bluuebunny/crossref_metadata_2025_split huggingface dataset:
Coleoborers (Curculionidae: Scolytinae) in native and homogeneous systems of Brazil nut (Bertholletia excelsabonpl.) in the Southern Amazon, Brazil
Authors: Martins e Silva Marcus Henrique , Garlet Juliana , Luis Silva Fernando , da Silva Paula Carla 
Published: May 2020

AbstractBrazil nut is one of the most important species of the Amazon due to its socioeconomic importance. Especially in homogeneous production systems, it may be susceptible to damage by wood-boring insects, as by the subfamily Scolytinae (Coleoptera: Curculionidae); thus, inadequate management conditions can cause economic damage. Therefore, the objective of the present work is to evaluate the occurrence of wood-boring insects (Curculionidae: Scolytinae) in native and homogeneous systems of Brazil nut in the Meridional Amazonian, Brazil. The study was conducted in three environments: Conserved Native Planting nut, Anthropized Native Planting nut and Homogeneous Planting nut. Twelve ethanol traps were installed in each environment during four sampling periods. The data were submitted to entomofaunistic analysis, Pearson’s correlation analysis and cluster analysis. A total of 2,243 individuals from 31 species were sampled, of which 23 were from the Anthropized Native Planting nut, 24 from the Homogeneous Planting nut and 26 from the Conserved Native Planting nut. In the faunistic analysis, we highlight the speciesXyleborus affinis(Eichhoff, 1868), which was the most representative one in the three environments and a super-dominant species in all four sampling periods. There was a greater similarity between the Anthropized Native Planting nut and the Conserved Native Planting nut; these two environments showed dissimilarity with the Homogeneous Planting nut. Monitoring coleoborers in Brazil nut agroecosystems is fundamental for the establishment of integrated pest management strategies.
N-Aryl Pyrido Cyanine derivatives: nuclear and organelle DNA markers for two-photon and super-resolution imaging
Authors: Uno Kakishi , Sugimoto Nagisa , Sato Yoshikatsu 
Published: May 2020

AbstractLive cell imaging using DNA-binding fluorescent probes is an essential molecular tool in various biological and biomedical fields. The major challenges in currently used DNA probes are to avoid UV light photo-excitation with high DNA selectivity and cell-permeability and are the availability of the cutting-edge imaging techniques such as a super-resolution microscopy. Herein we report new orange to red fluorogenic DNA probes having N-aryl pyrido cyanine (PC) moiety as a basic skeleton. Their DNA selectivity and cell-permeabilities are so high that organelle DNA as well as nuclear DNA can be clearly stained in various cell types and plant tissues with wash-free manner. PC dyes are also compatible with a stimulated emission depletion fluorescent lifetime imaging microscopy (STED-FLIM) for super-resolution imaging as well as two-photon microscopy for deep tissue imaging, should release the utilization limitation of synthetic DNA probes.
A selective autophagy pathway for phase separated endocytic protein deposits
Authors: Wilfling Florian , Lee Chia-Wei , Erdmann Philipp , Zheng Yumei , Jentsch Stefan , Pfander Boris , Schulman Brenda A. , Baumeister Wolfgang 
Published: May 2020

SummaryAutophagy eliminates cytoplasmic content selected by autophagy receptors, which link cargoes to the membrane bound autophagosomal ubiquitin-like protein Atg8/LC3. Here, we discover a selective autophagy pathway for protein condensates formed by endocytic proteins. In this pathway, the endocytic yeast protein Ede1 functions as a selective autophagy receptor. Distinct domains within Ede1 bind Atg8 and mediate phase separation into condensates. Both properties are necessary for an Ede1-dependent autophagy pathway for endocytic proteins, which differs from regular endocytosis, does not involve other known selective autophagy receptors, but requires the core autophagy machinery. Cryo-electron tomography of Ede1-containing condensates – at the plasma membrane and in autophagic bodies – shows a phase-separated compartment at the beginning and end of the Ede1-mediated selective autophagy pathway. Our data suggest a model for autophagic degradation of membraneless compartments by the action of intrinsic autophagy receptors.HighlightsEde1 is a selective autophagy receptor for aberrant CME protein assembliesAberrant CME assemblies form by liquid-liquid phase separationCore autophagy machinery and Ede1 are important for degradation of CME condensatesUltrastrucural view of a LLPS compartment at the PM and within autophagic bodies
Meltwater runoff from the Greenland Ice Sheet reveals microbial consortia from contrasting subglacial drainage systems
Authors: Lamarche-Gagnon Guillaume , Anesio Alexandre M. , Wadham Jemma L. , Zarsky Jakub D. , Kohler Tyler J. , Bagshaw Elizabeth A. , Telling Jon , Hawkings Jon R. , Stibal Marek 
Published: May 2020

