bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pallido-putaminal connectivity predicts outcomes of deep brain stimulation for cervical dystonia
Authors: Raghu Ashley L B , Eraifej John , Sarangmat Nagaraja , Stein John , FitzGerald James J , Payne Stephen , Aziz Tipu Z , Green Alexander L 
Published: July 2021

Abstract
Cervical dystonia is a non-degenerative movement disorder characterized by dysfunction of both motor and sensory cortico-basal ganglia networks. Deep brain stimulation targeted to the internal pallidum is an established treatment, but its specific mechanisms remain elusive, and response to therapy is highly variable. Modulation of key dysfunctional networks via axonal connections is likely important.
Fifteen patients underwent preoperative diffusion-MRI acquisitions and then progressed to bilateral deep brain stimulation targeting the posterior internal pallidum. Severity of disease was assessed preoperatively and later at follow-up. Scans were used to generate tractography-derived connectivity estimates between the bilateral regions of stimulation and relevant structures.
Connectivity to the putamen correlated with clinical improvement, and a series of cortical connectivity-based putaminal parcellations identified the primary motor putamen as the key node (r = 0.70, P = 0.004). A regression model with this connectivity and electrode coordinates explained 68% of the variance in outcomes (r = 0.83, P = 0.001), with both as significant explanatory variables.
We conclude that modulation of the primary motor putamen–posterior internal pallidum limb of the cortico-basal ganglia loop is characteristic of successful deep brain stimulation treatment of cervical dystonia. Preoperative diffusion imaging contains additional information that predicts outcomes, implying utility for patient selection and/or individualized targeting.
Determining the Incidence of Asymptomatic SARS-CoV-2 Among Early Recipients of COVID-19 Vaccines (DISCOVER-COVID-19): A Prospective Cohort Study of Healthcare Workers Before, During and After Vaccination
Authors: North Crystal M , Barczak Amy , Goldstein Robert H , Healy Brian C , Finkelstein Dianne M , Ding Delaney D , Kim Andy , Boucau Julie , Shaw Bennett , Gilbert Rebecca F , Vyas Tammy , Reynolds Zahra , Siddle Katherine J , MacInnis Bronwyn L , Regan James , Flynn James P , Choudhary Manish C , Vyas Jatin M , Laskowski Karl , Dighe Anand S , Lemieux Jacob E , Li Jonathan Z , Baden Lindsey R , Siedner Mark J , Woolley Ann E , Sacks Chana A 
Published: July 2021

Abstract
The impact of coronavirus disease 2019 vaccination on viral characteristics of breakthrough infections is unknown. In this prospective cohort study, incidence of severe acute respiratory syndrome coronavirus 2 infection decreased following vaccination. Although asymptomatic positive tests were observed following vaccination, the higher cycle thresholds, repeat negative tests, and inability to culture virus raise questions about their clinical significance.
The BNT162b2 mRNA Vaccine Elicits Robust Humoral and Cellular Immune Responses in People Living With Human Immunodeficiency Virus (HIV)
Authors: Woldemeskel Bezawit A , Karaba Andrew H , Garliss Caroline C , Beck Evan J , Wang Kristy H , Laeyendecker Oliver , Cox Andrea L , Blankson Joel N 
Published: July 2021

Abstract
Previous studies have shown that certain vaccines induce suboptimal responses in people living with human immunodeficiency virus (HIV, PLWH). However, responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines have not been fully characterized in these patients. Here we show that the BNT162b2 vaccine induces robust immune responses comparable to responses in healthy donors.
Monarch caterpillars are robust to combined exposure to the roadside micronutrients sodium and zinc
Authors: Shephard Alexander M , Mitchell Timothy S , Snell-Rood Emilie C 
Published: July 2021

