bluuebunny/crossref_metadata_2025 huggingface dataset:
Characterization ofPythiumSpecies Collected from a Multiple Time-Point Sampling of Cucurbits in South Carolina
Authors: Toporek Sean M. , Keinath Anthony P.
Published: May 2020

Species of Pythium cause root and stem rot in cucurbits, but no formal surveys have been conducted in the United States to identify which species are responsible. The cucurbit hosts bottle gourd, cucumber, Hubbard squash, and watermelon were transplanted in May, July, September, and November into sentinel plots in four and five different fields in 2017 and 2018, respectively, in South Carolina. Eight of the nine fields were replanted in March 2019. Isolates (600) were collected and identified by sequencing DNA of the mitochondrial cytochrome oxidase I region. The four most common species were P. spinosum (45.6% of all isolates), P. myriotylum (20.0%), P. irregulare (15.3%), and P. aphanidermatum (12.8%). P. myriotylum and P. aphanidermatum were predominantly isolated in May, July, and September, whereas P. spinosum and P. irregulare were predominantly isolated in November and March. Isolates of P. ultimum, P. irregulare, and P. spinosum were more virulent than isolates of P. myriotylum and P. aphanidermatum at 25°C. Representative isolates were screened in vitro for sensitivity to three fungicides: mefenoxam, propamocarb, and oxathiapiprolin. All isolates were sensitive to mefenoxam and propamocarb, but these same isolates were insensitive to oxathiapiprolin, except those classified taxonomically in Pythium clade I.
Nurses: Courageous, Committed, and Fed Up
Authors: Kennedy Maureen Shawn
Published: May 2020

The COVID-19 pandemic is a watershed moment for nurses.
Why a Nurse (and Mother) Didn't Know
Authors: Holmes Arlene
Published: May 2020

A striking plea for education in recognizing mental illness.
Original Research: The Relationship Between Food Insecurity and Cost-Related Medication Nonadherence in Older Adults: A Systematic Review
Authors: Caouette Shaunna , Boss Lisa , Lynn Monika
Published: May 2020

Background:

Food insecurity, which can be defined as having limited access to nutritional and safe foods as a result of a lack of financial resources, is believed to adversely influence health outcomes. Older adults, in particular, face rising health care costs and may be forced to choose between purchasing prescribed medications or using their limited financial resources for basic needs, such as food.

Purpose:

The purpose of this systematic review was to examine the relationship between food insecurity and cost-related medication nonadherence (CRN) in older adults living in a community setting.

Methods:

A comprehensive electronic review of the literature was performed. Criteria for inclusion were original quantitative or qualitative research, written in English, involving community-dwelling U.S. adults 60 years of age and older.

Results:

Six studies met all criteria and were included for analysis. Two studies reported a significant dose-response relationship between food insecurity and CRN, and a third reported an increased risk of CRN in subjects with persistent food insecurity. Three key predictors of food insecurity and CRN in older adults were identified: low income, health insurance gaps, and higher out-of-pocket prescription costs. Most studies reported that subjects with higher food insecurity and CRN were more likely to be young-old (ages 60 to 84), have lower income, and have relatively more chronic conditions.

Conclusion:

Overall, the findings indicate that older adults who have multiple chronic conditions and only receive Medicare are at increased risk for food insecurity and CRN. Finding ways for health care providers and organizations to help manage these risks is critical to improving health outcomes and reducing use of health care services. Nurses can be pivotal in taking the lead to develop appropriate interventions and programs for patients, and to advocate better government-funded health care and policy reform in order to improve outcomes in this vulnerable population.
CE: Opioid Use Disorder: Pathophysiology, Assessment, and Effective Interventions
Authors: Brown Kate Garland , Capili Bernadette
Published: May 2020

Opioid use disorder (OUD) is a chronic, relapsing disease. Genetic variability, dysregulated stress system response, and history of opioid experimentation or escalating exposure all contribute to the likelihood of developing OUD, which produces complex brain changes that make it difficult to stop opioid use. Understanding the neurobiology of OUD helps nurses anticipate the behaviors of patients with OUD and approach them with empathy. Here, the authors discuss the pathophysiology of OUD, available screening tools, medical treatments, and behavioral interventions that have demonstrated efficacy in reducing substance use.
Acid Suppressants Increase Risk of Colonization with Multidrug-Resistant Microorganisms
Authors: Rosenberg Karen
Published: May 2020

According to this study:

Use of acid suppressants is associated with a 75% increase in the risk of intestinal tract colonization with multidrug-resistant microorganisms in both the community and health care settings.

