bluuebunny/crossref_metadata_2025 huggingface dataset:
WormBase: a modern Model Organism Information Resource
Authors: Harris Todd W , Arnaboldi Valerio , Cain Scott , Chan Juancarlos , Chen Wen J , Cho Jaehyoung , Davis Paul , Gao Sibyl , Grove Christian A , Kishore Ranjana , Lee Raymond Y N , Muller Hans-Michael , Nakamura Cecilia , Nuin Paulo , Paulini Michael , Raciti Daniela , Rodgers Faye H , Russell Matthew , Schindelman Gary , Auken Kimberly V , Wang Qinghua , Williams Gary , Wright Adam J , Yook Karen , Howe Kevin L , Schedl Tim , Stein Lincoln , Sternberg Paul W
Published: October 2019

WormBase (https://wormbase.org/) is a mature Model Organism Information Resource supporting researchers using the nematode Caenorhabditis elegans as a model system for studies across a broad range of basic biological processes. Toward this mission, WormBase efforts are arranged in three primary facets: curation, user interface and architecture. In this update, we describe progress in each of these three areas. In particular, we discuss the status of literature curation and recently added data, detail new features of the web interface and options for users wishing to conduct data mining workflows, and discuss our efforts to build a robust and scalable architecture by leveraging commercial cloud offerings. We conclude with a description of WormBase's role as a founding member of the nascent Alliance of Genome Resources.
MBKbase for rice: an integrated omics knowledgebase for molecular breeding in rice
Authors: Peng Hua , Wang Kai , Chen Zhuo , Cao Yinghao , Gao Qiang , Li Yan , Li Xiuxiu , Lu Hongwei , Du Huilong , Lu Min , Yang Xin , Liang Chengzhi
Published: October 2019

To date, large amounts of genomic and phenotypic data have been accumulated in the fields of crop genetics and genomic research, and the data are increasing very quickly. However, the bottleneck to using big data in breeding is integrating the data and developing tools for revealing the relationship between genotypes and phenotypes. Here, we report a rice sub-database of an integrated omics knowledgebase (MBKbase-rice, www.mbkbase.org/rice), which integrates rice germplasm information, multiple reference genomes with a united set of gene loci, population sequencing data, phenotypic data, known alleles and gene expression data. In addition to basic data search functions, MBKbase provides advanced web tools for genotype searches at the population level and for visually displaying the relationship between genotypes and phenotypes. Furthermore, the database also provides online tools for comparing two samples by their genotypes and finding target germplasms by genotype or phenotype information, as well as for analyzing the user submitted SNP or sequence data to find important alleles in the germplasm. A soybean sub-database is planned for release in 3 months and wheat and maize will be added in 1–2 years. The data and tools integrated in MBKbase will facilitate research in crop functional genomics and molecular breeding.
AraPheno and the AraGWAS Catalog 2020: a major database update including RNA-Seq and knockout mutation data for Arabidopsis thaliana
Authors: Togninalli Matteo , Seren Ümit , Freudenthal Jan A , Monroe J Grey , Meng Dazhe , Nordborg Magnus , Weigel Detlef , Borgwardt Karsten , Korte Arthur , Grimm Dominik G
Published: October 2019

Genome-wide association studies (GWAS) are integral for studying genotype-phenotype relationships and gaining a deeper understanding of the genetic architecture underlying trait variation. A plethora of genetic associations between distinct loci and various traits have been successfully discovered and published for the model plant Arabidopsis thaliana. This success and the free availability of full genomes and phenotypic data for more than 1,000 different natural inbred lines led to the development of several data repositories. AraPheno (https://arapheno.1001genomes.org) serves as a central repository of population-scale phenotypes in A. thaliana, while the AraGWAS Catalog (https://aragwas.1001genomes.org) provides a publicly available, manually curated and standardized collection of marker-trait associations for all available phenotypes from AraPheno. In this major update, we introduce the next generation of both platforms, including new data, features and tools. We included novel results on associations between knockout-mutations and all AraPheno traits. Furthermore, AraPheno has been extended to display RNA-Seq data for hundreds of accessions, providing expression information for over 28 000 genes for these accessions. All data, including the imputed genotype matrix used for GWAS, are easily downloadable via the respective databases.
Assembly and annotation of the mitochondrial minicircle genome of a differentiation-competent strain of Trypanosoma brucei
Authors: Cooper Sinclair , Wadsworth Elizabeth S , Ochsenreiter Torsten , Ivens Alasdair , Savill Nicholas J , Schnaufer Achim
Published: October 2019

Kinetoplastids are protists defined by one of the most complex mitochondrial genomes in nature, the kinetoplast. In the sleeping sickness parasite Trypanosoma brucei, the kinetoplast is a chain mail-like network of two types of interlocked DNA molecules: a few dozen ∼23-kb maxicircles (homologs of the mitochondrial genome of other eukaryotes) and thousands of ∼1-kb minicircles. Maxicircles encode components of respiratory chain complexes and the mitoribosome. Several maxicircle-encoded mRNAs undergo extensive post-transcriptional RNA editing via addition and deletion of uridines. The process is mediated by hundreds of species of minicircle-encoded guide RNAs (gRNAs), but the precise number of minicircle classes and gRNA genes was unknown. Here we present the first essentially complete assembly and annotation of the kinetoplast genome of T. brucei. We have identified 391 minicircles, encoding not only ∼930 predicted ‘canonical’ gRNA genes that cover nearly all known editing events (accessible via the web at http://hank.bio.ed.ac.uk), but also ∼370 ‘non-canonical’ gRNA genes of unknown function. Small RNA transcriptome data confirmed expression of the majority of both categories of gRNAs. Finally, we have used our data set to refine definitions for minicircle structure and to explore dynamics of minicircle copy numbers.
Control of ϕC31 integrase-mediated site-specific recombination by protein trans-splicing
Authors: Olorunniji Femi J , Lawson-Williams Makeba , McPherson Arlene L , Paget Jane E , Stark W Marshall , Rosser Susan J
Published: October 2019

