bluuebunny/crossref_metadata_2025 huggingface dataset:
Trends in Acute Lymphoblastic Leukemia Incidence in the United States by Race/Ethnicity From 2000 to 2016
Authors: Feng Qianxi , de Smith Adam J , Vergara-Lluri Maria , Muskens Ivo S , McKean-Cowdin Roberta , Kogan Scott , Brynes Russell , Wiemels Joseph L
Published: October 2020

Incidence trends in acute lymphoblastic leukemia (ALL) demonstrate disparities by race and ethnicity. We used data from the Surveillance, Epidemiology, and End Results Registry to evaluate patterns in ALL incidence from 2000 to 2016, including the association between percentage of people born in a foreign country at the county level and ALL incidence. Among 23,829 persons of all ages diagnosed with ALL, 8,297 (34.8%) were Latinos, 11,714 (49.2%) were non-Latino (NL) Whites, and 1,639 (6.9%) were NL Blacks. Latinos had the largest increase in the age-adjusted incidence rate (AAIR) of ALL during this period compared with other races/ethnicities for both children and adults: The AAIR was 1.6 times higher for Latinos (AAIR = 2.43, 95% confidence interval (CI): 2.37, 2.49) than for NL Whites (AAIR = 1.56, 95% CI: 1.53, 1.59) (P < 0.01). The AAIR for all subjects increased approximately 1% per year from 2000 to 2016 (annual percent change = 0.97, 95% CI: 0.67, 1.27), with the highest increase being observed in Latinos (annual percent change = 1.18, 95% CI: 0.76, 1.60). In multivariable models evaluating the contribution of percentage of county residents who were foreign-born to ALL risk, a positive association was found for percentage foreign-born for NL Whites (P for trend < 0.01) and NL Blacks (P for trend < 0.01), but the reverse was found for Latinos (P for trend < 0.01); this is consistent with tenets of the “Hispanic paradox,” in which better health outcomes exist for foreign-born Latinos.
Do annual and perennial populations of an insect-pollinated plant species differ in mating system?
Authors: Ma Yue , Barrett Spencer C H , Wang Fang-Yuan , Deng Jun-Chen , Bai Wei-Ning
Published: October 2020

Background and Aims

Theory predicts that outcrossing should be more prevalent among perennials than annuals, a pattern confirmed by comparative evidence from diverse angiosperm families. However, intraspecific comparisons between annual and perennial populations are few because such variation is uncommon among flowering plants. Here, we test the hypothesis that perennial populations outcross more than annual populations by investigating Incarvillea sinensis, a wide-ranging insect-pollinated herb native to China. The occurrence of both allopatric and sympatric populations allows us to examine the stability of mating system differences between life histories under varying ecological conditions.

Methods

We estimated outcrossing rates and biparental inbreeding in 16 allopatric and five sympatric populations in which both life histories coexisted using 20 microsatellite loci. In each population we measured height, branch number, corolla size, tube length and herkogamy for ~30 individuals. In a sympatric population, we recorded daily flower number, pollinator visitation and the fruit and seed set of annual and perennial plants.

Key Results

As predicted, outcrossing rates (t) were considerably higher in perennial (mean = 0.76) than annual (mean = 0.09) populations. This difference in mating system was also maintained at sympatric sites where plants grew intermixed. In both allopatric and sympatric populations the degree of herkogamy was consistently larger in outcrossing than selfing plants. Perennials were more branched, with more and larger flowers than in annuals. In a sympatric population, annuals had a significantly higher fruit and seed set than perennials.

Conclusions

Genetically based differences in herkogamy between annuals and perennials appear to play a key role in governing outcrossing rates in populations, regardless of variation in local ecological conditions. The maintenance of mating system and life history trait differentiation between perennial and annual populations of I. sinensis probably results from correlated evolution in response to local environmental conditions.
Adjustment Disorder Amongst Welfare Social Service Clients: The Role of Period of Service Receipt and Social Worker’s Alternation
Authors: Mahat-Shamir Michal , Zychlinski Ester , Lavenda Osnat , Kagan Maya
Published: October 2020

Adjustment disorder is a maladaptive reaction to common life events. Levels of adjustment disorder can serve as one of the indicators of the effectiveness of social services interventions. Yet, the role of service receipt period and of social worker alternation in explaining levels of adjustment disorder remains unclear. In order to explore this issue, structured questionnaires were distributed to a random sample of 190 clients of a social services department in Israel. Whilst no significant differences were found between service receipt periods with regard to clients’ adjustment disorder, clients treated by a single social worker reported lower levels of adjustment disorder than those treated by alternating social workers. Furthermore, new and long-standing clients, treated by alternating social workers displayed higher levels of adjustment disorder than those treated by a single social worker. The importance of therapeutic alliance is discussed in light of the present findings.
Sustainable waste management for zero waste cities in China: potential, challenges and opportunities
Authors: Lee Roh Pin , Meyer Bernd , Huang Qiuliang , Voss Raoul
Published: October 2020

