bluuebunny/crossref_metadata_2025 huggingface dataset:
Starburst galaxies strike back: a multi-messenger analysis with Fermi-LAT and IceCube data
Authors: Ambrosone Antonio , Chianese Marco , Fiorillo Damiano F G , Marinelli Antonio , Miele Gennaro , Pisanti Ofelia
Published: March 2021

Starburst galaxies, which are known as ‘reservoirs’ of high-energy cosmic-rays, can represent an important high-energy neutrino ‘factory’ contributing to the diffuse neutrino flux observed by IceCube. In this paper, we revisit the constraints affecting the neutrino and gamma-ray hadronuclear emissions from this class of astrophysical objects. In particular, we go beyond the standard prototype-based approach leading to a simple power-law neutrino flux, and investigate a more realistic model based on a data-driven blending of spectral indexes, thereby capturing the observed changes in the properties of individual emitters. We then perform a multi-messenger analysis considering the extragalactic gamma-ray background (EGB) measured by Fermi-LAT and different IceCube data samples: the 7.5-yr high-energy starting events (HESE) and the 6-yr high-energy cascade data. Along with starburst galaxies, we take into account the contributions from blazars and radio galaxies as well as the secondary gamma-rays from electromagnetic cascades. Remarkably, we find that, differently from the highly-constrained prototype scenario, the spectral index blending allows starburst galaxies to account for up to $40{{\ \rm per\ cent}}$ of the HESE events at $95.4{{\ \rm per\ cent}}$ CL, while satisfying the limit on the non-blazar EGB component. Moreover, values of $\mathcal {O}(100\, \mathrm{PeV})$ for the maximal energy of accelerated cosmic-rays by supernovae remnants inside the starburst are disfavoured in our scenario. In broad terms, our analysis points out that a better modelling of astrophysical sources could alleviate the tension between neutrino and gamma-ray data interpretation.
Synchrotron micro-X-ray fluorescence imaging of arsenic in frozen-hydrated sections of a root of Pteris vittata
Authors: Kashiwabara Teruhiko , Kitajima Nobuyuki , Onuma Ryoko , Fukuda Naoki , Endo Satoshi , Terada Yasuko , Abe Tomoko , Hokura Akiko , Nakai Izumi
Published: March 2021

We performed micro-X-ray fluorescence imaging of frozen-hydrated sections of a root of Pteris vittata for the first time, to the best of our knowledge, to reveal the mechanism of arsenic (As) uptake. The As distribution was successfully visualized in cross sections of different parts of the root, which showed that (i) the major pathway of As uptake changes from symplastic to apoplastic transport in the direction of root growth, and (ii) As and K have different mobilities around the stele before xylem loading, despite their similar distributions outside the stele in the cross sections. These data can reasonably explain As reduction, axially observed around the root tip in the direction of root growth and radially observed in the endodermis in the cross sections, as a consequence of the incorporation of As into the cells or symplast of the root. In addition, previous observations of As species in the midrib can be reconciled by ascribing a reduction capacity to the root cells, which implies that As reduction mechanisms at the cellular level may be an important control on the peculiar root-to-shoot transport of As in P. vittata.
Saving Sensitivity
Authors: Topey Brett
Published: March 2021

Sensitivity has sometimes been thought to be a highly epistemologically significant property, serving as a proxy for a kind of responsiveness to the facts that ensure that the truth of our beliefs isn’t just a lucky coincidence. But it's an imperfect proxy: there are various well-known cases in which sensitivity-based anti-luck conditions return the wrong verdicts. And as a result of these failures, contemporary theorists often dismiss such conditions out of hand. I show here, though, that a sensitivity-based understanding of epistemic luck can be developed that respects what was attractive about sensitivity-based approaches in the first place but that's immune to these failures.
Post-16 Further Mathematics blended learning: learner self-regulation, mathematical resilience and technology
Authors: Lyakhova Sofya , Joubert Marie
Published: March 2021

This paper reports on a study set in Wales where the Further Mathematics Support Programme Wales supports the provision of an advanced qualification in mathematics for 16- to 18-year-old students with courses delivered in reduced teaching time. The study aimed to understand how the students experienced the Further Mathematics (FM) courses which are delivered either face-to-face or online and, more generally, to negotiate a place of alternative forms of delivery in post-16 mathematics curriculum. Sixteen students, eight of whom studied through the online course, were interviewed; overall, although they found the course challenging both in terms of the content and relatively limited teaching time, they enjoyed it and appeared to perceive benefits from taking the course. Most volunteered ‘tips’ about coping with the challenges of the course and the tips can be seen as strategies of self-regulation. Self-regulation strategies were reported more strongly by the students taking the course online than those attending face-to-face classes. In view of the evidence of technology creating new learning environments perceived as advantageous by students, it is hypothesized that introducing blended learning as part of post-16 mathematics curriculum could be beneficial. Improving learner self-regulation is discussed as means of improving access to FM. Other findings included the importance of support from peers, parents and schools and gender differences.
Mass Casualty Mini Drills on Trauma Surgery Department Staff Knowledge: An Educational Improvement Study
Authors: Hollister Lisa M. , Zhu Thein , Edwards Nancy , Good Becky , Hoeppner Sarah
Published: March 2021

Background:

Over the last decade, the United States has witnessed an increase in mass casualty incidents (MCIs). The outcome of an MCI depends upon hospital preparedness, yet many hospitals are unfamiliar with their facility MCI procedure. Educational training drills may be one method to improve staff knowledge of policy and procedure.

