bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prediction of the effects of the top 10 synonymous mutations from 26645 SARS-CoV-2 genomes
Authors: Boon Wan Xin , Sia Boon Zhan , Ng Chong Han 
Published: September 2022

Background: The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) had led to a global pandemic since December 2019. SARS-CoV-2 is a single-stranded RNA virus, which mutates at a higher rate. Multiple works had been done to study nonsynonymous mutations, which change protein sequences. However, there is little study on the effects of SARS-CoV-2 synonymous mutations, which may affect viral fitness. This study aims to predict the effect of synonymous mutations on the SARS-CoV-2 genome. Methods: A total of 26645 SARS-CoV-2 genomic sequences retrieved from Global Initiative on Sharing all Influenza Data (GISAID) database were aligned using MAFFT. Then, the mutations and their respective frequency were identified. Multiple RNA secondary structures prediction tools, namely RNAfold, IPknot++ and MXfold2 were applied to predict the effect of the mutations on RNA secondary structure and their base pair probabilities was estimated using MutaRNA. Relative synonymous codon usage (RSCU) analysis was also performed to measure the codon usage bias (CUB) of SARS-CoV-2. Results: A total of 150 synonymous mutations were identified. The synonymous mutation identified with the highest frequency is C3037U mutation in the nsp3 of ORF1a.. Of these top 10 highest frequency synonymous mutations, C913U, C3037U, U16176C and C18877U mutants show pronounced changes between wild type and mutant in all 3 RNA secondary structure prediction tools, suggesting these mutations may have some biological impact on viral fitness. These four mutations show changes in base pair probabilities. All mutations except U16176C change the codon to a more preferred codon, which may result in higher translation efficiency. Conclusion: Synonymous mutations in SARS-CoV-2 genome may affect RNA secondary structure, changing base pair probabilities and possibly resulting in a higher translation rate. However, lab experiments are required to validate the results obtained from prediction analysis.
Chromosome-scale assembly of the yellow mealworm genome
Authors: Eleftheriou Evangelia , Aury Jean-Marc , Vacherie Benoît , Istace Benjamin , Belser Caroline , Noel Benjamin , Moret Yannick , Rigaud Thierry , Berro Fabrice , Gasparian Sona , Labadie-Bretheau Karine , Lefebvre Thomas , Madoui Mohammed-Amin 
Published: September 2022

Background: The yellow mealworm beetle, Tenebrio molitor, is a promising alternative protein source for animal and human nutrition and its farming involves relatively low environmental costs. For these reasons, its industrial scale production started this century. However, to optimize and breed sustainable new T. molitor lines, the access to its genome remains essential. Methods: By combining Oxford Nanopore and Illumina Hi-C data, we constructed a high-quality chromosome-scale assembly of T. molitor. Then, we combined RNA-seq data and available coleoptera proteomes for gene prediction with GMOVE. Results: We produced a high-quality genome with a N50 = 21.9Mb with a completeness of 99.5% and predicted 21,435 genes with a median size of 1,780 bp. Gene orthology between T. molitor and Tribolium castaneum showed a highly conserved synteny between the two coleoptera and paralogs search revealed an expansion of histones in the T. molitor genome. Conclusions: The present genome will greatly help fundamental and applied research such as genetic breeding and will contribute to the sustainable production of the yellow mealworm.
Developing the University of Tartu in Estonia into a well-networked Patient Safety Research Centre (PATSAFE): A study protocol
Authors: PÕLLUSTE Kaja , Calsbeek Hiske , Orrego Carola , Ballester Marta , Suñol Rosa , Vall-Roqué Helena , Kangasniemi Mari , Läänelaid Siim , Starkopf Joel , van Tuijl Anne , Wollersheim Hub , Freimann Tiina , Mägi Liisi , Bañeres Joaquim , Fernández-Maillo María del Mar , Emond Yvette , Lember Margus 
Published: September 2022

