bluuebunny/crossref_metadata_2025_split huggingface dataset:
Herbicide resistance in China: a quantitative review
Authors: Liu Xiangying , Xiang Shihai , Zong Tao , Ma Guolan , Wu Lamei , Liu Kailin , Zhou Xuguo , Bai Lianyang 
Published: August 2019

AbstractThe widespread, rapid evolution of herbicide-resistant weeds is a serious and escalating agronomic problem worldwide. During China’s economic boom, the country became one of the most important herbicide producers and consumers in the world, and herbicide resistance has dramatically increased in the past decade and has become a serious threat to agriculture. Here, following an evidence-based PRISMA (preferred reporting items for systematic reviews and meta-analyses) approach, we carried out a systematic review to quantitatively assess herbicide resistance in China. Multiple weed species, including 26, 18, 11, 9, 5, 5, 4, and 3 species in rice (Oryza sativa L.), wheat (Triticum aestivum L.), soybean [Glycine max (L.) Merr.], corn (Zea mays L.), canola (Brassica napus L.), cotton (Gossypium hirsutum L.)., orchards, and peanut (Arachis hypogaea L.) fields, respectively, have developed herbicide resistance. Acetolactate synthase inhibitors, acetyl-CoA carboxylase inhibitors, and synthetic auxin herbicides are the most resistance-prone herbicides and are the most frequently used mechanisms of action, followed by 5-enolpyruvylshikimate-3-phosphate synthase inhibitors and protoporphyrinogen oxidase inhibitors. The lack of alternative herbicides to manage weeds that exhibit cross-resistance or multiple resistance (or both) is an emerging issue and poses one of the greatest threats challenging the crop production and food safety both in China and globally.
An Optimized Array Configuration of Tsunami Observation Network Off Southern Java, Indonesia
Authors: Mulia Iyan E. , Gusman Aditya Riadi , Williamson Amy L. , Satake Kenji 
Published: August 2019

AbstractHistorical records have proven that the southern coasts of Java, Indonesia, are prone to tsunamis. The existing tsunami observing system using bottom pressure gauges, also known as tsunameters, composes a global network but is too sparse for regional tsunami forecasts. The nearest tsunameter to Indonesia is located approximately 500‐km offshore, which is not very useful for the area, particularly for a tsunami source in eastern part of the Sunda megathrust. Here we propose a methodology to optimally place offshore tsunameters with the main consideration of operational costs, which is proportional to the number of observation points. We use a stochastic slip model of earthquakes with Mw 8.8–9.2 to generate multiple tsunami source realizations representing possible future events in the region. Based on the sources, we then identify a potential zone where an early tsunami detection is feasible. Furthermore, empirical orthogonal functions derived from tsunami simulations are used to determine the initial locations for tsunameter placement inside the specified zone. Finally, we apply an optimization scheme to improve the initial locations that facilitates both tsunami forecasts and source characterizations through a tsunami waveform inversion analysis. Our result indicates that six tsunameters are sufficient to efficiently cover the major seismogenic region in the study area.
Untangling the dynamics of persistence and colonization in microbial communities
Authors: Ranjeva Sylvia L , Mihaljevic Joseph R , Joseph Maxwell B , Giuliano Anna R , Dwyer Greg 
Published: August 2019

Abstract
A central goal of community ecology is to infer biotic interactions from observed distributions of co-occurring species. Evidence for biotic interactions, however, can be obscured by shared environmental requirements, posing a challenge for statistical inference. Here, we introduce a dynamic statistical model, based on probit regression, that quantifies the effects of spatial and temporal covariance in longitudinal co-occurrence data. We separate the fixed pairwise effects of species occurrences on persistence and colonization rates, a potential signal of direct interactions, from latent pairwise correlations in occurrence, a potential signal of shared environmental responses. We first validate our modeling framework with several simulation studies. Then, we apply the approach to a pressing epidemiological question by examining how human papillomavirus (HPV) types coexist. Our results suggest that while HPV types respond similarly to common host traits, direct interactions are sparse and weak, so that HPV type diversity depends largely on shared environmental drivers. Our modeling approach is widely applicable to microbial communities and provides valuable insights that should lead to more directed hypothesis testing and mechanistic modeling.
Rebalancing of actomyosin contractility enables mammary tumor formation upon loss of E-cadherin
Authors: Schipper Koen , Seinstra Danielle , Paulien Drenth Anne , van der Burg Eline , Ramovs Veronika , Sonnenberg Arnoud , van Rheenen Jacco , Nethe Micha , Jonkers Jos 
Published: August 2019

