bluuebunny/crossref_metadata_2025_split huggingface dataset:
Van der Waals ferromagnetic Josephson junctions
Authors: Ai Linfeng , Zhang Enze , Yang Jinshan , Xie Xiaoyi , Yang Yunkun , Jia Zehao , Zhang Yuda , Liu Shanshan , Li Zihan , Leng Pengliang , Cao Xiangyu , Sun Xingdan , Zhang Tongyao , Kou Xufeng , Han Zheng , Xiu Faxian , Dong Shaoming 
Published: November 2021

AbstractSuperconductor-ferromagnet interfaces in two-dimensional heterostructures present a unique opportunity to study the interplay between superconductivity and ferromagnetism. The realization of such nanoscale heterostructures in van der Waals (vdW) crystals remains largely unexplored due to the challenge of making atomically-sharp interfaces from their layered structures. Here, we build a vdW ferromagnetic Josephson junction (JJ) by inserting a few-layer ferromagnetic insulator Cr2Ge2Te6 into two layers of superconductor NbSe2. The critical current and corresponding junction resistance exhibit a hysteretic and oscillatory behavior against in-plane magnetic fields, manifesting itself as a strong Josephson coupling state. Also, we observe a central minimum of critical current in some JJ devices as well as a nontrivial phase shift in SQUID structures, evidencing the coexistence of 0 and π phase in the junction region. Our study paves the way to exploring sensitive probes of weak magnetism and multifunctional building-blocks for phase-related superconducting circuits using vdW heterostructures.
The effects of ideological value framing and symbolic racism on pro-environmental behavior
Authors: Makovi Kinga , Kasak-Gliboff Hannah 
Published: November 2021

Abstract
Environmental degradation continues to be one of the greatest threats to human well-being, posing a disproportionate burden on communities of color. Environmental action, however, fails to reflect this urgency, leaving social-behavioral research at the frontier of environmental conservation, as well as environmental justice. Broad societal consensus for environmental action is particularly sparse among conservatives. The lack of even small personal sacrifices in favor of the environment could be attributed to the relatively low salience of environmental threats to white Americans and the partisan nature of environmentalism in America. We evaluate if (1) environmental action is causally related to the ideological value framing of an environmental issue; and (2) if the perceived race of impacted communities influences environmental action as a function of racial resentment. With this large-scale, original survey experiment examining the case of air-pollution, we find weak support for the first, but we do not find evidence for the second. We advance our understanding of environmental justice advocacy and environmental inaction in the United States.

Protocol registration
The stage 1 protocol for this Registered Report was accepted in principle on 10 June 2021. The protocol, as accepted by the journal, can be found at https://doi.org/10.6084/m9.figshare.14769558.
Calculation of the Gibbs–Donnan factors for multi-ion solutions with non-permeating charge on both sides of a permselective membrane
Authors: Waniewski Jacek , Pietribiasi Mauro , Pstras Leszek 
Published: November 2021

AbstractSeparation of two ionic solutions with a permselective membrane that is impermeable to some of the ions leads to an uneven distribution of permeating ions on the two sides of the membrane described by the Gibbs–Donnan (G–D) equilibrium with the G–D factors relating ion concentrations in the two solutions. Here, we present a method of calculating the G–D factors for ideal electroneutral multi-ion solutions with different total charge of non-permeating species on each side of a permselective membrane separating two compartments. We discuss some special cases of G–D equilibrium for which an analytical solution may be found, and we prove the transitivity of G–D factors for multi-ion solutions in several compartments interconnected by permselective membranes. We show a few examples of calculation of the G–D factors for both simple and complex solutions, including the case of human blood plasma and interstitial fluid separated by capillary walls. The article is accompanied by an online tool that enables the calculation of the G–D factors and the equilibrium concentrations for multi-ion solutions with various composition in terms of permeating ions and non-permeating charge, according to the presented method.
The influence of rainfall and tillage on wheat yield parameters and weed population in monoculture versus rotation systems
Authors: Gandía María Luisa , Del Monte Juan Pablo , Tenorio José Luis , Santín-Montanyá María Inés 
Published: November 2021