Waste is a valuable secondary carbon resource. In the linear economy, it is predominantly landfilled or incinerated. These disposal routes not only lead to diverse climate, environmental and societal problems; they also represent a loss of carbon resources. In a circular carbon economy, waste is used as a secondary carbon feedstock to replace fossil resources for production. This contributes to environmental protection and resource conservation. It furthermore increases a nation’s independence from imported fossil energy sources. China is at the start of its transition from a linear to circular carbon economy. It can thus draw on waste management experiences of other economies and assess the opportunities for transference to support its development of ‘zero waste cities’. This paper has three main focuses. First is an assessment of drivers for China’s zero waste cities initiative and the approaches that have been implemented to combat its growing waste crisis. Second is a sharing of Germany’s experience—a forerunner in the implementation of the waste hierarchy (reduce–reuse–recycle–recover–landfill) with extensive experience in circular carbon technologies—in sustainable waste management. Last is an identification of transference opportunities for China’s zero waste cities. Specific transference opportunities identified range from measures to promote waste prevention, waste separation and waste reduction, generating additional value via mechanical recycling, implementing chemical recycling as a recycling option before energy recovery to extending energy recovery opportunities.
Tau and Amyloid Relationships with Resting-state Functional Connectivity in Atypical Alzheimer’s Disease
Authors: Sintini Irene , Graff-Radford Jonathan , Jones David T , Botha Hugo , Martin Peter R , Machulda Mary M , Schwarz Christopher G , Senjem Matthew L , Gunter Jeffrey L , Jack Clifford R , Lowe Val J , Josephs Keith A , Whitwell Jennifer L
Published: October 2020

The mechanisms through which tau and amyloid-beta (Aβ) accumulate in the brain of Alzheimer’s disease patients may differ but both are related to neuronal networks. We examined such mechanisms on neuroimaging in 58 participants with atypical Alzheimer’s disease (posterior cortical atrophy or logopenic progressive aphasia). Participants underwent Aβ-PET, longitudinal tau-PET, structural MRI and resting-state functional MRI, which was analyzed with graph theory. Regions with high levels of Aβ were more likely to be functional hubs, with a high number of functional connections important for resilience to cascading network failures. Regions with high levels of tau were more likely to have low clustering coefficients and degrees, suggesting a lack of trophic support or vulnerability to local network failures. Regions strongly functionally connected to the disease epicenters were more likely to have higher levels of tau and, less strongly, of Aβ. The regional rate of tau accumulation was associated with tau levels in functionally connected regions, in support of tau accumulation in a functional network. This study elucidates the relations of tau and Aβ to functional connectivity metrics in atypical Alzheimer’s disease, strengthening the hypothesis that the spread of the 2 proteins is driven by different biological mechanisms related to functional networks.
Ethnic Insults in YouTube Comments: Social Contagion and Selection Effects During the German “Refugee Crisis”
Authors: Spörlein Christoph , Schlueter Elmar
Published: October 2020

In this article, we investigate the extent to which ethnic insults propagate through comment networks in YouTube videos from four German political talk shows with the largest audience reach. We argue that comments using ethnic insults signal social norms and embolden others to emulate offensive behaviour, therefore potentially contributing the contagiousness of insulting commenting. Moreover, periods of highly salient intergroup conflict (i.e. sexual assaults and terrorist attacks), may further reduce inhibitions to publicly post insulting content further multiplying the spread of this behaviour. To evaluate our claims, we construct a repeated cross-sectional dataset from the comment networks in YouTube videos as well as a pseudo-panel of highly active users which is used to gauge the impact of social selection. Results indicate that the use of ethnic insults in online comment sections appears socially contagious. Specifically, we find that a larger presence of ethnic insults in preceding comments increases the prevalence of insulting comments by 2 percentage points which increases to 7 percentage points in the aftermath of violent incidents. However, findings based on the pseudo-user panel do show that using ethnic insults is socially contagious thus suggesting that the patterns found for the full sample are largely a function of social selection processes.
Durchfall, Auschwitz’s Unwritten Story: Filth and Excremental Violence in Tadeusz Borowski’s Postwar Fiction
Authors: Tietjen Jeanie
Published: October 2020

As an author central to postwar literature on the concentration and death camp experience, Tadeusz Borowski chose to depict the relatively taboo subject of excremental violence. Borowski’s documentary fiction depicted an aspect of history that was, especially in 1946 after his own incarceration and survival, both raw and controversial. Writing in Polish as part of a collective work, Borowski was intent on speaking in his native language to a shattered Polish nation. This article analyzes how Borowski drew attention to human rights violations by writing about excremental violence. It further examines how Borowski eschewed oversimplified postwar categories of perpetrators, victims, and resisters. Instead, drawing upon his own experiences in Auschwitz, Dautmergen, and Dachau, his works articulate the powerlessness of those in the camps and the dehumanizing conditions they faced, thus challenging any misleading narratives regarding heroic agency.
Midterm outcomes of endovascular treatment with bare metal stents for Leriche syndrome patients
Authors: Zhang Bihui , Niu Guochen , Yan Ziguang , Zou Yinghua , Tong Xiaoqiang , Yang Min
Published: October 2020

OBJECTIVES

This study was undertaken to evaluate the acute and midterm results of endovascular treatment with bare metal stents (BMS) for Leriche syndrome patients.

