bluuebunny/crossref_metadata_2025_split huggingface dataset:
TMEM30A is essential for hair cell polarity maintenance in postnatal mouse cochlea
Authors: Xing Yazhi , Peng Kun , Yi Qian , Yu Dongzhen , Shi Haibo , Yang Guang , Yin Shankai 
Published: March 2023

AbstractBackgroundPhosphatidylserine is translocated to the inner leaflet of the phospholipid bilayer membrane by the flippase function of type IV P-tape ATPase (P4-ATPase), which is critical to maintain cellular stability and homeostasis. Transmembrane protein 30A (TMEM30A) is the β-subunit of P4-ATPase. Loss of P4-ATPase function causes sensorineural hearing loss and visual dysfunction in human. However, the function of TMEM30A in the auditory system is unclear.MethodsP4-ATPase subtype expression in the cochlea was detected by immunofluorescence staining and quantitative real-time polymerase chain reaction (qRT-PCR) at different developmental stages. Hair cell specific TMEM30A knockout mice and wild-type littermates were used for the following functional and morphological analysis. Auditory function was evaluated by auditory brainstem response. We investigated hair cell and stereocilia morphological changes by immunofluorescence staining. Scanning electron microscopy was applied to observe the stereocilia ultrastructure. Differentially expressed transcriptomes were analyzed based on RNA-sequencing data from knockout and wild-type mouse cochleae. Differentially expressed genes were verified by qRT-PCR.ResultsTMEM30A and subtypes of P4-ATPase are expressed in the mouse cochlea in a temporal-dependent pattern. Deletion of TMEM30A in hair cells impaired hearing onset due to progressive hair cell loss. The disrupted kinocilia placement and irregular distribution of spectrin-α in cuticular plate indicated the hair cell planar polarity disruption in TMEM30A deletion hair cells. Hair cell degeneration begins at P7 and finishes around P14. Transcriptional analysis indicates that the focal adhesion pathway and stereocilium tip-related genes changed dramatically. Without the TMEM30A chaperone, excessive ATP8A2 accumulated in the cytoplasm, leading to overwhelming endoplasmic reticulum stress, which eventually contributed to hair cell death.ConclusionsDeletion of TMEM30A led to disrupted planar polarity and stereocilia bundles, and finally led to hair cell loss and auditory dysfunction. TMEM30A is essential for hair cell polarity maintenance and membrane homeostasis. Our study highlights a pivotal role of TMEM30A in the postnatal development of hair cells and reveals the possible mechanisms underlying P4-ATPase-related genetic hearing loss.
A review and comparative study of cancer detection using machine learning: SBERT and SimCSE application
Authors: Mokoatle Mpho , Marivate Vukosi , Mapiye Darlington , Bornman Riana , Hayes Vanessa. M. 
Published: March 2023

Abstract
Background
Using visual, biological, and electronic health records data as the sole input source, pretrained convolutional neural networks and conventional machine learning methods have been heavily employed for the identification of various malignancies. Initially, a series of preprocessing steps and image segmentation steps are performed to extract region of interest features from noisy features. Then, the extracted features are applied to several machine learning and deep learning methods for the detection of cancer.

Methods
In this work, a review of all the methods that have been applied to develop machine learning algorithms that detect cancer is provided. With more than 100 types of cancer, this study only examines research on the four most common and prevalent cancers worldwide: lung, breast, prostate, and colorectal cancer. Next, by using state-of-the-art sentence transformers namely: SBERT (2019) and the unsupervised SimCSE (2021), this study proposes a new methodology for detecting cancer. This method requires raw DNA sequences of matched tumor/normal pair as the only input. The learnt DNA representations retrieved from SBERT and SimCSE will then be sent to machine learning algorithms (XGBoost, Random Forest, LightGBM, and CNNs) for classification. As far as we are aware, SBERT and SimCSE transformers have not been applied to represent DNA sequences in cancer detection settings.