Background: Patient safety (PS) is a serious global public health problem affecting all countries. Estimates show that around 10 percent of the patients are harmed during hospital care, resulting in 23 million disability-adjusted life years lost per year. Experts emphasize research advancements as a key precondition for safer care. Aim: The Patient Safety Research Centre (PATSAFE) project enhances the Institute of Clinical Medicine of the University of Tartu’s (ICM-UT) research potential and capacities in PS in order to improve and strengthen knowledge and skills in methods, techniques and experience for PS research. Methods: A strategic partnership with Avedis Donabedian Research Institute in Spain, and IQ Healthcare in the Netherlands, both international leaders in PS research, enables the development of a long-lasting knowledge exchange, allowing the ICM-UT to capitalise on its current achievements and to overcome gaps in scientific excellence in the field of PS research. These twining activities will strengthen and raise the research profile of the ICM-UT academic staff and early-stage researchers (ESRs), by implementing the hands-on training on methods, techniques, and experience in PS research. The project also encourages the active participation of ESRs in PS research by increasing their soft skills, to ensure the continuity and sustainability of PS research in ICM-UT. Finally, development of the research strategy on PS contributes to the long-term sustainability of PS research in Estonia. To implement these activities, PATSAFE foresees a comprehensive strategy consisting of knowledge exchange, soft research skills capacity building, strategic planning, and strong dissemination and exploitation efforts. Expected results: As a result of the project, ICM-UT will have the capacity to carry out PS research using the appropriate methodology and the competences to apply state-of-the-art evidence-based strategies for PS research.
The potential for linking cohort participants to official criminal records: a pilot study using the Avon Longitudinal Study of Parents and Children (ALSPAC)
Authors: Boyd Andy , Teyhan Alison , Cornish Rosie P. , Croft Jazz , Thomas Richard , Brennan Iain , Macleod John 
Published: September 2022

Introduction: Linking longitudinal cohort resources with police-recorded records of criminal activity has the potential to inform public health style approaches to policing, and may reduce potential sources of bias from self-reported criminal data collected by cohort studies. A pilot linkage of police records to the Avon Longitudinal Study of Parents and Children (ALSPAC) allows us to consider the acceptability of this linkage, its utility as a data resource, differences in self-reported crime according to consent status for data linkage, and the appropriate governance mechanism to support such a linkage. Methods: We carried out a pilot study linking data from the ALSPAC birth cohort to Ministry of Justice (MoJ) records on criminal cautions and convictions. This pilot was conducted on a fully anonymous basis, meaning we cannot link the identified records to any participant or the wider information within the dataset. Using ALSPAC data, we used summary statistics to investigate differences in socio-economic background and self-reported criminal activity by consent status for crime linkage. We used MoJ records to identify the geographic and temporal concentration of criminality in the ALSPAC cohort. Results: We found that the linkage appears acceptable to participants (4% of the sample opted out), levels of criminal caution and conviction are high enough to support research, and that the majority of crimes occurred in Avon & Somerset (the policing area local to ALSPAC). Those who did not respond to consent requests had higher levels of self-reported criminal behaviour compared to participants who provided explicit consent. Conclusions: These findings suggest that data linkage in ALSPAC provides opportunities to study criminal behaviour and that linked individual-level records could provide robust research in the area. Our findings also suggest the potential for bias when only including participants who have explicitly consented to data linkage, highlighting the limitations of opt-in consent strategies.
Yiddish varieties in the Livonian contact area
Authors: Verschik Anna 
Published: September 2022

