bluuebunny/crossref_metadata_2025_split huggingface dataset:
Knowledge, attitudes and practices pertaining to urogenital schistosomiasis in Lambaréné and surrounding areas, Gabon
Authors: Dejon-Agobé Jean Claude , Zinsou Jeannot Fréjus , Honkpehedji Yabo Josiane , Edoa Jean Ronald , Adegbité Bayodé Roméo , Beh-Mba Romuald , Kremsner Peter Gottfried , Adegnika Ayola Akim , Grobusch Martin Peter 
Published: September 2021

Abstract
Background
Control of schistosomiasis remains a priority in endemic areas. Local epidemiological data are necessary for a tailored control programme, including data on population behaviour in relation to the disease. The objective of this study was to assess schistosomiasis-related knowledge, attitudes and practices in the general population of Lambaréné, a small city in Gabon, in order to optimise the design and implementation of a local control programme that is tailored to need.

Methods
The study was cross-sectional in nature. Eligible adults and children living in the study area who volunteered (with informed consent) to participate in the study were interviewed using standardised questionnaires, one of which was a simplified version of the primary questionnaire for participants aged 6–13 years. Data on the participants’ knowledge, attitudes and practices that enhance the risk for contracting schistosomiasis were collected.

Results
A total of 602 participants were included. The mean (± standard deviation) age was 21.2 (± 15.0) years, the female:male gender ratio was 1.6 and 289 (48%) participants completed the simplified version the questionnaire. Of the 602 participants, 554 (92%) reported past or current contact with freshwater, 218 (36%) reported a history of a diagnosis of schistosomiasis and 193 (32%) reported past intake of praziquantel medication. The overall levels of knowledge and adequate attitudes toward schistosomiasis among young adults and adults were 68 and 73%, respectively. The proportion of participants pursuing risk-enhancing practices (REP) was 60% among the whole study population. Location was significantly associated with differences in knowledge and REP levels. A history of confirmed schistosomiasis and larger family size were significantly associated with an increase in good knowledge and REP levels. However, the indication of freshwater-associated activities was only associated with a significant increase in the REP level.

Conclusions
The results of this survey reveal a high level of population exposure to schistosomiasis, which is in line with known prevalence of schistosomiasis in Lambaréné and its surroundings. The local population has a reasonable level of knowledge of and adequate attitudes toward schistosomiasis but the level of REP is high, particularly in areas where piped water is absent. In terms of interventions, improving hygiene should have the highest priority, but in a context where provision of safe water is difficult to achieve, the effectiveness of praziquantel treatment and the education of at-risk populations on the need for protective behaviours should be a prominent feature of any local control programme.

Graphical abstract
Upconverting phosphor technology-based lateral flow assay for the rapid and sensitive detection of anti-Trichinella spiralis IgG antibodies in pig serum
Authors: Li Jian , Ding Jing , Liu Xiao-Lei , Tang Bin , Bai Xue , Wang Yang , Qiao Wei-Dong , Liu Ming-Yuan , Wang Xue-Lin 
Published: September 2021

Abstract
Background
Trichinella spiralis is a zoonotic food-borne parasite. A disease caused by infection with T. spiralis is called trichinellosis in humans. It is important to investigate the epidemic situation and the surveillance of herds and then prevent infection in humans. Therefore, this study is to develop a rapid and sensitive diagnostic method for on-site test in domestic and wild animals.

Methods
Upconverting phosphor nanoparticles (UCNPs), an excellent optical label, were conjugated with the excretory-secretory (ES) antigens from T. spiralis muscle larvae (ML) or goat anti-rabbit IgG, and a lateral flow (LF) assay based on these probes (UCNPs-ES/goat anti-rabbit IgG) was developed for the rapid and sensitive detection of anti-T. spiralis IgG antibodies in pig serum. The assay is named the UPT-LF-ES assay. In addition, the probes were characterized, and the assay was optimized. A cut-off threshold of the assay was also identified by using 169 known negative pig samples. Performance of the assay to T. spiralis with different infective numbers, cross-reactivity with other parasitic infections, the single-blinded experiment, and coincidence were evaluated with the assay.