Results
The XGBoost model, which had the highest overall accuracy of 73 ± 0.13 % using SBERT embeddings and 75 ± 0.12 % using SimCSE embeddings, was the best performing classifier. In light of these findings, it can be concluded that incorporating sentence representations from SimCSE’s sentence transformer only marginally improved the performance of machine learning models.
CNN-Siam: multimodal siamese CNN-based deep learning approach for drug‒drug interaction prediction
Authors: Yang Zihao , Tong Kuiyuan , Jin Shiyu , Wang Shiyan , Yang Chao , Jiang Feng 
Published: March 2023

Abstract
Background
Drug‒drug interactions (DDIs) are reactions between two or more drugs, i.e., possible situations that occur when two or more drugs are used simultaneously. DDIs act as an important link in both drug development and clinical treatment. Since it is not possible to study the interactions of such a large number of drugs using experimental means, a computer-based deep learning solution is always worth investigating. We propose a deep learning-based model that uses twin convolutional neural networks to learn representations from multimodal drug data and to make predictions about the possible types of drug effects.

Results
In this paper, we propose a novel convolutional neural network algorithm using a Siamese network architecture called CNN-Siam. CNN-Siam uses a convolutional neural network (CNN) as a backbone network in the form of a twin network architecture to learn the feature representation of drug pairs from multimodal data of drugs (including chemical substructures, targets and enzymes). Moreover, this network is used to predict the types of drug interactions with the best optimization algorithms available (RAdam and LookAhead). The experimental data show that the CNN-Siam achieves an area under the precision-recall (AUPR) curve score of 0.96 on the benchmark dataset and a correct rate of 92%. These results are significant improvements compared to the state-of-the-art method (from 86 to 92%) and demonstrate the robustness of the CNN-Siam and the superiority of the new optimization algorithm through ablation experiments.

Conclusion
The experimental results show that our multimodal siamese convolutional neural network can accurately predict DDIs, and the Siamese network architecture is able to learn the feature representation of drug pairs better than individual networks. CNN-Siam outperforms other state-of-the-art algorithms with the combination of data enhancement and better optimizers. But at the same time, CNN-Siam has some drawbacks, longer training time, generalization needs to be improved, and poorer classification results on some classes.
Chromosome-level assembly of the Rangifer tarandus genome and validation of cervid and bovid evolution insights
Authors: Poisson William , Prunier Julien , Carrier Alexandra , Gilbert Isabelle , Mastromonaco Gabriela , Albert Vicky , Taillon Joëlle , Bourret Vincent , Droit Arnaud , Côté Steeve D. , Robert Claude 
Published: March 2023

AbstractBackgroundGenome assembly into chromosomes facilitates several analyses including cytogenetics, genomics and phylogenetics. Despite rapid development in bioinformatics, however, assembly beyond scaffolds remains challenging, especially in species without closely related well-assembled and available reference genomes. So far, four draft genomes ofRangifer tarandus(caribou or reindeer, a circumpolar distributed cervid species) have been published, but none with chromosome-level assembly. This emblematic northern species is of high interest in ecological studies and conservation since most populations are declining.ResultsWe have designed specific probes based on Oligopaint FISH technology to upgrade the latest published reindeer and caribou chromosome-level genomes. Using this oligonucleotide-based method, we found six mis-assembled scaffolds and physically mapped 68 of the largest scaffolds representing 78% of the most recentR. tarandusgenome assembly. Combining physical mapping and comparative genomics, it was possible to document chromosomal evolution among Cervidae and closely related bovids.ConclusionsOur results provide validation for the current chromosome-level genome assembly as well as resources to use chromosome banding in studies ofRangifer tarandus.
Genome-wide association study for the extractable phenolic profile and coat color of common bean seeds (Phaseolus vulgaris L.)
Authors: Campa Ana , Rodríguez Madrera Roberto , Jurado María , García-Fernández Carmen , Suárez Valles Belén , Ferreira Juan José 
Published: March 2023

Abstract
Background
A large variation in seed coat colors and seed phenolic metabolites is present in common bean (Phaseolus vulgaris L.). The study of the relationships between seed coat color phenotype and the phenolic profile is an important step in the elucidation of the gene network involved in the phenylpropanoid biosynthetic pathway. However, this relationship is still poorly understood in this species.