More prudent use of acid suppressants may help to reduce the risks of colonization with multidrug-resistant microorganisms.
Abnormal Basic Metabolic Panel Findings: Implications for Nursing
Authors: Bertschi Lydia A.
Published: May 2020

In this article, the second in a new series designed to improve acute care nurses' understanding of laboratory abnormalities, the author continues her discussion of important values in the basic metabolic panel (see Back to Basics, January, for a discussion of sodium and fluid balance). Here she addresses the electrolytes potassium and chloride as well as blood urea nitrogen and creatinine, four values that are best considered together because they both reflect and impact renal function as well as acid–base homeostasis. Important etiology, clinical manifestations, and treatment concerns are also presented. Three case studies are used to integrate select laboratory diagnostic tests with history and physical examination findings, allowing nurses to develop a thorough, focused plan of care for electrolyte abnormalities and kidney disorders commonly encountered in the medical–surgical setting.
How to Support the Nurse in Your Life
Authors: Sato Hui-Wen (Alina)
Published: May 2020

Updated several times a week with posts by a wide variety of authors, AJN's blog Off the Charts allows us to provide more timely—and often more personal—perspectives on professional, policy, and clinical issues. Best of the Blog is a regular column to draw the attention of AJN readers to posts we think deserve a wider audience. To read more, please visit: www.ajnoffthecharts.com.
Far from Home
Authors: Phipps Marcy
Published: May 2020

A flight nurse cares for one of COVID-19's many ‘peripheral victims.’
Next-Generation Sequencing of the Ocular Surface Microbiome: In Health, Contact Lens Wear, Diabetes, Trachoma, and Dry Eye
Authors: Okonkwo Arthur , Rimmer Victoria , Walkden Andrew , Brahma Arun , Carley Fiona , McBain Andrew J. , Radhakrishnan Hema
Published: May 2020

Objectives:

To assess publications examining the occurrence, composition, and clinical significance of a microbiome at the ocular surface.

Methods:

MEDLINE, EMBASE, and Google Scholar were searched. Reference lists of included articles were also searched for relevant citations. All publications up to June 1, 2019, were analyzed.

Results:

Eleven articles and 1 abstract were included, analyzing 661 patients. Articles generally report bacteria to the genus level. The presence of DNA associated with diverse bacterial species was reported including pathogenic species, such as Pseudomonas and Neisseria. Bacterial DNA that makes up the microbiome, such as Acinetobacter, Actinomyces, Aquabacterium, Bradyrhizobium, Corynebacterium, Sphingomonas, Staphylococcus, and Streptococcus, in other parts of the body was found. The putative ocular microbiome is consistent between right and left eyes and is affected by contact lens use (higher Pseudomonas levels) and blepharitis (higher Staphylococcus levels).

Conclusions:

There is a significant likelihood that there is at least a transitory ocular surface microbiome, with Acinetobacter, Corynebacterium, Propionibacterium, Staphylococcus, and Streptococcus detected in at least 7 of 11 studies. However, further investigation attempting to control for environmental and methodological contaminants (Aquabacterium and Bradyrhizobium are commonly identified as contaminants in DNA extraction kits) is required. Bacteria, such as Propionibacterium, Staphylococcus, and Streptococcus, capable of causing sight-threatening infections may reside on a healthy ocular surface. With greater understanding, we can establish whether elements of the ocular surface microbiome are harmful or protective (despite their small quantities); furthermore, new therapeutic agents can be identified to treat and prevent ocular surface infection and inflammation.
Arthrographis kalrae Keratitis Complicated by Endophthalmitis: A Case Report With Literature Review
Authors: Ting Darren Shu Jeng , Mckenna Michael , Sadiq Salman Naveed , Martin Jessica , Mudhar Hardeep S. , Meeney Adam , Patel Trushar
Published: May 2020

Objectives:

To report the first case of Arthrographis kalrae keratitis complicated by endophthalmitis in the UK and to review the current literature.

Methods:

A case report with literature review.

Results:

A 65-year-old male patient, with a background of treated B-cell lymphoma and herpes simplex virus-related neurotrophic keratopathy, presented with a large infiltrative corneal ulcer in the right eye. The patient was immediately commenced on empirical antifungal treatment in view of the clinical suspicion of fungal keratitis (FK). The initial corneal scrape identified the organism as nonspecific “mold,” and the identity of A. kalrae was subsequently confirmed using matrix-assisted laser/desorption ionization-time of flight-mass spectrometry (MALDI-TOF-MS). During the clinical course, the patient received topical, intrastromal, intracameral, and systemic antifungal treatment, repeat therapeutic corneal cross-linking treatment, and three penetrating keratoplasties. Although a temporary improvement was achieved with therapeutic corneal cross-linking treatment, the FK progressed relentlessly and was ultimately complicated by an endophthalmitis despite maximum medical and surgical treatment, eventuating in an enucleation.

Conclusions:

A. kalrae keratitis is an exceptionally rare clinical entity that poses significant therapeutic challenges. MALDI-TOF-MS serves as a useful diagnostic technique in identifying this rare organism. Although the literature suggested that A. kalrae keratitis may sometimes be controlled with antifungal medical treatment alone, this approach was proven to be futile in our immunocompromised patient with pre-existing neurotrophic keratopathy, suggesting that early surgical intervention such as therapeutic keratoplasty may be required in these cases.
Establishing a Geriatric Hip Fracture Program at a Level 1 Community Trauma Center
Authors: O'Mara-Gardner Kristin , Redfern Roberta E. , Bair Jeffrey M.
Published: May 2020

BACKGROUND:

Traditional care of patients with geriatric hip fracture has been fragmented with patients admitted under various specialty services and to different units within a hospital. This produces inconsistent care and leads to varying outcomes that can be associated with increased length of stay, delays in time from admission to surgery, and higher readmission rates.

