bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogenetic Concepts and Tools Applied to Epidemiologic Investigations of Infectious Diseases
Authors: Janies Daniel 
Published: July 2019

ABSTRACTIn this review, which is a part of theMicrobiology SpectrumCurated Collection: Advances in Molecular Epidemiology of Infectious Diseases, I present an overview of the principles used to classify organisms in the field of phylogenetics, highlight the methods used to infer the interrelationships of organisms, and summarize how these concepts are applied to molecular epidemiologic analyses. I present steps in analyses that come downstream of the assembly of a set of genomes or genes and the production of a multiple-sequence alignment or other matrices of putative orthologs for comparison. I focus on the history of the problem of phylogenetic reconstruction and debates within the field about the most appropriate methods. I illustrate methods that bridge the gap between molecular epidemiology and traditional epidemiology, including phylogenetic character evolution and geographic visualization. Finally, I provide practical advice on how to conduct an example analysis in the appendix.*This article is part of a curated collection.
Population Structure and Dynamics of Helminthic Infection: Schistosomiasis
Authors: Blanton Ronald E. 
Published: July 2019

ABSTRACT

While disease and outbreaks are mainly clonal for bacteria and other asexually reproducing organisms, sexual reproduction in schistosomes and other helminths usually results in unique individuals. For sexually reproducing organisms, the traits conserved in clones will instead be conserved in the group of organisms that tends to breed together, the population. While the same tools are applied to characterize DNA, how results are interpreted can be quite different at times (see another article in this collection,
http://www.asmscience.org/content/journal/microbiolspec/10.1128/microbiolspec.AME-0002-2018
). It is difficult to know what the real effect any control program has on the parasite population without assessing the health of this population, how they respond to the control measure, and how they recover, if they do. This review, part of the
Microbiology Spectrum
Curated Collection: Advances in Molecular Epidemiology of Infectious Diseases, concentrates on one approach using pooled samples to study schistosome populations and shows how this and other approaches have contributed to our understanding of this parasite family’s biology and epidemiology.

*
This article is part of a curated collection.
Critical role of caldera collapse in the formation of seafloor mineralization: The case of Brothers volcano
Authors: de Ronde Cornel E.J. , Humphris Susan E. , Höfig Tobias W. , Reyes Agnes G. ,   the IODP Expedition 376 Scientists
Published: July 2019

Abstract
Hydrothermal systems hosted by submarine arc volcanoes commonly include a large component of magmatic fluid. The high Cu-Au contents and strongly acidic fluids in these systems are similar to those that formed in the shallow parts of some porphyry copper and epithermal gold deposits mined today on land. Two main types of hydrothermal systems occur along the submarine portion of the Kermadec arc (offshore New Zealand): magmatically influenced and seawater-dominated systems. Brothers volcano hosts both types. Here, we report results from a series of drill holes cored by the International Ocean Discovery Program into these two types of hydrothermal systems. We show that the extent of hydrothermal alteration of the host dacitic volcaniclastics and lavas reflects primary lithological porosity and contrasting spatial and temporal contributions of magmatic fluid, hydrothermal fluid, and seawater. We present a two-step model that links the changes in hydrothermal fluid regime to the evolution of the volcano caldera. Initial hydrothermal activity, prior to caldera formation, was dominated by magmatic gases and hypersaline brines. The former mixed with seawater as they ascended toward the seafloor, and the latter remained sequestered in the subsurface. Following caldera collapse, seawater infiltrated the volcano through fault-controlled permeability, interacted with wall rock and the segregated brines, and transported associated metals toward the seafloor and formed Cu-Zn-Au–rich chimneys on the caldera walls and rim, a process continuing to the present day. This two-step process may be common in submarine arc caldera volcanoes that host volcanogenic massive sulfide deposits, and it is particularly efficient at focusing mineralization at, or near, the seafloor.
Long-term outcomes of functional neurological disorder in children
Authors: Raper Joseph , Currigan Victoria , Fothergill Sarah , Stone Jon , Forsyth Rob J 
Published: July 2019

