bluuebunny/crossref_metadata_2025_split huggingface dataset:
An electronic application to improve management of infections in low-income neonatal units: pilot implementation of the NeoTree Beta App in a public sector hospital in Zimbabwe
Authors: Gannon H , Chimhuya S , Chimhini G , Neal S. R. , Shaw L P , Crehan C , Bailey T Hull , Ferrand R. A. , Klein N , Sharland M , Robertson V , Borja M Cortina , Heys M. , Fitzgerald F 
Published: September 2020

AbstractThere are 2.9 million annual neonatal deaths worldwide. Simple, evidence-based interventions such as temperature control could prevent approximately two-thirds of these deaths. However, key problems in implementing these interventions are a lack of newborn-trained healthcare workers and a lack of data collection systems. NeoTree is a digital platform aiming to improve newborn care in low-resource settings through real-time data capture and feedback alongside education and data linkage. This project demonstrates proof of concept of the NeoTree as a real-time data capture tool replacing hand-written clinical paper notes over a 9-month period in a tertiary neonatal unit at Harare Central hospital, Zimbabwe. We aimed to deliver robust data for monthly mortality and morbidity meetings, and to improve turn-around time for blood culture results among other quality improvement indicators.There were 3222 admissions and discharges entered using the NeoTree software with 41 junior doctors and 9 laboratory staff trained over the 9-month period. The NeoTree app was fully integrated into the department for all admission and discharge documentation and the monthly presentations became routine, informing local practice. An essential factor for this success was local buy-in and ownership at each stage of the project development, as was monthly data analysis and presentations allowing us to rapidly troubleshoot emerging issues. However, the laboratory arm of the project was negatively affected by nationwide economic upheaval. Our successes and challenges piloting this digital tool have provided key insights for effective future roll-out in Zimbabwe and other low-income healthcare settings.
A Systematic Review of Randomised Controlled Trials on the Effectiveness of Ecotherapy Interventions for Treating Mental Disorders
Authors: Williams T. , Barnwell G.C. , Stein D.J. 
Published: September 2020

AbstractBackgroundSystematic reviews on ecotherapy interventions (i.e. environmental therapies and animal-assisted therapies) in the general population have demonstrated promising findings. However, there is a need for systematic assessment of the evidence for the use of these interventions in people living with mental disorders. Hence, we conducted a systematic review of randomised control trials (RCTs) on exposure to ecotherapy interventions (i.e. environmental therapy, animal-assisted therapy, wilderness therapy) for individuals with mental disorders.MethodsThe search was completed in September 2019 and comprised: Science Direct, PubMed Central, EBSCOHOST (via Academic Search Premier), the Cochrane Library, and Google Scholar. The primary outcomes that were assessed include: treatment efficacy (on the CGI-I or similar), symptom severity, and/or dropout rates. Secondary outcome measures assessed included self-efficacy, perceived control, hope, quality of life, life skills, and coping.ResultsA total of 2415 reports were identified, of which 94 were assessed for eligibility. Eight environmental therapy trials (i.e. gardening, forest therapy, horticultural therapy, nature adventure rehabilitation, and adventure-based therapy) and ten animal-assisted therapy trials (i.e. dogs, horses or dolphins) were included in the review. Risk of bias assessment was conducted, and qualitative analysis performed to describe the efficacy of the RCTs. The findings suggest that environmental therapies or animal-assisted therapies are efficacious in reducing symptoms of anxiety, depressive, substance-related and addictive, schizophrenia-spectrum and trauma- and stress-related disorders.ConclusionThere is suggestive, but not conclusive, evidence for the efficacy of some ecotherapy interventions in mental disorders. In particular, there are: four environmental therapy trials and five animal-assisted therapy trails for depression and/or anxiety; one environmental therapy trial for post-traumatic stress disorder; three environmental therapy and animal assisted therapy trials for general psychiatric disorders; one environmental therapy trial and two animal assisted therapy trials for substance use disorders; and, one environmental therapy and two animal-assisted trials for people living with schizophrenia spectrum disorder. The use of standard reporting guidelines may improve evidence quality of future ecotherapy RCTs, and provide a foundation meta-analysis of the evidence.
A combined oro-nasopharyngeal swab is more sensitive than mouthwash in detecting SARS-CoV-2 by a high-throughput PCR assay
Authors: Michel Wiebke , Färber Jacqueline , Dilas Milica , Tammer Ina , Baar Jannik , Kaasch Achim J. 
Published: September 2020

