bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evidence-based development of new qualification models for public health practice and science
Authors: Arnold L , Bimczok S , Dragano N , Götz S , Kietzmann A , Melville-Drewes A , Weyers S , Starke D 
Published: October 2022

Abstract

The Public Health Service (PHS) needs a sufficient and well-trained workforce to fulfill core public health activities. Given the multitude of complex challenges, from often short-term crisis management to long-term health promotion, a better integration of science and practice in the PHS is essential. In Germany, there is a lack of systematically established cooperations and integrated training concepts. However, both are essential to ensure continuous knowledge transfer between science and practice. In the EvidenzÖGD study, representatives from practice, teaching and science jointly develop and pilot new qualification models to qualify public health professionals for work at the interface of practice and science. Based on a systematic analysis of existing collaborations and qualification models, 23 expert interviews were conducted to identify qualification approaches that will enable future public health professionals to work at the interface between science and practice. In a stakeholder workshop planned for July 2022, a multistage decision-making process based on strategic orientation mapping will be conducted to prioritize the identified approaches and generate ideas for new qualification models. In total 17 papers were analyzed and inductively coded according to three main categories. In addition to (1) context-related aspects, such as credentialing, recruitment strategies and resources, also (2) content-related aspects, such as training forms and didactical concepts were extracted. Furthermore, criteria relevant for the further development and continuation of the models (3) could be identified. By strengthening the scientific nature of practice in PHS and anchoring PHS-relevant topics in academia, the EvidenzÖGD project contributes to a sustainable strengthening of evidence-informed approaches in PHS practice. The evidence-informed, participatory development of a tailored qualification model is intended to promote the pilot of the model, which is due in 2023.

Key messages
• Integrated qualification models support the strengthening of evidence-based approaches in the public health service (ÖGD) and promote the integration of ÖGD-relevant issues in science.
• Participatory approaches with explicit consideration of the perspective of young health professionals ensures that new qualification approaches meet the needs and requirements of future generations.
Suicidality among children and adolescents “in the COVID-19 era”: a worldwide metanalytic picture
Authors: Bersia M , Koumantakis E , Berchialla P , Charrier L , Dalmasso P , Comoretto RI 
Published: October 2022

Abstract

Background
The impact of the COVID-19 pandemic on adolescent suicidality is still controversial. The present systematic review and meta analysis aim to summarise findings from emerging literature about prevalences of the main suicidal outcomes among children and adolescents under 19 years old, and to compare them with the pre-pandemic period.

Methods
Five databases (PubMed, Embase, Scopus, CINAHL and Web of Science) were systematically searched for studies published in English from January 1st, 2020 until November 3rd, 2021, reporting prevalence for suicidal ideation (SI), suicidal behaviors (SB) and suicide (S) in the general population aged &lt;19 during the COVID-19 pandemic. Single-study prevalence data were pooled using random-effects meta-analysis. If studies reported prevalence estimates for both pre- and during-pandemic periods, prevalence ratio (PR) comparing the two periods has been computed and pooled.

Results
Sixteen observational studies were selected: 10 about SI, 9 about SB and 3 about S. During the pandemic, prevalence of SI among adolescents was 21% (95% CI 12-34%) while prevalence of SB was 3% (95% CI 1-10%). Comparing pre- and during- pandemic prevalences, a significant overall increase in SB was observed (PR 1.35; 95% CI 1.06-1.72) while the prevalence rates of SI remained substantially steady (PR 0.95; 95% CI 0.64-1.39). A narrative review on the population-based data on suicide rates suggested an escalating trend since Summer 2020, after an initial stability of the phenomenon.

Conclusions
During the COVID-19 pandemic SB showed a 35% increase and suicides rates escalated after a initial stability. School closures might be involved, representing an initial protective factor for suicidality, while after the reopenings we could have assisted to a suicide rebound, especially among the most vulnerable young people.

