bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conifer: clonal tree inference for tumor heterogeneity with single-cell and bulk sequencing data
Authors: Baghaarabani Leila , Goliaei Sama , Foroughmand-Araabi Mohammad-Hadi , Shariatpanahi Seyed Peyman , Goliaei Bahram 
Published: August 2021

Abstract
Background
Genetic heterogeneity of a cancer tumor that develops during clonal evolution is one of the reasons for cancer treatment failure, by increasing the chance of drug resistance. Clones are cell populations with different genotypes, resulting from differences in somatic mutations that occur and accumulate during cancer development. An appropriate approach for identifying clones is determining the variant allele frequency of mutations that occurred in the tumor. Although bulk sequencing data can be used to provide that information, the frequencies are not informative enough for identifying different clones with the same prevalence and their evolutionary relationships. On the other hand, single-cell sequencing data provides valuable information about branching events in the evolution of a cancerous tumor. However, the temporal order of mutations may be determined with ambiguities using only single-cell data, while variant allele frequencies from bulk sequencing data can provide beneficial information for inferring the temporal order of mutations with fewer ambiguities.

Result
In this study, a new method called Conifer (ClONal tree Inference For hEterogeneity of tumoR) is proposed which combines aggregated variant allele frequency from bulk sequencing data with branching event information from single-cell sequencing data to more accurately identify clones and their evolutionary relationships. It is proven that the accuracy of clone identification and clonal tree inference is increased by using Conifer compared to other existing methods on various sets of simulated data. In addition, it is discussed that the evolutionary tree provided by Conifer on real cancer data sets is highly consistent with information in both bulk and single-cell data.

Conclusions
In this study, we have provided an accurate and robust method to identify clones of tumor heterogeneity and their evolutionary history by combining single-cell and bulk sequencing data.
Experimental increase of worker diversity benefits brood production in ants
Authors: Psalti Marina N. , Gohlke Dustin , Libbrecht Romain 
Published: August 2021

Abstract
Background
The reproductive division of labor of eusocial insects, whereby one or several queens monopolize reproduction, evolved in a context of high genetic relatedness. However, many extant eusocial species have developed strategies that decrease genetic relatedness in their colonies, suggesting some benefits of the increased diversity. Multiple studies support this hypothesis by showing positive correlations between genetic diversity and colony fitness, as well as finding effects of experimental manipulations of diversity on colony performance. However, alternative explanations could account for most of these reports, and the benefits of diversity on performance in eusocial insects still await validation. In this study, we experimentally increased worker diversity in small colonies of the ant Lasius niger while controlling for typical confounding factors.

Results
We found that experimental colonies composed of workers coming from three different source colonies produced more larvae and showed more variation in size compared to groups of workers coming from a single colony.

Conclusions
We propose that the benefits of increased diversity stemmed from an improved division of labor. Our study confirms that worker diversity enhances colony performance, thus providing a possible explanation for the evolution of multiply mated queens and multiple-queen colonies in many species of eusocial insects.
A validated generally applicable approach using the systematic assessment of disease modules by GWAS reveals a multi-omic module strongly associated with risk factors in multiple sclerosis
Authors: Badam Tejaswi V. S. , de Weerd Hendrik A. , Martínez-Enguita David , Olsson Tomas , Alfredsson Lars , Kockum Ingrid , Jagodic Maja , Lubovac-Pilav Zelmina , Gustafsson Mika 
Published: August 2021

Abstract
Background
There exist few, if any, practical guidelines for predictive and falsifiable multi-omic data integration that systematically integrate existing knowledge. Disease modules are popular concepts for interpreting genome-wide studies in medicine but have so far not been systematically evaluated and may lead to corroborating multi-omic modules.