Serine integrases are emerging as core tools in synthetic biology and have applications in biotechnology and genome engineering. We have designed a split-intein serine integrase-based system with potential for regulation of site-specific recombination events at the protein level in vivo. The ϕC31 integrase was split into two extein domains, and intein sequences (Npu DnaEN and Ssp DnaEC) were attached to the two termini to be fused. Expression of these two components followed by post-translational protein trans-splicing in Escherichia coli generated a fully functional ϕC31 integrase. We showed that protein splicing is necessary for recombination activity; deletion of intein domains or mutation of key intein residues inactivated recombination. We used an invertible promoter reporter system to demonstrate a potential application of the split intein-regulated site-specific recombination system in building reversible genetic switches. We used the same split inteins to control the reconstitution of a split Integrase-Recombination Directionality Factor fusion (Integrase-RDF) that efficiently catalysed the reverse attR x attL recombination. This demonstrates the potential for split-intein regulation of the forward and reverse reactions using the integrase and the integrase-RDF fusion, respectively. The split-intein integrase is a potentially versatile, regulatable component for building synthetic genetic circuits and devices.
Bovine Genome Database: new annotation tools for a new reference genome
Authors: Shamimuzzaman Md , Le Tourneau Justin J , Unni Deepak R , Diesh Colin M , Triant Deborah A , Walsh Amy T , Tayal Aditi , Conant Gavin C , Hagen Darren E , Elsik Christine G
Published: October 2019

The Bovine Genome Database (BGD) (http://bovinegenome.org) has been the key community bovine genomics database for more than a decade. To accommodate the increasing amount and complexity of bovine genomics data, BGD continues to advance its practices in data acquisition, curation, integration and efficient data retrieval. BGD provides tools for genome browsing (JBrowse), genome annotation (Apollo), data mining (BovineMine) and sequence database searching (BLAST). To augment the BGD genome annotation capabilities, we have developed a new Apollo plug-in, called the Locus-Specific Alternate Assembly (LSAA) tool, which enables users to identify and report potential genome assembly errors and structural variants. BGD now hosts both the newest bovine reference genome assembly, ARS-UCD1.2, as well as the previous reference genome, UMD3.1.1, with cross-genome navigation and queries supported in JBrowse and BovineMine, respectively. Other notable enhancements to BovineMine include the incorporation of genomes and gene annotation datasets for non-bovine ruminant species (goat and sheep), support for multiple assemblies per organism in the Regions Search tool, integration of additional ontologies and development of many new template queries. To better serve the research community, we continue to focus on improving existing tools, developing new tools, adding new datasets and encouraging researchers to use these resources.
Arteriovenous access placement and renal function decline
Authors: Hahn Lundström Ulrika , Hedin Ulf , Gasparini Alessandro , Caskey Fergus J , Carrero Juan-Jesus , Evans Marie
Published: October 2019

Background

There is controversial evidence on whether arteriovenous access (AVA) placement may protect renal function and hence should be considered in the timing of access placement. This study aimed to investigate the association between AVA placement and estimated glomerular filtration rate (eGFR) decline as compared with the placement of a peritoneal dialysis catheter (PDC) at a similar time point.

Methods

We studied a cohort of 744 pre-dialysis patients in Stockholm, Sweden, who underwent surgery for AVA or PDC between 2006 and 2012. Data on comorbidity, medication and laboratory measures were collected 100 days before and after surgery. Patients were followed until dialysis start, death or 100 days, whichever came first. The primary outcome was difference in eGFR decline after AVA surgery compared with PDC. Decline in eGFR was estimated through linear mixed models with random intercept and slope, before and after surgery.

Results

There were 435 AVA and 309 PDC patients. The AVA patients had higher eGFR (8.1 mL/min/1.73 m2 versus 7.0 mL/min/1.73 m2) and less rapid eGFR decline before surgery (−5.6 mL/min/1.73 m2/year compared with −6.7 mL/min/1.73 m2/year for PDC). We found no difference in eGFR decline after surgery in AVA patients compared with PDC patients [AVA progressed 0.26 (95% confidence interval −0.88 to 0.35) mL/min/1.73 m2/year faster after surgery compared with PDC].

Conclusions

There was no significant difference in eGFR decline after placement of an AVA compared with a PDC. Both forms of access were associated with reduced eGFR decline in our population. The need for dialysis remains the main determinant for timing of access surgery.
Central Sensitization and Catastrophism Symptoms Are Associated with Chronic Myofascial Pain in the Gastrocnemius of Athletes
Authors: San-Antolín Marta , Rodríguez-Sanz David , Becerro-de-Bengoa-Vallejo Ricardo , Losa-Iglesias Marta Elena , Casado-Hernández Israel , López-López Daniel , Calvo-Lobo César
Published: October 2019

Objective

To compare central sensitization symptoms, presence of central sensitivity syndrome (CSS), catastrophism, rumination, magnification, and helplessness symptoms between athletes with gastrocnemius myofascial pain and healthy athletes. Furthermore, to predict central sensitization symptoms based on sociodemographic and descriptive data, catastrophism features, and presence of gastrocnemius myofascial pain in athletes.

Design

Case–control study.

Setting

Outpatient clinic.

Subjects

Fifty matched paired athletes were recruited and divided into patients with chronic (more than three months) gastrocnemius myofascial pain (N = 25) and healthy subjects (N = 25).