The aim of this article is to discuss the Yiddish varieties of Courland and Estonia in the general context of the co-territorial languages: Baltic German, Latvian, Livonian, and Estonian. As a rule, discussion of Yiddish in the region is mostly based on the classical descriptions of the Yiddish varieties from the beginning of the 20th century. It is demonstrated that common features in phonology and lexicon of Courland (and Estonian) Yiddish and Baltic German are, in fact, regional and attested at least in varieties of Estonian but often in Latvian and Livonian as well. It is argued that due to the multilingualism of Jews in the region, a wider perspective of modern contact linguistics and multilingualism and analysis is needed. In the 20th century, multilingual speech was a norm at least among Estonian Jews, and, based on fieldwork data from the 1990s among multilingual Estonian Jews, there is no clear preference of insertional or alternational code-switching. However, if alternational code-switching is preferred in a community, it might explain the low number of conventionalised lexical borrowings (as is the case for Latvian borrowings in Yiddish).
Kokkuvõte. Anna Verschik: Jidiši keelekujud liivi kontaktalal. Artikli eesmärk on kirjeldada Kuramaa ja Eesti jidiši keele variante naaberkeelte (s.o. baltisaksa, läti, liivi ja eesti keele) kontekstis. Reeglina põhineb kohalike jidiši keelekujude analüüs nn klassikalistel, 20. sajandi algusest pärit kirjeldustel. Artiklis näidatakse, et fonoloogilised ühisjooned Kuramaa ja Eesti jidišis ja baltisaksa keeles on tegelikult regionaalsed ning esinevad vähemalt eesti keeles, aga tihtilugu ka läti ja liivi keeles. Kuna tegu on mitmekeelsusega, oleks vaja laiemat, moodsa kontaktlingvistika põhist analüüsi. 20. sajandil oli vähemalt Eesti juutidele omane nn mitmekeelne kõne ning 1990ndatel kogutud välitööandmete põhjal saab väita, et ei ole kindlalt domineerivat koodivahetuse tüüpi (sisestav vs. vahelduv). Kuid siis, kui kogukonnas domineerib vahelduv koodivahetus, seletab see leksikaalsete laenude väikest arvu (nagu nt läti laenude puhul jidišis).
Kubbõvõttõks. Anna Verschik. Jidiš kīelvīțõd līvõ kīel kontaktõd arāl. Kēra merk um kēraldõ Kurmō ja Ēstimō jidiš kīel variantidi kāimad kīeld (s.t. Baltijmōd saksā, lețkīel, līvõ ja ēsti kīel) kontekstõs. Kūožpēļizt jidiš kīelvīțõd analīz alīzõks ātõ n.n. irdizt 20. āigastsadā īrgandõks kēraldõkst. Kēra nägțõb, ku ītizt fonolōgij eņtšsuglitõd Kurmō ja Ēstimō jidišõs ja Baltijmōd saksā kīels āt regionālizt ja nǟdõb ka ēsti kīels, saggõld ka lețkīels ja līvõ kīels. 20. āigastsadās Ēstimō zīḑõdõn vȯļ ummi n.n. setmiņkēļi rõk, ja 1990. āigastis kūoŗdõd tieut pǟl vaņtlõs võib kītõ, ku kīels pūtõb ikšāinagi dominīeriji kōd vaidimiz tīp (sizzõlpandõb vs. mõitantiji). Sīegid siz, až kubgõns dominīerõb mõitantiji kōd vaidimi, se sēļțab piškīzt leksikālizt täpīņtõkst luggõ (nägț. lețkīel täpīņtõkst jidiš kīels).
Spoon-shaped pendants in the culture of the Livonians and inhabitants of Ancient Russia in the 11th–13th centuries: preliminary study results
Authors: Spirgis Roberts , Kuznetsova Valentina , Sobolev Vladislav 
Published: September 2022