Objective:

This study aimed to improve knowledge gained through educational MCI mini drills of institutional mass casualty policy and procedure in surgery department staff at a level II trauma center.

Methods:

A pre-/posttest design was utilized. The hospital implemented MCI mini training drills as a quality improvement project using Plan-Do-Study-Act iterative cycles with prospective data collection. Knowledge scores were measured using a 12-item surgery department MCI policy and procedure questionnaire that was developed by the author and leadership.

Results:

A one-way analysis of covariance analysis in participants that mini drilled more than once indicated significant effect on mean cycle score differences among three cycles F
(2,21) = 12.96, p = .00. Multiple comparison using Games–Howell indicated the mean score for Cycle 4 (M = 96.15, SD = 6.54) was significantly different from Cycle 3 (M = 59.71, SD = 25.15). Gender, shift, and credentials of participants influenced knowledge improvement.

Conclusion:

Implementation of hospital MCI mini drills improved staff knowledge of institutional mass casualty policy and procedure in the surgery department and may be applied to surgery departments with similar policy, procedure, and participant characteristics. Hospital mass casualty response education and preparation is essential to saving lives.
Resuming Deceased Donor Kidney Transplantation in the COVID-19 Era: What Do Patients Want?
Authors: Thind Amarpreet K. , Beckwith Hannah , Dattani Rakesh , Dhutia Amrita , Gleeson Sarah , Martin Paul , Ryan Louise , Shuaib Rishana , Svetitsky Shuli , Dor Frank J.M.F. , Brown Edwina A. , Willicombe Michelle
Published: March 2021

Background.

The rapidly evolving novel coronavirus 2019 (COVID-19) pandemic bought many kidney transplant (KT) programs to a halt. Integral to resuming KT activity is understanding the perspectives of potential transplant candidates during this highly dynamic time.

Methods.

From June 1 to July 7, 2020, a telephone survey of KT candidates on the deceased donor waiting list at Imperial College Renal and Transplant Centre in West London was conducted. The survey captured ongoing COVID-19 exposure risks and patients’ views on waitlist (WL) reactivation and undergoing transplantation.

Results.

Two hundred seven responses were received. Of the respondents, 180 patients (87%) were happy to be reactivated onto the WL; with 141 patients (68%) willing to give consent to transplantation currently, while 53 patients (26%) felt unsure, and 13 patients (6%) would decline a KT. The vast majority of patients had no concerns. In the responses from those who were uncertain or who would decline a KT, concerns about COVID-19 infection and the need for reassurance from transplant units dominated. Universally patients wanted more information about COVID-19 infection risk with KT and the precautions being taken to reduce this risk.

Conclusions.

The majority of surveyed patients are in favor of reactivation and receiving a KT despite the ongoing COVID-19 pandemic. Reactivation of candidates cannot be assumed and should take an individualized approach, incorporating clinical risk with patient perspectives. Improved communication with KT candidates is highly requested.
Estimating the levels and trends of family planning indicators in 436 sub-national areas across 26 countries in sub-Saharan Africa
Authors: Proctor Joshua L. , Mercer Laina D.
Published: March 2021

Background

Scaling up access to safe, effective, and voluntary family planning (FP) services to achieve universal access for women and families will require increased commitment by countries and international organizations. On the way toward universal access, quantitative family planning goals have also been established by the United Nations through the sustainable development goals (SDGs). Here, we present a model-based framework that can help monitor progress toward these goals at the sub-national and demographic subgroup scale.

Methods

We utilize 90 demographic health surveys for 26 countries that contain associated geographic position system data. We extract survey cluster level data to fit multiple small area estimation models that estimate FP indicators by administrative unit one and two regions as well as different demographic subgroups.

Findings

We find significant variation of modern contraceptive prevalence rates (mCPR), unmet need, and demand satisfied by country, sub-national region, and demographic subgroup. Our model-based estimates show that on average for 436 administrative unit one regions, mCPR has increased at a rate of 0.75% per year and unmet need has decreased by 0.26% per year. There are also striking differences of FP indicators by demographic subgroup; for example, unmet need can be up to 40% different based on age and parity.

Interpretation

We have developed a framework to help monitor progress, provide insights about the inequitable progress by region and demographic groups, and account for the sparsity of available data. These results and framework can help policy-makers better allocate and target interventions to help achieve family planning goals.

Funding

This publication is based on models and data analysis performed by the Institute for Disease Modeling at the Bill & Melinda Gates Foundation.
T-cell Repertoire Characteristics of Asymptomatic and Re-detectable Positive COVID-19 Patients
Authors: Xu Jianhua , Shi Yaling , Wang Yongsi , Liu Yuntao , Lin Dongzi , Zhang Jiaqi , Lin Jing , Hu Wei , He Haolan , Wang Wei , Fan Wentao , Li Linlin , Lan Hai , Lei Chunliang , Wang Kejian , Wang Dawei
Published: March 2021

Background

The prevention of COVID-19 pandemic is highly complicated by the prevalence of asymptomatic and recurrent infection. Many previous immunological studies have focused on symptomatic and convalescent patients, while the immune responses in asymptomatic patients and re-detectable positive cases remain unclear.