Results
A genome-wide association study (GWAS) was used to investigate the genomic regions associated with the synthesis of 10 flavonoids (5 anthocyanins and 5 flavonols) and with 10 seed coat color traits using a set of 308 common bean lines of the Spanish Diversity Panel (SDP) which have been genotyped with 11,763 SNP markers.. A total of 31 significant SNP-trait associations (QTNs) were identified, grouped in 20 chromosome regions: 6 for phenolic metabolites on chromosomes Pv01, Pv02, Pv04, Pv08, and Pv09, 13 for seed coat color on chromosomes Pv01, Pv02, Pv06, Pv07, and Pv10, and 1 including both types of traits located on chromosome Pv08. In all, 58 candidate genes underlying these regions have been proposed, 31 of them previously described in the phenylpropanoid pathway in common bean, and 27 of them newly proposed in this work based on the association study and their homology with Arabidopsis anthocyanin genes.

Conclusions
Chromosome Pv08 was identified as the main chromosome involved in the phenylpropanoid pathway and in consequence in the common bean seed pigmentation, with three independent chromosome regions identified, Phe/C_Pv08(2.7) (expanding from 2.71 to 4.04 Mbp), C_Pv08(5.8) (5.89–6.59 Mbp), and Phe_Pv08(62.5) (62.58 to 63.28 Mbp). Candidate genes previously proposed by other authors for the color genes V and P were validated in this GWAS. Candidate genes have been tentatively proposed from this study for color genes B and Rk on Pv02, Asp on Pv07, and complex C on Pv08. These results help to clarify the complex network of genes involved in the genetic control of phenolic compounds and seed color in common bean and provide the opportunity for future validation studies.
Challenges, strategies and consequences from the perspective of German nursing home managers during the first wave of the COVID-19 pandemic - a qualitative interview study
Authors: Sander Marco , Dano Richard , Bieber Anja , Dammermann Anna , Fleischer Steffen , Dinand Claudia , Müller Martin , Möhler Ralph , Schultes Kristin , Köpke Sascha , Dichter Martin N. ,   on behalf of the HEICO-study group, Seismann-Petersen Swantje , Matthies Daniel , Sommerlatte Sabine , Meyer Gabriele , Steyer Linda , Isensee Sebastian , Balzer Katrin , Halek Margareta , Freytag Stefanie , Hrudey Ilona , Hasenpusch Claudia , Eich-Krohm Astrid , Meyer Sarah , Piotrowski Alexandra , Hoffmann Falk , Fassmer Alexander 
Published: March 2023

Abstract
Background
The first wave of the COVID-19 pandemic reached Germany between March and May 2020. In order to contain the spread of the virus and particularly protect vulnerable people, the government imposed a lockdown in March 2020. In addition to infection control measures, such as hygiene and social distancing requirements, a general ban on access to nursing homes for relatives and external service providers was issued.

Methods
To investigate the challenges and consequences of the enacted infection prevention measures and specific strategies for nursing homes in Germany, a multicentre cross-sectional qualitative interview study with nursing home managers and ward managers was conducted. Recorded audio data were transcribed, analysed using thematic framework analysis and reflected in peer debriefings.

Results
Seventy-eight interviews with 40 nursing home managers and 38 ward managers from 43 German nursing homes were conducted. At organisational level, the following six themes were identified: Appointing a multi-professional crisis task force, reorganizing the use of building and spatial structures, continuous adaption and implementation of hygiene plans, adapting staff deployment to dynamically changing demands, managing additional communicative demands and relying on and resorting to informal networks. To deal with the pandemic challenges also six themes can be described for the direct care level: Changed routines, taking over non-nursing tasks, increased medical responsibility, increased documentation demands, promoting social participation and increased communication demands. Also various negative consequences were identified (four themes): Psychological stress, negative emotional consequences, permanent feeling of responsibility and increased potential for conflicts. Positive emotional consequences were also reported (two themes): resources for the challenges and positive emotional consequences for home managers and staff.

