nils-herrmann/clean_scirepeval huggingface dataset:
Bayesian Joint Modeling of Multiple Brain Functional Networks

Investigating the similarity and changes in brain networks under different mental conditions has become increasingly important in neuroscience research. A standard separate estimation strategy fails to pool information across networks and hence has reduced estimation accuracy and power to detect between-network differences. Motivated by an fMRI Stroop task experiment that involves multiple related tasks, we develop an integrative Bayesian approach for jointly modeling multiple brain networks that provides a systematic inferential framework for network comparisons. The proposed approach explicitly models shared and differential patterns via flexible Dirichlet process-based priors on edge probabilities. Conditional on edges, the connection strengths are modeled via Bayesian spike-and-slab prior on the precision matrix off-diagonals. Numerical simulations illustrate that the proposed approach has increased power to detect true differential edges while providing adequate control on false positives and achieves greater network estimation accuracy compared to existing methods. The Stroop task data analysis reveals greater connectivity differences between task and fixation that are concentrated in brain regions previously identified as differentially activated in Stroop task, and more nuanced connectivity differences between exertion and relaxed task. In contrast, penalized modeling approaches involving computationally burdensome permutation tests reveal negligible network differences between conditions that seem biologically implausible.

Field of study: Mathematics
Unsettling the West: Violence and State Building in the Ohio Valley by Rob Harper (review)

Northwestern, and several are former students of Breen; many of the contributions, therefore, are grounded in Breen’s approach to the American Revolution or on the study of common persons in imperial settings. The recent work of both Brendan McConville (The King’s Three Faces, which is mentioned in a few citations but never directly discussed) and especially Eric Nelson (The Royalist Revolution) are overlooked, but both have argued for the importance of the crown in colonial culture and in interpreting the American Revolution, making important contributions in its social and ideological history. At times, the contributions seem to depart from the focuses in the introduction, making the collection somewhat disjointed; Breen, in his conclusion, directly engages with only a few of the essays. The volume suffers from something of an identity crisis: Is it about the American Revolution; the common person engaging with (any?) empire; or a tribute to Breen and his approach? If the answer is all three, it is too ambitious for an edited collection to accomplish. Nonetheless, this volume will benefit those who admire Breen’s work or wish to find recent scholarship that has adopted the imperial-revolutionary approach.

Field of study: History
Late Pleistocene, post-Vashon, alpine glaciation of the Nooksack drainage, North Cascades, Washington

During the maximum late Wisconsin glaciation ca. 15 000 14C yr B.P., the Cordilleran Ice Sheet overwhelmed the Nooksack drainage of the northwestern Cascades, leaving only peaks higher than 2000 m above the ice surface. Ice-sheet flow over the Nooksack drainage and the adjacent Puget Lowland was essentially north-south. Rapid deglaciation between 14 500 and 12 500 14C yr B.P. resulted in dropping of the ice-sheet surface below ridge crests in the Nooksack drainage, and glacial activity thereafter became topographically controlled. Long valley glaciers in the upper Nooksack Valley were no longer connected to the Cordilleran Ice Sheet, and the source area changed from the main ice sheet to Mount Baker, Mount Shuksan, and the Twin Sisters Range. At that time, the margin of the remnants of the Cordilleran Ice Sheet was 30 km to the northwest, separated from the Nooksack Valley glaciers by several ridges 1200 m higher than the surface of the ice sheet.

Moraines were built in all three forks of the Nooksack drainage, 25–45 km downvalley from their sources. The Middle Fork glacier stagnated 12 300 14C yr B.P. and deposited ice-contact drift that was later overridden when ice readvanced over ice-contact drift and deposited a prominent, 2-km-long, lateral moraine. Logs in a lateral moraine in the upper Middle Fork were dated at 10 680 ± 70 and 10 500 ± 70 14C yr B.P. The North Fork glacier, which originated at a large cirque on Mount Shuksan and was fed by glaciers from Mount Baker, extended to Kendall, where two moraines were deposited. Outwash from the younger moraine in the North Fork valley overlies glaciomarine drift, dated as 11 910 ± 80 14C yr B.P., and contains charcoal layers dated at 10 603 ± 69 and 10 788 ± 77 14C yr B.P. The South Fork glacier at its maximum was joined by ice from the Middle Fork and extended downvalley to Lake Whatcom and to Cranberry Lake. It retreated from its terminal position slightly before ca. 12 700 14C yr B.P.

