cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Hypertensive Disorders of Pregnancy (HDP) and the Risk of Common Cancers in Women: Evidence from the European Prospective Investigation into Cancer (EPIC)-Norfolk Prospective Population-Based Study
Creators: name: Pasdar, Zahra
name: Gamble, David T.
name: Myint, Phyo K.
name: Luben, Robert N.
name: Wareham, Nicholas J.
name: Khaw, Kay-Tee
name: Bhattacharya, Sohinee
Publisher: name: Apollo - University of Cambridge Repository
Year: 2020
Subjects: hypertension during pregnancy
pregnancy complications
cancer

description: Purpose: The purpose was to determine the association between HDP and cancer in a UK cohort. Methods: Between 1993 and 1997, participants from the EPIC-Norfolk cohort attended baseline health-checks and completed questionnaires, where a history of HDP was collected. Incident cancer cases were identified through NHS record linkage until March 2016. Univariable and multivariable logistic regression analyses were employed to determine the association between HDP and odds of cancer, with adjustment for potential confounders including co-morbidities, sociodemographic, lifestyle and reproductive factors. Results: 13,562 women were included after excluding prevalent cancer cases and women with no pregnancies. 2919 (21.5%) reported HDP and 2615 incident cancers occurred during mean follow up of 19 years. Median age (IQR) at baseline for incident cancer was 60.8 (±14.8) years. Among incident cancer cases, 578 (22.1%) had HDP. In multivariable analyses, HDP had odds ratio (OR) 1.06; 95% CI 0.95−1.18 for incident cancer. The ORs (95% CIs) for common site-specific cancers including breast, colorectal, lung, ovarian and endometrial cancers were 1.06 (0.88−1.28), 1.15 (0.92−1.45), 0.96 (0.68−1.35), 1.30 (0.93−1.83) and 1.16 (0.80−1.67). Conclusion: We found no association between HDP and cancer risk. Further studies are required to confirm and account for any underlying genetic factors involved in pregnancy-related exposures and cancer risk.
Exotic pairing state in quasicrystalline superconductors under magnetic field
Creators: name: Sakai, Shiro
name: Arita, Ryotaro
Publisher: name: arXiv
Year: 2019
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: Other Condensed Matter (cond-mat.other)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We theoretically study the effect of a magnetic field on quasicrystalline superconductors, by modelling them as the attractive Hubbard model on the Penrose-tiling structure. We find that at low temperatures and under a high magnetic field there appears an exotic superconducting state with the order parameter changing its sign in real space. We discuss the state in comparison with the Fulde-Ferrell-Larkin-Ovchinnikov state proposed many years ago for periodic systems, clarifying commonalities and differences. It is remarkable that, even in the absence of periodicity, the electronic system finds a way to keep a coherent superconducting state with a spatially sign-changing order parameter compatible with the underlying quasiperiodic structure.
description: 7 pages, 8 figures
Additional file 6 of Mechanism of Zn2+ regulation of cellulase production in Trichoderma reesei Rut-C30
Creators: name: Li, Ni
name: Li, Jing
name: Chen, Yumeng
name: Shen, Yaling
name: Wei, Dongzhi
name: Wang, Wei
Publisher: name: figshare
Year: 2023
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 6: Figure S5. Effect of 3 mM Zn2+ on zafA transcription level in RUT-C30 strain. Transcriptional level of zafA of the RUT-C30 strain were detected after culturing in liquid MM for 36, 48 or 60 h containing 0 or 3 mM Zn2+ with 1% (w/v) Avicel as the sole carbon source. The final values are presented as the mean±standard deviation (SD) of three independent experimental results. Asterisks indicate significant differences compared to the control (*P <0.05, according to Student’s t-test).
Determinants of Irrigation Technology Adoption in Soybean Production
Creators: name: Gautam, Tej
name: Paudel, Krishna
name: Guidry, Kurt
name: Gautam, Tej
name: Paudel, Krishna
name: Guidry, Kurt
Publisher: name: Unknown
Year: 2016
Subjects: subject: Crop Production/Industries
subject: Production Economics
subject: Resource /Energy Economics and Policy
subject: Irrigation technology
subject: Soybean
subject: Logit
subject: Survey

description: This study identifies factors affecting irrigation technology adoption among soybean producers in Louisiana. We conducted survey to collect information regarding irrigation practices and concerns among the soybean farmers, then estimated technology adoption model using logit framework and analyzed the impact of different factors on irrigation technology adoption. Our estimated results show that the predicted probability for adopting furrow irrigation increases as well depth and land holding size increase. Additionally, farming experience, farm revenue, well drilling cost, education, and maintenance cost have negative effect on adopting furrow irrigation technology.
Oil theft and pipeline vandalism in the Niger Delta Region of Nigeria, efects, solutions and recommendations..pdf
Creators: name: Obarafor, Victor
Publisher: name: figshare
Year: 2019
Subjects: Uncategorized

description: This research explains the issue of pipeline vandalism and oil theft in the Niger Delta Region of Nigeria, some causes of oil theft and pipeline vandalism, effects, and recommends solutions towards the above issue.
Deep learning for glioblastoma segmentation using preoperative magnetic resonance imaging identifies volumetric features associated with survival
Creators: name: Wan, Yizhou
name: Rahmat, Roushanak
name: Price, Stephen J.
Publisher: name: Apollo - University of Cambridge Repository
Year: 2020
Subjects: Original Article - Brain Tumors
Brain tumors
Glioblastoma
Volumetric
Segmentation
MRI
Survival
Deep learning