Result
We assessed eight module identification methods in 57 previously published expression and methylation studies of 19 diseases using GWAS enrichment analysis. Next, we applied the same strategy for multi-omic integration of 20 datasets of multiple sclerosis (MS), and further validated the resulting module using both GWAS and risk-factor-associated genes from several independent cohorts. Our benchmark of modules showed that in immune-associated diseases modules inferred from clique-based methods were the most enriched for GWAS genes. The multi-omic case study using MS data revealed the robust identification of a module of 220 genes. Strikingly, most genes of the module were differentially methylated upon the action of one or several environmental risk factors in MS (n = 217, P = 10− 47) and were also independently validated for association with five different risk factors of MS, which further stressed the high genetic and epigenetic relevance of the module for MS.

Conclusions
We believe our analysis provides a workflow for selecting modules and our benchmark study may help further improvement of disease module methods. Moreover, we also stress that our methodology is generally applicable for combining and assessing the performance of multi-omic approaches for complex diseases.
Light dominates the diurnal emissions of herbivore-induced volatiles in wild tobacco
Authors: He Jun , Halitschke Rayko , Schuman Meredith C. , Baldwin Ian T. 
Published: August 2021

Abstract
Background
Timing is everything when it comes to the fitness outcome of a plant’s ecological interactions, and accurate timing is particularly relevant for interactions with herbivores or mutualists that are based on ephemeral emissions of volatile organic compounds. Previous studies of the wild tobacco N. attenuata have found associations between the diurnal timing of volatile emissions, and daytime predation of herbivores by their natural enemies.

Results
Here, we investigated the role of light in regulating two biosynthetic groups of volatiles, terpenoids and green leaf volatiles (GLVs), which dominate the herbivore-induced bouquet of N. attenuata. Light deprivation strongly suppressed terpenoid emissions while enhancing GLV emissions, albeit with a time lag. Silencing the expression of photoreceptor genes did not alter terpenoid emission rhythms, but silencing expression of the phytochrome gene, NaPhyB1, disordered the emission of the GLV (Z)-3-hexenyl acetate. External abscisic acid (ABA) treatments increased stomatal resistance, but did not truncate the emission of terpenoid volatiles (recovered in the headspace). However, ABA treatment enhanced GLV emissions and leaf internal pools (recovered from tissue), and reduced internal linalool pools. In contrast to the pattern of diurnal terpenoid emissions and nocturnal GLV emissions, transcripts of herbivore-induced plant volatile (HIPV) biosynthetic genes peaked during the day. The promotor regions of these genes were populated with various cis-acting regulatory elements involved in light-, stress-, phytohormone- and circadian regulation.

Conclusions
This research provides insights into the complexity of the mechanisms involved in the regulation of HIPV bouquets, a mechanistic complexity which rivals the functional complexity of HIPVs, which includes repelling herbivores, calling for body guards, and attracting pollinators.
Adjuvant chemotherapy is an additional option for locally advanced gastric cancer after radical gastrectomy with D2 lymphadenectomy: a retrospective control study
Authors: Chen Lei , Zhang Chenghai , Yao Zhendan , Cui Ming , Xing Jiadi , Yang Hong , Zhang Nan , Liu Maoxing , Xu Kai , Tan Fei , Li Yuzhe , Jiang Beihai , Su Xiangqian 
Published: August 2021

Abstract
Background
This study compared the long-term efficacy of different durations of adjuvant chemotherapy for patients with gastric cancer after radical gastrectomy with D2 lymphadenectomy.

Methods
We retrospectively identified 428 patients with stage II–III gastric cancer who underwent D2 gastrectomy between 2009 and 2016. Patients were divided into four groups according to the duration of adjuvant chemotherapy, including 0 week (no adjuvant, group A), 20 to 24 weeks (completed 7–8 cycles every 3 weeks or 10–12 cycles every 2 weeks, group B), and 12 to18 weeks (completed 4–6 cycles every 3 weeks or 6–9 cycles every 2 weeks, group C), and less than 12 weeks (received up to 3 cycles every 3 weeks or 5 cycles every 2 weeks, group D). The chemotherapy regimens included XELOX, SOX, and FOLFOX. 5-year overall survival (OS) and disease-free survival (DFS) were analyzed.