Field of study: Geology
SHARED MASS DAMPER(STMD) USED TO REDUCE THE SEISMIC RESPONSE OF SECONDARY SYSTEMS

By considering that the strategy of Viscous Damper(VD) does not behave well in reducing the seismic response of secondary systems,a new strategy termed as Shared Mass Damper(STMD) is introduced in the paper.In the strategy,a shared mass connected by viscous dampers is placed between two adjacent secondary systems,dissipating earthquake energy by the relative displacement between the secondary systems and the shared mass.Meanwhile,two adjacent secondary systems are made to vibrate coordinately so as to avoid the pounding.The new strategy of Shared Mass Damper(STMD) can work well,especially when the frequencies of two secondary systems are close to each other.The effects of two strategies as well as the influencing factors of STMD and VD on reducing the seismic response of secondary systems are studied.

Field of study: Engineering
Direct inter-subdomain interactions switch between the closed and open forms of the Hsp70 nucleotide-binding domain in the nucleotide-free state.

The 70 kDa heat-shock proteins (Hsp70s) are highly conserved chaperones that are involved in several cellular processes, such as protein folding, disaggregation and translocation. In this study, the crystal structures of the human Hsp70 nucleotide-binding domain (NBD) fragment were determined in the nucleotide-free state and in complex with adenosine 5'-(beta,gamma-imido)triphosphate (AMPPNP). The structure of the nucleotide-free NBD fragment is similar to that of the AMPPNP-bound NBD fragment and is designated as the ;closed form'. In the nucleotide-free NBD fragment the closed form is intrinsically supported through interactions between Tyr15, Lys56 and Glu268 which connect subdomains IA, IB and IIB at the centre of the protein. Interaction with the substrate-binding domain (SBD) of Hsp70 or the BAG domain of BAG1 impairs this subdomain connection and triggers the rotation of subdomain IIA around a hydrophobic helix from subdomain IA. The subdomain rotation is limited by Asp199 and Asp206 from subdomain IIA and clearly defines the open form of the NBD. The open form is further stabilized by a new interaction between Gly230 from subdomain IIB and Ser340 from subdomain IIA. The structure of the NBD in the nucleotide-free state is determined by switching of the inter-subdomain interactions.

Field of study: Chemistry
Über die Quantenbedingungen

ZusammenfassungEs wird gezeigt, daß man die stationären Zustände einer allgemeinen Klasse von bedingt-periodischen Systemen mittels einer einzigen Bedingung festlegen kann, da diese Bedingung den Sommerfeld sehen Zustandsbedingungen: Ik=nkh (k=1, 2, ... u) äquivalent ist.

Field of study: Physics
Application of Online Monitoring System of Partial Discharge in GIS Based on Ultra High Frequency Method in 1000 kV GIS

The Operation and Maintenance of UHV substation main equipment is facing more serious problems than EHV substation,once happening the equipment failure will bring great loss,so the safety and reliability of UHV substation main equipment is specially in need of attention.An online monitoring system of partial discharge in GIS based on ultra high frequency method is introduced in this paper,it can be real-time monitoring the discharge of fixed particles,unbound particles,floating electrode and insulation defects,accurately reflecting the state of 1000kV GIS.It is a great help to 1000kV GIS operation and maintenance.

Field of study: Engineering, Physics
Strategies for Obtaining and Pruning Imputed Whole-Genome Sequence Data for Genomic Prediction

