bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular detection ofLeishmania donovani, Leishmania major, andTrypanosomaspp. inSergentomyia squamipleurissandflies from a visceral leishmaniasis focus in Merti sub-County, eastern Kenya
Authors: Owino Barrack O. , Mwangi Jackline Milkah , Kiplagat Steve , Mwangi Hannah Njiriku , Ingonga Johnstone M. , Chebet Alphine , Ngumbi Philip M. , Villinger Jaundouwe , Masiga Daniel K. , Matoke-Muhia Damaris 
Published: July 2020

AbstractBackgroundVisceral leishmaniasis (VL) and zoonotic cutaneous leishmaniasis (ZCL) are of public health concern in Merti sub-County, Kenya, but epidemiological data on transmission, vector abundance, distribution, and reservoir hosts remains limited. To better understand the disease and inform control measures to reduce transmission, we investigated the abundance and distribution of sandfly species responsible forLeishmaniatransmission in the sub-County, and their blood-meal hosts.MethodsWe conducted an entomological survey in five villages with reported cases of VL in Merti sub-County, Kenya, using CDC miniature light traps and castor oil sticky papers. Sandflies were dissected and identified to the species level using standard taxonomic keys and PCR analysis of the cytochrome c oxidase subunit 1 (COI) gene.Leishmaniaparasites were detected and identified by PCR and sequencing of internal transcribed spacer 1 (ITS1) genes. Bloodmeal sources of engorged females were identified by high-resolution melting analysis of vertebrate cytochrome b (cyt-b) gene PCR products.ResultsWe sampled 526 sandflies consisting of eight species,Phlebotomus orientalis(1.52%; n = 8) and sevenSergentomyiaspp.Sergentomyia squamipleuriswas the most abundant sandfly species (78.71%; n = 414) followed bySergentomyia clydei(10.46%; n = 55).Leishmania major, Leishmania donovani, andTrypanosomaDNA were detected inS. squamipleurisspecimens. Humans were the main sources of sandfly bloodmeals. However, we also detected mixed bloodmeals; oneS. squamipleurisspecimen had fed on both human and mouse (Mus musculus) blood, while twoPh. orientalisspecimens fed on human, hyrax (Procavia capensis), and mouse (Mus musculus) blood.ConclusionsOur findings implicate the potential involvement ofS. squamipleurisin the transmission ofLeishmaniaand question the dogma that human leishmaniases in the Old World are exclusively transmitted by sandflies of thePhlebotomusgenus. The presence ofTrypanosomaspp. may indicate mechanical transmission, whose efficiency should be investigated. Host preference analysis revealed the possibility of zoonotic transmission of leishmaniasis and other pathogens in the sub-County.Leishmania majorcauses ZCL whileL. donovaniis responsible for VL. However, the reservoir status of the parasites is not uniform. Further studies are needed to determine the reservoir hosts ofLeishmaniaspp. in the area.
The influence of microbial mats on travertine precipitation in active hydrothermal systems (Central Italy)
Authors: Porta Giovanna Della , Reitner Joachim 
Published: July 2020

ABSTRACTThe study of hydrothermal travertines contributes to the understanding of the interaction between physico-chemical processes and the role played by microbial mats and biofilms in influencing carbonate precipitation. Three active travertine sites were investigated in Central Italy to identify the types of carbonate precipitates and the associated microbial mats at varying physico-chemical parameters. Carbonate precipitated fabrics at the decimetre- to millimetre-scale and microbial mats vary with decreasing water temperature: a) at high temperature (55-44°C) calcite or aragonite crystals precipitate on microbial mats of sulphide oxidizing, sulphate reducing and anoxygenic phototrophic bacteria forming filamentous streamer fabrics, b) at intermediate temperature (44-40°C), rafts, coated gas bubbles and dendrites are associated withSpirulinacyanobacteria and other filamentous and rod-shaped cyanobacteria, c) low temperature (34-33°C) laminated crusts and oncoids in a terraced slope system are associated with diverse Oscillatoriales and Nostocales filamentous cyanobacteria, sparseSpirulinaand diatoms. At the microscale, carbonate precipitates are similar in the three sites consisting of prismatic calcite (40-100 μm long, 20-40 μm wide) or acicular aragonite crystals organized in radial spherulites, overlying or embedded within biofilm EPS (Extracellular Polymeric Substances). Microsparite and sparite crystal size decreases with decreasing temperature and clotted peloidal micrite dominates at temperatures < 40°C, also encrusting filamentous microbes. Carbonates are associated with gypsum and Ca-phosphate crystals; EPS elemental composition is enriched in Si, Al, Mg, Ca, P, S and authigenic aluminium-silicates form aggregates on EPS.This study confirms that microbial communities in hydrothermal travertine settings vary as a function of temperature. Carbonate precipitate types at the microscale do not vary considerably, despite different microbial communities suggesting that travertine precipitation, driven by CO2degassing, is influenced by biofilm EPS acting as template for crystal nucleation (EPS-mediated mineralization) and affecting the fabric types, independently from specific microbial metabolism.
SAMHD1 promotes oncogene-induced replication stress
Authors: Zhang Si Min , Calderón-Montaño Jose M , Rudd Sean G 
Published: July 2020