AbstractObjectivesThe optimal diagnostic specimen to detect SARS-CoV-2 by PCR in the upper respiratory tract is unclear. Mouthwash fluid has been reported as an alternative to nasopharyngeal and oropharyngeal swabs. We compared mouthwash fluid with a combined oro-nasopharyngeal swab regarding test performance.MethodsWe tested asymptomatic persons with a previous diagnosis of COVID-19 and their household contacts. First, a mouthwash (gargling for at least 5 sec) with sterile water was performed. Then, with a single flocked swab the back of the throat and subsequently the nasopharynx were sampled. Samples were inactivated and analysed on a Roche cobas 6800® system with the Roche SARS-CoV-2 test.ResultsOf 76 persons, 39 (51%) tested positive for SARS-CoV-2 by oro-nasopharyngeal swab. Mouthwash detected 13 (17%) of these infections but did not detect any additional infection. Samples that were positive in both tests, had lower cycle threshold (Ct)-values for oro-nasopharyngeal samples, indicating a higher virus concentration, compared to samples only positive in oro-nasopharyngeal swabs.ConclusionsMouthwash is not as sensitive as combined oro-nasopharyngeal swab in detecting upper respiratory tract infection.
Modeling COVID-19 as a National Dynamics with a SARS-CoV-2 Prevalent Variant: Brazil - A Study Case
Authors: Celaschi S. 
Published: September 2020

ABSTRACTCOVID-19 global dynamics is modeled by an adaptation of the deterministic SEIR Model, which takes into account two dominant lineages of the SARS-CoV-2, and a time-varying reproduction number to estimate the disease transmission behavior. Such a methodology can be applied worldwide to predict forecasts of the outbreak in any infected country. The pandemic in Brazil was selected as a first study case. Brazilian official published data from February 25th to August 30th, 2020 was used to adjust a few epidemiologic parameters. The estimated time-dependence mean value to the infected individuals (confirmed cases) presents - in logarithmic scale - standard deviation SD = 0.08 for over six orders of magnitude. Data points for additional three weeks were added after the model was complete, granting confidence on the outcomes. By the end of 2020, the predicted numbers of confirmed cases in Brazil, within 95% credible intervals, may reach 6 Million (5 -7), and fatalities would accounts for 180 (130 – 220) thousands. The total number of infected individuals is estimated to reach 13 ± 1 Million, 6.2% of the Brazilian population. Regarding the original SARS-CoV-2 form and its variant, the only model assumption is their distinct incubation rates. The variant form reaches a maximum of 96% of exposed individuals as previously reported for South America.
Pneumococcal vaccine uptake and vaccine effectiveness in older adults with invasive pneumococcal disease in Germany
Authors: Perniciaro Stephanie , van der Linden Mark 
Published: September 2020

AbstractBackgroundInvasive pneumococcal disease (IPD) in people ≥60 years old is on the rise in Germany. There has been a recommendation for pneumococcal vaccination in this age group since 1998.MethodsWe determined the vaccination status of people ≥60 years old with IPD in Germany. We assessed vaccine effectiveness (VE) of the recommended 23-valent polysaccharide vaccine (PPV23).ResultsThe rate of pneumococcal vaccination in older adults with IPD is low, 26%, with only 16% of people receiving a pneumococcal vaccine within the past 5 years. Age- and sex-adjusted vaccine effectiveness (VE) for PPV23 was 37% (95% confidence interval 12% - 55%). For people vaccinated with PPV23 less than 2 years prior to IPD, VE was - 20% (−131% - 34%), between 2-4 years prior to IPD, VE was 56% (20% - 76%), and 47% (17% - 63%) for those vaccinated ≥5 years ago. Excluding serotype 3, overall VE for the remaining serotypes in PPV23 was 63% (49% - 74%). For people receiving PPV23 within the past 2 years, VE against all serotypes except 3 was 49% (12% - 71%); for people vaccinated between 2-4 years prior to IPD 66% (37% - 82%); for those vaccinated ≥5 years ago, 69% (50% - 81%). VE of PPV23 against serotype 3 IPD only was -110% (- 198% - -47%).ConclusionsTo reduce IPD in older adults in Germany, we must increase the rate of pneumococcal vaccine uptake. For 22/23 serotypes, PPV23 was effective. Serotype 3 remains a major problem.
Correlation between serum 25(OH) vitamin D level and sleep quality in elderly patients with type 2 diabetes
Authors: Ma Hongyan , Fan Danni , Li Xiaofei , Qi Ying , Zhao Yang , Zhang Lin 
Published: September 2020