AbstractExtreme climate events (ECEs) of drought are becoming common in Mediterranean areas and farmers need adapt agricultural practices to achieve sustainability. This field study took place in to gain insight into the effects of seasonal rainfall, tillage and crop systems on wheat yield and weed parameters. Conventional (CT), minimum (MT) and no-tillage (NT) systems in wheat monoculture and rotation cropping systems were tested during 3 years of study (2014–2015, 2015–2016 and 2016–2017). Growing Season Rainfall (GSR) was the most influential factor on yield parameters and weed population. In 2016–2017, categorized as an extreme climate event by drought, the GSR accounted for 43.4% of the historical average. This year, the wheat yield (373 kg ha−1) and harvest index (0.18) were the lowest. In 2015–2016, scarcer autumn rainfall (44 mm) affected the weed germination period, reducing the density (17 plants m−2) and diversity of weed species (3 species m−2) while yield was favoured by high winter and spring rainfall (247 mm). Our study revealed that tillage effects was not significant on wheat yield, but NT systems consistently showed higher weed density and diversity than CT and MT despite the irregular GSR during this study. The rotation system presented higher values of wheat grain yield (781 kg/ha) and dry straw biomass (1803 kg/ha) but also weed biomass (48.54 g m−2) compared to monoculture (27.50 g m−2). NT and rotation combined increased the weed community although did not reduce the wheat yield compare to conventional systems even with an ECE of drought.
Clinical characteristics and outcomes for patients with non‑metastatic castration-resistant prostate cancer
Authors: Arnold Peter , Penaloza-Ramos Maria Cristina , Adedokun Lola , Rees Sarah , Lockhat Mohamed , Spary Lisa , Watkins Alan , Gnanapragasam Vincent , Crabb Simon J. 
Published: November 2021

AbstractThis study used linked, routinely-collected datasets to explore incidence, clinical characteristics and outcomes of prostate cancer (PC) patients who experience a rise in prostate-specific antigen (PSA) levels despite androgen deprivation therapy (ADT), without evidence of metastases in their patient record, termed non-metastatic castration-resistant PC (nmCRPC). Routinely collected administrative data in Wales were used to identify patients diagnosed with PC and nmCRPC from 2000–2015. Logrank tests and Cox proportional hazard models were used to compare time-to-events across subgroups defined by PSA doubling time and age. Of 38,021 patients identified with PC, 1,465 met nmCRPC criteria. PC incidence increased over the study period, while nmCRPC categorizations reduced. Median time from PC diagnosis to nmCRPC categorization was 3.07 years (95% confidence interval [CI] 2.91–3.26) and from nmCRPC categorization to metastases/death was 2.86 years (95% CI 2.67–3.09). Shorter PSA doubling time (≤ 10 months, versus > 10 months) was associated with reduced time to metastases or death (2.11 years [95% CI 1.92–2.30] versus 5.22 years [95% CI 4.87–5.51]). Age was not significantly associated with time to metastases/death. Our findings highlight key clinical characteristics and outcomes for patients with nmCRPC prior to the introduction of recently approved treatments.
Automatic vertebrae localization and segmentation in CT with a two-stage Dense-U-Net
Authors: Cheng Pengfei , Yang Yusheng , Yu Huiqiang , He Yongyi 
Published: November 2021

AbstractAutomatic vertebrae localization and segmentation in computed tomography (CT) are fundamental for spinal image analysis and spine surgery with computer-assisted surgery systems. But they remain challenging due to high variation in spinal anatomy among patients. In this paper, we proposed a deep-learning approach for automatic CT vertebrae localization and segmentation with a two-stage Dense-U-Net. The first stage used a 2D-Dense-U-Net to localize vertebrae by detecting the vertebrae centroids with dense labels and 2D slices. The second stage segmented the specific vertebra within a region-of-interest identified based on the centroid using 3D-Dense-U-Net. Finally, each segmented vertebra was merged into a complete spine and resampled to original resolution. We evaluated our method on the dataset from the CSI 2014 Workshop with 6 metrics: location error (1.69 ± 0.78 mm), detection rate (100%) for vertebrae localization; the dice coefficient (0.953 ± 0.014), intersection over union (0.911 ± 0.025), Hausdorff distance (4.013 ± 2.128 mm), pixel accuracy (0.998 ± 0.001) for vertebrae segmentation. The experimental results demonstrated the efficiency of the proposed method. Furthermore, evaluation on the dataset from the xVertSeg challenge with location error (4.12 ± 2.31), detection rate (100%), dice coefficient (0.877 ± 0.035) shows the generalizability of our method. In summary, our solution localized the vertebrae successfully by detecting the centroids of vertebrae and implemented instance segmentation of vertebrae in the whole spine.
Machining feature recognition based on deep neural networks to support tight integration with 3D CAD systems
Authors: Yeo Changmo , Kim Byung Chul , Cheon Sanguk , Lee Jinwon , Mun Duhwan 
Published: November 2021

