bluuebunny/crossref_metadata_2025_split huggingface dataset:
Early Signals of Vaccine-driven Perturbation Seen in Pneumococcal Carriage Population Genomic Data
Authors: Chaguza Chrispin , Heinsbroek Ellen , Gladstone Rebecca A , Tafatatha Terence , Alaerts Maaike , Peno Chikondi , Cornick Jennifer E , Musicha Patrick , Bar-Zeev Naor , Kamng’ona Arox , Kadioglu Aras , McGee Lesley , Hanage William P , Breiman Robert F , Heyderman Robert S , French Neil , Everett Dean B , Bentley Stephen D 
Published: May 2019

Abstract

Background
Pneumococcal conjugate vaccines (PCVs) have reduced pneumococcal diseases globally. Pneumococcal genomic surveys elucidate PCV effects on population structure but are rarely conducted in low-income settings despite the high disease burden.

Methods
We undertook whole-genome sequencing (WGS) of 660 pneumococcal isolates collected through surveys from healthy carriers 2 years from 13-valent PCV (PCV13) introduction and 1 year after rollout in northern Malawi. We investigated changes in population structure, within-lineage serotype dynamics, serotype diversity, and frequency of antibiotic resistance (ABR) and accessory genes.

Results
In children &lt;5 years of age, frequency and diversity of vaccine serotypes (VTs) decreased significantly post-PCV, but no significant changes occurred in persons ≥5 years of age. Clearance of VT serotypes was consistent across different genetic backgrounds (lineages). There was an increase of nonvaccine serotypes (NVTs)—namely 7C, 15B/C, and 23A—in children &lt;5 years of age, but 28F increased in both age groups. While carriage rates have been recently shown to remain stable post-PCV due to replacement serotypes, there was no change in diversity of NVTs. Additionally, frequency of intermediate-penicillin-resistant lineages decreased post-PCV. Although frequency of ABR genes remained stable, other accessory genes, especially those associated with mobile genetic element and bacteriocins, showed changes in frequency post-PCV.

Conclusions
We demonstrate evidence of significant population restructuring post-PCV driven by decreasing frequency of vaccine serotypes and increasing frequency of few NVTs mainly in children under 5. Continued surveillance with WGS remains crucial to fully understand dynamics of the residual VTs and replacement NVT serotypes post-PCV.
Clinical Impact of Rapid Species Identification From Positive Blood Cultures With Same-day Phenotypic Antimicrobial Susceptibility Testing on the Management and Outcome of Bloodstream Infections
Authors: Ehren Kathrin , Meißner Arne , Jazmati Nathalie , Wille Julia , Jung Norma , Vehreschild Jörg Janne , Hellmich Martin , Seifert Harald 
Published: May 2019

Abstract

Background
Timely availability of microbiological results from positive blood cultures is essential to enable early pathogen-directed therapy. The Accelerate Pheno system (ADX) is a novel technology using fluorescence in situ hybridization for rapid species identification (ID) and morphokinetic bacterial analysis for phenotypic antimicrobial susceptibility testing (AST), with promising results. Yet the impact of this technology on clinical management and patient outcome remains unclear.

Methods
We conducted a quasiexperimental before-and-after observational study and analyzed 3 groups with different diagnostic and therapeutic pathways following recent integration of ADX: conventional microbiological diagnostics with and without antimicrobial stewardship program (ASP) intervention, and rapid diagnostics (ADX in addition to conventional standard) with ASP intervention. Primary endpoints were time to adequate, to optimal and to step-down antimicrobial therapy. Secondary endpoints were antimicrobial consumption, in-hospital mortality, length of stay (LOS), and the incidence of Clostridioidesdifficile infection (CDI).

Results
Two hundred four patients (conventional diagnostics, n = 64; conventional diagnostics + ASP, n = 68; rapid diagnostics + ASP; n = 72) were evaluated. The use of ADX significantly decreased time from Gram stain to ID (median, 23 vs 2.2 hours, P &lt; .001) and AST (median, 23 vs 7.4 hours, P &lt; .001), from Gram stain to optimal therapy (median, 11 vs 7 hours, P = .024) and to step-down antimicrobial therapy (median, 27.8 vs 12 hours, P = .019). However, groups did not differ in antimicrobial consumption, duration of antimicrobial therapy, mortality, LOS, or incidence of CDI.