PURPOSE:

The purpose of this article is to describe the process taken to establish a successful geriatric hip fracture program (GFP) and the initial results observed in a single institution after its implementation.

METHODS:

All patients 60 years or older, with an osteoporotic hip fracture sustained from a low energy mechanism (defined as a fall from 3-ft height or less), were included in our program. Fracture patterns include femoral neck, intertrochanteric, pertrochanteric, and subtrochanteric femur fractures including displaced, nondisplaced, and periprosthetic fractures. Preprogram data included all patients admitted from January 1, 2012, through December 31, 2014; postprogram data were collected on patients admitted between May 1, 2016, and May 1, 2018.

RESULTS:

Demographic characteristics of the populations were similar. After the GFP was implemented, the proportion of patients who were treated surgically within 24 and 48 hours increased. The average number of hours between admission and surgery significantly reduced from 35.2 to 23.2 hours. Overall length of stay was decreased by 1.8 days and readmission within 30 days of discharge was lower. Reasons for readmission were similar in both timeframes. The rate of inpatient death was similar in the two groups. Mortality within 30 days of surgery appeared somewhat higher in the post-GFP period.

CONCLUSION:

Our program found that, with the utilization of a multidisciplinary approach, we could positively influence the care of patients with geriatric hip fracture through the implementation of evidence-based practice guidelines. In the first 2 years after initiation of the GFP, our institution saw a decrease in time from admission to surgery, length of stay, and blood transfusion requirements.
Geriatric Fracture Programs
Authors: Sedlock Jennifer , Green Jaymie , Diegel-Vacek Lauren
Published: May 2020

The successful implementation of a geriatric fracture program is dependent on engaging a multidisciplinary team. The goal of these programs is to address the unique needs of patients with geriatric fracture by providing the support necessary for return to their prefracture level of activities of daily living. Identifying the key stakeholders and clarifying their role in pre- and postoperative patient support are vital to the development of such an initiative. The purpose of this article is to discuss the steps to plan and implement a geriatric fracture program in a hospital and lessons learned from our experience initiating such a program.
Physical Health of Autistic Girls and Women: A Scoping Review
Authors: Kassee Caroline , Babinski Stephanie , Tint Ami , Lunsky Yona , Brown Hilary , Ameis Stephanie H. , Szatmari Peter , Lai Meng-Chuan , Einstein Gillian
Published: May 2020

Background: There is a growing recognition of sex and gender influences in autism. Increasingly, studies include comparisons between sexes or genders, but few have focused on clarifying the characteristics of autistic girls' and women's physical health.
Methods: A scoping review was conducted to determine what is currently known about the physical health of autistic girls and women. We screened 1,112 unique articles, with 40 studies meeting the inclusion criteria. We used a convergent iterative process to synthesize this content into broad thematic areas.
Results: Overall, autistic girls and women experience more physical health challenges compared to non-autistic girls and women, and to autistic boys and men. Preliminary evidence suggests increased neurological conditions (e.g., epilepsy) in autistic girls and women compared to autistic boys and men. As well, the literature suggests increased endocrine/reproductive conditions in autistic girls and women compared to non-autistic girls and women.
Limitations: The literature has substantial heterogeneity in how physical health conditions were assessed and reported. Further, our explicit focus on physical health may have constrained the ability to examine potential interactions between mental and physical health. In addition, the widely differing research aims and methodologies make it difficult to reach definitive conclusions. Nevertheless, in keeping with the goals of a scoping review, we were able to identify key themes to guide future research.
Conclusions: Emerging themes in the literature suggest that autistic girls and women have heightened rates of physical health challenges compared to autistic boys and men, and non-autistic girls and women. Clinicians should seek to provide holistic care for this population that includes a focus on physical health and recognizes that autistic girls and women have co-occurring conditions that differ from those of autistic boys and men.
Hospital-acquired infective endocarditis during Covid-19 pandemic
Authors: Ramos-Martinez Antonio , Fernndez-Cruz Ana , Dominguez Fernando , Forteza Alberto , Cobo Marta , Sanchez-Romero Isabel , asensio Angel
Published: May 2020

Background. The COVID pandemic has had a major impact on healthcare in hospitals, including the diagnosis and treatment of infections. Hospital-acquired infective endocarditis (HAIE) is a severe complication of medical procedures that has shown a progressive increase in recent years.
Objectives. to determine whether the incidence of HAIE during the first two months of the epidemic (March-April 2020) was higher than previously observed and to describe the clinical characteristics of these cases. The probability of studied event (HAIE) during the studied period was calculate by Poisson distribution.
Results. Four cases of HAIE were diagnosed in our institution during the study period. The incidence of HAIE during the study period was 2/patient-month and 0.25/patient-month during the previous 5 years (p=0.024). Two cases appeared during admission for COVID-19 with pulmonary involvement treated with metilprednisolone and tocilizumab. The other two cases were admitted to the hospital during the epidemic. All cases underwent central venous and urinary catheterization during admission. The etiology of HAIE was Enterococcus faecalis (2 cases), Staphylococcus aureus and Candida albicans (one case each). A source of infection was identified in three cases (central venous catheter, peripheral venous catheter, sternal wound infection, respectively). One patient was operated on. There were no fatalities during the first 30 days of follow-up.
Conclusion. The incidence of HAIE during COVID-19 pandemic in our institution was higher than usual. In order to reduce the risk of this serious infection, optimal catheter care, appropriate use of corticosteroids and interleukin antagonists and early treatment of every local infection should be prioritized during coronavirus outbreaks.
The correspondence between the structure of the terrestrial mobility network and the emergence of COVID-19 in Brazil
Authors: Freitas Vander L. S. , Konstantyner Thais C. R. O. , Feitosa Jeferson , Sepetauskas Catia S. N. , Santos Leonardo B. L.
Published: May 2020

BACKGROUND

the inter-cities mobility network serves as a proxy for the SARS-CoV-2 spreading network in a country.