AbstractHuman activities are increasing the environmental availability of micronutrients, including sodium and some essential metals. Micronutrients are often limiting in animal diets but may have negative effects when consumed in excess. Though prior research has documented how elevated exposure to individual micronutrients can impact organismal development and fitness, we know less about combined effects of multiple micronutrients. In the wild, monarch butterfly larvae (Danaus plexippus) commonly consume plants in roadside habitats that contain elevated levels of sodium (from road salt) and zinc (from vehicle wear-and-tear). We reared monarch caterpillars to adulthood to test individual and combined effects of dietary sodium and zinc on components of fitness, sodium-linked phenotypes (proxies for neural and flight muscle development) and concentrations of sodium and zinc in adult butterflies. Monarch survival was not impacted by elevated sodium or zinc individually or in combination. Yet, monarchs feeding on sodium-treated milkweed developed relatively larger eyes, consistent with a positive effect of sodium on neural development. Measurements of element concentrations in butterfly and plant tissue indicated that monarchs had higher zinc levels than those present in zinc-treated milkweed but lower sodium levels than those present in sodium-treated milkweed. Monarchs developing on sodium-treated milkweed also had prolonged development time, which might be a cost associated with developing extra neural tissue or investing in mechanisms to excrete excess dietary sodium during the larval stage. Our results indicate that sodium, more than zinc, is likely influencing phenotypic development and performance of insect pollinators in roadside habitats. Yet, in contrast to previous work, our experiment suggests that the highest levels of sodium found along roads are not always harmful for developing monarchs. Future work could consider how potentially stressful effects of micronutrients could be mitigated by increased macronutrient availability or how developmental factors such as migratory status might increase micronutrient requirements.
Clinical utility and applicability of circulating tumor DNA testing in esophageal cancer: a systematic review and meta-analysis
Authors: Chidambaram Swathikan , Markar Sheraz R 
Published: July 2021

SummaryEsophageal cancer is an aggressive malignancy with a relatively poor prognosis even after multimodality therapy. Currently, patients undergo a series of investigations that can be invasive and costly or pose secondary risks to their health. In other malignancies, liquid biopsies of circulating tumor DNA (ctDNA) are used in clinical practice for diagnostic and surveillance purposes. This systematic review summarizes the latest evidence for the clinical applicability of ctDNA technology in esophageal cancer. A systematic review of the literature was performed using MEDLINE, EMBASE, the Cochrane Review and Scopus databases. Articles were evaluated for the use of ctDNA for diagnosis and monitoring of patients with esophageal cancer. Quality assessment of studies was performed using the QUADAS-2 tool. A meta-analysis was performed to assess the diagnostic accuracy of sequencing methodologies. We included 15 studies that described the use of ctDNA technology in the qualitative synthesis and eight studies involving 414 patients in the quantitative analysis. Of these, four studies assessed its utility in cancer diagnosis, while four studies evaluated its use for prognosis and monitoring. The pooled sensitivity and specificity for diagnostic studies were 71.0% (55.7–82.6%) and 98.6% (33.9–99.9%), while the pooled sensitivity and specificity for surveillance purposes were 48.9% (29.4–68.8%) and 95.5% (90.6–97.9%). ctDNA technology is an acceptable method for diagnosis and monitoring with a moderate sensitivity and high specificity that is enhanced in combination with current imaging methods. Further work should demonstrate the practical integration of ctDNA in the diagnostic and surveillance clinical pathway.
Contrast in Post-Chill Eclosion Time Strategies Between Two Specialist Braconid Wasps (Hymenoptera: Braconidae) Attacking Rhagoletis Flies (Diptera: Tephritidae) in Western North America
Authors: Yee Wee L , Forbes Andrew A , Feder Jeffrey L 
Published: July 2021

Abstract
Parasitoids comprise a speciose insect group, displaying a wide array of life history strategies. In the Pacific Northwest of the United States, the tephritid fruit flies Rhagoletis tabellaria (Fitch) and Rhagoletis indifferens Curran infest red osier dogwood, Cornus sericea L. (Cornaceae), and bitter cherry, Prunus emarginata (Douglas ex Hooker) Eaton (Rosaceae), respectively. The flies are parasitized by different braconid wasps at different life stages; Utetes tabellariae (Fischer) oviposits into R. tabellaria eggs, whereas Diachasma muliebre (Muesebeck) oviposits into R. indifferens larvae feeding in cherries. Because Rhagoletis only have one major generation a year and the wasps attack temporally distinct fly life stages, we predicted that eclosion times of U. tabellariae should more closely follow that of its host than the larval-attacking D. muliebre. As predicted, U. tabellariae eclosed on average 6.0–12.5 d later than R. tabellaria, whereas D. muliebre eclosed on average 32.1 d after R. indifferens. Unexpectedly, however, longer chill duration differentially affected the systems; longer overwinters minimally influenced eclosion times of R. tabellaria and U. tabellariae but caused earlier eclosion of both R. indifferens and D. muliebre. Results imply that in temperate regions, diapause timing in braconid wasps evolves in response to both host life stage attacked and fly eclosion characteristics, possibly reflecting differential effects of winter on host plant fruiting phenology. Differences in phenological sensitivity of the lower host plant trophic level to variation in environmental conditions may have cascading effects, sequentially and differentially affecting eclosion times in higher frugivore (fly) and parasitoid (wasp) trophic levels.
Comparative analysis of surgical and percutaneous pulmonary valve implants over a 20-year period
Authors: Hribernik Ines , Thomson John , Ho Andrew , English Kate , Van Doorn Carin , Jaber Osama , Bentham James 
Published: July 2021

