bluuebunny/crossref_metadata_2025_split huggingface dataset:
Topological clustering of regulatory genes confers pathogenic tolerance to cassava brown streak virus (CBSV) in cassava
Authors: Jaemthaworn Thanakorn , Kalapanulak Saowalak , Saithong Treenut 
Published: April 2021

AbstractRobustness, a naïve property of biological systems, enables organisms to maintain functions during perturbation and is crucial for improving the resilience of crops to prevailing stress conditions and diseases, guaranteeing food security. Most studies of robustness in crops have focused on genetic superiority based upon individual genes, overlooking the collaborative actions of multiple responsive genes and the regulatory network topology. This research aims to uncover patterns of gene cooperation leading to organismal robustness by studying the topology of gene co-expression networks (GCNs) of both CBSV virus resistant and susceptible cassava cultivars. The resulting GCNs show higher topological clustering of cooperative genes in the resistant cultivar, suggesting that the network architecture is central to attaining robustness. Despite a reduction in the number of hub genes in the resistant cultivar following the perturbation, essential biological functions contained in the network were maintained through neighboring genes that withstood the shock. The susceptible cultivar seemingly coped by inducing more gene actions in the network but could not maintain the functions required for plant growth. These findings underscore the importance of regulatory network architecture in ensuring phenotypic robustness and deepen our understanding of transcriptional regulation.
An updated analysis of the epidemiologic trends of neuroendocrine tumors in Taiwan
Authors: Chang Jeffrey S. , Chen Li-Tzong , Shan Yan-Shen , Chu Pei-Yi , Tsai Chia-Rong , Tsai Hui-Jen 
Published: April 2021

AbstractThe incidence of neuroendocrine tumors (NETs) has been increasing in recent decades. Previously, we reported the incidence and survival of NETs in Taiwan by analyzing the 1996–2008 data from the Taiwan Cancer Registry. Here we performed an updated analysis on the incidence and survival of NETs in Taiwan from 1996 to 2015. The incidence of NETs was 0.244 per 100,000 in 1996 and increased to 3.162 per 100,000 in 2015. The most common site of NETs was rectum (29.65%), followed by lung/bronchus (17.22%), and pancreas (10.71%). The 5- and 10-year overall survival rates of all NETs were 54.6% and 45.3%, respectively. Female and younger NETs patients had a better survival. The survival of all NETs diagnosed between 2010 and 2015 was better than those diagnosed between 2004 and 2009. Among the common sites of NETs, an improved survival of pancreatic NETs diagnosed between 2010 and 2015 compared to those diagnosed between 2004 and 2009 was observed. Overall, the incidence of NETs in Taiwan has continued to increase. The survival of pancreatic NET has shown a recent improvement. The development of novel therapeutic agents has the potential to improve the prognosis of NETs of other sites in the near future.
Multisubstituted pyrimidines effectively inhibit bacterial growth and biofilm formation of Staphylococcus aureus
Authors: Provenzani Riccardo , San-Martin-Galindo Paola , Hassan Ghada , Legehar Ashenafi , Kallio Aleksi , Xhaard Henri , Fallarero Adyary , Yli-Kauhaluoma Jari 
Published: April 2021

AbstractBiofilms are multicellular communities of microorganisms that generally attach to surfaces in a self-produced matrix. Unlike planktonic cells, biofilms can withstand conventional antibiotics, causing significant challenges in the healthcare system. Currently, new chemical entities are urgently needed to develop novel anti-biofilm agents. In this study, we designed and synthesized a set of 2,4,5,6-tetrasubstituted pyrimidines and assessed their antibacterial activity against planktonic cells and biofilms formed by Staphylococcus aureus. Compounds 9e, 10d, and 10e displayed potent activity for inhibiting the onset of biofilm formation as well as for killing pre-formed biofilms of S. aureus ATCC 25923 and Newman strains, with half-maximal inhibitory concentration (IC50) values ranging from 11.6 to 62.0 µM. These pyrimidines, at 100 µM, not only decreased the number of viable bacteria within the pre-formed biofilm by 2–3 log10 but also reduced the amount of total biomass by 30–50%. Furthermore, these compounds were effective against planktonic cells with minimum inhibitory concentration (MIC) values lower than 60 µM for both staphylococcal strains. Compound 10d inhibited the growth of S. aureus ATCC 25923 in a concentration-dependent manner and displayed a bactericidal anti-staphylococcal activity. Taken together, our study highlights the value of multisubstituted pyrimidines to develop novel anti-biofilm agents.
Coeval primary and diagenetic carbonates in lacustrine sediments challenge palaeoclimate interpretations
Authors: McCormack Jeremy , Kwiecien Ola 
Published: April 2021

