Kohlensäure ÜberprÜft. Es wird eine befriedigende quantitative Übereinstimmung mit der Erfahrung gefunden.

Field of study: Physics
Calculation of a narrow resonance with the LIT method

The possibility to resolve narrow structures in reaction cross sections in calculations with the Lorentz integral-transform (LIT) method is studied. To this end we consider a fictitious two-nucleon problem with a low-lying and narrow resonance in the 3P1 nucleon-nucleon partial wave and calculate the corresponding “deuteron photoabsorption cross section”. In the LIT method the use of continuum wave functions is avoided and one works instead with a localized function $\widetilde{\Psi}$. In this case study it is investigated how far into the asymptotic region $\widetilde{\Psi}$ has to be determined in order to obtain a precise resolution of the artificially introduced E1 resonance. Comparing with the results of a conventional calculation with explicit neutron-proton continuum wave functions it is shown that the LIT approach leads to an excellent reproduction of the cross section in the resonance region and of further finer cross-section details at higher energies. To this end, however, for $\widetilde{\Psi}$ one has to take into account two-nucleon distances up to at least 30 fm.

Field of study: Physics
3-Aminopyrrolidine lithium amides as chiral ligands for alkyllithium derivatives: Synthesis, NMR analysis, and computational study of their mixed aggregates

An overview of the role of 3-aminopyrrolidine lithium amides (3-APLi's) as chiral ligands for alkyllithiums (AlkLi's) is presented. Synthetic developments as well as NMR characterizations and computational interpretations have been simultaneously and complementarily conducted to improve the ligand design for a model reaction that is the condensation of AlkLi's on o-tolualdehyde, for which enantiomeric excesses up to 80 % were obtained. This study describes the whole chain going from the synthesis of the chiral 3-aminopyrrolidines (3-APs) (18 different 3-APs synthesized) to the characterization of the noncovalent mixed aggregates resulting from the interaction between the organolithium partners (3-APLi:AlkLi). Finally, the docking of the aldehyde on one lithium of the aggregate was analyzed by theoretical means on simplified models, in an attempt to understand the structure of the fully loaded pretransition complexes.

Field of study: Chemistry
The FAO guidelines for the development and use of indicators for sustainable development of marine capture fisheries and an Australian example of their application

Guidelines for developing and implementing sustainability indicators for marine capture fisheries were drafted during a recent expert consultation jointly organised by Australia and FAO in Sydney (Australia). This paper provides an overview of the guidelines and illustrates their application with an Australian example. As a background to the guidelines, the concept of sustainable development (SD) for marine capture fisheries was discussed and an agreed set of definitions and usage of common terms developed. The guidelines then outline the five sequential steps that need to be addressed in developing a meaningful set of indicators in the context of a Sustainable Development Reference System (SDRS). The five steps are: 1. specifying the scope of the SDRS; 2. developing a framework to agree on components within the system; 3. specifying criteria, objectives, potential indicators and reference values; 4. choosing the set of indicators and reference values; 5. specifying the method of aggregation and visualisation. 
These steps are further elaborated in terms of how to scope the SDRS, define the dimensions and hierarchical levels to be included in the system, set multiple objectives and link these to indicators and reference values (e.g. targets, thresholds and/or standards). The guidelines also provide some examples of possible indicators, criteria for selecting some indicators over others and present ways of aggregating and visualising the indicators so that progress towards achieving sustainable development can be communicated easily to decision-makers.

Field of study: Environmental science
Experiment on data mining in composite flavor type formula in Chinese cuisine

This paper based on collecting Chinese cuisine in the typical compound flavor type formula for mining object,explores the method rule of the data mining technology compound flavor type formula deployment in the Chinese cuisine.Using the data preprocessing,recipe name and dosage of measurement standard.using the cluster analysis,the formula for different cuisines,the flavor types are classified.And using frequency set statistical constitute compound flavor type formula core seasonings,and its correlation corresponding rules.The results show that the obtained mining knowledge pattern for the realization of automatic cooking robot automatic seasoning process has certain theoretical significance and practical value.