AbstractOncogenes induce DNA replication stress in cancer cells. Although this was established more than a decade ago, we are still unravelling the molecular underpinnings of this phenomenon, which will be critical if we are to exploit this knowledge to improve cancer treatment. A key mediator of oncogene-induced replication stress is the availability of DNA precursors, which will limit ongoing DNA synthesis by cellular replicases. In this study, we identify a potential role for nucleotide catabolism in promoting replication stress induced by oncogenes. Specifically, we establish that the dNTPase SAMHD1 slows DNA replication fork speeds in human fibroblasts harbouring an oncogenic RAS allele, elevating levels of endogenous DNA damage, and ultimately limiting cell proliferation. We then show that oncogenic RAS-driven tumours express reduced SAMHD1 levels, suggesting they have overcome this tumour suppressor barrier, and that this correlates with worse overall survival for these patients.Abstract Figure
Functional and genetic determinants of mutation rate variability in regulatory elements of cancer genomes
Authors: Lee Christian A. , Abd-Rabbo Diala , Reimand Jüri 
Published: July 2020

ABSTRACTBackgroundCancer genomes are shaped by mutational processes with complex spatial variation at multiple scales. Entire classes of regulatory elements are affected by local variations in mutation frequency. However, the underlying mutational mechanisms with functional and genetic determinants remain poorly understood.ResultsWe characterised the mutational landscape of 1.3 million gene regulatory and chromatin architectural elements in 2,419 whole cancer genomes with transcriptional and pathway activity, functional conservation and recurrent driver events. We developed RM2, a statistical model that quantifies mutational enrichment or depletion in classes of genomic elements through genetic, trinucleotide and megabase-scale effects. We report a map of localised mutational processes affecting CTCF binding sites, transcription start sites (TSS) and tissue-specific open-chromatin regions. We show that increased mutational frequency in TSSs correlates with mRNA abundance in most cancer types, while open-chromatin regions are generally enriched in mutations. We identified ∼10,000 CTCF binding sites with core DNA motifs and constitutive binding in 66 cell types that represent focal points of local mutagenesis. We detected site-specific mutational signatures, such as SBS40 in open-chromatin regions in prostate cancer and SBS17b in CTCF binding sites in gastrointestinal cancers. We also proposed candidate drivers of localised mutagenesis:BRAFmutations associate with mutational enrichments at CTCF binding sites in melanoma, andARID1Amutations with TSS-specific mutations in pancreatic cancer.ConclusionsOur method and catalogue of localised mutational processes provide novel perspectives to cancer genome evolution, mutagenesis, DNA repair and driver discovery. Functional and genetic correlates of localised mutagenesis provide mechanistic hypotheses for future studies.
Exploring patterns of ongoing thought under naturalistic and task-based conditions
Authors: Konu Delali , Mckeown Brontë , Turnbull Adam , Ho Nerissa Siu Ping , Vanderwal Tamara , McCall Cade , Tipper Steven P. , Jefferies Elizabeth , Smallwood Jonathan 
Published: July 2020