description: Funder: National Institute for Health Research; doi: http://dx.doi.org/10.13039/501100000272
description: Abstract: Background: Measurement of volumetric features is challenging in glioblastoma. We investigate whether volumetric features derived from preoperative MRI using a convolutional neural network–assisted segmentation is correlated with survival. Methods: Preoperative MRI of 120 patients were scored using Visually Accessible Rembrandt Images (VASARI) features. We trained and tested a multilayer, multi-scale convolutional neural network on multimodal brain tumour segmentation challenge (BRATS) data, prior to testing on our dataset. The automated labels were manually edited to generate ground truth segmentations. Network performance for our data and BRATS data was compared. Multivariable Cox regression analysis corrected for multiple testing using the false discovery rate was performed to correlate clinical and imaging variables with overall survival. Results: Median Dice coefficients in our sample were (1) whole tumour 0.94 (IQR, 0.82–0.98) compared to 0.91 (IQR, 0.83–0.94 p = 0.012), (2) FLAIR region 0.84 (IQR, 0.63–0.95) compared to 0.81 (IQR, 0.69–0.8 p = 0.170), (3) contrast-enhancing region 0.91 (IQR, 0.74–0.98) compared to 0.83 (IQR, 0.78–0.89 p = 0.003) and (4) necrosis region were 0.82 (IQR, 0.47–0.97) compared to 0.67 (IQR, 0.42–0.81 p = 0.005). Contrast-enhancing region/tumour core ratio (HR 4.73 [95% CI, 1.67–13.40], corrected p = 0.017) and necrotic core/tumour core ratio (HR 8.13 [95% CI, 2.06–32.12], corrected p = 0.011) were independently associated with overall survival. Conclusion: Semi-automated segmentation of glioblastoma using a convolutional neural network trained on independent data is robust when applied to routine clinical data. The segmented volumes have prognostic significance.
A fast implicit difference scheme for solving the generalized time-space fractional diffusion equations with variable coefficients
Creators: name: Gu, Xian-Ming
name: Huang, Ting-Zhu
name: Zhao, Yong-Liang
name: Lyu, Pin
name: Carpentieri, Bruno
Publisher: name: arXiv
Year: 2019
Subjects: subject: Numerical Analysis (math.NA)
subject: FOS: Mathematics
subject: 65M06, 65N06, 65F08

description: In this paper, we first propose an unconditionally stable implicit difference scheme for solving generalized time-space fractional diffusion equations (GTSFDEs) with variable coefficients. The numerical scheme utilizes the $L1$-type formula for the generalized Caputo fractional derivative in time discretization and the second-order weighted and shifted Grünwald difference (WSGD) formula in spatial discretization, respectively. Theoretical results and numerical tests are conducted to verify the $(2 - γ)$-order and 2-order of temporal and spatial convergence with $γ\in(0,1)$ the order of Caputo fractional derivative, respectively. The fast sum-of-exponential approximation of the generalized Caputo fractional derivative and Toeplitz-like coefficient matrices are also developed to accelerate the proposed implicit difference scheme. Numerical experiments show the effectiveness of the proposed numerical scheme and its good potential for large-scale simulation of GTSFDEs.
description: 23 pages, 10 tables, 1 figure. Make several corrections again and have been submitted to a journal at Sept. 20, 2019. Version 2: Make some necessary corrections and symbols, 13 Jan. 2020. Revised manuscript has been resubmitted to journal
Additional file 1 of Mechanical circulatory support for refractory out-of-hospital cardiac arrest: a Danish nationwide multicenter study
Creators: name: Mørk, Sivagowry Rasalingam
name: Stengaard, Carsten
name: Linde, Louise
name: Møller, Jacob Eifer
name: Jensen, Lisette Okkels
name: Schmidt, Henrik
name: Riber, Lars Peter
name: Andreasen, Jo Bønding
name: Thomassen, Sisse Anette
name: Laugesen, Helle
name: Freeman, Phillip Michael
name: Christensen, Steffen
name: Greisen, Jacob Raben
name: Tang, Mariann
name: Møller-Sørensen, Peter Hasse
name: Holmvang, Lene
name: Gregers, Emilie
name: Kjaergaard, Jesper
name: Hassager, Christian
name: Eiskjær, Hans
name: Terkelsen, Christian Juhl
Publisher: name: figshare
Year: 2021
Subjects: subject: Medicine
subject: Cell Biology
subject: Biotechnology
subject: Immunology
subject: FOS: Clinical medicine
subject: Science Policy

description: Additional file 1. Table S1: National and regional indications for mechanical circulatory support in refractory normothermic cardiac arrest with presumed cardiac origin.
A Nonparametric Approach to Estimate Multiproduct and Product-specific Scale and Scope Economies for Agricultural Cooperatives
Creators: name: Pokharel, Krishna P
name: Featherstone, Allen M
name: Pokharel, Krishna P
name: Featherstone, Allen M
Publisher: name: Unknown
Year: 2016
Subjects: subject: Production Economics
subject: Multiproduct
subject: Product-specific
subject: Scale
subject: Scope
subject: Economies

description: The purpose of this research is to estimate product-specific and multiproduct economies of scale and economies of scope using a nonparametric data envelopment analysis (DEA) approach. Product-specific economies of scale exist for other product sales, but not for grain and farm inputs sales. Overall, multiproduct economies of scale and economies of scope exist. However, the median value of multiproduct scale economies are higher and greater than one for small cooperatives, which imply that cooperatives mergers likely to continue to exhaust the benefits from economies of scale.
The Roles of Risk and Honey Bee Colony Strength in Determining Almond Pollination Contract Provisions
Creators: name: Goodrich, Brittney
name: Goodrich, Brittney
Publisher: name: Unknown
Year: 2016
Subjects: subject: Crop Production/Industries
subject: Industrial Organization
subject: Production Economics
subject: Risk and Uncertainty
subject: Contracts
subject: Pollination
subject: Bees
subject: Ecosystem Services
subject: Colony Strength