Conclusions
Use of ADX significantly reduced time to ID and AST as well as time to optimal antimicrobial therapy but did not affect antimicrobial consumption and clinical outcome.
Stability and Resiliency of Biological Control of the Twospotted Spider Mite (Acari: Tetranychidae) in Hop
Authors: Iskra A E , Woods J L , Gent D H 
Published: May 2019

Abstract
The twospotted spider mite (Tetranychus urticae Koch) is a common pest in agricultural and ornamental crops. This pest can be controlled by resident predatory arthropods in certain situations. This research quantified the stability and resiliency of established conservation biological control of the twospotted spider mite in hop over a 5-yr period associated with nitrogen fertilization rate and use of a broad-spectrum insecticide. Biological control generally was stable and resilient over a sixfold range of nitrogen fertilization rates, and in only 1 of 5 yr did elevated nitrogen rates significantly affect populations of spider mites. In contrast, one application of the insecticide bifenthrin was associated with disruption of biological control and a severe outbreak of spider mites. The complex of natural enemies suppressed the outbreak during the same year in which bifenthrin was applied, but only after populations of spider mites exceeded levels associated with economic damage. However, in the following year the system returned to an equilibrium state where spider mites were suppressed below economically damaging levels. Therefore, conservation biological control in hop appears stable and robust to factors such as nitrogen fertilization that increase reproductive rates of spider mites but may be sensitive to factors such as nonselective insecticides that are lethal to natural enemies. Conservation biological control can be considered resilient to a single use of a nonselective insecticide in the year following the application, but not within the year of application.
Improved differential diagnosis of intracardiac and extracardiac shunts using acoustic intensity mapping of saline contrast studies
Authors: Rasalingam Ravi , Novak Eric , Rifkin Robert D 
Published: May 2019

Abstract

Aims
The aim of this study was to test the hypothesis that temporal patterns of saline contrast entry into, and exit from the left heart are significantly different in intra- and extra-cardiac shunts and can be used to differentiate the shunt mechanism when Valsalva manoeuvre cannot be performed, or is of uncertain quality. We propose a novel approach of mapping the temporal changes in acoustic intensity (AI) within the left and right heart to identify and define these unique patterns.

Methods and results
We screened cases of right to left shunting on resting agitated saline contrast echocardiograms with clinical criteria that identified the origin of shunting as either a patent foramen ovale or pulmonary arteriovenous malformation. Acoustic time-intensity curves were generated from the right and left heart chambers that reflected the change in saline contrast density over time. Several novel pre-specified parameters were measured from these curves, in addition to the standard heartbeat counting method, to characterize the entrance (wash-in) and exit (wash-out) patterns of saline contrast in the left heart. Statistical analysis showed that AI mapping provided superior differentiation of the two populations than did the traditional beat counting method.

Conclusion
Diagnosis of shunt mechanism from saline contrast studies can be improved over current methods through the use of AI mapping to define the rapidity that peak contrast effect develops, the speed that the contrast effect decays, and the contrast intensity late in the recording.
Minimally invasive versus conventional surgery of the ascending aorta and root: a systematic review and meta-analysis
Authors: Rayner Tom A , Harrison Sean , Rival Paul , Mahoney Dominic E , Caputo Massimo , Angelini Gianni D , Savović Jelena , Vohra Hunaid A 
Published: May 2019

Summary

Limited uptake of minimally invasive surgery (MIS) of the aorta hinders assessment of its efficacy compared to median sternotomy (MS). The objective of this systematic review is to compare operative and perioperative outcomes for MIS versus MS. Online databases Medline, EMBASE, Cochrane Library and Web of Science were searched from inception until July 2018. Both randomized and observational studies of patients undergoing aortic root, ascending aorta or aortic arch surgery by MIS versus MS were eligible for inclusion. Primary outcomes were 30-day mortality, reoperation for bleeding, perioperative renal impairment and neurological events. Intraoperative and postoperative timing measures were also evaluated. Thirteen observational studies were included comparing 1101 MIS and 1405 MS patients. The overall quality of evidence was very low for all outcomes. Mortality and the incidence of stroke were similar between the 2 cohorts. Meta-analysis demonstrated increased length of cardiopulmonary bypass (CPB) time for patients undergoing MS [standardized mean difference 0.36, 95% confidence interval (CI) 0.15–0.58; P = 0.001]. Patients receiving MS spent more time in hospital (standardized mean difference 0.30, 95% CI 0.17–0.43; P &lt; 0.001) and intensive care (standardized mean difference 0.17, 95% CI 0.06–0.27; P &lt; 0.001). Reoperation for bleeding (risk ratio 1.51, 95% CI 1.06–2.17; P = 0.024) and renal impairment (risk ratio 1.97, 95% CI 1.12–3.46; P = 0.019) were also greater for MS patients. There was substantial heterogeneity in meta-analyses for CPB and aortic cross-clamp timing outcomes. MIS may be associated with improved early clinical outcomes compared to MS, but the quality of the evidence is very low. Randomized evidence is needed to confirm these findings.
A null allele of Dnaaf2 displays embryonic lethality and mimics human ciliary dyskinesia
Authors: Cheong Agnes , Degani Rinat , Tremblay Kimberly D , Mager Jesse 
Published: May 2019

