bluuebunny/crossref_metadata_2025_split huggingface dataset:
Urbanization Exacerbated Rainfall Over European Suburbs Under a Warming Climate
Authors: Yang Long , Ni Guangheng , Tian Fuqiang , Niyogi Dev 
Published: October 2021

AbstractThe impacts of cities and climate warming on extreme rainfall under strong synoptic conditions are not well understood. Here, we carry out the first model‐based assessment of urban impacts on extreme flood‐producing storms for the European region. We identify contrasting roles of cities and climate warming in determining the space‐time variability of the July 14, 2021 storm over western Europe. While climate warming dominates the temporal rainfall variability over the domain, cities further enhance total rainfall over their suburbs by dynamically modifying the intensity and position of moisture convergence. There is a cyclonic structure of flow anomalies around the city induced by urban surface roughness. The rainfall anomaly induced by the interactive impacts of cities and climate warming is 50% larger than by those urban impacts alone. We highlight a need to develop a regional framework by reconciling the emerging urban‐rural contrasts in vulnerability and preparedness to hydrometeorological extremes.
Effects of maternal diet-induced obesity on metabolic disorders and age-associated miRNA expression in the liver of male mouse offspring
Authors: Mennitti Laís Vales , Carpenter Asha A. M. , Loche Elena , Pantaleão Lucas C. , Fernandez-Twinn Denise S. , Schoonejans Josca M. , Blackmore Heather L. , Ashmore Thomas J. , Pisani Luciana Pellegrini , Tadross John A. , Hargreaves Iain , Ozanne Susan E. 
Published: October 2021

Abstract
Objective
This study investigated the effect of maternal obesity on aged-male offspring liver phenotype and hepatic expression of a programmed miRNA.

Methods
A mouse model (C57BL/6 J) of maternal diet-induced obesity was used to investigate fasting-serum metabolites, hepatic lipid content, steatosis, and relative mRNA levels (RT-PCR) and protein expression (Western blotting) of key components involved in hepatic and mitochondrial metabolism in 12-month-old offspring. We also measured hepatic lipid peroxidation, mitochondrial content, fibrosis stage, and apoptosis in the offspring. To investigate potential mechanisms leading to the observed phenotype, we also measured the expression of miR-582 (a miRNA previously implicated in liver cirrhosis) in 8-week-old and 12-month-old offspring.

Results
Body weight and composition was similar between 8-week-old offspring, however, 12-month-old offspring from obese mothers had increased body weight and fat mass (19.5 ± 0.8 g versus 10.4 ± 0.9 g, p < 0.001), as well as elevated serum levels of LDL and leptin and hepatic lipid content (21.4 ± 2.1 g versus 12.9 ± 1.8 g, p < 0.01). This was accompanied by steatosis, increased Bax/Bcl-2 ratio, and overexpression of p-SAPK/JNK, Tgfβ1, Map3k14, and Col1a1 in the liver. Decreased levels of Bcl-2, p-AMPKα, total AMPKα and mitochondrial complexes were also observed. Maternal obesity was associated with increased hepatic miR-582-3p (p < 0.001) and miR-582-5p (p < 0.05). Age was also associated with an increase in both miR-582-3p and miR-582-5p, however, this was more pronounced in the offspring of obese dams, such that differences were greater in 12-month-old animals (−3p: 7.34 ± 1.35 versus 1.39 ± 0.50, p < 0.0001 and −5p: 4.66 ± 1.16 versus 1.63 ± 0.65, p < 0.05).

Conclusion
Our findings demonstrate that maternal diet-induced obesity has detrimental effects on offspring body composition as well as hepatic phenotype that may be indicative of accelerated-ageing phenotype. These whole-body and cellular phenotypes were associated with age-dependent changes in expression of miRNA-582 that might contribute mechanistically to the development of metabolic disorders in the older progeny.
Unravelling roles of error-prone DNA polymerases in shaping cancer genomes
Authors: Vaziri Cyrus , Rogozin Igor B. , Gu Qisheng , Wu Di , Day Tovah A. 
Published: October 2021