ObjectivesTo establish the incidence and long-term outcomes (up to 21 years) of children presenting to a University hospital paediatric neurology service with symptoms due to functional neurological disorder (FND) with particular reference to occurrence of FND or similar symptoms in adulthood.MethodsRetrospective chart review to determine characteristics of the original paediatric FND presentation plus record-linkage with providers of Child and Adolescent Mental Health Services. Chart review of adult medical records for documentation of functional symptoms in adulthood.Results124 individuals (56% female) met entry criteria. The most common presentations were seizures (18%), sensory loss (18%) and motor symptoms (16%). Frequency gradually increased with age of onset with an incidence in paediatric neurological services of 6 per 100 000 children under 16. In up to 21 years’ follow-up (median 8.3 years), 114/124 attained their 16th birthdays by the study census date and were thus eligible for inclusion in an analysis of symptom persistence/recurrence in adulthood. 26/114 (23%) showed evidence of FND in adulthood of sufficient significance to be recorded in medical records.ConclusionPaediatric FND is commoner than previous estimates. Even in this selected population of children reaching specialist paediatric neurology services, a high long-term remission rate is observed.
Observational study of cytomegalovirus from breast milk and necrotising enterocolitis
Authors: Patel Ravi Mangal , Shenvi Neeta , Knezevic Andrea , Hinkes Michael , Bugg George W , Stowell Sean R , Roback John D , Easley Kirk A , Josephson Cassandra 
Published: July 2019

ObjectiveTo evaluate the relationship between cytomegalovirus (CMV) exposure from breast milk and risk of necrotising enterocolitis (NEC).DesignSecondary analysis of a multicentre, observational cohort study. Maternal breast milk and infant serum or urine were serially evaluated by nucleic acid testing at scheduled intervals for CMV. Infants with evidence of congenital infection were excluded. Competing-risks Cox models, with adjustment for confounders, were used to evaluate the relationship between breast milk CMV exposure or postnatal CMV infection and NEC.SettingThree neonatal intensive care units in Atlanta, Georgia.PatientsInfants with a birth weight≤1500 grams.ExposuresMaximal CMV viral load in breast milk in the first 14 days after birth or postnatal CMV infection. Two different approaches were used to assess the timing of onset of CMV infection (midpoint or early).Main outcome measuresNEC, defined as Bell stage II or greater.ResultsAmong 596 enrolled infants, 457 (77%) were born to CMV seropositive mothers and 33 developed postnatal CMV infection (cumulative incidence 7.3%, 95% CI 5.0% to 10.1%). The incidence of NEC was 18% (6/33) among infants with CMV infection, compared with 7% (37/563) among infants without infection (adjusted cause-specific HR (CSHR): 2.81; 95% CI 0.73 to 10.9 (midpoint); 6.02; 95% CI 1.28 to 28.4 (early)). Exposure to higher breast milk CMV viral load was associated with a higher risk of NEC (adjusted CSHR per twofold increase 1.28; 95% CI 1.06 to 1.54).ConclusionsCMV exposure from breast milk may be associated with the development of NEC in very low birth weight infants.
Association of small for gestational age with retinopathy of prematurity: a systematic review and meta-analysis
Authors: Razak Abdul , Faden Maher 
Published: July 2019