Key messages
• The topic of suicidality among young people is still affected by a cultural stigma that hampers the development of both academic research, early detection and preventive policies.
• The increase in suicidal behaviors among youths after the COVID-19 outbreak highlights a major public health issue that requires adequate supporting policies to control and prevent this phenomenon.
Methodological choices in brucellosis burden of disease assessments: A systematic review
Authors: di Bari C , Venkateswaran N , Patterson G , Pigott D , Devleesschauwer B 
Published: October 2022

Abstract

Background
Foodborne and zoonotic diseases such as brucellosis present many challenges to public health and economic welfare. Increasingly, researchers and public health institutes use disability-adjusted life years (DALYs) to generate a comprehensive comparison of the population health impact of these conditions. DALY calculations entail several methodological choices and assumptions, with data gaps and uncertainties to accommodate. The following review identifies existing brucellosis burden studies and analyses their methodological choices and assumptions.

Methods/Findings
A systematic search for brucellosis burden calculations was conducted in pre-selected international and grey literature databases. Using a standardized reporting framework, we evaluated each estimate on a variety of key methodological assumptions necessary to compute a DALY. One study reported estimates at the global level, the rest (13) at national or subnational. Most studies retrieved brucellosis epidemiological data from administrative registries. Incidence data were often estimated based on laboratory-confirmed tests. Not all studies included mortality estimates (YLLs) in their assessments due to the lack of data or the assumption that brucellosis is not a fatal disease. Only two studies used a model with variable health states and corresponding disability weights. The rest used a simplified singular health state approach. Wide variation was seen in the duration chosen for brucellosis, ranging from 2 weeks to 4.5 years, irrespective of whether a chronic state was included.

Conclusions
Available brucellosis burden assessments vary widely in their methodology and assumptions. Further research is needed to characterize better the total clinical course of brucellosis and estimate case-fatality rate. In addition, reporting of methodological choices should be improved to enhance transparency and comparability of estimates. These steps will increase the value of these estimates for policymakers.

Key messages
• Inconsistencies in reporting methods and assumptions are found, which hinder transparency and understanding of the methodological choices and the reuse of estimates for prioritization purposes.
• Thus, there is a need for a more standardized reporting system for DALY estimates, which could resemble a checklist that reports the methodological choices and assumptions.
Interactions between Bacterial Inoculants and Native Soil Bacterial Community: the Case of Spore-formingBacillusspp.
Authors: Mawarda Panji Cahya , Mallon Cyrus A , Le Roux Xavier , van Elsas Jan Dirk , Salles Joana Falcão 
Published: October 2022

AbstractMicrobial diversity can restrict the invasion and impact of alien microbes into soils via resource competition. However, this theory has not been tested on various microbial invaders with different ecological traits, particularly spore-forming bacteria. Here we investigated the survival capacity of two introduced spore-forming bacteria, Bacillus mycoides (BM) and B. pumillus (BP) and their impact on the soil microbiome niches with low and high diversity. We hypothesized that higher soil bacterial diversity would better restrict Bacillus survival via resource competition, and the invasion would alter the resident bacterial communities’ niches only if inoculants do not escape competition with the soil community (e.g. through sporulation). Our findings showed that BP could not survive as viable propagules and transiently impacted the bacterial communities’ niche structure. This may be linked to its poor resource usage and low growth rate. Having better resource use capacities, BM better survived in soil, though its survival was weakly related to the remaining resources left for them by the soil community. BM strongly affected the community niche structure, ultimately in less diverse communities. These findings show that the inverse diversity-invasibility relationship can be valid for some spore-forming bacteria, but only when they have sufficient resource use capacity.
Proteomic profiling of extracellular vesicles derived from ARPE-19 cells challenged with Aspergillus flavus and Candida albicans: application in fungal endophthalmitis
Authors: Gandhi Jaishree , Joseph Joveeta 
Published: October 2022

Abstract
Extracellular vesicles (EVs) are nano-sized-particles that play an important role in cellular cross-talk. The aim of this study was to understand the proteomic cargo of EVs, released by Retinal Pigment Epithelial (RPE) cells challenged with Candida albicans (C-CA) and Aspergillus flavus (C-AF). EVs were isolated from culture supernatant of retinal cells infected with fungal pathogens and characterized by dynamic light scattering, SEM, and western blot. EV proteome was then evaluated by mass spectrometry (LC-MS/MS). Isolated EVs were approximately 120–150 nm and higher in number in infected group compared to control. Proteomic profiling of EVs from infected cells, showed a total of 419 and 254 differentially expressed proteins, of which 218 were upregulated in C-CA group and 81 proteins were upregulated in C-AF group. Gene ontology revealed majority of proteins associated with transport, cell migration, and in activation of innate immune response. Proteins identified were annexins, calpain, and Sorcin proteins. Additionally, KEGG analysis unveiled involvement of MAPK, HIF-1, and PI3K-AKT signalling pathways. Proteomic results indicate that EVs cargo derived from fungal-infected retinal cells can activate immune signalling pathways and might contribute to the pathogenesis of endophthalmitis, indicating the potential use of EVs as theranostic marker for management of fungal infections.
BrumiR: A toolkit for de novo discovery of microRNAs from sRNA-seq data
Authors: Moraga Carol , Sanchez Evelyn , Ferrarini Mariana Galvão , Gutierrez Rodrigo A , Vidal Elena A , Sagot Marie-France 
Published: October 2022

Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that are key players in the regulation of gene expression. In the past decade, with the increasing accessibility of high-throughput sequencing technologies, different methods have been developed to identify miRNAs, most of which rely on preexisting reference genomes. However, when a reference genome is absent or is not of high quality, such identification becomes more difficult. In this context, we developed BrumiR, an algorithm that is able to discover miRNAs directly and exclusively from small RNA (sRNA) sequencing (sRNA-seq) data. We benchmarked BrumiR with datasets encompassing animal and plant species using real and simulated sRNA-seq experiments. The results demonstrate that BrumiR reaches the highest recall for miRNA discovery, while at the same time being much faster and more efficient than the state-of-the-art tools evaluated. The latter allows BrumiR to analyze a large number of sRNA-seq experiments, from plants or animal species. Moreover, BrumiR detects additional information regarding other expressed sequences (sRNAs, isomiRs, etc.), thus maximizing the biological insight gained from sRNA-seq experiments. Additionally, when a reference genome is available, BrumiR provides a new mapping tool (BrumiR2reference) that performs an a posteriori exhaustive search to identify the precursor sequences. Finally, we also provide a machine learning classifier based on a random forest model that evaluates the sequence-derived features to further refine the prediction obtained from the BrumiR-core. The code of BrumiR and all the algorithms that compose the BrumiR toolkit are freely available at https://github.com/camoragaq/BrumiR.
Functional genomics analysis identifies loss ofHNF1Bfunction as a cause of Mayer–Rokitansky–Küster–Hauser syndrome
Authors: Thomson Ella , Tran Minh , Robevska Gorjana , Ayers Katie , van der Bergen Jocelyn , Gopalakrishnan Bhaskaran Prarthna , Haan Eric , Cereghini Silvia , Vash-Margita Alla , Margetts Miranda , Hensley Alison , Nguyen Quan , Sinclair Andrew , Koopman Peter , Pelosi Emanuele 
Published: October 2022

AbstractMayer–Rokitansky–Küster–Hauser (MRKH) syndrome is a congenital condition characterized by aplasia or hypoplasia of the uterus and vagina in women with a 46,XX karyotype. This condition can occur as type I when isolated or as type II when associated with extragenital anomalies including kidney and skeletal abnormalities. The genetic basis of MRKH syndrome remains unexplained and several candidate genes have been proposed to play a role in its etiology, including HNF1B, LHX1 and WNT4. Here, we conducted a microarray analysis of 13 women affected by MRKH syndrome, resulting in the identification of chromosomal changes, including the deletion at 17q12, which contains both HNF1B and LHX1. We focused on HNF1B for further investigation due to its known association with, but unknown etiological role in, MRKH syndrome. We ablated Hnf1b specifically in the epithelium of the Müllerian ducts in mice and found that this caused hypoplastic development of the uterus, as well as kidney anomalies, closely mirroring the MRKH type II phenotype. Using single-cell RNA sequencing of uterine tissue in the Hnf1b-ablated embryos, we analyzed the molecules and pathways downstream of Hnf1b, revealing a dysregulation of processes associated with cell proliferation, migration and differentiation. Thus, we establish that loss of Hnf1b function leads to an MRKH phenotype and generate the first mouse model of MRKH syndrome type II. Our results support the investigation of HNF1B in clinical genetic settings of MRKH syndrome and shed new light on the molecular mechanisms underlying this poorly understood condition in women’s reproductive health.
TgMIF Promotes Hepatocyte Pyroptosis and Recruitment of Proinflammatory Macrophages During Severe Liver Injury in Acute Toxoplasmosis
Authors: Zhou Nan , Chen Ying , Wang Jie , An Ran , Cai Haijian , Liu Shutong , Yao Lei , Tang Yuewen , Chen Lijian , Du Jian 
Published: October 2022

