bluuebunny/crossref_metadata_2025_split huggingface dataset:
Insertion variants missing in the human reference genome are widespread among human populations
Authors: Lee Young-gun , Lee Jin-young , Kim Junhyong , Kim Young-Joon 
Published: November 2020

Abstract
Background
Structural variants comprise diverse genomic arrangements including deletions, insertions, inversions, and translocations, which can generally be detected in humans through sequence comparison to the reference genome. Among structural variants, insertions are the least frequently identified variants, mainly due to ascertainment bias in the reference genome, lack of previous sequence knowledge, and low complexity of typical insertion sequences. Though recent developments in long-read sequencing deliver promise in annotating individual non-reference insertions, population-level catalogues on non-reference insertion variants have not been identified and the possible functional roles of these hidden variants remain elusive.

Results
To detect non-reference insertion variants, we developed a pipeline, InserTag, which generates non-reference contigs by local de novo assembly and then infers the full-sequence of insertion variants by tracing contigs from non-human primates and other human genome assemblies. Application of the pipeline to data from 2535 individuals of the 1000 Genomes Project helped identify 1696 non-reference insertion variants and re-classify the variants as retention of ancestral sequences or novel sequence insertions based on the ancestral state. Genotyping of the variants showed that individuals had, on average, 0.92-Mbp sequences missing from the reference genome, 92% of the variants were common (allele frequency > 5%) among human populations, and more than half of the variants were major alleles. Among human populations, African populations were the most divergent and had the most non-reference sequences, which was attributed to the greater prevalence of high-frequency insertion variants. The subsets of insertion variants were in high linkage disequilibrium with phenotype-associated SNPs and showed signals of recent continent-specific selection.

Conclusions
Non-reference insertion variants represent an important type of genetic variation in the human population, and our developed pipeline, InserTag, provides the frameworks for the detection and genotyping of non-reference sequences missing from human populations.
“We have a ticking time bomb”: a qualitative exploration of the impact of canine epilepsy on dog owners living in England
Authors: Pergande Amy E. , Belshaw Zoe , Volk Holger A. , Packer Rowena M. A. 
Published: November 2020

Abstract
Background
Idiopathic epilepsy is a common neurological condition in dogs. Previous research has focused on clinical aspects of seizure management in dogs with idiopathic epilepsy with little attention given to the emotional and logistical challenges for their owners. The current study aimed to explore the impacts of owning a dog with idiopathic epilepsy on owner quality of life and lifestyle, using qualitative methods.

Methods
Owners of dogs with idiopathic epilepsy living in England were recruited via social media and word of mouth, and then selected using purposive sampling to participate in face-to-face semi-structured interviews. Epilepsy management was explored through in-depth accounts of owner experiences and influencing factors. Interviews were recorded and transcribed verbatim and thematic analysis was used to construct key themes.

Results
Twenty-one interviews were completed. Almost all owners had made lifestyle changes in order to care for their dog, including substantial modifications to routines and, in some cases, employment. Many owners discussed a very emotionally close dog-owner bond, and described experiencing frequent feelings of fear, stress and uncertainty regarding their dog’s health. Friends, family and colleagues did not always understand the magnitude of commitment required to care for a dog with idiopathic epilepsy. This, combined with a fear of leaving their dog unsupervised, had social implications in some instances and lead to increased use of the Internet and online groups for peer support.

Conclusions
The commitment required to care for a dog with idiopathic epilepsy, and the lifestyle changes made by their owners, may be far greater than previously estimated. Further consideration of these factors by veterinary professionals and the friends and families of owners of dogs with idiopathic epilepsy could improve owner quality of life, and facilitate the provision of additional support.
Neighbourhood environment and depressive symptoms among the elderly in Hong Kong and Singapore
Authors: Lam Winnie W. Y. , Loo Becky P. Y. , Mahendran Rathi 
Published: November 2020