ContextThe association between small for gestational age (SGA) and retinopathy of prematurity (ROP) is unclear.ObjectiveA systematic review and meta-analysis was conducted to evaluate the association between ROP and SGA in preterm infants <37 weeks’ gestational age (GA) admitted to neonatal intensive care unit.MethodsMedline, PubMed, Web of Science and Cochrane Central databases were searched from inception through 15 January 2019. Studies reporting outcomes based on SGA as the primary exposure variable were included. Data were extracted independently by two coauthors. Modified Newcastle-Ottawa scale was used for risk of bias assessment.ResultsDatabase search yielded 536 records (Medline=152, PubMed=171, Web of Science=144 and Cochrane Central=69). Twenty-one studies evaluating 190 946 infants were included. SGA was associated with significantly higher odds of any stage of ROP on unadjusted analysis (unadjusted OR (uOR) 1.55; 95% CI 1.22 to 1.98; 10 studies) but not on adjusted analysis (adjusted OR (aOR) 2.16; 95% CI 0.66 to 7.11; 3 studies). SGA was associated with significantly higher odds of severe ROP (aOR 1.92; 95% CI 1.57 to 2.34; nine studies). SGA was also significantly associated with higher odds of treated ROP (aOR 1.39; 95% CI 1.18 to 1.65; three studies). In subgroup analysis of infants <29 weeks’ GA, SGA was significantly associated with increased odds of ROP (uOR 1.64; 95% CI 1.19 to 2.26; two studies), severe ROP (aOR 1.61; 95% CI 1.23 to 2.10; four studies) and treated ROP (aOR 1.37; 95% CI 1.16 to 1.62; two studies).ConclusionSGA was associated with increased odds of any stage of ROP, severe ROP and treated ROP in preterm infants. Neonatologists should incorporate SGA into the risk assessment during ROP evaluation and while providing counselling to the families of preterm SGA infants. ROP screening guidelines should look into the frequency of follow-up examination in SGA infants in aim to offer early detection and treatment.
The role of Müller cells in tractional macular disorders: an optical coherence tomography study and physical model of mechanical force transmission
Authors: Govetto Andrea , Hubschman Jean-Pierre , Sarraf David , Figueroa Marta S , Bottoni Ferdinando , dell'Omo Roberto , Curcio Christine A , Seidenari Patrizio , Delledonne Giulia , Gunzenhauser Robert , Ferrara Mariantonia , Au Adrian , Virgili Gianni , Scialdone Antonio , Repetto Rodolfo , Romano Mario R 
Published: July 2019

BackgroundTo explore the role of foveal and parafoveal Müller cells in the morphology and pathophysiology of tractional macular disorders with a mathematical model of mechanical force transmission.MethodsIn this retrospective observational study, spectral-domain optical coherence tomography images of tractional lamellar macular holes and patients with myopic foveoschisis were reviewed and analysed with a mathematical model of force transmission. Parafoveal z-shaped Müller cells were modelled as a structure composed of three rigid rods, named R1, R2 and R3. The angle formed between the rods was referred to as
θ
. R1, R2 and R3 lengths as well as the variation of the angle
θ
were measured and correlated with best corrected visual acuity (BCVA).ResultsIn tractional lamellar macular holes, there was a significant reduction of the angle
θ
towards the foveal centre (p<0.001). By contrast, there were no significant differences in
θ
in myopic foveoschisis (p=0.570). R2 segments were more vertical in myopic foveoschisis. There was a significant association between lower
θ
angles at 200 µm temporal and nasal to the fovea and lower BCVA (p<0.001 and p=0.005, respectively). The stiffness of parafoveal Müller cells was predicted to be function of the angle
θ
, and it grew very rapidly as the
θ
decreased.ConclusionParafoveal Müller cells in the Henle fibre layer may guarantee structural stability of the parafovea by increasing retinal compliance and resistance to mechanical stress. Small values of the angle
θ
were related to worse BCVA possibly due to damage to Müller cell processes and photoreceptor’s axons.
Natriuretic peptide-guided treatment for heart failure: a systematic review and meta-analysis
Authors: McLellan Julie , Bankhead Clare R , Oke Jason L , Hobbs F D Richard , Taylor Clare J , Perera Rafael 
Published: July 2019

BackgroundGUIDE-IT, the largest trial to date, published in August 2017, evaluating the effectiveness of natriuretic peptide (NP)-guided treatment of heart failure (HF), was stopped early for futility on a composite outcome. However, the reported effect sizes on individual outcomes of all-cause mortality and HF admissions are potentially clinically relevant.ObjectiveThis systematic review and meta-analysis aims to combine all available trial level evidence to determine if NP-guided treatment of HF reduces all-cause mortality and HF admissions in patients with HF.Study selectionEight databases, no language restrictions, up to November 2017 were searched for all randomised controlled trials comparing NP-guided treatment versus clinical assessment alone in adult patients with HF. No language restrictions were applied. Publications were independently double screened and extracted. Fixed-effect meta-analyses were conducted.Findings89 papers were included, reporting 19 trials (4554 participants), average ages 62–80 years. Pooled risk ratio estimates for all-cause mortality (16 trials, 4063 participants) were 0.87, 95% CI 0.77 to 0.99 and 0.80, 95% CI 0.72 to 0.89 for HF admissions (11 trials, 2822 participants). Sensitivity analyses, restricted to low risk of bias, produced similar estimates, but were no longer statistically significant.ConclusionsConsidering all the evidence to date, the pooled effects suggest that NP-guided treatment is beneficial in reducing HF admissions and all-cause mortality. However, there is still insufficient high-quality evidence to make definitive recommendations on the use of NP-guided treatment in clinical practice.Trial registration numberSystematic Review Cochrane Database Number: CD008966.
”For this one, let me take the risk”: why surgical staff continued to perform caesarean sections during the 2014–2016 Ebola epidemic in Sierra Leone
Authors: Drevin Gustaf , Mölsted Alvesson Helle , van Duinen Alex , Bolkan Håkon A , Koroma Alimamy P , Von Schreeb Johan 
Published: July 2019