AbstractPrevious research suggests that patterns of ongoing thought are heterogeneous, varying across situations and individuals. The current study investigated the influence of a wide range of tasks and individual affective style on ongoing patterns of thought. In total, we used 9 different tasks and measured ongoing thought using multidimensional experience sampling. A Principle Component Analysis of the experience sampling data revealed four patterns of ongoing thought. Linear Mixed Modelling was used to examine the contextual distribution of the thought patterns. Different thought patterns were found to relate to different types of conditions. Intrusive and negative thought pattern expression was found to be influenced by individual affective style (depression level). Overall, these data show that patterns of thought are subject to both contextual and intrinsic variation, suggesting that understanding these important features of experience across a broad range of situations will be useful in understanding their role in human experience.HighlightsPatterns of thought vary across different task contextsThought pattern expression is influenced by individual affective styleThere is a need to broaden the tasks used to study ongoing thought
Sero-prevalence and risk factors of leptospirosis in commercial cattle herds of Rupandehi district, Nepal
Authors: Gompo Tulsi Ram , Jyoti Sumit , Pandit Sudikchya , Sapkota Ram Chandra , Pandey Aditi 
Published: July 2020

AbstractNepal has an agrarian-based economy where the livestock sector contributes about 12 percent to the national GDP. Rupandehi district is one of the largest dairy pocket areas in the nation, but the disease, such as leptospirosis, posed a negative impact on their production and productivity. Despite the economic importance of cattle leptospirosis, the disease is concerned for the people’s occupational risk and food safety. Although leptospirosis is a priority zoonosis in Nepal, the effective implementation of the control program lacks both in animal and human health. A cross-sectional study was conducted to estimate the prevalence and identify associated risk factors of cattle leptospirosis from March 2019 to April 2020. Altogether, 206 cattle herds located in all the sixteen local levels of the district were visited. The owners were interviewed to record the cattle management system’s information and their knowledge of the zoonotic diseases. A total of 383 cattle serum samples were collected, and an indirect antibody ELISA was performed to estimate the infection status of leptospirosis in the cattle herds. All the data were analyzed by Open epi and R software for the descriptive and analytical study. Bivariate and multivariable logistic regression was applied to assess the potential herd level and animal level risk factors. Out of seven potential herd-level risk factors, the purchased cattle herds (OR: 7.2, 95% CI: 1.24-136.5, p=0.025) and cattle with herd size >10 (OR: 14.92, 95% CI: 2.61-283.38, p=0.025) were identified as significant risk factors for leptospirosis. At the animal level, the cattle taken for grazing in pastureland accessed by the community dog was a significant risk factor (OR: 4.16, 95% CI: 1.13-14.06, p=0.034). Surprisingly, none of the farmers had heard about leptospirosis before. The outcome of this research could be an epidemiological insight in control of priority zoonosis to protect the livestock economy and reduce their negative impact on public health.
A new molecular method for the exploration of hybrid zones between two toad species of conservation interest
Authors: Gál Zoltán , Kovács Tibor , Ujszegi János , Anthony Brandon P. , Vági Balázs , Hoffmann Orsolya I. 
Published: July 2020

AbstractAnalyzing hybrid zones between previously isolated lineages allows insight into processes determining the fate of re-encounter of these taxa. The distributions of Fire-bellied (Bombina bombina) and Yellow-bellied toads (B. variegata) meet in the Carpathian Basin resulting in a narrow contact zone in the foothill regions, where hybrids often appear. Our aim was to explore a transient zone betweenB. bombinaandB. variegatawithin the Carpathian Basin along a transect including the Börzsöny Hills in Hungary and Krupinská Planina in Slovakia. We visited 28 locations in these areas and collected altogether 230 specimens, photographed and sampled them using buccal swabs. In order to distinguish between the two species and determine hybrid individuals, we used mitochondrial markers and designed a novel technique based on the restriction of the Ncx-1 gene. The geographical distribution pattern of these two species delivered unexpected results, as Börzsöny Hills was completely colonised byB. bombinaincluding locations which can be classified as typical habitats ofB. variegata. Moreover, in Krupinská Planina many locations were also colonised byB. bombina, including high altitude ponds. The most remote sites still harbourB. variegatapopulations, but seven of these were found with hybrid individuals. This pattern may indicate the northward and altitudinal range expansion ofB. bombinaand the colonisation of habitats of its sister species in these areas. Our results warrant enhanced attention to hybrid zones, where introgression and changes in population composition may reflect recent rapid environmental alterations and redirect conservation focus.
Cutaneous inputs from perineal region facilitates and modulates spinal locomotor activity and reduces cutaneous reflexes from the foot in spinal cats
Authors: Merlet Angèle N , Harnie Jonathan , Macovei Madalina , Doelman Adam , Gaudreault Nathaly , Frigon Alain 
Published: July 2020