Methods

Central sensitization symptoms and CSS presence (≥40 points) were determined by the Central Sensitization Questionnaire (CSQ). Catastrophism symptoms and rumination, magnification, and helplessness domains were measured by the Pain Catastrophizing Scale (PCS). Statistical significance was set at P < 0.01 for a 99% confidence interval.

Results

Statistically significant differences (P ≤ 0.001) with a large effect size (d = 1.05–1.19) were shown for higher CSQ scores and PCS total and domain scores in athletes with gastrocnemius myofascial pain vs healthy athletes. Nevertheless, CSS presence (CSQ ≥ 40 points) did not show statistically significant differences (P = 0.050) between groups. A linear regression model (R2 = 0.560, P < 0.01) predicted higher CSQ scores based on PCS total score (R2 = 0.390), female sex (R2 = 0.095), and myofascial pain presence (R2 = 0.075).

Conclusions

Greater symptoms of central sensitization, catastrophism, rumination, magnification, and helplessness were shown in athletes with gastrocnemius myofascial pain compared with healthy athletes. Nevertheless, there was not a statistically significant presence of CSS comparing both groups. Greater central sensitization symptoms were predicted by catastrophism symptoms, female sex, and presence of gastrocnemius myofascial pain in athletes.
Complementary Information and Learning Traps*
Authors: Liang Annie , Mu Xiaosheng
Published: October 2019

We develop a model of social learning from complementary information: short-lived agents sequentially choose from a large set of flexibly correlated information sources for prediction of an unknown state, and information is passed down across periods. Will the community collectively acquire the best kinds of information? Long-run outcomes fall into one of two cases: (i) efficient information aggregation, where the community eventually learns as fast as possible; (ii) “learning traps,” where the community gets stuck observing suboptimal sources and information aggregation is inefficient. Our main results identify a simple property of the underlying informational complementarities that determines which occurs. In both regimes, we characterize which sources are observed in the long run and how often.
Tax incentives for R&D: supporting innovative scale-ups?
Authors: Mitchell Jessica , Testa Giuseppina , Sanchez Martinez Miguel , Cunningham Paul N , Szkuta Katarzyna
Published: October 2019

This article investigates the impact of tax incentives targeting young innovative firms and broader R&D tax incentives where effects on young firms are observed. It examines effects on R&D additionality, R&D wages, employment growth, turnover growth, and sales growth from innovative activities. It draws on academic literature and policy evaluation studies and uses a mixed-method approach based on evaluation synthesis. Evidence on the effectiveness of tax incentives on young and small firms’ employment and economic performance is relatively limited, largely due to a dearth of evaluations. This analysis, based on a limited number of studies, finds that with regard to R&D additionality, generic R&D tax incentives tend to have a larger, or at least as large, effect on young companies, both when compared with companies of average age (with the exception of a study on an Irish tax instrument), and when compared with grants and loans. Some evidence also shows a positive effect on wages. More limited evidence shows that R&D tax incentives targeted at young companies tend to have positive effects on R&D intensity and wages, but that effects decrease relatively if combined with other instruments such as subsidies. With regard to output additionality, generic R&D tax incentives have a limited impact on innovation for all companies and a positive impact on turnover, turnover share of new products or services and labour productivity. There is some evidence of positive effects on employment, productivity, sales and added-value of targeted measures, but these results should be validated using more robust methods.
The dual orexinergic receptor antagonist DORA-22 improves the sleep disruption and memory impairment produced by a rodent insomnia model
Authors: Gamble Mackenzie C , Katsuki Fumi , McCoy John G , Strecker Robert E , McKenna James Timothy
Published: October 2019

Insomnia-related sleep disruption can contribute to impaired learning and memory. Treatment of insomnia should ideally improve the sleep profile while minimally affecting mnemonic function, yet many hypnotic drugs (e.g. benzodiazepines) are known to impair memory. Here, we used a rat model of insomnia to determine whether the novel hypnotic drug DORA-22, a dual orexin receptor antagonist, improves mild stress-induced insomnia with minimal effect on memory. Animals were first trained to remember the location of a hidden platform (acquisition) in the Morris Water Maze and then administered DORA-22 (10, 30, or 100 mg/kg doses) or vehicle control. Animals were then subjected to a rodent insomnia model involving two exposures to dirty cages over a 6-hr time period (at time points 0 and 3 hr), followed immediately by a probe trial in which memory of the water maze platform location was evaluated. DORA-22 treatment improved the insomnia-related sleep disruption—wake was attenuated and NREM sleep was normalized. REM sleep amounts were enhanced compared with vehicle treatment for one dose (30 mg/kg). In the first hour of insomnia model exposure, DORA-22 promoted the number and average duration of NREM sleep spindles, which have been previously proposed to play a role in memory consolidation (all doses). Water maze measures revealed probe trial performance improvement for select doses of DORA-22, including increased time spent in the platform quadrant (10 and 30 mg/kg) and time spent in platform location and number of platform crossings (10 mg/kg only). In conclusion, DORA-22 treatment improved insomnia-related sleep disruption and memory consolidation deficits.
Clustering of Cardiometabolic Risk Factors among Children and Adolescents in a Rural Community in Ondo, Southwest Nigeria
Authors: Akinbodewa Akinwumi Ayodeji , Adejumo Ademola Oluseyi , Lamidi Oluwakemi Abiola , Adeyemi Ogunleye
Published: October 2019

Background

Clustering of cardiometabolic risk factors is rapidly becoming prevalent among children and adolescents with grave implications for their cardiovascular health. We set out to determine prevalence and pattern of clustering of risk factors and, identify factors (if any) that determine their clustering.