METHODS

Patients with Leriche syndrome treated with BMS from August 2008 to May 2017 were included in the study and followed up. The primary endpoints were primary restenosis-free survival rates at 1, 2 and 3 years. The secondary endpoints were secondary restenosis-free and freedom from target lesion revascularization survival rates at 1, 2 and 3 years; technical success rate; complication rate; procedure-related mortality rate; and clinical status improvement at follow-up.

RESULTS

Twenty patients were included and the follow-up duration was 34.7 ± 18.7 months (0–86 months). The 1-, 2- and 3-year primary restenosis-free survival rates were 94.4%, 88.1% and 73.5% and the secondary patency rates were 94.4%, 94.4% and 86.6%, respectively. The freedom from target lesion revascularization survival rates of patients at 1, 2 and 3 years were 94.4%, 88.1% and 79.3%, respectively. The aortoiliac lesions were successfully treated with BMS bilaterally in 17 patients (85.0%) and unilaterally in another 3 patients (15.0%). The complication rate was 10.0% and the procedure-related mortality rate was 0%. Mean ankle-brachial index increased significantly from 0.43 ± 0.20 before the procedure to 0.95 ± 0.21 after the procedure (P < 0.001), and to 1.00 ± 0.19 at the end of the follow-up (P < 0.001). Improvement in symptoms occurred in most patients soon after the endovascular procedure (95.0%) and at follow-up (88.2%).

CONCLUSIONS

Endovascular treatment with BMS is effective and safe for patients with Leriche syndrome according to 3-year follow-up results.
Effect of conventional and rapid-deployment aortic valve replacement on the distance from the aortic annulus to coronary arteries
Authors: Coti Iuliana , Maierhofer Udo , Rath Claus , Werner Paul , Loewe Christian , Kocher Alfred , Laufer Guenther , Andreas Martin
Published: October 2020

OBJECTIVES

This study aimed to compare the effect of surgical aortic valve replacement (SAVR) on coronary height in patients undergoing SAVR with rapid-deployment or SAVR with several standard sutured bioprostheses. This study may identify patients at higher risk of coronary obstruction during valve-in-valve procedures.

METHODS

We analysed 112 patients [mean age 71 (9 SD) years] who underwent SAVR with either a rapid-deployment aortic bioprosthesis (EDWARDS INTUITY Elite Valve) or other standard sutured biological valves. The coronary heights were assessed by computed tomography scan with the Philips 3D HeartNavigator system.

RESULTS

Two groups of patients were analysed: 51 (45.5%) patients implanted with an RD-AVR, which is a supra-annular valve that requires 3 anchoring sutures without the use of pledgets, and 61 (54.5%) patients implanted with a conventional supra-annular sutured bioprosthesis. The mean right and left coronary artery-to-annulus (RCAA and LCAA) heights at baseline were 16.9 (4.6 SD) and 14.2 (4.0 SD) mm in the standard sutured group and 16.3 (3.5 SD) and 12.8 (2.9 SD) mm in the RD-AVR group, respectively; a significantly shorter distance was observed for the left coronary artery in the rapid-deployment group (P = 0.420 for RCAA height and P = 0.044 for LCAA). Postoperatively, the mean RCAA and LCAA heights were significantly decreased in both groups compared to baseline. A mean of 11.5 (4.8 SD) mm for the RCAA and 7.9 (4.3 SD) mm for the LCAA in the standard sutured group as well as 14.4 (3.9 SD) mm for the RCAA and 9.0 (3.1 SD) mm for the LCAA in the RD-AVR group were observed (P < 0.001 for RCAA and LCAA in both the sutured and rapid-deployment groups). Despite the significant difference in the mean distance from the left coronary artery to annulus between the groups at baseline, the postoperative mean distance of the LCAA to the sewing ring was still higher in the RD-AVR group.

CONCLUSIONS

A significantly shorter coronary artery-to-aortic annulus distance for both the right and left main coronary arteries was observed after AVR with different conventional sutured supra-annular bioprostheses compared to AVR with rapid-deployment valves. These findings might be relevant for bioprosthesis selection, especially for young patients.
Changes in compensation claim contents following reorganization of emergency hospital care
Authors: Birkeland Søren , Brabrand Mikkel , Mikkelsen Kim Lyngby , Bie Bogh Søren
Published: October 2020

Objectives

To study the effects of the reorganization on patient compensation claim contents relating to health care quality and patient safety.

Design and settings

Danish emergency care has developed considerably over the past decades, including a major reorganization to improve health care quality and patient safety through ensuring easier access to specialist treatment. Analysis of compensation claim patterns is used to evaluate the effects of such health care system changes.

Participants, interventions and main outcome measures

A sample of 1613 compensation claims to the Danish Patient Assurance organization was reviewed using a standardized taxonomy (the Healthcare Complaints Analysis Tool [HCAT]). Using trend analysis, we compared the proportions of claims categorized under HCAT domains, problem categories and sub-categories before and after the reorganization, with particular emphasis on the ‘Clinical problems’ domain covering health care quality and patient safety issues.

Results

We observed a baseline increase in claims relating to clinical problems (P < 0.01), but this increase was less pronounced following the reorganization. This appeared to be driven mainly by a decrease in claims about clinician skills (P = 0.03) and health care neglects (P = 0.01). However, claims about diagnostic errors and patient outcomes showed a tendency (insignificant) to increase.