OBJECTIVE

to investigate the correspondences between the structure of the mobility network and the emergence of COVID-19 cases in Brazilian cities.

METHODS

we adopt the data from the Brazilian Health Ministry and the terrestrial flow of people between cities from the IBGE database in two scales: Brazilian cities without the North region and cities from the Sao Paulo state. Grounded on the complex networks approach, cities are represented as nodes and the flows as edges. Network centrality measures such as strength and degree are ranked and compared to the list of Brazilian cities, ordered according to the day that they confirmed the first case of COVID-19.

FINDINGS

The strength presents the best correspondences and the interiorization process of SARS-CoV-2 is captured in the Sao Paulo state when different thresholds are applied to the network flows.

MAIN CONCLUSIONS

the strength captures the cities with a higher vulnerability of receiving new cases of COVID-19. Some countryside cities such as Feira de Santana (Bahia state), Ribeirao Preto (Sao Paulo state), and Caruaru (Pernambuco state) have strength comparable to states’ capitals, making them potential super spreaders.

Financial support

São Paulo Research Foundation (FAPESP) Grant Numbers 2015/50122-0, 2018/06205-7 and 2020/06837-3; DFG-IRTG Grant Number 1740/2; CNPq Grant Numbers 420338/2018-7 and 101720/2020-3.
A Novel Approach to Data Driven Pandemic Recovery: The Pandemic Recovery Acceleration Model
Authors: Gold Jeffrey P , Wichman Christopher , Bayles Kenneth , Khan Ali S , Kratochvil Christopher , Lawler James V , Lowe John Martin , Schwedhelm Shelly , Grimm Brandon
Published: May 2020

A data driven approach to guide the global, regional and local pandemic recovery planning is key to the safety, efficacy and sustainability of all pandemic recovery efforts. The Pandemic Recovery Acceleration Model (PRAM) analytic tool was developed and implemented state wide in Nebraska to allow health officials, public officials, industry leaders and community leaders to capture a real time snapshot of how the COVID-19 pandemic is affecting their local community, a region or the state and use this novel lens to aid in making key mitigation and recovery decisions. This is done by using six commonly available metrics that are monitored daily across the state describing the pandemic impact: number of new cases, percent positive tests, deaths, occupied hospital beds, occupied intensive care beds and utilized ventilators, all directly related to confirmed COVID-19 patients.
Nebraska is separated into six Health Care Coalitions based on geography, public health and medical care systems. The PRAM aggregates the data for each of these geographic regions based on disease prevalence acceleration and health care resource utilization acceleration, producing real time analysis of the acceleration of change for each metric individually and also combined into a single weighted index, the PRAM Recovery Index. These indices are then shared daily with the state leadership, coalition leaders and public health directors and also tracked over time, aiding in real time regional and statewide decisions of resource allocation and the extent of use of comprehensive non-pharmacologic interventions.
Epidemiology of sleep disorders during COVID-19 pandemic: A systematic scoping review protocol
Authors: Tasnim Samia , Rahman Mariya , Pawar Priyanka , Zou Liye , Sultana Abida , McKyer E. Lisako J. , Ma Ping , Hossain Md Mahbub
Published: May 2020

Background: The coronavirus disease (COVID-19) is impacting human health globally. In addition to physical health problems, a growing burden of mental health problems has become a global concern amid this pandemic. Sleep disorders are major mental health problems associated with increased psychosocial stressors; however, no research synthesis is available on the epidemiology of sleep disorders. In this systematic scoping review, we aim to assess the current evidence on the epidemiological burden, associated factors, and interventions from the existing literature on sleep disorders.
Methods: We will search seven major health databases and additional sources to identify, evaluate, and synthesize empirical studies on the prevalence and correlates of sleep disorders and available interventions addressing the same. We will use the Joanna Briggs Institute Methodology for Scoping Review and report the findings using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR) checklist.
Conclusion: This review will identify the epidemiological burden of and interventions for sleep disorders. The findings of this review will be widely communicated with the research and professional community to facilitate future research and practice.
Requirement and functional redundancy of two large ribonucleotide reductase subunit genes for cell cycle, chloroplast biogenesis in tomato
Authors: Gu Mengjun , Liu Yi , Cui Man , Wu Huilan , Ling Hong-Qing
Published: May 2020