Methods

A cross-sectional study of children (3–9 years) and adolescents (10–17 years) in a rural, agrarian community. Their blood pressure, body mass index and lipids were measured. Data was analyzed with SPSS 20.

Results

A total of 114 (M : F, 1 : 1.1) subjects were studied. The mean age of children and adolescents were 5.6 ± 2.1 and 12.9 ± 2.2 years respectively. The most prevalent cardiometabolic risk factors were elevated non-high density lipoprotein-cholesterol (HDL-c; 39.5%), low HDL-c (33.3%), prehypertension (12.3%) and overweight (9.6%). The prevalence of hypertension was higher among females (11.9% vs. 1.8%, p = 0.024) and adolescents (13.2% vs. 1.6%, p = 0.037). Serum levels of non-HDL-c was higher among adolescents than children (50.9% vs. 29.5%, p = 0.013). At least one risk factor was present in 68.4% of the subjects. Clustering of two and three risk factors were present in 18.4% and 6.1%. The presence of prehypertension (χ2 23.93, p < .001), hypertension (χ2 12.19, p = 0.002), high serum non-HDL-c (χ2 6.336, p = 0.011) and high serum total cholesterol (TC; χ2 8.810, p < 0.001) were associated with clustering of cardiometabolic risk factors.

Conclusion

The burden of cardiometabolic risk factors among children and adolescents is high. Identified determinants of risk factor clustering were prehypertension, hypertension, non-HDL-c and TC.
The Genome Sequence of Five Genotypes ofFusarium oxysporumf. sp.vasinfectum: A Resource for Studies on Fusarium Wilt of Cotton
Authors: Seo Seungyeon , Pokhrel Ambika , Coleman Jeffrey J.
Published: October 2019

Fusarium oxysporum f. sp. vasinfectum is an important plant pathogen responsible for vascular wilt disease on cotton. Members of this group are known to carry supernumerary chromosomes that encode virulence factors. We sequenced the genomes of five F. oxysporum f. sp. vasinfectum isolates, including the genome of a representative of the highly virulent genotype race 4, at a high coverage to assemble reference-quality genomes. These genomes provide a necessary resource for comparative genomic analyses to identify genes or genome features that are involved in pathogenicity on cotton and may ultimately be used to identify improved management strategies.
Trigger finger
Authors: Matthews Amber , Smith Kristen , Read Laura , Nicholas Joyce , Schmidt Eric
Published: October 2019

Stenosing flexor tenosynovitis, more commonly known as trigger finger, is one of the most common causes of hand pain and dysfunction. Clinicians must be able to identify the disorder, know the broad range of treatment options, and counsel patients on the treatment best suited for their condition. Awareness of the economic burden each option entails is central to optimizing treatment outcomes and patient satisfaction.
Managing hyponatremia
Authors: Boyle Rebecca
Published: October 2019

Despite the high incidence of hyponatremia, the correct approach to management, particularly in patients with severe hyponatremia (serum sodium of 120 mEq/L or less), is controversial. This article reviews two major consensus guidelines and recent studies that can help clinicians make evidence-based treatment decisions and reduce patient risk for iatrogenic osmotic demyelination from overly aggressive treatment.
Years of Life Lost due to Opioid Overdose in Ohio: Temporal and Geographic Patterns of Excess Mortality
Authors: Hall O. Trent , Hall Orman E. , McGrath Ryan P. , Haile Zelalem T.
Published: October 2019

Objectives:

The aim of the study was to quantify the burden of premature mortality because of opioid overdose in Ohio, document the role of fentanyl poisoning in contribution to this evolving epidemic, examine geographic, demographic, and temporal patterns of mortality burden within Ohio, and measure the effect of opioid overdose on lifespan in the state.

Methods:

A serial cross-sectional analysis was performed for all fatal opioid poisonings (N = 12,782) in the state of Ohio between January 1, 2010 and December 31, 2016. The burden of fatal opioid overdose was calculated in Years of Life Lost (YLL). YLL were mapped with respect to geographic and cultural region. The geographic spread of fentanyl poisoning was also mapped, and the shifting contribution of fentanyl poisoning to overall opioid mortality burden was assessed over time. Finally, the negative effect of opioid overdose on average lifespan was calculated.

Results:

Opioid overdose resulted in 508,451 total YLL. In the year 2016 alone, there were 136,679 YLL attributable to opioid poisoning. Fentanyl-related YLL rose from 7.5% of all YLL because of opioid overdose in 2010 to 69.0% in 2016. In the same year, opioid overdose lowered the lifespan of an average Ohioan by 0.97 years.

Conclusions:

Fatal opioid overdose accounted for over half a million YLL in Ohio during the 7-year study period. Opioid overdose mortality rose annually. Fentanyl involved overdoses accounted for a growing proportion of excess mortality. Burden was not equally distributed within the state. Two distinct geographical clusters of excess mortality were identified in the northeast and south.
Conformity and Changes in the Radiological Neck and Shoulder Balance Parameters Throughout 3-Year Follow-up Period
Authors: Chiu Chee Kidd , Chan Chris Yin Wei , Tan Pheng Hian , Goh Saw Huan , Ng Sherwin Johan , Chian Xue Han , Ng Yun Hui , Ler Xin Yi , Chandren Josephine Rebecca , Chung Weng Hong , Kwan Mun Keong
Published: October 2019

Study Design.

Retrospective study.

Objective.

The primary objective of this study was to assess the conformity of the radiological neck and shoulder balance parameters throughout a follow-up period of more than 2 years.

Summary of Background Data.

Postoperative shoulder and neck imbalance are undesirable features among Adolescent Idiopathic Scoliosis patients who underwent Posterior Spinal Fusion. There are many clinical and radiological parameters used to assess this clinical outcome. However, we do not know whether these radiological parameters conform throughout the entire follow-up period.