AbstractThe dynein axonemal assembly factor (Dnaaf) protein family is involved in preassembly and stability of dynein arms before they are transported into the cilia. In humans, mutations in DNAAF genes lead to several diseases related to cilia defects such as primary ciliary dyskinesia (PCD; OMIM: 612518). Patients with PCD experience malfunctions in cilia motility, which can result in inflammation and infection of the respiratory tract among other defects. Previous studies have identified that a mutation in DNAAF2 results in PCD and that 40% of these patients also experience laterality defects. In an outbred genetic background, Dnaaf2 homozygotes die after birth and have left/right defects among other phenotypes. Here we characterize a novel null allele of Dnaaf2 obtained from the International Mouse Phenotyping Consortium. Our data indicate that on a defined C57bl/6NJ genetic background, homozygous Dnaaf2 mouse embryos fail to progress beyond organogenesis stages with many abnormalities including left–right patterning defects. These findings support studies indicating that hypomorphic mutations of human DNAAF2 can result in ciliary dyskinesia and identify Dnaaf2 as an essential component of cilia function in vivo.
Altered calcium dynamics and glutamate receptor properties in iPSC-derived motor neurons from ALS patients with C9orf72, FUS, SOD1 or TDP43 mutations
Authors: Bursch Franziska , Kalmbach Norman , Naujock Maximilian , Staege Selma , Eggenschwiler Reto , Abo-Rady Masin , Japtok Julia , Guo Wenting , Hensel Niko , Reinhardt Peter , Boeckers Tobias M , Cantz Tobias , Sterneckert Jared , Van Den Bosch Ludo , Hermann Andreas , Petri Susanne , Wegner Florian 
Published: May 2019

AbstractThe fatal neurodegenerative disease amyotrophic lateral sclerosis (ALS) is characterized by a profound loss of motor neurons (MNs). Until now only riluzole minimally extends life expectancy in ALS, presumably by inhibiting glutamatergic neurotransmission and calcium overload of MNs. Therefore, the aim of this study was to investigate the glutamate receptor properties and key aspects of intracellular calcium dynamics in induced pluripotent stem cell (iPSC)-derived MNs from ALS patients with C9orf72 (n = 4 cell lines), fused in sarcoma (FUS) (n = 9), superoxide dismutase 1 (SOD1) (n = 3) or transactive response DNA-binding protein 43 (TDP43) (n = 3) mutations as well as healthy (n = 7 cell lines) and isogenic controls (n = 3). Using calcium imaging, we most frequently observed spontaneous transients in mutant C9orf72 MNs. Basal intracellular calcium levels and α-amino-3-hydroxy-5-methylisoxazole-4-propionic acid (AMPA)-induced signal amplitudes were elevated in mutant TDP43 MNs. Besides, a majority of mutant TDP43 MNs responded to 3.5-dihydroxyphenylglycine as metabotropic glutamate receptor agonist. Quantitative real-time PCR demonstrated significantly increased expression levels of AMPA and kainate receptors in mutant FUS cells compared to healthy and isogenic controls. Furthermore, the expression of kainate receptors and voltage gated calcium channels in mutant C9orf72 MNs as well as metabotropic glutamate receptors in mutant SOD1 cells was markedly elevated compared to controls. Our data of iPSC-derived MNs from familial ALS patients revealed several mutation-specific alterations in glutamate receptor properties and calcium dynamics that could play a role in ALS pathogenesis and may lead to future translational strategies with individual stratification of neuroprotective ALS treatments.
Return of the Inconsistent Application of the ‘Essential Security Interest’ Clause in Investment Treaty Arbitration: CC/Devas v India and Deutsche Telekom v India
Authors: Kabra Ridhi 
Published: May 2019

