bluuebunny/crossref_metadata_2025_split huggingface dataset:
A workflow for accurate metabarcoding using nanopore MinION sequencing
Authors: Baloğlu Bilgenur , Chen Zhewei , Elbrecht Vasco , Braukmann Thomas , MacDonald Shanna , Steinke Dirk 
Published: May 2020

AbstractMetabarcoding has become a common approach to the rapid identification of the species composition in a mixed sample. The majority of studies use established short-read high-throughput sequencing platforms. The Oxford Nanopore MinION™, a portable sequencing platform, represents a low-cost alternative allowing researchers to generate sequence data in the field. However, a major drawback is the high raw read error rate that can range from 10% to 22%.To test if the MinION™ represents a viable alternative to other sequencing platforms we used rolling circle amplification (RCA) to generate full-length consensus DNA barcodes (658bp of cytochrome oxidase I - COI) for a bulk mock sample of 50 aquatic invertebrate species. By applying two different laboratory protocols, we generated two MinION™ runs that were used to build consensus sequences. We also developed a novel Python pipeline, ASHURE, for processing, consensus building, clustering, and taxonomic assignment of the resulting reads.We were able to show that it is possible to reduce error rates to a median accuracy of up to 99.3% for long RCA fragments (>45 barcodes). Our pipeline successfully identified all 50 species in the mock community and exhibited comparable sensitivity and accuracy to MiSeq. The use of RCA was integral for increasing consensus accuracy, but it was also the most time-consuming step during the laboratory workflow and most RCA reads were skewed towards a shorter read length range with a median RCA fragment length of up to 1262bp. Our study demonstrates that Nanopore sequencing can be used for metabarcoding but we recommend the exploration of other isothermal amplification procedures to improve consensus length.
Brain tissue transcriptomic analysis of SIV-infected macaques identifies several altered metabolic pathways linked to neuropathogenesis, and Poly (ADP-ribose) polymerases (PARPs) as potential therapeutic targets
Authors: Mavian Carla , Ramirez-Mata Andrea S. , Dollar James Jarad , Nolan David J. , White Kevin , Rich Shannan N. , Magalis Brittany Rife , Cash Melanie , Marini Simone , Prosperi Mattia C. F. , Amador David Moraga , Riva Alberto , Williams Kenneth C. , Salemi Marco 
Published: May 2020

AbstractBackgroundDespite improvements in antiretroviral therapy, human immunodeficiency virus type 1 (HIV-1)-associated neurocognitive disorders (HAND) remain prevalent in subjects undergoing therapy. HAND significantly affects individuals’ quality of life, as well as adherence to therapy, and, despite the increasing understanding of neuropathogenesis, no definitive diagnostic or prognostic marker has been identified.ResultsWe investigated transcriptomic profiles in frontal cortex tissues of Simian immunodeficiency virus (SIV)-infected Rhesus macaques sacrificed at different stages of infection. Gene expression was compared among SIV-infected animals (n=11), with or without CD8+ lymphocyte depletion, based on detectable (n=6) or non-detectable (n=5) presence of the virus in frontal cortex tissues. Significant enrichment in activation of monocyte and macrophage cellular pathways was found in animals with detectable brain infection, independently from CD8+ lymphocyte depletion. In addition, transcripts of four poly (ADP-ribose) polymerases (PARPs) were up-regulated in the frontal cortex, which was confirmed by real-time polymerase chain reaction.ConclusionsOur results shed light on involvement of PARPs in SIV infection of the brain and their role in SIV-associated neurodegenerative processes. Inhibition of PARPs may provide an effective novel therapeutic target for HIV-related neuropathology.
Development of novel apoptosis-assisted lung tissue decellularization methods
Authors: Song Young Hye , Maynes Mark A , Hlavac Nora , Visosevic Daniel , Daramola Kaitlyn O , Porvasnik Stacy L , Schmidt Christine E 
Published: May 2020

