bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolution of echocardiographic and cardiac magnetic resonance imaging abnormalities during follow-up in patients with multisystem inflammatory syndrome in children
Authors: Sirico D , Basso A , Sabatino J , Reffo E , Cavaliere A , Biffanti R , Cerutti A , Castaldi B , Zulian F , Da Dalt L , Di Salvo G 
Published: May 2022

Abstract

Aims
Multisystem inflammatory syndrome in children (MIS-C) with cardiovascular manifestations are frequent. However, there is lacking evidence regarding cardiological follow-up of this cohort of patients. The aim of our study was to describe the early and mid-term cardiac abnormalities assessed by standard and speckle-tracking echocardiography (STE), and cardiac MRI (CMR).

Methods and results
We enrolled 32 patients (21 male, 11 female), mean age 8.25 ± 4years, with diagnosis of MIS-C. During admission, all children underwent TTE, STE with analysis of left ventricle global longitudinal strain (GLS) and CMR. Patients underwent cardiological evaluation at 2 (T1) and 6 months (T2) after discharge. Cardiac MRI was repeated at 6 months after discharge. Mean left ventricular ejection fraction (LVEF) at baseline was 58.8 ± 10% with 10 patients (31%) below 55%. Speckle-tracking echocardiography showed reduced mean LV GLS (−17.4 ± 4%). On CMR, late gadolinium enhancement (LGE) with non-ischaemic pattern was evident in 8 of 23 patients (35%). Follow-up data showed rapid improvement of LVEF at T1 (62.5 ± 7.5 vs. 58.8 ± 10.6%, P-value 0.044) with only three patients (10%) below ≤ 55% at T1. Left ventricular (LV) GLS remained impaired at T1 (−17.2 ± 2.7 vs.−17.4 ± 4, P-value 0.71) and significantly improved at T2 (−19 ± 2.6% vs. −17.4 ± 4%, P-value 0.009). LV GLS was impaired (&gt;−18%) in 53% of patients at baseline and T1, whereas only 13% showed persistent LV GLS reduction at T2. Follow-up CMR showed LGE persistence in 33.4% of cases.

Conclusion
Early cardiac involvement significantly improves during follow-up of MIS-C patients. However, subclinical myocardial dysfunction seems to be still detectable after 6 months of follow-up in a not negligible proportion of them.
Molecular approaches improving our understanding ofBrettanomycesphysiology
Authors: Varela Cristian , Borneman Anthony R 
Published: May 2022

AbstractBrettanomyces species, and particularly B. bruxellensis as the most studied representative, are strongly linked to industrial fermentation processes. This association is considered either positive or undesirable depending on the industry. While in some brewing applications and in kombucha production Brettanomyces yeasts contribute to the flavour and aroma profile of these beverages, in winemaking and bioethanol production Brettanomyces is considered a spoilage or contaminant microorganism. Nevertheless, understanding Brettanomyces biology and metabolism in detail will benefit all industries. This review discusses recent molecular biology tools including genomics, transcriptomics, and genetic engineering techniques that can improve our understanding of Brettanomyces physiology and how these approaches can be used to make the industrial potential of this species a reality.
Highly efficient site-specific integration of DNA fragments into the honeybee genome using CRISPR/Cas9
Authors: Wagner Anna , Seiler Jana , Beye Martin 
Published: May 2022

AbstractFunctional genetic studies in honeybees have been limited to transposon mediated transformation and site directed mutagenesis tools. However, site- and sequence-specific manipulations that insert DNA fragments or replace sequences at specific target sites are lacking. Such tools would enable the tagging of proteins, the expression of reporters and site-specific amino acid changes, which are all gold standard manipulations for physiological, organismal, and genetic studies. However, such manipulations must be very efficient in honeybees since screening and crossing procedures are laborious due to their social organization. Here, we report an accurate and remarkably efficient site-specific integration of DNA-sequences into the honeybee genome using clustered regularly interspaced short palindromic repeat/clustered regularly interspaced short palindromic repeat-associated protein 9-mediated homology-directed repair. We employed early embryonic injections and selected a highly efficient sgRNA in order to insert 294 and 729 bp long DNA sequences into a specific locus at the dsx gene. These sequences were locus-specifically integrated in 57% and 59% of injected bees. Most importantly, 21% and 25% of the individuals lacked the wildtype sequence demonstrating that we generated homozygous mutants in which all cells are affected (no mosaicism). The highly efficient, locus-specific insertions of nucleotide sequences generating homozygous mutants demonstrate that systematic molecular studies for honeybees are in hand that allow somatic mutation approaches via workers or studies in the next generation using queens with their worker progeny. The employment of early embryonic injections and screenings of highly efficient sgRNAs may offer the prospect of highly successful sequence- and locus-specific mutations also in other organisms.
The Drosophila melanogaster enzyme glycerol-3-phosphate dehydrogenase 1 is required for oogenesis, embryonic development, and amino acid homeostasis
Authors: Rai Madhulika , Carter Sarah M , Shefali Shefali A , Mahmoudzadeh Nader H , Pepin Robert , Tennessen Jason M 
Published: May 2022