Abstract
Investment treaty arbitration is currently undergoing a backlash, precipitated in large measure by the problem of inconsistency in investment awards. Inconsistent reasoning and decisions have proved particularly problematic when different shareholders of an affected company pursue claims for reflective loss before different tribunals concerning the same dispute. This article examines two recent investment treaty cases—CC/Devas v India and Deutsche Telekom v India—that are a critical example of this very real problem.
The first part of this article assesses the inconsistent interpretation and application of essential security interest clauses in those cases. As this article shows, the disagreement between the tribunals is explained by contradictory assessments of the same facts.
The second part critically evaluates the impact of the two cases on the development of the precise criteria for successfully invoking an essential security interest clause. Such clauses comprise two elements: (i) the existence of such an interest; and (ii) the nexus between the interest and the measure adopted. These elements have hitherto been subject to inconsistent interpretations, leaving the exact contours of such clauses unclear. This article uncovers which security interests can qualify as ‘essential’ interests, focusing particularly on the question whether such an interest encompasses protection of strategic resources for military and non-military use. It also examines the meaning of the nexus requirement of ‘necessary’, and explores the difference(s) between the nexus requirements of ‘directed to’ and ‘necessary’.
Updating HIPAA for the electronic medical record era
Authors: Rosenbloom S Trent , Smith Jeffery R L , Bowen Rita , Burns Janelle , Riplinger Lauren , Payne Thomas H 
Published: May 2019

Abstract
With advances in technology, patients increasingly expect to access their health information on their phones and computers seamlessly, whenever needed, to meet their clinical needs. The 1996 passage of the Health Insurance Portability and Accountability Act (HIPAA), modifications made by the Health Information Technology for Economic and Clinical Health Act (HITECH), and the recent 21st Century Cures Act (Cures) promise to make patients’ health information available to them without special effort and at no cost. However, inconsistencies among these policies' definitions of what is included in “health information”, widespread variation in electronic health record system capabilities, and differences in local health system policies around health data release have created a confusing landscape for patients, health care providers, and third parties who reuse health information. In this article, we present relevant regulatory history, describe challenges to health data portability and fluidity, and present the authors’ policy recommendations for lawmakers to consider so that the vision of HIPAA, HITECH, and Cures may be fulfilled.
Matrin3 promotes homologous recombinational repair by regulation of RAD51
Authors: Shi Lin , Sun Jiying , Kinomura Aiko , Fukuto Atsuhiko , Horikoshi Yasunori , Tashiro Satoshi 
Published: May 2019

Abstract
Matrin3 is a highly conserved inner nuclear matrix protein involved in multiple stages of RNA metabolism. Although Matrin3 may also play a role in DNA repair, its precise roles have remained unclear. In this study, we showed that the depletion of Matrin3 led to decreased homologous recombination (HR) efficiency and increased radiation sensitivity of cells. Matrin3-depleted cells showed impaired DNA damage-dependent focus formation of RAD51, a key protein in HR. These findings suggest that Matrin3 promotes HR by regulating RAD51.
First evidence of Cardinium (Sphingobacteria) in non-marine ostracods from Turkey
Authors: Çelen Ebru , Külköylüoğlu Okan , Yavuzatmaca Mehmet , Akdemir Derya , Yılmaz Ozan 
Published: May 2019

ABSTRACTEndosymbiotic bacteria are extremely common and diverse in arthropods. Cardinium, maternally transmitted intracellular bacteria, can contribute to the fitness of the host and can manipulate its reproduction by feminization, cytoplasmic incompatibility, and thelytokous parthenogenesis. Non-marine ostracods can reproduce asexually as well as sexually. We studied the presence of Cardinium in non-marine ostracods collected from 43 sites in Turkey between 2014 and 2017. The presence of Cardinium in 64 specimens belonging to 24 ostracod species were tested by PCR protocol using 16S rRNA-specific primers. A total of 59 specimens belonging to 22 species showed positive result for the presence of Cardinium, with the sequences of the partial 16S rRNA assigned to the bacteria. Results showed that that majority (92 %) of ostracod species tested were found to be infected by Cardinium. It appears that the bacteria can be seen in both sexes depending on species. We report the first evidence of the presence of Cardinium in non-marine ostracods.
The Role of Minor Pheromone Components in Segregating 14 Species of Longhorned Beetles (Coleoptera: Cerambycidae) of the Subfamily Cerambycinae
Authors: Hanks Lawrence M , Mongold-Diers Judith A , Mitchell Robert F , Zou Yunfan , Wong Joseph C H , Meier Linnea R , Johnson Todd D , Millar Jocelyn G 
Published: May 2019

