bluuebunny/crossref_metadata_2025 huggingface dataset:
Sustainable Utilization of Hoya species and other bioresources in Ketori, Sanggau, West Kalimantan, Indonesia
Authors: Rahayu Sri
Published: August 2019

Indonesia has a high diversity of Hoya species especially in Kalimantan. The Hoyas have been used as ornamental plant and trades internationally, while in local community, some species have been used as medicinal plant. Recently, two new species found in Sanggau, West Kalimantan and has high value as ornamental plant. The species grows in specific habitat i.e. heath forest of the Ketori community forest. The local community was practicing rules in maintaining the biodiversity in their forest, i.e. only members of the community are allowed to use biodiversity (woods, logs, medicinal plant and so on). They controlled also the number of biodiversity used. This practices lead to the conservation and sustainable use of the biodiversity of the forest . The community forest is believed as source of their needs and water shed.
Case-Only Analysis of Gene-Environment Interactions Using Polygenic Risk Scores
Authors: Meisner Allison , Kundu Prosenjit , Chatterjee Nilanjan
Published: August 2019

Investigations of gene (G)-environment (E) interactions have led to limited findings to date, possibly due to weak effects of individual genetic variants. Polygenic risk scores (PRS), which capture the genetic susceptibility associated with a set of variants, can be a powerful tool for detecting global patterns of interaction. Motivated by the case-only method for evaluating interactions with a single variant, we propose a case-only method for the analysis of interactions with a PRS in case-control studies. Assuming the PRS and E are independent, we show how a linear regression of the PRS on E in a sample of cases can be used to efficiently estimate the interaction parameter. Furthermore, if an estimate of the mean of the PRS in the underlying population is available, the proposed method can estimate the PRS main effect. Extensions allow for PRS-E dependence due to associations between variants in the PRS and E. Simulation studies indicate the proposed method offers appreciable gains in efficiency over logistic regression and can recover much of the efficiency of a cohort study. We applied the proposed method to investigate interactions between a PRS and epidemiologic factors on breast cancer risk in the UK Biobank (United Kingdom, recruited 2006–2010).
circMeta: a unified computational framework for genomic feature annotation and differential expression analysis of circular RNAs
Authors: Chen Li , Wang Feng , Bruggeman Emily C , Li Chao , Yao Bing
Published: August 2019

Motivation

Circular RNAs (circRNAs), a class of non-coding RNAs generated from non-canonical back-splicing events, have emerged to play key roles in many biological processes. Though numerous tools have been developed to detect circRNAs from rRNA-depleted RNA-seq data based on back-splicing junction-spanning reads, computational tools to identify critical genomic features regulating circRNA biogenesis are still lacking. In addition, rigorous statistical methods to perform differential expression (DE) analysis of circRNAs remain under-developed.

Results

We present circMeta, a unified computational framework for circRNA analyses. circMeta has three primary functional modules: (i) a pipeline for comprehensive genomic feature annotation related to circRNA biogenesis, including length of introns flanking circularized exons, repetitive elements such as Alu elements and SINEs, competition score for forming circulation and RNA editing in back-splicing flanking introns; (ii) a two-stage DE approach of circRNAs based on circular junction reads to quantitatively compare circRNA levels and (iii) a Bayesian hierarchical model for DE analysis of circRNAs based on the ratio of circular reads to linear reads in back-splicing sites to study spatial and temporal regulation of circRNA production. Both proposed DE methods without and with considering host genes outperform existing methods by obtaining better control of false discovery rate and comparable statistical power. Moreover, the identified DE circRNAs by the proposed two-stage DE approach display potential biological functions in Gene Ontology and circRNA-miRNA–mRNA networks that are not able to be detected using existing mRNA DE methods. Furthermore, top DE circRNAs have been further validated by RT-qPCR using divergent primers spanning back-splicing junctions.

Availability and implementation

The software circMeta is freely available at https://github.com/lichen-lab/circMeta.

Supplementary information

Supplementary data are available at Bioinformatics online.
PyRanges: efficient comparison of genomic intervals in Python
Authors: Stovner Endre Bakken , Sætrom Pål
Published: August 2019

Complex genomic analyses often use sequences of simple set operations like intersection, overlap and nearest on genomic intervals. These operations, coupled with some custom programming, allow a wide range of analyses to be performed. To this end, we have written PyRanges, a data structure for representing and manipulating genomic intervals and their associated data in Python. Run single threaded on binary set operations, PyRanges is in median 2.3–9.6 times faster than the popular R GenomicRanges library and is equally memory efficient; run multi-threaded on 8 cores, our library is up to 123 times faster. PyRanges is therefore ideally suited both for individual analyses and as a foundation for future genomic libraries in Python.

