bluuebunny/crossref_metadata_2025 huggingface dataset:
Genome-Wide Association Studies Reveal the Genetic Basis of Fertility Restoration of CMS-WA and CMS-HL in xian/indica and aus Accessions of Rice (Oryza sativa L.)
Authors: Li Pingbo , Zhou Hao , Yang Hanyuan , Xia Duo , Liu Rongjia , Sun Ping , Wang Quanxiu , Gao Guanjun , Zhang Qinglu , Wang Gongwei , He Yuqing
Published: February 2020

Background

Wild-abortive cytoplasmic male sterility (CMS-WA) and Honglian CMS (CMS-HL) are the two main CMS types utilized in production of three-line hybrid rice in xian/indica (XI) rice. Dissection of the genetic basis of fertility restoration of CMS-WA and CMS-HL in the core germplasm population would provide valuable gene and material resources for development of three-line hybrid combinations.

Results

In this study, two F1 populations with CMS-WA and CMS-HL background respectively were developed using 337 XI and aus accessions being paternal parents. Genome-wide association studies on three fertility-related traits of the two populations for two consecutive years revealed that both fertility restoration of CMS-WA and CMS-HL were controlled by a major locus and several minor loci respectively. The major locus for fertility restoration of CMS-WA was co-located with Rf4, and that for fertility restoration of CMS-HL was co-located with Rf5, which are cloned major restorer of fertility (Rf) genes. Furthermore, haplotype analysis of Rf4, Rf5 and Rf6, the three cloned major Rf genes, were conducted using the 337 paternal accessions. Four main haplotypes were identified for Rf4, and displayed different subgroup preferences. Two main haplotypes were identified for Rf5, and the functional type was carried by the majority of paternal accessions. In addition, eight haplotypes were identified for Rf6.

Conclusions

Haplotype analysis of three Rf genes, Rf4, Rf5 and Rf6, could provide valuable sequence variations that can be utilized in marker-aided selection of corresponding genes in rice breeding. Meanwhile, fertility evaluation of 337 accessions under the background of CMS could provide material resources for development of maintainer lines and restorers.
Role of Tamsulosin with or without Deflazacort to facilitate stone clearance after ESWL: a single-center randomized controlled study
Authors: Jain Saurabh , Singh Mahendra , Khanna Sudhir , Rasool Shahnawaz , Gupta Manu , Kathuria Sachin , Pathak Amrendra , Pandey Himanshu
Published: February 2020

Background

Extracorporeal shock wave lithotripsy (ESWL) is the treatment of choice for upper tract calculi of moderate size. After ESWL, various factors affect the passage of small fragments through ureter like fragment’s size and location. To facilitate fragment passage, a lot of medications have been tried and few have stood the test of the time. In this prospective study, we evaluated the role of Tamsulosin with or without Deflazacort versus no treatment after ESWL for ureteric and renal stones in terms of requirement of the number of ESWL sessions, stone clearance rate, stone expulsion time and analgesia requirements.

Results

Patients presenting between age-groups of 18–70 years with solitary renal/ureteric calculus of size between 6 and 15 mm in major axis with Hounsfield unit less than 1000 were recruited in one of the three groups (A, B and C) randomly. Patients in Group A were prescribed Tamsulosin (0.4 mg once daily) with Deflazacort (30 mg once daily), Group B were given Tamsulosin (0.4 mg once daily), and Group C received no treatment (analgesics SOS and hydration therapy) after undergoing ESWL. Two hundred and twenty-five patients were recruited in Group A, and 240 patients were recruited in Group B and Group C each. There was an insignificant difference for required mean ESWL sessions and stone clearance rate between three groups. There was an early clearance of stone fragments in Group A than in Groups B and C, and it was statistically significant between Group A and Group C, specifically in the subgroup of stone size 10.1–15 mm. The requirement of mean analgesic tablets difference was significant between Groups A and C.