Conclusions
The results of the described challenges, strategies and consequences allow recommendations as basis for possible approaches and successful adaptation processes in nursing home care in the future. In particular, there is a need for local networks to act in a coordinated way and a need for quantitative and qualitative support for nurses, such as staff support as well as advanced nursing practice, to cope with the challenges of the pandemic.
Development of a UK core dataset for geriatric medicine research: a position statement and results from a Delphi consensus process
Authors: Welch Carly , Wilson Daisy , Sayer Avan A. , Witham Miles D. , Jackson Thomas A. ,   on behalf of the UK Geriatric Medicine Core Dataset Extended Working Group, Rajkumar Raj , Dhesi Jugdeep , Lochlainn Mary Ni , Aspray Terry , Dodds Richard , Frith James , Richardson Sarah , Tullo Ellen , Yarnall Alison , Walker Richard , Cunningham Emma , Prynn Josephine , Patel Harnish , Tiwari Divya , Makin Stephen , Myint Phyo , Henderson Emily , Keevil Victoria , Walesby Katherine , Allan Louise , Masoli Jane , Quinn Terry , Clegg Andrew P. , Hale Matthew , Conroy Simon , Taylor Joanne , Gladman John , Gordon Adam , Harwood Rowan , Cox Natalie , Roberts Helen 
Published: March 2023

Abstract
Background
There is lack of standardisation in assessment tools used in geriatric medicine research, which makes pooling of data and cross-study comparisons difficult.

Methods
We conducted a modified Delphi process to establish measures to be included within core and extended datasets for geriatric medicine research in the United Kingdom (UK). This included three complete questionnaire rounds, and one consensus meeting. Participants were selected from attendance at the NIHR Newcastle Biomedical Research Centre meeting, May 2019, and academic geriatric medicine e-mailing lists. Literature review was used to develop the initial questionnaire, with all responses then included in the second questionnaire. The third questionnaire used refined options from the second questionnaire with response ranking.

Results
Ninety-eight responses were obtained across all questionnaire rounds (Initial: 19, Second: 21, Third: 58) from experienced and early career researchers in geriatric medicine. The initial questionnaire included 18 questions with short text responses, including one question for responders to suggest additional items. Twenty-six questions were included in the second questionnaire, with 108 within category options. The third questionnaire included three ranking, seven final agreement, and four binary option questions. Results were discussed at the consensus meeting. In our position statement, the final consensus dataset includes six core domains: demographics (age, gender, ethnicity, socioeconomic status), specified morbidities, functional ability (Barthel and/or Nottingham Extended Activities of Daily Living), Clinical Frailty Scale (CFS), cognition, and patient-reported outcome measures (dependent on research question). We also propose how additional variables should be measured within an extended dataset.

Conclusions
Our core and extended datasets represent current consensus opinion of academic geriatric medicine clinicians across the UK. We consider the development and further use of these datasets will strengthen collaboration between researchers and academic institutions.
A novel homozygous missense substitution p.Thr313Ile in the PDE6B gene underlies autosomal recessive retinitis pigmentosa in a consanguineous Pakistani family
Authors: Aziz Nobia , Ullah Mukhtar , Rashid Abdur , Hussain Zubair , Shah Khadim , Awan Azeem , Khan Muhammad , Ullah Inam , Rehman Atta Ur 
Published: March 2023

Abstract
Background
Retinitis pigmentosa (RP) is one of the most frequent hereditary retinal diseases that often starts with night blindness and eventually leads to legal blindness. Our study aimed to identify the underlying genetic cause of autosomal recessive retinitis pigmentosa (arRP) in a consanguineous Pakistani family.

Methods
Following a detailed ophthalmological examination of the patients by an ophthalmologist, whole-exome sequencing was performed on the proband’s DNA to delineate the genetic cause of RP in the family. In-depth computational methods, in-silico analysis, and familial co-segregation study were performed for variant detection and validation.

Results
We studied an inbred Pakistani family with two siblings affected by retinitis pigmentosa. The proband, a 32 years old female, was clinically diagnosed with RP at the age of 6 years. A classical night blindness symptom was reported in the proband since her early childhood. OCT report showed a major reduction in the outer nuclear layer and the ellipsoid zone width, leading to the progression of the disease. Exome sequencing revealed a novel homozygous missense mutation (c.938C > T;p.Thr313Ile) in exon 12 of the PDE6B gene. The mutation p.Thr313Ile co-segregated with RP phenotype in the family. The altered residue (p.Thr313) was super conserved evolutionarily across different vertebrate species, and all available in silico tools classified the mutation as highly pathogenic.