AbstractBackgroundGeriatric depression is a growing public health issue worldwide. This study aims at identifying the relevant neighbourhood attributes, separate from the individual-level characteristics, that are related to the onset of depressive disorders among the geriatric population.MethodsThis study adopts a structural equation modelling (SEM) approach to understand the effect of the neighbourhood environment on geriatric depression, as identified by data collected from community-dwelling elderly living in Hong Kong and Singapore. Using network buffers as the unit of analysis, different features of the neighbourhood environment are captured and analysed. SEM also examines the strength and direction of the relationships using different parameters at both the individual and neighbourhood levels, as well as the prevalence of depressive symptoms among the elderly.ResultsThe total sample size is 347, with 173 and 174 elderly people in Hong Kong and Singapore respectively. The results show that in addition to one’s physical health status, both objective and subjective neighbourhood factors including the size of parks, land use mix, walkability, and connectivity are all statistically significant influential factors in geriatric depression. In particular, enhancing walkability and providing more parks at the neighbourhood level can bring mental health benefits.ConclusionsPublic health policy initiatives aimed at tackling geriatric depression can be achieved by adopting a holistic and integrative approach to better prepare the neighbourhood environment in an ageing society.
Favorable short-term oncologic outcomes following laparoscopic surgery for small T4 colon cancer: a multicenter comparative study
Authors:   on behalf of the Seoul Colorectal Research Group (SECOG), Park Sung Sil , Lee Joon Sang , Park Hyoung-Chul , Park Sung Chan , Sohn Dae Kyung , Oh Jae Hwan , Han Kyung Su , Lee Dong-Won , Lee Dong-Eun , Kang Sung-Bum , Park Kyu Joo , Jeong Seung-Yong 
Published: November 2020

Abstract
Background
Laparoscopic surgery for T4 colon cancer may be safe in selected patients. We hypothesized that small tumor size might preoperatively predict a good laparoscopic surgery outcome. Herein, we compared the clinicopathologic and oncologic outcomes of laparoscopic and open surgery in small T4 colon cancer.

Methods
In a retrospective multicenter study, we reviewed the data of 449 patients, including 117 patients with tumors ≤ 4.0 cm who underwent surgery for T4 colon cancer between January 2014 and December 2017. We compared the clinicopathologic and 3-year oncologic outcomes between the laparoscopic and open groups. Survival curves were estimated using the Kaplan–Meier method and compared using the log-rank test. Univariate and multivariate analyses were performed using the Cox proportional hazards model. A p < 0.05 was considered statistically significant.

Results
Blood loss, length of hospital stay, and postoperative morbidity were lower in the laparoscopic group than in the open group (median [range], 50 [0–700] vs. 100 [0–4000] mL, p < 0.001; 8 vs. 10 days, p < 0.001; and 18.0 vs. 29.5%, p = 0.005, respectively). There were no intergroup differences in 3-year overall survival or disease-free survival (86.6 vs. 83.2%, p = 0.180, and 71.7 vs. 75.1%, p = 0.720, respectively). Among patients with tumor size ≤ 4.0 cm, blood loss was significantly lower in the laparoscopic group than in the open group (median [range], 50 [0–530] vs. 50 [0–1000] mL, p = 0.003). Despite no statistical difference observed in the 3-year overall survival rate (83.3 vs. 78.7%, p = 0.538), the laparoscopic group had a significantly higher 3-year disease-free survival rate (79.2 vs. 53.2%, p = 0.012).

Conclusions
Laparoscopic surgery showed similar outcomes to open surgery in T4 colon cancer patients and may have favorable short-term oncologic outcomes in patients with tumors ≤ 4.0 cm.
Ocular macrophage origin and heterogeneity during steady state and experimental choroidal neovascularization
Authors: Droho Steven , Thomson Benjamin R. , Makinde Hadijat M. , Cuda Carla M. , Perlman Harris , Lavine Jeremy A. 
Published: November 2020

Abstract
Background
Neovascular age-related macular degeneration (nAMD) commonly causes vision loss from aberrant angiogenesis, termed choroidal neovascularization (CNV). Macrophages are heterogeneous cells that are necessary for experimental CNV, present in human CNV samples, and can display diverse functions, which are dependent upon both their origin and tissue microenvironment. Despite these associations, choroidal macrophage heterogeneity remains unexplored.

Methods
We performed multi-parameter flow cytometry on wildtype (WT) and Ccr2−/− mice after laser injury to identify macrophage subtypes, and determine which subsets originate from classical monocytes. To fate map tissue resident macrophages at steady state and after laser injury, we used the Cx3cr1CreER/+ ; Rosa26zsGFP/+ mouse model. We reanalyzed previously published single-cell RNA-seq of human choroid samples from healthy and nAMD patients to investigate human macrophage heterogeneity, disease association, and function.