Ribonucleotide reductase (RNR), functioning in thede novosynthesis of dNTPs, is crucial for DNA replication and cell cycle progression. However, the knowledge about the RNR in plants is still limited. In this study, we isolatedylc1(youngleafchlorosis1) mutant, which exhibited many development defects such as dwarf stature, chlorotic young leaf, and smaller fruits. Map-based cloning, complementation, and knocking-out experiments confirmed thatYLC1encodes a large subunit of RNR (SlRNRL1), an enzyme involved in thede novobiosynthesis of dNTPs. Physiological and transcriptomic analyses indicate that SlRNRL1 plays a crucial role in the regulation of cell cycle, chloroplast biogenesis, and photosynthesis in tomato. In addition, we knocked outSlRNRL2(aSlRNRL1homolog) using CRISPR-Cas9 technology in the tomato genome, and found that SlRNRL2, possessing a redundant function with SlRNRL1, played a weak role in the formation of RNR complex due to its low expression intensity. Genetic analysis reveals that SlRNRL1 and SlRNRL2 are essential for tomato growth and development as the double mutantslrnrl1slrnrl2is lethal. This also implies that thede novosynthesis of dNTPs is required for seed development in tomato. Overall, our results provide a new insight for understanding the SlRNRL1 and SlRNRL2 functions and the mechanism ofde novobiosynthesis of dNTPs in plants.
Doxycycline and Hydroxychloroquine as Treatment for High-Risk COVID-19 Patients: Experience from Case Series of 54 Patients in Long-Term Care Facilities
Authors: Ahmad Imtiaz , Alam Mohammud , Saadi Ryan , Mahmud Saborny , Saadi Emily
Published: May 2020

Importance

Patients in long-term care facilities (LTCF) are at a high-risk of contracting COVID-19 due to advanced age and multiple comorbidities. Without effective treatments, outbreaks in such facilities will become commonplace and will result in severe morbidity and mortality. The effectiveness of doxycycline (DOXY) and hydroxychloroquine (HCQ) combination therapy in high risk COVID-19 patients in longterm care facilities is not yet understood.

Objective

The goal of this analysis is to describe outcomes after use of DOXY-HCQ combination in high-risk COVID-19 patients in LTCF.

Design

Case-series analysis.

Setting

Three (3) LTCFs in New York.

Participants

From March 19 to March 30, 2020, fifty-four (54) patients, residents of three (3) LTCFs in New York and diagnosed (confirmed or presumed) with COVID-19, were included in this analysis.

Exposure

All patients who were diagnosed (confirmed or presumed) with COVID-19 received DOXY-HCQ combination therapy along with standard of care.

Main Outcomes and Measures

Patients characteristics, clinical recovery, radiological improvements, medication side-effects, hospital transfer, and death were assessed as outcome measures.

Results

A series of fifty-four (54) high-risk patients, who developed a sudden onset of fever, cough, and shortness of breath (SOB) and were diagnosed or presumed to have COVID-19, were started with a combination of DOXY-HCQ and 85% (n=46) patients showed clinical recovery defined as: resolution of fever and SOB, or a return to baseline setting if patients are ventilator-dependent. A total of 11% (n=6) patients were transferred to acute care hospitals due to clinical deterioration and 6% (n=3) patients died in the facilities. Naive Indirect Comparison suggests these data were significantly better outcomes than the data reported in MMWR (reported on March 26, 2020) from a long-term care facility in King County, Washington where 57% patients were hospitalized, and 22% patients died.

Conclusion

The clinical experience of this case series indicates DOXY-HCQ treatment in high-risk COVID-19 patients is associated with a reduction in clinical recovery, decreased transfer to hospital and decreased mortality were observed after treatment with DOXY-HCQ.
COVID-19 in Great Britain: epidemiological and clinical characteristics of the first few hundred (FF100) cases: a descriptive case series and case control analysis
Authors: Boddington Nicola L , Charlett Andre , Elgohari Suzanne , Walker Jemma L , Mcdonald Helen , Byers Chloe , Coughlan Laura , Garcia Vilaplana Tatiana , Whillock Rosie , Sinnathamby Mary , Panagiotopoulos Nikolaos , Letley Louise , MacDonald Pauline , Vivancos Roberto , Edeghere Obaghe , Shingleton Joseph , Bennett Emma , Grint Daniel J , Strongman Helen , Mansfield Kathryn E , Rentsch Christopher , Minassian Caroline , Douglas Ian J , Mathur Rohini , Peppa Maria , Cottrell Simon , McMenamin Jim , Zambon Maria , Ramsay Mary , Dabrera Gavin , Saliba Vanessa , Lopez Bernal Jamie
Published: May 2020