description: Managed honey bee colonies provide pollination services, which are an essential input in production of many crops in the United States. Over the last decade, U.S. honey bee colony populations have become volatile as a result of many colony health inhibitors. This paper investigates the impact that colony supply uncertainty has on the California almond pollination market, the largest user of managed pollinators in the world. I develop a theoretical model and find that almond growers can reduce moral hazard in pollination agreements by paying beekeepers according to delivered colony strength. Additionally, I utilize two unique datasets to empirically explore determinants of almond pollination fees. Using the California State Beekeeper's Association pollination fee survey for years 2008-2015, I find that providing low strength colonies for almond pollination results in lower fees collected by the beekeeper. I pair the beekeeper-reported data analysis with an empirical study of an almond grower pollination contract survey that I conducted at the 2015 Almond Conference. The results of the almond grower data analysis suggest that growers whose almond pollination contracts specify minimum colony strength requirements pay higher pollination fees compared to those who have no colony strength requirements. The empirical results support the theoretical model finding that almond growers use colony strength requirements to elicit optimal beekeeper effort. Since almond pollination represents a fraction of beekeepers' yearly income, this paper highlights the need for additional research on the total economic impact of volatility of U.S. honey bee colony populations to effectively implement policies that promote managed pollinator health.
Value of information: costs and returns of precision corn production in Livingston County, Illinois
Creators: name: Osei, Edward
name: Li, Huijun
name: Osei, Edward
name: Li, Huijun
Publisher: name: Unknown
Year: 2016
Subjects: subject: Production Economics
subject: Research Methods/ Statistical Methods
subject: precision farming
subject: VRT
subject: APEX
subject: FEM
subject: GIS
subject: computer modeling

description: Despite the intuitive appeal of precision farming, adoption of precision technology options has been well below expectations. A review of precision farming studies suggests as expected that precision farming becomes more profitable as in-field spatial variability increases. However, no studies have attempted to quantify infield variability at any reasonable scale beyond a few experimental fields. This study contributes to the assessment of precision farming by introducing an approach that can help characterize the relative profitability of precision farming methods as compared to conventional farming. Using readily available geographic information systems databases on crop cover, soil type, and weather, we use a fully-linked biophysical-economic modeling system to assess the viability of precision nitrogen applications on corn in Livingston County, Illinois. Livingston County was selected because of its role as a major corn producing county in Illinois. We find little evidence, in general, for viability of precision nitrogen applications in contrast to uniform application rates, largely because of the lack of significant in-field spatial variability in soil types. However, precision application methods may be viable in specific situations.
Additional file 6 of Bacterial microbiome of faecal samples of naked mole-rat collected from the toilet chamber
Creators: name: Chua, Kah-Ooi
name: Fatima, Iqra
name: Lau, Yin Yin
name: Hong, Kar Wai
name: Yin, Wai-Fong
name: Mardaryev, Andrei
name: Chan, Kok-Gan
name: Chang, Chien-Yi
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 6: Figure S3. The bacterial microbiomes of faecal samples from wild individual NMRs and the toilet chamber of a laboratory NMR colony. Barplot showing the relative abundance of bacterial taxa at the rank of family.
Supplementary Figures from Osteocyte TSC1 promotes sclerostin secretion to restrain osteogenesis in mice
Creators: name: Liu, Wen
name: Wang, Zhenyu
name: Yang, Jun
name: Wang, Yongkui
name: Li, Kai
name: Huang, Bin
name: Yan, Bo
name: Wang, Ting
name: Li, Mangmang
name: Zou, Zhipeng
name: Yang, Jian
name: Xiao, Guozhi
name: Cui, Zhong-Kai
name: Liu, Anling
name: Bai, Xiaochun
Publisher: name: The Royal Society
Year: 2019

description: Figure S1. Generation of mice with osteocyte-specific deletion of TSC1. (A) Schematic of deletion of TSC1 by DMP1-Cre-mediated recombination. This mutant carries a "floxed" allele of Tsc1, when combined with a mutant carrying DMP1-Cre recombinase gene, exons 17 and 18 of Tsc1 are deleted in osteocytes. (B) Genotyping the offspring after mating transgenic Cre and loxp mice. Original image of agarose gel electrophoresis. The expected band of mutant carrying a DMP1-Cre-recombinase gene is nearly 800 bp and floxed Tsc1 allele is nearly 200 bp. M, molecular weight marker. DMP1-Tsc1f/f: control mice/DTCL, DMP1+Tsc1f/f: knockout mice/Tsc1 CKO. (C) Osteocyte deletion of TSC1 was confirmed in cortical sections from Rosa-DMP1 mice. Red signal indicates DMP1 expression in osteocytes. Boxed area was magnified on the right. Scale bar, 50 µm (n = 6); Figure S2. General phenotypes of Tsc1 CKO mice. (A) Body length and (B) weight in 10-week-old control and Tsc1 CKO mice. No difference was detected in control and Tsc1 CKO mice (t test, p=0.1235 and p=0.0873, n = 6). ns, no significance. (C-D) Representative micro-computed tomography (micro-CT) 2D images of (C) vertebral column, (D) metaphyseal trabecular bone of 4-, 8-, and 12-week-old control and Tsc1 CKO mice. Scale bar, 1 mm (n = 6).Data represent mean ± SD.* P < 0.05 ** P < 0.01, ***P < 0.001 by Student's t test.; Figure S3 . Thickness of cortical bone in DTCL and Tsc1 CKO mice. (A) H&E staining of cortical bone of femora from 4-, 8- and 12-week-old control and Tsc1 CKO mice. The boxed area was magnified in the panel below. The scale bar represents 100 µm and 50 µm (n = 6). (B-C) Histomorphometric measurements showed that (B) the mineralizing surface/bone surface (MS/BS, t test, p = 0.0087) and (C) bone formation rate (BFR, t test, p = 0.0003) of control mice were lower than that of Tsc1 CKO mice (n = 6). (D) mRNA expression of TSC1 in DTCL and Tsc1 CKO mice (t test, p = 0.0007). Data are represented as mean ± SD, **p < 0.01, and ***p < 0.001.; Figure S4 . TSC1 deletion induced H3K9 acetylation of the Sost promoter. (A)CHIP-qPCR detected TSC1 binding to the Sost promotor region in MLO-Y4 with control or TSC1 shRNA lentivirus infection. (t test, -3602-3728, p = 0.1476; -761-844, p = 0.7348; -998-1115, p = 0.1037; -1245-1361, p = 0.0141;-1828-1940, p = 0.0209; n = 3) .Data are represented as mean ± SD. * p < 0.05.
Decomposing Irrigation Water Use Changes in Equilibrium Models
Creators: name: Haqiqi, Iman
name: Hertel, Thomas W.
name: Haqiqi, Iman
name: Hertel, Thomas W.
Publisher: name: Unknown
Year: 2016
Subjects: subject: Environmental Economics and Policy
subject: International Relations/Trade
subject: Land Economics/Use
subject: Resource /Energy Economics and Policy
subject: Water intensity
subject: International agricultural trade
subject: Irrigation
subject: Adaptation
subject: Heckscher–Ohlin
subject: Melitz