Conclusions

Emergency care reorganization apparently has been followed by a shift in claim contents towards fewer claims about health care neglect and staff competencies, although claims about other matters may have become more common. Present analyses of compensation claim trends should be supplemented by effect studies using traditional outcome measures such as mortality and readmission rates.
Key genetic elements, single and in clusters, underlying geographically dependent SARS-CoV-2 genetic adaptation and their impact on binding affinity for drugs and immune control
Authors: Salpini Romina , Alkhatib Mohammad , Costa Giosuè , Piermatteo Lorenzo , Ambrosio Francesca Alessandra , Di Maio Velia Chiara , Scutari Rossana , Duca Leonardo , Berno Giulia , Fabeni Lavinia , Alcaro Stefano , Ceccherini-Silberstein Francesca , Artese Anna , Svicher Valentina
Published: October 2020

Objectives

To define key genetic elements, single or in clusters, underlying SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2) evolutionary diversification across continents, and their impact on drug-binding affinity and viral antigenicity.

Methods

A total of 12 150 SARS-CoV-2 sequences (publicly available) from 69 countries were analysed. Mutational clusters were assessed by hierarchical clustering. Structure-based virtual screening (SBVS) was used to select the best inhibitors of 3-chymotrypsin-like protease (3CL-Pr) and RNA-dependent RNA polymerase (RdRp) among the FDA-approved drugs and to evaluate the impact of mutations on binding affinity of these drugs. The impact of mutations on epitope recognition was predicted following Grifoni et al. (Cell Host Microbe 2020;

27

671–80.)

Results

Thirty-five key mutations were identified (prevalence: ≥0.5%), residing in different viral proteins. Sixteen out of 35 formed tight clusters involving multiple SARS-CoV-2 proteins, highlighting intergenic co-evolution. Some clusters (including D614GSpike + P323LRdRp + R203KN + G204RN) occurred in all continents, while others showed a geographically restricted circulation (T1198KPL-Pr + P13LN + A97VRdRp in Asia, L84SORF-8 + S197LN in Europe, Y541CHel + H504CHel + L84SORF-8 in America and Oceania). SBVS identified 20 best RdRp inhibitors and 21 best 3CL-Pr inhibitors belonging to different drug classes. Notably, mutations in RdRp or 3CL-Pr modulate, positively or negatively, the binding affinity of these drugs. Among them, P323LRdRp (prevalence: 61.9%) reduced the binding affinity of specific compounds including remdesivir while it increased the binding affinity of the purine analogues penciclovir and tenofovir, suggesting potential hypersusceptibility. Finally, specific mutations (including Y541CHel + H504CHel) strongly hampered recognition of Class I/II epitopes, while D614GSpike profoundly altered the structural stability of a recently identified B cell epitope target of neutralizing antibodies (amino acids 592–620).

Conclusions

Key genetic elements reflect geographically dependent SARS-CoV-2 genetic adaptation, and may play a potential role in modulating drug susceptibility and hampering viral antigenicity. Thus, a close monitoring of SARS-CoV-2 mutational patterns is crucial to ensure the effectiveness of treatments and vaccines worldwide.
SynTEG: a framework for temporal structured electronic health data simulation
Authors: Zhang Ziqi , Yan Chao , Lasko Thomas A , Sun Jimeng , Malin Bradley A
Published: October 2020

Objective

Simulating electronic health record data offers an opportunity to resolve the tension between data sharing and patient privacy. Recent techniques based on generative adversarial networks have shown promise but neglect the temporal aspect of healthcare. We introduce a generative framework for simulating the trajectory of patients’ diagnoses and measures to evaluate utility and privacy.

Materials and Methods

The framework simulates date-stamped diagnosis sequences based on a 2-stage process that 1) sequentially extracts temporal patterns from clinical visits and 2) generates synthetic data conditioned on the learned patterns. We designed 3 utility measures to characterize the extent to which the framework maintains feature correlations and temporal patterns in clinical events. We evaluated the framework with billing codes, represented as phenome-wide association study codes (phecodes), from over 500 000 Vanderbilt University Medical Center electronic health records. We further assessed the privacy risks based on membership inference and attribute disclosure attacks.

Results

The simulated temporal sequences exhibited similar characteristics to real sequences on the utility measures. Notably, diagnosis prediction models based on real versus synthetic temporal data exhibited an average relative difference in area under the ROC curve of 1.6% with standard deviation of 3.8% for 1276 phecodes. Additionally, the relative difference in the mean occurrence age and time between visits were 4.9% and 4.2%, respectively. The privacy risks in synthetic data, with respect to the membership and attribute inference were negligible.