Results
The UPT-LF-ES assay was successfully constructed and optimized based on the probes of UCNPs-ES/goat anti-rabbit IgG. In the pigs infected with 100, 1000, and 10,000 ML, positive results were first presented at 35 days post-infection (dpi), 30 dpi, and 25 dpi, respectively. The assay had no cross-reaction with other parasitic infections. A single-blinded experiment indicated that the sensitivity and specificity of the UPT-LF-ES assay were 100% and 100%, respectively, the area under the receiver operating characteristic (ROC) curve was 1.000. In addition, the value detected by the UPT-LF-ES assay was significantly different between positive and negative samples. Moreover, compared with the “gold standard” magnetic stirrer method, the coincidence rate of the UPT-LF-ES assay was 87.27%, and the kappa (K) coefficient was 0.7454, showing a substantial agreement.

Conclusions
The UPT-LF-ES assay is a useful point-of-care test (POCT) with T. spiralis in the detection of pig, which contributes to preventing human trichinellosis.

Graphical Abstract
Changes in serum biomarkers of inflammation in bovine besnoitiosis
Authors: González-Barrio David , Huertas-López Ana , Diezma-Díaz Carlos , Ferre Ignacio , Cerón José Joaquín , Ortega-Mora Luis Miguel , Álvarez-García Gema 
Published: September 2021

Abstract
Background
Acute and chronic besnoitiosis in extensive natural-service herds can have relevant effects in the health of bulls and negative consequences in their productive performance. Recent progress has been made in order to elucidate the pathogenesis of this disease. In this context, the study of biomarkers of inflammation in serum would contribute to gaining knowledge about the physiopathology of bovine besnoitiosis. Serological biomarkers could help in early diagnosis and prognosis, as seropositive bulls may have mild or severe testicular lesions.

Methods
Herein, we have investigated the diagnostic and/or prognostic value of a panel of serum (serological) biomarkers related to inflammation, including total protein, globulin and albumin, haptoglobin (Hp), adenosine deaminase (ADA) paraoxonase-1 (PON-1) and acetylcholinesterase (AChE) in naturally and experimentally B. besnoiti-infected males classified according to different clinical phases of the disease (acute, chronic and subclinical besnoitiosis).

Results
Results showed a similar response pattern in these biomarkers for naturally and experimentally infected cattle, with a few relevant variations. Most significant changes occurred during the acute phase of infection, although significant changes in a few biomarkers were also observed during the chronic infection. Haptoglobin, albumin, PON-1 and ADA were identified as the biomarkers that showed changes of higher magnitude in the acute phase of the infection, whereas high total protein and globulin values were found in chronically infected cattle. We have described the changes of a panel of inflammatory biomarkers of acute and chronic bovine besnoitiosis.

Conclusions
In summary, several biomarkers with promising diagnostic value have been identified. The biomarkers associated with acute infection are related to previously reported molecular biomarkers in testicular parenchyma of infected bulls and could help in the diagnosis of early infections and complement results from specific immunoglobulin M (IgM) detection.

Graphical abstract
API2CAN: a dataset & service for canonical utterance generation for REST APIs
Authors: Yaghoub-Zadeh-Fard Mohammad-Ali , Benatallah Boualem 
Published: September 2021

Abstract
Objectives
Recently natural language interfaces (e.g., chatbots) have gained enormous attention. Such interfaces execute underlying application programming interfaces (APIs) based on the user's utterances to perform tasks (e.g., reporting weather). Supervised approaches for building such interfaces rely upon a large set of user utterances paired with APIs. Collecting such pairs is typically starts with obtaining initial utterances for a given API method. Generating initial utterances can be considered as a machine translation task in which an API method is translated into an utterance. However, the key challenge is the lack of training samples for training domain-independent translation models. In this paper, we propose a dataset for training supervised models to generate initial utterances for APIs.

