bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing genomic diversity and signatures of selection in Jiaxian Red cattle using whole-genome sequencing data
Authors: Xia Xiaoting , Zhang Shunjin , Zhang Huaju , Zhang Zijing , Chen Ningbo , Li Zhigang , Sun Hongxia , Liu Xian , Lyu Shijie , Wang Xianwei , Li Zhiming , Yang Peng , Xu Jiawei , Ding Xiaoting , Shi Qiaoting , Wang Eryao , Ru Baorui , Xu Zejun , Lei Chuzhao , Chen Hong , Huang Yongzhen 
Published: January 2021

Abstract
Background
Native cattle breeds are an important source of genetic variation because they might carry alleles that enable them to adapt to local environment and tough feeding conditions. Jiaxian Red, a Chinese native cattle breed, is reported to have originated from crossbreeding between taurine and indicine cattle; their history as a draft and meat animal dates back at least 30 years. Using whole-genome sequencing (WGS) data of 30 animals from the core breeding farm, we investigated the genetic diversity, population structure and genomic regions under selection of Jiaxian Red cattle. Furthermore, we used 131 published genomes of world-wide cattle to characterize the genomic variation of Jiaxian Red cattle.

Results
The population structure analysis revealed that Jiaxian Red cattle harboured the ancestry with East Asian taurine (0.493), Chinese indicine (0.379), European taurine (0.095) and Indian indicine (0.033). Three methods (nucleotide diversity, linkage disequilibrium decay and runs of homozygosity) implied the relatively high genomic diversity in Jiaxian Red cattle. We used θπ, CLR, FST and XP-EHH methods to look for the candidate signatures of positive selection in Jiaxian Red cattle. A total number of 171 (θπ and CLR) and 17 (FST and XP-EHH) shared genes were identified using different detection strategies. Functional annotation analysis revealed that these genes are potentially responsible for growth and feed efficiency (CCSER1), meat quality traits (ROCK2, PPP1R12A, CYB5R4, EYA3, PHACTR1), fertility (RFX4, SRD5A2) and immune system response (SLAMF1, CD84 and SLAMF6).

Conclusion
We provide a comprehensive overview of sequence variations in Jiaxian Red cattle genomes. Selection signatures were detected in genomic regions that are possibly related to economically important traits in Jiaxian Red cattle. We observed a high level of genomic diversity and low inbreeding in Jiaxian Red cattle. These results provide a basis for further resource protection and breeding improvement of this breed.
Interaction study of Pasteurella multocida with culturable aerobic bacteria isolated from porcine respiratory tracts using coculture in conditioned media
Authors: Hanchanachai Nonzee , Chumnanpuen Pramote , E-kobon Teerasak 
Published: January 2021

Abstract
Background
The porcine respiratory tract harbours multiple microorganisms, and the interactions between these organisms could be associated with animal health status. Pasteurella multocida is a culturable facultative anaerobic bacterium isolated from healthy and diseased porcine respiratory tracts. The interaction between P. multocida and other aerobic commensal bacteria in the porcine respiratory tract is not well understood. This study aimed to determine the interactions between porcine P. multocida capsular serotype A and D strains and other culturable aerobic bacteria isolated from porcine respiratory tracts using a coculture assay in conditioned media followed by calculation of the growth rates and interaction parameters.

Results
One hundred and sixteen bacterial samples were isolated from five porcine respiratory tracts, and 93 isolates were identified and phylogenetically classified into fourteen genera based on 16S rRNA sequences. Thirteen isolates from Gram-negative bacterial genera and two isolates from the Gram-positive bacterial genus were selected for coculture with P. multocida. From 17 × 17 (289) interaction pairs, the majority of 220 pairs had negative interactions indicating competition for nutrients and space, while 17 pairs were identified as mild cooperative or positive interactions indicating their coexistence. All conditioned media, except those of Acinetobacter, could inhibit P. multocida growth. Conversely, the conditioned media of P. multocida also inhibited the growth of nine isolates plus themselves.