description: This paper measures the importance of different drivers of change in irrigation water use regionally and globally. We followed Heckscher–Ohlin theory, Ricardian specific-factor model, and Melitz-type theories of trade to introduce a method for decomposing irrigated water use. We apply the decomposition method on the results of Liu et al. (2014) on the impacts of future irrigation shortfalls. We find that rain fed substitution (specific-factor impact) contributes to 62% of change in water use; substitution to non-crops (Heckscher–Ohlin impact) accounts for 16% of the change; and moving to farms with higher water productivity (Melitz impact) contributes to 7% of it, globally. The importance of drivers varies by region but usually these three drivers are the most important factors in adaptation to water shocks.
Listroderes montanus Germain 1895
Creators: name: Morrone, Juan J.
Publisher: name: Zenodo
Year: 2011
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Curculionidae
Listroderes
Listroderes montanus

description: Listroderes montanus Germain, 1895
 Listroderes montanus Germain, 1895: 99 (type locality: Chile: Cordillera Aculeo; type material: L: MHNS and PL: 1 MHNS and 1 NZAC).
 Distribution. Central Chile (Morrone, 1995b).
description: Published as part of Morrone, Juan J., 2011, Annotated checklist of the tribe Listroderini (Coleoptera: Curculionidae: Cyclominae) 3119, pp. 1-68 in Zootaxa 3119 (1) on page 31, DOI: 10.11646/zootaxa.3119.1.1, http://zenodo.org/record/5246257
Higher-order topological phases in a spring-mass model on a breathing kagome lattice
Creators: name: Wakao, Hiromasa
name: Yoshida, Tsuneya
name: Araki, Hiromu
name: Mizoguchi, Tomonari
name: Hatsugai, Yasuhiro
Publisher: name: arXiv
Year: 2019
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We propose a realization of higher-order topological phases in a spring-mass model with a breathing kagome structure. To demonstrate the existence of the higher-order topological phases, we characterize the topological properties and show that the corner states appear under the fixed boundary condition. To characterize the topological properties, we introduce a formula for the $\mathbb{Z}_3$ Berry phases in the Brillouin zone. From the numerical result of this $\mathbb{Z}_3$ Berry phase, we have elucidated that coupling between the longitudinal and transverse modes yields a state characterized by the Berry phase $\frac{2π}{3}$ for our mechanical breathing kagome model. In addition, we suggest that the corner states can be detected experimentally through a forced vibration.
description: 9 pages, 10 figures
Spindle pole body duplication defective yeast cells are more prone to membrane damage
Creators: name: Konuk, Hatice Büşra
name: Ergüden, Bengü
Publisher: name: Taylor & Francis
Year: 2019
Subjects: subject: Biochemistry
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Pharmacology
subject: Biotechnology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology

description: Correct separation of chromosomes during mitosis is essential for preventing genetic instability and aneuploidy. Such separation is dependent on correct duplication of the nuclear-associated microtubular organizing center, i.e., spindle pole body (SPB), in fungi. MonoPolar Spindle 2 (MPS2) is an essential gene, encoding a membrane protein required for the insertion of SPB into the nuclear envelope. We recently reported that the SESA complex, which is composed of Smy2, Eap1, Scp160, and Asc1, suppresses the essential role of MPS2 (Sezen et al. 2009, Genes & Development 23:1559–1570), i.e., in SESA-active cells Mps2 becomes nonessential. We also proposed that the SESA network facilitates this insertion by altering the membrane lipid composition (Sezen 2015, FEMS Yeast Research 15:fov089). In addition, we are interested in the antifungal properties of essential oils and previously reported that membrane integrity of yeast cells is impaired upon exposure to turpentine, thyme, oregano, and orange peel essential oils (Konuk and Ergüden 2017, BioCell 41:13–18). Due to our continuing interest in the SESA system and the mechanisms by which essential oils affect yeast cells, we aimed to investigate the effects of essential oils on yeast cell membranes. Herein, we show that mps2∆ 2µm-SMY2 and mps2∆ pom34∆ cells, in which the SESA complex is active and SPB duplication is defective, are more prone to membrane damage upon treatment with essential oils.
Additional file 9 of Mechanism of Zn2+ regulation of cellulase production in Trichoderma reesei Rut-C30
Creators: name: Li, Ni
name: Li, Jing
name: Chen, Yumeng
name: Shen, Yaling
name: Wei, Dongzhi
name: Wang, Wei
Publisher: name: figshare
Year: 2023
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 9: Figure S6. Effect of 3 mM Zn2+ on two major antioxidant enzyme gene transcription levels in RUT-C30 strain. Transcriptional levels of sod1 (a) and cat1 (b) of the RUT-C30 strain were determined after culturing in liquid MM for 36, 48 or 60 h containing 0 or 3 mM Zn2+ with 1% (w/v) Avicel as the sole carbon source. The final values are presented as the mean±standard deviation (SD) of three independent experimental results. Asterisks indicate significant differences compared to the control (*P <0.05, according to Student’s t-test).
Characterisation of proguanylin expressing cells in the intestine – evidence for constitutive luminal secretion
Creators: name: Dye, Florent Serge
name: Larraufie, Pierre
name: Kay, Richard
name: Darwish, Tamana
name: Rievaj, Juraj
name: Goldspink, Deborah A.
name: Meek, Claire L.
name: Middleton, Stephen J.
name: Hardwick, Richard H.
name: Roberts, Geoffrey P.
name: Percival-Alwyn, Jennifer L.
name: Vaughan, Tris
name: Ferraro, Franco
name: Challis, Benjamin G.
name: O’Rahilly, Stephen
name: Groves, Maria
name: Gribble, Fiona M.
name: Reimann, Frank
Publisher: name: Apollo - University of Cambridge Repository
Year: 2019
Subjects: Article
/692/4020/198
/692/163/2778
/64/110
/38/91
/14/35
/14/63
/82/58
/82/1
/96/31
/96/95
article

description: Abstract: Guanylin, a peptide implicated in regulation of intestinal fluid secretion, is expressed in the mucosa, but the exact cellular origin remains controversial. In a new transgenic mouse model fluorescent reporter protein expression driven by the proguanylin promoter was observed throughout the small intestine and colon in goblet and Paneth(-like) cells and, except in duodenum, in mature enterocytes. In Ussing chamber experiments employing both human and mouse intestinal tissue, proguanylin was released predominantly in the luminal direction. Measurements of proguanylin expression and secretion in cell lines and organoids indicated that secretion is largely constitutive and requires ER to Golgi transport but was not acutely regulated by salt or other stimuli. Using a newly-developed proguanylin assay, we found plasma levels to be raised in humans after total gastrectomy or intestinal transplantation, but largely unresponsive to nutrient ingestion. By LC-MS/MS we identified processed forms in tissue and luminal extracts, but in plasma we only detected full-length proguanylin. Our transgenic approach provides information about the cellular origins of proguanylin, complementing previous immunohistochemical and in-situ hybridisation results. The identification of processed forms of proguanylin in the intestinal lumen but not in plasma supports the notion that the primary site of action is the gut itself.
Can food safety shortfalls disrupt nutritional gains from increased animal-source food consumption? Evidence from Eid al-Adha
Creators: name: Schwab, Benjamin
name: Armah, Ralph
name: Schwab, Benjamin
name: Armah, Ralph
Publisher: name: Unknown
Year: 2016
Subjects: subject: Agricultural and Food Policy
subject: Food Consumption/Nutrition/Food Safety
subject: Food Security and Poverty
subject: International Development
subject: Food Safety
subject: Agriculture for Nutrition
subject: Child Nutrition
subject: Meat Consumption

description: The international health community has recently increased the focus on raising the consumption of animal-source foods in developing countries. While much of the literature has highlighted the high nutritional potential of such foods, little attention has been paid to infrastructure deficiencies for handling and processing animal-sourced foods, particularly meat. Such shortfalls in food safety have the potential to counteract some health gains, especially if renewed international efforts to increase animal consumption are not combined with improved processing capacity. The spike in meat consumption among Muslims worldwide on Eid al-Adha provides a natural experiment to test the extent to which such food safety concerns are justified. Meat processing on this holiday often exceeds the capacity of formal slaughter and processing infrastructure, and thus provides an excellent opportunity to observe the implications of a rapid intensification of meat production and consumption across several countries. Using Demographic and Health Survey (DHS) data from nine countries in Africa and Asia, we estimate the impact of meat consumption during this holiday on the incidence of diarrheal illness among children. Eid al-Adha provides a plausibly exogenous source of variation in meat consumption among Muslims, a natural comparison group (Non-Muslims) and independence from seasonal influences (the holiday follows the lunar Islamic calendar). We find that Eid al-Adha increases the incidence of diarrhea in Muslim children, relative to non-Muslims, by approximately 20 percent. These findings lend suggest food safety issues should be an important consideration for livestock intensification programs.
Additional file 2 of Mechanical circulatory support for refractory out-of-hospital cardiac arrest: a Danish nationwide multicenter study
Creators: name: Mørk, Sivagowry Rasalingam
name: Stengaard, Carsten
name: Linde, Louise
name: Møller, Jacob Eifer
name: Jensen, Lisette Okkels
name: Schmidt, Henrik
name: Riber, Lars Peter
name: Andreasen, Jo Bønding
name: Thomassen, Sisse Anette
name: Laugesen, Helle
name: Freeman, Phillip Michael
name: Christensen, Steffen
name: Greisen, Jacob Raben
name: Tang, Mariann
name: Møller-Sørensen, Peter Hasse
name: Holmvang, Lene
name: Gregers, Emilie
name: Kjaergaard, Jesper
name: Hassager, Christian
name: Eiskjær, Hans
name: Terkelsen, Christian Juhl
Publisher: name: figshare
Year: 2021
Subjects: subject: Medicine
subject: Cell Biology
subject: Biotechnology
subject: Immunology
subject: FOS: Clinical medicine
subject: Science Policy