AbstractLakes are sensitive to climate change and their sediments play a pivotal role as environmental recorders. The oxygen and carbon isotope composition (δ18O and δ13C) of carbonates from alkaline lakes is featured in numerous studies attempting a quantitative reconstruction of rainfall, temperature and precipitation-evaporation changes. An often-overlooked challenge consists in the mineralogically mixed nature of carbonates themselves. We document a large variability of carbonate components and their respective distinct δ18O and δ13C values from sediments of Lake Van (Turkey) covering the last 150 kyr. The carbonate inventory consists of primary (1) inorganic calcite and aragonite precipitating in the surface-water, (2) biogenic calcite ostracod valves; and post-depositional phases: (3) dolomite forming in the sediment, and previously overlooked, (4) aragonite encrustations formed rapidly around decaying organic matter. We find a systematic relation between the lithology and the dominant deep-water carbonate phase formed recurrently under specific hydrological conditions. The presence of the different carbonates is never mutually exclusive, and the isotopic composition of each phase forms a distinctive cluster characteristic for the depth and timing of their formation. Our findings stretch the envelope of mechanisms forming lacustrine carbonates and highlight the urge to identify and separate carbonate components prior to geochemical analyses.
Constitutive depletion of Slc34a2/NaPi-IIb in rats causes perinatal mortality
Authors: Pastor-Arroyo Eva Maria , Rodriguez Josep M. Monné , Pellegrini Giovanni , Bettoni Carla , Levi Moshe , Hernando Nati , Wagner Carsten A. 
Published: April 2021

AbstractAbsorption of dietary phosphate (Pi) across intestinal epithelia is a regulated process mediated by transcellular and paracellular pathways. Although hyperphosphatemia is a risk factor for the development of cardiovascular disease, the amount of ingested Pi in a typical Western diet is above physiological needs. While blocking intestinal absorption has been suggested as a therapeutic approach to prevent hyperphosphatemia, a complete picture regarding the identity and regulation of the mechanism(s) responsible for intestinal absorption of Pi is missing. The Na+/Pi cotransporter NaPi-IIb is a secondary active transporter encoded by the Slc34a2 gene. This transporter has a wide tissue distribution and within the intestinal tract is located at the apical membrane of epithelial cells. Based on mouse models deficient in NaPi-IIb, this cotransporter is assumed to mediate the bulk of active intestinal absorption of Pi. However, whether or not this is also applicable to humans is unknown, since human patients with inactivating mutations in SLC34A2 have not been reported to suffer from Pi depletion. Thus, mice may not be the most appropriate experimental model for the translation of intestinal Pi handling to humans. Here, we describe the generation of a rat model with Crispr/Cas-driven constitutive depletion of Slc34a2. Slc34a2 heterozygous rats were indistinguishable from wild type animals under standard dietary conditions as well as upon 3 days feeding on low Pi. However, unlike in humans, homozygosity resulted in perinatal lethality.
Fusion and fission events regulate endosome maturation and viral escape
Authors: Castro Mario , Lythe Grant , Smit Jolanda , Molina-París Carmen 
Published: April 2021

AbstractEndosomes are intracellular vesicles that mediate the communication of the cell with its extracellular environment. They are an essential part of the cell’s machinery regulating intracellular trafficking via the endocytic pathway. Many viruses, which in order to replicate require a host cell, attach themselves to the cellular membrane; an event which usually initiates uptake of a viral particle through the endocytic pathway. In this way viruses hijack endosomes for their journey towards intracellular sites of replication and avoid degradation without host detection by escaping the endosomal compartment. Recent experimental techniques have defined the role of endosomal maturation in the ability of enveloped viruses to release their genetic material into the cytoplasm. Endosome maturation depends on a family of small hydrolase enzymes (or GTPases) called Rab proteins, arranged on the cytoplasmic surface of its membrane. Here, we model endosomes as intracellular compartments described by two variables (its levels of active Rab5 and Rab7 proteins) and which can undergo coagulation (or fusion) and fragmentation (or fission). The key element in our approach is the “per-cell endosomal distribution” and its dynamical (Boltzmann) equation. The Boltzmann equation allows us to derive the dynamics of the total number of endosomes in a cell, as well as the mean and the standard deviation of its active Rab5 and Rab7 levels. We compare our mathematical results with experiments of Dengue viral escape from endosomes. The relationship between endosomal active Rab levels and pH suggests a mechanism that can account for the observed variability in viral escape times, which in turn regulate the viability of a viral intracellular infection.
The association of enteric neuropathy with gut phenotypes in acute and progressive models of Parkinson’s disease
Authors: McQuade Rachel M. , Singleton Lewis M. , Wu Hongyi , Lee Sophie , Constable Remy , Di Natale Madeleine , Ringuet Mitchell T. , Berger Joel P. , Kauhausen Jessica , Parish Clare L. , Finkelstein David I. , Furness John B. , Diwakarla Shanti 
Published: April 2021