AbstractDecellularized tissues hold great potential for both regenerative medicine and disease modeling applications. The acellular extracellular matrix (ECM)-enriched scaffolds can be recellularized with patient-derived cells prior to transplantation, or digested to create thermally-gelling hydrogels for 3D cell culture. Current methods of decellularization clear cellular components using detergents, which can result in loss of ECM proteins and tissue architectural integrity. Recently, an alternative approach utilizing apoptosis to decellularize excised murine sciatic nerves resulted in superior ECM preservation, cell removal, and immune tolerancein vivo. However, this apoptosis-assisted decellularization approach has not been optimized for other tissues with a more complex geometry, such as lungs. To this end, we developed an apoptosis-assisted lung tissue decellularization method using a combination of camptothecin and sulfobetaine-10 (SB-10) to induce apoptosis and facilitate gentle and effective removal of cell debris, respectively. Importantly, combination of the two agents resulted in superior cell removal and ECM preservation compared to either of the treatments alone, presumably because of pulmonary surfactants. In addition, our method was superior in cell removal compared to a previously established detergent-based decellularization protocol. Furthermore, thermally-gelling lung ECM proteins supported high viability of rat lung epithelial cells for up to 2 weeks in culture. This work demonstrates that apoptosis-based lung tissue decellularization is a superior technique that warrants further utilization for both regenerative medicine and disease modeling applications.
Natural Genetic Variation inDrosophila melanogasterReveals Genes Associated withCoxiella burnetiiInfection
Authors: Guzman Rosa M. , Howard Zachary P. , Liu Ziying , Oliveira Ryan D. , Massa Alisha T. , Omsland Anders , White Stephen N. , Goodman Alan G. 
Published: May 2020

ABSTRACTThe gram-negative bacteriumCoxiella burnetiiis the causative agent of Query (Q) fever in humans and coxiellosis in livestock. Association between host genetic background andCoxiella burnetiipathogenesis has been demonstrated both in humans and animals; however, specific genes associated with severity of infection remain unknown. We employed theDrosophilaGenetics Reference Panel to perform a genome-wide association study and identify host genetic variants that affectCoxiella burnetiiinfection outcome. The analysis resulted in 64 genome-wide suggestive (P < 10−5) single nucleotide polymorphisms or gene variants in 25 unique genes. We examined the role of each gene inCoxiella burnetiiinfection using flies carrying a null mutation or RNAi knockdown of each gene and monitoring survival. Of the 25 candidate genes, 15 validated using at least one method. For many, this is the first report establishing involvement of these genes or their homologs withCoxiella burnetiisusceptibility in any system. Among the validated genes,FERandtaraplay roles in the JAK-STAT, JNK, and decapentaplegic/TGF-β signaling pathways that are associated with the innate immune response toCoxiella burnetiiinfection. Two other two validated genes,CG42673andDIP-ɛ, play roles in bacterial infection and synaptic signaling but no previous association withCoxiella burnetiipathogenesis. Furthermore, since the mammalian ortholog ofCG13404(PLGRKT) is an important regulator of macrophage function,CG13404could play a role inCoxiella burnetiisusceptibility through hemocyte regulation. These insights provide a foundation for further investigation of genetics ofCoxiella burnetiisusceptibility across a wide variety of hosts.
BRAFV600Einduces reversible mitotic arrest in human melanocytes via microRNA-mediated suppression of AURKB
Authors: McNeal Andrew S. , Belote Rachel L. , Zeng Hanlin , Urquijo Marcus , Barker Kendra , Torres Rodrigo , Curtin Meghan , Shain A. Hunter , Andtbacka Robert H. I. , Holmen Sheri L. , Lum David H. , McCalmont Timothy H. , VanBrocklin Matthew W. , Grossman Douglas , Wei Maria L. , Lang Ursula E. , Judson-Torres Robert L. 
Published: May 2020

AbstractBenign melanocytic nevi frequently emerge when an acquiredBRAFV600Emutation triggers unchecked proliferation and subsequent arrest in melanocytes. Recent observations have challenged the role of oncogene-induced senescence in melanocytic nevus formation, necessitating investigations into alternative mechanisms for the establishment and maintenance of proliferation arrest in nevi. We compared the transcriptomes of melanocytes from healthy human skin, nevi, and melanomas arisen from nevi and identified a set of microRNAs as highly expressed nevus-enriched transcripts. Two of these microRNAs – MIR211-5p and MIR328-3p – induced mitotic failure, genome duplication and proliferation arrest in human melanocytes through convergent targeting of AURKB. We demonstrate thatBRAFV600Einduces a similar proliferation arrest in primary human melanocytes that is both reversible and conditional. Specifically,BRAFV600Eexpression stimulates either arrest or proliferation depending on the differentiation state of the melanocyte. We report genome duplication in human melanocytic nevi, reciprocal expression of AURKB and microRNAs in nevi and melanomas, and rescue of arrested human nevus cells with AURKB expression. Together, our data describe an alternative molecular mechanism for melanocytic nevus formation that is congruent with both experimental and clinical observations.
Effect of leaf temperature on estimating physiological traits of wheat leaves from hyperspectral reflectance
Authors: Khan Hammad A , Nakamura Yukiko , Furbank Robert T , Evans John R 
Published: May 2020