AbstractMutagenesis is a key hallmark and enabling characteristic of cancer cells, yet the diverse underlying mutagenic mechanisms that shape cancer genomes are not understood. This review will consider the emerging challenge of determining how DNA damage response pathways—both tolerance and repair—act upon specific forms of DNA damage to generate mutations characteristic of tumors. DNA polymerases are typically the ultimate mutagenic effectors of DNA repair pathways. Therefore, understanding the contributions of DNA polymerases is critical to develop a more comprehensive picture of mutagenic mechanisms in tumors. Selection of an appropriate DNA polymerase—whether error-free or error-prone—for a particular DNA template is critical to the maintenance of genome stability. We review different modes of DNA polymerase dysregulation including mutation, polymorphism, and over-expression of the polymerases themselves or their associated activators. Based upon recent findings connecting DNA polymerases with specific mechanisms of mutagenesis, we propose that compensation for DNA repair defects by error-prone polymerases may be a general paradigm molding the mutational landscape of cancer cells. Notably, we demonstrate that correlation of error-prone polymerase expression with mutation burden in a subset of patient tumors from The Cancer Genome Atlas can identify mechanistic hypotheses for further testing. We contrast experimental approaches from broad, genome-wide strategies to approaches with a narrower focus on a few hundred base pairs of DNA. In addition, we consider recent developments in computational annotation of patient tumor data to identify patterns of mutagenesis. Finally, we discuss the innovations and future experiments that will develop a more comprehensive portrait of mutagenic mechanisms in human tumors.
Single-cell RNA sequencing reveals distinct tumor microenvironmental patterns in lung adenocarcinoma
Authors: Bischoff Philip , Trinks Alexandra , Obermayer Benedikt , Pett Jan Patrick , Wiederspahn Jennifer , Uhlitz Florian , Liang Xizi , Lehmann Annika , Jurmeister Philipp , Elsner Aron , Dziodzio Tomasz , Rückert Jens-Carsten , Neudecker Jens , Falk Christine , Beule Dieter , Sers Christine , Morkel Markus , Horst David , Blüthgen Nils , Klauschen Frederick 
Published: October 2021

AbstractRecent developments in immuno-oncology demonstrate that not only cancer cells, but also the tumor microenvironment can guide precision medicine. A comprehensive and in-depth characterization of the tumor microenvironment is challenging since its cell populations are diverse and can be important even if scarce. To identify clinically relevant microenvironmental and cancer features, we applied single-cell RNA sequencing to ten human lung adenocarcinomas and ten normal control tissues. Our analyses revealed heterogeneous carcinoma cell transcriptomes reflecting histological grade and oncogenic pathway activities, and two distinct microenvironmental patterns. The immune-activated CP²E microenvironment was composed of cancer-associated myofibroblasts, proinflammatory monocyte-derived macrophages, plasmacytoid dendritic cells and exhausted CD8+ T cells, and was prognostically unfavorable. In contrast, the inert N³MC microenvironment was characterized by normal-like myofibroblasts, non-inflammatory monocyte-derived macrophages, NK cells, myeloid dendritic cells and conventional T cells, and was associated with a favorable prognosis. Microenvironmental marker genes and signatures identified in single-cell profiles had progonostic value in bulk tumor profiles. In summary, single-cell RNA profiling of lung adenocarcinoma provides additional prognostic information based on the microenvironment, and may help to predict therapy response and to reveal possible target cell populations for future therapeutic approaches.
The role of R-spondin proteins in cancer biology
Authors: ter Steege Eline J. , Bakker Elvira R. M. 
Published: October 2021

AbstractR-spondin (RSPO) proteins constitute a family of four secreted glycoproteins (RSPO1–4) that have appeared as multipotent signaling ligands. The best-known molecular function of RSPOs lie within their capacity to agonize the Wnt/β-catenin signaling pathway. As RSPOs act upon cognate receptors LGR4/5/6 that are typically expressed by stem cells and progenitor cells, RSPO proteins importantly potentiate Wnt/β-catenin signaling especially within these proliferative stem cell compartments. Since multiple organs express LGR4/5/6 receptors and RSPO ligands within their stem cell niches, RSPOs can exert an influential role in stem cell regulation throughout the body. Inherently, over the last decade a multitude of reports implicated the deregulation of RSPOs in cancer development. First, RSPO2 and RSPO3 gene fusions with concomitant enhanced expression have been identified in colon cancer patients, and proposed as an alternative driver of Wnt/β-catenin hyperactivation that earmarks cancer in the colorectal tract. Moreover, the causal oncogenic capacity of RSPO3 overactivation has been demonstrated in the mouse intestine. As a paradigm organ in this field, most of current knowledge about RSPOs in cancer is derived from studies in the intestinal tract. However, RSPO gene fusions as well as enhanced RSPO expression have been reported in multiple additional cancer types, affecting different organs that involve divergent stem cell hierarchies. Importantly, the emerging oncogenic role of RSPO and its potential clinical utility as a therapeutic target have been recognized and investigated in preclinical and clinical settings. This review provides a survey of current knowledge on the role of RSPOs in cancer biology, addressing the different organs implicated, and of efforts made to explore intervention opportunities in cancer cases with RSPO overrepresentation, including the potential utilization of RSPO as novel therapeutic target itself.
Prefrontal Aβ pathology influencing the pathway from apathy to cognitive decline in non-dementia elderly
Authors: Sun Lin , Li Wei , Li Guanjun , Xiao Shifu ,   Alzheimer’s Disease Neuroimaging Initiative
Published: October 2021