Conclusion

This investigation indicates that temporal diagnosis code sequences can be simulated in a manner that provides utility and respects privacy.
Quantification of Classic, Prescription and Synthetic Opioids in Hair by LC–MS-MS
Authors: Platosz Natalia A , Binz Tina M , Baumgartner Markus R , Lendoiro Elena , de Castro Ana , Concheiro Marta
Published: October 2020

The current use and misuse of synthetic and prescription opioids in the USA has reached epidemic status. According to the US Department of Health and Human Services, every day more than 130 people in the USA die after overdosing on opioids, and 2.1 million had an opioid use disorder in 2018. Hair is becoming an alternative matrix of increasing interest in forensic toxicology to investigate drug use and abuse patterns due to its long window of detection. The focus of this project was to develop and validate a method that simultaneously detects and quantifies 27 classic, prescription and synthetic opioids in hair by liquid chromatography–tandem mass spectrometry (LC–MS-MS). Hair samples were decontaminated and pulverized in a bead mill. Twenty-five milligrams of hair powder were incubated in a buffer overnight. Mixed mode cation exchange solid phase extraction was carried out before undergoing reversed-phase chromatographic separation, successfully resolving isobaric opioids. We used two multiple reaction monitoring transitions in positive mode to identify each analyte. The linearity range was 1–500 pg/mg for fentanyl and synthetic opioids and 10–500 pg/mg for prescription and classic opioids. Imprecision was <17.5% and bias ranged from −13.6 to 12.0%. Majority of compounds showed extraction efficiency >50%, and ion suppression from −89.2 to −26.6% (CV < 19%, n = 10). This method was applied to 64 authentic cases, identifying 13 compounds from our panel. A sensitive and specific method was developed for the identification and quantification of 27 classic, prescription and synthetic opioids in hair by LC–MS-MS.
Feasibility of Patient-Created Orff Chant as a Music-Based Intervention in Supportive Cancer Care
Authors: Colwell Cynthia M , Fiore Jennifer
Published: October 2020

A cancer diagnosis and subsequent treatment can produce distress symptoms, including pain, anxiety, fatigue, and altered mood. These symptoms can have a negative psychological and physiological impact on patients. Patients may need to engage in supportive care with opportunities for emotional responses associated with the disease and chemotherapy treatment to ameliorate distress symptoms. The purpose of the current study was to assess the feasibility of 2 music-based interventions, 1 traditional and 1 novel, and explore the preliminary efficacy of these interventions as supportive care of cancer patients in outpatient treatment rooms. Supportive care options were: standard care (control), patient-selected singing with accompaniment (traditional), and patient-created chant using the Orff process (novel). Distress outcomes measured were: pain and fatigue using a 0–10 numerical rating scale, the State-Trait Anxiety Inventory (state form), and the Profile of Mood States 2 Short Form (for mood and fatigue). After obtaining consent, participants engaged in a single-session of 1 of 3 conditions lasting approximately 30 min. Feasibility measures indicated that the traditional and novel interventions were appropriate for the setting. Results indicated that although not always statistically significant, there were positive changes in pain, fatigue, anxiety, and mood for the 2 music-based conditions over standard care. Conclusions indicate the patient-selected condition was more impactful for pain, anxiety, and mood, while the patient-created chant using the Orff process was more impactful for fatigue. These conclusions might be clinically relevant for therapists pending cancer-related symptoms present during the assessment.
Decision-Making in Collaborative Governance Networks: Pathways to Input and Throughput Legitimacy
Authors: Mosley Jennifer E , Wong Jade
Published: October 2020

Participants may lose faith in collaborative governance processes if they do not perceive internal decision-making processes to be legitimate. Yet, understanding how to assess internal legitimacy and what network characteristics are associated with it has been an enduring challenge. In this article, we propose conceptualizing internal legitimacy as multi-vectored, contrasting input legitimacy—the degree of openness and access that participants experience in their attempt to offer voice—with throughput legitimacy—the quality of the decision-making process itself. Using data from a comparative case study of 18 different US Department of Housing and Urban Development (HUD)-mandated Continuums of Care, we assess this framework with a mixed-methods approach, combining thematic analysis of interview data (n = 145) with Qualitative Comparative Analysis (QCA) to show (1) differences in how participants experience input and throughput legitimacy, (2) the nature of the relationship between input and throughput legitimacy, and (3) what specific network characteristics are associated with positive assessments of each. Our findings indicate that input and throughput legitimacy are distinct but related—throughput legitimacy is harder to achieve and dependent on positive assessments of input legitimacy. Some network characteristics, particularly large size and commissioner-style network management, pose challenges, but a focus on in-person engagement can help ameliorate them. We conclude that distinguishing between input and throughput legitimacy can help managers identify where and how to intervene in order to improve the legitimacy of decision-making processes in collaborative governance networks.
A new branch of understanding for barley inflorescence development
Authors: Levin Kara A , Boden Scott A
Published: October 2020

This article comments on:

Shang Y, Yuan L, Di Y, Jia Y, Zhang Z, Li S, Xing L, Qi Z, Wang X, Zhu J, Hua W, Wu X, Zhu M, Li G, Li C. 2020. A CYC/TB1 type TCP transcription factor controls spikelet meristem identity in barley. Journal of Experimental Botany 71, 7118–7131.
Analysis of a phase-variable restriction modification system of the human gut symbiont Bacteroides fragilis
Authors: Ben-Assa Nadav , Coyne Michael J , Fomenkov Alexey , Livny Jonathan , Robins William P , Muniesa Maite , Carey Vincent , Carasso Shaqed , Gefen Tal , Jofre Juan , Roberts Richard J , Comstock Laurie E , Geva-Zatorsky Naama
Published: October 2020

