bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prediction of multiple drug resistant pulmonary tuberculosis against drug sensitive pulmonary tuberculosis by CT nodular consolidation sign
Authors: Huang Xi-Ling , Skrahin Aliaksandr , Lu Pu-Xuan , Alexandru Sofia , Crudu Valeriu , Astrovko Andrei , Skrahina Alena , Taaffe Jessica , Harris Michael , Long Alyssa , Wollenberg Kurt , Engle Eric , Hurt Darrell E. , Akhundova Irada , Ismayilov Sharafat , Mammadbayov Elcan , Gadirova Hagigat , Abuzarov Rafik , Seyfaddinova Mehriban , Avaliani Zaza , Vashakidze Sergo , Shubladze Natalia , Nanava Ucha , Strambu Irina , Zaharia Dragos , Muntean Alexandru , Ghita Eugenia , Bogdan Miron , Mindru Roxana , Spinu Victor , Sora Alexandra , Ene Catalina , Sergueev Eugene , Kirichenko Valery , Lapitski Vladzimir , Snezhko Eduard , Kovalev Vassili , Tuzikov Alexander , Gabrielian Andrei , Rosenthal Alex , Tartakovsky Michael , Wang Yi Xiang J 
Published: November 2019

AbstractMultidrug-resistant tuberculosis (mdrtb) refers to TB infection resistant to at least two most powerful anti-TB drugs, isoniazid and rifampincin. It has been estimated that globally 3.5% (which can be much higher in some regions) of newly diagnosed TB patients, and 20.5% of previously treated patients had mdrtb. Extensively drug-resistant TB (xdrtb) has resistance to rifampin and isoniazid, as well as to any member of the quinolone family and at least one of the second line injectable drugs: kanamycin, amikacin and capreomycin. xdrtb accounts for 4-20% of mdrtb. Early detection and targeted treatment are priorities for mdrtb/xdrtb control. The suspicion of mdr/xdr -pulmonary TB (mdrptb or xdrptb) by chest imaging shall suggest intensive diagnostic testing for mdrptb/xdrptb. We hypothesize that multiple nodular consolidation (NC) may serve one of the differentiators for separating dsptb vs mdrptb/xdrptb cases. For this study, mdrptb cases (n=310) and XDR-PTB cases (⋂=I58) were from the NIAID TB Portals Program (TBPP) <https://tbportals.niaid.nih.gov>. Drug sensitive pulmonary TB (dsptb) cases were from the TBPP collection (n=112) as well as the Shenzhen Center for Chronic Disease Control (n=111), Shenzhen, China, and we excluded patients with HIV(+) status. Our study shows NC, particularly multiple NCs, is more common in mdrptb than in dsptb, and more common in xdrptb than in mdrptb. For example, 2.24% of dsptb patients, 13.23% of mdrptb patients, and 20.89% of xdrptb patients, respectively, have NCs with diameter >= 10mm equal or more than 2 in number.
A novel resistance pathway for calcineurin inhibitors in the human pathogenic MucoralesMucor circinelloides
Authors: Vellanki Sandeep , Billmyre R. Blake , Lorenzen Alejandra , Campbell Micaela , Turner Broderick , Huh Eun Young , Heitman Joseph , Lee Soo Chan 
Published: November 2019