AbstractE-cadherin (CDH1) is a master regulator of epithelial cell adherence junctions and a well-established tumor suppressor in Invasive Lobular Carcinoma (ILC). Intriguingly, somatic inactivation of E-cadherin alone in mouse mammary epithelial cells (MMECs) is insufficient to induce tumor formation. Here we show that E-cadherin loss induces extrusion of luminal MMECs to the basal lamina. Remarkably, E-cadherin-deficient MMECs can breach the basal lamina but do not disseminate into the surrounding fat pad. Basal lamina components laminin and collagen IV supported adhesion and survival of E-cadherin-deficient MMECs while collagen I, the principle component of the mammary stromal micro-environment did not. We uncovered that relaxation of actomyosin contractility mediates adhesion and survival of E-cadherin-deficient MMECs on collagen I, thereby allowing ILC development. Together, these findings unmask the direct consequences of E-cadherin inactivation in the mammary gland and identify aberrant actomyosin contractility as a critical barrier to ILC formation.
Cell-type-specific genomics reveals histone modification dynamics in mammalian meiosis
Authors: Lam Kwan-Wood Gabriel , Brick Kevin , Cheng Gang , Pratto Florencia , Camerini-Otero R. Daniel 
Published: August 2019

AbstractMeiosis is the specialized cell division during which parental genomes recombine to create genotypically unique gametes. Despite its importance, mammalian meiosis cannot be studied in vitro, greatly limiting mechanistic studies. In vivo, meiocytes progress asynchronously through meiosis and therefore the study of specific stages of meiosis is a challenge. Here, we describe a method for isolating pure sub-populations of nuclei that allows for detailed study of meiotic substages. Interrogating the H3K4me3 landscape revealed dynamic chromatin transitions between substages of meiotic prophase I, both at sites of genetic recombination and at gene promoters. We also leveraged this method to perform the first comprehensive, genome-wide survey of histone marks in meiotic prophase, revealing a heretofore unappreciated complexity of the epigenetic landscape at meiotic recombination hotspots. Ultimately, this study presents a straightforward, scalable framework for interrogating the complexities of mammalian meiosis.
Impact of low lethal concentrations of buprofezin on biological traits and expression profile of chitin synthase 1 gene (CHS1) in melon aphid, Aphis gossypii
Authors: Ullah Farman , Gul Hina , Yousaf Hafiz Kamran , Xiu Wang , Qian Ding , Gao Xiwu , Tariq Kaleem , Han Peng , Desneux Nicolas , Song Dunlun 
Published: August 2019

AbstractBuprofezin, a chitin synthesis inhibitor that can be used for the control of hemipteran pests, especially melon aphid, Aphis gossypii. The impact of low lethal concentrations of buprofezin on the biological parameters and expression profile of CHS1 gene were estimated for two successive generations of A. gossypii. The present result shows that the LC15 and LC30 of buprofezin significantly decreased the fecundity and longevity of both generations. Exposure of F0 individuals to both concentrations delay the developmental period in F1. Furthermore, the survival rate, intrinsic rate of increase (r), finite rate of increase (λ), and net reproductive rate (R0) were reduced significantly in progeny generation at both concentrations. However, the reduction in gross reproductive rate (GRR) was observed only at LC30. Although, the mean generation time (T) prolonged substantially at LC30. Additionally, expression of the CHS1 gene was significantly increased in F0 adults. Significant increase in the relative abundance of CHS1 mRNA transcript was also observed at the juvenile and adult stages of F1 generation following exposure to LC15 and LC30. Therefore, our results show that buprofezin could affect the biological traits by diminishing the chitin contents owing to the inhibition of chitin synthase activity in the succeeding generation of melon aphid.
Nano-mechanical mapping of interdependent cell and ECM mechanics by AFM force spectroscopy
Authors: Viji Babu Prem Kumar , Rianna Carmela , Mirastschijski Ursula , Radmacher Manfred 
Published: August 2019