Results
We identified 4 macrophage subsets in mice: microglia, MHCII+CD11c−, MHCII+CD11c+, and MHCII−. Microglia are tissue resident macrophages at steady state and unaffected by laser injury. At steady state, MHCII− macrophages are long lived, tissue resident macrophages, while MHCII+CD11c− and MHCII+CD11c+ macrophages are partially replenished from blood monocytes. After laser injury, MHCII+CD11c− macrophages are entirely derived from classical monocytes, MHCII− macrophages originate from classical monocytes (90%) and an expansion of tissue resident macrophages (10%), and MHCII+CD11c+ macrophages are derived from classical monocytes (70%), non-classical monocytes (10%), and an expansion of tissue resident macrophages (20%). Single-cell RNA-seq analysis of human choroid found 5 macrophage subsets: two MHCII+CD11C− and three MHCII+CD11C+ populations. One MHCII+CD11C+ subset was 78% derived from a patient with nAMD. Differential expression analysis identified up-regulation of pro-angiogenic gene expression in one MHCII+CD11C− and two MHCII+CD11C+ subsets, including the disease-associated cluster. The upregulated MHCII+CD11C− pro-angiogenic genes were unique compared to the increased MHCII+CD11C+ angiogenesis genes.

Conclusions
Macrophage origin impacts heterogeneity at steady state and after laser injury in mice. Both mice and human patients demonstrate similar macrophage subtypes. Two discrete pro-angiogenic macrophage populations exist in the human choroid. Targeting specific, pro-angiogenic macrophage subsets is a potential novel therapeutic for nAMD.
A clinical study of curative partial breast irradiation for stage I breast cancer using carbon ion radiotherapy
Authors: Karasawa Kumiko , Omatsu Tokuhiko , Shiba Shintaro , Irie Daisuke , Wakatsuki Masaru , Fukuda Shigekazu 
Published: November 2020

Abstract
Background and purpose
Our institute initiated carbon ion radiotherapy research for patients with stage I breast cancer in April 2013. The purpose of this article is to evaluate the treatment outcome of cases treated outside clinical trial up to May 2020.

Materials and methods
Eligibility criteria of the patients were having untreated stage I breast cancer and being unsuitable for operation for physical or mental reasons. The irradiated volume was defined as the gross tumor including intraductal components. The dose escalation study was initially conducted four times a week for a total of 52.8 Gy [relative biological efficacy (RBE)]. After confirming that adverse effects were within acceptable range, the total dose was increased to 60.0 Gy (RBE).

Results
Between April 2013 and November 2015, 14 cases were treated. The median follow up period was 61 months. No adverse toxicities were observed except for grade 1 acute skin reaction in 10 cases. The time required from carbonion radiotherapy to tumor disappearance was 3 months in 1 case, 6 months in 3 cases, 12 months in 4 cases, and 24 months in 5 cases. The third case developed local recurrence 6 months after radiotherapy. Twelve patients with luminal subtype received 5-year endocrine therapy. Thirteen of 14 tumors have been maintaining complete response with excellent cosmetic results.

Conclusions
The time from carbon ion radiotherapy to tumor disappearance was longer than expected, but complete tumor disappearance was observed except for one high-grade case. With careful patient selection, carbonion radiotherapy in patients with stage I breast cancer is deemed effective and safe, and further research is recommended.
Touchscreen-based location discrimination and paired associate learning tasks detect cognitive impairment at an early stage in an App knock-in mouse model of Alzheimer’s disease
Authors: Saifullah Md. Ali Bin , Komine Okiru , Dong Yutao , Fukumoto Kazuya , Sobue Akira , Endo Fumito , Saito Takashi , Saido Takaomi C. , Yamanaka Koji , Mizoguchi Hiroyuki 
Published: November 2020