IntroductionRoutine health service provision decreased during the 2014–2016 Ebola virus disease (EVD) outbreak in Sierra Leone, while caesarean section (CS) rates at public hospitals did not. It is unknown what made staff provide CS despite the risks of contracting EVD. This study explores Sierra Leonean health worker perspectives of why they continued to provide CS.MethodsThis qualitative study documents the experiences of 15 CS providers who worked during the EVD outbreak. We interviewed surgical and non-surgical CS providers who worked at public hospitals that either increased or decreased CS volumes during the outbreak. Hospitals in all four administrative areas of Sierra Leone were included. Semistructured interviews averaged 97 min and healthcare experience 21 years. Transcripts were analysed by modified framework analysis in the NVivo V.11.4.1 software.ResultsWe identified two themes that may explain why providers performed CS despite EVD risks: (1) clinical adaptability and (2) overcoming the moral dilemmas. CS providers reported being overworked and exposed to infection hazards. However, they developed clinical workarounds to the lack of surgical materials, protective equipment and standard operating procedures until the broader international response introduced formal personal protective equipment and infection prevention and control practices. CS providers reported that dutifulness and sense of responsibility for one’s community increased during EVD, which helped them justify taking the risk of being infected. Although most surgical activities were reduced to minimise staff exposure to EVD, staff at public hospitals tended to prioritise performing CS surgery for women with acute obstetric complications.ConclusionThis study found that CS surgery during EVD in Sierra Leone may be explained by remarkable decisions by individual CS providers at public hospitals. They adapted practically to material limitations exacerbated by the outbreak and overcame the moral dilemmas of performing CS despite the risk of being infected with EVD.
Epidemiological transition in morbidity: 10-year data from emergency consultations in Dakar, Senegal
Authors: Gaye Bamba , Diop Massamba , Narayanan Kumar , Offredo Lucile , Reese Peter , Antignac Marie , Diop Vasenta , Mbacké Ahmadoul Badaviyou , Boyer Chatenet Louise , Marijon Eloi , Singh-Manoux Archana , Diop Ibrahima Bara , Jouven Xavier 
Published: July 2019

BackgroundIt is thought that low-income countries are undergoing an epidemiological transition from infectious to non-communicable diseases; however, this phenomenon is yet to be examined with long-term data on morbidity.MethodsWe performed a prospective evaluation of all emergency medical consultations at a major emergency service provider in Dakar, Senegal from 2005 to 2014. Using standardised definitions, the primary diagnosis for each consultation was classified using the International Classification of Diseases-10 and then broadly categorised as ‘infectious’, ‘non-communicable’ and ‘other’ diseases. Morbidity rates for each year in the 10-year observation period were plotted to depict the epidemiological transition over time. To quantify the yearly rate ratios of non-communicable over infectious diagnosis, we used a generalised Poisson mixed model.ResultsComplete data were obtained from 49 702 visits by African patients. The mean age was 36.5±23.2 and 34.8±24.3 years for women and men, respectively. Overall, infections accounted for 46.3% and 42.9% and non-communicable conditions 32.2% and 40.1% of consultations in women and men, respectively. Consultation for non-communicable compared with infectious conditions increased by 7% every year (95% CI: 5% to 9%; p<0.0001) over the 10 years. Consultations for non-communicable condition were more likely in women compared with men (RR=1.29, 95% CI: 1.18, 1.40) and at older ages (RR=1.27; 95% CI 1.25, 1.29 for 10-year increase in age).ConclusionUsing high-quality disease morbidity data over a decade, we provide novel data showing the epidemiological transition of diseases as manifested in emergency service consultations in a large Sub-Saharan African city. These results can help reorientation of healthcare policy in Sub-Saharan Africa.
Protocol for a non-randomised pilot and feasibility study evaluating a multicomponent intervention to simplify medication regimens for people receiving community-based home care services
Authors: Sluggett Janet Kathleen , Page Amy Theresa , Chen Esa Y H , Ilomäki Jenni , Corlis Megan , Van Emden Jan , Hogan Michelle , Caporale Tessa , Angley Manya , Hilmer Sarah N , Ooi Choon Ean , Bell J Simon 
Published: July 2019