Methods.

This was a retrospective study done in a single academic institution. Inclusion criteria were patients with scoliosis who underwent posterior instrumented spinal fusion with pedicle screw fixation and attended all scheduled follow-ups for at least 24 months postoperatively. Radiological shoulder parameters were measured from both preoperative antero-posterior and postoperative antero-posterior radiographs. Lateral shoulder parameters were: Radiographic Shoulder Height, Clavicle Angle (Cla-A), Clavicle-Rib Intersection Difference, and Coracoid Height Difference. Medial shoulder and neck parameters were: T1 Tilt and Cervical Axis (CA).

Results.

The radiographs of 50 patients who had surgery done from November 2013 to November 2015 were analyzed. Mean age of this cohort was 16.3 ± 7.0 years. There were 38 (76%) female patients and 12 (24%) male patients. Mean final follow-up was 38.6 ± 5.8 months. When conformity assessment of the radiological parameter using the interclass coefficient correlation was done, we found that all parameters had significant correlation (P < 0.05). T1 tilt (0.78) had good reliability, CA (0.47), Clavicle-Rib Intersection Difference (0.43), and Coracoid Height Difference (0.40) had moderate reliability and Radiographic Shoulder Height (0.22) and Cla-A (0.13) had poor reliability.

Conclusion.

All the radiological shoulder and neck balance parameters studied were conformed and suitable to be used to assess the patient postoperatively. Amongst these radiological parameters, T1 tilt followed by CA recorded to be the most reliable parameters over time.

Level of Evidence: 4
Panniculitis-Like Presentation of Extracavitary Primary Effusion Lymphoma
Authors: Saggini Andrea , Di Prete Monia , Facchetti Simone , Rapisarda Vito Mario , Anemona Lucia
Published: October 2019

Primary effusion lymphoma (PEL) is defined as a HHV-8-associated large B-cell lymphoma, which favors HIV-infected young adults, typically presenting as a serous (pleural, pericardial, or peritoneal) effusion with no identifiable tumor mass. Uncommon instances of lymphoid proliferations with the same morphology, immunophenotype, and molecular features as PEL, but occurring as a solid tumor mass without serous cavities involvement, have been termed extracavitary (or solid) variant of PEL. We hereby report the exceptional case of a HIV-associated extracavitary PEL primarily localized to the skin and exhibiting a panniculitis-like presentation. Primary cutaneous presentation of extracavitary PEL is exceedingly uncommon, with only 6 cases previously described in the literature. In light of its atypical immunophenotype, the differential diagnosis in case of skin involvement by extracavitary PEL is challenging: demonstration of HHV-8 infection in neoplastic cells is of pivotal importance. Our case is further atypical in that the lymphoid proliferation underwent complete and protracted regression solely by establishment of highly active antiretroviral therapy.
Effects of high-quality nursing care on psychological outcomes in patients with chronic heart failure
Authors: Li Xiao-Qing
Published: October 2019

Background:

This study will assess the effects of high quality nursing care (HQNC) on psychological outcomes (PCO) in patients with chronic heart failure (CHF).

Methods:

We will carry out a through search in 7 databases: PUBMED, EMBASE, Cochrane Library, Web of Science, Chinese Biomedical Literature Database, WANGFANG, and China National Knowledge Infrastructure. Eligibility criteria will be randomized controlled trials on assessing effects of HQNC on PCO in patients with CHF. Cochrane risk of bias evaluation will be utilized for methodological quality.

Results:

This proposed study will summarize a rational synthesis of current evidence for HQNC on PCO in patients with CHF.

Conclusion:

The results of this study will provide convinced evidence for judging the effects of HQNC on PCO in patients with CHF.
Obstetric and perinatal outcomes of intracytoplasmic sperm injection for infertile men with Y chromosome microdeletions
Authors: Xi Qi , Zhang Zhihong , Wang Ruixue , Li Linlin , Li Leilei , Zhu Haibo , Liu Ruizhi , Luo Lili
Published: October 2019

Background:

To evaluate the safety of intracytoplasmic sperm injection (ICSI) for men with Y chromosome azoospermia factor (AZF) microdeletions.

Methods:

Twenty-five men with Y chromosome microdeletions and their partners underwent ICSI treatment. These subjects were matched against 50 ICSI cycles in which the patients had normal Y chromosomes.

Results:

Among the 25 couples, 17 achieved a clinical pregnancy of which 14 continued to a live birth. Sixteen men had deletions of AZFc markers (sY152, sY254, and sY255), 1 had a deletion of sY152, 3 had a deletion of sY254, sY255, 1 had a deletion of sY152, sY239, Sy242, sY254, and sY255, and 3 had deletions of sY152, sY254, sY255, and sY157. AZFb microdeletions (sY127, sY134, and sY143) were found in 1 patient. AZF microdeletions had no adverse effects on the clinical pregnancy, implantation or delivery rates, birth weight, gestational age, or sex ratio when compared with the control group. Overall, the multiple gestation and preterm delivery rates of the AZF microdeletion group were similar to those in the control group.

Conclusion:

Men with AZF microdeletions can achieve the delivery of healthy children using ICSI. In this series, it produced good implantation rate and obstetric and perinatal outcomes.
Lowest Case Fatality Rate for Patients With Acute Pancreatitis Admitted in Gastroenterology Units in Veneto Region, Italy
Authors: Cavallaro Lucas Giovanni , Germanà Bastianello , Venerito Marino , Frulloni Luca , Farinati Fabio , Gabbrielli Armando , Saia Mario
Published: October 2019

Objectives

This study aimed to evaluate trends in hospitalizations and outcomes of acute pancreatitis (AP) according to first admitting hospital unit and hospital volumes.