Objectives:
Following detection of the first virologically-confirmed cases of COVID-19 in Great Britain, an enhanced surveillance study was initiated by Public Health England to describe the clinical presentation, course of disease and identify risk factors for infection of the first few hundred cases.
Methods:
Information was collected on the first COVID-19 cases according to the First Few X WHO protocol. Case-control analyses of the sensitivity, specificity and predictive value of symptoms and risk factors for infection were conducted. Point prevalences of underlying health conditions among the UK general population were presented.
Findings:
The majority of FF100 cases were imported (51.4%), of which the majority had recent travel to Italy (71.4%). 24.7% were secondary cases acquired mainly through household contact (40.4%). Children had lower odds of COVID-19 infection compared with the general population.
The clinical presentation of cases was dominated by cough, fever and fatigue. Non-linear relationships with age were observed for fever, and sensitivity and specificity of symptoms varied by age.
Conditions associated with higher odds of COVID-19 infection (after adjusting for age and sex) were chronic heart disease, immunosuppression and multimorbidity.
Conclusion:
This study presents the first epidemiological and clinical summary of COVID-19 cases in Great Britain. The FFX study design enabled systematic data collection. The study was able to characterize the risk factors for infection with population prevalence estimates setting these relative risks into a public health context. It also provides important evidence for generating case definitions to support public health risk assessment, clinical triage and diagnostic algorithms.
GWAS of Depression Phenotypes in the Million Veteran Program and Meta-analysis in More than 1.2 Million Participants Yields 178 Independent Risk Loci
Authors: Levey Daniel F. , Stein Murray B. , Wendt Frank R. , Pathak Gita A. , Zhou Hang , Aslan Mihaela , Quaden Rachel , Harrington Kelly M. , Sanacora Gerard , McIntosh Andrew M. , Concato John , Polimanti Renato , Gelernter Joel
Published: May 2020

We report a large meta-analysis of depression using data from the Million Veteran Program (MVP), 23andMe Inc., UK Biobank, and FinnGen; including individuals of European ancestry (n=1,154,267; 340,591 cases) and African ancestry (n=59,600; 25,843 cases). We identified 223 and 233 independent SNPs associated with depression in European ancestry and transancestral analysis, respectively. Genetic correlations within the MVP cohort across electronic health records diagnosis, survey self-report of diagnosis, and a 2-item depression screen exceeded 0.81. Using transcriptome-wide association study (TWAS) we found significant associations for gene expression in several brain regions, including hypothalamus (NEGR1, p=3.19×10−25) and nucleus accumbens (DRD2, p=1.87×10−20). 178 genomic risk loci were fine-mapped to find likely causal variants. We identified likely pathogenicity in these variants and overlapping gene expression for 17 genes from our TWAS, including TRAF3. This study sheds light on the genetic architecture of depression and provides new insight into the interrelatedness of complex psychiatric traits.
Biomarkers of Parkinson's Disease: Screening Vital Signs and Routine Blood Tests
Authors: IWAKI Hirotaka , Leonard Hampton L. , Bandres Ciga Sara , Blauwendraat Cornelis , Makarious Mary B. , Scholz Sonja W. , Nishikawa Noriko , Faghri Faraz , Frasier Mark , Gibbs J. Raphael , Singleton Andrew B. , Nalls Mike A. , Hernandez Dena G.
Published: May 2020

BACKGROUND: There is a need for reliable, objective, and easily accessible biomarkers for Parkinson's disease.
OBJECTIVES: The purpose of this study was to screen biomarkers from vital signs and routine blood tests.
METHODS: Longitudinal data of up to 7 years of vital signs and routine blood tests from 418 patients with Parkinson's disease (PD) untreated at baseline and 185 individuals without any neurological disease were analyzed using linear mixed models. We nominated the biomarkers whose main associations with the measurements were significant as differentiating biomarkers. Similarly, we nominated the interaction effects between biomarkers and time from baseline as progression biomarkers. We tested for 49 biomarkers, and multiple comparison was corrected with the false-discovery-rate of 0.05. We further evaluated the potential biomarkers with regard to their importance in diagnosis prediction and their association with sub-scores on the Movement Disorder Society-Unified Parkinson's Disease Rating Scale (MDS-UPDRS). We also assessed the relationship of the associations using bioinformatics.
RESULTS: Heart rate, systolic blood pressure, white blood cell fractions, neutrophil counts, serum albumin, sodium and AST were different between PD and controls. The causality or genetic correlations of these biomarkers to PD were not observed. Chronological changes in height, albumin, hemoglobin, and bicarbonate were different in PD. These biomarkers were associated with MDS-UPDRS sub-scores.
Conclusions In this study, the potential of some easily accessible biomarkers for diagnosis and disease progression was presented. Further investigation of the mechanisms underlying these associations is important for a deeper understanding of the disease and the better management of patients.
An Interpretable Machine Learning Framework for Accurate Severe vs Non-severe COVID-19 Clinical Type Classification
Authors: Chen Yuanfang , Ouyang Liu , Bao Sheng , Li Qian , Han Lei , Zhang Hengdong , Zhu Baoli , Xu Ming , Liu Jie , Ge Yaorong , Chen Shi
Published: May 2020