Methods

Here we comprehensively analyzed the peripheral T-cell receptor (TCR) repertoire of 54 COVID-19 patients in different phases, including asymptomatic, symptomatic, convalescent and re-detectable positive cases.

Results

We found progressed immune responses from asymptomatic to symptomatic phase. Furthermore, the TCR profiles of re-detectable positive cases were highly similar to those of asymptomatic patients, which could predict the risk of recurrent infection.

Conclusion

Therefore, TCR repertoire surveillance has the potential to strengthen the clinical management and the immunotherapy development for COVID-19.

Funding

The Science and Technology Innovation Project of Foshan Municipality (2020001000431) and the National Key Research and Development Project (2020YFA0708001).
Proteasome maturation factor UMP1 confers broad-spectrum disease resistance by modulating H2O2accumulation in rice
Authors: Hu Xiao-Hong , Fan Jing , Wu Jin-Long , Shen Shuai , He Jia-Xue , Liu Jie , Wang He , Zhu Yong , Li Guo-Bang , Zhao Jing-Hao , Xu Jie , Li De-Qiang , Pu Mei , Zhao Zhi-Xue , Zhou Shi-Xin , Zhang Ji-Wei , Huang Yan-Yan , Li Yan , Lu Yan-Li , Huang Fu , Wang Wen-Ming
Published: March 2021

Crops with broad-spectrum resistance (BSR) to diseases are highly desirable in agricultural production. Identification of BSR loci and dissection of the underlying mechanisms are fundamental for crop resistance breeding. Here, we describe the identification and characterization of a riceUMP1allele, which confers race-nonspecific BSR against blast pathogenMagnaporthe oryzae.OsUMP1encodes a proteasome maturation factor that contributes to 26S proteasome abundance and activity in rice. Modulation ofOsUMP1expression leads to proteome changes, particularly affects the amounts and activities of H2O2-degrading enzymes. Consequently, H2O2accumulation and disease resistance are enhanced inOsUMP1-overexpressing rice but reduced in loss-of-function mutants. Elevation ofOsUMP1expression also promotes rice resistance to foliar pathogensRhizoctonia solaniandXanthomonas oryzaepv.oryzaeand a floral pathogenUstilaginoidea virenswithout observable yield penalty. These results indicate a BSR pathway linking the proteasome machinery and H2O2homeostasis, and provide a candidate gene for balancing BSR and yield traits in rice breeding.

One Sentence Summary

A natural allele of rice UMP1 promotes resistance to multiple pathogens by boosting H2O2accumulation.
Present and Future Ecological Niche Modeling of Rift Valley fever in East Africa in Response to Climate Change
Authors: Muema Caroline , Ngarega Boniface K. , Muturi Elishiba , Wei Hongping , Yang Hang
Published: March 2021

Rift Valley fever (RVF) has been linked with recurrent outbreaks among humans and livestock in several parts of the globe. Predicting RVF’s habitat suitability under different climate scenarios offers vital information for developing informed management schemes. The present study evaluated the probable impacts of climate change on the distribution of RVF disease in East Africa (E. A.), using the maximum entropy (MaxEnt) model and the disease outbreak cases. Considering the potential of the spread of the disease in the East Africa region, we utilized two representative concentration pathways (RCP 4.5 and RCP 8.5) climate scenarios in the 2050s and 2070s (average for 2041-2060, and 2061-2080), respectively. All models had satisfactory AUC values of more than 0.809, which are considered excellent. Jackknife tests revealed that Bio4 (temperature seasonality), land use, and population density were the main factors influencing RVF distribution in the region. From the risk maps generated, we infer that, without regulations, this disease might establish itself across more extensive areas in the region, including most of Rwanda and Burundi. The ongoing trade between East African countries and changing climates could intensify RVF spread into new geographic extents with suitable habitats for the important zoonosis. The predicted suitable areas for RVF in eastern Kenya, southern Tanzania, and Somalia overlaps to a large extent where cattle keeping and pastoralism are highly practiced, thereby signifying the urgency to manage and control the disease. This work validates RVF outbreak cases’ effectiveness to map the disease’s distribution, thus contributing to enhanced ecological modeling and improved disease tracking and control efforts in East Africa.
The role of H3K36 methylation and associated methyltransferases in chromosome-specific gene regulation
Authors: Lindehell Henrik , Glotov Alexander , Dorafshan Eshagh , Schwartz Yuri B. , Larsson Jan
Published: March 2021

In Drosophila, two chromosomes require special mechanisms to balance their transcriptional output to the rest of the genome. These are the male-specific lethal complex targeting the male X-chromosome, and Painting of fourth targeting chromosome 4. The two systems are evolutionarily linked to dosage compensation of the X-chromosome and the chromosomes involved display specific chromatin structures. Here we explore the role of histone H3 tri-methylated at lysine 36 (H3K36me3) and the associated methyltransferases in these two chromosome-specific systems.

We show that the loss of Set2 impairs the MSL complex mediated dosage compensation; however, the effect is not recapitulated by H3K36 replacement and indicates an alternative target of Set2. Unexpectedly, balanced transcriptional output from the 4th chromosome requires intact H3K36 and depends on the additive functions of NSD and the Trithorax group protein Ash1.