Methods

Hospital discharge records of patients with AP admitted in the Veneto Region (Northeast Italy) during the period 2001–2015 were examined.

Results

A total of 23,389 patients (54% males; mean age, 62.2 years; standard deviation, 19.3 years) were admitted for AP. Both hospitalization (32.4 to 29.5/100,000 inhabitants per year; P < 0.05) and in-hospital mortality (1.41 to 0.79/100,000 inhabitants per year; P < 0.05) decreased over the study period. Case fatality rate was altogether 3.2%. The percentages of patients admitted in surgery, nongastroenterology medical units, gastroenterology, and intensive care were 52%, 30%, 16%, and 2%, respectively. Fewer fatalities were observed in gastroenterology units (1.7%) compared with nongastroenterology medical units (4.3%; odds ratio, 0.37; 95% confidence interval, 0.28–0.49) and surgical units (2.7%; odds ratio, 0.61; 95% confidence interval, 0.47–0.80). Fatalities decreased progressively with increasing hospital volumes from 3.7% to 2.9% (P < 0.05).

Conclusion

In the Veneto Region, both hospitalizations and in-hospital mortality for AP significantly decreased over the last 15 years. Case fatality rate was lowest for patients admitted in gastroenterology units.
Acupuncture for Acute Pancreatitis
Authors: Zhang Kai , Gao Chao , Li Chengyu , Li Yan , Wang Shenjun , Tang Qilin , Zhao Chen , Zhai Jingbo
Published: October 2019

Objective

The objective of this study was to assess the efficacy and safety of acupuncture plus routine treatment (RT) for acute pancreatitis (AP).

Methods

Literature searches were performed in 8 databases up to October 31, 2018. Randomized controlled trials comparing acupuncture plus RT with RT alone for AP were included.

Results

Twelve eligible studies were included finally. The meta-analysis showed that acupuncture plus RT compared with RT alone could significantly improve the total effective rate and gastrointestinal function and reduce the Acute Physiology, Age, Chronic Health Evaluation II score, tumor necrosis factor α count, the time of resuming to diets, and the length of hospital stay. Only 3 of the studies reported adverse events or reactions.

Conclusions

This study suggested that acupuncture combined with RT may be effective for AP. However, more rigorously designed randomized controlled trials are warranted to confirm the current findings.
Validation of an Affordable Handheld Wavefront Autorefractor
Authors: Rubio Marcos , Hernández Carlos S. , Seco Enrique , Perez-Merino Pablo , Casares Ignacio , Dave Shivang R. , Lim Daryl , Durr Nicholas J. , Lage Eduardo
Published: October 2019

SIGNIFICANCE

There is a critical need for tools that increase the accessibility of eye care to address the most common cause of vision impairment: uncorrected refractive errors. This work assesses the performance of an affordable autorefractor, which could help reduce the burden of this health care problem in low-resource communities.

PURPOSE

The purpose of this study was to validate the commercial version of a portable wavefront autorefractor for measuring refractive errors.

METHODS

Refraction was performed without cycloplegia using (1) a standard clinical procedure consisting of an objective measurement with a desktop autorefractor followed by subjective refraction (SR) and (2) with the handheld autorefractor. Agreement between both methods was evaluated using Bland-Altman analysis and by comparing the visual acuity (VA) with trial frames set to the resulting measurements.

RESULTS

The study was conducted on 54 patients (33.9 ± 14.1 years of age) with a spherical equivalent (M) refraction determined by SR ranging from −7.25 to 4.25 D (mean ± SD, −0.93 ± 1.95 D). Mean differences between the portable autorefractor and SR were 0.09 ± 0.39, −0.06 ± 0.13, and 0.02 ± 0.12 D for M, J
0, and J
45, respectively. The device agreed within 0.5 D of SR in 87% of the eyes for spherical equivalent power. The average VAs achieved from trial lenses set to the wavefront autorefractor and SR results were 0.02 ± 0.015 and 0.015 ± 0.042 logMAR units, respectively. Visual acuity resulting from correction based on the device was the same as or better than that achieved by SR in 87% of the eyes.

CONCLUSIONS

This study found excellent agreement between the measurements obtained with the portable autorefractor and the prescriptions based on SR and only small differences between the VA achieved by either method.
Validation of a Clinical Aberrometer Using Pyramidal Wavefront Sensing
Authors: Singh Neeraj K. , Jaskulski Matt , Ramasubramanian Viswanathan , Meyer Dawn , Reed Olivia , Rickert Martin E. , Bradley Arthur , Kollbaum Pete S.
Published: October 2019

SIGNIFICANCE

Measurement of ocular aberrations is a critical component of many optical corrections.

PURPOSE

This study examines the accuracy and repeatability of a newly available high-resolution pyramidal wavefront sensor–based aberrometer (Osiris by Costruzione Strumenti Oftalmici, Firenze, Italy).

METHODS

An engineered model eye and a dilated presbyopic eye were used to assess accuracy and repeatability of aberration measurements after systematic introduction of lower- and higher-order aberrations with calibrated trial lenses (sphere +10.00 to −10.00 D, and astigmatic −4.00 and −2.00 D with axis 180, 90, and 45°) and phase plates (−0.57 to 0.60 μm of Seidel spherical aberration defined over a 6-mm pupil diameter). Osiris aberration measurements were compared with those acquired on a previously calibrated COAS-HD aberrometer for foveal and peripheral optics both with and without multizone dual-focus contact lenses. The impact of simulated axial and lateral misalignment was evaluated.