Genomic prediction with imputed whole-genome sequencing (WGS) data is an attractive approach to improve predictive ability with low cost. However, high accuracy has not been realized using this method in livestock. In this study, we imputed 435 individuals from 600K single nucleotide polymorphism (SNP) chip data to WGS data using different reference panels. We also investigated the prediction accuracy of genomic best linear unbiased prediction (GBLUP) using imputed WGS data from different reference panels, linkage disequilibrium (LD)-based marker pruning, and pre-selected variants based on Genome-wide association society (GWAS) results. Results showed that the imputation accuracies from 600K to WGS data were 0.873 ± 0.038, 0.906 ± 0.036, and 0.979 ± 0.010 for the internal, external, and combined reference panels, respectively. In most traits of chickens, the prediction accuracy of imputed WGS data obtained from the internal reference panel was greater than or equal to that of the combined reference panel; the external reference panel had the lowest prediction accuracy. Compared with 600K chip data, GBLUP with imputed WGS data had only a small increase (1-3%) in prediction accuracy. Using only variants selected from imputed WGS data based on GWAS results resulted in almost no increase for most traits and even increased the bias of the regression coefficient. The impact of the degree of LD of selected and remaining variants on prediction accuracy was different. For average daily gain (ADG), residual feed intake (RFI), intestine length (IL), and body weight in 91 days (BW91), the accuracy of GBLUP increased as the degree of LD of selected variants decreased, but the opposite relationship occurred for the remaining variants. But for breast muscle weight (BMW) and average daily feed intake (ADFI), the accuracy of GBLUP increased as the degree of LD of selected variants increased, and the degree of LD of remaining variants had a small effect on prediction accuracy. Overall, the optimal imputation strategy to obtain WGS data for genomic prediction should consider the relationship between selected individuals and target population individuals to avoid heterogeneity of imputation. LD-based marker pruning can be used to improve the accuracy of genomic prediction using imputed WGS data.

Field of study: Biology
Impacts of land use/land cover change on climate and future research priorities

Several recommendations have been proposed for detecting land use and land cover change (LULCC) on the environment from, observed climatic records and to modeling to improve its understanding and its impacts on climate. Researchers need to detect LULCCs accurately at appropriate scales within a specified time period to better understand their impacts on climate and provide improved estimates of future climate. The US Climate Reference Network (USCRN) can be helpful in monitoring impacts of LULCC on near-surface atmospheric conditions, including temperature. The USCRN measures temperature, precipitation, solar radiation, and ground or skin temperature. It is recommended that the National Climatic Data Center (NCDC) and other climate monitoring agencies develop plans and seek funds to address any monitoring biases that are identified and for which detailed analyses have not been completed.

Field of study: Environmental science
Dependability of the immune system and the problem of secondary immunologic deficiency

: Based on the own materials and reported data the author defines the reliability of the immune system, regards possible mechanisms that ensure the reliability. Acquired immunodeficiency is viewed as the result of a decrease of the reliability of the immune system. The author defines the acquired immunodeficiency syndrome, bases the clinical and laboratory criteria for diagnosing the acquired immunodeficiency syndrome. Describes the principles of the treatment of the acquired immunodeficiency syndrome.

Field of study: Medicine
New states in heavy Cd isotopes and evidence for weakening of the N = 82 shell structure

A chemically selective laser ion source has been used in a β-decay study of heavy Ag isotopes into even-even Cd nuclides. Gamma-spectroscopic techniques in time-resolving event-by-event and multiscaling modes have permitted the identification of the first 2+ and 4+ levels in 126Cd78, 128Cd80, and tentatively the 2+ state in 130Cd82. From a comparison of these new states in 48Cd with the E(2+) and E(4+)/E(2+) level systematics of 46Pd and 52Te isotopes and several recent model predictions, possible evidence for a weakening of the spherical N = 82 neutron-shell below double-magic 132Sn is obtained.

Field of study: Physics
Global reprogramming of transcription and metabolism in Medicago truncatula during progressive drought and after rewatering

Medicago truncatula is a model legume forage crop native to the arid and semi-arid environments of the Mediterranean. Given its drought-adapted nature, it is an ideal candidate to study the molecular and biochemical mechanisms conferring drought resistance in plants. Medicago plants were subjected to a progressive drought stress over 14 d of water withholding followed by rewatering under controlled environmental conditions. Based on physiological measurements of plant water status and changes in morphology, plants experienced mild, moderate and severe water stress before rehydration. Transcriptome analysis of roots and shoots from control, mildly, moderately and severely stressed, and rewatered plants, identified many thousands of genes that were altered in expression in response to drought. Many genes with expression tightly coupled to the plant water potential (i.e. drought intensity) were identified suggesting an involvement in Medicago drought adaptation responses. Metabolite profiling of drought-stressed plants revealed the presence of 135 polar and 165 non-polar compounds in roots and shoots. Combining Medicago metabolomic data with transcriptomic data yielded insight into the regulation of metabolic pathways operating under drought stress. Among the metabolites detected in drought-stressed Medicago plants, myo-inositol and proline had striking regulatory profiles indicating involvement in Medicago drought tolerance. Global transcriptional and metabolic responses to drought and rewatering were investigated in Medicago truncatula, a naturally drought-adapted model legume species. Integration of metabolomic and transcriptomic data yielded insights into the regulation of metabolic pathways underlying drought-stress adaptation. Many genes and metabolites with expression tightly coupled to drought intensity were identified, suggesting active involvement in Medicago drought resistance. These could prove useful targets for future translational approaches to improve closely related crop plants such as common bean, soybean and pea.