Effectively and efficiently diagnosing COVID-19 patients with accurate clinical type is essential to achieve optimal outcomes of the patients as well as reducing the risk of overloading the healthcare system. Currently, severe and non-severe COVID-19 types are differentiated by only a few clinical features, which do not comprehensively characterize complicated pathological, physiological, and immunological responses to SARS-CoV-2 invasion in different types. In this study, we recruited 214 confirmed COVID-19 patients in non-severe and 148 in severe type, from Wuhan, China. The patients' comorbidity and symptoms (26 features), and blood biochemistry (26 features) upon admission were acquired as two input modalities. Exploratory analyses demonstrated that these features differed substantially between two clinical types. Machine learning random forest (RF) models using features in each modality were developed and validated to classify COVID-19 clinical types. Using comorbidity/symptom and biochemistry as input independently, RF models achieved >90% and >95% predictive accuracy, respectively. Input features' importance based on Gini impurity were further evaluated and top five features from each modality were identified (age, hypertension, cardiovascular disease, gender, diabetes; D-Dimer, hsTNI, neutrophil, IL-6, and LDH). Combining top 10 multimodal features, RF model achieved >99% predictive accuracy. These findings shed light on how the human body reacts to SARS-CoV-2 invasion as a unity and provide insights on effectively evaluating COVID-19 patient's severity and developing treatment plans accordingly. We suggest that symptoms and comorbidities can be used as an initial screening tool for triaging, while biochemistry and features combined are applied when accuracy is the priority.
Field evaluation of biocontrol agents against black-foot and Petri diseases of grapevine
Authors: del Pilar Martínez-Diz María , Díaz-Losada Emilia , Andrés-Sodupe Marcos , Bujanda Rebeca , Maldonado-González María Mercedes , Ojeda Sonia , Yacoub Amira , Rey Patrice , Gramaje David
Published: May 2020

BACKGROUND

Black-foot and Petri diseases are the main fungal diseases associated with young grapevine decline. Two field experiments were established to evaluate the preventive effect of two potential biocontrol agents (BCAs), i.e.Streptomycessp. E1 + R4 andPythium oligandrumPo37, and three BCA-commercial products containingTrichoderma atrovirideSC1,Trichoderma koningiiTK7 andPseudomonas fluorescens+Bacillus atrophaeuson fungal infection in grafted plants and plant growth parameters.

RESULTS

The effectiveness of some BCA in reducing the incidence and severity of both diseases was dependent on the plant part analyzed and the plant age. No single BCA application was able to control both diseases.Streptomycessp. E1+R4 were able to reduce significantly black-foot disease infection whileP. oligandrumPo37 andTrichodermaspp. were able to reduce significantly Petri disease infection. BCA treatments had no effect on the shoot weight, and root weight was significantly lower in all BCA treatments with respect to the control.

CONCLUSIONS

The combination of the disease-suppressive activity of two or more beneficial microbes in a biocontrol preparation is required to prevent infection by black-foot and Petri disease fungi in vineyards.
Network reconstruction for trans acting genetic loci using multi-omics data and prior information
Authors: Hawe Johann S. , Saha Ashis , Waldenberger Melanie , Kunze Sonja , Wahl Simone , Müller-Nurasyid Martina , Prokisch Holger , Grallert Harald , Herder Christian , Peters Annette , Strauch Konstantin , Theis Fabian J. , Gieger Christian , Chambers John , Battle Alexis , Heinig Matthias
Published: May 2020

Background

Molecular multi-omics data provide an in-depth view on biological systems, and their integration is crucial to gain insights in complex regulatory processes. These data can be used to explain disease related genetic variants by linking them to intermediate molecular traits (quantitative trait loci, QTL). Molecular networks regulating cellular processes leave footprints in QTL results as so-calledtrans-QTL hotspots. Reconstructing these networks is a complex endeavor and use of biological prior information has been proposed to alleviate network inference. However, previous efforts were limited in the types of priors used or have only been applied to model systems. In this study, we reconstruct the regulatory networks underlyingtrans-QTL hotspots using human cohort data and data-driven prior information.

Results

We devised a strategy to integrate QTL with human population scale multi-omics data and comprehensively curated prior information from large-scale biological databases. State-of-the art network inference methods applied to these data and priors were used to recover the regulatory networks underlyingtrans-QTL hotspots. We benchmarked inference methods and showed, that Bayesian strategies using biologically-informed priors outperform methods without prior data in simulated data and show better replication across datasets. Application of our approach to human cohort data highlighted two novel regulatory networks related to schizophrenia and lean body mass for which we generated novel functional hypotheses.

Conclusion

We demonstrate, that existing biological knowledge can be leveraged for the integrative analysis of networks underlyingtransassociations to deduce novel hypotheses on cell regulatory mechanisms.
To pool or not to pool: Can we ignore cross-trial variability in FMRI?
Authors: Chen Gang , Padmala Srikanth , Chen Yi , Taylor Paul A , Cox Robert W , Pessoa Luiz
Published: May 2020

In this work, we investigate the importance of explicitly accounting for cross-trial variability in neuroimaging data analysis. To attempt to obtain reliable estimates in a task-based experiment, each condition is usually repeated across many trials. The investigator may be interested in (a) condition-level effects, (b) trial-level effects, or (c) the association of trial-level effects with the corresponding behavior data. The typical strategy for condition-level modeling is to create one regressor per condition at the subject level with the underlying assumption that responses do not change across trials. In this methodology ofcomplete pooling, all cross-trial variability is ignored and dismissed as random noise that is swept under the rug of model residuals. Unfortunately, this framework invalidates the generalizability from the confine of specific trials (e.g., particular faces) to the associated stimulus category (“face”), and may inflate the statistical evidence when the trial sample size is not large enough. Here we propose an adaptive and computationally tractable framework that meshes well with the current two-level pipeline and explicitly accounts for trial-by-trial variability. The trial-level effects are first estimated per subject throughno pooling. To allow generalizing beyond the particular stimulus set employed, the cross-trial variability is modeled at the population level throughpartial poolingin a multilevel model, which permits accurate effect estimation and characterization. Alternatively, trial-level estimates can be used to investigate, for example, brain-behavior associations or correlations between brain regions. Furthermore, our approach allows appropriate accounting for serial correlation, handling outliers, adapting to data skew, and capturing nonlinear brain-behavior relationships. By applying a Bayesian multilevel model framework at the level of regions of interest to an experimental dataset, we show how multiple testing can be addressed and full results reported without arbitrary dichotomization. Our approach revealed important differences compared to the conventional method at the condition level, including how the latter can distort effect magnitude and precision. Notably, in some cases our approach led to increased statistical sensitivity. In summary, our proposed framework provides an effective strategy to capture trial-by-trial responses that should be of interest to a wide community of experimentalists.
Mismatch Negativity Predicts Pattern Separation
Authors: Herman Deena , Baker Stevenson , Cazes Jaime , Alain Claude , Rosenbaum R. Shayna
Published: May 2020