Conclusions

Tamsulosin with Deflazacort decreases the number of required ESWL sessions and improves complete stone clearance, but the difference is not significant. There were significant improvement in facilitating early stone clearance and decrease in requirement of mean analgesic tablets after ESWL with Tamsulosin and Deflazacort. Thus, Tamsulosin with Deflazacort can be used safely to facilitate stone clearance without increased complication rate.
Correction to: SLR: a scaffolding algorithm based on long reads and contig classification
Authors: Luo Junwei , Lyu Mengna , Chen Ranran , Zhang Xiaohong , Luo Huimin , Yan Chaokun
Published: February 2020

Following publication of the original article [1], the author reported that there is an error in the original article.
The draft genome of horseshoe crab Tachypleus tridentatus reveals its evolutionary scenario and well-developed innate immunity
Authors: Zhou Yan , Liang Yuan , Yan Qing , Zhang Liang , Chen Dianbao , Ruan Lingwei , Kong Yuan , Shi Hong , Chen Mingliang , Chen Jianming
Published: February 2020

Background

Horseshoe crabs are ancient marine arthropods with a long evolutionary history extending back approximately 450 million years, which may benefit from their innate immune systems. However, the genetic mechanisms underlying their abilities of distinguishing and defending against invading microbes are still unclear.

Results

Here, we describe the 2.06 Gbp genome assembly ofTachypleus tridentatuswith 24,222 predicted protein-coding genes. Comparative genomics shows thatT. tridentatusand the Atlantic horseshoe crabLimulus polyphemushave the most orthologues shared among two species, including genes involved in the immune-related JAK-STAT signalling pathway. Divergence time dating results show that the last common ancestor of Asian horseshoe crabs (includingT. tridentatusandC. rotundicauda) andL. polyphemusappeared approximately 130 Mya (121–141), and the split of the two Asian horseshoe crabs was dated to approximately 63 Mya (57–69). Hox gene analysis suggests two clusters in both horseshoe crab assemblies. Surprisingly, selective analysis of immune-related gene families revealed the high expansion of conserved pattern recognition receptors. Genes involved in the IMD and JAK-STAT signal transduction pathways also exhibited a certain degree of expansion in both genomes. Intact coagulation cascade-related genes were present in theT. tridentatusgenome with a higher number of coagulation factor genes. Moreover, most reported antibacterial peptides have been identified inT. tridentatuswith their potentially effective antimicrobial sites.

Conclusions

The draft genome ofT. tridentatuswould provide important evidence for further clarifying the taxonomy and evolutionary relationship of Chelicerata. The expansion of conserved immune signalling pathway genes, coagulation factors and intact antimicrobial peptides inT. tridentatusconstitutes its robust and effective innate immunity for self-defence in marine environments with an enormous number of invading pathogens and may affect the quality of the adaptive properties with regard to complicated marine environments.
STELAR: a statistically consistent coalescent-based species tree estimation method by maximizing triplet consistency
Authors: Islam Mazharul , Sarker Kowshika , Das Trisha , Reaz Rezwana , Bayzid Md. Shamsuzzoha
Published: February 2020

Background

Species tree estimation is frequently based on phylogenomic approaches that use multiple genes from throughout the genome. However, estimating a species tree from a collection of gene trees can be complicated due to the presence of gene tree incongruence resulting from incomplete lineage sorting (ILS), which is modelled by the multi-species coalescent process. Maximum likelihood and Bayesian MCMC methods can potentially result in accurate trees, but they do not scale well to large datasets.

Results

We present STELAR (Species Tree Estimation by maximizing tripLet AgReement), a new fast and highly accurate statistically consistent coalescent-based method for estimating species trees from a collection of gene trees. We formalized the constrained triplet consensus (CTC) problem and showed that the solution to the CTC problem is a statistically consistent estimate of the species tree under the multi-species coalescent (MSC) model. STELAR is an efficient dynamic programming based solution to the CTC problem which is highly accurate and scalable. We evaluated the accuracy of STELAR in comparison with SuperTriplets, which is an alternate fast and highly accurate triplet-based supertree method, and with MP-EST and ASTRAL – two of the most popular and accurate coalescent-based methods. Experimental results suggest that STELAR matches the accuracy of ASTRAL and improves on MP-EST and SuperTriplets.

Conclusions

Theoretical and empirical results (on both simulated and real biological datasets) suggest that STELAR is a valuable technique for species tree estimation from gene tree distributions.
From methylglyoxal to pyruvate: a genome-wide study for the identification of glyoxalases and D-lactate dehydrogenases in Sorghum bicolor
Authors: Bhowal Bidisha , Singla-Pareek Sneh L. , Sopory Sudhir K. , Kaur Charanpreet
Published: February 2020