AbstractA growing number of leaf traits can be predicted from hyperspectral reflectance data. These include structural and compositional traits, such as leaf mass per area, nitrogen and chlorophyll content, but also physiological traits such a Rubisco carboxylation activity, electron transport rate and respiration rate. Since physiological traits vary with leaf temperature, how does this impact on predictions made from reflectance measurements? We investigated this with two wheat varieties, by repeatedly measuring each leaf through a sequence of temperatures imposed by varying the air temperature in a growth room. The function predicting Rubisco capacity normalised to 25 °C predicted the same value, regardless of leaf temperatures ranging from 20 to 35°C. Leaf temperature affected none of the predicted traits: Vcmax25, J, chlorophyll content, LMA, N content per unit leaf area or Vcmax25/N. However, as others have derived models to predict Rubisco activity that includes variation associated with leaf temperature, we discuss whether these functions may include a temperature signal within the reflectance spectra.
Hidden components of microbiome diversity revealed by cell wall lysis with Adaptive Focused Acoustics
Authors: Wallace Giselle F. , Ahluwalia Sonia , Thovarai Vishal , Laugharn James , Khoja Hamid , Sen Shurjo K. 
Published: May 2020

AbstractWithin the rapidly evolving field of microbiome sequencing, a primary need exists for experimentally capturing microbiota in a manner as close as possible to theirin vivocomposition. During microbiome profiling, the first step necessarily involves lysis of the cell wall, releasing nucleic acids for next-generation sequencing. Microbial cell wall thicknesses can vary between 5nm to 80nm; while some species are quite easy to lyse, others are particularly resistant to lysis. Despite this, current chemical/mechanical lysis protocols ignore the possibility that species with different cell wall thicknesses are lysed at differential rates. This creates noise in species compositions and possibly skews current microbiome results in ways that are not currently understood. To develop a cell wall thickness-agnostic lysis protocol, we used Adaptive Focused Acoustics (AFA), a tunable acoustic methodology for processing of biological samples. Using identical aliquots of mouse stool homogenate as the lysis substrate, we compared AFA with chemical/mechanical lysis methodology routinely used in microbiome studies and found that AFA-mediated lysis substantially increases both microbial DNA yield as well as alpha and beta diversity. By starting with lower AFA energy levels, sequentially removing aliquots at each step, and subjecting the remainder to progressively stronger AFA treatment, we developed a sequential lysis method that accounts for differences in cell wall thickness. This method revealed even greater levels of diversity than single-timepoint AFA treatment. 16S sequencing results from the above experiments were verified by shotgun metagenome sequencing of a subset of the AFA samples. We found that lysis-induced noise affects not just species compositaions, but also functional characterization of shotgun metagenome data. AFA samples also showed a higher detection of eukaryotic and fungal DNA. We suggest that AFA-mediated lysis produces a truer representation of the native microbiota, and that this method deserves consideration as a potential addition to microbiome lysis protocols.
Antihypertensive medication uses and serum ACE2 levels
Authors: Emilsson Valur , Gudmundsson Elias F. , Aspelund Thor , Jonsson Brynjolfur G. , Gudjonsson Alexander , Launer Lenore J. , Jennings Lori L. , Gudmundsdottir Valborg , Gudnason Vilmundur 
Published: May 2020