description: Additional file 2. Figure S1: National trend in the use of mechanical circulatory support for OHCA in Denmark.
A simple way to generate high order vacuum graphs
Creators: name: Kajantie, K.
name: Laine, M.
name: Schroder, Y.
Publisher: name: arXiv
Year: 2001
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We describe an efficient practical procedure for enumerating and regrouping vacuum Feynman graphs of a given order in perturbation theory. The method is based on a combination of Schwinger-Dyson equations and the two-particle-irreducible ("skeleton") expansion. The regrouping leads to skeletons containing only free propagators, together with "ring diagrams" containing all the self-energy insertions. As a consequence, relatively few diagrams need to be drawn and integrations carried out at any single stage of the computation and, in low dimensions, overlapping ultraviolet/infrared subdivergences can be cleanly isolated. As an illustration we enumerate the graphs contributing to the 4-loop free energy in QCD, explicitly in a continuum and more compactly in a lattice regularization.
description: 19 pages. Reference added. To appear in Phys.Rev.D
Listroderes nodifer Boheman 1842
Creators: name: Morrone, Juan J.
Publisher: name: Zenodo
Year: 2011
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Curculionidae
Listroderes
Listroderes nodifer

description: Listroderes nodifer Boheman, 1842
 Listroderes nodifer Boheman, 1842: 194 (type locality: Chile; type material: H: NHRS).
 Listroderes chalceatus Blanchard, 1851: 342 (type locality: Chile: Santiago; type material: type material: H: MNHN); Kuschel, 1946: 139 (= L. nodifer).
 Listroderes calceatus Lacordaire, 1863: 345 (lapsus).
 Distribution. Central Chile and Peru (Morrone, 1993e).
description: Published as part of Morrone, Juan J., 2011, Annotated checklist of the tribe Listroderini (Coleoptera: Curculionidae: Cyclominae) 3119, pp. 1-68 in Zootaxa 3119 (1) on page 31, DOI: 10.11646/zootaxa.3119.1.1, http://zenodo.org/record/5246257
Additional file 3 of Mechanical circulatory support for refractory out-of-hospital cardiac arrest: a Danish nationwide multicenter study
Creators: name: Mørk, Sivagowry Rasalingam
name: Stengaard, Carsten
name: Linde, Louise
name: Møller, Jacob Eifer
name: Jensen, Lisette Okkels
name: Schmidt, Henrik
name: Riber, Lars Peter
name: Andreasen, Jo Bønding
name: Thomassen, Sisse Anette
name: Laugesen, Helle
name: Freeman, Phillip Michael
name: Christensen, Steffen
name: Greisen, Jacob Raben
name: Tang, Mariann
name: Møller-Sørensen, Peter Hasse
name: Holmvang, Lene
name: Gregers, Emilie
name: Kjaergaard, Jesper
name: Hassager, Christian
name: Eiskjær, Hans
name: Terkelsen, Christian Juhl
Publisher: name: figshare
Year: 2021
Subjects: subject: Medicine
subject: Cell Biology
subject: Biotechnology
subject: Immunology
subject: FOS: Clinical medicine
subject: Science Policy

description: Additional file 3. Figure S2: Kaplan-Meier survival curves of patients who had out-of-hospital cardiac arrest and received mechanical circulatory support.
Synthesis of functionalized selenazole derivatives via a three-component condensation of ethyl-2-chloro-3-oxo-butyrate, potassium selenocyanate and hydrazine or hydrazide derivatives
Creators: name: Pourmosavi, Marziyeh
name: Mosslemin, Mohammad H.
name: Alireza Hassanabadi
Publisher: name: Taylor & Francis
Year: 2019
Subjects: subject: Biochemistry
subject: Space Science
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Neuroscience
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: 110309 Infectious Diseases
subject: 60506 Virology

description: A simple, one-pot synthesis of five highly functionalized selenazole derivatives has been achieved in moderate-to-good yields via a three-component condensation of ethyl-2-chloro-3-oxo-butyrate, potassium selenocyanate and various substituted hydrazines or hydrazides in acetone at room temperature.
Additional file 1 of Mechanism of Zn2+ regulation of cellulase production in Trichoderma reesei Rut-C30
Creators: name: Li, Ni
name: Li, Jing
name: Chen, Yumeng
name: Shen, Yaling
name: Wei, Dongzhi
name: Wang, Wei
Publisher: name: figshare
Year: 2023
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Figure S1. The heat map showed the correlation between the biological replicates of each sample in RNA‑seq analysis. The value in the square is the correlation coefficient between the two samples. The larger the value, the greater the correlation between the two samples and the closer they are. These results mean that the RNA‑seq data is very reliable.
De-biased graphical Lasso for high-frequency data
Creators: name: Koike, Yuta
Publisher: name: arXiv
Year: 2019
Subjects: subject: Statistics Theory (math.ST)
subject: FOS: Mathematics
subject: 62J07, 62E20, 60H07