AbstractExtracellular matrix (ECM), as a dynamic component of the tissue, influences cell behavior and plays an important role in cell mechanics and tissue homeostasis. Reciprocally, this three-dimensional scaffold is dynamically, structurally and mechanically modified by cells. In the field of biophysics, the independent role of cell and ECM mechanics has been largely investigated; however, there is a lack of experimental data reporting the interdependent interplay between cell and ECM mechanics, measured simultaneously. Here, using Atomic Force Microscopy (AFM) we have characterized five different decellularized matrices diverse in their topography, ECM composition and stiffness and cultured them with normal and pathological fibroblasts (scar and Dupuytren’s). We investigated the change in topography and elasticity of these matrices due to cell seeding, by using AFM peak force imaging and mechanical mapping, respectively. We found normal fibroblasts soften these matrices more than pathological fibroblasts, suggesting that pathological fibroblasts are profoundly influencing tissue stiffening in fibrosis. We detected different ECM composition of decellularized matrices used here influences fibroblast stiffness, thus highlighting that cell mechanics not only depends on ECM stiffness but also on their composition. We used confocal microscopy to assess fibroblasts invasion and found pathological fibroblasts were invading the matrices deeper than normal fibroblasts.
HIV-1 DNA-capture-seq is a useful tool for the comprehensive characterization of HIV-1 provirus
Authors: Iwase Saori C. , Miyazato Paola , Katsuya Hiroo , Islam Saiful , Yang Benjy Tan Jek , Ito Jumpei , Matsuo Misaki , Takeuchi Hiroaki , Ishida Takaomi , Matsuda Kouki , Maeda Kenji , Satou Yorifumi 
Published: August 2019

AbstractRegardless of recent advances in the development of anti-retroviral drugs, it is still extremely difficult to eradicate HIV-1 from infected individuals. The characterization of the HIV-1 provirus, a type of viral reservoir, with a high resolution is key to HIV-1 cure research. Here, we demonstrate that DNA-capture-seq is a powerful tool to obtain comprehensive information on the HIV-1 provirus. We use biotinylated DNA probes targeting the entire HIV-1 sequence to capture fragments containing HIV-1 sequences from DNA-seq libraries prepared for high throughput sequencing. We demonstrate that the protocol provided the entire proviral sequence from the beginning of the 5′ LTR to the end of the 3′ LTR. Since HIV-1 DNA-probes can hybridize not only viral fragments but also virus-host chimeric ones, the viral integration site information can also be obtained. We verify the efficiency of the protocol by using latently infected cell lines, such as ACH-2 and J1.1, and newly generated ones. The results reveal that the 2 new clones that we analyse harbour one copy of replication-competent provirus, suggesting that latency is not caused by genetic mutations or deletions of the provirus. In conclusion, HIV-1 DNA-capture-seq is a powerful tool to characterize the HIV-1 provirus at a single nucleotide resolution and therefore might be useful for various experiments aiming for an HIV-1 cure.
Sequential adjustment of cytotoxic T lymphocyte densities improves efficacy in controlling tumor growth
Authors: Khazen Roxana , Müller Sabina , Lafouresse Fanny , Valitutti Salvatore , Cussat-Blanc Sylvain 
Published: August 2019

AbstractUnderstanding the human cytotoxic T lymphocyte (CTL) biology is crucial to develop novel strategies aiming at maximizing their lytic capacity against cancer cells. Here we introduce an agent-based model, calibrated on population-scale experimental data that allows quantifying human CTL per capita killing. Our model highlights higher individual CTL killing capacity at lower CTL densities and fits experimental data of human melanoma cell killing. The model allows extending the analysis over prolonged time frames, difficult to investigate experimentally, and reveals that initial high CTL densities hamper efficacy to control melanoma growth. Computational analysis forecasts that sequential addition of fresh CTL cohorts improves tumor growth control. In vivo experimental data, obtained in a mouse melanoma model, confirm this prediction. Taken together, our results unveil the impact that sequential adjustment of cellular densities has on enhancing CTL efficacy over long-term confrontation with tumor cells. In perspective, they can be instrumental to refine CTL-based therapeutic strategies aiming at controlling tumor growth.
A high-sugar diet rapidly enhances susceptibility to colitis via depletion of luminal short-chain fatty acids in mice
Authors: Laffin Michael , Fedorak Robert , Zalasky Aiden , Park Heekuk , Gill Amanpreet , Agrawal Ambika , Keshteli Ammar , Hotte Naomi , Madsen Karen L. 
Published: August 2019