Field of study: Environmental science
Cloning, expression, crystallization and initial crystallographic analysis of the C-terminal domain of the amyloid precursor protein APP.

Alzheimer's disease is associated with typical brain deposits (senile plaques) consisting mainly of neurotoxic amyloid beta-peptides. These are proteolytically derived from the large type I transmembrane protein amyloid precursor protein (APP), which is possibly involved in signal transduction. The large C-terminal domain CAPPD of the human APP ectodomain has been cloned, expressed in large amounts in Escherichia coli and purified to homogeneity. Well diffracting tetragonal crystals have been obtained and native data have been collected to 2.1 A. Initial experimental phases from a three-wavelength MAD experiment using (NH(4))(2)OsCl(6)-derivatized crystals are of good quality and show mostly alpha-helical conformations.

Field of study: Chemistry
On impulsive control with long run average cost criterion

The impulsive control with long run average cost criterion was considered first by M. Robin in , for Markov processes having nice ergodic properties. The aim of this paper is to complete and extend the results of paper . In particular we show that for Fellerien Markov processes the optimal value is constant and find optimal or ɛ-optimal strategies. We also prove, that the use of general stopping times, instead of those of the form τi = τi−1 + σi ° \(\tau _i = \tau _{i - 1} + \sigma _i \circ \theta \tau _{\tau _{_{i - 1} } }\) as in the paper  does not change the optimal value of the functional. Results are only reported here and the detailed proofs will appear elsewhere, see .

Field of study: Mathematics
Influence of the Type of Epoxy Resin and Concentration of Glycidylisobutyl-POSS in the Properties of Nanocomposites

Epoxy resin is one of the most used resins for obtaining composites and coatings. Its properties have been modified using many materials, mainly based on nanotechnology, such as clays and polyhedral oligomeric silsesquioxanes (POSS). POSS may increase thermal and mechanical resistance and hydrophobicity of the epoxy resin. This study aims at characterizing epoxy nanocomposites, using two distinct resins (DGEBA and DGEBF) and an addition of glycidylisobutyl-POSS in contents of 2.5% and 5% (w/w), through X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), thermogravimetric analysis (TGA) and dynamic mechanical analysis (DMA). Samples showed an amorphous halo due to the epoxy resin and a characteristic peak of POSS. TGA results showed a greater residual mass in DGEBF systems due to its wider formation of crosslinks. FTIR spectra demonstrated a higher amplitude of the hydroxyl band in DGEBF 5% system, which may affect its hydrophilic behavior because of the molecular mobility and resin weight reduction. DMA results showed that DGEBA systems are more flexible than DGEBF.

Field of study: Materials science
Anti‐tissue transglutaminase, anti‐endomysium and anti‐R1‐reticulin autoantibodies—the antibody trinity of coeliac disease