AbstractRecently, studies applying deep learning technology to recognize the machining feature of three-dimensional (3D) computer-aided design (CAD) models are increasing. Since the direct utilization of boundary representation (B-rep) models as input data for neural networks in terms of data structure is difficult, B-rep models are generally converted into a voxel, mesh, or point cloud model and used as inputs for neural networks for the application of 3D models to deep learning. However, the model’s resolution decreases during the format conversion of 3D models, causing the loss of some features or difficulties in identifying areas of the converted model corresponding to a specific face of the B-rep model. To solve these problems, this study proposes a method enabling tight integration of a 3D CAD system with a deep neural network using feature descriptors as inputs to neural networks for recognizing machining features. Feature descriptor denotes an explicit representation of the main property items of a face. We constructed 2236 data to train and evaluate the deep neural network. Of these, 1430 were used for training the deep neural network, and 358 were used for validation. And 448 were used to evaluate the performance of the trained deep neural network. In addition, we conducted an experiment to recognize a total of 17 types (16 types of machining features and a non-feature) from the B-rep model, and the types for all 75 test cases were successfully recognized.
Isolation, phenotypic characterization and comparative genomic analysis of 2019SD1, a polyvalent enterobacteria phage
Authors: Kumar Prince , Meghvansi Mukesh K. , Kamboj D. V. 
Published: November 2021

AbstractShigellahas the remarkable capability to acquire antibiotic resistance rapidly thereby posing a significant public health challenge for the effective treatment of dysentery (Shigellosis). The phage therapy has been proven as an effective alternative strategy for controllingShigellainfections. In this study, we illustrate the isolation and detailed characterization of a polyvalent phage 2019SD1, which demonstrates lytic activity againstShigella dysenteriae,Escherichia coli, Vibrio cholerae, Enterococcus saccharolyticusandEnterococcus faecium.The newly isolated phage 2019SD1 shows adsorption time < 6 min, a latent period of 20 min and burst size of 151 PFU per bacterial cell. 2019SD1 exhibits considerable stability in a wide pH range and survives an hour at 50 °C. Under transmission electron microscope, 2019SD1 shows an icosahedral capsid (60 nm dia) and a 140 nm long tail. Further, detailed bioinformatic analyses of whole genome sequence data obtained through Oxford Nanopore platform revealed that 2019SD1 belongs to genusHanrivervirusof subfamilyTempevirinaeunder the familyDrexlerviridae. The concatenated protein phylogeny of 2019SD1 with the members ofDrexlerviridaetaking four genes (DNA Primase, ATP Dependent DNA Helicase, Large Terminase Protein, and Portal Protein) using the maximum parsimony method also suggested that 2019SD1 formed a distinct clade with the closest match of the taxa belonging to the genusHanrivervirus.The genome analysis data indicate the occurrence of putative tail fiber proteins and DNA methylation mechanism. In addition, 2019SD1 has a well-established anti-host defence system as suggested through identification of putative anti-CRISPR and anti-restriction endonuclease systems thereby also indicating its biocontrol potential.
Acoustic differentiation and classification of wild belugas and narwhals using echolocation clicks
Authors: Zahn Marie J. , Rankin Shannon , McCullough Jennifer L. K. , Koblitz Jens C. , Archer Frederick , Rasmussen Marianne H. , Laidre Kristin L. 
Published: November 2021

AbstractBelugas (Delphinapterus leucas) and narwhals (Monodon monoceros) are highly social Arctic toothed whales with large vocal repertoires and similar acoustic profiles. Passive Acoustic Monitoring (PAM) that uses multiple hydrophones over large spatiotemporal scales has been a primary method to study their populations, particularly in response to rapid climate change and increasing underwater noise. This study marks the first acoustic comparison between wild belugas and narwhals from the same location and reveals that they can be acoustically differentiated and classified solely by echolocation clicks. Acoustic recordings were made in the pack ice of Baffin Bay, West Greenland, during 2013. Multivariate analyses and Random Forests classification models were applied to eighty-one single-species acoustic events comprised of numerous echolocation clicks. Results demonstrate a significant difference between species’ acoustic parameters where beluga echolocation was distinguished by higher frequency content, evidenced by higher peak frequencies, center frequencies, and frequency minimums and maximums. Spectral peaks, troughs, and center frequencies for beluga clicks were generally > 60 kHz and narwhal clicks < 60 kHz with overlap between 40–60 kHz. Classification model predictive performance was strong with an overall correct classification rate of 97.5% for the best model. The most important predictors for species assignment were defined by peaks and notches in frequency spectra. Our results provide strong support for the use of echolocation in PAM efforts to differentiate belugas and narwhals acoustically.
Adaptive neurons compute confidence in a decision network
Authors: Li Luozheng , Wang DaHui 
Published: November 2021