AbstractWestern-style diets have been implicated in triggering inflammatory bowel disease activity. The aim of this study was to identify the effect of a short-term diet high in sugar on susceptibility to colitis. Adult wild-type mice were placed on chow or a high sugar diet (50% sucrose) ± acetate. After two days of diet, mice were treated with dextran sodium sulfate (DSS) to induce colitis. Disease severity was assessed daily. Colonic tissues were analyzed for cytokine expression using the MesoScale discovery platform. Intestinal dextran permeability and serum lipopolysaccharide levels (LPS) were measured. Gut microbiota were analyzed by 16s rRNA sequencing and short chain fatty acid (SCFA) concentrations by gas chromatography. Bone marrow-derived macrophages (BMDM) were incubated with LPS and cytokine secretion measured. Mice on a high sugar diet had increased gut permeability, decreased microbial diversity and reduced SCFA. BMDM derived from high sugar fed mice were highly responsive to LPS. High sugar fed mice had increased susceptibility to colitis and pro-inflammatory cytokine concentrations. Oral acetate significantly attenuated colitis in mice by restoring permeability. In conclusion, short term exposure to a high sugar diet increases susceptibility to colitis by reducing short-chain fatty acids and increasing gut permeability.
Anticipatory postural adjustments during joint action coordination
Authors: Nogueira-Campos A. A. , Hilt P. M. , Fadiga L. , Veronesi C. , D’Ausilio A. , Pozzo T. 
Published: August 2019

AbstractThere is a current claim that humans are able to effortlessly detect others’ hidden mental state by simply observing their movements and transforming the visual input into motor knowledge to predict behaviour. Using a classical paradigm quantifying motor predictions, we tested the role of vision feedback during a reach and load-lifting task performed either alone or with the help of a partner. Wrist flexor and extensor muscle activities were recorded on the supporting hand. Early muscle changes preventing limb instabilities when participants performed the task by themselves revealed the contribution of the visual input in postural anticipation. When the partner performed the unloading, a condition mimicking a split-brain situation, motor prediction followed a pattern evolving along the task course and changing with the integration of successive somatosensory feedback. Our findings demonstrate that during social behaviour, in addition to self-motor representations, individuals cooperate by continuously integrating sensory signals from various sources.
Orangutans show active voicing through a membranophone
Authors: Lameira Adriano R. , Shumaker Robert W. 
Published: August 2019

AbstractActive voicing – voluntary control over vocal fold oscillation – is essential for speech. Nonhuman great apes can learn new consonant- and vowel-like calls, but active voicing by our closest relatives has historically been the hardest evidence to concede to. To resolve this controversy, a diagnostic test for active voicing is reached here through the use of a membranophone: a musical instrument where a player’s voice flares a membrane’s vibration through oscillating air pressure. We gave the opportunity to use a membranophone to six orangutans (with no effective training), three of whom produced a priori novel (species-atypical) individual-specific vocalizations. After 11 and 34 min, two subjects were successful by producing their novel vocalizations into the instrument, hence, confirming active voicing. Beyond expectation, however, within <1 hour, both subjects found opposite strategies to significantly alter their voice duration and frequency to better activate the membranophone, further demonstrating plastic voice control as a result of experience with the instrument. Results highlight how individual differences in vocal proficiency between great apes may affect performance in experimental tests. Failing to adjust a test’s difficulty level to individuals’ vocal skill may lead to false negatives, which may have largely been the case in past studies now used as “textbook fact” for great ape “missing” vocal capacities. Results qualitatively differ from small changes that can be caused in innate monkey calls by intensive months-long conditional training. Our findings verify that active voicing beyond the typical range of the species’ repertoire, which in our species underpins the acquisition of new voiced speech sounds, is not uniquely human among great apes.
Evaluating scale effects of topographic variables in landslide susceptibility models using GIS-based machine learning techniques
Authors: Chang Kuan-Tsung , Merghadi Abdelaziz , Yunus Ali P. , Pham Binh Thai , Dou Jie 
Published: August 2019