RESULTS

Root-mean-square errors for paraxial sphere (corneal plane), cylinder, and axis were, respectively, 0.07, 0.11 D, and 1.8° for the engineered model and 0.15, 0.26 D, and 2.7° for the presbyopic eye. Repeatability estimates (i.e., standard deviation of 10 repeat measures) for the model and presbyopic eyes were 0.026 and 0.039 D for spherical error. Root-mean-square errors of 0.01 and 0.02 μm, respectively, were observed for primary spherical aberration and horizontal coma (model eye). Foveal and peripheral measures of higher- and lower-order aberrations measured with the Osiris closely matched parallel data collected with the COAS-HD aberrometer both with and without dual-focus zonal bifocal contact lenses. Operator errors of focus and alignment introduced changes of 0.018 and 0.02 D/mm in sphere estimates.

CONCLUSIONS

The newly available clinical pyramidal aberrometer provided accurate and repeatable measures of lower- and higher-order aberrations, even in the challenging but clinically important cases of peripheral retina and multifocal optics.
Molecular Epidemiology, Diagnostics and Mechanisms of Antibiotic Resistance inMycobacterium tuberculosiscomplex in Africa: A Systematic Review of Current Reports
Authors: Sekyere John Osei , Reta Melese Abate , Maningi Nontuthuko Excellent , Fourie Petrus Bernard
Published: October 2019

Background

Tuberculosis (TB) remains a main global public health problem. However, a systematic review of TB resistance epidemiology in Africa is wanting.

Methods

A comprehensive systematic search of PubMed, Web of Science and ScienceDirect for English research articles reporting on the molecular epidemiology ofMycobacterium tuberculosiscomplex resistance in Africa from January 2007 to December 2018 was undertaken.

Results and conclusion

Qualitative and quantitative synthesis were respectively undertaken with 232 and 186 included articles, representing 32 countries. TB monoresistance rate was highest for isoniazid (59%) and rifampicin (27%), particularly in Zimbabwe (100%), Swaziland (100%), and Sudan (67.9%) whilst multidrug resistance (MDR) rate was substantial in Zimbabwe (100%), Sudan (34.6%), Ivory Coast (24.5%) and Ethiopia (23.9%). Resistance-conferring mutations were commonly found inkatG(n=3694),rpoB(n=3591),rrs(n=1272),inhA(n=1065),pncA(n=1063) andembB(n=705) in almost all included countries: S315G/I/N/R/T, V473D/F/G/I, Q471H/Q/R/Y, S303C/L etc. inkatG;S531A/F/S/G, H526A/C/D/G, D516A/E/G etc. inrpoB;A1401G, A513C etc. inrrs;C15T, G17A/T, -A16G etc. ininhA;Ins456C, Ins172G, L172P, C14R, Ins515G etc inpncA. Commonest lineages and families such as T (n=8139), LAM (n=5243), Beijing (n=5471), Cameroon (n=3315), CAS (n=2021), H (n=1773) etc., with the exception of T, were not fairly distributed; Beijing, Cameroon and CAS were prevalent in South Africa (n=4964), Ghana (n=2306), and Ethiopia/Tanzania (n=799/635) respectively. Resistance mutations were not lineage-specific and sputum (96.2%) were mainly used for diagnosing TB resistance using the LPA (38.5%), GeneXpert (17.2%), whole-genome sequencing (12.3%) and PCR/amplicon sequencing (9%/23%). Intercountry spread of strains were limited while intra-country dissemination was common. TB resistance and its diagnosis remain a major threat in Africa, necessitating urgent action to contain this global menace.
Diagnosing Cornelia de Lange syndrome and related neurodevelopmental disorders using RNA-sequencing
Authors: Rentas Stefan , Rathi Komal S. , Kaur Maninder , Raman Pichai , Krantz Ian D. , Sarmady Mahdi , Tayoun Ahmad Abou
Published: October 2019

Purpose

Neurodevelopmental phenotypes represent major indications for children undergoing clinical exome sequencing. However, 50% of cases remain undiagnosed even upon exome reanalysis. Here we show RNA sequencing (RNA-seq) on human B lymphoblastoid cell lines (LCL) is highly suitable for neurodevelopmental Mendelian gene testing and demonstrate the utility of this approach in suspected cases of Cornelia de Lange syndrome (CdLS).

Methods

Genotype-Tissue Expression project transcriptome data for LCL, blood, and brain was assessed for neurodevelopmental Mendelian gene expression. Detection of abnormal splicing and pathogenic variants in these genes was performed with a novel RNA-seq diagnostic pipeline and using a validation CdLS-LCL cohort (n=10) and test cohort of patients who carry a clinical diagnosis of CdLS but negative genetic testing (n=5).

Results

LCLs share isoform diversity of brain tissue for a large subset of neurodevelopmental genes and express 1.8-fold more of these genes compared to blood (LCL, n=1706; whole blood, n=917). This enables testing of over 1000 genetic syndromes. The RNA-seq pipeline had 90% sensitivity for detecting pathogenic events and revealed novel diagnoses such as abnormal splice products in NIPBL and pathogenic coding variants in BRD4 and ANKRD11.

Conclusion

The LCL transcriptome enables robust frontline and/or reflexive diagnostic testing for neurodevelopmental disorders.
APOE interacts with tau PET to influence memory independently of amyloid PET
Authors: Weigand Alexandra J. , Thomas Kelsey R. , Bangen Katherine J. , Eglit Graham M.L. , Delano-Wood Lisa , Gilbert Paul E. , Brickman Adam M. , Bondi Mark W. ,   for the Alzheimer’s Disease Neuroimaging Initiative
Published: October 2019

Objective

Apolipoprotein E (APOE) interacts with AD pathology to promote disease progression. Studies of APOE risk primarily focus on amyloid, however, and little research has assessed its interaction with tau pathology independent of amyloid. The current study investigated the moderating effect of APOE genotype on independent associations of amyloid and tau PET with cognition.