AbstractMucormycosis is an emerging lethal fungal infection in immunocompromised patients.Mucor circinelloidesis a causal agent of mucormycosis and serves as a model system to understand genetics in Mucorales. Calcineurin is a conserved virulence factor in many pathogenic fungi and calcineurin inhibition or deletion of the calcineurin regulatory subunit (CnbR) inMucorresults in a shift from hyphal to yeast growth. We analyzed thirty-six calcineurin inhibitor resistant or bypass mutants that exhibited hyphal growth in the presence of calcineurin inhibitors or in the yeast-lockedcnbRΔ mutant background without carrying any mutations in known calcineurin components. We found that a majority of the mutants had altered sequence in a gene, named herebycA(bypass ofcalcineurinA).bycAencodes an amino acid permease. We verified that bothbycAΔ, and thebycAΔcnbRΔ double mutant are resistant to the calcineurin inhibitor FK506, thereby demonstrating a novel resistance mechanism against calcineurin inhibitors. We also found that the expression ofbycAwas significantly higher in the wild type strain treated with FK506 and in thecnbRΔ mutants, but significantly lower in the wild type without FK506. These findings suggest thatbycAis a negative regulator of hyphal growth and/or a positive regulator of yeast growth inMucorand calcineurin suppresses thebycAgene at the mRNA level to promote hyphal growth. BycA is involved in theMucorhyphal-yeast transition as our data demonstrates a positive correlation betweenbycAexpression, protein kinase A activity, andMucoryeast-growth. Also calcineurin, independent of its role in morphogenesis, contributes to virulence traits including phagosome maturation blockade, host cell damages, and pro-angiogenic growth factor induction during interactions with hosts.ImportanceMucoris intrinsically resistant to most known antifungals, which makes mucormycosis treatment challenging. Calcineurin is a serine/threonine phosphatase widely conserved across eukaryotes. When calcineurin function is inhibited inMucor, growth shifts to a less-virulent yeast growth form which makes calcineurin an attractive target for development of new antifungal drugs. Previously we identified two distinct mechanisms through whichMucorcan become resistant to calcineurin inhibitors involving Mendelian mutations in the gene for FKBP12, calcineurin A or B subunits and epimutations silencing the FKBP12 gene. Here, we identified a third novel mechanism where loss of function mutations in the amino acid permease encoding thebycAgene contribute to resistance against calcineurin inhibitors. When calcineurin activity is absent, BycA can activate PKA to promote yeast growth via a cAMP-independent pathway. Our data also shows that calcineurin activity, primarily contributes to host - pathogen interactions in the pathogenesis ofMucor.
Improving tuberculosis surveillance by detecting international transmission using publicly available whole-genome sequencing data
Authors: Sanchini Andrea , Jandrasits Christine , Tembrockhaus Julius , Kohl Thomas Andreas , Utpatel Christian , Maurer Florian P. , Niemann Stefan , Haas Walter , Renard Bernhard Y. , Kröger Stefan 
Published: November 2019

AbstractIntroductionImproving the surveillance of tuberculosis (TB) is especially important for multidrug-resistant (MDR) and extensively drug-resistant (XDR)-TB. The large amount of publicly available whole-genome sequencing (WGS) data for TB gives us the chance to re-use data and to perform additional analysis at a large scale.AimWe assessed the usefulness of raw WGS data of global MDR/XDR-TB isolates available from public repositories to improve TB surveillance.MethodsWe extracted raw WGS data and the related metadata of Mycobacterium tuberculosis isolates available from the Sequence Read Archive. We compared this public dataset with WGS data and metadata of 131 MDR- and XDR-TB isolates from Germany in 2012-2013.ResultsWe aggregated a dataset that includes 1,081 MDR and 250 XDR isolates among which we identified 133 molecular clusters. In 16 clusters, the isolates were from at least two different countries. For example, cluster2 included 56 MDR/XDR isolates from Moldova, Georgia, and Germany. By comparing the WGS data from Germany and the public dataset, we found that 11 clusters contained at least one isolate from Germany and at least one isolate from another country. We could, therefore, connect TB cases despite missing epidemiological information.ConclusionWe demonstrated the added value of using WGS raw data from public repositories to contribute to TB surveillance. By comparing the German and the public dataset, we identified potential international transmission events. Thus, using this approach might support the interpretation of national surveillance results in an international context.
Comparative Anatomical, Ultrasonographical and Radiological studies of the biliary system of Rabbits and Domestic cats in Egypt
Authors: Reem R.T. , Maher M.A. , Alaa H.E. , Farghali H.A. 
Published: November 2019