IntroductionManaging medication regimens is one of the most complex and burdensome tasks performed by older people, and can be prone to errors. People living with dementia may require medication administration assistance from formal and informal caregivers. Simplified medication regimens maintain the same therapeutic intent, but have less complex instructions and administration schedules. This protocol paper outlines a study to determine the feasibility of a multicomponent intervention to simplify medication regimens for people receiving community-based home care services.Methods and analysisThis is a non-randomised pilot and feasibility study. Research nurses will recruit 50 people receiving community-based home care services. All participants will receive the intervention from a clinical pharmacist, who will undertake medication reconciliation, assess each participant’s capacity to self-manage their medication regimen and apply a structured tool to identify opportunities for medication simplification. The pharmacist will communicate recommendations regarding medication simplification to registered nurses at the community-based home care provider organisation. The primary outcome will be a description of study feasibility (recruitment and retention rates, protocol adherence and stakeholder acceptability). Secondary outcomes include the change in number of medication administration times per day, medication adherence, quality of life, participant satisfaction, medication incidents, falls and healthcare utilisation at 4 months.Ethics and disseminationEthical approval was obtained from the Monash University Human Research Ethics Committee and the community-based home care provider organisation’s ethical review panel. Research findings will be disseminated to consumers and caregivers, health professionals, researchers and healthcare providers through the National Health and Medical Research Council Cognitive Decline Partnership Centre and through conference presentations, lay summaries and peer-reviewed publications. This study will enable an improved understanding of medication management and administration among people receiving community-based home care services. This study will inform the decision to proceed with a randomised controlled trial to assess the effect of this intervention.Trial registration numberACTRN12618001130257; Pre-results.
Prescribing quality in secondary care patients with different stages of chronic kidney disease: a retrospective study in the Netherlands
Authors: Smits Kirsten PJ , Sidorenkov Grigory , van Ittersum Frans J , Waanders Femke , Bilo Henk JG , Navis Gerjan J , Denig Petra 
Published: July 2019

ObjectivesInsight in the prescribing quality for patients with chronic kidney disease (CKD) in secondary care is limited. The aim of this study is to assess the prescribing quality in secondary care patients with CKD stages 3–5 and possible differences in quality between CKD stages.DesignThis was a retrospective cohort study.SettingData were collected at two university (n=569 and n=845) and one non-university nephrology outpatient clinic (n=1718) in the Netherlands.ParticipantsBetween March 2015 and August 2016, data were collected from patients with stages 3a–5 CKD seen at the clinics. Blood pressure measurements, laboratory measurements and prescription data were extracted from medical records. For each prescribing quality indicator, patients with incomplete data required for calculation were excluded.Outcome measuresPotentially appropriate prescribing of antihypertensives, renin-angiotensin-aldosterone system (RAAS) inhibitors, statins, phosphate binders and potentially inappropriate prescribing according to prevailing guidelines was assessed using prescribing quality indicators. Χ2or Fisher’s exact tests were used to test for differences in prescribing quality.ResultsRAAS inhibitors alone or in combination with diuretics (57% or 52%, respectively) and statins (42%) were prescribed less often than phosphate binders (72%) or antihypertensives (94%) when indicated. Active vitamin D was relatively often prescribed when potentially not indicated (19%). Patients with high CKD stages were less likely to receive RAAS inhibitors but more likely to receive statins when indicated than stage 3 CKD patients. They also received more active vitamin D and erythropoietin-stimulating agents when potentially not indicated.ConclusionsPriority areas for improvement of prescribing in CKD outpatients include potential underprescribing of RAAS inhibitors and statins, and potential overprescribing of active vitamin D. CKD stage should be taken into account when assessing prescribing quality.