Results
The 5-year OS rates for groups A, B, C, and D were 52.3, 73.7, 72.0, and 53.3%, respectively, and the 5-year DFS rates were 50.0, 68.0, 65.4, and 50.0%, respectively. OS and DFS were higher in group B than in groups A and D. Similarly, patients in group C were more likely to have higher OS and DFS than those in groups A and D. Meanwhile, there were no significant differences in OS and DFS between groups B and C. The multivariate analysis confirmed with high statistical significance the efficacy of complete courses of adjuvant chemotherapy, and, among them, the similar impact of 4–6/6–9 and 7–8/10–12 cycles, resulting in similar HRs vs Group A (0.52 and 0.42, respectively).

Conclusions
To reduce toxicity and maintain efficacy, XELOX or SOX chemotherapy regimens administered for 4–6 cycles every 3 weeks or FOLFOX regimen for 6–9 cycles every 2 weeks might be a favorable option for patients with stage II–III gastric cancer after D2 gastrectomy. Prospective multicenter clinical trials with adequate sample sizes are necessary to verify these findings.
Genetic predisposition to male breast cancer in Poland
Authors: Szwiec Marek , Tomiczek-Szwiec Joanna , Kluźniak Wojciech , Wokołorczyk Dominika , Osowiecka Karolina , Sibilski Robert , Wachowiak Małgorzata , Gronwald Jacek , Gronwald Helena , Lubiński Jan , Cybulski Cezary , Narod Steven A. , Huzarski Tomasz 
Published: August 2021

Abstract
Background
Breast cancer in men accounts for fewer than 1 % of all breast cancer cases diagnosed in men and women. Genes which predispose to male breast cancer include BRCA1 and BRCA2. The role of other genes is less clear. In Poland, 20 founder mutations in BRCA1, BRCA2, CHEK2, PALB2, NBN, RECQL are responsible for the majority of hereditary breast cancer cases in women, but the utility this genes panel has not been tested in men.

Methods
We estimated the prevalence of 20 alleles in six genes (BRCA1, BRCA2, CHEK2, PALB2, NBN, RECQL) in 165 Polish male breast cancer patients. We compared the frequency of selected variants in male breast cancer cases and controls.

Results
One of the 20 mutations was seen in 22 of 165 cases (13.3%). Only one BRCA1 mutation and two BRCA2 mutations were found. We observed statistically significant associations for PALB2 and CHEK2 truncating mutations. A PALB2 mutation was detected in four cases (OR = 11.66; p < 0.001). A CHEK2 truncating mutation was detected in five cases (OR = 2.93;p = 0.02).

Conclusion
In conclusion, we recommend that a molecular test for BRCA1, BRCA2, PALB2 and CHEK2 recurrent mutations should be offered to male breast cancer patients in Poland.
Demographic and prognostic factors of optic nerve astrocytoma: a retrospective study of surveillance, epidemiology, and end results (SEER)
Authors: Zhang Mingui , Chen Tao , Zhong Yisheng 
Published: August 2021

Abstract
Background
Optic nerve astrocytomas (ONAs) are neurological neoplasms in the central nervous system (CNS), and they have the highest incidence rate among all the tumor types in the visual pathway. In this study, we conducted a Surveillance, Epidemiology, and End Results (SEER) -based research to explore the demographic, survival, and prognostic factors of patients diagnosed with ONAs.

Methods
Utilizing the SEER database, we retrospectively evaluated data of patients diagnosed with ONAs of all ages from 1984 to 2016. We used the Student’s t distribution to test variables of patients and various characteristics, and Kaplan-Meier curve to illustrate overall survival (OS) with 95.0% confidence intervals (CIs). We also performed univariate and multivariate analyses to evaluate various variables’ validity on overall survival.

Results
A total of 1004 cases were analyzed, and revealed that age (P<0.001, hazard ratio (HR) = 8.830, 95% CI: 4.088–19.073), tumor grade (P<0.001, HR = 1.927, 95% CI: 1.516–2.450), diagnostic confirmation (P<0.001, HR = 2.444, 95% CI: 1.632–3.660), and histology type (P = 0.046, HR = 1.563, 95% CI: 1.008–2.424) of the tumor were associated with decreased survival.