ABSTRACTUnder the prevailing overall Conditions of all veterinarians for the diagnosis of biliary diseases, application of surgical procedures and liver transplantation in Cats as carnivorous pet animal, and Rabbits as herbivorous pet animal and also as a human model in research. The present study was constructed on twelve native breeds of rabbits (Oryctolagus cuniculus) and eighteen adult domestic cats (Felis catus domesticus). We concluded that, in brief; the rabbit gall bladder was relatively small, fixed by several small hepato-cystic ducts to its fossa. The rabbit bile duct was formed commonly by the junction of the left hepatic duct and the cystic duct. The cystic duct was commonly fairly large, received the right hepatic duct that collected the right lobe in its route to enter the duodenum, the bile duct receives the branch of the caudate process of the caudate lobe. The present study revealed other four anatomic variations dealing with the shape and size of the feline native breed’s gall bladder from fundic duplication, bilobed, truncated fundus and distended rounded fundus. Commonly, the bile duct was formed by the triple convergence of the left and the right hepatic ducts with the cystic duct. However, in some exceptional cases a short common hepatic duct was formed. Sonographically, the normal gall bladder in rabbit appeared small, elongated with anechoic lumen bordered by right lobe laterally and quadrate lobe medially and has no visible wall, but in cat varied in conformation, bordered by the right medial lobe laterally and the quadrate lobe medially surrounded by echogenic wall.
mRNA decapping machinery targetsLBD3/ASL9transcripts to authorize developmental reprogramming in Arabidopsis
Authors: Zuo Zhangli , Roux Milena Edna , Chevalier Jonathan Renaud , Dagdas Yasin F. , Yamashino Takafumi , Højgaard Søren Diers , Knight Emilie , Østergaard Lars , Petersen Morten 
Published: November 2019

AbstractMulticellular organisms perceive and transduce multiple cues to optimize developmental reprogramming and cell state switching. Key transcription factors drive developmental changes, but transitions also require the attenuation of previous states. Here, we demonstrate that the mRNA levels of theLATERAL ORGAN BOUNDARIES DOMAIN 3 (LBD3) / ASYMMETRIC LEAVES 2-LIKE 9 (ASL9)transcription factor are directly regulated by mRNA decapping. CappedASL9transcripts accumulate in decapping deficient plants andASL9mRNAs are found together with decapping components. Accumulation ofASL9inhibits apical hook and lateral roots formation and interestingly, exogenous auxin application restores lateral roots formation in bothASL9overexpressor and mRNA decay-deficient mutants. Moreover, mutations in the cytokinin transcription factors type-B ARABIDOPSIS RESPONSE REGULATORS (B-ARRs)ARR10andARR12restore the developmental defects in apical hooking and lateral root formation caused by over-accumulation of cappedASL9transcript uponASL9overexpression. Thus, the mRNA decay machinery directly targetsASL9transcripts for decay to balance cytokinin/auxin responses during developmental reprogramming.
Characterizing the floral resources of a North American metropolis using a honey bee foraging assay
Authors: Sponsler Douglas B. , Shump Don , Richardson Rodney T. , Grozinger Christina M. 
Published: November 2019

AbstractRoughly a third of described insect species visit flowers, making the flower-insect interface one of the chief pillars of global biodiversity. Studying flower-insect relationships at the scale of communities and landscapes has been hindered, however, by the methodological challenges of quantifying landscape-scale floral resources. This challenge is especially acute in urban landscapes, where traditional floral surveying techniques are ill-suited to the unique constraints of built environments. To surmount these challenges, we devised a “honey bee foraging assay” approach to floral resource surveying, wherein continuous colony weight tracking and DNA metabarcoding of pollen samples are used to capture both the overall availability and taxonomic composition of floral resources. We deploy this methodology in the complex urban ecosystem of Philadelphia, PA, U.S. Our results reveal distinct seasonality of floral resource availability, with pulses of high availability in May, June, and September, and a period of prolonged scarcity in August. Pollen genus richness mirrored this pattern, with peak richness in May and June. The taxonomic composition of pollen samples varied seasonally, reflecting underlying floral phenology, with especially strong turnover between May and June samples and between August and September samples delineating well-defined spring, summer, and fall floral resource communities. Trait analysis also revealed marked seasonal structure, with spring samples characterized by trees and shrubs, summer samples including a stronger presence of herbaceous “weeds”, and fall samples dominated by woody vines. Native flora predominated in spring, giving way to a preponderance of exotic flora in summer and fall. Our study provides a detailed portrait of floral resources in a complex urban environment. At a basic level, this yields insight into the assembly of novel urban floral resource communities, showcasing, for example, the emergence of a woody-vine-dominated fall flora. At an applied level, our data can inform urban land management, such as the design of ecologically functional ornamental plantings, while also providing practical guidance to beekeepers seeking to adapt their management activities to floral resource seasonality. Methodologically, our study demonstrates the potential of the honey bee foraging assay as an efficient and standardizable technique for landscape-scale floral resource surveying.
Generation and molecular characterization of CRISPR/Cas9-induced mutations in 63 immunity-associated genes in tomato reveals specificity and a range of gene modifications
Authors: Zhang Ning , Roberts Holly M. , Van Eck Joyce , Martin Gregory B. 
Published: November 2019