AbstractImportanceRecent reports have shown that hypertension is the most common comorbidity associated with mortality in the current coronavirus disease 2019 (COVID-19). This has been related to the use of angiotensin-converting enzyme inhibitors (ACEIs) and angiotensin II receptor blockers (ARBs) as animal studies indicate that these medications increase levels of ACE2, the cellular entry point for the coronavirus SARS-CoV-2. This has prompted clinicians to recommend discontinuing ACEIs and ARBs.ObjectiveTo examine the effect of ACEIs or ARBs treatment on serum levels of ACE2 and other key enzymes in the renin-angiotensin system (RAS).Design, Setting, and ParticipantsA single center population-based study of 5457 Icelanders from the Age, Gene/Environment Susceptibility Reykjavik Study (AGES-RS) of the elderly (mean age 75±6 years) stratified by ACEIs (N = 699) or ARBs (N = 753) treatment.Main Outcomes and MeasuresThe AGES-RS study population was stratified by ACEIs and ARBs medication use and compared for age, body mass index (BMI) (kg/m2), hypertension and type 2 diabetes (T2D) as well as serum levels of renin, ACE and ACE2.ResultsWhile renin and ACE levels were significantly raised in serum of individuals on ACEIs or ARBs treatments, the ACE2 levels remained unaffected.Conclusions and RelevanceTreatment with ACEIs or ARBs does not raise ACE2 levels in serum. Therefore, the present study does not support the proposed discontinuation of these medications among patients affected with COVID-19.Key PointsQuestionDoes treatment with the antihypertensive medications angiotensin-converting enzyme inhibitors (ACEIs) and angiotensin II receptor blockers (ARBs) result in elevated levels of the cellular receptor for the coronavirus SARS-CoV-2, ACE2?FindingsIn a single center population-based cohort (AGES-RS), 699 and 753 individuals were either on ACEIs or ARBs treatment, respectively. The serum levels of the key enzymes in the renin-angiotensin system (RAS), renin, ACE and ACE2 were measured in 5457 subjects of the AGES-RS and their serum levels in individuals on ACEIs or ARBs treatment compared to those not using these medications. While renin and ACE were significantly raised in serum of ACEIs and ARBs users, the levels of ACE2 remained unaffected.MeaningThese results do not support the proposed routine discontinuation of ACEIs or ARBs among patients affected with COVID-19.
Hydroxychloroquine and Tocilizumab Therapy in COVID-19 Patients – An Observational Study
Authors: Ip Andrew , Berry Donald A. , Hansen Eric , Goy Andre H. , Pecora Andrew L , Sinclaire Brittany A , Bednarz Urszula , Marafelias Michael , Berry Scott M. , Berry Nicholas S. , Mathura Shivam , Sawczuk Ihor S , Biran Noa , Go Ronaldo C , Sperber Steven , Piwoz Julia A , Balani Bindu , Cicogna Cristina , Sebti Rani , Zuckerman Jerry , Rose Keith M , Tank Lisa , Jacobs Laurie G , Korcak Jason , Timmapuri Sarah L. , Underwood Joseph P. , Sugalski Gregory , Barsky Carol , Varga Daniel W. , Asif Arif , Landolfi Joseph C , Goldberg Stuart L 
Published: May 2020

AbstractBackgroundHydroxychloroquine has been touted as a COVID-19 treatment. Tocilizumab, an inhibitor of IL-6, has been proposed as a treatment of critically ill patients.ObjectiveTo describe the association between mortality and hydroxychloroquine or tocilizumab therapy among hospitalized COVID-19 patients.DesignRetrospective observational cohort study of electronic health records Setting: 13-hospital network spanning the state of New Jersey.ParticipantsPatients hospitalized between March 1, 2020 and April 22, 2020 with positive polymerase chain reaction results for SARS-CoV-2. Follow up was through May 5, 2020.Main OutcomesThe primary outcome was death.ResultsAmong 2512 hospitalized patients with COVID-19 there have been 547 deaths (22%), 1539 (61%) discharges and 426 (17%) remain hospitalized. 1914 (76%) received at least one dose of hydroxychloroquine and 1473 (59%) received hydroxychloroquine with azithromycin. After adjusting for imbalances via propensity modeling, compared to receiving neither drug, there were no significant differences in associated mortality for patients receiving any hydroxychloroquine during the hospitalization (HR, 0.99 [95% CI, 0.80-1.22]), hydroxychloroquine alone (HR, 1.02 [95% CI, 0.83-1.27]), or hydroxychloroquine with azithromycin (HR, 0.98 [95% CI, 0.75-1.28]). The 30-day unadjusted mortality for patients receiving hydroxychloroquine alone, azithromycin alone, the combination or neither drug was 25%, 20%, 18%, and 20%, respectively. Among 547 evaluable ICU patients, including 134 receiving tocilizumab in the ICU, an exploratory analysis found a trend towards an improved survival association with tocilizumab treatment (adjusted HR, 0.76 [95% CI, 0.57-1.00]), with 30 day unadjusted mortality with and without tocilizumab of 46% versus 56%.ConclusionsThis observational cohort study suggests hydroxychloroquine, either alone or in combination with azithromycin, was not associated with a survival benefit among hospitalized COVID-19 patients. Tocilizumab demonstrated a trend association towards reduced mortality among ICU patients. Our findings are limited to hospitalized patients and must be interpreted with caution while awaiting results of randomized trials.Trial RegistrationClinicaltrials.gov Identifier: NCT04347993
Comparison of horizontal corneal diameter measurements using Orbscan IIz, OPD Scan III, and IOLMaster 700
Authors: Cruz Sebastian , Valenzuela Felipe , Stoppel Juan , Maul Eugenio , Gibbons Allister 
Published: May 2020