description: This paper develops a new statistical inference theory for the precision matrix of high-frequency data in a high-dimensional setting. The focus is not only on point estimation but also on interval estimation and hypothesis testing for entries of the precision matrix. To accomplish this purpose, we establish an abstract asymptotic theory for the weighted graphical Lasso and its de-biased version without specifying the form of the initial covariance estimator. We also extend the scope of the theory to the case that a known factor structure is present in the data. The developed theory is applied to the concrete situation where we can use the realized covariance matrix as the initial covariance estimator, and we obtain a feasible asymptotic distribution theory to construct (simultaneous) confidence intervals and (multiple) testing procedures for entries of the precision matrix.
description: 38 pages
OptiJ: Open-source optical projection tomography of large organ samples
Creators: name: Vallejo Ramirez, Pedro P.
name: Zammit, Joseph
name: Vanderpoorten, Oliver
name: Riche, Fergus
name: Blé, Francois-Xavier
name: Zhou, Xiao-Hong
name: Spiridon, Bogdan
name: Valentine, Christopher
name: Spasov, Simeon E.
name: Oluwasanya, Pelumi W.
name: Goodfellow, Gemma
name: Fantham, Marcus J.
name: Siddiqui, Omid
name: Alimagham, Farah
name: Robbins, Miranda
name: Stretton, Andrew
name: Simatos, Dimitrios
name: Hadeler, Oliver
name: Rees, Eric J.
name: Ströhl, Florian
name: Laine, Romain F.
name: Kaminski, Clemens F.
Publisher: name: Apollo - University of Cambridge Repository
Year: 2019
Subjects: Article
/639/766/930/2735
/631/57/2267
/14/63
article

description: Abstract: The three-dimensional imaging of mesoscopic samples with Optical Projection Tomography (OPT) has become a powerful tool for biomedical phenotyping studies. OPT uses visible light to visualize the 3D morphology of large transparent samples. To enable a wider application of OPT, we present OptiJ, a low-cost, fully open-source OPT system capable of imaging large transparent specimens up to 13 mm tall and 8 mm deep with 50 µm resolution. OptiJ is based on off-the-shelf, easy-to-assemble optical components and an ImageJ plugin library for OPT data reconstruction. The software includes novel correction routines for uneven illumination and sample jitter in addition to CPU/GPU accelerated reconstruction for large datasets. We demonstrate the use of OptiJ to image and reconstruct cleared lung lobes from adult mice. We provide a detailed set of instructions to set up and use the OptiJ framework. Our hardware and software design are modular and easy to implement, allowing for further open microscopy developments for imaging large organ samples.
Formation and Collapse of False Vacuum Bubbles in Relativistic Heavy-Ion Collisions
Creators: name: Ray, Rajarshi
name: Sanyal, Soma
name: Srivastava, Ajit M.
Publisher: name: arXiv
Year: 2001
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Theory (hep-th)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: It is possible that under certain situations, in a relativistic heavy-ion collision, partons may expand out forming a shell like structure. We analyze the process of hadronization in such a picture for the case when the quark-hadron transition is of first order, and argue that the inside region of such a shell must correspond to a supercooled (to $T = 0$) deconfined vacuum. Hadrons from that region escape out, leaving a bubble of pure deconfined vacuum with large vacuum energy. This bubble undergoes relativistic collapse, with highly Lorentz contracted bubble walls, and may concentrate the entire energy into extremely small regions. Eventually different portions of bubble wall collide, with the energy being released in the form of particle production. Thermalization of this system can lead to very high temperatures. With a reasonably conservative set of parameters, at LHC, the temperature of the hot spot can reach as high as 3 GeV, and well above it with more optimistic parameters. Such a hot spot can leave signals like large $P_T$ partons, dileptons, and enhanced production of heavy quarks. We also briefly discuss a speculative possibility where the electroweak symmetry may get restored in the highly dense region resulting from the decay of the bubble wall via the phenomenon of non-thermal symmetry restoration (which is usually employed in models of pre-heating after inflation). If that could happen then the possibility may arise of observing sphaleron induced baryon number violation in relativistic heavy-ion collisions.
description: 32 pages, 9 figures, title changed, discussion added about equilibration of decay products of bubble wall, discussions of baryon violation significantly modified, new references added. (Version to appear in Nucl.Phys.A)
Validation of the BOADICEA model and a 313-variant polygenic risk score for breast cancer risk prediction in a Dutch prospective cohort
Creators: name: Lakeman, Inge M. M.
name: Rodríguez-Girondo, Mar
name: Lee, Andrew
name: Ruiter, Rikje
name: Stricker, Bruno H.
name: Wijnant, Sara R. A.
name: Kavousi, Maryam
name: Antoniou, Antonis C.
name: Schmidt, Marjanka K.
name: Uitterlinden, André G.
name: Van Rooij, Jeroen
name: Devilee, Peter
Publisher: name: Apollo - University of Cambridge Repository
Year: 2020
Subjects: Article
article
breast cancer
polygenic risk score
prospective cohort
risk assessment