We conclude that H3K36 methylation and the associated methyltransferases are important factors to balance transcriptional output of the male X-chromosome and the 4th chromosome. Furthermore, our study highlights the pleiotropic effects of these enzymes.
Optimization of an LNP-mRNA vaccine candidate targeting SARS-CoV-2 receptor-binding domain
Authors: Kobiyama Kouji , Imai Masaki , Jounai Nao , Nakayama Misako , Hioki Kou , Iwatsuki-Horimoto Kiyoko , Yamayoshi Seiya , Tsuchida Jun , Niwa Takako , Suzuki Takashi , Ito Mutsumi , Yamada Shinya , Watanabe Tokiko , Kiso Maki , Negishi Hideo , Temizoz Burcu , Ishigaki Hirohito , Kitagawa Yoshinori , Nguyen Cong Thanh , Itoh Yasushi , Takeshita Fumihiko , Kawaoka Yoshihiro , Ishii Ken J.
Published: March 2021

In 2020, two mRNA-based vaccines, encoding the full length of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein, have been introduced for control of the coronavirus disease (COVID-19) pandemic1,2. However, reactogenicity, such as fever, caused by innate immune responses to the vaccine formulation remains to be improved. Here, we optimized a lipid nanoparticle (LNP)-based mRNA vaccine candidate, encoding the SARS-CoV-2 spike protein receptor-binding domain (LNP-mRNA-RBD), which showed improved immunogenicity by removing reactogenic materials from the vaccine formulation and protective potential against SARS-CoV-2 infection in cynomolgus macaques. LNP-mRNA-RBD induced robust antigen-specific B cells and follicular helper T cells in the BALB/c strain but not in the C57BL/6 strain; the two strains have contrasting abilities to induce type I interferon production by dendritic cells. Removal of reactogenic materials from original synthesized mRNA by HPLC reduced type I interferon (IFN) production by dendritic cells, which improved immunogenicity. Immunization of cynomolgus macaques with an LNP encapsulating HPLC-purified mRNA induced robust anti-RBD IgG in the plasma and in various mucosal areas, including airways, thereby conferring protection against SARS-CoV-2 infection. Therefore, fine-tuning the balance between the immunogenic and reactogenic activity of mRNA-based vaccine formulations may offer safer and more efficacious outcomes.
Transcriptional regulation of schizophrenia risk gene TCF4 in inhibitory neurons during neurodevelopment
Authors: Wang Yuanyuan , Lin Mingyan
Published: March 2021

The pathology underlying schizophrenia (SCZ) involves cell type-specific and developmental stage-specific dysregulation of multiple gene regulatory networks dominated by some key transcription factors, such as SCZ risk gene transcription factor 4 (TCF4). Previous studies on the regulatory mechanism of TCF4 use SY5Y as the cellular model, which could not reflect its cell typespecific role in the real world. Using the transcriptional profile of whole brain during development stages and single-cell transcriptome data in the developing human prefrontal cortex, we found that TCF4 was preferentially expressed in the interneuron. Chromatin immunoprecipitation combined with sequencing (ChIP-Seq) in human embryonic stem cells (hESC)-derived interneurons revealed that TCF4 primarily activate transcription of genes associated with cortex development and telencephalon regionalization in a long-range manner. As expected, the downstream targets of TCF4 were distinct in inhibitory neurons and neural stem cells during early neurodevelopment, justifying the importance of our study. Deeper investigation further revealed that TCF4 regulate genes related to neurotransmission distally in interneuron in a c-FOS dependent manner, while TCF4 and TCF3 synergistically regulate genes associated with cell proliferation associated proximally in neural stem cells. Our findings suggested that defects in development of interneuron, for instance as a result of TCF4 abnormality, may break excitation and inhibition balance and contribute significantly to the risk of SCZ.
scCorr: A graph-based k-partitioning approach for single-cell gene-gene correlation analysis
Authors: Xu Heng , Hu Ying , Zhang Xinyu , Aouizerat Bradley E. , Yan Chunhua , Xu Ke
Published: March 2021

An important challenge in single-cell RNA-sequencing analysis is the abundance of zero values, which results in biased estimation of gene-gene correlations for downstream analyses. Here, we present a novel graph-based k-partitioning method by merging “homology” cells to reduce the number of zero values. Our method is robust and reliable for the detection of correlated gene pairs, which is fundamental to network construction, gene-gene interaction, and cellular -omic analyses.
Deep Diffusion MRI Registration (DDMReg): A Deep Learning Method for Diffusion MRI Registration
Authors: Zhang Fan , Wells William M. , O’Donnell Lauren J.
Published: March 2021