AbstractHumans and many animals have the ability to assess the confidence of their decisions. However, little is known about the underlying neural substrate and mechanism. In this study we propose a computational model consisting of a group of ’confidence neurons’ with adaptation, which are able to assess the confidence of decisions by detecting the slope of ramping activities of decision neurons. The simulated activities of ’confidence neurons’ in our simple model capture the typical features of confidence observed in humans and animals experiments. Our results indicate that confidence could be online formed along with the decision formation, and the adaptation properties could be used to monitor the formation of confidence during the decision making.
Prenatal exposure to persistent organic pollutants and metals and problematic child behavior at 3–5 years of age: a Greenlandic cohort study
Authors: Kornvig Simon , Wielsøe Maria , Long Manhai , Bonefeld-Jørgensen Eva Cecilie 
Published: November 2021

AbstractHigh levels of persistent organic pollutants (POPs) and heavy metals are found in Arctic populations. POP and heavy metals are linked to impaired cognitive development. This study examined associations between prenatal POP and metals exposure and problematic child behavior using the Strength and Difficulties Questionnaire (SDQ). POPs and metals were measured in 102 pregnant Greenlandic women. During follow-up at 3–5 years, parents answered an assisted questionnaire including children’s SDQ scores. Associations were analyzed using linear and logistic regression analyses and adjusted for maternal plasma cotinine, educational level and age at delivery. In the adjusted analyses, the medium tertile of hexachlorobenzene (β = 3.06,p = 0.010), β-hexachlorocyclohexane (β = 3.58,p = 0.004) and trans-nonachlor (β = 2.06,p = 0.082) were positively associated with SDQ scores. The continuous cis-nonachlor (OR = 1.09,p = 0.079), dichloro-diphenyl-dichloroethylene (OR = 1.01,p = 0.077), trans-nonachlor (OR = 1.01,p = 0.091), and sum Organochlorine-Pesticides (OR = 1.00,p = 0.094) were positively associated with abnormal SDQ score and the continuous mirex (OR = 1.28,p = 0.096), oxychlordane (OR = 1.04,p = 0.066), and trans-nonachlor (OR = 1.02,p = 0.071) with abnormal hyperactivity score. We found no consistent evidence of associations between polychlorinated biphenyls, perfluoroalkylated substances and heavy metals and problematic behavior. Prenatal organochlorine pesticide exposure associated significantly with problematic behavior in 3–5 year old children.
Prevalence of Toxoplasma gondii infection among small mammals in Tatarstan, Russian Federation
Authors: Shamaev Nikolai D. , Shuralev Eduard A. , Nikitin Oleg V. , Mukminov Malik N. , Davidyuk Yuriy N. , Belyaev Alexander N. , Isaeva Guzel Sh. , Ziatdinov Vasil B. , Khammadov Nail I. , Safina Regina F. , Salmanova Gaysha R. , Akhmedova Guzel M. , Khaertynov Kamil S. , Saito Taizo , Kitoh Katsuya , Takashima Yasuhiro 
Published: November 2021

AbstractToxoplasma gondii is a zoonotic parasite with a wide host range that includes humans, domestic animals and wild animals. Small mammals serve as intermediate hosts for T. gondii and may contribute to the persistence of this parasite in the environment. Mass mortality in wild animals and deaths in rare endemic species make the study of this parasite of growing importance. In this study, T. gondii infection prevalence was evaluated in brain tissues from 474 small mammals captured at 26 trapping points in urban and rural areas of Tatarstan, Russian Federation. Nested PCR was used to detect the T. gondii B1 gene in the samples. Overall, 40/474 samples (8.44%) showed B1 gene positivity. T. gondii infection among the wild small mammals trapped in the rural area was significantly higher as a whole than that of the urban area as a whole. Multivariate logistical regression analysis also showed that the trapping area (rural or urban) significantly contributed to T. gondii positivity. Vegetation in the trapping points, small mammal species, sex, age or distance from the trapping points to the nearest human settlements did not significantly affect T. gondii positivity in the sampled small mammals.
Unraveling the stepwise maturation of the yeast telomerase including a Cse1 and Mtr10 mediated quality control checkpoint
Authors: Hirsch Anna Greta , Becker Daniel , Lamping Jan-Philipp , Krebber Heike 
Published: November 2021