AbstractThe quality of digital elevation models (DEMs), as well as their spatial resolution, are important issues in geomorphic studies. However, their influence on landslide susceptibility mapping (LSM) remains poorly constrained. This work determined the scale dependency of DEM-derived geomorphometric factors in LSM using a 5 m LiDAR DEM, LiDAR resampled 30 m DEM, and a 30 m ASTER DEM. To verify the validity of our approach, we first compiled an inventory map comprising of 267 landslides for Sihjhong watershed, Taiwan, from 2004 to 2014. Twelve landslide causative factors were then generated from the DEMs and ancillary data. Afterward, popular statistical and machine learning techniques, namely, logistic regression (LR), random forest (RF), and support vector machine (SVM) were implemented to produce the LSM. The accuracies of models were evaluated by overall accuracy, kappa index and the receiver operating characteristic curve indicators. The highest accuracy was attained from the resampled 30 m LiDAR DEM derivatives, indicating a fine-resolution topographic data does not necessarily achieve the best performance. Additionally, RF attained superior performance between the three presented models. Our findings could contribute to opt for an appropriate DEM resolution for mapping landslide hazard in vulnerable areas.
Harnessing the tissue and plasma lncRNA-peptidome to discover peptide-based cancer biomarkers
Authors: Chakraborty Sajib , Andrieux Geoffroy , Hasan A. M. Mahmudul , Ahmed Musaddeque , Hosen Md. Ismail , Rahman Tania , Hossain M. Anwar , Boerries Melanie 
Published: August 2019

AbstractProteome-centric studies, although have identified numerous lncRNA-encoded polypeptides, lack differential expression analysis of lncRNA-peptidome across primary tissues, cell lines and cancer states. We established a computational-proteogenomic workflow involving re-processing of publicly available LC-MS/MS data, which facilitated the identification of tissue-specific and universally expressed (UExp) lncRNA-polypeptides across 14 primary human tissues and 11 cell lines. The utility of lncRNA-peptidome as cancer-biomarkers was investigated by re-processing LC-MS/MS data from 92 colon-adenocarcinoma (COAD) and 30 normal colon-epithelium tissues. Intriguingly, a significant upregulation of five lncRNA UExp-polypeptides in COAD tissues was observed. Furthermore, clustering of the UExp-polypeptides led to the classification of COAD patients that coincided with the clinical stratification, underlining the prognostic potential of the UExp-polypeptides. Lastly, we identified differential abundance of the UExp-polypeptides in the plasma of prostate-cancer patients highlighting their potential as plasma-biomarker. The analysis of lncRNA-peptidome may pave the way to identify effective tissue/plasma biomarkers for different cancer types.
Low-molecular-weight-heparin increases Th1- and Th17-associated chemokine levels during pregnancy in women with unexplained recurrent pregnancy loss: a randomised controlled trial
Authors: Rasmark Roepke E. , Bruno V. , Nedstrand E. , Boij R. , Strid C. Petersson , Piccione E. , Berg G. , Svensson-Arvelund J. , Jenmalm M. C. , Rubér M. , Ernerudh J. 
Published: August 2019

AbstractLow-molecular-weight heparin (LMWH) is widely used to treat recurrent pregnancy loss (RPL) because of its anti-coagulant effects. Although in vitro studies have suggested additional immunological effects, these are debated. We therefore investigated whether LMWH could modulate immune responses in vivo during pregnancy of women with unexplained RPL. A Swedish open multi-centre randomised controlled trial included 45 women treated with tinzaparin and 42 untreated women. Longitudinally collected plasma samples were obtained at gestational weeks (gw) 6, 18, 28 and 34 and analysed by multiplex bead technology for levels of 11 cytokines and chemokines, chosen to represent inflammation and T-helper subset-associated immunity. Mixed linear models test on LMWH-treated and untreated women showed differences during pregnancy of the Th1-associated chemokines CXCL10 (p = 0.01), CXCL11 (p < 0.001) and the Th17-associated chemokine CCL20 (p = 0.04), while CCL2, CCL17, CCL22, CXCL1, CXCL8, CXCL12, CXCL13 and IL-6 did not differ. Subsequent Student’s t-test showed significantly higher plasma levels of CXCL10 and CXCL11 in treated than untreated women at gw 28 and 34. The consistent increase in the two Th1-associated chemokines suggests a potential proinflammatory and unfavourable effect of LMWH treatment during later stages of pregnancy, when Th1 immunity is known to disrupt immunological tolerance.