In this paper, we present a deep learning method, DDMReg, for accurate registration between diffusion MRI (dMRI) datasets. In dMRI registration, the goal is to spatially align brain anatomical structures while ensuring that local fiber orientations remain consistent with the underlying white matter fiber tract anatomy. DDMReg is a novel method that uses joint whole-brain and tract-specific information for dMRI registration. Based on the successful VoxelMorph framework for image registration, we propose a novel registration architecture that leverages not only whole brain information but also tract-specific fiber orientation information. DDMReg is an unsupervised method for deformable registration between pairs of dMRI datasets: it does not require nonlinearly pre-registered training data or the corresponding deformation fields as ground truth. We perform comparisons with four state-of-the-art registration methods on multiple independently acquired datasets from different populations (including teenagers, young and elderly adults) and different imaging protocols and scanners. We evaluate the registration performance by assessing the ability to align anatomically corresponding brain structures and ensure fiber spatial agreement between different subjects after registration. Experimental results show that DDMReg obtains significantly improved registration performance compared to the state-of-the-art methods. Importantly, we demonstrate successful generalization of DDMReg to dMRI data from different populations with varying ages and acquired using different acquisition protocols and different scanners.
Correlative light and electron microscopy reveals that mutant huntingtin dysregulates the endolysosomal pathway in presymptomatic Huntington’s disease
Authors: Zhou Ya , Peskett Thomas R. , Landles Christian , Warner John B. , Sathasivam Kirupa , Smith Edward J. , Chen Shu , Wetzel Ronald , Lashuel Hilal A. , Bates Gillian P. , Saibil Helen R.
Published: March 2021

Huntington’s disease (HD) is a late onset, inherited neurodegenerative disorder for which early pathogenic events remain poorly understood. Here we show that mutant exon 1 HTT proteins are recruited to a subset of cytoplasmic aggregates in the cell bodies of neurons in brain sections from presymptomatic HD, but not wild-type, mice. This occurred in a disease stage and polyglutamine-length dependent manner. We successfully adapted a high-resolution correlative light and electron microscopy methodology, originally developed for mammalian and yeast cells, to allow us to correlate light microscopy and electron microscopy images on the same brain section within an accuracy of 100 nm. Using this approach, we identified these recruitment sites as single membrane bound, vesicle-rich endolysosomal organelles, specifically as (i) multivesicular bodies (MVBs), or amphisomes and (ii) autolysosomes or residual bodies. The organelles were often found in close proximity to phagophore-like structures. Immunogold labeling localized mutant HTT to non-fibrillar, electron lucent structures within the lumen of these organelles. In presymptomatic HD, the recruitment organelles were predominantly MVBs/amphisomes, whereas in late-stage HD, there were more autolysosomes or residual bodies. Electron tomograms indicated the fusion of small vesicles with the vacuole within the lumen, suggesting that MVBs develop into residual bodies. We found that markers of MVB-related exocytosis were depleted in presymptomatic mice and throughout the disease course. This suggests that endolysosomal homeostasis has moved away from exocytosis toward lysosome fusion and degradation, in response to the need to clear the chronically aggregating mutant HTT protein, and that this occurs at an early stage in HD pathogenesis.
Experimental study on friction coefficient and temperature rise of heavy-load grease-lubricated spherical plain bearings with surface texture
Authors: Shen Jinlong , Zhang Tong , Xu Jimin , LIU Xiaojun , Liu Kun
Published: March 2021

Purpose

This paper aims to improve the tribological performance of grease-lubricated spherical plain bearings (SPBs) under heavy load, dimple-type textures were prepared by laser on the outer surface of the inner ring. The influence of roughness parameters of a textured surface on reducing friction coefficient and temperature rise was also explored.

Design/methodology/approach

This study adopts a laser processing method to fabricate dimple-type textures. Three-dimensional roughness parameters were used to characterize the textured surfaces. The friction coefficients of five SPBs with surface texture and one original commercially available SPB without surface texture under different nominal loads were measured on a self-established test rig. The data of temperature rise were obtained by nine embedded thermal couples.

Findings

The results indicate that SPBs with textures generally exhibit lower friction coefficients than the original SPB without textures. The dimple depth has a significant influence on improving the tribological performance, which coincides with the analysis by surface roughness parameters. A textured surface with negative Ssk and high Vvc has the minimum temperature rise.

Originality/value

As it is too difficult to arrange sensors into heavy-load SPBs, there are few reports about the temperature characteristics. Through nine embedded thermal couples, the distribution of temperature rise on the inner ring of SPBs was given in this study. The positive effect of surface texture on reducing temperature rise and friction coefficient was verified, which is beneficial for the design of heavy-load SPBs.
Revisiting a ‘simple’ fungal metabolic pathway reveals redundancy, complexity and diversity
Authors: Chroumpi Tania , Peng Mao , Aguilar‐Pontes Maria Victoria , Müller Astrid , Wang Mei , Yan Juying , Lipzen Anna , Ng Vivian , Grigoriev Igor V. , Mäkelä Miia R. , de Vries Ronald P.
Published: March 2021

Next to d‐glucose, the pentoses l‐arabinose and d‐xylose are the main monosaccharide components of plant cell wall polysaccharides and are therefore of major importance in biotechnological applications that use plant biomass as a substrate. Pentose catabolism is one of the best‐studied pathways of primary metabolism of Aspergillus niger, and an initial outline of this pathway with individual enzymes covering each step of the pathway has been previously established. However, although growth on l‐arabinose and/or d‐xylose of most pentose catabolic pathway (PCP) single deletion mutants of A. niger has been shown to be negatively affected, it was not abolished, suggesting the involvement of additional enzymes. Detailed analysis of the single deletion mutants of the known A. niger PCP genes led to the identification of additional genes involved in the pathway. These results reveal a high level of complexity and redundancy in this pathway, emphasizing the need for a comprehensive understanding of metabolic pathways before entering metabolic engineering of such pathways for the generation of more efficient fungal cell factories.
EigenGWAS: An online visualizing and interactive application for detecting genomic signatures of natural selection
Authors: Qi Guo‐An , Zheng Yuan‐Ting , Lin Feng , Huang Xin , Duan Li‐Wen , You Yue , Liu Hailan , Wang Ying , Xu Hai‐Ming , Chen Guo‐Bo
Published: March 2021