Methods

Participants included 297 older adults without dementia from the Alzheimer’s Disease Neuroimaging Initiative. Regression equations modeled associations between cognitive domains and (1) cortical Aβ PET levels adjusting for tau PET and (2) medial temporal lobe (MTL) tau PET levels adjusting for Aβ PET, including interactions with APOE ε4 carrier status.

Results

Adjusting for tau PET, Aβ was not associated with cognition and did not interact with ε4 status. In contrast, adjusting for Aβ PET, MTL tau PET was significantly associated with all cognitive domains. Further, there was a moderating effect of ε4 status on MTL tau and memory with the strongest negative associations in ε4 carriers and at high levels of tau. This interaction persisted even among only Aβ negative individuals.

Interpretation

APOE ε4 genotype strengthens the negative association between MTL tau and memory independently of Aβ, although the converse is not observed, and this association may be particularly strong at high levels of tau. These findings suggest that APOE may interact with tau independently of Aβ and that elevated MTL tau confers negative cognitive consequences in Aβ negative ε4 carriers.
Evolution of crab eye structures and the utility of ommatidia morphology in resolving phylogeny
Authors: Luque Javier , Allison W. Ted , Bracken-Grissom Heather D. , Jenkins Kelsey M. , Palmer A. Richard , Porter Megan L. , Wolfe Joanna M.
Published: October 2019

Image-forming compound eyes are such a valuable adaptation that similar visual systems have evolved independently across crustaceans. But if different compound eye types have evolved independently multiple times, how useful are eye structures and ommatidia morphology for resolving phylogenetic relationships? Crabs are ideal study organisms to explore these questions because they have a good fossil record extending back into the Jurassic, they possess a great variety of optical designs, and details of eye form can be compared between extant and fossil groups. True crabs, or Brachyura, have been traditionally divided into two groups based on the position of the sexual openings in males and females: the so-called ‘Podotremata’ (females bearing their sexual openings on the legs), and the Eubrachyura, or ‘higher’ true crabs (females bearing their sexual openings on the thorax). Although Eubrachyura appears to be monophyletic, the monophyly of podotreme crabs remains controversial and therefore requires exploration of new character systems. The earliest podotremous lineages share the plesiomorphic condition of ‘mirror’ reflecting superposition eyes with most shrimp, lobsters, and anomurans (false crabs and allies). The optical mechanisms of fossil and extant podotreme groups more closely related to Eubrachyura, however, are still poorly investigated. To better judge the phylogenetic utility of compound eye form, we investigated the distribution of eye types in fossil and extant podotreme crabs. Our findings suggest the plesiomorphic ‘mirror’ eyes—seen in most decapod crustaceans including the earliest true crabs—has been lost in several ‘higher’ podotremes and in eubrachyurans. We conclude that the secondary retention of larval apposition eyes has existed in eubrachyurans and some podotremes since at least the Early Cretaceous, and that the distribution of eye types among true crabs supports a paraphyletic podotreme grade, as suggested by recent molecular and morphological phylogenetic studies. We also review photoreceptor structure and visual pigment evolution, currently known in crabs exclusively from eubrachyuran representatives. These topics are critical for future expansion of research on podotremes to deeply investigate the homology of eye types across crabs.
Molecular and histologic outcomes following spinal cord injury in spiny mice,Acomys cahirinus
Authors: Streeter K.A. , Sunshine M.D. , Brant J.O. , Sandoval M. A.G.W. , Maden M. , Fuller D.D.
Published: October 2019

The spiny mouse (Acomys cahirinus)appears to be unique among mammals by showing little scarring or fibrosis after skin or muscle injury, but theAcomysresponse to spinal cord injury (SCI) is unknown. We tested the hypothesis thatAcomyswould have molecular and immunohistochemical evidence of reduced spinal inflammation and fibrosis following SCI as compared to C57BL/6 mice (Mus), which similar to all mammals studied to date exhibits spinal scarring following SCI. Initial experiments used two pathway-focused RT-PCR gene arrays (“wound healing” and “neurogenesis”) to evaluate tissue samples from the C2-C6 spinal cord 3-days after a C3/C4 hemi-crush injury (C3Hc). Based on the gene array, specific genes were selected for RT-qPCR evaluation using species-specific primers. The results supported our hypothesis by showing increased inflammation and fibrosis related gene expression (Serpine 1, Plau, Timp1)inMusas compared toAcomys(P<0.05). RT-qPCR also showed enhanced stem cell and axonal guidance related gene expression(Bmp2, GDNF, Shh)inAcomyscompared toMus(P<0.05). Immunohistochemical evaluation of the spinal lesion at 4-wks post-injury indicated reduced collagen IV immunostaining inAcomys(P<0.05). Glial fibrillary acidic protein (GFAP) and ionized calcium binding adaptor molecule 1(IBA1) immunostaining indicated morphological differences in the appearance of astrocytes and macrophages/microglia inAcomys. Collectively, the molecular and histologic results support the hypothesis thatAcomyshas reduced spinal inflammation and fibrosis following SCI. We suggest thatAcomysmay be a useful comparative model to study adaptive responses to SCI.

Highlights

Spiny mice (Acomys cahirinus)and C57BL/6 (Mus) were studied after spinal injury

RT-PCR gene arrays suggested different molecular response inAcomys

RTq-PCR with species-specific primers showed increased neurogenesis-related signaling

Histology indicates reduced scarring and fibrosis inAcomys

Acomysmay be a useful comparative model to study SCI