Availability and implementation

PyRanges is available as open source under the MIT license at https://github.com/biocore-NTNU/pyranges and the documentation exists at https://biocore-NTNU.github.io/pyranges/

Supplementary information

Supplementary data are available at Bioinformatics online.
Invasive toads adopt marked capital breeding when introduced to a cooler, more seasonal environment
Authors: Vimercati Giovanni , Davies Sarah J , Measey John
Published: August 2019

Amphibians from cold and seasonal environments show marked capital breeding and sustained resource allocation to growth when compared with conspecifics from warmer, less seasonal environments. Capital breeding fuels reproduction by using only stored energy, and larger sizes and masses confer higher fecundity, starvation resistance and heat and water retention. Invasive populations act as experiments to explore how resources are allocated in novel environments. We investigated resource allocation of the southern African toad Sclerophrys gutturalis in a native source population (Durban) and in an invasive population recently (< 20 years) established in a cooler, more seasonal climate (Cape Town). After dissection, lean structural mass (bones and muscles), gonadal mass, liver mass and body fat percentage were measured in 161 native and invasive animals sampled at the beginning and the end of the breeding season. As expected, female gonadal mass decreased throughout the breeding season only in the invaded range. Thus, invasive female toads adopt a more marked capital breeding strategy than native conspecifics. Conversely, males from both populations appear to be income breeders. Also, male and female toads from the invaded range allocate more resources to growth than their native counterparts. Such a novel allocation strategy might be a response to the low temperatures, reduced rainfall and heightened seasonality encountered by the invasive population.
Omega-3 polyunsaturated fatty acids impinge on CD4+ T cell motility and adipose tissue distribution via direct and lipid mediator-dependent effects
Authors: Cucchi Danilo , Camacho-Muñoz Dolores , Certo Michelangelo , Niven Jennifer , Smith Joanne , Nicolaou Anna , Mauro Claudio
Published: August 2019

Aims

Adaptive immunity contributes to the pathogenesis of cardiovascular metabolic disorders (CVMD). The omega-3 polyunsaturated fatty acids (n-3PUFA) are beneficial for cardiovascular health, with potential to improve the dysregulated adaptive immune responses associated with metabolic imbalance. We aimed to explore the mechanisms through which n-3PUFA may alter T cell motility and tissue distribution to promote a less inflammatory environment and improve lymphocyte function in CVMD.

Methods and results

Using mass spectrometry lipidomics, cellular, biochemical, and in vivo and ex vivo analyses, we investigated how eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), the main n-3PUFA, modify the trafficking patterns of activated CD4+ T cells. In mice subjected to allogeneic immunization, a 3-week n-3PUFA-enriched diet reduced the number of effector memory CD4+ T cells found in adipose tissue, and changed the profiles of eicosanoids, octadecanoids, docosanoids, endocannabinoids, 2-monoacylglycerols, N-acyl ethanolamines, and ceramides, in plasma, lymphoid organs, and fat tissues. These bioactive lipids exhibited differing chemotactic properties when tested in chemotaxis assays with activated CD4+ T cells in vitro. Furthermore, CD4+ T cells treated with EPA and DHA showed a significant reduction in chemokinesis, as assessed by trans-endothelial migration assays, and, when implanted in recipient mice, demonstrated less efficient migration to the inflamed peritoneum. Finally, EPA and DHA treatments reduced the number of polarized CD4+ T cells in vitro, altered the phospholipid composition of membrane microdomains and decreased the activity of small Rho GTPases, Rhoα, and Rac1 instrumental in cytoskeletal dynamics.

Conclusions

Our findings suggest that EPA and DHA affect the motility of CD4+ T cells and modify their ability to reach target tissues by interfering with the cytoskeletal rearrangements required for cell migration. This can explain, at least in part, the anti-inflammatory effects of n-3PUFA supporting their potential use in interventions aiming to address adipocyte low-grade inflammation associated with cardiovascular metabolic disease.
Emotional Functioning, Positive Relationships, and Language Use in Deaf Adults
Authors: Peñacoba Cecilia , Garvi Daniel , Gómez Lourdes , Álvarez Ana
Published: August 2019

This study aimed to explore emotional regulation, alexithymia, and interpersonal relations in a Spanish sample of 146 adult deaf participants and 146 typical hearing participants. For the deaf sample, the associations between type of language used and the above variables were also analyzed. Results showed that deaf participants scored higher on alexithymia and lower for positive relationships. However, no differences were found between deaf and typical hearing participants on emotional regulation. Regarding language use (Spanish Oral Language, SOL; Spanish Sign Language; or both), deaf participants used both languages in most contexts. Deaf participants who reported using SOL as their main mode of expression showed greater positive relationships than deaf participants who use both languages. Deaf participants who reported using both languages scored higher in emotional attention and emotional repair. These results evidence an association between the language use of deaf participants and alexithymia.
An integrated respiratory microbial gene catalogue to better understand the microbial aetiology of Mycoplasma pneumoniae pneumonia
Authors: Dai Wenkui , Wang Heping , Zhou Qian , Li Dongfang , Feng Xin , Yang Zhenyu , Wang Wenjian , Qiu Chuangzhao , Lu Zhiwei , Xu Ximing , Lyu Mengxuan , Xie Gan , Li Yinhu , Bao Yanmin , Liu Yanhong , Shen Kunling , Yao Kaihu , Feng Xikang , Yang Yonghong , Zhou Ke , Li Shuaicheng , Zheng Yuejie
Published: August 2019

Background

The imbalanced respiratory microbiota observed in pneumonia causes high morbidity and mortality in childhood. Respiratory metagenomic analysis demands a comprehensive microbial gene catalogue, which will significantly advance our understanding of host–microorganism interactions.