AbstractAlzheimer's disease (AD) is a progressive neurodegenerative disorder characterized by cognitive decline with accumulation of amyloid beta (Aβ) and neurofibrillary tangles that usually begins 15–30 years before clinical diagnosis. Rodent models that recapitulate aggressive Aβ and/or the pathology of neurofibrillary tangles are essential for AD research. Accordingly, non-invasive early detection systems in these animal models are required to evaluate the phenotypic changes, elucidate the mechanism of disease progression, and facilitate development of novel therapeutic approaches. Although many behavioral tests efficiently reveal cognitive impairments at the later stage of the disease in AD models, it has been challenging to detect such impairments at the early stage. To address this issue, we subjected 4–6-month-old male AppNL−G−F/NL−G−F knock-in (App-KI) mice to touchscreen-based location discrimination (LD), different object–location paired-associate learning (dPAL), and reversal learning tests, and compared the results with those of the classical Morris water maze test. These tests are mainly dependent on the brain regions prone to Aβ accumulation at the earliest stages of the disease. At 4–6 months, considered to represent the early stage of disease when mice exhibit initial deposition of Aβ and slight gliosis, the classical Morris water maze test revealed no difference between groups, whereas touchscreen-based LD and dPAL tasks revealed significant impairments in task performance. Our report is the first to confirm that a systematic touchscreen-based behavioral test battery can sensitively detect the early stage of cognitive decline in an AD-linked App-KI mouse model. This system could be applied in future translational research.
New insights in gene expression alteration as effect of doxorubicin drug resistance in triple negative breast cancer cells
Authors: Ciocan-Cartita Cristina Alexandra , Jurj Ancuta , Zanoaga Oana , Cojocneanu Roxana , Pop Laura-Ancuta , Moldovan Alin , Moldovan Cristian , Zimta Alina Andreea , Raduly Lajos , Pop-Bica Cecilia , Buse Mihail , Budisan Liviuta , Virag Piroska , Irimie Alexandru , Gomes Dias Sandra Martha , Berindan-Neagoe Ioana , Braicu Cornelia 
Published: November 2020

Abstract
Background
Triple negative breast cancer (TNBC) is a heterogeneous disease with aggressive behavior and an unfavorable prognosis rate. Due to the lack of surface receptors, TNBC must be intensely investigated in order to establish a suitable treatment for patients with this pathology. Chemoresistance is an important reason for therapeutic failure in TNBC.

Method
The aim of this study was to investigate the effect of doxorubicin in TNBC cell lines and to highlight cellular and molecular alterations after a long exposure to doxorubicin.

Results
The results revealed that doxorubicin significantly increased the half maximal inhibitory concentration (IC50) values at P12 and P24 compared to parenteral cells P0. Modifications in gene expression were investigated through microarray technique, and for detection of mutational pattern was used Next Generation Sequencing (NGS). 196 upregulated and 115 downregulated genes were observed as effect of multiple dose exposure, and 15 overexpressed genes were found to be involved in drug resistance. Also, the presence of some additional mutations in both cell lines was observed.

Conclusion
The outcomes of this research may provide novel biomarkers for drug resistance in TNBC. Also, this activity can highlight the potential mechanisms associated with drug resistance, as well as the potential therapies to counteract these mechanisms.
Targeting HMGB3/hTERT axis for radioresistance in cervical cancer
Authors: Li Zongjuan , Zhang Yang , Sui Silei , Hua Yijun , Zhao Anshi , Tian Xiaoyuan , Wang Ruonan , Guo Wei , Yu Wendan , Zou Kun , Deng Wuguo , He Liru , Zou Lijuan 
Published: November 2020

Abstract
Background
Radiotherapy is regarded as a milestone for the cure of cervical cancer. However, clinical outcome heavily be hindered by radioresistance. So, exploring the underlying mechanism of radioresistance, and find potential target, well deserve fully emphasis.

Methods
In this study, we developed two novel radiation resistance cervical cancer cell lines, which could mimic clinical radioresistance. In order to find new potential targets, RNA-Seq, database analysis, streptavidin-agarose and LC/MS were used. Pull-down, luciferase and rescue assays were conducted to explore the regulatory mechanisms. To further evaluate the correlation between therapeutic responses and HMGB3/hTERT expression, 172 cervical cancer patients were recruited.

Results
Knockdown of HMGB3 significantly inhibit the DNA damage repair and induced more γH2AX foci, leading to enhanced chemo- and radio-sensitivity in vitro and in vivo, whereas HMGB3 overexpression has the opposite effects. HMGB3 promotes cell growth and radioresistance by transcriptionally up-regulating hTERT via the specifical binding of HMGB3 at the hTERT promoter region from − 902 to − 321. HMGB3 knockdown-mediated radiosensitization could be reversed by the overexpressed hTERT in both cervical cancer cell lines and xenograft tumor mouse model. Furthermore, clinical data from 172 cervical cancer patients proved that there was a positive correlation between HMGB3 and hTERT expression, and high expression of HMGB3/hTERT predicted poor response to radiotherapy, worse TNM stages and shorter survival time.