Detecting genetic regions under selection in structured populations is of great importance in ecology, evolutionary biology and breeding programmes. We recently proposed EigenGWAS, an unsupervised genomic scanning approach that is similar to but does not require grouping information of the population, for detection of genomic regions under selection. The original EigenGWAS is designed for the random mating population, and here we extend its use to inbred populations. We also show in theory and simulation that eigenvalues, the previous corrector for genetic drift in EigenGWAS, are overcorrected for genetic drift, and the genomic inflation factor is a better option for this adjustment. Applying the updated algorithm, we introduce the new EigenGWAS online platform with highly efficient core implementation. Our online computational tool accepts plink data in a standard binary format that can be easily converted from the original sequencing data, provides the users with graphical results via the R‐Shiny user‐friendly interface. We applied the proposed method and tool to various data sets, and biologically interpretable results as well as caveats that may lead to an unsatisfactory outcome are given. The EigenGWAS online platform is available at www.eigengwas.com, and can be localized and scaled up via R (recommended) or docker.
Habitats determining local frog assemblages within aquatic macrophyte meadows in Amazonia, through species traits filtering
Authors: Ganança Pedro Henrique Salomão , Santos Alfredo P. , Kawashita‐Ribeiro Ricardo A. , de Vasconcelos Neto Lourival Baía , dos Santos Júnior Ivan Alves , Guedes Daniel de Sousa , de Fraga Rafael
Published: March 2021

Investigating non‐random assemblages emerging in response to environmental gradients is relevant to understand mechanisms and processes affecting biodiversity. Species may be filtered from fractions of environmental gradients that limit dispersal, survival or ontogenetic development, which ultimately leads to biotic complementarities among sites. Non‐random assemblages as a response to environmental filtering have been widely demonstrated in Amazonian forests, but are rarely assessed in non‐forest ecosystems such as macrophyte meadows covering lakes. In this study, we sampled 50 plots (50 m long, 6 m wide) along continuous macrophyte meadows in a lake system in the lower Amazon River. Our main goal is to test the effects of distance from the lake bank, macrophyte height and composition (frequency of morphotype occurrence), air temperature and physicochemical properties of water (pH, dissolved oxygen, depth and temperature) on frog α and β‐diversity estimates, and frequency of species traits occurrence (abundance‐weighted body size, toe pads, foot webbing and tadpole habit). We found 16 species, for which local assemblages quantified by α and β‐diversity estimates were not random, but predicted by macrophyte height, morphotype composition and water depth. We have explicitly shown that species are filtered from fractions of these gradients through ecomorphological relationships, since morphological traits and tadpole habits were also selected by the vertical stratification provided by the vegetation cover and water depth. Overall, we present an investigation of assemblage ecology that is relevant to conservation, because the results suggest biotic complementarities within habitats that are rarely considered as distinct biogeographic units from the surrounding várzea forests.

Abstract in Portuguese is available with online material.
Potential functional variants in AHR signaling pathways are associated with age at puberty in swine
Authors: Nonneman Dan , Lents Clay A. , Rempel Lea A. , Rohrer Gary A.
Published: March 2021

Puberty in female pigs is defined as age at first estrus and gilts that have an earlier age at puberty are more likely to have greater lifetime productivity. Because age at puberty is predictive for sow longevity and lifetime productivity, but not routinely measured in commercial herds, it would be beneficial to use genomic or marker‐assisted selection to improve these traits. A GWAS at the US Meat Animal Research Center (USMARC) identified several loci associated with age at puberty in pigs. Candidate genes in these regions were scanned for potential functional variants using sequence information from the USMARC swine population founder animals and public databases. In total, 135 variants (SNP and insertion/deletions) in 39 genes were genotyped in 1284 phenotyped animals from a validation population sired by Landrace and Yorkshire industry semen using the Agena MassArray system. Twelve variants in eight genes were associated with age at puberty (P < 0.005) with estimated additive SNP effects ranging from 1.6 to 5.3 days. Nine of these variants were non‐synonymous coding changes in AHR, CYP1A2, OR2M4, SDCCAG8, TBC1D1 and ZNF608, two variants were deletions of one and four codons in aryl hydrocarbon receptor, AHR, and the most significant SNP was near an acceptor splice site in the acetyl‐CoA carboxylase alpha, ACACA. Several of the loci identified have a physiological and a genetic role in sexual maturation in humans and other animals and are involved in AHR‐mediated pathways. Further functional validation of these variants could identify causative mutations that influence age at puberty in gilts and possibly sow lifetime productivity.
Downward Hypothetical Bias in the Willingness to Accept Measure for Private Goods: Evidence from a Field Experiment
Authors: Liu Pengfei , Tian Xiaohui
Published: March 2021