Results

We collected 334 respiratory microbial samples from 171 healthy children and 76 children with pneumonia. The respiratory microbial gene catalogue we established comprised 2.25 million non-redundant microbial genes, covering 90.52% of prevalent genes. The major oropharyngeal microbial species found in healthy children were Prevotella and Streptococcus. In children with Mycoplasma pneumoniae pneumonia (MPP), oropharyngeal microbial diversity and associated gene numbers decreased compared with those of healthy children. The concurrence network of oropharyngeal microorganisms in patients predominantly featured Staphylococcus spp. and M. pneumoniae. Functional orthologues, which are associated with the metabolism of various lipids, membrane transport, and signal transduction, accumulated in the oropharyngeal microbiome of children with pneumonia. Several antibiotic resistance genes and virulence factor genes were identified in the genomes of M. pneumoniae and 13 other microorganisms reconstructed via metagenomic data. Although the common macrolide/β-lactam resistance genes were not identified in the assembled M. pneumoniae genome, a single-nucleotide polymorphism (A2063G) related to macrolide resistance was identified in a 23S ribosomal RNA gene.

Conclusions

The results of this study will facilitate exploration of unknown microbial components and host–microorganism interactions in studies of the respiratory microbiome. They will also yield further insights into the microbial aetiology of MPP.
Geo-clustered chronic affinity: pathways from socio-economic disadvantages to health disparities
Authors: Shin Eun Kyong , Kwon Youngsang , Shaban-Nejad Arash
Published: August 2019

Objective

Our objective was to develop and test a new concept (affinity) analogous to multimorbidity of chronic conditions for individuals at census tract level in Memphis, TN. The use of affinity will improve the surveillance of multiple chronic conditions and facilitate the design of effective interventions.

Methods

We used publicly available chronic condition data (Center for Disease Control and Prevention 500 Cities project), socio-demographic data (US Census Bureau), and demographics data (Environmental Systems Research Institute). We examined the geographic pattern of the affinity of chronic conditions using global Moran’s I and Getis-Ord Gi* statistics and its association with socio-economic disadvantage (poverty, unemployment, and crime) using robust regression models. We also used the most common behavioral factor, smoking, and other demographic factors (percent of the male population, percent of the population 67 years, and over and total population size) as control variables in the model.

Results

A geo-distinctive pattern of clustered chronic affinity associated with socio-economic deprivation was observed. Statistical results confirmed that neighborhoods with higher rates of crime, poverty, and unemployment were associated with an increased likelihood of having a higher affinity among major chronic conditions. With the inclusion of smoking in the model, however, only the crime prevalence was statistically significantly associated with the chronic affinity.

Conclusion

Chronic affinity disadvantages were disproportionately accumulated in socially disadvantaged areas. We showed links between commonly co-observed chronic diseases at the population level and systematically explored the complexity of affinity and socio-economic disparities. Our affinity score, based on publicly available datasets, served as a surrogate for multimorbidity at the population level, which may assist policymakers and public health planners to identify urgent hot spots for chronic disease and allocate clinical, medical and healthcare resources efficiently.
Elevated Heterozygosity in Adults Relative to Juveniles Provides Evidence of Viability Selection on Eagles and Falcons
Authors: Doyle Jacqueline M , Willoughby Janna R , Bell Douglas A , Bloom Peter H , Bragin Evgeny A , Fernandez Nadia B , Katzner Todd E , Leonard Kolbe , DeWoody J Andrew
Published: August 2019

Viability selection yields adult populations that are more genetically variable than those of juveniles, producing a positive correlation between heterozygosity and survival. Viability selection could be the result of decreased heterozygosity across many loci in inbred individuals and a subsequent decrease in survivorship resulting from the expression of the deleterious alleles. Alternatively, locus-specific differences in genetic variability between adults and juveniles may be driven by forms of balancing selection, including heterozygote advantage, frequency-dependent selection, or selection across temporal and spatial scales. We use a pooled-sequencing approach to compare genome-wide and locus-specific genetic variability between 74 golden eagle (Aquila chrysaetos), 62 imperial eagle (Aquila heliaca), and 69 prairie falcon (Falco mexicanus) juveniles and adults. Although genome-wide genetic variability is comparable between juvenile and adult golden eagles and prairie falcons, imperial eagle adults are significantly more heterozygous than juveniles. This evidence of viability selection may stem from a relatively smaller imperial eagle effective population size and potentially greater genetic load. We additionally identify ~2000 single-nucleotide polymorphisms across the 3 species with extreme differences in heterozygosity between juveniles and adults. Many of these markers are associated with genes implicated in immune function or olfaction. These loci represent potential targets for studies of how heterozygote advantage, frequency-dependent selection, and selection over spatial and temporal scales influence survivorship in avian species. Overall, our genome-wide data extend previous studies that used allozyme or microsatellite markers and indicate that viability selection may be a more common evolutionary phenomenon than often appreciated.
Barley cysteine protease PAP14 plays a role in degradation of chloroplast proteins
Authors: Frank Susann , Hollmann Julien , Mulisch Maria , Matros Andrea , Carrión Cristian C , Mock Hans-Peter , Hensel Götz , Krupinska Karin
Published: August 2019