Conclusion
Negative interaction was the major interactions among the coculture of these 15 representative isolates and the coculture with P. multocida. The conditioned media in this study might be further analysed to identify critical molecules and examined by the in vivo experiments. The study proposed the possibility of using these molecules in conditioned media to control P. multocida growth.
Survey of perceptions and educational needs of primary care providers regarding management of patients with class II and III obesity in Ontario, Canada
Authors: Zevin Boris , Martin Mary , Dalgarno Nancy , Chan Linda , Sivapalan Nardhana , Houlden Robyn , Birtwhistle Richard , Smith Karen , Barber David 
Published: January 2021

AbstractBackgroundPrimary care providers (PCPs) are typically the primary contact for patients with obesity seeking medical and surgical weight loss interventions; however, previous studies suggest that fewer than 7% of eligible adult patients are referred to publically funded medical and surgical weight loss interventions (MSWLI).MethodsWe performed an anonymous survey study between October 2017 and June 2018 to explore the knowledge, experiences, perceptions, and educational needs of PCPs in Southeastern Ontario in managing patients with class II and III obesity.ResultsSurveys were distributed to 591 PCPs (n = 538 family physicians;n = 53 nurse practitioners) identified as practicing in the Southeastern Ontario and 92 (15.6%) participated. PCPs serving a rural population estimated that 14.2 ± 10.9% of patients would qualify for MSWLI compared to 9.9 ± 8.5% of patients of PCPs serving an urban population (p = .049). Overall, 57.5% of respondents did not feel competent prescribing MSWLI to patients with class II/III obesity, while 69.8% stated they had ‘good’ knowledge of the referral criteria for MSWLI. 22.2% of respondents were hesitant to refer patients for bariatric surgery (BS) due to concerns about postoperative surgical complications and risks associated with surgery. Only 25% of respondents were comfortable providing long-term follow up after BS, and only 39.1% had participated in continuing education on management of patients with class II/III obesity in the past 5 years.ConclusionThe majority of PCPs believe there is a need for additional education about MSWLI for patients with class II/III obesity. Future studies are needed to develop and compare the effectiveness of additional education and professional development around risks of contemporary BS, indications to consider referral for MSWLI, management and long-term follow-up of patients after BS.
Design characteristics and inclusion of evidence-based exercise recommendation in fall prevention community exercise programs for older adults in Canada: a national descriptive self-report study
Authors: Touchette Alexie J. , Oates Alison R. , Menec Verena H. , Sibley Kathryn M. 
Published: January 2021

Abstract
Background
Training balance through exercise is an effective strategy to reduce falls in community-dwelling older adults. Evidence-based fall prevention exercise recommendations have been proposed, specifying that exercise programs should: (1) provide a high challenge to balance, (2) be offered for a least three hours per week, (3) be provided on an ongoing basis. Community exercise programs have the potential to deliver effective fall prevention exercise; however, current design characteristics and whether they include the recommendations is not known. This study described design characteristics of fall prevention community exercise programs for older adults (50 years and older) across Canada, and explored whether these programs included the three evidence-based exercise recommendations.

Methods
Instructors of fall prevention community exercise programs completed electronic self-report questionnaires following a modified Dillman recruitment approach. Questions explored program characteristics, exercise content, target population, and program and instructor demographic information. Using a previously developed coding scheme based on recommendations, exercises were coded for balance challenge.

Results
One hundred fourty completed eligible questionnaires were analyzed (74% response rate). One hundred thirty-three programs (95%) included the challenge recommendation by prescribing mostly moderate or high challenge balance exercises, 16 programs (11%) included at least three hours of exercise a week, and 59 programs (42%) were offered on an ongoing basis. Eight programs (6%) included all three recommendations.

Conclusions
Most programs included at least one recommendation for effective fall prevention exercise. Future studies should examine organizational barriers and facilitators to incorporating evidence-based exercise recommendations and explore the use of mixed home/in-class strategies to include the recommendations.
Do cognitive performance and physical function differ between individuals with motoric cognitive risk syndrome and those with mild cognitive impairment?
Authors: Cheng Fang-Yu , Chang Yuanmay , Cheng Shih-Jung , Shaw Jin-Siang , Lee Chuo-Yu , Chen Pei-Hao 
Published: January 2021

Abstract
Background
Motoric cognitive risk syndrome (MCR) is defined by slow gait speed combined with subjective cognitive complaint. MCR is a predementia syndrome, similar to mild cognitive impairment (MCI). However, there is currently no study comparing the differences in cognitive performance and physical function between these two types of cognitive impairment. Thus, the aim of this study is to compare cognitive performance and physical function in individuals with MCR versus MCI.