ABSTRACTPurposeTo compare 3 automated devices for measuring the horizontal corneal diameter [white-to-white (WTW) distance].SettingFundacion Oftalmologica Los Andes, Santiago, Chile.Study DesignRetrospective.MethodsIn 65 eyes of 38 patients, the WTW distance was measured independently using Orbscan IIz tomography system (Bausch & Lomb), IOLMaster 700 (Carl Zeiss Meditec) and OPD Scan III (NIDEK). We tested for systematic differences in measurements and estimated the limits of agreement (LoA) using linear mixed effects models.ResultsThe mean WTW distance was 11.8 ± 0.40 mm with Orbscan IIz, 12.1 ± 0.5 mm with IOLMaster 700 and 12.0 ± 0.4 mm with OPD Scan III. The mean difference between IOLMaster 700 and Orbscan IIz was 0.33 (95% CI 0.28;0.38) (p<0.001), between OPD Scan III and Orbscan IIz was 0.24 mm (95% CI 0.21;0.28) (p<0.001), and between IOL Master 700 and OPD Scan III was 0.09 (95% CI 0.05;0.12) (p<0.001). The 95% LoA for Orbscan IIz versus IOLMaster 700 was −0.69 mm to 0.03 mm, Orbscan IIz versus OPD Scan III was −0.52 mm to −0.03 mm, and OPD versus IOLMaster 700 was −0.39 mm to 0.22 mm. Switching to IOLMaster 700 or OPD Scan III measurements led to a selection of a longer phakic IOL length (Visian ICL, STAAR) in 34% and 33% of the cases, respectively compared to Orbscan IIz.ConclusionsThe data suggests that these devices are not interchangeable for usual clinical practice. Adjustments based on mean differences was not enough to compensate for inter-instrument discrepancy in WTW measurements.
Pituitary stem cells produce paracrine WNT signals to control the expansion of their descendant progenitor cells
Authors: Russell John Parkin , Lim Xinhong , Santambrogio Alice , Yianni Val , Kemkem Yasmine , Wang Bruce , Fish Matthew , Haston Scott , Grabek Anaëlle , Hallang Shirleen , Lodge Emily Jane , Patist Amanda Louise , Schedl Andreas , Mollard Patrice , Nusse Roeland , Andoniadou Cynthia Lilian 
Published: May 2020

ABSTRACTIn response to physiological demand, the pituitary gland generates new hormone-secreting cells from committed progenitor cells throughout life. It remains unclear to what extent pituitary stem cells (PSCs), which uniquely express SOX2, contribute to pituitary growth and renewal. Moreover, neither the signals that drive proliferation nor their sources have been elucidated. We have used genetic approaches in the mouse, showing that the WNT pathway is essential for proliferation of all lineages in the gland. We reveal that SOX2+stem cells are a key source of WNT ligands. By blocking secretion of WNTs from SOX2+PSCsin vivo, we demonstrate that proliferation of neighbouring committed progenitor cells declines, demonstrating that progenitor multiplication depends on the paracrine WNT secretion from SOX2+PSCs. Our results indicate that stem cells can hold additional roles in tissue expansion and homeostasis, acting as paracrine signalling centres to coordinate the proliferation of neighbouring cells.
Development of new cowpea (Vigna unguiculata) mutant genotypes, analysis of their agromorphological variation, genetic diversity and Population structure
Authors: Diouf Made , Diallo Sara , Badiane François Abaye , Diack Oumar , Diouf Diaga 
Published: May 2020

AbstractCowpea is one of the most important legume grain in the SubSaharian region of Africa used for human consumption and animal feeding but its production is hampered by biotic and abiotic constraints raising the need to broaden its genetic basis. For this purpose, the seeds of two cowpea varieties Melakh and Yacine were respectively irradiated with 300 and 340 Gy. The developed mutant populations were agromorphologically characterized from M5 to M7 while the genetic diversity of the last were evaluated using 13 ISSR markers. Based on agromorphological characterization, variation of flower color, pod length, seed coat color and seed weight with respectively 78.01, 68.29, 94.48 and 57.58% heritability were recorded in the mutant lines. PCA analyses allowed to identify the elite mutants based on their agromorphological traits while Pearson’s correlation results revealed a positive correlation between yield component traits. Three subpopulations were identified through STRUCTURE analyses but assignment of the individuals in each group was improved using DAPC. Analysis of Molecular Variance revealed that the majority (85%) of the variance rather existed within group than among (15%) group. Finally, our study allowed to select new promising mutant genotypes which could be tested for multi local trials to evaluate their agronomic performance.