Background

The glyoxalase pathway is evolutionarily conserved and involved in the glutathione-dependent detoxification of methylglyoxal (MG), a cytotoxic by-product of glycolysis. It acts via two metallo-enzymes, glyoxalase I (GLYI) and glyoxalase II (GLYII), to convert MG into D-lactate, which is further metabolized to pyruvate by D-lactate dehydrogenases (D-LDH). Since D-lactate formation occurs solely by the action of glyoxalase enzymes, its metabolism may be considered as the ultimate step of MG detoxification. By maintaining steady state levels of MG and other reactive dicarbonyl compounds, the glyoxalase pathway serves as an important line of defence against glycation and oxidative stress in living organisms. Therefore, considering the general role of glyoxalases in stress adaptation and the ability of Sorghum bicolor to withstand prolonged drought, the sorghum glyoxalase pathway warrants an in-depth investigation with regard to the presence, regulation and distribution of glyoxalase and D-LDH genes.

Result

Through this study, we have identified 15 GLYI and 6 GLYII genes in sorghum. In addition, 4 D-LDH genes were also identified, forming the first ever report on genome-wide identification of any plant D-LDH family. Our in silico analysis indicates homology of putatively active SbGLYI, SbGLYII and SbDLDH proteins to several functionally characterised glyoxalases and D-LDHs from Arabidopsis and rice. Further, these three gene families exhibit development and tissue-specific variations in their expression patterns. Importantly, we could predict the distribution of putatively active SbGLYI, SbGLYII and SbDLDH proteins in at least four different sub-cellular compartments namely, cytoplasm, chloroplast, nucleus and mitochondria. Most of the members of the sorghum glyoxalase and D-LDH gene families are indeed found to be highly stress responsive.

Conclusion

This study emphasizes the role of glyoxalases as well as that of D-LDH in the complete detoxification of MG in sorghum. In particular, we propose that D-LDH which metabolizes the specific end product of glyoxalases pathway is essential for complete MG detoxification. By proposing a cellular model for detoxification of MG via glyoxalase pathway in sorghum, we suggest that different sub-cellular organelles are actively involved in MG metabolism in plants.
Non-alcoholic fatty liver disease among patients with sleep disorders: a Nationwide study of Taiwan
Authors: Wei Yu-Ting , Lee Peng-Yi , Lin Cheng-Yu , Chen Hsuan-Ju , Lin Che-Chen , Wu Jin-Shang , Chang Yin-Fan , Wu Chen-Long , Guo How-Ran
Published: February 2020

Background

Nonalcoholic fatty liver disease (NAFLD) is one of the most common chronic liver diseases. Studies have shown that sleep apnea is associated with NAFLD. However, studies on the association between sleep disorders in general and NAFLD are limited. We conducted a nationwide population-based longitudinal study to evaluate this potential association.

Methods

We identified patients diagnosed with sleep disorders in the years 2000 through 2005 in Taiwan using the National Health Insurance Research Database and selected an equal number of patients without sleep disorders from the same database as the comparison cohort. The patients were followed from the index date to the diagnosis of NAFLD or the end of 2013. We used Cox proportional hazards models to estimate the risk of NAFLD associated with sleep disorders.

Results

A total of 33,045 patients with sleep disorders were identified. The incidence of NAFLD was 14.0 per 10,000 person-year in patients with sleep disorders and 6.2 per 10,000 person-year in the comparison cohort. The adjusted hazard ratio (AHR) of NAFLD associated with sleep disorders was 1.78 (95% confidence interval [95%CI]: 1.46–2.16), and other independent risk factors included male sex (AHR = 1.31, 95%CI: 1.12–1.54), age 40–59 years (AHR = 1.49, 95%CI: 1.21–1.82), and dyslipidemia (AHR = 2.51, 95%CI: 2.08–3.04). In the subgroup analyses, both patients with (AHR = 2.24, 95%CI: 1.05–4.77) and without (AHR = 1.77, 95%CI: 1.46–2.15) sleep apnea had an increased risk of NAFLD.

Conclusions

Sleep disorders are associated with NAFLD, even in patients without sleep apnea. Further studies are warranted to explore the mechanisms of the association.
Correction to: Association of CMV genomic mutations with symptomatic infection and hearing loss in congenital CMV infection
Authors: Dobbins G. Clement , Patki Amit , Chen Dongquan , Tiwari Hemant K. , Hendrickson Curtis , Britt William J. , Fowler Karen , Chen Jake Y. , Boppana Suresh B. , Ross Shannon A.
Published: February 2020

After publication of the original article [1], we were notified that Fig. 3 has “Fig. 1” posted on the top of it and Figs. 4 and 5 have “Genomic Position” in a different spot.
Epidemiological and clinical characteristics of healthcare-associated infection in elderly patients in a large Chinese tertiary hospital: a 3-year surveillance study
Authors: Zhao Xia , Wang Lihong , Wei Nan , Zhang Jingli , Ma Wenhui , Zhao Huijie , Han Xu
Published: February 2020

Background

We analyzed the results of a 3-year surveillance study on the epidemiological and clinical characteristics of healthcare associated-infections (HAIs) in elderly inpatients in a large tertiary hospital in China.