HvPAP14 is a cysteine protease found in association with thylakoid membranes. Among its putative substrates are proteins such as LHCB1, LHCB5, PSBO, and RbcL, as revealed in overexpressing barley plants.
Interpreting Crab Nebula’s synchrotron spectrum: two acceleration mechanisms
Authors: Lyutikov Maxim , Temim Tea , Komissarov Sergey , Slane Patrick , Sironi Lorenzo , Comisso Luca
Published: August 2019

We outline a model of the Crab pulsar wind nebula with two different populations of synchrotron emitting particles, arising from two different acceleration mechanisms: (i) Component-I due to Fermi-I acceleration at the equatorial portion of the termination shock, with particle spectral index pI ≈ 2.2 above the injection break corresponding to γwindσwind ∼ 105, peaking in the ultraviolet (UV, γwind ∼ 102 is the bulk Lorentz factor of the wind, σwind ∼ 103 is wind magnetization); and (ii) Component-II due to acceleration at reconnection layers in the bulk of the turbulent Nebula, with particle index pII ≈ 1.6. The model requires relatively slow but highly magnetized wind. For both components, the overall cooling break is in the infrared at ∼0.01 eV, so that the Component-I is in the fast cooling regime (cooling frequency below the peak frequency). In the optical band, Component-I produces emission with the cooling spectral index of αo ≈ 0.5, softening towards the edges due to radiative losses. Above the cooling break, in the optical, UV, and X-rays, Component-I mostly overwhelms Component-II. We hypothesize that acceleration at large-scale current sheets in the turbulent nebula (Component-II) extends to the synchrotron burn-off limit of ϵs ∼ 100 MeV. Thus in our model acceleration in turbulent reconnection (Component-II) can produce both hard radio spectra and occasional gamma-ray flares. This model may be applicable to a broader class of high-energy astrophysical objects, like active galactic nuclei and gamma-ray burst jets, where often radio electrons form a different population from the high-energy electrons.
Rejuvenated galaxies with very old bulges at the origin of the bending of the main sequence and of the ‘green valley’
Authors: Mancini Chiara , Daddi Emanuele , Juneau Stéphanie , Renzini Alvio , Rodighiero Giulia , Cappellari Michele , Rodríguez-Muñoz Lucía , Liu Daizhong , Pannella Maurilio , Baronchelli Ivano , Franceschini Alberto , Bergamini Pietro , D’Eugenio Chiara , Puglisi Annagrazia
Published: August 2019

We investigate the nature of star-forming galaxies with reduced specific star formation rate (sSFR) and high stellar masses, those ‘green valley’ objects that seemingly cause a reported bending, or flattening, of the star-forming main sequence. The fact that such objects host large bulges recently led some to suggest that the internal formation of bulges was a late event that induced the sSFRs of massive galaxies to drop in a slow downfall, and thus the main sequence to bend. We have studied in detail a sample of 10 galaxies at 0.45 < z < 1 with secure SFR from Herschel, deep Keck optical spectroscopy, and HST imaging from CANDELS allowing us to perform multiwavelength bulge to disc decomposition, and to derive star formation histories for the separated bulge and disc components. We find that the bulges hosted in these systems below main sequence are virtually all maximally old, with ages approaching the age of the Universe at the time of observation, while discs are young (〈 T50〉 ∼ 1.5 Gyr). We conclude that, at least based on our sample, the bending of the main sequence is, for a major part, due to rejuvenation, and we disfavour mechanisms that postulate the internal formation of bulges at late times. The very old stellar ages of our bulges suggest a number density of early-type galaxies at z = 1–3 higher than actually observed. If confirmed, this might represent one of the first direct validations of hierarchical assembly of bulges at high redshifts.
Evolution of relativistic thin discs with a finite ISCO stress – II. Late time behaviour
Authors: Mummery Andrew , Balbus Steven A
Published: August 2019

We present solutions to the relativistic thin disc evolutionary equation using a modified description of the mean fluid flow within the disc. The model takes into account the effects of sub-circular velocities in the innermost disc regions, and resolves otherwise unsustainable behaviour present in simple finite innermost stable circular orbit (ISCO) stress disc models. We show that the behaviour of a relativistic thin disc evolving with a finite ISCO stress is comprised of three distinct stages which join the ordinarily distinct finite and vanishing ISCO stress solutions into a fully continuous model parametrization. The most important prediction of our model is the existence of an intermediate stage of ‘stalled accretion’, controlled by a single dimensionless parameter. The hallmarks of this evolutionary phase appear to have been seen in General Relativistic MHD simulations as well as in the late time X-ray observations of tidal disruption events, but dedicated simulations and extended observations are needed for a deeper understanding.
ATP/ADP modulates gp16–pRNA conformational change in the Phi29 DNA packaging motor
Authors: Cai Rujie , Price Ian R , Ding Fang , Wu Feifei , Chen Ting , Zhang Yunlong , Liu Guangfeng , Jardine Paul J , Lu Changrui , Ke Ailong
Published: August 2019