Conclusions
From this large, comparative study of ONAs, we found that younger age may be considered as a protective indicator, while high-grade astrocytic tumors have a worse prognosis. We also found that diagnostic confirmation and tumor grade were independent prognostic factors in this patient population.
Understanding perception and acceptance of Sinopharm vaccine and vaccination against COVID–19 in the UAE
Authors: Ahamed Faheem , Ganesan Subhashini , James Anila , Zaher Walid Abbas 
Published: August 2021

Abstract
Background
In the current COVID-19 pandemic, the world has reached an important milestone where vaccinations are discovered and are proven to be effective against SARS-COV-2 infections. Though vaccines against COVID-19 are now available, around the globe there is some hesitancy in getting the vaccine. This hesitancy to get vaccinated against COVID-19 is a complex phenomenon with various factors playing a role. This study aims at understanding the perception and expectations of the people about COVID-19 vaccine and the factors influencing the vaccine acceptance. This information is crucial to challenge vaccine hesitancy and to win the combat against the COVID-19 Pandemic through voluntary vaccine efforts.

Methods
A cross-sectional survey among the residents of the UAE to understand the expectations and perception on vaccination against COVID-19. The survey was conducted online, and the survey design included participant samples to be representative of UAE’s demographics. The results of the survey were analysed with various demographical variables of interest.

Results
The survey showed that people were more likely to get vaccinated when vaccines are (i) endorsed by trusted government health authorities, (ii) recommended by physicians and family doctors, and (iii) the merits are effectively communicated through government websites and trusted news channels. Availability of vaccines at multiple sites and providing vaccines free of charges are likely to improve the rate of vaccination. The perceptions, expectations and the motivational factors needed for people to get vaccinated differed with age, gender, marital status, income level, and employment status.

Conclusion
To attain herd immunity against COVID-19, a large proportion of the population needs to be vaccinated and to achieve this the vaccination campaigns should target on specific expectations and motivational factors pertaining to each target group to successfully overcome the challenge of vaccine hesitancy.
The relationship between postmenopausal women’s body image and the severity of menopausal symptoms
Authors: Nazarpour Soheila , Simbar Masoumeh , Majd Hamid Alavi , Torkamani Zahra Jafari , Andarvar Khadijeh Dodel , Rahnemaei Fatemeh 
Published: August 2021

Abstract
Background
Body image is the main element of an individual’s personality that may be influenced by many factors during menopause. We aimed to assess the relationship between postmenopausal women’s body image with the severity of menopausal symptoms.

Methods
This was a cross-sectional study on 300 postmenopausal women, aged 45 to 65 years old, in Tehran, Iran. We recruited the samples using the multi-stage sampling method. Tools for data collection were: 1) the Menopausal Rating Scale (MRS), 2) the Fisher’s Body Image questionnaire and 3) a socio-demographic questionnaire. We analyzed data using the independent samples t-test, Pearson correlation coefficient, Spearman’s correlation coefficient, and multiple linear regression tests.

Results
Three hundred women aged 55.11 ± 3.99 years old, participated in the study. Mean scores for body image and MRS were 163.07 ± 21.17 (Range: 46–230) and 16.45 ± 8.38 (Range: 0–44), respectively. About 50% of women had severe symptoms of menopause (MRS score ≥ 17). There was a negative correlation between the total score and the score of all dimensions of body image with the total score and all dimensions of MRS (P < 0.001). There were also significant relationships between women’s body image with: their education (P < 0.001, r = 0.20) the spouse’s education (P < 0.001, r = 0.26), adequacy of monthly household income (P < 0.001, r = 0.32), marital status (P = 0.36), their occupation (P = 0.007) and housing status (P = 0.012). There was also a significant negative correlation between women’s lower body organs image with the number of children (P = 0.017, r = − 0.14). According to the multiple linear regressions model, severity of menopausal symptoms (Beta = − 0.45, P < 0.001) and adequacy of monthly household income (Beta = 0.15, P = 0.005) are the significant related factors with postmenopausal women’s body image.