Abstract
As the fruit fly, Drosophila melanogaster, progresses from one life stage to the next, many of the enzymes that compose intermediary metabolism undergo substantial changes in both expression and activity. These predictable shifts in metabolic flux allow the fly meet stage-specific requirements for energy production and biosynthesis. In this regard, the enzyme glycerol-3-phosphate dehydrogenase 1 (GPDH1) has been the focus of biochemical genetics studies for several decades and, as a result, is one of the most well-characterized Drosophila enzymes. Among the findings of these earlier studies is that GPDH1 acts throughout the fly lifecycle to promote mitochondrial energy production and triglyceride accumulation while also serving a key role in maintaining redox balance. Here, we expand upon the known roles of GPDH1 during fly development by examining how depletion of both the maternal and zygotic pools of this enzyme influences development, metabolism, and viability. Our findings not only confirm previous observations that Gpdh1 mutants exhibit defects in larval development, lifespan, and fat storage but also reveal that GPDH1 serves essential roles in oogenesis and embryogenesis. Moreover, metabolomics analysis reveals that a Gpdh1 mutant stock maintained in a homozygous state exhibits larval metabolic defects that significantly differ from those observed in the F1 mutant generation. Overall, our findings highlight unappreciated roles for GPDH1 in early development and uncover previously undescribed metabolic adaptations that could allow flies to survive the loss of this key enzyme.
Population Genetics of Reproductive Genes in Haplodiploid Species
Authors: Dapper Amy L. , Slater Garett P. , Shores Katherynne , Harpur Brock A. 
Published: May 2022

Abstract
Many animal species are haplodiploid: their fertilized eggs develop into diploid females and their unfertilized eggs develop into haploid males. The unique genetic features of haplodiploidy raise the prospect that these systems can be used to disentangle the population genetic consequences of haploid and diploid selection. To this end, sex-specific reproductive genes are of particular interest because, while they are shared within the same genome, they consistently experience selection in different ploidal environments. However, other features of these genes, including sex-specific expression and putative involvement in postcopulatory sexual selection, are potentially confounding factors because they may also impact the efficacy of selection asymmetrically between the sexes. Thus, to properly interpret evolutionary genomic patterns, it is necessary to generate a null expectation for the relative amount of polymorphism and divergence we expect to observe among sex-specific genes in haplodiploid species, given differences in ploidal environment, sex-limited expression, and their potential role in sexual selection. Here, we derive the theoretical expectation for the rate of evolution of sex-specific genes in haplodiploid species, under the assumption that they experience the same selective environment as genes expressed in both sexes. We find that the null expectation is that reproductive genes evolve more rapidly than constitutively expressed genes in haplodiploid genomes. However, despite the aforementioned differences, the null expectation does not differ between male- and female-specific reproductive genes, when assuming additivity. Our theoretical results provide an important baseline expectation that should be used in molecular evolution studies comparing rates of evolution among classes of genes in haplodiploid species.
BioKIT: a versatile toolkit for processing and analyzing diverse types of sequence data
Authors: Steenwyk Jacob L , Buida Thomas J , Gonçalves Carla , Goltz Dayna C , Morales Grace , Mead Matthew E , LaBella Abigail L , Chavez Christina M , Schmitz Jonathan E , Hadjifrangiskou Maria , Li Yuanning , Rokas Antonis 
Published: May 2022