We are so tuned to sensory changes that we can detect novelty within hundreds of milliseconds. To what extent does our capacity to automatically discriminate auditory inputs influence encoding of long-term memories? We recorded mismatch negativity (MMN), an event-related potential (ERP) indexing perceptual discrimination, as participants were presented with sound patterns while watching a muted movie. MMN strength predicted how well naïve listeners separated the previously heard from new micropatterns on a subsequent recognition test, providing evidence that the MMN translates into mnemonic pattern separation. Our investigation is the first to show that our capacity to discriminate auditory inputs, as measured by MMN, gives rise to unique memories.
When do opposites attract? A model uncovering the evolution of disassortative mating
Authors: Maisonneuve Ludovic Claude , Beneteau Thomas , Joron Mathieu , Smadi Charline , Llaurens Violaine
Published: May 2020

Disassortative mating is a rare form of mate preference that promotes the persistence of polymorphism. While the evolution of assortative mating, and its consequences on trait variation and speciation have been extensively studied, the conditions enabling the evolution of disassortative mating are still poorly understood. Mate preferences increase the risk of missing mating opportunities, a cost that can be compensated by a greater fitness of offspring. Heterozygote advantage should therefore promote the evolution of disassortative mating, which maximizes the number of heterozygous offspring. From the analysis of a two-locus diploid model, with one locus controlling the mating cue under viability selection and the other locus coding for the level of disassortative preference, we show that heterozygote advantage and negative frequency-dependent viability selection acting at the cue locus promote the fixation of disassortative preferences. The conditions predicted to enable the evolution of disassortative mating in our model match the selection regimes acting on traits subject to disassortative mating behavior in the wild. In sharp contrast with the evolution of assortative preferences, we also show that disassortative mating generates a negative frequency-dependent sexual selection, which in turn disadvantages heterozygotes at the cue locus, limiting the evolution of disassortative preferences. This negative feedback loop could explain why this behavior is rare in natural populations.
Resolving the heterogeneity of diaphragmatic mesenchyme: a novel mouse model of congenital diaphragmatic hernia
Authors: Cleal Louise , Martinez-Estrada Ofelia , Chau You-Ying
Published: May 2020

Congenital diaphragmatic hernia (CDH) is a relatively common developmental defect with considerable mortality and morbidity. Diaphragm formation is a complex process, involving several cell types, each with different developmental origins. Due to this complexity, the aetiology of CDH is not well understood. The pleuroperitoneal folds (PPFs) and the post hepatic mesenchymal plate (PHMP) are transient structures that are essential during diaphragm development. Using several mouse models including lineage tracing, we demonstrate the heterogeneous nature of the cells that make up the PPFs. The conditional deletion ofWt1(Wilms’ Tumour gene) in the non-muscle mesenchyme of the PPFs results in CDH. We show that the fusion of the PPFs and the PHMP to form a continuous band of tissue involves migration of cells from both sources. The PPFs of mutant mice fail to fuse with the PHMP and exhibit increased RALDH2 expression. However, no changes in the expression of genes implicated in epithelial-to-mesenchymal transition (EMT) are observed. Additionally, the mutant PPFs lack migrating myoblasts and muscle connective tissue fibroblasts (TCF4+/GATA4+), suggesting possible interactions between these cell types. Our study demonstrates the importance of the non-muscle mesenchyme in diaphragm development.

Author Summary

Congenital diaphragmatic hernia (CDH) is a frequent developmental defect and it remains one of the most difficult problems of perinatology. The defect can be repaired by surgery but it is often associated with complications and total mortalities are still high (50-60%). The causes of CDH are largely unknown. Body cavity formation is a carefully regulated process, and diaphragm formation defines the thoracic and abdominal cavities. Connective tissue and muscle fibres are the known major players involved in diaphragm formation. Our current study emphasises another player, the mesenchymal cells. We manipulate the expression of an important developmental regulator,Wt1(Wilms’ tumour gene), in mesenchymal cells in a tissue specific manner using transgenic mouse models. We found that mutant mice can survive till birth, develop diaphragmatic hernia, and die shortly after birth. AblatingWt1in the mesenchymal cells leads to ceased movement, and the failure to form a continuous band of tissue. In our model, disruption of mesenchymal cell movement leads to the attenuation of migration of connective tissue fibroblasts and myoblasts, suggesting possible interactions between these cell types.