AbstractIt is well known that mechanically stimulating the perineal region potently facilitates hindlimb locomotion and weight support in mammals with a spinal transection (spinal mammals). However, how perineal stimulation mediates this excitatory effect is poorly understood. We evaluated the effect of mechanically stimulating (vibration or pinch) the perineal region on ipsilateral (9-14 ms onset) and contralateral (14-18 ms onset) short-latency cutaneous reflex responses evoked by electrically stimulating the superficial peroneal or distal tibial nerve in seven adult spinal cats where hindlimb movement was restrained. Cutaneous reflexes were evoked before, during, and after mechanical stimulation of the perineal region. We found that vibration or pinch of the perineal region effectively triggered rhythmic activity, unilateral and bilateral to nerve stimulation. When electrically stimulating nerves, adding perineal stimulation modulated rhythmic activity by decreasing cycle and burst durations and by increasing the amplitude of flexors and extensors. Perineal stimulation also disrupted the timing of the ipsilateral rhythm, which had been entrained by nerve stimulation. Mechanically stimulating the perineal region decreased ipsilateral and contralateral short-latency reflex responses evoked by cutaneous inputs, a phenomenon we observed in muscles crossing different joints and located in different limbs. The results suggest that the excitatory effect of perineal stimulation on locomotion and weight support is not mediated by increasing cutaneous reflex gain and instead points to an excitation of central pattern-generating circuitry. Our results are consistent with a state-dependent modulation of reflexes by spinal interneuronal circuits.Significance StatementMechanically stimulating the skin of the perineal region strongly facilitates hindlimb locomotion in mammals following a complete spinal cord injury (SCI). Despite its remarkable effectiveness in promoting hindlimb locomotion in spinal cord-injured mammals, we do not know how this is mediated. The present study provides data on how inputs from the perineal region interact with neuronal circuits that generate locomotor-like activity and reflexes from the foot. A better understanding of how inputs from the perineal region interact with neuronal circuits of the spinal cord could lead to non-invasive approaches to restore walking in people with SCI.
The genetic variant analyses of SARS-CoV-2 strains; circulating in Bangladesh
Authors: Mohmmad Mahmud Abu Sayeed , Taznin Tarannum , Hasan Sarkar Md. Murshed , Uzzaman Mohammad Samir , Osman Eshrar , Habib Md. Ahasan , Akter Shahina , Banu Tanjina Akhter , Goswami Barna , Jahan Iffat , Hossain Md. Saddam , Khan Md. Salim 
Published: July 2020

AbstractGenomic mutation of the virus may impact the viral adaptation to the local environment, their transmission, disease manifestation, and the effectiveness of existing treatment and vaccination. The objectives of this study were to characterize genomic variations, non-synonymous amino acid substitutions, especially in target proteins, mutation events per samples, mutation rate, and overall scenario of coronaviruses across the country. To investigate the genetic diversity, a total of 184 genomes of virus strains sampled from different divisions of Bangladesh with sampling dates between the 10th of May 2020 and the 27thof June 2020 were analyzed. To date, a total of 634 mutations located along the entire genome resulting in non-synonymous 274 amino acid substitutions in 22 different proteins were detected with nucleotide mutation rate estimated to be 23.715 substitutions per year. The highest non-synonymous amino acid substitutions were observed at 48 different positions of the papain-like protease (nsp3). Although no mutations were found in nsp7, nsp9, nsp10, and nsp11, yet orf1ab accounts for 56% of total mutations. Among the structural proteins, the highest non-synonymous amino acid substitution (at 36 positions) observed in spike proteins, in which 9 unique locations were detected relative to the global strains, including 516E>Q in the boundary of the ACE2 binding region. The most dominated variant G614 (95%) based in spike protein is circulating across the country with co-evolving other variants including L323 (94%) in RNA dependent RNA polymerase (RdRp), K203 (82%) and R204 (82%) in nucleocapsid, and F120 (78%) in NSP2. These variants are mostly seen as linked mutations and are part of a haplotype observed in Europe. Data suggest effective containment of clade G strains (4.8%) with sub-clusters GR 82.4%, and GH clade 6.4%.HighlightsWe have sequenced 137 and analyzed 184 whole-genomes sequences of SARS-CoV-2 strains from different divisions of Bangladesh.A total of 634 mutation sites across the SARS-CoV-2 genome and 274 non-synonymous amino acid substitutions were detected.The mutation rate of SARS-CoV-2 estimated to be 23.715 nucleotide substitutions per year.Nine unique variants were detected based on non-anonymous amino acid substitutions in spike protein relative to the global SARS-CoV-2 strains.
Dynamic Configuration of Coactive Micropatterns in the Default Mode Network during Wakefulness and Sleep
Authors: Cui Yan , Li Min , Biswal Bharat , Jing Wei , Zhou Changsong , Liu Huixiao , Guo Daqing , Xia Yang , Yao Dezhong 
Published: July 2020