Abstract
Bioinformatic analysis—such as genome assembly quality assessment, alignment summary statistics, relative synonymous codon usage, file format conversion, and processing and analysis—is integrated into diverse disciplines in the biological sciences. Several command-line pieces of software have been developed to conduct some of these individual analyses, but unified toolkits that conduct all these analyses are lacking. To address this gap, we introduce BioKIT, a versatile command line toolkit that has, upon publication, 42 functions, several of which were community-sourced, that conduct routine and novel processing and analysis of genome assemblies, multiple sequence alignments, coding sequences, sequencing data, and more. To demonstrate the utility of BioKIT, we conducted a comprehensive examination of relative synonymous codon usage across 171 fungal genomes that use alternative genetic codes, showed that the novel metric of gene-wise relative synonymous codon usage can accurately estimate gene-wise codon optimization, evaluated the quality and characteristics of 901 eukaryotic genome assemblies, and calculated alignment summary statistics for 10 phylogenomic data matrices. BioKIT will be helpful in facilitating and streamlining sequence analysis workflows. BioKIT is freely available under the MIT license from GitHub (https://github.com/JLSteenwyk/BioKIT), PyPi (https://pypi.org/project/jlsteenwyk-biokit/), and the Anaconda Cloud (https://anaconda.org/jlsteenwyk/jlsteenwyk-biokit). Documentation, user tutorials, and instructions for requesting new features are available online (https://jlsteenwyk.com/BioKIT).
Tobacco advertisement, promotion and sponsorship in Arabic media between 2017 and 2019
Authors: Monshi Sarah S , Collins Bradley N , Wu Jingwei , Alzahrani Mona Ahmed J , Ibrahim Jennifer K 
Published: May 2022

Abstract
Nineteen out of 22 countries in the Eastern Mediterranean region, including the Gulf Cooperation Council countries, have ratified the World Health Organization Framework Convention on Tobacco Control (FCTC) treaty. One of FCTC’s provisions prohibits tobacco advertisement, promotion and sponsorship (TAPS). The TAPS provision requires nations to ban direct and indirect tobacco ads in media, as exposure to tobacco use in the media encourages smoking initiation. A limited number of studies have examined TAPS in Arabic media. This study examined the occurrence of tobacco use across Arabic television (TV) series released between January 2017 and December 2019 to assess compliance with the FCTC provision banning TAPS. The content analysis examined incidents of tobacco use in Arabic TV series, types of tobacco products used and the portrayal of second-hand smoking exposure. Out of 92 Arabic TV series (2952 episodes), there were 32 044 incidents of tobacco use. Incidents of tobacco use per episode fluctuated over time. During Ramadan, the median number of tobacco incidents declined from 6 in 2017 to 3 in 2019; however, it increased to 8 in 2018. Regular cigarettes and water pipes were the most common tobacco products used in TV series. While 27% of tobacco use showed characters who smoked tobacco products alone, 13% of the incidents portrayed characters who were smoking in the presence of children. This study concludes that tobacco imagery is not completely banned in Arabic media and its continued representation weakens tobacco control measures.
Understanding the child mortality decline in Guinea-Bissau: the role of population-level nutritional status measured by mid-upper arm circumference
Authors: Rieckmann Andreas , Fisker Ane Bærent , Øland Christian Bjerregård , Nielsen Sebastian , Wibaek Rasmus , Sørensen Tina Bonde , Martins Cesário Lourenço , Benn Christine Stabell , Aaby Peter 
Published: May 2022

Abstract

Background
Malnutrition is considered an important contributing factor to child mortality, and the mid-upper arm circumference (MUAC) is regarded as one of the better anthropometric predictors of child mortality. We explored whether the decline in child mortality over recent decades could be explained by changes in children’s MUAC.

Methods
This prospective study analysed individual-level data from 47 731 children from the capital of Guinea-Bissau followed from 3 months until 36 months of age over 2003 to 2016. We used standardization to compare the mortality rate as if only the MUAC distribution had changed between an early period (2003–05) and a late period (2014–16). We adjusted the analyses for age, sex, socioeconomic-related possessions and maternal education.

Results
A total of 949 deaths were included in the analysis. The adjusted mortality rate was 18.9 [95% confidence interval (CI) 14.3-23.3] deaths per 1000 person-years (pyrs) in the early period and declined to 4.4 (95% CI 2.9-6.0) deaths per 1000 pyrs in the late period, a 77% (95% CI 71-83%) reduction in the mortality rate. At all calendar years, the MUAC distribution in the population was close to the WHO reference population. MUAC below -1 z-score was associated with increased child mortality. The change in MUAC distribution from the early period to the late period (in the early period mortality standardization) corresponded to 1.5 (95% CI 1.0-2.2) fewer deaths per 1000 pyrs, equivalent to 11% (95% CI 7-14%) of the observed change in child mortality.