AbstractParkinson’s disease (PD) is associated with neuronal damage in the brain and gut. This work compares changes in the enteric nervous system (ENS) of commonly used mouse models of PD that exhibit central neuropathy and a gut phenotype. Enteric neuropathy was assessed in five mouse models: peripheral injection of MPTP; intracerebral injection of 6-OHDA; oral rotenone; and mice transgenic for A53T variant human α-synuclein with and without rotenone. Changes in the ENS of the colon were quantified using pan-neuronal marker, Hu, and neuronal nitric oxide synthase (nNOS) and were correlated with GI function. MPTP had no effect on the number of Hu+ neurons but was associated with an increase in Hu+ nuclear translocation (P < 0.04). 6-OHDA lesioned mice had significantly fewer Hu+ neurons/ganglion (P < 0.02) and a reduced proportion of nNOS+ neurons in colon (P < 0.001). A53T mice had significantly fewer Hu+ neurons/area (P < 0.001) and exhibited larger soma size (P < 0.03). Treatment with rotenone reduced the number of Hu+ cells/mm2in WT mice (P < 0.006) and increased the proportion of Hu+ translocated cells in both WT (P < 0.02) and A53T mice (P < 0.04). All PD models exhibited a degree of enteric neuropathy, the extent and type of damage to the ENS, however, was dependent on the model.
Accessible chromatin reveals regulatory mechanisms underlying cell fate decisions during early embryogenesis
Authors: Fan Tongqiang , Huang Youjun 
Published: April 2021

AbstractThis study was conducted to investigate epigenetic landscape across multiple species and identify transcription factors (TFs) and their roles in controlling cell fate decision events during early embryogenesis. We made a comprehensively joint-research of chromatin accessibility of five species during embryogenesis by integration of ATAC-seq and RNA-seq datasets. Regulatory roles of candidate early embryonic TFs were investigated. Widespread accessible chromatin in early embryos overlapped with putative cis-regulatory sequences. Sets of cell-fate-determining TFs were identified. YOX1, a key cell cycle regulator, were found to homologous to clusters of TFs that are involved in neuron and epidermal cell-fate determination. Our research provides an intriguing insight into evolution of cell-fate decision during early embryogenesis among organisms.
Higher order mode supercontinuum generation in tantalum pentoxide (Ta2O5) channel waveguide
Authors: Fan Ranran , Lin Yuan-Yao , Chang Lin , Boes Andreas , Bowers John , Liu Jia-Wei , Lin Chao-Hong , Wang Te-Keng , Qiao Junpeng , Kuo Hao-Chung , Lin Gong-Ru , Shih Min-Hsiung , Hung Yung-Jr , Chiu Yi-Jen , Lee Chao-Kuei 
Published: April 2021

AbstractWe fabricated tantalum pentoxide (Ta2O5) channel waveguides and used them to experimentally demonstrate higher-order mode supercontinuum (SC) generation. The Ta2O5 waveguide has a high nonlinear refractive index which was in an order magnitude of 10–14 cm2/W and was designed to be anomalously dispersive at the pumping wavelength. To the best of our knowledge, this is the first time a higher-order mode femtosecond pump based broadband SC has been measured from a nonlinear waveguide using the phase-matching method. This enabled us to demonstrate a SC spectrum spanning from 842 to 1462 nm (at − 30 dB), which corresponds to 0.83 octaves, when using the TM10 waveguide mode. When using the TE10 mode, the SC bandwidth is slightly reduced for the same excitation peak power. In addition, we theoretically estimated and discussed the possibility of using the broadband higher-order modes emitted from the Ta2O5 waveguide for trapping nanoparticles. Hence, we believe that demonstrated Ta2O5 waveguide are a promising broadband light source for optical applications such as frequency metrology, Raman spectroscopy, molecular spectroscopy and optical coherence tomography.
Efficacy of broflanilide (VECTRON T500), a new meta-diamide insecticide, for indoor residual spraying against pyrethroid-resistant malaria vectors
Authors: Ngufor Corine , Govoetchan Renaud , Fongnikin Augustin , Vigninou Estelle , Syme Thomas , Akogbeto Martin , Rowland Mark 
Published: April 2021