AbstractThe default mode network (DMN) is a prominent intrinsic network that is observable in many mammalian brains. However, few studies have investigated the temporal dynamics of this network based on direct physiological recordings. Herein, we addressed this issue by characterizing the dynamics of local field potentials (LFPs) from the rat DMN during wakefulness and sleep with an exploratory analysis. We constructed a novel coactive micropattern (CAMP) algorithm to evaluate the configurations of rat DMN dynamics and further revealed the relationship between DMN dynamics with different wakefulness and alertness levels. From the gamma activity (40-80 Hz) in the DMN across wakefulness and sleep, three spatially stable CAMPs were detected: a common low-activity level micropattern (cDMN), an anterior high-activity level micropattern (aDMN) and a posterior high-activity level micropattern (pDMN). A dynamic balance across CAMPs emerged during wakefulness and was disrupted in sleep stages. In the slow-wave sleep (SWS) stage, cDMN became the primary activity pattern, whereas aDMN and pDMN were the major activity patterns in the rapid eye movement sleep (REM) stage. Additionally, further investigation revealed phasic relationships between CAMPs and the up-down states of the slow DMN activity in the SWS stage. Our study revealed that the dynamic configurations of CAMPs were highly associated with different stages of wakefulness and provided a potential three-state model to describe the DMN dynamics for wakefulness and alertness.Impact StatementIn the current study, a novel coactive micropattern method (CAMP) was developed to elucidate fast DMN dynamics during wakefulness and sleep. Our findings demonstrated that the dynamic configurations of DMN activity are specific to different wakefulness stages and provided a three-state DMN CAMP model to depict wakefulness levels, thus revealing a potentially new neurophysiological representation of alertness levels. This work could elucidate the DMN dynamics underlying different stages of wakefulness and have important implications for the theoretical understanding of the neural mechanism of wakefulness and alertness.
On the Validity of the Saccharum Complex and the Saccharinae Subtribe: A Re-assesment
Authors: Evans Dyfed Lloyd , Joshi Shailesh Vinay 
Published: July 2020

AbstractThe ‘Saccharum Complex’ represents an hypothetical collective of species that were supposedly responsible, through interbreeding, for the origins of sugarcane. Though recent phylogenetic studies have cast doubt on the veracity of this hypothesis, it has cast a long shadow over the taxonomics of the Andropogoneae and the Saccharinae subtribe. Though evidence suggests that Saccharum s.s. is comprised of only three true species, according to Kew’s GrassBase there are as many as 34 species inSaccharum s.l. Our recent work has shown that many of these species are millions of years divergent from Saccharum. As the Saccharum complex represents the species that sugarcane breeders attempt to introgress into sugarcane, and as the Saccharinae, in its current form, covers almst 12 million years of Andropogoneae evolution an update on the extents of the Taxonomic and customary groupings is much needed. Based on the latest sequence based phylogenies and the inclusion of traditional taxonomics we develop an integrated view of the Saccharinae + Saccharum complex species in the context of the major groupings within the Andropogoneae. We use this phylogeny to re-circumscribe the limits of both the Saccharinae subtribe and the Saccharum complex group of interbreeding species.