AbstractThe CRISPR/Cas9 system is a powerful tool for targeted gene editing in many organisms including plants. However, most of the reported uses of CRISPR/Cas9 in plants have focused on modifying one or a few genes, and thus the overall specificity, types of mutations, and heritability of gene alterations remain unclear. Here we describe the molecular characterization of 361 T0 transgenic tomato plants that were generated using CRISPR/Cas9 to induce mutations in 63 immunity-associated genes. Among the T0 transformed plants, 245 carried mutations (68%), with 20% of those plants being homozygous for the mutation, 30% being heterozygous, 32% having two different mutations (biallelic) and 18% having multiple mutations (chimeric). The mutations were predominantly short insertions or deletions, with 87% of the affected sequences being smaller than 10 bp. The majority of 1 bp insertions were A (50%) or T (29%). The mutations from the T0 generation were stably transmitted to later generations, although new mutations were detected in some T1 plants. No mutations were detected in 18 potential off-target sites among 144 plants. Our study provides a broad and detailed view into the effectiveness of CRISPR/Cas9 for genome editing in an economically important plant species.
Optimising Renewal Models for Real-Time Epidemic Prediction and Estimation
Authors: Parag KV , Donnelly CA 
Published: November 2019

AbstractThe effective reproduction number, Rt, is an important prognostic for infectious disease epidemics. Significant changes in Rt can forewarn about new transmissions or predict the efficacy of interventions. The renewal model infers Rt from incidence data and has been applied to Ebola virus disease and pandemic influenza outbreaks, among others. This model estimates Rt using a sliding window of length k. While this facilitates real-time detection of statistically significant Rt fluctuations, inference is highly k -sensitive. Models with too large or small k might ignore meaningful changes or over-interpret noise-induced ones. No principled k -selection scheme exists. We develop a practical yet rigorous scheme using the accumulated prediction error (APE) metric from information theory. We derive exact incidence prediction distributions and integrate these within an APE framework to identify the k best supported by available data. We find that this k optimises short-term prediction accuracy and expose how common, heuristic k -choices, which seem sensible, could be misleading.
Dual indexed design of in-Drop single-cell RNA-seq libraries improves sequencing quality and throughput
Authors: Smith Austin N. Southard , Simmons Alan J. , Chen Bob , Jones Angela L. , Solano Marisol A. Ramirez , Vega Paige N. , Scurrah Cherie’ R. , Zhao Yue , Brenan Michael J. , Xuan Jiekun , Porter Ely B. , Chen Xi , Brenan Colin J.H. , Liu Qi , Quigley Lauren N.M. , Lau Ken S. 
Published: November 2019

AbstractThe increasing demand of single-cell RNA-sequencing (scRNA-seq) experiments, such as the number of experiments and cells queried per experiment, necessitates higher sequencing depth coupled to high data quality. New high-throughput sequencers, such as the Illumina NovaSeq 6000, enables this demand to be filled in a cost-effective manner. However, current scRNA-seq library designs present compatibility challenges with newer sequencing technologies, such as index-hopping, and their ability to generate high quality data has yet to be systematically evaluated. Here, we engineered a new dual-indexed library structure, called TruDrop, on top of the inDrop scRNA-seq platform to solve these compatibility challenges, such that TruDrop libraries and standard Illumina libraries can be sequenced alongside each other on the NovaSeq. We overcame the index-hopping issue, demonstrated significant improvements in base-calling accuracy, and provided an example of multiplexing twenty-four scRNA-seq libraries simultaneously. We showed favorable comparisons in transcriptional diversity of TruDrop compared with prior library structures. Our approach enables cost-effective, high throughput generation of sequencing data with high quality, which should enable more routine use of scRNA-seq technologies.
Data-driven inference of crosstalk in the tumor microenvironment
Authors: Ghoshdastider Umesh , Naeini Marjan Mojtabavi , Rohatgi Neha , Revkov Egor , Wong Angeline , Solai Sundar , Nguyen Tin Trung , Yeong Joe , Iqbal Jabed , Tan Puay Hoon , Chowbay Balram , DasGupta Ramanuj , Skanderup Anders Jacobsen 
Published: November 2019