AbstractTelomerases elongate the ends of chromosomes required for cell immortality through their reverse transcriptase activity. By using the model organism Saccharomyces cerevisiae we defined the order in which the holoenzyme matures. First, a longer precursor of the telomerase RNA, TLC1 is transcribed and exported into the cytoplasm, where it associates with the protecting Sm-ring, the Est and the Pop proteins. This partly matured telomerase is re-imported into the nucleus via Mtr10 and a novel TLC1-import factor, the karyopherin Cse1. Remarkably, while mutations in all known transport factors result in short telomere ends, mutation in CSE1 leads to the amplification of Y′ elements in the terminal chromosome regions and thus elongated telomere ends. Cse1 does not only support TLC1 import, but also the Sm-ring stabilization on the RNA enableling Mtr10 contact and nuclear import. Thus, Sm-ring formation and import factor contact resembles a quality control step in the maturation process of the telomerase. The re-imported immature TLC1 is finally trimmed into the 1158 nucleotides long mature form via the nuclear exosome. TMG-capping of TLC1 finalizes maturation, leading to mature telomerase.
The analysis of reference genes expression stability in susceptible and resistant Apera spica-venti populations under herbicide treatment
Authors: Wrzesińska Barbara , Kościelniak Karolina , Frąckowiak Patryk , Praczyk Tadeusz , Obrępalska-Stęplowska Aleksandra 
Published: November 2021

AbstractWeed resistance to herbicides constitutes a serious problem to world crop production. One of the weeds that are significantly threatening the crops’ yield and quality isApera spica-venti. The target-site resistance (TSR) mechanism ofA. spica-ventihas been widely studied, though, little is known about its non-target-site resistance (NTSR) mechanisms at the molecular level. Molecular examination of NTSR is, to a great extent, based on the expression profiles of selected genes, e.g. those participating in detoxification. However, to obtain reliable results of gene expression analysis, the use of a normalizer is required. The aim of this study was to select the best reference genes inA. spica-ventiplants of both populations, susceptible and resistant to ALS inhibitor, under treatment with herbicide. Eleven housekeeping genes were chosen for their expression stability assessment. The efficiency correction of raw quantification cycles (Cq) was included in the gene expression stability analyses, which resulted in indicating the TATA-box binding protein (TBP), glyceraldehyde-3-phosphate dehydrogenase, cytosolic (GAPC), and peptidyl-prolylcis–transisomerase CYP28 (CYP28) genes as the most stably expressed reference genes. The obtained results are of vital importance for future studies on the expression of genes associated with the non-target-site resistance mechanisms in theA. spica-ventipopulations susceptible and resistant to herbicides.
Fatigue after acquired brain injury impacts health-related quality of life: an exploratory cohort study
Authors: Åkerlund Elisabeth , Sunnerhagen Katharina S. , Persson Hanna C. 
Published: November 2021

AbstractThis study aimed to identify the consequences of fatigue, fatigability, cognitive and executive functioning, and emotional state on health-related quality of life (HRQoL) in a clinical group of outpatients after acquired brain injury (ABI). This cross-sectional retrospective study included assessing outpatients at a rehabilitation clinic with WAIS-III working memory and coding subtests, and self-rating scales (Fatigue Impact Scale, Dysexecutive Questionnaire, Hospital Anxiety and Depression Scale, and the dimension of health-related quality of life from EQ-5D-3L). The predictive variables were investigated using a binary logistic regression with HRQoL as the dependent variable. Descriptive statistics and correlations were analyzed. Participants reported a lower than average HRQoL (95%), fatigue (90%), and executive dysfunction (75%). Fatigue had a significant impact and explained 20–33% of the variance in HRQoL with a moderate significance on depression (p = 0.579) and executive dysfunction (p = 0.555). Cognitive and executive function and emotional state showed no association with HRQoL. A lower HRQoL, as well as fatigue and cognitive and executive dysfunctions, are common after ABI, with fatigue is a partial explanation of a lower HRQoL.