AbstractThe rotational use of insecticides with different modes of action for indoor residual spraying (IRS) is recommended for improving malaria vector control and managing insecticide resistance. Insecticides with new chemistries are urgently needed. Broflanilide is a newly discovered insecticide under consideration. We investigated the efficacy of a wettable powder (WP) formulation of broflanilide (VECTRON T500) for IRS on mud and cement wall substrates in laboratory and experimental hut studies against pyrethroid-resistant malaria vectors in Benin, in comparison with pirimiphos-methyl CS (Actellic 300CS). There was no evidence of cross-resistance to pyrethroids and broflanilide in CDC bottle bioassays. In laboratory cone bioassays, broflanilide WP-treated substrates killed > 80% of susceptible and pyrethroid-resistant An. gambiae sl for 6–14 months. At application rates of 100 mg/m2 and 150 mg/m2, mortality of wild pyrethroid-resistant An. gambiae sl entering experimental huts in Covè, Benin treated with VECTRON T500 was similar to pirimiphos-methyl CS (57–66% vs. 56%, P > 0.05). Throughout the 6-month hut trial, monthly wall cone bioassay mortality on VECTRON T500 treated hut walls remained > 80%. IRS with broflanilide shows potential to significantly improve the control of malaria transmitted by pyrethroid-resistant mosquito vectors and could thus be a crucial addition to the current portfolio of IRS insecticides.
Trees outside forests are an underestimated resource in a country with low forest cover
Authors: Thomas Nathan , Baltezar Priscilla , Lagomasino David , Stovall Atticus , Iqbal Zaheer , Fatoyinbo Lola 
Published: April 2021

AbstractTrees outside forests (TOF) are an underrepresented resource in forest poor nations. As a result of their frequent omission from national forest resource assessments and a lack of readily available very-high-resolution remotely sensed imagery, TOF status and characterization has until now, been unknown. Here, we assess the capacity of openly available 10 m ESA Sentinel constellation satellite imagery for mapping TOF extent at the national level in Bangladesh. In addition, we estimate canopy height for TOF using a TanDEM-X DEM. We map 2,233,578 ha of TOF in Bangladesh with a mean canopy height of 7.3 m. We map 31 and 53% more TOF than existing estimates of TOF and forest, respectively. We find TOF in Bangladesh is nationally fragmented as a consequence of agricultural activity, yet is capable of maintaining connectedness between remaining stands. Now, TOF accounting is feasible at the national scale using readily available datasets, enabling the mainstream inclusion of TOF in national forest resource assessments for other countries.
Serum sodium variation is a major determinant of peridialytic blood pressure trends in haemodialysis outpatients
Authors: Jaques David A. , Davenport Andrew 
Published: April 2021

AbstractIntradialytic hypotension (IDH) and peridialytic blood pressure (BP) trends are associated with morbidity and mortality in haemodialysis (HD) patients. We aimed to characterise the respective influence of volume status and small solutes variation on peridialytic systolic BP (SBP) trends during HD. We retrospectively analysed the relative peridialytic SBP decrease in 647 prevalent outpatients attending for their mid-week session with corresponding pre- and post-HD bioelectrical impedance analysis. Mean SBP decreased by 10.5 ± 23.6 mmHg. Factors positively associated with the relative decrease in SBP were: serum sodium (Na) decrease, body mass index, serum albumin, dialysis vintage, ultrafiltration rate and urea Kt/V (p < 0.05 for all). Antihypertensive medications and higher dialysate calcium were negatively associated with the relative decrease in SBP (p < 0.05 for both). Age had a quadratic relationship with SBP trends (p < 0.05). Pre-HD volume status measured by extracellular to total body water ratio was not associated with SBP variation (p = 0.216). Peridialytic SBP trends represent a continuum with serum Na variation being a major determinant while volume status has negligible influence. Middle-aged and overweight patients are particularly prone to SBP decline. Tailoring Na and calcium dialysate concentrations could influence haemodynamic stability during HD and improve patient experience and outcomes.
Coexistence of inhibitory and activating killer-cell immunoglobulin-like receptors to the same cognate HLA-C2 and Bw4 ligands confer breast cancer risk
Authors: Ashouri Elham , Rajalingam Karan , Barani Shaghik , Farjadian Shirin , Ghaderi Abbas , Rajalingam Raja 
Published: April 2021