Packaging of phage phi29 genome requires the ATPase gp16 and prohead RNA (pRNA). The highly conserved pRNA forms the interface between the connector complex and gp16. Understanding how pRNA interacts with gp16 under packaging conditions can shed light on the molecular mechanism of the packaging motor. Here, we present 3D models of the pRNA–gp16 complex and its conformation change in response to ATP or ADP binding. Using a combination of crystallography, small angle X-ray scattering and chemical probing, we find that the pRNA and gp16 forms a ‘Z’-shaped complex, with gp16 specifically binds to pRNA domain II. The whole complex closes in the presence of ATP, and pRNA domain II rotates open as ATP hydrolyzes, before resetting after ADP is released. Our results suggest that pRNA domain II actively participates in the packaging process.
Remodeling of the Caenorhabditis elegans non-coding RNA transcriptome by heat shock
Authors: Schreiner William P , Pagliuso Delaney C , Garrigues Jacob M , Chen Jerry S , Aalto Antti P , Pasquinelli Amy E
Published: August 2019

Elevated temperatures activate a heat shock response (HSR) to protect cells from the pathological effects of protein mis-folding, cellular mis-organization, organelle dysfunction and altered membrane fluidity. This response includes activation of the conserved transcription factor heat shock factor 1 (HSF-1), which binds heat shock elements (HSEs) in the promoters of genes induced by heat shock (HS). The upregulation of protein-coding genes (PCGs), such as heat shock proteins and cytoskeletal regulators, is critical for cellular survival during elevated temperatures. While the transcriptional response of PCGs to HS has been comprehensively analyzed in a variety of organisms, the effect of this stress on the expression of non-coding RNAs (ncRNAs) has not been systematically examined. Here we show that in Caenorhabditis elegans HS induces up- and downregulation of specific ncRNAs from multiple classes, including miRNA, piRNA, lincRNA, pseudogene and repeat elements. Moreover, some ncRNA genes appear to be direct targets of the HSR, as they contain HSF-1 bound HSEs in their promoters and their expression is regulated by this factor during HS. These results demonstrate that multiple ncRNA genes respond to HS, some as direct HSF-1 targets, providing new candidates that may contribute to organismal survival during this stress.
Habit-based workplace physical activity intervention: a pilot study
Authors: Hamilton K , Fraser E , Hannan T
Published: August 2019

Background

Increasing workplace physical activity has important implications for workers’ health and well-being. However, few interventions targeting physical activity in the workplace are grounded in behavioural theory.

Aims

The aim of this study was to develop and pilot a 6-week habit-based intervention designed to promote the development of workplace physical activity habits and increase average weekly step counts. Changes in the strength of workplace physical activity habit and weekly step counts were assessed at 1 and 6 weeks following the intervention.

Methods

The study was a prospective three-wave within-subjects single-arm intervention study that ran for 12 weeks (baseline, 7 weeks, 12 weeks). During the 6-week intervention, participants received information regarding 10 top tips (10TT) to increase and promote habit formation and wore a pedometer during work hours. Differences in workplace physical activity habit and weekly step counts were compared across baseline (T1), 1 (T2) and 6 weeks (T3) post-intervention using repeated measures analyses of variance.

Results

Data from 20 sedentary office workers at a large Australian University were included. The average strength of workplace physical activity habits significantly increased from baseline (M = 3.90) to 1 week post-intervention (M = 4.45), and these effects were maintained 6 weeks later (M = 4.72). No significant increase in step counts were observed across any of the time points (all P > 0.05).

Conclusions

The results of this pilot study reveal that workplace physical activity habits can be strengthened via a habit-based intervention. Further research is needed to replicate these findings in larger cohorts of office workers.
The Geopolitics of Social Reproduction and Depletion: The Case of Iraq and Palestine
Authors: Chilmeran Yasmin , Pratt Nicola
Published: August 2019

This article explores the relationships between social reproduction, depletion, and geopolitical processes, drawing on two case studies: Iraq and Palestine. It underlines the importance of social reproduction to geopolitical processes and of particular geopolitical contexts to how states intervene in social reproduction, with differential implications for depletion. It argues that Iraqi state measures targeting social reproduction have sought to organize and instrumentalize the life of Iraqi citizens in the service of postcolonial state building and war-making, whilst, by contrast, Israeli state measures targeting Palestinian social reproduction have largely sought to erase Palestinian life in line with a settler colonial logic.
Short-term weight trajectories and long-term weight outcomes from a lifestyle intervention in real-world clinical practice
Authors: Romanelli Robert J , Sudat Sylvia , Huang Qiwen , Ma Jun , Venditti Elizabeth M , Greenwood Deborah A , Pressman Alice R , Azar Kristen M J
Published: August 2019