Abstract
Liver injury is a common complication during infection of Toxoplasma gondii. However, the Toxoplasma effector proteins involved remain unknown. Herein, we identified that T. gondii macrophage migration inhibitory factor (TgMIF) is a critical pathogenic factor of liver injury in acute toxoplasmosis mouse model induced by a less virulent strain, which is widely prevalent in humans. We show that TgMIF is a novel activator of nucleotide-binding oligomerization domain-like receptor pyrin domain containing 3 (NLRP3) inflammasome in hepatocytes, resulting in subsequent pyroptosis. Furthermore, T. gondii promotes the TgMIF-dependent infiltration of Ly6Chi proinflammatory macrophages to release cytokines, leading to hepatocyte apoptosis. Although the intense inflammation induced by TgMIF inhibits the proliferation of intracellular parasites, it results in fatal liver damage. In contrast, parasites with TgMIF gene deletion significantly alleviate liver injury and prolong mice survival. The discovery of novel Toxoplasma virulence factor may expedite the development of human toxoplasmosis control strategies.
Outpatient Clonal Propagation and Rapid Regional Establishment of an Emergent Carbapenem-Resistant Acinetobacter baumannnii Lineage Sequence Type 499Pas
Authors: Calix Juan J , de Almeida Maria C Stockler , Potter Robert F , Wallace Meghan A , Burnham Carey-Ann D , Dantas Gautam 
Published: October 2022

Abstract
Eliminating carbapenem-resistant Acinetobacter baumannii (CRAb) disease requires comprehensive knowledge of how this noncommensal organism propagates among at-risk hosts. We molecularly characterized an ongoing surge of CRAb cases among patients in a Midwest US healthcare system, which coincided with sustained reductions in hospital-acquired CRAb infections and falloffs of cases associated with distinctly more resistant antibiotypes. Genome sequencing revealed surge isolates belonged to an emergent Pasteur scheme sequence type 499 and comprised multiple contemporaneous clonal clusters. Detailed query of health records revealed no consistent hospital source but instead identified various outpatient healthcare settings linked to cluster cases. We show that CRAb can rapidly establish a regional presence even without gains in breadth of antibiotic resistance and negligible contribution from sustained intrahospital transmission. As CRAb lineages may sidestep control efforts via outpatient epidemiological niches, our approach can be implemented to investigate outpatient CRAb propagation and inform subsequent local surveillance outside hospital settings.
Looking into the Laboratory Staffing Issues that Affected Ambulatory Care Clinical Laboratory Operations during the COVID-19 Pandemic
Authors: Huq Ronny Faisal M , Sherpa Tshering , Choesang Tenzin , Ahmad Shana 
Published: October 2022

Abstract

Objective
Our New York City Municipal Public Health System-based multisite ambulatory and school-based Gotham Health clinics offer waived point-of-care tests and provider-performed microscopy to the local communities. Our Gotham Health laboratory service conducts system-wide centralized implementation, monitoring, and oversight of the POCT operations. Laboratory staffing has always been an issue for us as there is a decades-long shortage of laboratory staff, primarily licensed medical technologists and technicians, in New York, like many other states. Our clinical laboratory operations team struggled to hire qualified people even before the COVID-19 pandemic onset. It has faced more significant challenges with the emergence of SARS-CoV-2 pandemic cases in New York City and across the country since mid-March 2020.

Methods
As staffing continues to be a struggle, it directly affected the POCT performances and a system-wide reduction in the test numbers during the pandemic. We investigated to identify the factors that made staffing more challenging.

Results
The impact on our POCT started after laboratory staff relocated to the acute care hospital laboratories to provide testing support during the pandemic’s peak. That caused significant delays or complete cessation of POCT operations in the clinics due to a lack of oversight support. We also experienced the risk of more vacated positions where staff already feel overworked, overwhelmed, and emotionally drained, causing professional burnout. The significant challenges identified are noncompliance with vaccine mandates resulting in job dismissal and voluntary resignations in exchange for higher-paying laboratories. Finally, the other challenges identified were frequent sick calls due to mental fatigue, retirement of seasoned staff, and inability to attract qualified technologists to meet the demands of increasing test-ordering patterns.