Conclusions
From 2003 to 2016, child mortality in urban Guinea-Bissau declined considerably but, though a low MUAC was associated with increased mortality, changes in the MUAC distribution in the population explained little of the decline. Understanding the driving factors of child mortality decline can help scope tomorrow’s interventions.
Formative service evaluation of transfer of care service for care home residents after hospital discharge
Authors: Kandiah Janani , Nazar Hamde , Wright David 
Published: May 2022

Abstract

Objectives
This study provides a service description and analysis of a pilot across two sites involving pharmacists aiming to support care home residents with their medications post-discharge.

Methods
An interview with the pilot coordinator was undertaken to understand the pilot service. Service data (March 2020–June 2021) were analysed to investigate what was actually delivered to the care home residents.

Key findings
One hundred eighty-eight inpatients were referred and 132 received the post-discharge service. One hundred three residents received medicines reconciliation and 29 received an additional structured medication review. The latter cohort was significantly more likely to receive medicines and illness-related information and have medicines stopped.

Conclusions
The service facilitates the provision of medicines information and medicines-related interventions. Further evaluation is required to evidence the value of medicines review alongside the medicines reconciliation.
Influence of daptomycin doses on the outcomes of VRE bloodstream infection treated with high-dose daptomycin
Authors: Chuang Yu Chung , Lin Hsin Yi , Yang Jia Ling , Lin Chi Ying , Huang Sung Hsi , Wang Jann Tay , Chen Yee Chun , Chang Shan Chwen 
Published: May 2022

Abstract

Objectives
The CLSI recommended high-dose daptomycin (8–12 mg/kg) for treating Enterococcus faecium bloodstream infections (BSI). The current study was designed to determine the safety and efficacy of increasing the daptomycin dose for VRE BSI patients receiving ≥8 mg/kg.

Methods
We conducted a multicentre prospective observational study of patients who received a ≥8 mg/kg dose of daptomycin for treatment of VRE BSI. The primary outcome was 28 day mortality.

Results
A total of 661 patients were included. The 28 day mortality rate was 45.1%. The survivors received higher doses of daptomycin than non-survivors (10.1 versus 9.8 mg/kg; P &lt; 0.001). An increase in the daptomycin dose independently predicted lower mortality [adjusted OR (aOR) = 0.85; 95% CI = 0.73–0.99; P = 0.03]. Eighty-six survivors (23.7%) and 43 non-survivors (14.4%) received a ≥11 mg/kg dose of daptomycin (P = 0.003). The 8 to &lt;11 and ≥11 mg/kg doses of daptomycin differed in the 28 day mortality in the higher MIC group (≥2 mg/L) (49.4% versus 33.3%; P = 0.004), but not in the lower MIC group (≤1 mg/L) (29.3% versus 29.4%; P = 0.99). A dose of ≥11 mg/kg was associated with a higher (3.9%) rate of highly elevated creatine kinase (&gt;2000 U/L) compared with 1.1% with 8 to &lt;11 mg/kg (P = 0.04).

Conclusions
The efficacy of daptomycin is dose dependent. A high daptomycin dose, especially at ≥11 mg/kg, improved survival in patients with VRE BSI, but was associated with highly elevated creatine kinase. We recommend a ≥11 mg/kg dose of daptomycin be considered for treatment of VRE BSI, particularly for isolates with higher MICs.
dPQL: a lossless distributed algorithm for generalized linear mixed model with application to privacy-preserving hospital profiling
Authors: Luo Chongliang , Islam Md Nazmul , Sheils Natalie E , Buresh John , Schuemie Martijn J , Doshi Jalpa A , Werner Rachel M , Asch David A , Chen Yong 
Published: May 2022