Centers for Disease Control and Prevention aligned lifestyle change programs are effective in promoting weight loss among those with elevated cardiometabolic risk; yet, variability in weight outcomes among participants is high. Little is known about heterogeneity of short-term weight changes among participants in real-world clinical practice. We sought to identify short-term weight trajectory clusters among lifestyle change program participants in real-world clinical practice and to examine the relationship between cluster membership and long-term weight outcomes. We identified participants from the electronic health records (2010–2017) with weight measured ≤30 days prior to program initiation (baseline) and in four intervals (3-week segments) in the 12 weeks after baseline. Clustering analysis was performed to identify distinct trajectories in percent weight change over 12 weeks. Cluster-specific differences in weight change at 12 and 52 weeks were assessed. Among 1,148 participants, across 18 clinic sites, three clusters were identified: minimal-to-no weight loss (MWL), delayed-minimal weight loss (DWL), and steady-moderate weight loss (SWL), corresponding to mean weight changes of 0.4%, −2.3%, and −4.8% at 12 weeks follow-up, respectively. Mean weight changes were 0.4%, −1.8%, and −5.1% for MWL, DWL, and SWL clusters, respectively, at 52 weeks follow-up, which correlated in direction and magnitude with short-term weight changes. Clustering analysis reveals heterogeneous, short-term weight trajectories among lifestyle change program participants in real-world clinical practice. Given the relationship between the magnitudes of short- and long-term weight change, individual participant weight trajectories may be useful in identifying potential non-responders in need of adjunctive or alternative therapy.
‘Googling’ anaphylaxis
Authors: Kornafeld Anna , Gonzalez-Estrada Alexei , Dimov Ves
Published: August 2019

Purpose of review

Anaphylaxis is a systemic allergic reaction and without the appropriate treatment can progress fast and may be fatal. Information about allergy and immunology topics including anaphylaxis can be easily found online and are widely searched by patients as well as medical personnel. Social media and search engines not only bring a number of benefits to users but also carry risks for breaches of confidentiality and privacy, unprofessional behaviour, malpractice and litigation. Social media use by medical healthcare workers has liability risks and can result in malpractice.

Recent findings

We used PubMed with the terms anaphylaxis; social network; mobile apps that revealed a very small number of publications addressing the use of these platforms and anaphylaxis. Google Trends and KWFinder were used to analyse the relative search interest and absolute search volumes on ‘anaphylaxis’.

Multiple sources exist on the Internet for health-related searches for both healthcare providers and patients. We analysed different websites, mobile apps, Facebook, YouTube and Twitter. To avoid any posting of patient identifiers, it is imperative to be aware of the 18 HIPAA identifiers. We list websites with accurate information about anaphylaxis for the use of both patients and healthcare professionals for purposes of patient education. Further research on health information-seeking behaviour is clearly needed.
The Role of Lexical Tone Information in the Recognition of Mandarin Sentences in Listeners With Hearing Aids
Authors: Chen Yuan , Wong Lena L. N. , Qian Jinyu , Kuehnel Volker , Christina Voss Solveig , Chen Fei
Published: August 2019

Objectives:

Lexical tone information provides redundant cues for the recognition of Mandarin sentences in listeners with normal hearing in quiet conditions. The contribution of lexical tones to Mandarin sentence recognition in listeners with hearing aids (HAs) is unclear. This study aimed to remove lexical tone information and examine the effects on Mandarin sentence intelligibility in HA users. The second objective was to investigate the contribution of cognitive abilities (i.e., general cognitive ability, working memory, and attention) on Mandarin sentence perception when the presentation of lexical tone information was mismatched.

Design:

A text-to-speech synthesis engine was used to manipulate Mandarin sentences into three test conditions: (1) a Normal Tone test condition, where no alterations were made to lexical tones within sentences; (2) a Flat Tone test condition, where lexical tones were all changed into tone 1 (i.e., the flat tone); and (3) a Random Tone test condition, where each word in test sentences was randomly assigned one of four Mandarin lexical tones. The manipulated sentence signals were presented to 32 listeners with HAs in both quiet and noisy environments at an 8 dB signal to noise ratio.

Results:

Speech intelligibility was reduced significantly (by approximately 40 percentage points) in the presence of mismatched lexical tone information in both quiet and noise. The difficulty in correctly identifying sentences with mismatched lexical tones among adults with hearing loss was significantly greater than that of adults with normal hearing. Cognitive function was not significantly related to a decline in speech recognition scores.

Conclusions:

Contextual and other phonemic cues (i.e., consonants and vowels) are inadequate for HA users to perceive sentences with mismatched lexical tone contours in quiet or noise. Also, HA users with better cognitive function could not compensate for the loss of lexical tone information. These results highlight the importance of accurately representing lexical tone information for Mandarin speakers using HAs.
Mortality Risk Profiles for Sepsis: A Novel Longitudinal and Multivariable Approach
Authors: Liaw Patricia C. , Fox-Robichaud Alison E. , Liaw Kao-Lee , McDonald Ellen , Dwivedi Dhruva J. , Zamir Nasim M. , Pepler Laura , Gould Travis J. , Xu Michael , Zytaruk Nicole , Medeiros Sarah K. , McIntyre Lauralyn , Tsang Jennifer , Dodek Peter M. , Winston Brent W. , Martin Claudio , Fraser Douglas D. , Weitz Jeffrey I. , Lellouche Francois , Cook Deborah J. , Marshall John
Published: August 2019

Objectives:

To determine if a set of time-varying biological indicators can be used to: 1) predict the sepsis mortality risk over time and 2) generate mortality risk profiles.

Design:

Prospective observational study.

Setting:

Nine Canadian ICUs.

Subjects:

Three-hundred fifty-six septic patients.

Interventions:

None.