Conclusions
Determining the factors that culminated in the staffing issues becoming more challenging during the COVID-19 pandemic in our ambulatory care clinic laboratory operations will help us in future crisis planning and mitigation.
Photometric redshift estimation of galaxies in the DESI Legacy Imaging Surveys
Authors: Li Changhua , Zhang Yanxia , Cui Chenzhou , Fan Dongwei , Zhao Yongheng , Wu Xue-Bing , Zhang Jing-Yi , Tao Yihan , Han Jun , Xu Yunfei , Li Shanshan , Mi Linying , He Boliang , Kang Zihan , Wang Youfen , Yang Hanxi , Yang Sisi 
Published: October 2022

ABSTRACT
The accurate estimation of photometric redshifts plays a crucial role in accomplishing science objectives of the large survey projects. Template-fitting and machine learning are the two main types of methods applied currently. Based on the training set obtained by cross-correlating the DESI Legacy Imaging Surveys DR9 galaxy catalogue and the SDSS DR16 galaxy catalogue, the two kinds of methods are used and optimized, such as eazy for template-fitting approach and catboost for machine learning. Then, the created models are tested by the cross-matched samples of the DESI Legacy Imaging Surveys DR9 galaxy catalogue with LAMOST DR7, GAMA DR3, and WiggleZ galaxy catalogues. Moreover, three machine learning methods (catboost, Multi-Layer Perceptron, and Random Forest) are compared; catboost shows its superiority for our case. By feature selection and optimization of model parameters, catboost can obtain higher accuracy with optical and infrared photometric information, the best performance ($\rm MSE=0.0032$, σNMAD = 0.0156, and $O=0.88{{\ \rm per\ cent}}$) with g ≤ 24.0, r ≤ 23.4, and z ≤ 22.5 is achieved. But eazy can provide more accurate photometric redshift estimation for high redshift galaxies, especially beyond the redshift range of training sample. Finally, we finish the redshift estimation of all DESI Legacy Imaging Surveys DR9 galaxies with catboost and eazy, which will contribute to the further study of galaxies and their properties.
Neutron star crust can support a large ellipticity
Authors: Morales J A , Horowitz C J 
Published: October 2022

ABSTRACT
Non-axisymmetrical deformations of the crust on rapidly rotating neutron stars are one of the main targets of searches for continuous gravitational waves. The maximum ellipticity, or fractional difference in moments of inertia, which can be supported by deformations of the crust (known as ‘mountains’), provides an important upper limit on the strength of these continuous gravitational wave sources. We use the formalism developed by Gittins and Andersson, along with a deforming force that acts mainly in the transverse direction, to obtain a maximum ellipticity of 7.4 × 10−6. This is larger than the original results that Gittins and Andersson obtained but consistent with earlier calculations by Ushomirsky, Cutler, and Bildsten. This suggests that rotating neutron stars could be strong sources of continuous gravitational waves.
Pulse frequency fluctuations of persistent accretion powered pulsars
Authors: Serim D , Serim M M , Baykal A 
Published: October 2022

ABSTRACT
In this study, we examine the long-term torque noise fluctuations of persistent X-ray binaries Her X-1, Vela X-1, GX 301-2, Cen X-3, 4U 1538-53, OAO 1657-415, and 4U 1626-67 using the historical pulse frequency measurements provided by CGRO/BATSE and Fermi/GBM. We find that known disc-fed sources exhibit a 1/ω2 red noise component in their power density spectra which is saturated over long time-scales. On the other hand, wind-fed sources form a clear white noise component, and the wind-fed sources with occasional transient disc formation imprint 1/ω type flicker noise. We discuss their long-term timing noise properties based on the models to describe the power density spectrum of pulse frequency derivative fluctuations in terms of monochromatic and coloured noise processes. Furthermore, we investigate the relation between measured timing noise strengths and other independently measured physical parameters. Despite the low number of sample sources, we suggest that the noise strengths of these sources are correlated with their luminosities and uncorrelated with their magnetic field strengths, implying that the dominant noise-generating mechanism is accretion.