In the culture of the ancient Livonians and Russians there was a particular group of pendants in the shape of household utensils, mostly made of copper alloys. This article deals with spoon-shaped pendants discovered in the settlements and burials of the second part of the 11th–13th century. Spoon-shaped pendants were rather rare for ancient Livonians. We have collected information about 19 finds from the Daugava region. In the territory of ancient Russia, about one hundred items have been found. In the historiography, spoon-shaped pendants were regarded as pagan amulets associated with the idea of satiation, wealth, and well-being. In our opinion, due to the late date of the items and their widespread distribution in Christian lands, they could be miniatures of the Eucharist spoons used in Orthodox communion.
Kokkuvõte. Roberts Spirģis, Valentina Kuznetsova, Vladislav Sobolev: Lusikakujulised ripatsehted 11.–13. sajandi liivi kultuuris ja muistse Venemaa asukatel: esialgsed uurimistulemused. Muistsete liivlaste ja venelaste kultuuris oli eripärane rühm majapidamisesemete kujulisi ripatseid, mis oli tehtud peamiselt vasesulamitest. See artikkel vaatleb lusikakujulisi ripatseid, mida on leitud 11. sajandi teise poole kuni 13. sajandi asulakohtadest ja haudadest. Lusikripatsid olid muistsetel liivlastel üsna haruldased. Autorid on kogunud teavet 19 leiu kohta Daugava piirkonnast. Muinasvene alalt on leitud kokku ligikaudu sada sellist eset. Historiograafias on lusikripatseid peetud paganlikeks amulettideks, mida on seostatud külluse, tervise ja heaolu taotlusega. Autorite arvates võisid hilise esinemisaja ja kristlikes maades laialdase leviku tõttu olla need aga armulaualusika miniatuursed kujutised ortodoksses ühenduses.
Kubbõvõttõks. Roberts Spirģis, Valentina Kuznetsova, Vladislav Sobolev: Kōjvīțlizt tänktõkst 11.–13. āigastsadā līvõd kultūrs ja muiniz Krīevmō jelānikād jūs. Ežmizt tuņšlimizt rezultātõd. Līvõd ja muinizt krīevõd kultūrs īžki kūož um pǟmizõld bronzõst vaļmõstõd kuodažād vīțlizt tänktõkst gruppõn. Kēras sōbõd vaņtõltõd tänktõkst-kōjd, mis sōbõd lieudtõd 11. ā.s. tuoiz pūol – 13. ā.s. jeltõbkūožis agā matūkstkūožis. Līvõd jūs tänktõkstkōjḑi līedab ōrald. Kēras ātõ īdõkubbõ pandõd tieutõd iļ 19 lieudtõd tänktõkst Vēna joug immõrgouțs. Muinizõs Krīevmōl um lieudtõd immõr sadā tänktõkst. Tieudlizõs kērandõksõs aŗŗõbõd, ku tänktõkst-kōjd ātõ pagānd amuletõd, mis ātõ mõttõltõd rikūz ja jõvāvȯlmiz lūomiz pierāst. Sīen vastõ rõkāndõb se, ku tänktõkst ātõ obbizt ja jo laigāld lieudtõb rištusk mōši. Sīepierāst autōrd aŗŗõbõd, ku tänktõkst-kōjd võikst vȱlda pareiznikād usk jumāllōda liturgijs kȭlbatõb kōjd miniatūrd.
Rhinovirus/enterovirus was the most common respiratory virus detected in adults with severe acute respiratory infections pre-COVID-19 in Kuala Lumpur, Malaysia
Authors: Chong Yoong Min , Chan Yoke Fun , Jamaluddin Mohamad Fadhil Hadi , Hasan M. Shahnaz , Pang Yong Kek , Ponnampalavanar Sasheela , Syed Omar Sharifah Faridah , Sam I-Ching 
Published: September 2022

Background
Severe acute respiratory infections (SARI) pose a great global burden. The contribution of respiratory viruses to adult SARI is relatively understudied in Asia. We aimed to determine viral aetiology of adult SARI patients in Kuala Lumpur, Malaysia.

Methods
The prevalence of 20 common (mainly viral) respiratory pathogens, and MERS-CoV, SARS-CoV and 5 bacterial select agents was investigated from May 2017 to October 2019 in 489 SARI adult patients in Kuala Lumpur, Malaysia, using molecular assays (Luminex NxTAG-RPP kit and qPCR assays). Viral metagenomics analysis was performed on 105 negative samples.