Methods
A total of 77 participants, free of dementia, were recruited from the neurological outpatient clinic of a medical center in Taiwan. Participants were separated into 2 groups, MCR (n = 33) and MCI (n = 44) groups, based on definition criteria from previous studies. The priority was to assign a diagnosis of MCR first, followed by MCI. Hence, “pure” MCI had no overlap with MCR syndrome. Cognitive performance, including executive function, attention, working memory, episode memory, visuospatial function, and language, were measured. Physical functions such as activities in daily living, the Tinetti Assessment Scale, and the Timed Up and Go test were also measured.

Results
Executive function, attention, working memory, episodic memory and language were all significantly lower in the MCR group than the MCI group. Abilities related to physical function, including those measured by the Tinetti Assessment Scale and the Timed Up and Go test, were significantly lower in the MCR group than the MCI group.

Conclusions
We noted that cognitive performance and physical function were lower in MCR individuals than MCI but without MCR syndrome. However, the conclusions were based on the enrollment procedure of participants prioritizes the MCR syndrome. Because of the overlap of MCR and MCI, future studies should use different enrollment strategies to further clarify the status of these two populations.
The effective screening tools for detecting hearing loss in elderly population: HHIE-ST Versus TSQ
Authors: Chayaopas Nichtima , Kasemsiri Pornthep , Thanawirattananit Panida , Piromchai Patorn , Yimtae Kwanchanok 
Published: January 2021

Abstract
Background
Globally increasing number of elders is concerned. Hearing loss process in older adults cannot be avoided. An effective screening tool for hearing loss is essential for proper diagnosis and rehabilitation, which can improve QOL in older adults.

Methods
This prospective-diagnostic test study evaluates the diagnostic value of Thai version of the Hearing Handicap Inventory for Elderly Screening (HHIE-ST) and the Thai Single Question (TSQ) surveys in screening hearing disability in 1109 Thai participants aged 60 years and older in communities in four provinces in Thailand. The HHIE-ST consisted of 10 selected questions from the validated HHIE-Thai version. A TSQ survey was developed to have the same meaning as an English Single Question survey. The participants answered both questionnaires, and a standard audiometry test assessed with air conduction from 250 to 8000 Hz was included as a gold standard.

Results
The prevalence of hearing disability was 38.34%. The HHIE-ST achieved a sensitivity of 88.96% (95% CI 85.77–91.64) and specificity of 52.19% (95% CI 48.24–56.13) for diagnosis hearing disability in Thai older adults, whereas the TSQ yielded a sensitivity of 88.73% and a specificity of 55.93%. A combined test including the HHIE-ST and TSQ achieved better performance with sensitivity of 85.29% and specificity of 60.13%.

Conclusions
Either the HHIE-ST or the TSQ is a sensitive and useful tool for screening hearing disability in Thai older adults. Using the HHIE-ST together with the TSQ resulted in a better screening tool for detecting moderate hearing loss older adults who will benefit and recommended for hearing rehabilitation.

Trial registration
The study is registered with the following number in the Thai Clinical Trials Registry: TCTR20151015003. Date of registration October 14, 2015.
Increased investment in gametocytes in asymptomatic Plasmodium falciparum infections in the wet season
Authors: Oduma Colins O. , Ogolla Sidney , Atieli Harrysone , Ondigo Bartholomew N. , Lee Ming-Chieh , Githeko Andrew K. , Dent Arlene E. , Kazura James W. , Yan Guiyun , Koepfli Cristian 
Published: January 2021

Abstract
Background
Transmission stemming from asymptomatic infections is increasingly being recognized as a threat to malaria elimination. In many regions, malaria transmission is seasonal. It is not well understood whether Plasmodium falciparum modulates its investment in transmission to coincide with seasonal vector abundance.

Methods
We sampled 1116 asymptomatic individuals in the wet season, when vectors are abundant, and 1743 in the dry season, in two sites in western Kenya, representing different transmission intensities (Chulaimbo, moderate transmission, and Homa Bay, low transmission). Blood samples were screened for P. falciparum by qPCR, and gametocytes by pfs25 RT-qPCR.

Results
Parasite prevalence by qPCR was 27.1% (Chulaimbo, dry), 48.2% (Chulaimbo, wet), 9.4% (Homabay, dry), and 7.8% (Homabay, wet). Mean parasite densities did not differ between seasons (P = 0.562). pfs25 transcripts were detected in 119/456 (26.1%) of infections. In the wet season, fewer infections harbored detectable gametocytes (22.3% vs. 33.8%, P = 0.009), but densities were 3-fold higher (wet: 3.46 transcripts/uL, dry: 1.05 transcripts/uL, P < 0.001). In the dry season, 4.0% of infections carried gametocytes at moderate-to-high densities likely infective (> 1 gametocyte per 2 uL blood), compared to 7.9% in the wet season. Children aged 5–15 years harbored 76.7% of infections with gametocytes at moderate-to-high densities.