AbstractThe purpose of this study is to investigate the complex connection between apathy and cognitive decline that remains unclear. A total of 1057 non-dementia elderly from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) database received up to 13 years of follow-up and were divided into an apathy negative (−) group of 943 participants and an apathy positive (+) group of 114 participants through the Neuropsychiatric Inventory (NPI)-apathy subitem. Cerebrospinal fluid (CSF) AD biomarkers and amyloid β (Aβ) PET were measured, and their longitudinal changes were assessed using linear mixed-effects models. Risk factors for cognitive decline and apathy conversion were explored through the Cox proportional hazards model. Mediation effects of Aβ pathology on cognition were investigated using the causal mediation analysis. Apathy syndrome was associated with faster impairment of cognition and elevation of the Aβ burden. The effects of apathy on cognitive function and life quality were mediated by Aβ pathology, including CSF Aβ42/total tau ratio, and Aβ deposition in the prefrontal regions. Apathy syndrome was the risk factor for cognitive deterioration; meanwhile, frontal Aβ burden was the risk factor for apathy conversion. Apathy syndrome is an early manifestation of cognitive decline and there are bidirectional roles between apathy syndrome and Aβ pathology. Prefrontal Aβ pathology influenced the pathway from apathy to cognitive decline.
Retrospective analysis of Schlafen11 (SLFN11) to predict the outcomes to therapies affecting the DNA damage response
Authors: Willis Sophie E. , Winkler Claudia , Roudier Martine P. , Baird Tarrion , Marco-Casanova Paola , Jones Emma V. , Rowe Philip , Rodriguez-Canales Jaime , Angell Helen K. , Ng Felicia S. L. , Waring Paul M. , Hodgson Darren , Ledermann Jonathan A. , Weberpals Johanne I. , Dean Emma , Harrington Elizabeth A. , Barrett J. Carl , Pierce Andrew J. , Leo Elisabetta , Jones Gemma N. 
Published: October 2021

Abstract
Background
The absence of the putative DNA/RNA helicase Schlafen11 (SLFN11) is thought to cause resistance to DNA-damaging agents (DDAs) and PARP inhibitors.

Methods
We developed and validated a clinically applicable SLFN11 immunohistochemistry assay and retrospectively correlated SLFN11 tumour levels to patient outcome to the standard of care therapies and olaparib maintenance.

Results
High SLFN11 associated with improved prognosis to the first-line treatment with DDAs platinum-plus-etoposide in SCLC patients, but was not strongly linked to paclitaxel–platinum response in ovarian cancer patients. Multivariate analysis of patients with relapsed platinum-sensitive ovarian cancer from the randomised, placebo-controlled Phase II olaparib maintenance Study19 showed SLFN11 tumour levels associated with sensitivity to olaparib. Study19 patients with high SLFN11 had a lower progression-free survival (PFS) hazard ratio compared to patients with low SLFN11, although both groups had the benefit of olaparib over placebo. Whilst caveated by small sample size, this trend was maintained for PFS, but not overall survival, when adjusting for BRCA status across the olaparib and placebo treatment groups, a key driver of PARP inhibitor sensitivity.