AbstractIce sheets overlay active and putatively widespread microbial ecosystems. An active subglacial biota has the potential to impact strongly on the (bio)geochemistry of local as well as downstream environments. Such impacts partly depend on the distribution of microbial populations, the types of habitats present beneath the ice, and their connectivity. In the ablation zone of the Greenland Ice Sheet (GrIS), supraglacial meltwaters are routed to the ice-sheet bed during the melt season, flushing out subglacial waters, sediments, and cells to proglacial environments via runoff. Here, we report on the diversity, composition, and niche differentiation of microbial assemblages exported in bulk runoff from a large (~600 km2) GrIS catchment. Proglacial river samples were collected over a period of subglacial drainage evolution in order to capture potential shifts in exported microbial community alongside hydrochemical transitions. We use high-resolution hydrochemical and hydrological information from the proglacial river to guide microbial (16S rRNA gene) interpretations. Core populations closely matched sequences previously isolated from other (pro)glacial environments, and phylogenetic characterisation of main OTUs alluded to a central role for subglacial iron, sulphur, and methane cycling. Whilst results indicate that bulk populations exported are likely true members of sub ice-sheet communities, we also find evidence of a supraglacial signature influencing composition of exported assemblages. Changes in assemblage structure accompanied those of major hydrological periods, with enhanced subglacial flushing coinciding with distinct shifts in microbial composition. Timing of sampling therefore matters when attempting to infer more nuanced changes in exported communities, or reveal the biogeochemical processes likely occurring in regions of the bed less influenced by surface melt. This is likely especially true when studying larger glacial systems, which experience complex hydrological changes throughout the melt-season, and that periods of extensive subglacial flushing offer opportunities to assess diversity from more isolated regions of the bed. Still, an apparent strong buffering signal from marginal zones appear to mask some of the diversity intrinsic to more remote, likely anoxic, subglacial niches, which may ultimately only be sampled via direct access to the subsurface.
Assessing the Utility and Accuracy of ICD10-CM Nontraumatic Subarachnoid Hemorrhage Codes for Intracranial Aneurysm Research
Authors: Roark Christopher , Wilson Melissa P. , Kubes Sheila , Mayer David , Wiley Laura K. 
Published: May 2020

ABSTRACTBackgroundThe 10th revision of International Classification of Disease, Clinical Modification (ICD10-CM) increased the number of codes to identify nontraumatic subarachnoid hemorrhage from one to twenty-two. ICD10-CM codes are able to specify the location of aneurysms causing subarachnoid hemorrhage (aSAH), however it is not clear how frequently or accurately these codes are being used in practice.ObjectiveTo systematically evaluate the usage and accuracy of location-specific ICD10-CM codes for aSAH.MethodsWe extracted all uses of ICD10-CM codes for nontraumatic subarachnoid hemorrhage (I60.x) during the first three years following the implementation of ICD10-CM from the billing module of the EHR for UCHealth. For those codes that specified aSAH location (I60.0-I60.6), EHR documentation was reviewed to determine whether there was an active aSAH, any patient history of aSAH, or unruptured intracranial aneurysm/s and the locations of those outcomes.ResultsBetween October 1, 2015 – September 30, 2018, there were 3,119 instances of nontraumatic subarachnoid hemorrhage ICD10-CM codes (I60.00-I60.9), of which 297 (9.5%) code instances identified aSAH location (I60.0-I60.6). These codes accurately identified current aSAH (64%), any patient history of aSAH (84%), and any patient history of intracranial aneurysm (87%). The accuracy of identified outcome location was 53% in current aSAH, 72% for any history of aSAH, and 76% for any history of an intracranial artery.ConclusionsResearchers should use ICD10-CM codes with caution when attempting to detect active aSAH and/or aneurysm location.
Efficacy and harms of remdesivir for the treatment of COVID-19: a systematic review and meta-analysis
Authors: Piscoya Alejandro , Ng-Sueng Luis Fernando , Riego Angela Parra del , Cerna-Viacava Renato , Pasupuleti Vinay , Roman Yuani M. , Thota Priyaleela , White C. Michael , Hernandez Adrian V. 
Published: May 2020