description: Abstract: Purpose: We evaluated the performance of the recently extended Breast and Ovarian Analysis of Disease Incidence and Carrier Estimation Algorithm (BOADICEA version 5) in a Dutch prospective cohort, using a polygenic risk score (PRS) based on 313 breast cancer (BC)–associated variants (PRS313) and other, nongenetic risk factors. Methods: Since 1989, 6522 women without BC aged 45 or older of European descent have been included in the Rotterdam Study. The PRS313 was calculated per 1 SD in controls from the Breast Cancer Association Consortium (BCAC). Cox regression analysis was performed to estimate the association between the PRS313 and incident BC risk. Cumulative 10-year risks were calculated with BOADICEA including different sets of variables (age, risk factors and PRS313). C-statistics were used to evaluate discriminative ability. Results: In total, 320 women developed BC. The PRS313 was significantly associated with BC (hazard ratio [HR] per SD of 1.56, 95% confidence interval [CI] [1.40–1.73]). Using 10-year risk estimates including age and the PRS313, other risk factors improved the discriminatory ability of the BOADICEA model marginally, from a C-statistic of 0.636 to 0.653. Conclusions: The effect size of the PRS313 is highly reproducible in the Dutch population. Our results validate the BOADICEA v5 model for BC risk assessment in the Dutch general population.
Non-invasive light focusing in scattering media using speckle variance optimization
Creators: name: Boniface, Antoine
name: Blochet, Baptiste
name: Dong, Jonathan
name: Gigan, Sylvain
Publisher: name: arXiv
Year: 2019
Subjects: subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: Optical imaging deep inside scattering media remains a fundamental problem in bio-imaging. While wavefront shaping has been shown to allow focusing of coherent light at depth, achieving it non-invasively remains a challenge. Various feedback mechanisms, in particular acoustic or non-linear fluorescence-based, have been put forward for this purpose. Non-invasive focusing at depth on fluorescent objects with linear excitation is, however, still unresolved. Here we report a simple method for focusing inside a scattering medium in an epi-detection geometry with a linear signal: optimizing the spatial variance of low contrast speckle patterns emitted by a set of fluorescent sources. Experimentally, we demonstrate robust and efficient focusing of scattered light on a single source, and show that this variance optimization method is formally equivalent to previous optimization strategies based on two-photon fluorescence. Our technique should generalize to a large variety of incoherent contrast mechanisms and holds interesting prospects for deep bio-imaging.
Magnetoconductance, Quantum Hall Effect, and Coulomb Blockade in Topological Insulator Nanocones
Creators: name: Kozlovsky, Raphael
name: Graf, Ansgar
name: Kochan, Denis
name: Richter, Klaus
name: Gorini, Cosimo
Publisher: name: arXiv
Year: 2019
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Magnetotransport through cylindrical topological insulator (TI) nanowires is governed by the interplay between quantum confinement and geometric (Aharonov-Bohm and Berry) phases. Here, we argue that the much broader class of TI nanowires with varying radius -- for which a homogeneous coaxial magnetic field induces a varying Aharonov-Bohm flux that gives rise to a non-trivial mass-like potential along the wire -- is accessible by studying its simplest member, a TI nanocone. Such nanocones allow to observe intriguing mesoscopic transport phenomena: While the conductance in a perpendicular magnetic field is quantized due to higher-order topological hinge states, it shows resonant transmission through Dirac Landau levels in a coaxial magnetic field. Furthermore, it may act as a quantum magnetic bottle, confining surface Dirac electrons and leading to a largely interaction-dominated regime of Coulomb blockade type. We show numerically that the above-mentioned effects occur for experimentally accessible values of system size and magnetic field, suggesting that TI nanocone junctions may serve as building blocks for Dirac electron optics setups.
An Adaptive Optics Survey of M8-M9 Stars: Discovery of 4 Very Low mass Binaries With at Least One System Containing a Brown Dwarf Companion
Creators: name: Close, Laird M.
name: Siegler, Nick
name: Potter, Dan
name: Brandner, Wolfgang
name: Liebert, James
Publisher: name: arXiv
Year: 2002
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: Use of the highly sensitive Hokupa'a/Gemini curvature wavefront sensor has allowed for the first time direct adaptive optics (AO) guiding on M8-M9 very low mass (VLM) stars. An initial survey of 20 such objects (SpT=M8-M9) discovered 4 binaries. Three of the systems have separations of less than 4.2 AU and similar mass ratios (Delta K<0.8 mag; 0.853 AU. This is likely consistent with the 23+/-5% measured for more massive (M0-M6) stars over the same separation range. It appears M8-M9 binaries have a much smaller semi-major axis distribution peak (~4 AU; with no systems wider than 15 AU) compared to M and G stars which have a broad peak at larger \~30 AU separations.
description: Accepted in Astrophysical Letters (March). 12 pages, 2 figures
Integrated genome and transcriptome analyses reveal the mechanism of genome instability in ataxia with oculomotor apraxia 2.
Creators: name: Kanagaraj, Radhakrishnan
name: Mitter, Richard
name: Kantidakis, Theodoros
name: Edwards, Matthew M
name: Benitez, Anaid
name: Chakravarty, Probir
name: Fu, Beiyuan
name: Becherel, Olivier
name: Yang, Fengtang
name: Lavin, Martin F
name: Koren, Amnon
name: Stewart, Aengus
name: West, Stephen C
Publisher: name: The Francis Crick Institute
Year: 2022
Subjects: Biochemistry & Proteomics
Tumour Biology
Genetics & Genomics
Genome Integrity & Repair
Structural Biology & Biophysics
Cell Biology
Cell Cycle & Chromosomes
Chemical Biology & High Throughput
Computational & Systems Biology

description: Mutations in the SETX gene, which encodes Senataxin, are associated with the progressive neurodegenerative diseases ataxia with oculomotor apraxia 2 (AOA2) and amyotrophic lateral sclerosis 4 (ALS4). To identify the causal defect in AOA2, patient-derived cells and SETX knockouts (human and mouse) were analyzed using integrated genomic and transcriptomic approaches. A genome-wide increase in chromosome instability (gains and losses) within genes and at chromosome fragile sites was observed, resulting in changes to gene-expression profiles. Transcription stress near promoters correlated with high GCskew and the accumulation of R-loops at promoter-proximal regions, which localized with chromosomal regions where gains and losses were observed. In the absence of Senataxin, the Cockayne syndrome protein CSB was required for the recruitment of the transcription-coupled repair endonucleases (XPG and XPF) and RAD52 recombination protein to target and resolve transcription bubbles containing R-loops, leading to genomic instability. These results show that transcription stress is an important contributor to SETX mutation-associated chromosome fragility and AOA2.