Data description
The dataset contains 14,370 pairs of API methods and utterances. It is built automatically by converting method descriptions of a large number of APIs to user utterances; and it is cleaned manually to ensure quality. The dataset is also accompanied with a set of microservices (e.g., translating API methods to utterances) which can facilitate the process of collecting training samples for building natural language interfaces.
Problematic familial alcohol use and heavy episodic drinking among upper secondary students: a moderator analysis of teacher-rated school ethos
Authors: Olsson Gabriella , Brolin Låftman Sara , Wahlström Joakim , Modin Bitte 
Published: September 2021

AbstractObjectiveBuilding on findings reported in a previous publication, the objective of this study is to explore if teacher-rated indicators of school ethos modify the association between problematic familial alcohol use and heavy episodic drinking among upper secondary students. Data were based on combined information from two separate surveys conducted in 2016 among 4709 students and 1061 teachers in 46 Stockholm upper secondary schools, with linked school-level information from administrative registers. Multilevel binary logistic regression analyses were performed.ResultsProblematic familial alcohol use was associated with an increased likelihood of heavy episodic drinking among upper secondary students (OR 1.36, 95% CI 1.12–1.65). Cross-level interactions revealed that the association was weaker among students attending schools with higher levels of teacher-rated ethos. This was true for overall school ethos (OR 0.79, 95% CI 0.65–0.97) and for four of five studied sub-dimensions of ethos: staff stability (OR 0.78, 95% CI 0.65–0.95); teacher morale (OR 0.79, 95% CI 0.65–0.97); student focus (OR 0.80, 95% CI 0.65–0.97); and academic atmosphere (OR 0.79, 95% CI 0.65–0.96). The sub-dimension “structure and order for dealing with unwanted behaviour” did however not moderate the association between problematic familial alcohol use and heavy episodic drinking (OR 0.95, 95% CI 0.77–1.18).
Epidemiology of comorbidities and their association with asthma control
Authors: Tomisa Gábor , Horváth Alpár , Sánta Balázs , Keglevich András , Tamási Lilla 
Published: September 2021

Abstract
Background
The prevalence of comorbidities and their relation to asthma control and treatment is a topic of increasing interest, however comprehensive studies are scarce. We aimed to determine the prevalence of the most common comorbidities in asthma in relation to patient characteristics (age, gender and body mass index [BMI]) and their association with asthma control in a large, specialist-managed representative patient population.

Methods
A secondary, exploratory analysis of the Asthma Reality (ARL), across-sectional, non-interventional real-life study was conducted. Basic patient characteristics, the prevalence of comorbidities and data on asthma control and risk factors had been collected and their interactions examined. Descriptive statistics and binomial regression were used to assess the distribution of the prevalence of comorbidities and propensity matching was applied to assess their effect on asthma control.

Results
Overall, 12,743 patients were enrolled in our study in 187 treatment centres covering all regions of Hungary. Most comorbidities showed significantly different distribution for all basic patient characteristics. Gender, age group, smoking status, BMI and the duration of asthma had a significant impact on asthma control. The frequency of uncontrolled asthma was higher in females (37.1%), in the age group of 46–65 years (39.6%), in severely obese patients (43.2%), in patients who had been diagnosed with asthma for more than 20 years (40.4%), and in active heavy smokers (55%), compared with respective groups in the same category. Based on the binomial regression with propensity score matching, concomitant chronic obstructive pulmonary disease (COPD) (odds ratio [OR] = 2.06, 95% confidence interval [CI] 1.80–2.36), ischaemic heart disease (OR = 1.86, 95% CI 1.64–2.10) and cerebrovascular events (OR = 1.85, 95% CI 1.47–2.32) had the strongest negative effect on asthma control, with the presence of all of these conditions increasing the risk of uncontrolled asthma.

Conclusions
This evaluation of comorbidity data of more than 12,000, adult asthmatic patients has provided a clearer picture of diseases that can frequently co-exist with asthma, and their influence on asthma control, assessed by the prevalence of symptoms. Our study suggests that most asthmatic patients have at least one comorbidity, and the presence of comorbidities may have a high impact on asthma control measures.
In vitro genome editing rescues parkinsonism phenotypes in induced pluripotent stem cells-derived dopaminergic neurons carrying LRRK2 p.G2019S mutation
Authors: Chang Kuo-Hsuan , Huang Cheng-Yen , Ou-Yang Chih-Hsin , Ho Chang-Han , Lin Han-Yi , Hsu Chia-Lang , Chen You-Tzung , Chou Yu-Chi , Chen Yi-Jing , Chen Ying , Lin Jia-Li , Wang Ji-Kuan , Lin Pei-Wen , Lin Ying-Ru , Lin Miao-Hsia , Tseng Chi-Kang , Lin Chin-Hsien 
Published: September 2021