The genomes of gut Bacteroidales contain numerous invertible regions, many of which contain promoters that dictate phase-variable synthesis of surface molecules such as polysaccharides, fimbriae, and outer surface proteins. Here, we characterize a different type of phase-variable system of Bacteroides fragilis, a Type I restriction modification system (R-M). We show that reversible DNA inversions within this R-M locus leads to the generation of eight specificity proteins with distinct recognition sites. In vitro grown bacteria have a different proportion of specificity gene combinations at the expression locus than bacteria isolated from the mammalian gut. By creating mutants, each able to produce only one specificity protein from this region, we identified the R-M recognition sites of four of these S-proteins using SMRT sequencing. Transcriptome analysis revealed that the locked specificity mutants, whether grown in vitro or isolated from the mammalian gut, have distinct transcriptional profiles, likely creating different phenotypes, one of which was confirmed. Genomic analyses of diverse strains of Bacteroidetes from both host-associated and environmental sources reveal the ubiquity of phase-variable R-M systems in this phylum.
SMART: recent updates, new developments and status in 2020
Authors: Letunic Ivica , Khedkar Supriya , Bork Peer
Published: October 2020

SMART (Simple Modular Architecture Research Tool) is a web resource (https://smart.embl.de) for the identification and annotation of protein domains and the analysis of protein domain architectures. SMART version 9 contains manually curated models for more than 1300 protein domains, with a topical set of 68 new models added since our last update article (1). All the new models are for diverse recombinase families and subfamilies and as a set they provide a comprehensive overview of mobile element recombinases namely transposase, integrase, relaxase, resolvase, cas1 casposase and Xer like cellular recombinase. Further updates include the synchronization of the underlying protein databases with UniProt (2), Ensembl (3) and STRING (4), greatly increasing the total number of annotated domains and other protein features available in architecture analysis mode. Furthermore, SMART’s vector-based protein display engine has been extended and updated to use the latest web technologies and the domain architecture analysis components have been optimized to handle the increased number of protein features available.
How to tackle health literacy problems in chronic kidney disease patients? A systematic review to identify promising intervention targets and strategies
Authors: Boonstra Marco D , Reijneveld Sijmen A , Foitzik Elisabeth M , Westerhuis Ralf , Navis Gerjan , de Winter Andrea F
Published: October 2020

Background

Limited health literacy (LHL) is associated with multiple adverse health outcomes in chronic kidney disease (CKD). Interventions are needed to improve this situation, but evidence on intervention targets and strategies is lacking. This systematic review aims to identify potential targets and strategies by summarizing the evidence on: (i) patient- and system-level factors potentially mediating the relation between LHL and health outcomes; and (ii) the effectiveness of health literacy interventions customized to CKD patients.

Methods

We performed a systematic review of peer-reviewed research articles in Medline, Embase and Web of Science, 2009–19. We assessed the quality of the studies and conducted a best-evidence synthesis.

Results

We identified 860 publications and included 48 studies. Most studies were of low quality (n = 26) and focused on dialysis and transplantation (n = 38). We found strong evidence for an association of LHL with smoking and having a suboptimal transplantation process. Evidence was weak for associations between LHL and a variety of factors related to self-care management (n = 25), utilization of care (n = 23), patient–provider interaction (n = 8) and social context (n = 5). Six interventions were aimed at improving knowledge, decision-making and health behaviours, but evidence for their effectiveness was weak.

Conclusions

Study heterogeneity, low quality and focus on kidney failure largely impede the identification of intervention targets and strategies for LHL. More and higher quality studies in earlier CKD stages are needed to unravel how LHL leads to worse health outcomes, and to identify targets and strategies to prevent disease deterioration. Healthcare organizations need to develop and evaluate efforts to support LHL patients.
PCB126 Exposure Revealed Alterations in m6A RNA Modifications in Transcripts Associated With AHR Activation
Authors: Aluru Neelakanteswar , Karchner Sibel I
Published: October 2020

Chemical modifications of proteins, DNA, and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests the RNA modifications (epitranscriptomics) have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6-methyladenosine (m6A). In a subset of mRNAs, m6A sites are preferentially enriched near stop codons, in 3′ UTRs, and within exons, suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes, it is important to understand the effects of exposure on this important layer of gene regulation. Hence, the objective of this study was to characterize the acute effects of developmental exposure to PCB126, an environmentally relevant dioxin-like PCB, on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for 6 h starting from 72 h post fertilization and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing (MeRIP-seq). Our analysis revealed 117 and 217 m6A peaks in the DMSO and PCB126 samples (false discovery rate 5%), respectively. The majority of the peaks were preferentially located around the 3′ UTR and stop codons. Statistical analysis revealed 15 m6A marked transcripts to be differentially methylated by PCB126 exposure. These include transcripts that are known to be activated by AHR agonists (eg, ahrra, tiparp, nfe2l2b) as well as others that are important for normal development (vgf, cebpd, sned1). These results suggest that environmental chemicals such as dioxin-like PCBs could affect developmental gene expression patterns by altering m6A levels. Further studies are necessary to understand the functional consequences of exposure-associated alterations in m6A levels.
The tight genome size of ants: diversity and evolution under ancestral state reconstruction and base composition
Authors: Moura Mariana Neves , Cardoso Danon Clemes , Cristiano Maykon Passos
Published: October 2020