Abstract

OBJECTIVES
Since percutaneous pulmonary valve implantation (PPVI) was introduced to prolong the lifetime of surgically placed right ventricular to pulmonary artery conduits, valve technology has evolved and the indications for PPVI expanded to native and larger right ventricular outflow tracts. We explore how indications, patient populations and outcomes compare to surgical pulmonary valve replacement (PVR).

METHODS
This is a retrospective cohort study of PPVI and PVR procedures between 1998 and 2020 at a single UK centre. One hundred and twenty-eight patients underwent PPVI and 365 patients PVR. Primary outcome measures were survival, infective endocarditis and reintervention.

RESULTS
The most common indication for PVR was replacement of the native pulmonary valve for pulmonary regurgitation whereas PPVI was more commonly used to treat pulmonary stenosis in a previously placed bioprosthetic conduit or valve. Treatment indications for PPVI expanded over the study to include the native right ventricular outflow tract. Survival was similar for PPVI and PVR (92% PPVI and 96.8% PVR at 5 years; 85.8% PPVI and 95.1% PVR at 10 years). Preprocedural New York Heart Association class 3 and 4 was the most important predictor of poor outcome. Annualized infective endocarditis rate was significantly higher for the Melody PPVI (0.024 vs 0.0024/person/year for PVR, P &lt; 0.05). Both groups showed significant symptomatic improvement postprocedure with remodelling of ventricular volumes and improvement in cardiac output. Long-term follow-up for PVR showed half of patients will need replacement at 10–15 years post-index procedure.

CONCLUSIONS
An increasing number of patients requiring PVR can now be treated percutaneously. A lifetime strategy for re-valving should be considered at the first valve implant.
Sex-specific differences and postoperative outcomes of minimally invasive and sternotomy valve surgery
Authors: Moscarelli Marco , Lorusso Roberto , Angelini Gianni D , Di Bari Nicola , Paparella Domenico , Fattouch Khalil , Albertini Alberto , Nasso Giuseppe , Fiorentino Francesca , Speziale Giuseppe 
Published: July 2021

Abstract

OBJECTIVES
Female sex is an established risk factor for postoperative complications after heart surgery, but the influence of sex on outcomes after minimally invasive cardiac surgery (MICS) for valvular replacement/repair remains controversial. We examined whether the role of sex as a risk factor varies by surgical approach [MICS vs conventional sternotomy (ST)] and further assessed outcomes among female patients including in-hospital mortality and postoperative complications by surgical approach.

METHODS
We analysed data from a multicentre registry for patients who underwent isolated aortic valve and mitral surgery with MICS or ST. The primary outcome was in-hospital mortality. Propensity score matching was used to minimize between-group differences.

RESULTS
Among the 15 155 patients included in the study, 7674 underwent MICS (50.6%). Female sex was equally distributed in the MICS and ST groups (47.3% vs 47.6%, respectively). Risk for surgery was higher in the ST group than in the MICS group {EuroSCORE II: 4.0 [standard deviation (SD): 6.8] vs 3.7 [SD: 6.4]; P = 0.005}, including among female patients only [ST vs MICS 4.6 (SD: 6.9) vs 4.2 (SD: 6.3); P = 0.04]. Mortality did not significantly vary by procedure among women [MICS vs ST, 2.4% vs 2.8%; hazard ratio 1.09, 95% confidence interval 0.71–1.73; P (surgical approach × sex) = 0.51]. The results also did not vary after adjusting for confounders.

CONCLUSIONS
Female sex was associated with higher mortality in patients undergoing valve surgery, regardless of surgical approach. In female patients, MICS did not provide any benefits over ST in terms of in-hospital deaths or postoperative complications.