Abstract
Background
The c.G6055A (p.G2019S) mutation in leucine-rich repeat kinase 2 (LRRK2) is the most prevalent genetic cause of Parkinson’s disease (PD). CRISPR/Cas9-mediated genome editing by homology-directed repair (HDR) has been applied to correct the mutation but may create small insertions and deletions (indels) due to double-strand DNA breaks. Adenine base editors (ABEs) could convert targeted A·T to G·C in genomic DNA without double-strand breaks. However, the correction efficiency of ABE in LRRK2 c.G6055A (p.G2019S) mutation remains unknown yet. This study aimed to compare the mutation correction efficiencies and off-target effects between HDR and ABEs in induced pluripotent stem cells (iPSCs) carrying LRRK2 c.G6055A (p.G2019S) mutation.

Methods
A set of mutation-corrected isogenic lines by editing the LRRK2 c.G6055A (p.G2019S) mutation in a PD patient-derived iPSC line using HDR or ABE were established. The mutation correction efficacies, off-target effects, and indels between HDR and ABE were compared. Comparative transcriptomic and proteomic analyses between the LRRK2 p.G2019S iPSCs and isogenic control cells were performed to identify novel molecular targets involved in LRRK2-parkinsonism pathways.

Results
ABE had a higher correction rate (13/53 clones, 24.5%) than HDR (3/47 clones, 6.4%). Twenty-seven HDR clones (57.4%), but no ABE clones, had deletions, though 14 ABE clones (26.4%) had off-target mutations. The corrected isogenic iPSC-derived dopaminergic neurons exhibited reduced LRRK2 kinase activity, decreased phospho-α-synuclein expression, and mitigated neurite shrinkage and apoptosis. Comparative transcriptomic and proteomic analysis identified different gene expression patterns in energy metabolism, protein degradation, and peroxisome proliferator-activated receptor pathways between the mutant and isogenic control cells.

Conclusions
The results of this study envision that ABE could directly correct the pathogenic mutation in iPSCs for reversing disease-related phenotypes in neuropathology and exploring novel pathophysiological targets in PD.
DTi2Vec: Drug–target interaction prediction using network embedding and ensemble learning
Authors: Thafar Maha A. , Olayan Rawan S. , Albaradei Somayah , Bajic Vladimir B. , Gojobori Takashi , Essack Magbubah , Gao Xin 
Published: September 2021

AbstractDrug–target interaction (DTI) prediction is a crucial step in drug discovery and repositioning as it reduces experimental validation costs if done right. Thus, developingin-silicomethods to predict potential DTI has become a competitive research niche, with one of its main focuses being improving the prediction accuracy. Using machine learning (ML) models for this task, specifically network-based approaches, is effective and has shown great advantages over the other computational methods. However, ML model development involves upstream hand-crafted feature extraction and other processes that impact prediction accuracy. Thus, network-based representation learning techniques that provide automated feature extraction combined with traditional ML classifiers dealing with downstream link prediction tasks may be better-suited paradigms. Here, we present such a method, DTi2Vec, which identifies DTIs using network representation learning and ensemble learning techniques. DTi2Vec constructs the heterogeneous network, and then it automatically generates features for each drug and target using the nodes embedding technique. DTi2Vec demonstrated its ability in drug–target link prediction compared to several state-of-the-art network-based methods, using four benchmark datasets and large-scale data compiled from DrugBank. DTi2Vec showed a statistically significant increase in the prediction performances in terms of AUPR. We verified the "novel" predicted DTIs using several databases and scientific literature. DTi2Vec is a simple yet effective method that provides high DTI prediction performance while being scalable and efficient in computation, translating into a powerful drug repositioning tool.
Improved CRISPR/Cas9 gene editing in primary human myoblasts using low confluency cultures on Matrigel
Authors: Goullée Hayley , Taylor Rhonda L. , Forrest Alistair R. R. , Laing Nigel G. , Ravenscroft Gianina , Clayton Joshua S. 
Published: September 2021

Abstract
Background
CRISPR/Cas9 is an invaluable tool for studying cell biology and the development of molecular therapies. However, delivery of CRISPR/Cas9 components into some cell types remains a major hurdle. Primary human myoblasts are a valuable cell model for muscle studies, but are notoriously difficult to transfect. There are currently no commercial lipofection protocols tailored for primary myoblasts, and most generic guidelines simply recommend transfecting healthy cells at high confluency. This study aimed to maximize CRISPR/Cas9 transfection and editing in primary human myoblasts.