AbstractBackgroundUntreated sleep disorders have been linked with type 2 diabetes in previous evidence. This study was to investigate the correlation between serum 25(OH) vitamin D level and sleep quality in elderly patients with type 2 diabetes and reveal the therapeutic potential of 25(OH) vitamin D-based treatments to improve sleeping quality and its effect on diabetes management.MethodsThe sleep quality of 186 elderly patients with type 2 diabetes were assessed by questionaires of Pittsburgh sleep index (PSQI), with a cutoff point of PSQI • 7 defined as poor sleep. The measurement of serum 25(OH) vitamin D, fasting blood glucose, glycosylated hemoglobin, serum creatinine, total cholesterol, triglyceride, low-density lipoprotein cholesterol, and urinary albumin/creatinine ratio were collected. History of diabetic nephropathy, diabetic retinopathy, peripheral neuropathy, blood pressure, height, weight, hypoglycemic drug use, and the duration of diabetes also were recorded. Both univariate and multivariate logistic regression analysis was used to investigate the relationship of serum 25(OH) vitamin D and sleep quality in elderly patients with type 2 diabetes.ResultsThe age of elderly patients with type 2 diabetes was 73.6±4.3 years., and duration of diabetes was 8.8 ± 3.0 years. In the study, inadequate quality of sleep was reported in 63% elderly patients with type 2 diabetes. This study revealed that lower level of 25(OH) vitamin D was significantly associated with poor sleep quality in type 2 diabetes patients(P < 0.05). Multivariate logistic regression analysis showed that 25(OH) vitamin D deficiency and the use of insulin were risk factors for of inadequate sleep quality in elderly patients with type 2 diabetes.ConclusionsElderly type 2 diabetic patients with 25(OH) vitamin D deficiency showed a high incidence of poor sleep quality, low-level of 25(OH) vitamin D was a risk factor for inadequate quality of sleep in elderly patients with type 2 diabetes.
Kinetics of SARS-CoV-2 infection in the human upper and lower respiratory tracts and their relationship with infectiousness
Authors: Ke Ruian , Zitzmann Carolin , Ribeiro Ruy M. , Perelson Alan S. 
Published: September 2020

AbstractSARS-CoV-2 is a human pathogen that causes infection in both the upper respiratory tract (URT) and the lower respiratory tract (LRT). The viral kinetics of SARS-CoV-2 infection and how they relate to infectiousness and disease progression are not well understood. Here, we develop data-driven viral dynamic models of SARS-CoV-2 infection in both the URT and LRT. We fit the models to viral load data from patients with likely infection dates known, we estimated that infected individuals with a longer incubation period had lower rates of viral growth, took longer to reach peak viremia in the URT, and had higher chances of presymptomatic transmission. We then developed a model linking viral load to infectiousness. We found that to explain the substantial fraction of transmissions occurring presymptomatically, a person’s infectiousness should depend on a saturating function of the viral load, making the logarithm of the URT viral load a better surrogate of infectiousness than the viral load itself. Comparing the roles of target-cell limitation, the innate immune response, proliferation of target cells and spatial infection in the LRT, we found that spatial dissemination in the lungs is likely to be an important process in sustaining the prolonged high viral loads. Overall, our models provide a quantitative framework for predicting how SARS-CoV-2 within-host dynamics determine infectiousness and represent a step towards quantifying how viral load dynamics and the immune responses determine disease severity.SignificanceA quantitative understanding of the kinetics of SARS-CoV-2 infection is key to understanding the development of infectiousness and disease symptoms. To address this need, we developed data-driven within-host models of SARS-CoV-2 infection and showed that lower rates of viral growth lead to longer incubation periods and higher chances of presymptomatic transmission. We found that the logarithm of the URT viral load serves an appropriate surrogate for a person’s infectiousness. We then developed a mechanistic model for infectiousness and showed that a saturation effect in the dependence of transmission on viral load gives rise to this relationship. We also provide evidence of spatial dissemination in the lungs as an important process in sustaining prolonged high viral loads in the LRT.
Deep Immune Profiling of MIS-C demonstrates marked but transient immune activation compared to adult and pediatric COVID-19
Authors: Vella Laura A. , Giles Josephine R. , Baxter Amy E. , Oldridge Derek A. , Diorio Caroline , Kuri-Cervantes Leticia , Alanio Cécile , Pampena M. Betina , Wu Jennifer E. , Chen Zeyu , Huang Yinghui Jane , Anderson Elizabeth M. , Gouma Sigrid , McNerney Kevin O. , Chase Julie , Burudpakdee Chakkapong , Lee Jessica H. , Apostolidis Sokratis A. , Huang Alexander C. , Mathew Divij , Kuthuru Oliva , Goodwin Eileen C. , Weirick Madison E. , Bolton Marcus J. , Arevalo Claudia P. , Ramos Andre , Jasen Cristina , Giannini Heather M. , D’Andrea Kurt ,   The UPenn COVID Processing Unit, Meyer Nuala J. , Behrens Edward M. , Bassiri Hamid , Hensley Scott E. , Henrickson Sarah E. , Teachey David T. , Betts Michael R. , Wherry E. John 
Published: September 2020