Conclusion
We present a novel homozygous pathogenic mutation in the PDE6B gene as the underlying cause of arRP in a consanguineous Pakistani family. Our findings highlight the importance of missense mutations in the PDE6B gene and expand the known mutational repertoire of PDE6B-related RP.
Clinicians’ perceptions and practices of diagnostic assessment in psychiatric services
Authors: Bohman Benjamin 
Published: March 2023

Abstract
Background
Diagnostic assessment in psychiatric services typically involves applying clinical judgment to information collected from patients using multiple sources, including anamnesis and structured diagnostic interviews. Research shows that clinicians’ perceptions of diagnostic assessment are associated with their diagnostic practices, and that perceptions and practices may vary according to clinician characteristics. Examining clinicians’ perceptions and practices of diagnostic assessment is important for quality improvement in psychiatric services, including implementation of evidence-based practice procedures. The purpose of the present study was to evaluate clinicians’ perceptions and practices of diagnostic assessment in psychiatric services and examine whether these perceptions and practices varied according to profession and age, with the aim of providing a basis for quality improvement.

Methods
A total of 183 (53.2%) clinicians in community-based adult psychiatric services in Stockholm, Sweden participated in an online survey. Differences between professions were analyzed using Kruskal-Wallis tests and effect sizes were calculated. Associations of clinicians’ perceptions with their age were examined using Spearman correlations.

Results
Overall, clinicians had positive attitudes toward diagnostic assessment, and they considered themselves as competent. Differences were as most pronounced between nurses and other professions. Nursed had conducted fewer assessments, perceived themselves as less competent, and reported to a smaller extent to be able to determine which diagnosis should be the target for treatment in patients with multiple diagnoses. There were no associations of clinicians’ perceptions with their age. Some potential areas of improvement were identified, including clinician qualifications, education in diagnostic assessment, and contents of diagnostic assessment.

Conclusions
The results of the present study may provide a basis for quality improvement in psychiatric services. For example, it may be important to pay attention to potential differences in perceptions and practices between professions in efforts to improve quality of assessment and care.
Differences in child and adolescent exposure to unhealthy food and beverage advertising on television in a self-regulatory environment
Authors: Potvin Kent Monique , Soares Guimaraes Julia , Pritchard Meghan , Remedios Lauren , Pauzé Elise , L’Abbé Mary , Mulligan Christine , Vergeer Laura , Weippert Madyson 
Published: March 2023

Abstract
Background
Food and beverage promotion is a contributor to children’s dietary behaviours, and ultimately, downstream health consequences. Broadcast television remains an important source of such advertising. The objective of this study was to examine and compare children and adolescent’s exposure to food advertising on television in Canada over an entire year in a self-regulatory environment.

Methods
Television advertising data for 57 selected food and beverage categories were licensed from Numerator for 36 stations in Toronto, for 2019. The estimated average number of advertisements viewed by children aged 2–11 and adolescents aged 12–17 was determined overall, by food category, and by marketing technique. The healthfulness of advertisements was also assessed using Health Canada’s Nutrient Profile Model.

Results
Overall in 2019, children viewed 2234.4 food ads/person/yr while adolescents viewed 1631.7 ads, exposure for both groups stemmed primarily from stations with general appeal, and both age groups were exposed to a range of powerful marketing techniques. Exposure to advertising for restaurants, snacks, breakfast food and candy and chocolate was high among both age groups and the healthfulness of most advertised products was considered poor. Adolescents were exposed to 36.4% more food products classified as unhealthy, had higher exposure to all marketing techniques examined, and were exposed to substantially more child-related marketing techniques compared to children.

Conclusion
Children and adolescents were heavily exposed to food advertisements on television in 2019. Despite current self-regulatory policies, children’s exposure to unhealthy food and beverages remains high. Differences in exposure to food advertisements by food category and healthfulness may suggest that adolescents are being disproportionately targeted by food companies as a result of self-regulatory marketing restrictions.