Methods

Real-time surveillance was performed from January 1, 2015 to December 31, 2017. All HAIs were identified by infection control practitioners and doctors. Inpatient data were collected with an automatic surveillance system.

Results

A total of 134,637 inpatients including 60,332 (44.8%) elderly ≥60 years were included. The overall incidence of HAI was 2.0%. The incidence of HAI in elderly patients was significantly higher than that in non-elderly patients (2.6% vs. 1.5%, χ2 = 202.421, P < 0.01) and increased with age. The top five sites of HAIs in the elderly were the lower respiratory tract, urinary tract, blood stream, antibiotic-associated diarrhea, and surgical site. The five most common pathogens detected in elderly HAI patients were Candida albicans, Klebsiella pneumonia, Acinetobacter baumannii, Escherichia coli, and Pseudomonas aeruginosa. The incidence of ventilator-associated pneumonia in the elderly was lower than in the non-elderly, catheter-associated urinary tract infections were more common in elderly patients, and the rate of central line-associated bloodstream infection was similar between groups. The numbers of male patients and patients with comorbidities and special medical procedures (e.g., intensive care unit admission, cerebrovascular disease, brain neoplasms, hypertension, hyperlipidemia, diabetes mellitus, coronary artery disease, chronic obstructive pulmonary disease, malignant tumor, malignant hematonosis, and osteoarthropathy) were significantly higher in the elderly group, but the number of patients who underwent surgery was lower.

Conclusion

We observed a significantly higher overall incidence of HAI in elderly inpatients ≥60 compared to non-elderly inpatients < 60 years, but the trend was different for device-associated HAIs, which was attributed to the higher rates of comorbidities and special medical procedures in the elderly group. The main HAI sites in elderly inpatients were the lower respiratory tract, urinary tract, and bloodstream, and the main pathogens were gram-negative bacilli and Candida albicans.
Correction to: Adrenocortical carcinoma complicated by renal thrombotic microangiopathy, a case-series
Authors: de Nattes Tristan , Moreau-Grangé Lucile , Vezzosi Delphine , Hadoux Julien , Hie Miguel , Guerrot Dominique , Grangé Steven
Published: February 2020

Following publication of the original article [1], we have been notified that the name of one author was spelled incorrectly as Julien Haddoux, when the correct spelling is Julien Hadoux.
Healthy pregnancies and essential fats: focus group discussions with Zambian women on dietary need and acceptability of a novel RUSF containing fish oil DHA
Authors: Chunda-Liyoka Catherine , Lubeya Mwansa Ketty , Imakando Mercy , Kisling Sophia , Majid Sonoor , Willis Mary S. , Wood Charles , Kankasa Chipepo , DiRusso Concetta C.
Published: February 2020

Background

Nut butter-based Ready to Use Supplemental Foods (RUSF) are an effective way to add nutrients and calories to diets of malnourished and food insecure populations. The RUSF formulations have been further modified to add micronutrients including iron and folic acid needed during pregnancy and lactation. Because docosahexaenoic acid (DHA, C22:6 n-3) enhances fetal development and birth outcomes, it has been suggested that perhaps RUSF formulations for pregnancy should also include this Omega 3 fatty acid. The goal of the present study was to gain an understanding of Zambian women’s knowledge of nutritional needs in pregnancy through structured focus group discussions, and to formulate and determine the acceptability of a RUSF with DHA.

Methods

Structured focus group sessions were conducted among women attending an antenatal clinic at the University Teaching Hospitals in Lusaka, Zambia. Dietary and nutrition knowledge was surveyed through structured dialogue that was recorded by audio and transcribed verbatim. An RUSF containing 400 mg DHA from fish oil in 50 g RUSF was designed and assessed for fatty acid content and product stability. Participants then sampled the RUSF-DHA, provided feedback on taste, and were surveyed about willingness to consume the novel formula using a standardized hedonic instrument.