AbstractObjectiveTo develop a lossless distributed algorithm for generalized linear mixed model (GLMM) with application to privacy-preserving hospital profiling.Materials and MethodsThe GLMM is often fitted to implement hospital profiling, using clinical or administrative claims data. Due to individual patient data (IPD) privacy regulations and the computational complexity of GLMM, a distributed algorithm for hospital profiling is needed. We develop a novel distributed penalized quasi-likelihood (dPQL) algorithm to fit GLMM when only aggregated data, rather than IPD, can be shared across hospitals. We also show that the standardized mortality rates, which are often reported as the results of hospital profiling, can also be calculated distributively without sharing IPD. We demonstrate the applicability of the proposed dPQL algorithm by ranking 929 hospitals for coronavirus disease 2019 (COVID-19) mortality or referral to hospice that have been previously studied.ResultsThe proposed dPQL algorithm is mathematically proven to be lossless, that is, it obtains identical results as if IPD were pooled from all hospitals. In the example of hospital profiling regarding COVID-19 mortality, the dPQL algorithm reached convergence with only 5 iterations, and the estimation of fixed effects, random effects, and mortality rates were identical to that of the PQL from pooled data.ConclusionThe dPQL algorithm is lossless, privacy-preserving and fast-converging for fitting GLMM. It provides an extremely suitable and convenient distributed approach for hospital profiling.
Characterization and utilization of methyltransferase for apramycin production in Streptoalloteichus tenebrarius
Authors: Sun Junyang , Gao Hongjing , Yan Danyang , Liu Yu , Ni Xianpu , Xia Huanzhang 
Published: May 2022

Abstract
A structurally unique aminoglycoside produced in Streptoalloteichus tenebrarius, Apramycin is used in veterinary medicine or the treatment of Salmonella, Escherichia coli, and Pasteurella multocida infections. Although apramycin was discovered nearly 50 years ago, many biosynthetic steps of apramycin remain unknown. In this study, we identified a HemK family methyltransferase, AprI, to be the 7’-N-methyltransferase in apramycin biosynthetic pathway. Biochemical experiments showed that AprI converted demethyl-aprosamine to aprosamine. Through gene disruption of aprI, we identified a new aminoglycoside antibiotic demethyl-apramycin as the main product in aprI disruption strain. The demethyl-apramycin is an impurity in apramycin product. In addition to demethyl-apramycin, carbamyltobramycin is another major impurity. However, unlike demethyl-apramycin, tobramycin is biosynthesized by an independent biosynthetic pathway in S. tenebrarius. The titer and rate of apramycin were improved by overexpression of the aprI and disruption of the tobM2, which is a crucial gene for tobramycin biosynthesis. The titer of apramycin increased from 2227 ± 320 mg/L to 2331 ± 210 mg/L, while the titer of product impurity demethyl-apramycin decreased from 196 ± 36 mg/L to 51 ± 9 mg/L. Moreover, the carbamyltobramycin titer of the wild-type strain was 607 ± 111 mg/L and that of the engineering strain was null. The rate of apramycin increased from 68% to 87% and that of demethyl-apramycin decreased from 1.17% to 0.34%.
Bioethics and the Contours of Autonomy
Authors: Estes Derek 
Published: May 2022

AbstractThe principle of respect for autonomy often dominates the bioethical discourse. Yet despite its prominence, the exact contours are not always well defined. Widespread disagreement about the nature of autonomy has led some to conclude that autonomy is hopelessly vague and therefore ought to be abandoned in contemporary bioethics. Despite calls to move beyond it, autonomy remains at the center of bioethical reflection. The challenge, then, if autonomy is to function as a bedrock of contemporary bioethics, is to define more clearly the shape of autonomy, to mark more precisely its conceptual boundaries, and to delineate more carefully how best autonomy is put into practice in medical ethics. In this article, I raise questions about the ways autonomy is used in theory, as well as the ways that it is operationalized in practice.
Rare giant female adnexal tumor of probable Wolffian origin: a case report
Authors: Brzika Sanela , Rašić Ismar , Bektešević Admir , Gavrankapetanović Ali , Hasić Nedim , Pašović Salko 
Published: May 2022

Abstract
Female adnexal tumors of probable Wolffian origin (FATWOs) are extremely rare tumors, with only around 100 cases published worldwide. FATWOs are most frequently found in the broad ligament, but these can also appear in the mesosalpinx, Fallopian tube, ovary, paravaginal region or peritoneum. We present a case of a 68-year-old female with a history of painless abdominal distension and frequent urination, with palpable big abdominal mass. Initial diagnosis was made using ultrasound and computed tomography scan that showed 22 × 21-cm tumor with solid and cystic components. Blood test showed elevated serum levels of CA 125, HE4 and Roma index. Intraoperatively, a large abdominopelvic encapsulated mass, fixated to surrounding tissue, was found. Our patient underwent hysterectomy 12 years ago. Total tumor resection, including bilateral adnexectomy, was performed. At 6 months of following, there was no evidence of disease. Here, we report extremely rare abdominal tumors and one of the biggest FATWOs reported so far.