AbstractHuman leukocyte antigen (HLA) class I-specific killer-cell immunoglobulin-like receptors (KIR) regulate natural killer (NK) cell function in eliminating malignancy. Breast cancer (BC) patients exhibit reduced NK-cytotoxicity in peripheral blood. To test the hypothesis that certain KIR-HLA combinations impairing NK-cytotoxicity predispose to BC risk, we analyzed KIR and HLA polymorphisms in 162 women with BC and 278 controls. KIR-Bx genotypes increased significantly in BC than controls (83.3% vs. 71.9%, OR 1.95), and the increase was more pronounced in advanced-cancer (OR 5.3). No difference was observed with inhibitory KIR (iKIR) and HLA-ligand combinations. The activating KIR (aKIR) and HLA-ligand combinations, 2DS1 + C2 (OR 2.98) and 3DS1 + Bw4 (OR 2.6), were significantly increased in advanced-BC. All patients with advanced-cancer carrying 2DS1 + C2 or 3DS1 + Bw4 also have their iKIR counterparts 2DL1 and 3DL1, respectively. Contrarily, the 2DL1 + C2 and 3DL1 + Bw4 pairs without their aKIR counterparts are significantly higher in controls. These data suggest that NK cells expressing iKIR to the cognate HLA-ligands in the absence of putative aKIR counterpart are instrumental in antitumor response. These data provide a new framework for improving the utility of genetic risk scores for individualized surveillance.
Reduced dispersibility of flushable wet wipes after wet storage
Authors: Harter Thomas , Bernt Ingo , Winkler Stefanie , Hirn Ulrich 
Published: April 2021

AbstractScientific publications and newsfeeds recently focused on flushable wet wipes and their role in sewage system blockages. It is stated that although products are marked as flushable, they do not disintegrate after being disposed of via the toilet. In this work it is shown that wetlaid hydroentangled wet wipes lose their initially good dispersive properties during their storage in wet condition. As a consequence, we are suggesting to add tests after defined times of wet storage when assessing the flushability of wet wipes. Loss of dispersibility is found for both, wet wipes from industrial pilot production and wipes produced on laboratory pilot facilities. We found it quite surprising that the wet wipes’ dispersibility is deteriorating after storage in exactly the same liquid they are dispersed in, i.e. water. This is probably why the effect of wet storage has not been investigated earlier. It is demonstrated that the deteriorating dispersibility of these wipes is linked to the used type of short cellulosic fibres — only wipes containing unbleached softwood pulp as short fibre component were preserving good dispersibility during wet storage. Possible mechanisms that might be responsible are discussed, e.g. long term fiber swelling causing a tightening of the fiber network, or surface interdiffusion.
Incidental detection of prostate cancer with computed tomography scans
Authors: Korevaar Steven , Tennakoon Ruwan , Page Mark , Brotchie Peter , Thangarajah John , Florescu Cosmin , Sutherland Tom , Kam Ning Mao , Bab-Hadiashar Alireza 
Published: April 2021

AbstractProstate cancer (PCa) is the second most frequent type of cancer found in men worldwide, with around one in nine men being diagnosed with PCa within their lifetime. PCa often shows no symptoms in its early stages and its diagnosis techniques are either invasive, resource intensive, or has low efficacy, making widespread early detection onerous. Inspired by the recent success of deep convolutional neural networks (CNN) in computer aided detection (CADe), we propose a new CNN based framework for incidental detection of clinically significant prostate cancer (csPCa) in patients who had a CT scan of the abdomen/pelvis for other reasons. While CT is generally considered insufficient to diagnose PCa due to its inferior soft tissue characterisation, our evaluations on a relatively large dataset consisting of 139 clinically significant PCa patients and 432 controls show that the proposed deep neural network pipeline can detect csPCa patients at a level that is suitable for incidental detection. The proposed pipeline achieved an area under the receiver operating characteristic curve (ROC-AUC) of 0.88 (95% Confidence Interval: 0.86–0.90) at patient level csPCa detection on CT, significantly higher than the AUCs achieved by two radiologists (0.61 and 0.70) on the same task.