Conclusions
Parasites increase their investment in transmission in the wet season, reflected by higher gametocyte densities. Despite increased gametocyte densities, parasite density remained similar across seasons and were often below the limit of detection of microscopy or rapid diagnostic test, thus a large proportion of infective infections would escape population screening in the wet season. Seasonal changes of gametocytemia in asymptomatic infections need to be considered when designing malaria control measures.
Relationship of socio-demographics, comorbidities, symptoms and healthcare access with early COVID-19 presentation and disease severity
Authors: Vaughan Laura , Veruttipong Darlene , Shaw Jonathan G. , Levy Noemie , Edwards Lauren , Winget Marcy 
Published: January 2021

Abstract
Background
COVID-19 studies are primarily from the inpatient setting, skewing towards severe disease. Race and comorbidities predict hospitalization, however, ambulatory presentation of milder COVID-19 disease and characteristics associated with progression to severe disease is not well-understood.

Methods
We conducted a retrospective chart review including all COVID-19 positive cases from Stanford Health Care (SHC) in March 2020 to assess demographics, comorbidities and symptoms in relationship to: 1) their access point of testing (outpatient, inpatient, and emergency room (ER)) and 2) development of severe disease.

Results
Two hundred fifty-seven patients tested positive: 127 (49%), 96 (37%), and 34 (13%) at outpatient, ER and inpatient, respectively. Overall, 61% were age < 55; age > 75 was rarer in outpatient setting (11%) than ER (14%) or inpatient (24%). Most patients presented with cough (86%), fever/chills (76%), or fatigue (63%). 65% of inpatients reported shortness of breath compared to 30–32% of outpatients and ER patients. Ethnic/minority patients had a significantly higher risk of developing severe disease (Asian OR = 4.8 [1.6–14.2], Hispanic OR = 3.6 [1.1–11.9]). Medicare-insured patients were marginally more likely (OR = 4.0 [0.9–17.8]). Other factors associated with developing severe disease included kidney disease (OR = 6.1 [1.0–38.1]), cardiovascular disease (OR = 4.7 [1.0–22.1], shortness of breath (OR = 5.4 [2.3–12.6]) and GI symptoms (OR = 3.3 [1.4–7.7]; hypertension without concomitant CVD or kidney disease was marginally significant (OR = 2.3 [0.8–6.5]).

Conclusions
Early widespread symptomatic testing for COVID-19 in Silicon Valley included many less severely ill patients. Thorough manual review of symptomatology reconfirms the heterogeneity of COVID-19 symptoms, and challenges in using clinical characteristics to predict decline. We re-demonstrate that socio-demographics are consistently associated with severity.
LncRNA LINC00240 suppresses invasion and migration in non-small cell lung cancer by sponging miR-7-5p
Authors: Ku Gwan Woo , Kang Yujin , Yu Seong-Lan , Park Joonghoon , Park Sejin , Jeong In Beom , Kang Min Woong , Son Ji Woong , Kang Jaeku 
Published: January 2021

Abstract
Background
lncRNAs have important roles in regulating cancer biology. Accumulating evidence has established a link between the dysregulation of lncRNAs and microRNA in cancer progression. In previous studies, miR-7-5p has been found to be significantly down-regulated in mesenchymal-like lung cancer cell lines and directly regulated EGFR. In this work, we investigated the lncRNA partner of miR-7-5p in the progression of lung cancer.

Methods
We investigated the expression of miR-7-5p and the lncRNA after transfection with an miR-7-5p mimics using a microarray. The microarray results were validated using quantitative real time-polymerase Chain Reaction (qRT-PCR). The regulatory effects of lncRNA on miR-7-5p and its target were evaluated by changes in the expression of miR-7-5p after transfection with siRNAs for lncRNA and the synthesis of full-length lncRNA. The effect of miR-7-5p on lncRNA and the miRNA target was evaluated after transfection with miRNA mimic and inhibitor. The role of lncRNA in cancer progression was determined using invasion and migration assays. The level of lncRNA and EGFR in lung cancer and normal lung tissue was analyzed using TCGA data.