Subject collection
117, 125.
Improved draft reference genome for the Glassy-winged Sharpshooter (Homalodisca vitripennis), a vector for Pierce’s disease
Authors: Ettinger Cassandra L , Byrne Frank J , Collin Matthew A , Carter-House Derreck , Walling Linda L , Atkinson Peter W , Redak Rick A , Stajich Jason E 
Published: July 2021

Abstract
Homalodisca vitripennis (Hemiptera: Cicadellidae), known as the glassy-winged sharpshooter, is a xylem feeding leafhopper and an important agricultural pest as a vector of Xylella fastidiosa, which causes Pierce’s disease in grapes and a variety of other scorch diseases. The current H. vitripennis reference genome from the Baylor College of Medicine's i5k pilot project is a 1.4-Gb assembly with 110,000 scaffolds, which still has significant gaps making identification of genes difficult. To improve on this effort, we used a combination of Oxford Nanopore long-read sequencing technology combined with Illumina sequencing reads to generate a better assembly and first-pass annotation of the whole genome sequence of a wild-caught Californian (Tulare County) individual of H. vitripennis. The improved reference genome assembly for H. vitripennis is 1.93-Gb in length (21,254 scaffolds, N50 = 650 Mb, BUSCO completeness = 94.3%), with 33.06% of the genome masked as repetitive. In total, 108,762 gene models were predicted including 98,296 protein-coding genes and 10,466 tRNA genes. As an additional community resource, we identified 27 orthologous candidate genes of interest for future experimental work including phenotypic marker genes like white. Furthermore, as part of the assembly process, we generated four endosymbiont metagenome-assembled genomes, including a high-quality near complete 1.7-Mb Wolbachia sp. genome (1 scaffold, CheckM completeness = 99.4%). The improved genome assembly and annotation for H. vitripennis, curated set of candidate genes, and endosymbiont MAGs will be invaluable resources for future research of H. vitripennis.
The Pseudoalteromonas multipartite genome: distribution and expression of pangene categories, and a hypothesis for the origin and evolution of the chromid
Authors: Sonnenberg Cecilie Bækkedal , Haugen Peik 
Published: July 2021

Abstract
Bacterial genomes typically consist of one large chromosome, but can also include secondary replicons. These so-called multipartite genomes are scattered on the bacterial tree of life with the majority of cases belonging to Proteobacteria. Within the class gamma-proteobacteria, multipartite genomes are restricted to the two families Vibrionaceae and Pseudoalteromonadaceae. Whereas the genome of vibrios is well studied, information on the Pseudoalteromonadaceae genome is much scarcer. We have studied Pseudoalteromonadaceae with respect to the origin of the chromid, how pangene categories are distributed, how genes are expressed relative to their genomic location, and identified chromid hallmark genes. We calculated the Pseudoalteromonadaceae pangenome based on 25 complete genomes and found that core/softcore are significantly overrepresented in late replicating sectors of the chromid, regardless of how the chromid is replicated. On the chromosome, core/softcore and shell/cloud genes are only weakly overrepresented at the chromosomal replication origin and termination sequences, respectively. Gene expression is trending downwards with increasing distance from the chromosomal oriC, whereas the chromidal expression pattern is more complex. Moreover, we identified 78 chromid hallmark genes, and BLASTp searches suggest that the majority of them were acquired from the ancestral gene pool of Alteromonadales. Finally, our data strongly suggest that the chromid originates from a plasmid that was acquired in a relatively recent event. In summary, this study extends our knowledge on multipartite genomes, and helps us understand how and why secondary replicons are acquired, why they are maintained, and how they are shaped by evolution.
Optimizing the Care and Management of Older Offenders: A Scoping Review
Authors: Hagos Amanuel K , Butler Tony G , Howie Adam , Withall Adrienne L 
Published: July 2021

Abstract

Background and Objectives
The rapid increase in the number of older offenders in many countries presents unique challenges to both correctional and health care systems. In the absence of strong empirical evidence on effective interventions, identifying best practices can help optimize the care and management of this segment of the prisoner population.

Research Design and Methods
We conducted a scoping review of care models, prison programs, and different interventions designed to improve the care and management of older offenders. We searched 5 bibliographic databases and other data sources including OpenGrey, agency documents, and government reports published until December 2020. This review employed commonly used steps for conducting a scoping review and applied additional tools to enhance the methodology.