AbstractBackgroundWe evaluated the efficacy and safety of remdesivir for the treatment of COVID-19.MethodsSystematic review in five engines, pre-print webpages and RCT registries until May 22, 2020 for randomized controlled trials (RCTs) and observational studies evaluating remdesivir on confirmed, COVID-19 adults with pneumonia and/or respiratory insufficiency. Primary outcomes were all-cause mortality, clinical improvement or recovery, need for invasive ventilation, and serious adverse events (SAE). Secondary outcomes included length of hospital stay, progression of pneumonia, and adverse events (AE). Inverse variance random effects meta-analyses were performed.ResultsTwo placebo-controlled RCTs (n=1300) and two case series (n=88) were included. All studies used remdesivir 200mg IV the first day and 100mg IV for 9 more days, and followed up until 28 days. Wang et al. RCT was stopped early due to AEs; ACTT-1 was preliminary reported at 15-day follow up. Time to clinical improvement was not decreased in Wang et al. RCT, but median time to recovery was decreased by 4 days in ACTT-1. Remdesivir did not decrease all-cause mortality (RR 0.71, 95%CI 0.39 to 1.28) and need for invasive ventilation at 14 days (RR 0.57, 95%CI 0.23 to 1.42), but had fewer SAEs (RR 0.77, 95%CI 0.63 to 0.94). AEs were similar between remdesivir and placebo arms. Risk of bias ranged from some concerns to high risk in RCTs.InterpretationThere is paucity of adequately powered and fully reported RCTs evaluating effects of remdesivir in adult, hospitalized COVID-19 patients. Remdesivir should not be recommended for the treatment of severe COVID-19.
Saliva as a Candidate for COVID-19 Diagnostic Testing: A Meta-Analysis
Authors: Czumbel László Márk , Kiss Szabolcs , Farkas Nelli , Mandel Iván , Hegyi Anita , Nagy Ákos , Lohinai Zsolt , Szakács Zsolt , Hegyi Péter , Steward Martin C. , Varga Gábor 
Published: May 2020

AbstractObjectivesOur aim was to conduct a meta-analysis on the reliability and consistency of SARS-CoV-2 viral RNA detection in saliva specimens.MethodsWe reported our meta-analysis according to the Cochrane Handbook. We searched the Cochrane Library, Embase, Pubmed, Scopus, Web of Science and clinical trial registries for eligible studies published between 1 January and 25 April 2020. The number of positive tests and total number of conducted tests were collected as raw data. The proportion of positive tests in the pooled data were calculated by score confidence interval estimation with the Freeman-Tukey transformation. Heterogeneity was assessed using the I2 measure and the χ2 test.ResultsThe systematic search revealed 96 records after removal of duplicates. 26 records were included for qualitative analysis and 5 records for quantitative synthesis. We found 91% (95%CI = 80%-99%) sensitivity for saliva tests and 98% (95%CI 89%-100%) sensitivity for nasopharyngeal swab (NPS) tests in previously confirmed COVID-19 infected patients, with moderate heterogeneity among studies. Additionally, we identified 18 registered, ongoing clinical trials on saliva-based tests for detection of the virus.ConclusionSaliva tests offer a promising alternative to NPS for COVID-19 diagnosis. However, further diagnostic accuracy studies are needed to improve their specificity and sensitivity.
Seek COVER: Development and validation of a personalized risk calculator for COVID-19 outcomes in an international network
Authors: Williams Ross D. , Markus Aniek F. , Yang Cynthia , Salles Talita Duarte , DuVall Scott L. , Falconer Thomas , Jonnagaddala Jitendra , Kim Chungsoo , Rho Yeunsook , Williams Andrew , Alberga Amanda , An Min Ho , Aragón María , Areia Carlos , Burn Edward , Choi Young Hwa , Drakos Iannis , Fernandes Abrahão Maria Tereza , Fernández-Bertolín Sergio , Hripcsak George , Kaas-Hansen Benjamin Skov , Kandukuri Prasanna L , Kors Jan A. , Kostka Kristin , Liaw Siaw-Teng , Lynch Kristine E. , Machnicki Gerardo , Matheny Michael E. , Morales Daniel , Nyberg Fredrik , Park Rae Woong , Prats-Uribe Albert , Pratt Nicole , Rao Gowtham , Reich Christian G. , Rivera Marcela , Seinen Tom , Shoaibi Azza , Spotnitz Matthew E , Steyerberg Ewout W. , Suchard Marc A. , You Seng Chan , Zhang Lin , Zhou Lili , Ryan Patrick B. , Prieto-Alhambra Daniel , Reps Jenna M. , Rijnbeek Peter R. 
Published: May 2020