The mechanisms and processes driving change and variation in the genome size (GS) are not well known, and only a small set of ant species has been studied. Ants are an ecologically successful insect group present in most distinct ecosystems worldwide. Considering their wide distribution and ecological plasticity in different environmental contexts, we aimed to expand GS estimation within Formicidae to examine distribution patterns and variation in GS and base composition and to reconstruct the ancestral state of this character in an attempt to elucidate the generalized pattern of genomic expansions. Genome size estimates were generated for 99 ant species, including new GS estimates for 91 species of ants, and the mean GS of Formicidae was found to be 0.38 pg. The AT/GC ratio was 62.40/37.60. The phylogenetic reconstruction suggested an ancestral GS of 0.38 pg according to the Bayesian inference/Markov chain Monte Carlo method and 0.37 pg according to maximum likelihood and parsimony methods; significant differences in GS were observed between the subfamilies sampled. Our results suggest that the evolution of GS in Formicidae occurred through loss and accumulation of non-coding regions, mainly transposable elements, and occasionally by whole genome duplication. However, further studies are needed to verify whether these changes in DNA content are related to colonization processes, as suggested at the intraspecific level.
Evaluation of Dried Amniotic Membrane on Wound Healing at Split-Thickness Skin Graft Donor Sites: A Randomized, Placebo-Controlled, Double-blind Trial
Authors: Vaheb Mojtaba , Kohestani Bahareh Mohajer , Karrabi Maryam , Khosrojerdi Maryam , Khajeh Mahtab , Shahrestanaki Ehsan , Sahebkar Mohammad
Published: October 2020

OBJECTIVE

To evaluate the effect of amniotic membrane (AM) at split-thickness skin graft (STSG) donor sites.

METHODS

This double-blind randomized controlled trial was conducted on 35 eligible participants referred to the burn unit of Vasei Hospital of Sabzevar, Iran, during 2017 and 2018. Each STSG donor site was divided into two sides, and the respective halves were covered with either a dried AM or petrolatum gauze (control). Outcomes were evaluated on postprocedure days 10, 20, and 30 using the Vancouver Scar Scale.

RESULTS

The mean age of the patients was 39.4 ± 13.97 years, and 62.8% (n = 22) were male. There was no statistically significant difference in wound healing rate on day 10 (P = .261), 20 (P = .214), or 30 (P = .187) between groups. The intervention group had significantly better epithelialization than the control group on day 10 (investigator 1, 1.62 ± 0.59 vs 1.40 ± 0.88 [P = .009); investigator 2, 1.22 ± 0.84 vs 0.91 ± 0.85 [P = .003]), as well as pain reduction (P < .001 during the follow-up period). However, there was no statistically significant difference between groups in terms of pigmentation or vascularization (P > .05).

CONCLUSIONS

Findings suggest that the use of AM is not superior to petrolatum gauze in terms of STSG healing rate; however, AM achieved better pain reduction and epithelialization on day 10.
Predictors of Long-Term Pain After Hip Arthroplasty in Patients With Femoral Neck Fractures: A Cohort Study
Authors: Noori Atefeh , Sprague Sheila , Bzovsky Sofia , Schemitsch Emil H. , Poolman Rudolf W. , Frihagen Frede , Axelrod Daniel , Heels-Ansdell Diane , Bhandari Mohit , Busse Jason W. ,   on behalf of the HEALTH Investigators
Published: October 2020

Objectives:

To identify factors associated with the development of prolonged pain after hip fracture surgery.

Design:

Secondary analysis of a randomized controlled trial.

Setting:

Eighty hospitals in 10 countries.

Patients/Participants:

One thousand four hundred forty-one hip fracture patients in the HEALTH trial.

Interventions:

Total hip arthroplasty or hemiarthroplasty.

Main Outcome Measures:

Moderate-to-severe pain (at least 2 activities on the Western Ontario and McMaster Universities Osteoarthritis questionnaire pain subscale with scores ≥2) at 12 and 24 months after hip arthroplasty.

Results:

Of 840 and 726 patients with complete baseline data and outcomes at 1-year and 2-year follow-up, 96 (11.4%) and 80 (11.0%) reported moderate-to-severe pain, respectively. An increased risk of pain at both 1 and 2 years after surgery was associated with reporting moderate-to-severe hip pain before fracture [absolute risk increase (ARI) 15.3%, 95% confidence interval (CI) 6.44%–24.35%; ARI 12.5%, 95% CI 2.85%–22.12%, respectively] and prefracture opioid use (ARI 15.6%, 95% CI 5.41%–25.89%; ARI 21.1%; 95% CI 8.23%–34.02%, respectively). Female sex was associated with an increased risk of persistent pain at 1 year (ARI 6.2%, 95% CI 3.53%–8.84%). A greater risk of persistent pain at 2 years was associated with younger age (≤79-year-old; ARI 6.3%; 95% CI 2.67%–9.91%) and higher prefacture functional status (ARI 10.7%; 95% CI 3.80%–17.64%).