Field of study: Agricultural and Food sciences
Microbial community networks.

This FEMS Microbiology Ecology Thematic Issue on Bacterial Genetics and Ecology: ‘Microbial community networks’ compiles contributions presented at the BAGECO-9 meeting held in Wernigerode, Germany (23–27 June 2007). The issue contains one MiniReview and 14 research papers.

The history of the European-based BAGECO meetings dates back to the 1980s. Although there is no society associated with BAGECO meetings, their continuity is ensured by microbial ecologists who appreciate their particular atmosphere and spirit. One secret of the success of the meetings is the mix of excellent science, open and lively discussion and scientific community networking. Although the number of participants has increased continuously, the current size of the BAGECO meeting (around 300 participants in Wernigerode) allows plenary nonparallel sessions giving not only invited speakers but also Ph.D. students the chance to present their work in front of all other participants.

A major reason for establishing these meetings …

Field of study: Biology, Environmental science
Altered brain activation by a false recognition task in young abstinent patients with alcohol dependence.

Heavy alcohol intake induces both structural and functional changes in the central nervous system. Recent research developments converged on the idea that even in patients with alcohol dependence without apparent structural brain changes, some cognitive impairment exists, and associated functional change could be visualized by neuroimaging techniques. However, these data were from old (more than 50 years) patients using working memory and response inhibition tasks. Whether young abstinent patients show aberrant signs of brain activation is a matter of interest, specifically by the long-term memory retrieval task.



Subjects were 9 young patients with alcohol dependence with long-term abstinent (8 males and 1 female) and age- and education-matched 9 healthy controls (7 males and 2 females). We used a modified false recognition task in a functional MRI study.



The young patients with alcohol dependence showed reduced activation in the right dorsolateral prefrontal cortex, anterior cingulate cortex (ACC), left pulvinar in the thalamus, and in the right ventral striatum, although behavioral performances and regional patterns of brain activation were similar between patients and controls.



Long-term memory retrieval induced altered activations in prefrontal lobes, ACC, thalamus, and ventral striatum in young patients with alcohol dependence. These findings were correspondent to deficits of goal directed behavior, monitoring the erroneous responses, memory function, and drug-seeking behavior. Furthermore, these reduced activations can be considered as latent "lesions," suggesting subclinical pathology in alcoholic brains.

Field of study: Medicine
Polarization Gradient Study of Interstellar Medium Turbulence Using the Canadian Galactic Plane Survey

We have investigated the magneto-ionic turbulence in the interstellar medium through spatial gradients of the complex radio polarization vector in the Canadian Galactic Plane Survey (CGPS). The CGPS data cover 1300 square degrees, over the range , , with an extension to in the range , and arcminute resolution at 1420 MHz. Previous studies found a correlation between the skewness and kurtosis of the polarization gradient and the Mach number of the turbulence, or assumed this correlation to deduce the Mach number of an observed turbulent region. We present polarization gradient images of the entire CGPS data set, and analyze the dependence of these images on angular resolution. The polarization gradients are filamentary, and the length of these filaments is largest toward the Galactic anti-center, with the smallest toward the inner Galaxy. This may imply that small-scale turbulence is stronger in the inner Galaxy, or that we observe more distant features at low Galactic longitudes. For every resolution studied, the skewness of the polarization gradient is influenced by the edges of bright polarization gradient regions, which are not related to the turbulence revealed by the polarization gradients. We also find that the skewness of the polarization gradient is sensitive to the size of the box used to calculate the skewness, but insensitive to Galactic longitude, implying that the skewness only probes the number and magnitude of the inhomogeneities within the box. We conclude that the skewness and kurtosis of the polarization gradient are not ideal statistics for probing natural magneto-ionic turbulence.

Field of study: Physics