Results

The participants’ knowledge of foods recommended for use in pregnancy included fruits, vegetables, meat, and fish. Most women reported eating fish at least once per week, although the specific type of fish varied. Most did not have prior knowledge of the importance of consuming fish during pregnancy or that some fish types were more nutritional than others as they included omega 3 fatty acids. The participants were uniformly accepting of the RUSF-DHA for the purpose of enhancing birth and developmental outcomes, but were critical of the aroma in hedonic testing.

Conclusions

Women were committed to consuming a healthy diet that would impact the outcome of pregnancy, and were receptive to advice on the importance of consuming foods such as fish as a source of DHA. The RUSF-DHA formulation was acceptable due to the potential benefits for the developing infant, however, the fishy odor may be limiting for long-term daily use.
Young-onset colorectal cancer in the North East of Scotland: survival, clinico-pathological features and genetics
Authors: Perrott Sarah , Laurie Kirsten , Laws Kirsten , Johnes Annie , Miedzybrodzka Zosia , Samuel Leslie
Published: February 2020

Background

Colorectal cancer (CRC) in patients aged under 55 years is on the rise, constituting approximately 10% of cases. Our aim was to determine the survival and clinico-pathological details of young-onset CRC (yCRC), as well as audit the referral rate to genetic services and thus establish the incidence of inherited cancer syndromes.

Methods

A retrospective case note review was conducted for patients aged under 55 years who were diagnosed with CRC between 2005 and 2015 in the North East of Scotland. Cases were identified by pathology records and data was obtained from patient notes. Analysis was performed using SPSS version 25 (IBM, New York, USA) to produce Kaplan-Meier survival estimates, descriptive statistics and markers predictive for genetic referral.

Results

Data from 345 patients (age range 22–54 years) were identified. The one year, five year and overall survival rates were found to be 89, 63 and 55%, respectively. Most patients (61%) presented with advanced disease. Of 201 patients that met criteria for genetic referral, only 93 (46%) were referred to genetic services. Microsatellite instability (MSI) was identified in 14% of those referred.

Conclusion

Survival in yCRC was found to be better than that in later onset disease, despite higher rates of advanced disease. Patients were under-referred to genetic services, where a significant proportion were found to be MSI positive and investigated for Lynch syndrome.
Persistent depressive disorder across the adult lifespan: results from clinical and population-based surveys in Germany
Authors: Nübel Julia , Guhn Anne , Müllender Susanne , Le Hong Duyen , Cohrdes Caroline , Köhler Stephan
Published: February 2020

Background

Although the individual and economic disease burden of depression is particularly high for long-term symptoms, little is known of the lifetime course of chronic depression. Most evidence derives from clinical samples, and the diagnostic distinction between persistent depressive disorder (PDD) and non-chronic major depression (NCMDD) is still debated. Thus, we examined characteristics of PDD among clinical vs. non-clinical cases, and the associated disease burden at a population level.

Methods

Data were drawn from the mental health module of the German Health Interview and Examination Survey for Adults (DEGS1-MH, 2009–2012, n = 4483) and a clinical sample of PDD inpatients at Charité – Universitätsmedizin Berlin (2018–2019, n = 45). The DSM-5 definition of PDD was operationalized a priori to the study using interview-based DSM-IV diagnoses of dysthymia and major depression lasting at least 2 years in both surveys. Additional depression characteristics (depression onset, self-classified course, suicidality, comorbid mental disorders, treatment history and current depressive symptoms [Patient Health Questionnaire-9]) were assessed. In the DEGS1-MH, health-related quality of life (Short Form Health Survey-36, SF-36), chronic somatic conditions, number of sick days (past 12 months) or days with limitations in normal daily life activities (past 4 weeks), and health service utilization (past 12 months) were compared for PDD vs. NCMDD.

Results

PDD cases from the clinical sample had a significantly earlier depression onset, a higher proportion of self-classification as persistent course, and treatment resistance than PDD and NCMDD cases in DEGS1-MH. At a population level, PDD cases showed worse outcomes compared with NCMDD cases in terms of somatic comorbidity, SF-36 mental component score, and activity limitations owing to mental health problems, as well as a higher risk for outpatient mental health care contact.