AbstractWe present research on the chemical ecology of 14 species of longhorned beetles (Coleoptera: Cerambycidae), in four tribes of the subfamily Cerambycinae, conducted in east-central Illinois over 8 yr. Adult males produce aggregation-sex pheromones that attract both sexes. Twenty independent field bioassays explored the pheromone chemistry of the species and tested the possible attractive or antagonistic effects of compounds that are not produced by a given species, but are pheromone components of other species. Analyses of beetle-produced volatiles revealed compounds that had not been reported previously from several of the species. The most common pheromone component was (R)-3-hydroxyhexan-2-one, but pheromones of some species included isomers of the related 2,3-hexanediols. Males of the congeners Phymatodes amoenus (Say) and Phymatodes testaceus (L.) produced pure (R)-2-methylbutan-1-ol. Enantiomers of 2-methylbutan-1-ol also proved to be powerful synergists for Megacyllene caryae (Gahan), Sarosesthes fulminans (F.), and Xylotrechus colonus (F.). The major components of pheromone blends were consistently present in collections of headspace volatiles from male beetles, and only the major components were inherently attractive to a subset of species when tested as single components. Minor components of some species acted as powerful synergists, but in other cases appeared not to influence attraction. Among the minor components identified in headspace extracts from males, 2,3-hexanedione and 2-hydroxyhexan-3-one appeared to be analytical artifacts or biosynthetic by-products, and were neither attractants nor synergists. The antagonistic effects of minor compounds produced by heterospecific males suggest that these compounds serve to maintain prezygotic reproductive isolation among some species that share pheromone components.
A particle swarm optimization method for interpreting self-potential anomalies
Authors: Essa Khalid S 
Published: May 2019

Abstract
This paper describes the use of the particle swarm optimization (PSO) method for interpreting observed self-potential anomalies measured along a profile. First, the technique applies the second moving average to the observed self-potential data in order to eradicate the possible influence of the regional anomaly (up to the third-order polynomial effect) via the filter of consecutive window lengths (s-values) and to calculate the residual anomaly. Following that, the PSO method is applied to the residual response to infer the source parameters: amplitude coefficient (K), depth (z), polarization angle (θ) and the shape factor (q) of the underlying buried target. The technique has been applied to three different theoretical and two field examples from the USA and Turkey. Comparisons have shown that the source parameters retrieved from the technique described here are in good agreement with the available geologic and geophysical information.
State Variation in Early-Onset Colorectal Cancer in the United States, 1995–2015
Authors: Siegel Rebecca L , Medhanie Genet A , Fedewa Stacey A , Jemal Ahmedin 
Published: May 2019

Abstract
The extent to which the increase in early-onset colorectal cancer (CRC) in the United States varies geographically is unknown. We analyzed changes in CRC incidence and risk factors among people aged 20–49 years by state using high-quality population-based cancer registry data provided by the North American Association of Central Cancer Registries and national survey data, respectively. Early-onset CRC incidence was mostly stable among blacks and Hispanics but increased in 40 of 47 states among non-Hispanic whites, most prominently in western states. For example, rates increased in Washington from 6.7 (per 100 000) during 1995–1996 to 11.5 during 2014–2015 (rate ratio = 1.73, 95% confidence interval = 1.48 to 2.01) and in Colorado from 6.0 to 9.5 (rate ratio = 1.57, 95% confidence interval = 1.30 to 1.91). Nevertheless, current CRC incidence was highest in southern states. From 1995 to 2005, increases occurred in obesity prevalence in all states and heavy alcohol consumption in one-third of states, but neither were correlated with CRC incidence trends. Early-onset CRC is increasing most rapidly among whites in western states. Etiologic studies are needed to explore early life colorectal carcinogenesis.