Measurements and Main Results:

Clinical data and plasma levels of biomarkers were collected longitudinally. We used a complementary log-log model to account for the daily mortality risk of each patient until death in ICU/hospital, discharge, or 28 days after admission. The model, which is a versatile version of the Cox model for gaining longitudinal insights, created a composite indicator (the daily hazard of dying) from the “day 1” and “change” variables of six time-varying biological indicators (cell-free DNA, protein C, platelet count, creatinine, Glasgow Coma Scale score, and lactate) and a set of contextual variables (age, presence of chronic lung disease or previous brain injury, and duration of stay), achieving a high predictive power (conventional area under the curve, 0.90; 95% CI, 0.86–0.94). Including change variables avoided misleading inferences about the effects of day 1 variables, signifying the importance of the longitudinal approach. We then generated mortality risk profiles that highlight the relative contributions among the time-varying biological indicators to overall mortality risk. The tool was validated in 28 nonseptic patients from the same ICUs who became septic later and was subject to 10-fold cross-validation, achieving similarly high area under the curve.

Conclusions:

Using a novel version of the Cox model, we created a prognostic tool for septic patients that yields not only a predicted probability of dying but also a mortality risk profile that reveals how six time-varying biological indicators differentially and longitudinally account for the patient’s overall daily mortality risk.
Qualitative Research
Authors: Cypress Brigitte S.
Published: August 2019

Considering the inductive nature of qualitative studies, the research process can be challenging to novices and doctoral students at every step. Appropriate planning should be in place before the commencement of the fieldwork, as well as to be able to address any methodological contingencies that emerge during the process. Challenges and dilemmas occur at different stages of the endeavor, namely, when selecting a topic, exploring the literature, selecting the setting, protecting the rights of participants, choosing a methodology and a research design, and collecting, managing, and analyzing data. This article aims to illuminate the quandaries of a naturalistic inquiry and to teach and recommend approaches to better address them. Providing researchers with the necessary and appropriate skills may help provide applicable and trustworthy study findings and outcomes. Hence, these recommendations need to be well defined and presented.
Emerging technologies in pediatric gynecology: new paradigms in women's health care
Authors: Wancura Megan , McCracken Jennifer M. , Steen Emily , Cosgriff-Hernandez Elizabeth , Keswani Sundeep , Hakim Julie C.-E.
Published: August 2019

Purpose of review

The current review highlights the complexity of the pediatric and adolescent gynecology subspecialty as well as the recent and exciting opportunities for innovation within the field.

Recent findings

The opportunities for concept, treatment, instrument, and knowledge-transfer innovation to better serve the specific needs of pediatric gynecology patients include novel approaches to neovagina creation using magnets, improving postoperative vaginal wound healing through newly designed and degradable vaginal stents, and complex Mullerian reconstructive surgical planning using virtual reality immersive experiential training.

There is a significant window of opportunity to address the needs of pediatric, adolescent and adult gynecological patients with new innovative concepts and tools.
Are We Ready to Treat Diffuse Large B‐cell and High‐Grade Lymphoma According to Major Genetic Subtypes?
Authors: Chiappella Annalisa , Crombie Jennifer , Guidetti Anna , Vitolo Umberto , Armand Philippe , Corradini Paolo
Published: August 2019

Diffuse Large B‐Cell Lymphoma (DLBCL) is a clinically and biologically heterogeneous disease. The revised Classification of Lymphoproliferative diseases published in 2016 (WHO, 2016) refined the previous DLBLC subtypes and identified four categories: DLBCL not otherwise specified (NOS), other lymphomas of large B cells, high grade B‐cell lymphoma, and B‐cell lymphoma unclassifiable. High grade B‐cell lymphomas include the entities carrying MYC, BCL2 and/or BCL6 translocations or cases with blastoid morphology without DH translocations. This classification also acknowledges the cell of origin (COO) classification, that has only a limited impact on the choice of frontline treatment for DLBCL, as most patients still receive R‐CHOP chemoimmunotherapy. Attempts to improve the outcomes of specific subgroups, especially COO groups, have so far had limited success. Newer analyses have further subdivided DLBCL into genomically distinct subsets, not yet incorporated in the WHO classification, which may facilitate targeted approaches to therapy. In this review, we discuss the subgroups that are recognized by the WHO 2016 classification, review the newer genomic data, and speculate on how this could alter the treatment landscape of DLBCL in the future. We also discuss novel approaches to salvage therapy in the broad context of the heterogeneity of DLBCL.
Results and implications from a gender minority health education module for advance practice nursing students
Authors: Klotzbaugh Ralph J. , Ballout Suha , Spencer Gale
Published: August 2019

Nursing literature has recognized deficits in lesbian, gay, bisexual, transgender, queer-specific care. Of particular concern is lack of knowledge about gender minorities. Lack of knowledge remains despite this populations' increased health disparities. This pilot study investigates pre- and post-knowledge of medical guidelines, disparities, policies, and attitudes specific to gender minorities among advanced practice nursing students attending a gender minority health module. All participants in this pilot study completed a questionnaire on content and a transphobia scale to evaluate its effect on attitudes. Students were also surveyed on previous experience with gender minority patients. Students indicated sex and gender identity as female, with a mean age of 33.5 years. Twenty-seven percent of the students reported experience with gender minority patients. Wilcoxon signed rank test indicated statistically significant improvement in knowledge and improved scores on transphobia. This study demonstrated a module on the health of gender minorities is an effective method for increasing student knowledge of gender minority health care.
Surgical site infections: current management and role of new antibiotics
Authors: Mellinghoff Sibylle C. , Otto Christina , Cornely Oliver A.
Published: August 2019

Purpose of review

Management of SSI comprises prevention, extensive diagnosis, and appropriate treatment as well as follow-up. All these are interrelated matters. This review gives a brief update on the latest developments in the field, specifically on new antibiotics that may find a place in this complex field.