Anti‐tissue transglutaminase has been recently described as the predominant autoantigen in coeliac disease. We purified serum anti‐tissue transglutaminase antibodies from three patients with coeliac disease by column chromatography and eluted tissue section‐bound R1‐anti‐reticulin antibodies from sections of rat tissue for two of these. Lastly, we generated seven mouse MoAbs to guinea pig tissue transglutaminase. Each preparation was examined for anti‐tissue transglutaminase, anti‐endomysium, anti‐R1 reticulin and anti‐gliadin antibodies. Column‐purified patient antibodies and 2/7 mouse MoAbs gave characteristic anti‐endomysium/anti‐R1 reticulin reactivity on rat, monkey and human tissue. All positive sera gave indistinguishable patterns of immunofluorescence on rat liver, kidney and stomach, monkey oesophagus, and human umbilical cord. Anti‐R1‐reticulin eluted from sections showed anti‐tissue transglutaminase reactivity in 2/2 cases, but 0/2 showed anti‐gliadin reactivity. In both, tissue section‐eluted anti‐R1 reticulin gave endomysial staining on monkey oesophagus. None of the mouse monoclonals, or any of the purified patient's anti‐tissue transglutaminase or anti‐R1‐reticulin antibody showed any reactivity with gliadin. These data confirm tissue transglutaminase as the predominant autoantigen in coeliac disease and suggest that both anti‐endomysium and anti‐R1 reticulin reactivities seen in coeliac disease arise due to an immune response to tissue transglutaminase. Rigorous immunoabsorption was sufficient to abrogate reactivity in the tissue transglutaminase ELISA, but failed to completely absorb anti‐endomysium and anti‐reticulin activity. The possibility remains that some of the anti‐endomysium and anti‐reticulin activity was directed against antigens other than tissue transglutaminase.

Field of study: Biology, Medicine
Quasicrystals: a new class of ordered structures

A quasicrystal is the natural extension of the notion of a crystal to structures with quasiperiodic, rather than periodic, translational order. We classify two- and three-dimensional quasicrystals by their symmetry under rotation and show that many disallowed crystal symmetries are allowed quasicrystal symmetries. We analytically compute the diffraction pattern of an ideal quasicrystal and show that the recently observed electron diffraction pattern of an Al-Mn alloy is closely related to that of an icosahedral quasicrystal.

Field of study: Physics
Development and Assessment of an Interprofessional Curriculum for Managing Diabetes During Ramadan

To develop an educational module that would optimize the diabetic management of individuals observing Ramadan, and to evaluate the effectiveness of the module based on the special needs of fasting individuals.  A needs assessment was conducted to understand the knowledge gaps of health care professionals and the perceived usefulness of an interprofessional curriculum focused on the management of diabetes during Ramadan. Following this assessment, an interdisciplinary team developed and implemented a comprehensive curriculum. Pre- and post-surveys were completed to evaluate the course and assess the changes in skill level and knowledge measured on a Likert scale of 0-5 from “none” to “mastery.”  One hundred percent of residents and 75% of staff who completed pre- and post-test surveys reported at least one point of increased skill in the item: adjusting medication for patients with diabetes during Ramadan.  Residents and staff demonstrated a need for improved educational curriculum to address diabetes during Ramadan. For both residents and staff, self-reported confidence in their skillset improved upon completing the curriculum.

Field of study: Education, Medicine
Electrical qualification of new ultrathin integration techniques

The aim of this paper is to analyze the feasibility of ultrathin packages through the electrical qualification of the technological process used, i.e. mechanical lapping. It considers polysilicon bipolar transistors which thickness can reach values lower than 10 μm. Forward mode and reverse mode characterizations show no significant degradation of pertinent characteristics, thus allowing to find applications in new compact packaging concept.

Field of study: Engineering
Physicochemical characteristics of gummy added with sutchi catfish (Pangasius hypophthalmus) gelatin.

Gelatin from sutchi catfish (Pangasius hypophthalmus) skin was extracted and applied in the preparation of gummy in order to determine the suitability of sutchi catfish gelatin in gummy production. The skin was subjected to pre-treatment in the following sequence; 0.8M NaCl, 0.19 N NaOH followed by 0.12 N acetic acid prior to 12 hours extraction in distilled water at 50oC. The physicochemical characteristics of sutchi catfish gelatin was analysed and compared with the commercial bovine gelatin. Gummy added with sutchi catfish gelatin was also compared with gummy added with commercial gelatin. Analysis comprises of yield, gel strength, setting point and setting time, amino acid composition, texture profile analysis and sensory evaluation. The extraction resulted in 14.47% yield of gelatin. Sutchi catfish gelatin showed higher gel strength value (360.86 g) compared to the commercial gelatin (217.37 g) which is in accordance with proline content. Texture profile analysis showed that gummies prepared using sutchi catfish gelatin had significantly higher (p<0.05) gumminess value while amino acid compositions such as proline, glycine and lysine were also higher. Sensory analysis indicated that both gummies were equally acceptable. Therefore, sutchi catfish gelatin can be successfully used as a future gelling agent in food.

Field of study: Agricultural and Food sciences