Conclusion
We provide clinical evidence supporting the role of SLFN11 as a DDA therapy selection biomarker in SCLC and highlight the need for further clinical investigation into SLFN11 as a PARP inhibitor predictive biomarker.
Carbon dioxide levels in initial nests of the leaf-cutting ant Atta sexdens (Hymenoptera: Formicidae)
Authors: Sousa Kátia K. A. , Camargo Roberto S. , Caldato Nadia , Farias Adriano P. , Matos Carlos A. O. , Zanuncio José C. , Santos Isabel C. L. , Forti Luiz C. 
Published: October 2021

AbstractClaustral foundation of nests by Atta sexdens Forel (Hymenoptera: Formicidae) involves great effort by its queens, solely responsible for the cultivation of the fungus and care for her offspring at this stage. The minimum workers, after 4 months, open access to the external environment to foraging plants to cultivate the symbiotic fungus, which decomposes the plant fragments and produces gongilidea nodules as food for the individuals in the colony. Colony gas exchange and decomposition of organic matter in underground ant nests generate carbon dioxide (CO2) emitted into the atmosphere. We described the carbon dioxide concentration in colonies in the field. The objective was to evaluate the carbon dioxide concentration in initial A. sexdens colonies, in the field, and their development. The CO2 level was also measured in 4-month-old colonies in the field, using an open respirometric system fitted with an atmospheric air inlet. The CO2 level of the respirometric container was read by introducing a tube into the nest inlet hole and the air sucked by a peristaltic pump into the CO2 meter box. The CO2 concentration in the initial colony was also measured after 4 months of age, when the offspring production (number of eggs, larvae, pupae and adult workers) stabilized. Ten perforations (15 cm deep) was carried out in the adjacent soil, without a nest of ants nearby, to determine the concentration of CO2. The composition of the nests in the field was evaluated after excavating them using a gardening shovel and they were stored in 250 ml pots with 1 cm of moistened plaster at the bottom. The CO2 concentration was higher in field nest than in adjacent soil. The concentration of carbon dioxide in A. sexdens nests in the field is higher than in those in the soil, due to the production of CO2 by the fungus garden and colony.
Graphene coated magnetic nanoparticles facilitate the release of biofuels and oleochemicals from yeast cell factories
Authors: Pandit Santosh , Konzock Oliver , Leistner Kirsten , Mokkapati VRSS , Merlo Alessandra , Sun Jie , Mijakovic Ivan 
Published: October 2021

AbstractEngineering of microbial cells to produce high value chemicals is rapidly advancing. Yeast, bacteria and microalgae are being used to produce high value chemicals by utilizing widely available carbon sources. However, current extraction processes of many high value products from these cells are time- and labor-consuming and require toxic chemicals. This makes the extraction processes detrimental to the environment and not economically feasible. Hence, there is a demand for the development of simple, effective, and environmentally friendly method for the extraction of high value chemicals from these cell factories. Herein, we hypothesized that atomically thin edges of graphene having ability to interact with hydrophobic materials, could be used to extract high value lipids from cell factories. To achieve this, array of axially oriented graphene was deposited on iron nanoparticles. These coated nanoparticles were used to facilitate the release of intracellular lipids from Yarrowia lipolytica cells. Our treatment process can be integrated with the growth procedure and achieved the release of 50% of total cellular lipids from Y. lipolytica cells. Based on this result, we propose that nanoparticles coated with axially oriented graphene could pave efficient, environmentally friendly, and cost-effective way to release intracellular lipids from yeast cell factories.
Disclosure of salicylic acid and jasmonic acid-responsive genes provides a molecular tool for deciphering stress responses in soybean
Authors: Beyer Sebastian F. , Bel Paloma Sánchez , Flors Victor , Schultheiss Holger , Conrath Uwe , Langenbach Caspar J. G. 
Published: October 2021

AbstractHormones orchestrate the physiology of organisms. Measuring the activity of defense hormone-responsive genes can help understanding immune signaling and facilitate breeding for plant health. However, different from model species like Arabidopsis, genes that respond to defense hormones salicylic acid (SA) and jasmonic acid (JA) have not been disclosed in the soybean crop. We performed global transcriptome analyses to fill this knowledge gap. Upon exogenous application, endogenous levels of SA and JA increased in leaves. SA predominantly activated genes linked to systemic acquired resistance and defense signaling whereas JA mainly activated wound response-associated genes. In general, SA-responsive genes were activated earlier than those responding to JA. Consistent with the paradigm of biotrophic pathogens predominantly activating SA responses, free SA and here identified most robust SA marker genes GmNIMIN1, GmNIMIN1.2 and GmWRK40 were induced upon inoculation with Phakopsora pachyrhizi, whereas JA marker genes did not respond to infection with the biotrophic fungus. Spodoptera exigua larvae caused a strong accumulation of JA-Ile and JA-specific mRNA transcripts of GmBPI1, GmKTI1 and GmAAT whereas neither free SA nor SA-marker gene transcripts accumulated upon insect feeding. Our study provides molecular tools for monitoring the dynamic accumulation of SA and JA, e.g. in a given stress condition.
Research on time series characteristics of the gas drainage evaluation index based on lasso regression
Authors: Song Shuang , Li Shugang , Zhang Tianjun , Ma Li , Zhang Lei , Pan Shaobo 
Published: October 2021