Results
Viral respiratory pathogens were detected by PCR in 279 cases (57.1%), including 10 (2.0%) additional detections by metagenomics analysis. The most detected viruses were rhinovirus/enterovirus (RV/EV) (49.1%) and influenza virus (7.4%). Three melioidosis cases were detected but no SARS-CoV, MERS-CoV or other bacterial select agents. Bacterial/viral co-detections and viral co-detections were found in 44 (9.0%) and 27 (5.5%) cases respectively, mostly involving RV/EV. Independent predictors of critical disease were male gender, chronic lung disease, lack of runny nose and positive blood culture with a significant bacterial pathogen. Asthma and sore throat were associated with increased risk of RV/EV detection, while among RV/EV cases, males and those with neurological disease were at increased risk of critical disease.

Conclusions
Prior to the COVID-19 pandemic, the high prevalence of respiratory viruses in adults with SARI was mainly attributed to RV/EV. Continued surveillance of respiratory virus trends contributes to effective diagnostic, prevention, and treatment strategies.
Changes in the proteome and secretome of rat liver sinusoidal endothelial cells during early primary culture and effects of dexamethasone
Authors: Li Ruomei , Bhandari Sabin , Martinez-Zubiaurre Inigo , Bruun Jack-Ansgar , Urbarova Ilona , Smedsrød Bård , Simón-Santamaría Jaione , Sørensen Karen Kristine 
Published: September 2022

Introduction
Liver sinusoidal endothelial cells (LSECs) are specialized fenestrated scavenger endothelial cells involved in the elimination of modified plasma proteins and tissue turnover waste macromolecules from blood. LSECs also participate in liver immune responses. A challenge when studying LSEC biology is the rapid loss of the in vivo phenotype in culture. In this study, we have examined biological processes and pathways affected during early-stage primary culture of rat LSECs and checked for cell responses to the pro-inflammatory cytokine interleukin (IL)-1β and the anti-inflammatory drug dexamethasone.

Methods
LSECs from male Sprague Dawley rats were cultured on type I collagen in 5% oxygen atmosphere in DMEM with serum-free supplements for 2 and 24 h. Quantitative proteomics using tandem mass tag technology was used to examine proteins in cells and supernatants. Validation was done with qPCR, ELISA, multiplex immunoassay, and caspase 3/7 assay. Cell ultrastructure was examined by scanning electron microscopy, and scavenger function by quantitative endocytosis assays.

Results
LSECs cultured for 24 h showed a characteristic pro-inflammatory phenotype both in the presence and absence of IL-1β, with upregulation of cellular responses to cytokines and interferon-γ, cell-cell adhesion, and glycolysis, increased expression of fatty acid binding proteins (FABP4, FABP5), and downregulation of several membrane receptors (STAB1, STAB2, LYVE1, CLEC4G) and proteins in pyruvate metabolism, citric acid cycle, fatty acid elongation, amino acid metabolism, and oxidation-reduction processes. Dexamethasone inhibited apoptosis and improved LSEC viability in culture, repressed inflammatory and immune regulatory pathways and secretion of IL-1β and IL-6, and further upregulated FABP4 and FABP5 compared to time-matched controls. The LSEC porosity and endocytic activity were reduced at 24 h both with and without dexamethasone but the dexamethasone-treated cells showed a less stressed phenotype.

Conclusion
Rat LSECs become activated towards a pro-inflammatory phenotype during early culture. Dexamethasone represses LSEC activation, inhibits apoptosis, and improves cell viability.
Familial hypercholesterolaemia and coronary risk factors among patients with angiogram-proven premature coronary artery disease in an Asian cohort
Authors: Nazli Sukma Azureen , Chua Yung-An , Mohd Kasim Noor Alicezah , Ismail Zaliha , Md Radzi Ahmad Bakhtiar , Ibrahim Khairul Shafiq , Kasim Sazzli Shahlan , Rosman Azhari , Nawawi Hapizah 
Published: September 2022

Background
Familial hypercholesterolaemia (FH) patients have elevated levels of low-density lipoprotein cholesterol, rendering them at high risk of premature coronary artery disease (PCAD). However, the FH prevalence among angiogram-proven PCAD (AP-PCAD) patients and their status of coronary risk factors (CRFs) have not been reported in the Asian population.