ObjectiveTo develop and externally validate COVID-19 Estimated Risk (COVER) scores that quantify a patient’s risk of hospital admission (COVER-H), requiring intensive services (COVER-I), or fatality (COVER-F) in the 30-days following COVID-19 diagnosis.MethodsWe analyzed a federated network of electronic medical records and administrative claims data from 14 data sources and 6 countries. We developed and validated 3 scores using 6,869,127 patients with a general practice, emergency room, or outpatient visit with diagnosed influenza or flu-like symptoms any time prior to 2020. The scores were validated on patients with confirmed or suspected COVID-19 diagnosis across five databases from South Korea, Spain and the United States. Outcomes included i) hospitalization with pneumonia, ii) hospitalization with pneumonia requiring intensive services or death iii) death in the 30 days after index date.ResultsOverall, 44,507 COVID-19 patients were included for model validation. We identified 7 predictors (history of cancer, chronic obstructive pulmonary disease, diabetes, heart disease, hypertension, hyperlipidemia, kidney disease) which combined with age and sex discriminated which patients would experience any of our three outcomes. The models achieved high performance in influenza. When transported to COVID-19 cohorts, the AUC ranges were, COVER-H: 0.69-0.81, COVER-I: 0.73-0.91, and COVER-F: 0.72-0.90. Calibration was overall acceptable.ConclusionsA 9-predictor model performs well for COVID-19 patients for predicting hospitalization, intensive services and fatality. The models could aid in providing reassurance for low risk patients and shield high risk patients from COVID-19 during de-confinement to reduce the virus’ impact on morbidity and mortality.
Deteriorated Covid19 control due to delayed lockdown resulting from strategic interactions between Governments and oppositions
Authors: Carrozzo-Magli Alessio , d’Onofrio Alberto , Manfredi Piero 
Published: May 2020

AbstractBackgroundIn many European countries and the US, the burden of Covid-19 epidemic could be much lower if Governments had been able to learn from the China and Lombardy stories and to declare full lockdown without delays.MethodsWe use a simple game-theoretic framework for the strategic interaction between the Government, political oppositions and lobbies, combined with a Covid-19 transmission model, to analyse the role of political factors delaying the lockdown declaration, depending on the degrees of “responsibility” of political actors.ResultsThe lockdown can always be declared immediately (i.e., without delay) as sustained transmission arises, only if the government feels fully “responsible” towards all citizens. If this is not the case, epidemic growth will eventually dominate the agents’ payoffs, so that sooner or later the lockdown will always be declared i.e., both the government and the opposition will be forced by the epidemic to switch towards a higher degree of responsibility, but with a delay. There is a further nontrivial situation where the lockdown can be declared without delay, occurring when the political opposition is at least as responsible as the Government. This however requires the solution of a coordination issue, which cannot be taken for granted. Eventually, a vicious circle emerges, where the delayed lockdown requires a much longer lockdown period to achieve adequate control results, thereby causing the explosion of economic losses and so calling for unlocking long before it should.ConclusionsLockdown delays have dramatically worsened the impact of the current Covid-19 wave in a number of countries. Citizens should be made cogently aware of this to claim maximal responsibility from political actors and economic lobbies to avoid that such stories repeat in the future when further threats, due to Covid-19 itself or other pathogens, will re-appear.
Frailty and mortality in hospitalized older adults with COVID-19: retrospective observational study
Authors: Smet Robert De , Mellaerts Bea , Vandewinckele Hannelore , Lybeert Peter , Frans Eric , Ombelet Sara , Lemahieu Wim , Symons Rolf , Ho Erwin , Frans Johan , Smismans Annick , Laurent Michaël R. 
Published: May 2020