Results
We found that LINC00240 was downregulated in lung cancer cell line after miR-7-5p transfection with an miR-7-5p mimic. Further investigations revealed that the knockdown of LINC00240 induced the overexpression of miR-7-5p. The overexpression of miR-7-5p diminished cancer invasion and migration. The EGFR expression was down regulated after siRNA treatment for LINC00240. Silencing LINC00240 suppressed the invasion and migration of lung cancer cells, whereas LINC00240 overexpression exerted the opposite effect. The lower expression of LINC00240 in squamous lung cancer was analyzed using TCGA data.

Conclusions
Taken together, LINC00240 acted as a sponge for miR-7-5p and induced the overexpression of EGFR. LINC00240 may represent a potential target for the treatment of lung cancer.
The impact of ICAM-1, CCL2 and TGM2 gene polymorphisms on differentiation syndrome in acute promyelocytic leukemia
Authors: Mohammadzadeh Zahra , Omidkhoda Azadeh , Chahardouli Bahram , Hoseinzadeh Ghazaleh , Moghaddam Kamran Ali , Mousavi Seyed Asadollah , Rostami Shahrbano 
Published: January 2021

Abstract
Background
Although arsenic trioxide (ATO) and all-trans retinoic acid (ATRA) are well-tolerated and effective treatments for Acute Promyelocytic Leukemia (APL), Differentiation Syndrome (DS) is a lethal side effect in some patients. The pathogenesis of DS is complex and not well understood; however, it is considered as an inflammatory response due to cytokines release of differentiated cells. Moreover, adhesion molecules that are widely expressed on the surface of differentiated cells and gene expression changes of transglutaminase2 (TGM2) are mechanisms involved in the development of DS. The purpose of this study was to assess the association of single nucleotide polymorphisms (SNP) of Intercellular Adhesion Molecule-1 (ICAM-1), chemokine (C-C motif) ligand 2 (CCL2) and TGM2 as inflammatory factors with differentiation syndrome susceptibility.

Methods
DNA was extracted from 133 APL patients and 100 normal controls. Assessment according to the PETHEMA criteria revealed that 13.5% of these patients experienced differentiation syndrome. Tetra-ARMS PCR and PCR-RFLP were done to amplify DNA fragments in APL patients with and without DS. Then DNA sequencing was done to validate the results. SNPStats, SPSS and Finch TV were used to analyze the results.

Results
A significant correlation was found between rs4811528 in the TGM2 gene and differentiation syndrome susceptibility (P = 0.002, 95% CI = 1.74–18.81, OR = 5.72) while rs5498 in ICAM-1, rs1024611 in CCL2, and rs7270785 in TGM2 genes showed no correlation with differentiation syndrome. The G allele of rs7270785 and rs4811528 showed a haplotypic association with differentiation syndrome (P = 0.03, 95% CI = 1.13–13.86, OR = 3.96).

Conclusions
AA genotype of the TGM2 SNP (rs4811528) may be a risk factor for development of DS in patients with APL following the use of ATRA/ATO.
Optic neuritis of MOG-IgG-associated autoimmune disorders: a case report
Authors: Li Tiantian , Zhou Jian , Yan Xiaoling , Duan Ran , Zhu Xiaobo 
Published: January 2021

Abstract
Background
The diagnosis of immunoglobulin G serum antibodies to myelin oligodendrocyte glycoprotein (MOG-IgG) associated inflammatory demyelinating disorders can be confirmed by the presence of MOG-IgG, yet its general cut-off concentration had not yet to be defined. Whether it is significant that a seropositive lower titer level for MOG-IgG could cause disease is still unknown.

Case presentation
A 55-year-old Chinese woman presented with acute optic neuritis manifestations in the left eye. MRI showed a left optic nerve demyelination image and a T2 hyperintensity at C7 vertebral segment without any extra specific lesions. AQP4-IgG was tested seronegative, while the MOG-IgG was positive, titer 1:10, by indirect immunofluorescence. Considering the lower concentration, we retested serum MOG-IgG after 6 months of steroid therapy, using cell-based assay, then we still got the same result which was also barely above the negative cut-off value. So, the clinical diagnose was “possible MOG-IgG-associated encephalomyelitis”. The woman’s condition improved by steroid therapy without relapse.

Conclusions
Seropositive MOG-IgG, even at a lower level, could lead to an autoimmune inflammatory demyelination. In adults, it commonly presents as ON and myelitis. Although the patient had a considerable reaction, steroid therapy could not make MOG-IgG seronegative, instead, the antibody may persist even during remission and flare-ups can recur after steroid withdrawal. Therefore, a long-term follow-up is necessary to monitor the patient’s prognosis.