Methods
Since increased cell proliferation is associated with increased transfection efficiency, we investigated two factors known to influence myoblast proliferation: cell confluency, and a basement membrane matrix, Matrigel. CRISPR/Cas9 editing was performed by delivering Cas9 ribonucleoprotein complexes via lipofection into primary human myoblasts, cultured in wells with or without a Matrigel coating, at low (~ 40%) or high (~ 80%) confluency.

Results
Cells transfected at low confluency on Matrigel-coated wells had the highest levels of transfection, and were most effectively edited across three different target loci, achieving a maximum editing efficiency of 93.8%. On average, editing under these conditions was >4-fold higher compared to commercial recommendations (high confluency, uncoated wells).

Conclusion
This study presents a simple, effective and economical method of maximizing CRISPR/Cas9-mediated gene editing in primary human myoblasts. This protocol could be a valuable tool for improving the genetic manipulation of cultured human skeletal muscle cells, and potentially be adapted for use in other cell types.
Benefits and harms of implementing [18F]FDG-PET/CT for diagnosing recurrent breast cancer: a prospective clinical study
Authors: Vogsen Marianne , Jensen Jeanette Dupont , Gerke Oke , Jylling Anne Marie Bak , Asmussen Jon Thor , Christensen Ivar Yannick , Braad Poul-Erik , Thye-Rønn Peter , Søe Katrine Lydolph , Ewertz Marianne , Hildebrandt Malene Grubbe 
Published: September 2021

Abstract
Background
[18F]-fluorodeoxyglucose-positron emission tomography/computed tomography ([18F]FDG-PET/CT) has been implemented sporadically in hospital settings as the standard of care examination for recurrent breast cancer. We aimed to explore the clinical impact of implementing [18F]FDG-PET/CT for patients with clinically suspected recurrent breast cancer and validate the diagnostic accuracy.

Methods
Women with suspected distant recurrent breast cancer were prospectively enrolled in the study between September 2017 and August 2019. [18F]FDG-PET/CT was performed, and the appearance of incidental benign and malignant findings was registered. Additional examinations, complications, and the final diagnosis were registered to reflect the clinical consequence of such findings. The diagnostic accuracy of [18F]FDG-PET/CT as a stand-alone examination was analyzed. Biopsy and follow-up were used as a reference standard.

Results
[18F]FDG-PET/CT reported breast cancer metastases in 72 of 225 women (32.0%), and metastases were verified by biopsy in 52 (52/225, 23.1%). Prior probability and posterior probability of a positive test for suspected metastatic cancer and incidental malignancies were 27%/85% and 4%/20%, respectively. Suspected malignant incidental findings were reported in 46 patients (46/225, 20.4%), leading to further examinations and final detection of nine synchronous cancers (9/225, 4.0%). These cancers originated from the lung, thyroid, skin, pancreas, peritoneum, breast, kidney, one was malignant melanoma, and one was hematological cancer. False-positive incidental malignant findings were examined in 37/225 patients (16.4%), mainly in the colon (n = 12) and thyroid gland (n = 12). Ten incidental findings suspicious for benign disease were suggested by [18F]FDG-PET/CT, and further examinations resulted in the detection of three benign conditions requiring treatment. Sensitivity, specificity, and AUC-ROC for diagnosing distant metastases were 1.00 (0.93–1.0), 0.88 (0.82–0.92), and 0.98 (95% CI 0.97–0.99), respectively.

Conclusion
[18F]FDG-PET/CT provided a high posterior probability of positive test, and a negative test was able to rule out distant metastases in women with clinically suspected recurrent breast cancer. One-fifth of patients examined for incidental findings detected on [18F]FDG-PET/CT were diagnosed with clinically relevant conditions. Further examinations of false-positive incidental findings in one of six women should be weighed against the high accuracy for diagnosing metastatic breast cancer.
Trial registration Clinical.Trials.gov. NCT03358589. Registered 30 November 2017—Retrospectively registered, http://www.ClinicalTrials.gov