bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic features of Mycoplasma bovis subtypes currently circulating in France
Authors: Ambroset Chloé , Peticca Aurélie , Tricot Agnès , Tardy Florence 
Published: August 2022

Abstract
Background
Mycoplasma (M.) bovis is a major etiological agent of bovine respiratory disease, which is the most economically costly disease of cattle worldwide. Cattle disease surveillance on M. bovis is increasingly using gene-based techniques, such as multilocus sequence typing (MLST), or genome-based techniques such as core genome MLST that both require only partial genomic data. However, accurate up-to-date surveillance also demands complete, circular genomes that can be used as reference to track the evolution of the different lineages. Yet, in France, two of the main subtypes currently circulating still have no representing genome in public databases. Here, to address this gap, we provide and compare three new complete M. bovis genomes obtained from recent clinical isolates that represent major subtypes circulating in France and Europe.

Results
Genomes were obtained using a hybrid assembly strategy (Illumina and Nanopore) with fine-tuning of settings and inputs used in the Unicycler assembly pipeline, such as size selection of reads and quality trimming of the FASTQ files. The main characteristics and synteny of the genomes were compared. The three genomes mainly differed by their content in terms of mobile genetic elements, i.e. integrative conjugative elements (ICE) and insertion sequences (IS), a feature that impacts their structure. For instance, strain L15527, representing subtype3 (st3), harbours an exceptionally high number of ICEs, which results in a bigger-sized genome than all those previously described and could be associated with the propensity of st3 to gain and fix mutations through chromosomal transfer mechanisms. In contrast, strain F9160, of st1, is very close to the PG45 type strain isolated in 1961 in the USA, and harbours a huge number of IS. These features may be associated with an evolution towards a host-restricted state or in a “closed” host or environment reservoir until a recent re-emergence.

Conclusions
Whole-genome comparison of the three French M. bovis subtypes provides valuable resources for future studies combining epidemiology, phylogenetic data, and phylodynamic methods.
A tale of two lineages: how the strains of the earliest divergent symbiotic Frankia clade spread over the world
Authors: Berckx Fede , Nguyen Thanh Van , Bandong Cyndi Mae , Lin Hsiao-Han , Yamanaka Takashi , Katayama Sae , Wibberg Daniel , Blom Jochen , Kalinowski Jörn , Tateno Masaki , Simbahan Jessica , Liu Chi-Te , Brachmann Andreas , Pawlowski Katharina 
Published: August 2022

AbstractIt is currently assumed that around 100 million years ago, the common ancestor to the Fabales, Fagales, Rosales and Cucurbitales in Gondwana, developed a root nodule symbiosis with a nitrogen-fixing bacterium. The symbiotic trait evolved first inFrankiacluster-2; thus, strains belonging to this cluster are the best extant representatives of this original symbiont. Most cluster-2 strains could not be cultured to date, except forFrankia coriariae,and therefore many aspects of the symbiosis are still elusive. Based on phylogenetics of cluster-2 metagenome-assembled genomes (MAGs), it has been shown that the genomes of strains originating in Eurasia are highly conserved. These MAGs are more closely related toFrankiacluster-2 in North America than to the single genome available thus far from the southern hemisphere, i.e., from Papua New Guinea.To unravel more biodiversity withinFrankiacluster-2 and predict routes of dispersal from Gondwana, we sequenced and analysed the MAGs ofFrankiacluster-2 fromCoriaria japonicaandCoriaria intermediagrowing in Japan, Taiwan and the Philippines. Phylogenetic analyses indicate there is a clear split withinFrankiacluster-2, separating a continental from an island lineage. Presumably, these lineages already diverged in Gondwana.Based on fossil data on the host plants, we propose that these two lineages dispersed via at least two routes. While the continental lineage reached Eurasia together with their host plants via the Indian subcontinent, the island lineage spread towards Japan with an unknown host plant.
Comparing the effects of SMS-based education with group-based education and control group on diabetes management: a randomized educational program
Authors: Haghighinejad Hourvash , Liaghat Leila , Malekpour Fatemeh , Jafari Peyman , Taghipour Kaveh , Rezaie Mehrdad , Jooya Parisa , Ghazipoor Hamidreza , Ramzi Mani 
Published: August 2022

Abstract
Background
The high prevalence of diabetes and the importance of long-term follow-up of these patients encourage finding an inexpensive and applicable educational method to control the disease. Distance education based on mobile technology and Short message service (SMS) can be an effective way to manage this disease by eliminating time and place limitations. Due to the world’s high penetration rate, SMS is one of the best ways to transfer information and health education.