This paper documents a downward hypothetical bias in the willingness to accept measure for a private good using the Becker‐DeGroot‐Marschak (BDM) method. We first construct a theoretical framework that predicts an upward hypothetical bias for the willingness to pay and a downward hypothetical bias for the willingness to accept measure. Based on a field experiment on livestock trading in China, we compare four experiment treatments, including a hypothetical treatment wherein responses are not consequential, two consequential treatments with probabilistic implementation wherein responses have a 25% or 75% probability of being consequential, and a consequential treatment with full implementation wherein responses are 100% consequential. Consistent with our theoretical predictions, the empirical results show that respondents report significant lower (about 12% lower) values in the hypothetical treatment compared with the consequential treatment with full implementation using the willingness to accept measure. The reported values also increase as the implementation probability increases. Our study contributes to the research on hypothetical bias in the willingness to accept by allowing exogenous changes in the consequential probability.
Able and Mostly Willing: An Empirical Anatomy of Information's Effect on Voter‐Driven Accountability in Senegal
Authors: Bhandari Abhit , Larreguy Horacio , Marshall John
Published: March 2021

Political accountability may be constrained by the reach and relevance of information campaigns in developing democracies and—upon receiving information—voters' ability and will to hold politicians accountable. To illuminate voter‐level constraints and information relevance absent dissemination constraints, we conducted a field experiment around Senegal's 2017 parliamentary elections to examine the core theoretical steps linking receiving different types of incumbent performance information to electoral and nonelectoral accountability. Voters immediately processed information as Bayesians, found temporally benchmarked local performance outcomes particularly informative, and updated their beliefs for at least a month. Learning that incumbents generally performed better than expected, voters durably requested greater politician contact after elections while incumbent vote choice increased among likely voters and voters prioritizing local projects when appraising incumbents. In contrast, information about incumbent duties did not systematically influence beliefs or accountability. These findings suggest voters were able and mostly willing to use relevant information to hold politicians to account.
Tree encroachment impacts on seed predator selection and seedling establishment in degraded pine woodlands
Authors: Willis John L. , Schnake David K. , DePerno Christopher S. , Lashley Marcus A. , Wetzstein Branson , Yow Justin
Published: March 2021

Questions

While much is known about the impact of tree encroachment on flammability in degraded pine woodlands, little is known about how encroachment is impacting other important ecosystem functions. We investigated how the availability of seed from four encroaching tree species and the presence of a midstorey and litter layer affect seed predator selection. Additionally, we investigated how seed predators, the midstorey, overstorey basal area, substrate availability, and vegetation cover affect germination for a foundational species (Pinus palustris) compared to an encroaching species (Pinus taeda).

Location

Sandhills Ecoregion, NC, USA (35°3′34.6932″ N, 79°22′22.0872″ W).

Methods

We measured seed depredation of Pinus palustris, Pinus taeda, Liquidambar styraciflua, Acer rubrum, and Quercus nigra in cafeteria trials. Each trial was held within a 2 × 2 factorial involving vertebrate seed predator exclusion and midstorey and litter layer removal across a gradient of overstorey basal area (6–25 m2). Additionally, we measured Pinus palustris and Pinus taeda germination within each treatment and correlated germinant density to substrate and understorey vegetation cover.

Results

Granivory generally varied inversely with seed size, with small‐seeded Liquidambar styraciflua experiencing the highest (27%) and large‐seeded Quercus nigra (7%) and Acer rubrum (6%) the lowest depredation pressure. Pinus palustris and Pinus taeda germinant density was significantly highest where vertebrate seed predators were excluded and the midstorey and litter layer were removed. For both pine species, this result corresponded with a significant positive association with mineral soil and negative associations with hardwood and pine litter where vertebrate predators were excluded. Basal area did not affect granivory or germination for any species.

Conclusions

Our results demonstrate that granivores did not select Pinus palustris, and that large‐seeded species encroachment was less inhibited by seed predators. Pinus palustris and Pinus taeda are depredated at comparable rates and germinate best under similar understorey conditions.
Barter markets, indivisibilities, and Markovian core
Authors: Fujishige Satoru , Yang Zaifu
Published: March 2021

We study a general barter market where every agent is endowed with several heterogeneous indivisible items and wishes to exchange. There is no medium of exchange like money. Agents have general preferences over their interested bundles of items and may acquire several items. We propose a practical and sensible solution called a Markovian core, generalizing the classical notion of the core. A Markovian core allocation is individually rational, Pareto‐efficient, and stable against any coalition deviation by comparison with their current assignments instead of their initial endowments and is shown to be a natural outcome of a decentralized market process.
Geographical sampling bias on the assessment of endemism areas for marine meiobenthic fauna
Authors: Garraffoni André , Sørensen Martin V. , Worsaae Katrine , Di Domenico Maikon , Sales Lilian P. , Santos Jessie , Lourenço Anete
Published: March 2021