ABSTRACTBackgroundOlder adults with coronavirus disease 2019 (COVID-19) face an increased risk of adverse health outcomes including mortality. Ethical guidelines consider allocation of limited resources based on likelihood of survival, frilty, co-morbidities and age. However, the association of frailty with clinical outcomes in older COVID-19 patients remains unclear.ObjectivesTo determine the association between frailty and short-term mortality in older adults hospitalized for COVID-19.DesignRetrospective single-center observational study.Setting and participantsN = 81 patients with COVID-19 confirmed by reverse-transcriptase polymerase chain reaction (RT-PCR), at the Geriatrics department of Imelda general hospital, Belgium.MeasurementsFrailty was graded according to the Rockwood Clinical Frailty Scale (CFS). Demographic, biochemical and radiological variables, co-morbidities, symptoms and treatment were extracted from electronic medical records.ResultsParticipants (N = 48 women, 59%) had a median age of 85 years (range 65-97 years), median CFS score of 7 (range 2 - 9), and 42 (52%) were long-term care residents. Within six weeks, eighteen patients died. Mortality was significantly but weakly associated with age (Spearman r = 0.241, P = 0.03) and CFS score (r = 0.282, P = 0.011), baseline lactate dehydrogenase (LDH) (r = 0.301, P = 0.009), lymphocyte count (r = -0.262, P = 0.02) and RT-PCR Ct value (r = -0.285, P = 0.015). Mortality was not associated with long-term care residence, dementia, delirium or polypharmacy. In multivariable logistic regression analyses, CFS, LDH and RT-PCR Ct values (but not age) remained independently associated with mortality. Both age and frailty had poor specificity to predict survival. A multivariable model combining age, CFS, LDH and viral load significantly predicted survival.Conclusions and implicationsAlthough their prognosis is worse, even the oldest and most severely frail patients may benefit from hospitalization for COVID-19, if sufficient resources are available.BRIEF SUMMARYOutcomes of frail older adults hospitalized for COVID-19, particularly long-term care residents, remain unclear. In this retrospective cohort, frailty predicted mortality independently of age or established biomarkers.
Changes in the stool and oropharyngeal microbiome in obsessive-compulsive disorder
Authors: Domènech Laura , Willis Jesse , Alemany Maria , Morell Marta , Real Eva , Escaramís Geòrgia , Bertolín Sara , Chinchilla Daniel Sánchez , Balcells Susanna , Segalàs Cinto , Estivill Xavier , Menchón Jose M , Gabaldón Toni , Alonso Pino , Rabionet Raquel 
Published: May 2020

ABSTRACTAlthough the etiology of obsessive-compulsive disorder (OCD) is largely unknown, it is accepted that OCD is a complex disorder. There is a known bi-directional interaction between the gut microbiome and brain activity. Several authors have reported associations between changes in gut microbiota and neuropsychiatric disorders, including depression or autism. Furthermore, a pediatric-onset neuropsychiatric OCD-related syndrome occurs after streptococcal infection, which might indicate that exposure to certain microbes could be involved in OCD susceptibility. However, only one study has investigated the microbiome of OCD patients to date. We performed 16S ribosomal RNA gene-based metagenomic sequencing to analyze the stool and oropharyngeal microbiome composition of 32 OCD cases and 32 age and gender matched controls. We estimated different α- and β-diversity measures and performed LEfSe and Wilcoxon tests to assess differences in bacterial distribution. OCD stool samples showed a trend towards lower bacterial α-diversity, as well as an increase of the relative abundance of Rikenellaceae, particularly of the genus Alistipes, and lower relative abundance of Prevotellaceae, and two genera within the Lachnospiraceae: Agathobacer and Coprococcus. However, we did not observe a different Bacteroidetes to Firmicutes ratio between OCD cases and controls. Analysis of the oropharyngeal microbiome composition showed a lower Fusobacteria to Actinobacteria ratio in OCD cases. In conclusion, we observed an imbalance in the gut and oropharyngeal microbiomes of OCD cases, including, in stool, an increase of bacteria from the Rikenellaceae family, associated with gut inflammation, and a decrease of bacteria from the Coprococcus genus, associated with DOPAC synthesis.
RT-qPCR analyses on the osteogenic differentiation from human iPS cells: An investigation of reference genes
Authors: Okamura Kensuke , Inagaki Yusuke , Matsui Takeshi K. , Matsubayashi Masaya , Komeda Tomoya , Ogawa Munehiro , Mori Eiichiro , Tanaka Yasuhito 
Published: May 2020

AbstractReverse transcription quantitative PCR (RT-qPCR) is used to quantify gene expression and require standardization with reference genes. We sought to identify the reference genes best suited for experiments that induce osteogenic differentiation from human induced pluripotent stem (iPS) cells. They were cultured in an undifferentiated maintenance medium and after confluence, further cultured in an osteogenic differentiation medium for 28 days. RT-qPCR was performed on undifferentiation markers, osteoblast and osteocyte differentiation markers, and reference gene candidates. The expression stability of each reference gene candidate was ranked using four algorithms. General rankings identified TATA box binding protein (TBP) in the first place, followed by transferrin receptor (TFRC), ribosomal protein large P0 (RPLP0), and finally, beta-2-microglobulin (B2M), which was revealed as the least stable. Interestingly, universally used GAPDH and ACTB were found to be unsuitable. Our findings strongly suggest a need to evaluate the expression stability of reference gene candidates for each experiment.