Objective
This study aimed to compare the effect of SMS- and group-based education in managing diabetes type 2 and compare them with a control group.

Method
A total of 168 patients with diabetes type 2 under the coverage of three family physician clinics were randomly allocated into three groups. The education was conducted in 12 one-hour sessions once a week in the group-based arm, and a daily short message was sent to the participants in the SMS group. The control group also underwent routine care at the family physician clinic. The duration of the education was 3 months. At baseline and 3 months later, fasting blood sugar (FBS), 2 hours postprandial sugar (2hppBS), and HBA1c, as well as diabetes self-management questionnaire score (DSMQ), were measured.

Results
The comparison of the three groups in terms of changes in FBS (P-value: 0.001), 2hppBS (8 P-value: < 0.001) and HbA1c (P-value: < 0.001) were significantly different after 3 months. In pairwise analysis, 2hppBS was the only significantly different parameter between the group- and SMS-based education (P-value: 0.035).

Conclusion
Although the effect of both educational methods via SMS or group education was better than the control group in controlling diabetes, these two methods were not statistically different. Due to spending a lot of time and money on group-based education, it is better to replace it with education by SMS.
Mixed genotypes of Orientia tsutsugamushi in conserved genes and a single immune-dominant tsa56 genotype discovered from a patient with scrub typhus in Hainan Island, China: a case report
Authors: Tang Chuanning , Zhang Liyuan , Huang Yi , Mai Wenhui , Xue Liying , Wang Gaoyu , Wen Shu , Peng Ruoyan , Wu Kunliang , Tian Xiuying , Pei Hua , Du Jiang , Yuen Kwok-Yung , Chan Jasper Fuk-Woo , Du Yongguo , Yin Feifei 
Published: August 2022

Abstract
Background
Orientia tsutsugamushi (O. tsutsugamushi), an obligate intracellular bacterium, is transmitted to humans through infected larval trombiculid mite bites, causing scrub typhus. Mixed genotypes of O. tsutsugamushi in canonical conserved genes were reported in 8–25% of blood samples from patients. Yet, there are few clinical descriptions of these mixed O. tsutsugamushi-infected patients.

Case presentation
We report a patient with scrub typhus complicated with pulmonary involvement and hepatic dysfunction, who carried mixed genotypes of the conserved genes but had a single immune-dominant 56-kDa type-specific antigen (tsa56) genotype. The patient was successfully recovered by doxycycline treatment.

Conclusions
In this reported case, both patient’s eschar and blood samples have repeatedly shown the same results, i.e., no variants were discovered in tsa56 gene that bears multiple hypervariable regions. Whereas the selected highly conserved genes were identified with up to 32 variants in a 2700 base-pair concatenated sequence. The prevalence, disease severity and mechanism of these single-tsa56-genotype mixed infections remain to be investigated on a large scale with more cases.
Further validation of the Cognitive Biases Questionnaire for psychosis
Authors: Samson Crystal , Achim Amélie M. , Sicard Veronik , Gilker Andy , Francoeur Audrey , Franck Nicolas , Cloutier Briana , Giguère Charles-Edouard , Jean-Baptiste Francelyne , Lecomte Tania 
Published: August 2022

Abstract
Background
Cognitive biases are recognized as important treatment targets for reducing symptoms associated with severe mental disorders. Although cognitive biases have been linked to symptoms in most studies, few studies have looked at such biases transdiagnostically. The Cognitive Bias Questionnaire for psychosis (CBQp) is a self-reported questionnaire that assesses cognitive biases amongst individuals with a psychotic disorder, as well as individuals with other severe mental disorders. The current study aims to validate a French version of the CBQp and to explore transdiagnostic cognitive biases in individuals with psychotic disorders, individuals with depression, and in healthy controls.

Methods
The CBQp was translated into French following a protocol based on international standards. Discriminant validity and internal consistency were determined for total score and each subscale score. Confirmatory factor analyses were performed to test construct validity. Finally, cluster analyses were conducted to investigate cognitive biases across diagnostic groups.