Results
After title and abstract screening and full-text review, a total of 34 studies were included in the analysis. Four themes emerged from the review: (a) institutional logics, (b) adaptations, (c) multidisciplinary teams, and (d) person-centered care and management.

Discussion and Implications
Best practices identified in this review can help optimize the care and management of older offenders in mainstream prisons. Further action research is recommended to adapt and scale up the interventions.
Enhancing the interoperability of glycan data flow between ChEBI, PubChem, and GlyGen
Authors: Navelkar Rahi , Owen Gareth , Mutherkrishnan Venkatesh , Thiessen Paul , Cheng Tiejun , Bolton Evan , Edwards Nathan , Tiemeyer Michael , Campbell Matthew P , Martin Maria , Vora Jeet , Kahsay Robel , Mazumder Raja 
Published: July 2021

Abstract
Glycans play a vital role in health, disease, bioenergy, biomaterials, and bio-therapeutics. As a result, there is keen interest to identify and increase glycan data in bioinformatics databases like ChEBI and PubChem, and connecting them to resources at the EMBL-EBI and NCBI to facilitate access to important annotations at a global level. GlyTouCan is a comprehensive archival database that contains glycans obtained primarily through batch upload from glycan repositories, glycoprotein databases, and individual laboratories. In many instances, the glycan structures deposited in GlyTouCan may not be fully defined or have supporting experimental evidence and citations. Databases like ChEBI and PubChem were designed to accommodate complete atomistic structures with well-defined chemical linkages. As a result, they cannot easily accommodate the structural ambiguity inherent in glycan databases. Consequently, there is a need to improve the organization of glycan data coherently to enhance connectivity across the major NCBI, EMBL-EBI, and glycoscience databases.
This paper outlines a workflow developed in collaboration between GlyGen, ChEBI, and PubChem to improve the visibility and connectivity of glycan data across these resources. GlyGen hosts a subset of glycans (~29,000) from the GlyTouCan database and has submitted valuable glycan annotations to the PubChem database and integrated over 10,500 (including ambiguously defined) glycans into the ChEBI database. The integrated glycans were prioritized based on links to PubChem and connectivity to glycoprotein data. The pipeline provides a blueprint for how glycan data can be harmonized between different resources. The current PubChem, ChEBI, and GlyTouCan mappings can be downloaded from GlyGen (https://data.glygen.org).
National multisectoral governance challenges of implementing the Philippines’ Reproductive Health Law
Authors: Siy Van Vanessa T , Uy Jhanna , Bagas Joy , Ulep Valerie Gilbert T 
Published: July 2021

Abstract
In recognition of the role of reproductive health in individual and national development, the Responsible Parenthood and Reproductive Health (RPRH) Law of 2012 was passed in the Philippines after 30 years of opposition and debate. Seven years later, this article examined the cohesiveness of national multi-sectoral governance among state and non-state actors and identified challenges in coordination as part of the first comprehensive evaluation of the landmark policy. Using a qualitative intrinsic case study design and guided by the World Health Organization’s systems checklist for governing health equity as our theoretical perspective, we conducted 20 semi-structured interviews with national implementers from health agencies (n = 11), non-health agencies (n = 6) and non-state actors (n = 3) that included civil society organizations (CSOs). Key themes identified through thematic analysis were supported with document reviews of policy issuances, accomplishment reports and meeting transcripts of the RPRH National Implementation Team (NIT). The study found that despite aspirations for vibrant multi-sectoral coordination, the implementation of the RPRH Law in the Philippines was incohesive. National leaders, particularly the health sector, were neither able to rally non-health sector actors around RPRH nor strategically harness the power of CSOs. Local resource limitations associated with decentralization were exacerbated by paternalistic financing, coordination, and monitoring. The absence of multi-agency plans fostered a culture of siloed opportunism, without consideration to integrated implementation. This case study shows that for neutral policies without conflicts in sector objectives, the interest and buy-in of non-health state actors, even with a national law, cannot be assumed. Moreover, possible conflicts in interests and perspectives between state and civil society actors must be managed in national governance bodies. Overall, there is need for participatory policymaking and health-sector advocacy to set health equity as an intersectoral goal, involving subnational leaders in developing concrete action plans, and strengthening NIT’s formal accountability systems.