Species distribution patterns are constrained by historical and ecological processes in space and time, but very often the species range sizes are geographical sampling biases resulting from unequal sampling effort. One of the most common definitions of endemism is based on the “congruence of distributional areas” criterion, when two or more species have the same distributional limits. By acknowledging that available data of marine meiobenthic species are prone to geographical sampling bias and that can affect the accuracy of the biogeographical signals, the present study combines analyses of inventory incompleteness and recognition of spatial congruence of Gastrotricha, Kinorhyncha, meiobenthic Annelida and Tardigrada in order to better understand the large‐scale distribution of these organisms in coastal and shelf areas of the world. We used the marine bioregionalization framework for geographical operative units to quantify the inventory incompleteness effect (by modelling spatial predictions of species richness) and to recognize areas of endemism. Our models showed that the difference between observed and expected species richness in the Southern Hemisphere is much higher than in the Northern Hemisphere. Parsimony Analysis of Endemicity delimited 20 areas of endemism, most found in the Northern Hemisphere. Distribution patterns of meiobenthic species are shown to respond to events of geographical barriers and abiotic features, and their distribution is far from homogeneous throughout the world. Also, our data show that ecoregions with distinct biotas have at least some cohesion over evolutionary time. However, we found that inventory incompleteness may significantly affect the explanatory power of areas of endemism delimitation in both hemispheres. Yet, whereas future increases in sampling efforts are likely to change the spatial congruence ranges in the Southern Hemisphere, patterns for the Northern Hemisphere may prove to be relatively more resilient.
Government economic policy uncertainty and corporate debt contracting
Authors: Tran Dung T. T. , Phan Hieu V.
Published: March 2021

We examine the relation between government economic policy uncertainty and debt contracting of U.S. public firms. We find that policy uncertainty is associated with more stringent debt terms, such as shorter debt maturity, higher cost of debt, and more restrictive debt covenants, and these relations are concentrated in financially constrained firms. Further analysis indicates that the negative real effects of policy uncertainty documented in the literature are more pronounced for financially constrained firms. Overall, our evidence suggests that policy uncertainty dampens external financing and exacerbates firms' financial constraints, leading to their investment delays.
Microclimate and habitat heterogeneity as important drivers of soil Collembola in a karst collapse doline in the temperate zone
Authors: Marcin Michal , Raschmanová Natália , Miklisová Dana , Kováč Ľubomír
Published: March 2021

Changes in well‐delimited Collembola communities along a steep microclimatic gradient at the entrance of Silická ľadnica Ice Cave, Slovakia, were investigated after 10 years (2007, 2017). We focused on the occurrence of psychrophilic and endemic species occupying this unique karst collapse doline and their response to climatic singularities in the given years as well as the increasing trend in regional air temperature. The soil temperature means at sites across the doline slope corresponded with climatic trends in the periods 2006–2007 and 2016–2017. Significantly lower average soil temperatures but significantly higher mean abundances, species richness, and diversity indices of the collembolan communities were recorded at sites during the second study period, which was characterized by more favorable soil microclimatic conditions (temperature and moisture content) compared to the first period. The dominance structure and community composition of the studied assemblages appeared to be relatively constant after 10 years, indicating stable collembolan communities, especially at cold sites at the bottom of the doline. Redundancy ordination analysis documented a clear delimitation of the communities in relation to the soil temperature, pH, and C:N ratio in both periods. Long‐term (30‐year) regional climatic data showed an increasing trend of annual air temperature means and precipitation. However, an increase in the number and abundance of xerothermophilous species and a decline in psychrophilic species (mostly endemic) along the gradient as a potential response of the increasing regional temperature were not observed, suggesting the high resilience of these communities. Microclimate and habitat heterogeneity are probably major drivers of soil Collembola communities along the steep microclimatic gradient of a karst collapse doline, which was observed by the repeated sampling after 10 years. Karst dolines as potentially important local sources of ɑ‐diversity will likely become increasingly indispensable refugia for local biodiversity under ongoing global warming, thus deserving reliable conservation.
Identification of hub genes associated with neutrophils infiltration in colorectal cancer
Authors: Su Hao , Cai Tianyi , Zhang Sen , Yan Xialin , Zhou Leqi , He Zirui , Xue Pei , Li Jianwen , Zheng Minhua , Yang Xiao , Feng Bo
Published: March 2021

Colorectal cancer (CRC) is the leading cause of cancer‐related mortality in the world. Accumulating evidence indicate that tumour infiltrating immune cells participated in cancer progression. Among them, tumour infiltrating neutrophils (TINs) are reported to play crucial role in various cancers. In this study, we used CIBERSORTx, a digital cytometry tool to evaluate the neutrophils infiltration in CRC based on gene expression data of CRC tissues from GSE39582 data set and The Cancer Genome Atlas data set (TCGA‐COAD and TCGA‐READ). Weighted gene co‐expression network analysis (WGCNA) was conducted in GSE39582 data set to identify hub genes associated with neutrophil infiltration. The association of hub gene and neutrophils was then validated in TCGA cohorts and an independent RJ cohort. Functional analysis was performed to investigate the molecular mechanisms of the interested hub gene. We found that neutrophil infiltration is elevated in CRC tissues, and it is related to a poorer prognosis. A total of 18 gene modules are identified by WGCNA in GSE39582 data set, among which lightcyan module is significantly correlated with neutrophils infiltration. Furthermore, Superoxide Dismutase 2 (SOD2) in lightcyan module was proved to correlated with neutrophils infiltration in various cancer types. In addition, SOD2 expression is highly associated with several chemokines, including CXCL8, a neutrophils‐related attractant, and functional analysis revealed that SOD2 is involved in neutrophils recruitment biological process. These results indicate that an ‘SOD2‐CXCL8‐neutrophil recruitment’ axis plays a potential role in colorectal cancer progression.