ABSTRACTPediatric COVID-19 following SARS-CoV-2 infection is associated with fewer hospitalizations and often milder disease than in adults. A subset of children, however, present with Multisystem Inflammatory Syndrome in Children (MIS-C) that can lead to vascular complications and shock, but rarely death. The immune features of MIS-C compared to pediatric COVID-19 or adult disease remain poorly understood. We analyzed peripheral blood immune responses in hospitalized SARS-CoV-2 infected pediatric patients (pediatric COVID-19) and patients with MIS-C. MIS-C patients had patterns of T cell-biased lymphopenia and T cell activation similar to severely ill adults, and all patients with MIS-C had SARS-CoV-2 spike-specific antibodies at admission. A distinct feature of MIS-C patients was robust activation of vascular patrolling CX3CR1+ CD8 T cells that correlated with use of vasoactive medication. Finally, whereas pediatric COVID-19 patients with acute respiratory distress syndrome (ARDS) had sustained immune activation, MIS-C patients displayed clinical improvement over time, concomitant with decreasing immune activation. Thus, non-MIS-C versus MIS-C SARS-CoV-2 associated illnesses are characterized by divergent immune signatures that are temporally distinct and implicate CD8 T cells in clinical presentation and trajectory of MIS-C.One Sentence SummaryMIS-C is defined by generalized lymphocyte activation that corrects during hospitalization, including elevated plasmablast frequencies and marked activation of vascular patrolling CX3CR1+ CD8 T cells.
Dynamic Modeling of Reported COVID-19 Cases and Deaths with Continuously Varying Case Fatality and Transmission Rate Functions
Authors: Lyu Mingdong , Hall Randolph 
Published: September 2020

AbstractIn this paper, we propose an enhanced SEIRD (Susceptible-Exposed-Infectious-Recovered-Death) model with time varying case fatality and transmission rates for confirmed cases and deaths from COVID-19. We show that when case fatalities and transmission rates are represented by simple Sigmoid functions, historical cases and fatalities can be fit with a relative-root-mean-squared-error accuracy on the order of 2% for most American states over the period from initial cases to July 28 (2020). We find that the model is most accurate for states that so far had not shown signs of multiple waves of the disease (such as New York), and least accurate for states where transmission rates increased after initially declining (such as Hawaii). For such states, we propose an alternate multi-phase model. Both the base model and multi-phase model provide a way to explain historical reported cases and deaths with a small set of parameters, which in the future can enable analyses of uncertainty and variations in disease progression across regions.
Granulosa cell genes that regulate ovarian follicle development beyond the antral stage: the role of estrogen receptor β
Authors: Chakravarthi V. Praveen , Borosha Shaon , Ghosh Subhra , Roby Katherine F. , Wolfe Michael W. , Christenson Lane K. , Karim Rumi M. A. 
Published: September 2020