Recent findings

Avibactam and dalbavancin are novel antiinfectives. Although randomized controlled trials in SSI are lacking to date, preliminary data show that new drugs may be alternatives to existing treatment. Currently, they should be used only on the ground of susceptibility testing, and if standard drugs are inappropriate.

Correct diagnosis of SSI depends on the type of procedure performed. However, early detection is of great importance for proper management across all surgical interventions. The management of SSI includes consistent antibiotic therapy, wound drainage, and rigorous wound debridement as appropriate. Specific wound management thereafter depends on the location and nature of infection. If available, culture findings guide changes in antibiotic therapy. Avibactam and dalbavancin are novel antiinfectives that should be used on ground of susceptibility testing in the absence of appropriate alternatives. Follow-up is particularly important in patients with prosthesis in place. The most promising approach of postdischarge surveillance is a matter of ongoing debate.
Characterization of Age-Related Injury Patterns and Surgical Treatment of Pediatric Facial Fractures: Analysis of the National Trauma Data Bank
Authors: Gebran Selim G. , Wasicek Philip J. , Elegbede Adekunle , Ngaage Ledibabari M. , Liang Yuanyuan , Ottochian Marcus , Morrison Jonathan J. , Rasko Yvonne M. , Liang Fan , Grant Michael P. , Nam Arthur J.
Published: August 2019

Background:

Presentation of pediatric facial fractures varies widely and many injuries are encountered infrequently by most practitioners. This study summarizes injury patterns in a large cohort of facial fractures and their subsequent surgical management.

Methods:

Demographic and clinical characteristics of patients 18 years of age or younger admitted between 2009 and 2015 to trauma centers participating in the National Trauma Data Bank were examined. Craniofacial fractures and reconstructive procedures performed at index admission were selected based on ICD-9 and AIS codes. A multivariable analysis was used to determine independent determinants of surgical repair.

Results:

Out of 60,094 pediatric patients evaluated in the US emergency departments, 48,821 patients were admitted and underwent open treatment (n = 8364; 17.1%) or closed treatment (n = 4244; 8.7%) of facial fractures. Falls were the most common mechanism of injury in infants and toddlers (<2-year-old, 44.4%, P <0.001), while motor vehicle collisions (32.9%, P <0.001) and assault (22.1%, P <0.001) were most commonly seen in adolescents (12–18-year-old). The frequency and odds of repair of facial fractures increased with advancing age, more so with open than closed treatment in adolescents (73.0%) as compared to infants and toddlers (50.3%). Children who sustained mandible fractures are the most likely to require surgical treatment at index-admission (odds ratio = 13.9, 95% confidence interval 13.1–14.8, P <0.001).

Conclusions:

Population-based data shows that pediatric fracture patterns and associated early repair vary significantly with age. Patient demographics and hospital characteristics are significant determinants of surgical treatment that should be related to clinical outcomes in future studies.
Failure in Revision Dacryocystorhinostomy: A Study of Surgical Technique and Etiology
Authors: Altin Ekin Meryem , Karadeniz Ugurlu Seyda , Aytogan Hasan , Sahin Atik Sevinc
Published: August 2019

The aim of this study is to assess the etiologic factors of primary dacryocystorhinostomy (DCR) failure according to DCR techniques and also to determine risk factors for the prediction of failure in revision external DCR. Retrospective review was performed in patients who underwent revision external DCR for previous DCR failure between 2008 and 2018. All patients underwent full ophthalmic and intranasal examination, lacrimal probing, and irrigation. Patients were classified into following groups according to previous DCR type: external, endoscopic endonasal, and transcanalicular laser DCR. Potential etiologic factors were compared between 3 groups. Multivariate analysis was performed to identify risk factors for failure in revision external DCR. About 115 eyes from 109 patients constituted the external (50.4%), endonasal (31.3%), and laser (18.3%) DCR groups. Among 27 (23.5%) patients with intranasal pathologies, septal deviation (33.3%) is the most common finding. The commonest cause of failure was inadequate ostium size in external (37.9%), endonasal (36.1%), and laser (66.7%) DCR groups. Inadequate ostium size and cicatricial lacrimal ostium scarring were observed significantly more common in the laser (P = 0.047) and external DCR group (P = 0.043), respectively. The success rate for revision external DCR was 85.2%. Canalicular or common canalicular obstruction (P = 0.032), intranasal pathology (P = 0.003), and bilateral obstruction (P = 0.025) demonstrated a significant independent association with failure in revision external DCR. Inadequate ostium size was the most common cause of failure in primary external, endonasal, and laser DCR. Canalicular or common canalicular obstruction, intranasal pathology, and bilateral lacrimal obstruction were significant predictors of failure in revision external DCR.