Results
Our results were similar to those of the original authors, with the one-factor solution (assessment of a general thinking bias) being the strongest, but the two-factor solution (assessing biases within two themes relating to psychosis) and the five-factor solution (assessment of multiple distinct biases) being clinically more interesting. A six-cluster solution emerged, suggesting that individuals with similar diagnoses score differently on all cognitive biases, and that individuals with different diagnoses might have similar cognitive biases.

Conclusions
The current findings support the validity of the French translation of the CBQp. Our cluster analyses overall support the transdiagnostic presence of cognitive biases.
Protocol: evaluation of an optimised couples-focused intervention to increase testing for HIV in rural KwaZulu-Natal, South Africa, the Igugu Lethu (‘Our treasure’) cohort study
Authors: McGrath Nuala , Ngcobo Nathi , Feng Zhixin , Joseph Phillip , Dladla Pumla , Ngubane Thulani , Hosegood Victoria , Morton Katherine , Van Rooyen Heidi , Van Heerden Alastair 
Published: August 2022

AbstractBackgroundBetween 2012 and 2015, the Uthando Lwethu (UL) study demonstrated that a theory-based behavioural couples-focused intervention significantly increased participation in couples HIV testing and counselling (CHTC) among South African couples who had never previously tested for HIV together or mutually disclosed their HIV status, 42% compared to 12% of the control group at 9 months follow-up. Although effective, we were nonetheless concerned that in this high prevalence setting the majority (58%) of intervention couples chose not to test together. In response we optimised the UL intervention and in a new study, ‘Igugu Lethu’, we are evaluating the success of the optimised intervention in promoting CHTC.MethodsOne hundred eighty heterosexual couples, who have been in a relationship together for at least 6 months, are being recruited and offered the optimised couples-focused intervention. In the Igugu Lethu study, we have expanded the health screening visit offered to couples to include other health conditions in addition to CHTC. Enrolled couples who choose to schedule CHTC will also have the opportunity to undertake a random blood glucose test, blood pressure and BMI measurements, and self-sample for STI testing as part of their health screening. Individual surveys are administered at baseline, 4 weeks and 4 months follow-up. The proportion of couples who decide to test together for HIV will be compared to the results of the intervention arm in the UL study (historical controls). To facilitate this comparison, we will use the same recruitment and follow-up strategies in the same community as the previous UL study.DiscussionBy strengthening communication and functioning within the relationship, the Igugu Lethu study, like the previous UL study, aims to transform the motivation of individual partners from a focus on their own health to shared health as a couple. The Igugu Lethu study findings will answer whether the optimised couples-focused behavioural intervention and offering CHTC as part of a broader health screening for couples can increase uptake of CHTC by 40%, an outcome that would be highly desirable in populations with high HIV prevalence.Trial registrationRetrospectively registered. ISRCTN Registry ISRCTN 46162564 Registered on 26th May 2022.
Cross-training needs among community-based clinicians in HIV and substance use
Authors: Claborn Kasey , Scott Kelli , Becker Sara J. 
Published: August 2022

Abstract
Background
People with double burden of HIV and substance use have poorer treatment engagement and worse treatment outcomes. Cross-training of HIV and substance use disorder clinicians can potentially enhance the scale up and quality of integrated care. Research is needed on clinicians’ areas of greatest training need in order to inform training development.

Methods
Data from semi-structured individual interviews with 16 HIV and 13 substance use disorder clinicians (N = 29) examining clinician perspectives on their training needs were analyzed using thematic analysis focused on both a priori and emergent subthemes.

Results
Several key emergent subthemes were identified across the a priori themes of: 1) past training experiences; 2) gaps in training; and 3) training and supervision format/structure. Both HIV and substance use clinicians reported they had received minimal formal cross-training and had mostly been trained “on the job.” Clinicians also emphasized gaps in training regarding sensitivity and anti-stigma, the latest medications for opioid use disorder, and HIV prevention/treatment and referral resources. Regarding training and supervision format, clinicians cited didactic workshops and ongoing supervision as appealing strategies.