Conclusion
Here, we have identified HMGB3/hTERT signaling axis as a new target for cervical cancer radioresistance. Our results provide new insights into the mechanism of cervical cancer radioresistance and indicate that targeting the HMGB3/hTERT signaling axis may benefit cervical cancer patients.
PD-L1 correlates with chemokines and cytokines in gingival crevicular fluid from healthy and diseased sites in subjects with periodontitis
Authors: Shelby Andrew , Pendleton Chandler , Thayer Emma , Johnson Georgia K. , Xie Xian Jin , Brogden Kim A. 
Published: November 2020

AbstractObjectivePD-L1 is an immune checkpoint molecule that regulates immune and inflammatory responses. While cells of periodontal tissues express PD-L1, its presence in GCF is not known. The purpose of this study was to measure the PD-L1 values in GCF and correlate values with the presence of chemokine and cytokine values from periodontally diseased subjects and periodontally healthy subjects.ResultsPD-L1 values (pg/30 s), determined in triplicate using a fluorescent microparticle-based immunoassay ranged from 0.04–31.65 pg/30 s. PD-L1 correlated with 15 out of 22 chemokine and cytokine responses. In 85 healthy sites in 31 subjects, PD-L1 values were negatively correlated with IL6, CXCL8, IL10, and CCL3 values. In 53 diseased sites in 20 subjects, PD-L1 values were positively correlated with CCL11, CSF2, IFNG, IL1A, IL1B, IL2, IL7, IL15, and CCL5 values and negatively correlated with IL12A and IL5 values. Gene ontology (GO) annotations identified roles of PD-L1 in Th1 and Th2 activation and T-cell exhaustion signaling canonical pathways. PD-L1 values were correlated with the expression of chemokines and cytokines, which likely regulates immune cell trafficking and protects the periodontium from uncontrolled immune responses to pathogens and inflammation-induced tissue damage.
Entrepreneurial intent among prospective graduates of higher education institution: an exploratory investigation in Kafa, Sheka, and Bench-Maji Zones, SNNPR, Ethiopia
Authors: Issa Edomgenet Hiba , Tesfaye Zerebruk Zewdu 
Published: November 2020

AbstractThe purpose of this paper is to present results of an exploratory study conducted on entrepreneurial intent among graduating class students of higher education institutions in Kafa, Sheka, and Bench-Maji Zones, Southern Nation Nationalities Peoples’ Region (SNNPR), Ethiopia. The research design of the study was a cross-sectional survey design where relevant data were collected through questionnaires from a sample of 347 University and Technical and Vocational Education and Training (TVET) College graduating class students. The data were analyzed using both descriptive statistics (bar graph and pie chart) and inferential statistics (chi-square goodness-of-fit test, independent samplesttest, and one-way between-group analysis of variance). The study found out that among prospective graduates of higher education institutions in the study area, only 45.4–50.6% had low, 24–33.7% had moderate, and 18–25% had a high level of entrepreneurial intent. The study also showed that the level of higher education, prior experience of self-employment, and the chance of taking extracurricular entrepreneurship courses were the three demographic and other distal variables that explained the difference in entrepreneurial intent among the study population. The study, however, showed gender, the chance of taking entrepreneurship courses as part of curriculum, college, department, parent’s occupation, and level of education had no statistically significant association with entrepreneurial intent of the study population. The study is expected to hold relevant inputs to politicians and national policy-makers, the Ministry of Science and Higher Education, entrepreneurial intent researchers, and model developers.
Supervising third-party control bodies for certification: the case of organic farming in Italy
Authors: Zezza Annalisa , Demaria Federica , Laureti Tiziana , Secondi Luca 
Published: November 2020

AbstractThe organic food certification system in Italy, based on the EU legislation, relies on private control bodies (CBs) that are supervised by national authorities. The aim of this paper is to investigate whether it is possible to test for differences in controls outcome based on CBs’ behavior. To this extent, we use a multinomial logit model estimated on data corresponding to the results of the inspections in the year 2015 in Italy. The model controls for two fixed effects represented by the type of operator and a contextual variable, i.e., the region where a firm is located. Significant variability in CBs behavior could induce adverse selection in the choice of the CB by organic operators. In this vein, we discuss some implications in terms of policies and consequences for supervision in the conclusions.