ABSTRACTFollicle development beyond the preantral stage is dependent on gonadotropins. FSH signaling is crucial for the advancement of preantral follicles to the antral stage, and LH signaling is essential for further maturation of preovulatory follicles. Estrogen is intricately tied to gonadotropin signaling during the advanced stages of folliculogenesis. We observed thatErβnullovarian follicles fail to develop beyond the antral stage, even after exogenous gonadotropin stimulation. As ERβ is primarily expressed in the granulosa cells (GCs), we explored the gonadotropin-regulated GC genes that induce maturation of antral follicles. Synchronized follicle development was induced by administration of exogenous gonadotropins to wildtype 4-wk-old female rats. The GC transcriptome was analyzed via RNA-sequencing before and after gonadotropin stimulation. AnErβnullmutant model that fails to show follicle maturation was also included in order to identify the ERβ-regulated genes involved at this step. We observed that specific groups of genes were differentially expressed in response to PMSG or hCG administration in wildtype rats. While some of the PMSG or hCG-induced genes showed a similar expression pattern inErβnullGCs, a subset of PMSG- or hCG-induced genes showed a differential expression inErβnullGCs. These latter ERβ-regulated genes included previously known FSH or LH target genes includingLhcgr, Cyp11a1, Cyp19a1, Pgr, Runx2, Egfr, Kiss1, andPtgs2, which are involved in follicle development, oocyte maturation, and ovulation. We also identified novel ERβ-regulated genes includingJaml, Galnt6, Znf750, Dusp9, Wnt16, andMageb16that failed to respond to gonadotropin stimulation inErβnullGCs. Our findings indicate that the gonadotropin-induced spatiotemporal pattern of gene expression is essential for ovarian follicle maturation beyond the antral stage. However, expression of a subset of those gonadotropin-induced genes is dependent on transcriptional regulation by ERβ.
A tale of two transcriptomic responses in agricultural pests via host defenses and viral replication
Authors: Pantha Pramod , Chalivendra Subbaiah , Oh Dong-Ha , Elderd Bret , Dassanayake Maheshi 
Published: September 2020

AbstractBackgroundAutographa californicaMultiple Nucleopolyhedrovirus (AcMNPV) is a baculovirus with a high potential for its use as a biopesticide against arthropod pests. The budded form of the virus causes a systemic infection when it escapes the midgut to enter the hemolymph of susceptible hosts. Yet, the specific molecular processes underlying the biocidal activity of AcMNPV on its insect hosts are largely unknown.ResultsIn this study, we describe the transcriptional responses in two major pests,Spodoptera frugiperdaandTrichoplusia ni, to determine the host-pathogen responses during AcMNPV infection, concurrently with the viral response to the host. We assembled species-specificde novoreference transcriptomes of the hemolymph to identify key transcripts that respond during pathogenesis in these arthropod models where genomic resources are sparse. We found that the suppression of transcriptional processes related to chitin, a metabolite critical for basement membrane stability and tracheal development are central in establishing a systemic infection. Synergistic transcriptional support was observed to suggest suppression of immune responses and induction of oxidative stress indicating disease progression in the host. The entire AcMNPV core genome was expressed in the host hemolymph and viral genes predominantly associated with the budded virus replication, structure, and movement were more abundant than those associated with the occlusion-derived virus. Genes known to directly arrest host cell cycle and development were among the most abundant AcMNPV transcripts in infected hosts. Interestingly, several of the host genes (e.g.Chitin synthase) that were targeted by the pathogen as revealed by our study are also targets of several chemical insecticides currently used commercially to control arthropod pests.ConclusionsOur results reveal an extensive overlap between biological processes represented by genes differently expressed in both hosts, as well as convergence on highly abundant viral genes expressed in the two hosts, providing an overview of the host-pathogen transcriptomic landscape during systemic infection. Given the diversity of AcMNPV strains that infect a wide range of insect hosts, our study provides a framework where pathogen strains could be selected to target specific host genes that facilitates modulation of the infection strength and specificity of the susceptible hosts.
Species-specific assembly of root-associated bacterial microbiota mediated by a combination of plant specialized metabolites
Authors: Shimasaki Tomohisa , Masuda Sachiko , Garrido-Oter Ruben , Kawasaki Takashi , Aoki Yuichi , Shibata Arisa , Suda Wataru , Shirasu Ken , Yazaki Kazufumi , Nakano Ryohei Thomas , Sugiyama Akifumi 
Published: September 2020

AbstractPlant specialized metabolites (PSMs) influence the taxonomic compositions of the root-associated microbiota; however, the underlying molecular mechanisms and evolutionary trajectories remain elusive. Here, we show that the bacterial genusArthrobacteris predominant in the tobacco endosphere, and that its enrichment is mediated by a combination of two tobacco-specific PSMs, santhopine and nicotine The isolation and whole genome sequencing of a representative set ofArthrobacterstrains identified independent genomic features, including but not limited to genes for santhopine and nicotine catabolism, which are associated with the colonization competence of tobacco roots. Taken together, these data suggest that plant species-specific root microbiota assembly is mediated by bacterial catabolism of a cocktail of PSMs synthesized by the host plant.