Objectives
This study aimed to (1) determine the prevalence of clinically diagnosed FH among AP-PCAD patients, (2) compare CRFs between AP-PCAD patients with control groups, and (3) identify the independent predictors of PCAD.

Methods
AP-PCAD patients and FH patients without PCAD were recruited from Cardiology and Specialist Lipid Clinics. Subjects were divided into AP-PCAD with FH (G1), AP-PCAD without FH (G2), FH without PCAD (G3) and normal controls (G4). Medical records were collected from the clinic database and standardised questionnaires. FH was clinically diagnosed using Dutch Lipid Clinic Network Criteria.

Results
A total of 572 subjects were recruited (males:86.4%; mean±SD age: 55.6±8.5years). The prevalence of Definite, Potential and All FH among AP-PCAD patients were 6%(19/319), 16% (51/319) and 45.5% (145/319) respectively. G1 had higher central obesity, family history of PCAD and family history of hypercholesterolaemia compared to other groups. Among all subjects, diabetes [OR(95% CI): 4.7(2.9,7.7)], hypertension [OR(95% CI): 14.1(7.8,25.6)], FH [OR(95% CI): 2.9(1.5,5.5)] and Potential (Definite and Probable) FH [OR(95% CI): 4.5(2.1,9.6)] were independent predictors for PCAD. Among FH patients, family history of PCAD [OR(95% CI): 3.0(1.4,6.3)] and Definite FH [OR(95% CI): 7.1(1.9,27.4)] were independent predictors for PCAD.

Conclusion
Potential FH is common among AP-PCAD patients and contributes greatly to the AP-PCAD. FH-PCAD subjects have greater proportions of various risk factors compared to other groups. Presence of FH, diabetes, hypertension, obesity and family history of PCAD are independent predictors of PCAD. FH with PCAD is in very-high-risk category, hence, early management of modifiable CRFs in these patients are warranted.
HUBUNGAN ANTARA SIBLING RIVALRY DENGAN PENYESUAIAN SOSIAL PADA SISWA KELAS X DI SMA NEGERI 3 CILACAP
Authors: Dewi Zelmaiddha Edmirani , Fauziah Nailul 
Published: September 2022

Remaja memiliki tugas perkembangan yang harus diselesaikan dengan baik agar tugas perkembangan selanjutnya tidak terganggu. Remaja yang memasuki dunia SMA memiliki lingkungan baru sehingga dibutuhkannya kemampuan penyesuaian social pada diri mereka. Penelitian ini bertujuan untuk mengetahui hubungan antara sibling rivalry dengan penyesuaian sosial pada siswa kelas X SMA Negeri 3 Cilacap. Sibling rivalry merupakan sikap individu berupa kecemburuan, persaingan, dan perasaan marah terhadap saudara kandung. Penyesuaian sosial ialah kemampuan individu dalam menyesuaian diri dan bereaksi efektif terhadap lingkungan sekitar. Populasi penelitian ini adalah siswa kelas X SMA Negeri 3 Cilacap sejumlah 360 siswa. Sampel penelitian ini terdiri dari 187 siswa yang diperoleh dengan metode cluster random sampling. Metode pengambilan data menggunakan dua alat ukur yaitu skala sibling rivalry (18 aitem, α= 0,851) dan skala penyesuaian sosial (21 aitem, α= 0,854). Hasil pengolahan data menggunakan uji non parametric rank spearman diperoleh rxy= -0,529 dengan nilai p = 0,000 (p < 0,05). Hasil penelitian ini menunjukan bahwa terdapat hubungan negative antara sibling rivalry dengan penyesuaian sosial. Semakin tinggi sibling rivalry maka akan semakin rendah penyesuaian sosial dan sebaliknya.