Conclusions
Body image is correlated with menopausal symptoms of women during menopause. Therefore, it seems that interventions aimed at relieving the annoying symptoms of menopause can help to improve their body image. Also, body image could be influenced by some socio-demographic factors which should be considered in menopause health promotion programs.
Treatment of Fabella syndrome with arthroscopic fabellectomy: a case series and literature review
Authors: Weng Shuo-Po , Wu Tsung-Mu , Chien Chi-Sheng , Lin Sheng-Hui 
Published: August 2021

AbstractBackgroundThe fabella is a sesamoid bone in the posterolateral capsule of the human knee joint. In quadrupedal mammals, the fabella is believed to have a role similar to the patella in redirecting extension forces of the knee joint from one point to another. In bipeds, the fabella is not touching the back of the bent knee, and therefore the role in redirecting forces declines. Posterolateral knee pain can be associated with the irritation between the fabella and lateral femoral condyle, a phenomenon also known as fabella syndrome. In cases that are unresponsive to conservative management, surgical fabellectomy can be a successful treatment option. Among the surgical approaches, open resection is most commonly seen. There are also literature reporting arthroscopic-assisted open resection, but seldom mentioned the all-arthroscopic fabellectomy.Case presentationWe present 3 patients with a long history (> 12 month) of posterolateral knee pain under suspicion of different pain origins. The diagnosis of fabella impingement was eventually made by ruling out of other causes. All the patients underwent all-arthroscopic fabellectomy for diagnosis and treatment. Investigations of the resected fabella suggested chronic impingement with apparent osteophyte formation and cartilage wearing of the articular side. All patients have been continually followed up at our outpatient department and reported to be pain free after the procedure.ConclusionsIn the patients presenting posterolateral pain, fabella syndrome cannot be ignored due to its relative higher presence in Asian population. In our experience, the all-arthroscopic fabellectomy offers a smaller wound size, less post-operative pain, fewer days of hospitalization and quicker time to rehabilitation for the patients with chronic posterolateral knee pain caused by fabella syndrome.
Efficient framework for predicting MiRNA-disease associations based on improved hybrid collaborative filtering
Authors: Nie Ru , Li Zhengwei , You Zhu-hong , Bao Wenzheng , Li Jiashu 
Published: August 2021

Abstract
Background
Accumulating studies indicates that microRNAs (miRNAs) play vital roles in the process of development and progression of many human complex diseases. However, traditional biochemical experimental methods for identifying disease-related miRNAs cost large amount of time, manpower, material and financial resources.

Methods
In this study, we developed a framework named hybrid collaborative filtering for miRNA-disease association prediction (HCFMDA) by integrating heterogeneous data, e.g., miRNA functional similarity, disease semantic similarity, known miRNA-disease association networks, and Gaussian kernel similarity of miRNAs and diseases. To capture the intrinsic interaction patterns embedded in the sparse association matrix, we prioritized the predictive score by fusing three types of information: similar disease associations, similar miRNA associations, and similar disease-miRNA associations. Meanwhile, singular value decomposition was adopted to reduce the impact of noise and accelerate predictive speed.

Results
We then validated HCFMDA with leave-one-out cross-validation (LOOCV) and two types of case studies. In the LOOCV, we achieved 0.8379 of AUC (area under the curve). To evaluate the performance of HCFMDA on real diseases, we further implemented the first type of case validation over three important human diseases: Colon Neoplasms, Esophageal Neoplasms and Prostate Neoplasms. As a result, 44, 46 and 44 out of the top 50 predicted disease-related miRNAs were confirmed by experimental evidence. Moreover, the second type of case validation on Breast Neoplasms indicates that HCFMDA could also be applied to predict potential miRNAs towards those diseases without any known associated miRNA.

Conclusions
The satisfactory prediction performance demonstrates that our model could serve as a reliable tool to guide the following research for identifying candidate miRNAs associated with human diseases.