Conclusions
Results show that lack of formal and updated training for clinicians is an important gap in providing integrated HIV and substance use treatment. Didactic workshops and ongoing support strategies that address stigma, medications for HIV and substance use disorder, and referral resources are likely to be particularly valuable.
Reliability of predictive models to support early decision making in the emergency department for patients with confirmed diagnosis of COVID-19: the Pescara Covid Hospital score
Authors: Polilli Ennio , Frattari Antonella , Esposito Jessica Elisabetta , D’Amato Milena , Rapacchiale Giorgia , D’Intino Angela , Albani Alberto , Di Iorio Giancarlo , Carinci Fabrizio , Parruti Giustino 
Published: August 2022

Abstract
Background
The hospital management of patients diagnosed with COVID-19 can be hampered by heterogeneous characteristics at entry into the emergency department. We aimed to identify demographic, clinical and laboratory parameters associated with higher risks of hospitalisation, oxygen support, admission to intensive care and death, to build a risk score for clinical decision making at presentation to the emergency department.

Methods
We carried out a retrospective study using linked administrative data and laboratory parameters available in the initial phase of the pandemic at the emergency department of the regional reference hospital of Pescara, Abruzzo, Italy, March–June 2020. Logistic regression and Cox modelling were used to identify independent predictors for risk stratification. Validation was carried out collecting data from an extended timeframe covering other variants of concern, including Alpha (December 2020–January 2021) and Delta/Omicron (January–March 2022).

Results
Several clinical and laboratory parameters were significantly associated to the outcomes of interest, independently from age and gender. The strongest predictors were: for hospitalisation, monocyte distribution width ≥ 22 (4.09; 2.21–7.72) and diabetes (OR = 3.04; 1.09–9.84); for oxygen support: saturation < 95% (OR = 11.01; 3.75–41.14), lactate dehydrogenase≥237 U/L (OR = 5.93; 2.40–15.39) and lymphocytes< 1.2 × 103/μL (OR = 4.49; 1.84–11.53); for intensive care, end stage renal disease (OR = 59.42; 2.43–2230.60), lactate dehydrogenase≥334 U/L (OR = 5.59; 2.46–13.84), D-dimer≥2.37 mg/L (OR = 5.18; 1.14–26.36), monocyte distribution width ≥ 25 (OR = 3.32; 1.39–8.50); for death, procalcitonin≥0.2 ng/mL (HR = 2.86; 1.95–4.19) and saturation < 96% (HR = 2.74; 1.76–4.28). Risk scores derived from predictive models using optimal thresholds achieved values of the area under the curve between 81 and 91%. Validation of the scoring algorithm for the evolving virus achieved accuracy between 65 and 84%.

Conclusions
A set of parameters that are normally available at emergency departments of any hospital can be used to stratify patients with COVID-19 at risk of severe conditions. The method shall be calibrated to support timely clinical decision during the first hours of admission with different variants of concern.
Knockdown of HSP110 attenuates hypoxia-induced pulmonary hypertension in mice through suppression of YAP/TAZ-TEAD4 pathway
Authors: Liu Haitao , Zhang Sha , Liu Yi , Ma Jing , Chen Wei , Yin Tao , Li Tongbin , Liang Bin , Tao Ling 
Published: August 2022

Abstract
Background
Pulmonary hypertension (PH) is a progressive and fatal cardiopulmonary disease characterized by pulmonary vascular remodeling and increased pulmonary vascular resistance and artery pressure. Vascular remodeling is associated with the excessive cell proliferation and migration of pulmonary artery smooth muscle cells (PASMCs). In this paper, the effects of heat shock protein-110 (HSP110) on PH were investigated.

Methods
The C57BL/6 mice and human PASMCs (HPASMCs) were respectively exposed to hypoxia to establish and simulate PH model in vivo and cell experiment in vitro. To HSP110 knockdown, the hypoxia mice and HPASMCs were infected with adeno-associated virus or adenovirus carring the shRNAs (short hairpin RNAs) for HSP110 (shHSP110). For HSP110 and yes-associated protein (YAP) overexpression, HPASMCs were infected with adenovirus vector carring the cDNA of HSP110 or YAP. The effects of HSP110 on PH development in mice and cell proliferation, migration and autophagy of PASMCs under hypoxia were assessed. Moreover, the regulatory mechanisms among HSP110, YAP and TEA domain transcription factor 4 (TEAD4) were investigated.