AbstractThe evaluation of the coal mine gas drainage effect is affected by many factors, such as flow rate, wind speed, drainage negative pressure, concentration, and temperature. This paper starts from actual coal mine production monitoring data and based on the lasso regression algorithm, features selection of multiple parameters of the preprocessed gas concentration time series to construct gas concentration feature selection based on the algorithm. The three-time smoothing index method is used to fill in the missing values. Aiming at the problem of different dimensions in the gas concentration time series, the MinMaxScaler method is used to normalize the data. The lasso regression algorithm is used to perform feature selection on the multivariable gas concentration time series, and the gas concentration time series selected by the lasso feature and the gas concentration time series without feature selection are input. The performance of the ANN algorithm for gas concentration prediction is compared and analyzed. The optimal α value and L1 norm are selected based on the grid search method to determine the strong explanatory gas concentration time series feature set of the working face, and an experimental comparison of the gas concentration prediction results before and after the lasso feature selection is performed. We verify the effectiveness of the algorithm.
Effectiveness of using representative subsets of global climate models in future crop yield projections
Authors: Qian Budong , Jing Qi , Cannon Alex J. , Smith Ward , Grant Brian , Semenov Mikhail A. , Xu Yue-Ping , Ma Di 
Published: October 2021

AbstractRepresentative subsets of global climate models (GCMs) are often used in climate change impact studies to account for uncertainty in ensemble climate projections. However, the effectiveness of such subsets has seldom been assessed for the estimations of either the mean or the spread of the full ensembles. We assessed two different approaches that were employed to select 5 GCMs from a 20-member ensemble of GCMs from the CMIP5 ensemble for projecting canola and spring wheat yields across Canada under RCP 4.5 and 8.5 emission scenarios in the periods 2040–2069 and 2070–2099, based on crop simulation models. Averages and spreads of the simulated crop yields using the 5-GCM subsets selected by T&P and KKZ approaches were compared with the full 20-GCM ensemble. Our results showed that the 5-GCM subsets selected by the two approaches could produce full-ensemble means with a relative absolute error of 2.9–4.7% for canola and 1.5–2.2% for spring wheat, and covers 61.8–91.1% and 66.1–80.8% of the full-ensemble spread for canola and spring wheat, respectively. Our results also demonstrated that both approaches were very likely to outperform a subset of randomly selected 5 GCMs in terms of a smaller error and a larger range.
Novel﻿ eco-friendly low cost and energy efficient synthesis of (Nd–Pr–Dy)2Fe14B magnetic powder from monazite concentrate
Authors: Haider Syed Kamran , Lee Jin-Young , Pawar Amol Uttam , Kim Dongsoo , Kang Young Soo 
Published: October 2021

AbstractSyntheses of Nd2Fe14B magnetic powder by conventional method is a complicated multi-step process, which produces harmful pollutants and consumes a huge amount of energy and resources. Herein we report a simple chemical route for the preparation of (Nd–Pr)2Fe14B magnetic powder using monazite concentrate as a precursor. Th, U, Sm, and La impurities were removed from monazite leachate by roasting, solvent extraction and leaching the concentrate. Purified leachate consisting of Nd and Pr Chlorides was added to the FeCl3 solution, and the solution produced was co-precipitated with NaOH. RE and Fe hydroxide precipitates were converted to the oxides by annealing at 700 °C. Boric acid and CaH2 were added in the RE and Fe oxides produced, and this mixture was reduced and diffused to (Nd–Pr)2Fe14B. Magnetic properties of the (Nd–Pr)2Fe14B produced were enhanced by introducing antiferromagnetic coupling, induced by Dy addition and efficient removal of CaO byproduct through ball milling in ethanol which increased the BHmax from 3.9 to 11.45 MGOe. Process reported is energy efficient, environment-friendly, time saving and low-cost.