Conclusions:

Among hip fracture patients undergoing arthroplasty, approximately one in 10 will experience moderate-to-severe pain up to 2 years after surgery. Younger age, female sex, higher functioning prefracture, living with hip pain prefracture, and use of prescription opioids were predictive of persistent pain.

Level of Evidence:

Prognostic Level II. See Instructions for Authors for a complete description of levels of evidence.
What Factors Increase Revision Surgery Risk When Treating Displaced Femoral Neck Fractures With Arthroplasty: A Secondary Analysis of the HEALTH Trial
Authors: Blankstein Michael , Schemitsch Emil H. , Bzovsky Sofia , Poolman Rudolf W. , Frihagen Frede , Axelrod Daniel , Heels-Ansdell Diane , Bhandari Mohit , Sprague Sheila , Schottel Patrick C. ,   on behalf of the HEALTH Investigators
Published: October 2020

Objectives:

HEALTH was a randomized controlled trial comparing total hip arthroplasty with hemiarthroplasty in low-energy displaced femoral neck fracture patients aged ≥50 years with unplanned revision surgery within 24 months of the initial procedure being the primary outcome. No significant short-term differences between treatment arms were observed. The primary objective of this secondary HEALTH trial analysis was to determine if any patient and surgical factors were associated with increased risk of revision surgery within 24 months after hip fracture.

Methods:

We analyzed 9 potential factors chosen a priori that could be associated with revision surgery. The factors included age, body mass index, major comorbidities, independent ambulation, type of surgical approach, length of operation, use of femoral cement, femoral head size, and degree of femoral stem offset. Our statistical analysis was a multivariable Cox regression using reoperation within 24 months of index surgery as the dependent variable.

Results:

Of the 1441 patients included in this analysis, 8.1% (117/1441) experienced reoperation within 24 months. None of the studied factors were found to be predictors of revision surgery (P > 0.05).

Conclusion:

Both total and partial hip replacements are successful procedures in low-energy displaced femoral neck fracture patients. We were unable to identify any patient or surgeon-controlled factors that significantly increased the need for revision surgery in our elderly and predominately female patient population. One should not generalize our findings to an active physiologically younger femoral neck fracture population.

Level of Evidence:

Prognostic Level II. See Instructions for Authors for a complete description of levels of evidence.
Pediatric and Neonatal Invasive Candidiasis
Authors: Jantarabenjakul Watsamon , Yodkitudomying Chatnapa , Chindamporn Ariya , Suchartlikitwong Pintip , Anugulruengkitt Suvaporn , Pancharoen Chitsanu , Puthanakit Thanyawee
Published: October 2020

Background:

Invasive candidiasis (IC) is a serious infection among children with underlying medical conditions. A shift from C. albicans to non-albicans Candida has been observed worldwide. This study aims to identify species of Candida and factors associated with the overall 30-day mortality rate.

Methods:

A retrospective chart review was conducted among children with culture-confirmed IC from birth to 15 years of age at King Chulalongkorn Memorial Hospital, Thailand. Multivariate Cox regression analysis was performed to determine associated factors with 30-day mortality.

Results:

From 2003 to 2019, 102 episodes of IC in pediatric group with a median age of 16 months (interquartile range 4–65) and 12 episodes of IC in neonatal group with a median age of 18 days (interquartile range 12–22). The species distribution were Candida albicans (35%), Candida parapsilosis (26%), Candida tropicalis (22%), Candida glabrata (6%) and other/unspecified species (11%). Antifungal treatment was given in 88% (67% Amphotericin B deoxycholate, 28% Fluconazole). Overall 30-day mortality rates were 28.5% [95% confidence interval (CI) 20.8%–38.4%] and 8.3% (95% CI 1.2%–46.1%) in pediatrics and neonates, respectively. Mortality rate among the neutropenic group was significantly higher than non-neutropenic group (46.4% vs. 20.6%, P = 0.005). Factors associated with 30-day mortality in pediatric IC were shock [adjusted hazard ratio (aHR) 4.2; 95% CI 1.8–9.4], thrombocytopenia (aHR 7.7; 95% CI 1.8–33.9) and no antifungal treatment (aHR 4.6; 95% CI 1.7–12.1).

Conclusions:

Two-third of children with IC were diagnosed with non-albicans Candida. Children with high mortality rate included those with neutropenia, presented with shock or thrombocytopenia, such that the proper empiric antifungal treatment is recommended.
Relationship Between Job Satisfaction and Burnout Based on a Structural Equation Model
Authors: Song Xiaohua , Xiang Minrong , Liu Yan , Yu Chuanhua
Published: October 2020

Objectives:

To understand the relationship between job burnout and job satisfaction for medical workers and analyse the influencing factors.

Methods:

We used two scales to examine medical workers in Hengyang mental hospitals. Multivariate logistic regression and structural equation model were used to evaluate the relevant factors of job satisfaction, and the relationship between job satisfaction and job burnout.

Results:

The total job satisfaction was at the moderate level. For job burnout was in the middle burnout level. Job satisfaction can have a negative prediction function for job burnout (direct effect −0.684). The relevant factors of job burnout and job satisfaction was as follows: nature of the work, pay, benefits and communication impacted job satisfaction and job burnout.

Conclusions:

The current level of job satisfaction is relatively low, job satisfaction has a negative effect on job burnout.