Results
We demonstrated that expression of HSP110 was significantly increased in the pulmonary arteries of mice and HPASMCs under hypoxia. Moreover, knockdown of HSP110 alleviated hypoxia-induced right ventricle systolic pressure, vascular wall thickening, right ventricular hypertrophy, autophagy and proliferation of PASMCs in mice. In addition, knockdown of HSP110 inhibited the increases of proliferation, migration and autophagy of HPASMCs that induced by hypoxia in vitro. Mechanistically, HSP110 knockdown inhibited YAP and transcriptional co-activator with PDZ-binding motif (TAZ) activity and TEAD4 nuclear expression under hypoxia. However, overexpression of HSP110 exhibited the opposite results in HPASMCs. Additionally, overexpression of YAP partially restored the effects of shHSP110 on HPASMCs. The interaction of HSP110 and YAP was verified. Moreover, TEAD4 could promote the transcriptional activity of HSP110 by binding to the HSP110 promoter under hypoxia.

Conclusions
Our findings suggest that HSP110 might contribute to the development of PH by regulating the proliferation, migration and autophagy of PASMCs through YAP/TAZ-TEAD4 pathway, which may help to understand deeper the pathogenic mechanism in PH development.
Is population frequency a useful criterion to assign pathogenicity to newly described mitochondrial DNA variants?
Authors: Bayona-Bafaluy M. Pilar , López-Gallardo Ester , Emperador Sonia , Pacheu-Grau David , Montoya Julio , Ruiz-Pesini Eduardo 
Published: August 2022

AbstractPopulation frequency has been one of the most widely used criteria to help assign pathogenicity to newly described mitochondrial DNA variants. However, after sequencing this molecule in thousands of healthy individuals, it has been observed that a very large number of genetic variants have a very low population frequency, which has raised doubts about the utility of this criterion. By analyzing the genetic variation of mitochondrial DNA-encoded genes for oxidative phosphorylation subunits in 195,983 individuals from HelixMTdb that were not sequenced based on any medical phenotype, we show that rare variants are deleterious and, along with other criteria, population frequency is still a useful criterion to assign pathogenicity to newly described variants.
Tumor associated macrophages-derived exosomes facilitate hepatocellular carcinoma malignance by transferring lncMMPA to tumor cells and activating glycolysis pathway
Authors: Xu Minghao , Zhou Chenhao , Weng Jialei , Chen Zhaoshuo , Zhou Qiang , Gao Jian , Shi Guoming , Ke Aiwu , Ren Ning , Sun Huichuan , Shen Yinghao 
Published: August 2022

Abstract
Background
Tumor-associated macrophages (TAMs), which form a large part of the tumor microenvironment, are normally regulated by metabolic reprogramming. However, the potential mechanisms of the immune-metabolism interaction between hepatocellular carcinoma (HCC) cells and TAMs remain unclear.

Methods
The candidate long non-coding RNAs (lncRNAs) were screened by Smart-seq based scRNA-seq method and then validated by qPCR. Immunostaining analysis was done to examine the levels of markers for TAMs and glycolysis. Exosomes from primary TAMs of human HCC tissues were isolated by centrifugation, and their internalization with lncRNAs was confirmed by immunofluorescence. The underlying mechanism of TAMs-derived exosomal lncRNA to HCC was confirmed by luciferase reporter assay and RNA immunoprecipitation. Metabolism regulation was evaluated through glucose consumption, lactate productions and extracellular acidification rates (ECARs). Mouse xenograft models were used to elucidate the in vivo effect of candidate lncRNAs on tumor growth.

Results
TAMs augment the aerobic glycolysis in HCC cells and their proliferation by the extracellular exosome transmission of a myeloid-derived lncRNA, M2 macrophage polarization associated lncRNA (lncMMPA). Mechanistically, lncMMPA not only could polarize M2 macrophage, but also could act as an microRNA sponge to interact with miR-548 s and increase the mRNA level of ALDH1A3, then further promote glucose metabolism and cell proliferation in HCC. Moreover, lncMMPA increased HCC cell multiplication through interacting with miR-548 s in vivo. Clinically, lncMMPA expression associates with glycolysis in TAMs and reduced survival of HCC patients.

Conclusion
LncMMPA plays an important role in regulating HCC malignancy and metabolic reprogramming of miR-548 s/ALDH1A3 pathway.