AbstractSignaling between cancer and nonmalignant (stromal) cells in the tumor microenvironment (TME) is key to tumorigenesis yet challenging to decipher from tumor transcriptomes. Here, we report an unbiased, data-driven approach to deconvolute bulk tumor transcriptomes and predict crosstalk between ligands and receptors on cancer and stromal cells in the TME of 20 solid tumor types. Our approach recovers known transcriptional hallmarks of cancer and stromal cells and is concordant with single-cell and immunohistochemistry data, underlining its robustness. Pan-cancer analysis reveals previously unrecognized features of cancer-stromal crosstalk. We find that autocrine cancer cell cross-talk varied between tissues but often converged on known cancer signaling pathways. In contrast, many stromal cross-talk interactions were highly conserved across tumor types. Interestingly, the immune checkpoint ligand PD-L1 was overexpressed in stromal rather than cancer cells across all tumor types. Moreover, we predicted and experimentally validated aberrant ligand and receptor expression in cancer cells of basal and luminal breast cancer, respectively. Collectively, our findings validate a data-driven method for tumor transcriptome deconvolution and establishes a new resource for hypothesis generation and downstream functional interrogation of the TME in tumorigenesis and disease progression.
The Genome of the Charophyte AlgaPenium margaritaceumBears Footprints of the Evolutionary Origins of Land Plants
Authors: Jiao Chen , Sørensen Iben , Sun Xuepeng , Sun Honghe , Behar Hila , Alseekh Saleh , Philippe Glenn , Lopez Kattia Palacio , Sun Li , Reed Reagan , Jeon Susan , Kiyonami Reiko , Zhang Sheng , Fernie Alisdair R. , Brumer Harry , Domozych David S. , Fei Zhangjun , Rose Jocelyn K. C. 
Published: November 2019

ABSTRACTThe colonization of land by plants was a pivotal event in the history of the biosphere, and yet the underlying evolutionary features and innovations of the first land plant ancestors are not well understood. Here we present the genome sequence of the unicellular algaPenium margaritaceum, a member of the Zygnematophyceae, the sister lineage to land plants. TheP. margaritaceumgenome has a high proportion of repeat sequences, which are associated with massive segmental gene duplications, likely facilitating neofunctionalization. Compared with earlier diverging plant lineages,P. margaritaceumhas uniquely expanded repertoires of gene families, signaling networks and adaptive responses, supporting its phylogenetic placement and highlighting the evolutionary trajectory towards terrestrialization. These encompass a broad range of physiological processes and cellular structures, such as large families of extracellular polymer biosynthetic and modifying enzymes involved in cell wall assembly and remodeling. Transcriptome profiling of cells exposed to conditions that are common in terrestrial habitats, namely high light and desiccation, further elucidated key adaptations to the semi-aquatic ecosystems that are home to the Zygnematophyceae. Such habitats, in which a simpler body plan would be advantageous, likely provided the evolutionary crucible in which selective pressures shaped the transition to land. Earlier diverging charophyte lineages that are characterized by more complex land plant-like anatomies have either remained exclusively aquatic, or developed alternative life styles that allow periods of desiccation.
Analysis of combined passively and actively morphing blade root chord length and blade taper for helicopter control
Authors: Sal Firat 
Published: November 2019

Purpose
The purpose of this study is to examine the effect of passive and active morphing of blade root chord length and blade taper on the control effort of the flight control system (FCS) of a helicopter.

Design/methodology/approach
Physics-based helicopter models, which are functions of passive and active morphing, are created and applied in helicopter FCS design to determine the control effort.

Findings
Helicopters, having both passively and actively morphing blade root chord length and blade taper, experience less control effort than the ones having either only passively morphing blade root chord length or only blade taper or only actively morphing blade root chord length and blade taper.

Practical implications
Both passively and actively morphing blade root chord length and blade taper can be implemented for more economical autonomous helicopter flights.

Originality/value
Main novelty of our article is simultaneous application of passive and active morphing ideas on helicopter root chord length and blade taper. It is also proved in this study that using both passive and active morphing ideas on helicopter blade root chord and blade taper causes much less energy consumption than using either only passive morphing idea on helicopter blade root chord and blade taper or only active morphing idea on helicopter blade root chord and blade taper. This also reduces fuel consumption and also makes environment cleaner.