Conclusions

The distinction between PDD and NCMDD proposed for DSM-5 seems warranted. Early onset depression, self-classification as persistent depressive course, and treatment resistance are suggested as markers of more severe and chronic depression courses. At a population level, PDD is associated with remarkably higher individual and economic disease burden than NCMDD, highlighting the need to improve medical recognition of chronic courses and establish specific treatment concepts for chronic depression.
Barriers to teaching communication skills in Spanish medical schools: a qualitative study with academic leaders
Authors: Ruiz Moral Roger , García de Leonardo Cristina , Cerro Pérez Alvaro , Caballero Martínez Fernando , Monge Martín Diana
Published: February 2020

Background

In recent years, Spanish medical schools (MSs) have incorporated training in communication skills (CS), but how this training is being carried out has not yet been evaluated.

Objective

To identify the barriers to the introduction and development of CS teaching in Spanish MSs.

Methods

In a previous study, 34 MSs (83% of all MSs in Spain) were invited to participate in a study that explored the factual aspects of teaching CS in these schools. The person responsible for teaching CS at each school was contacted again for this study and asked to respond to a single open-ended question. Two researchers independently conducted a thematic analysis of the responses.

Results

We received responses from 30 MSs (85.7% of those contacted and 73% of all MSs in Spain). Five main thematic areas were identified, each with different sub-areas: negative attitudes of teachers and academic leaders; organisation, structure and presence of CS training in the curriculum; negative attitudes of students; a lack of trained teachers; and problems linked to teaching methods and necessary educational logistics.

Conclusions

The identified barriers and problems indicate that there are areas for improvement in teaching CS in most Spanish MSs. There seems to be a vicious circle based on the dynamic relationship and interdependence of all these problems that should be faced with different strategies and that requires a significant cultural shift as well as decisive institutional support at the local and national levels. The incorporation of CS training into MS curricula represents a major challenge that must be addressed for students to learn CS more effectively and avoid negative attitudes towards learning CS.
Germline variants in DNA repair genes associated with hereditary breast and ovarian cancer syndrome: analysis of a 21 gene panel in the Brazilian population
Authors: da Costa e Silva Carvalho Simone , Cury Nathalia Moreno , Brotto Danielle Barbosa , de Araujo Luiza Ferreira , Rosa Reginaldo Cruz Alves , Texeira Lorena Alves , Plaça Jessica Rodrigues , Marques Adriana Aparecida , Peronni Kamila Chagas , Ruy Patricia de Cássia , Molfetta Greice Andreotti , Moriguti Julio Cesar , Carraro Dirce Maria , Palmero Edenir Inêz , Ashton-Prolla Patricia , de Faria Ferraz Victor Evangelista , Silva Jr Wilson Araujo
Published: February 2020

Background

The Hereditary Breast and Ovarian Cancer Syndrome (HBOC) occurs in families with a history of breast/ovarian cancer, presenting an autosomal dominant inheritance pattern.BRCA1andBRCA2are high penetrance genes associated with an increased risk of up to 20-fold for breast and ovarian cancer. However, only 20–30% of HBOC cases present pathogenic variants in those genes, and other DNA repair genes have emerged as increasing the risk for HBOC. In Brazil, variants inATM, ATR, CHEK2, MLH1, MSH2, MSH6, POLQ, PTEN,andTP53genes have been reported in up to 7.35% of the studied cases. Here we screened and characterized variants in 21 DNA repair genes in HBOC patients.

Methods

We systematically analyzed 708 amplicons encompassing the coding and flanking regions of 21 genes related to DNA repair pathways (ABRAXAS1,ATM, ATR, BARD1, BRCA1, BRCA2, BRIP1, CDH1, CHEK2, MLH1, MRE11, MSH2, MSH6, NBN, PALB2, PMS2, PTEN, RAD50, RAD51, TP53andUIMC1). A total of 95 individuals with HBOC syndrome clinical suspicion in Southeast Brazil were sequenced, and 25 samples were evaluated for insertions/deletions inBRCA1/BRCA2genes. Identified variants were assessed in terms of population allele frequency and their functional effects were predicted through in silico algorithms.

Results

We identified 80 variants in 19 genes. About 23.4% of the patients presented pathogenic variants inBRCA1, BRCA2andTP53, a frequency higher than that identified among previous studies in Brazil. We identified a novel variant inATR, which was predicted as pathogenic by in silico tools. The association analysis revealed 13 missense variants inABRAXAS1, BARD1, BRCA2, CHEK2, CDH1, MLH1, PALB2,andPMS2genes, as significantly associated with increased risk to HBOC, and the patients carrying those variants did not present large insertions or deletions inBRCA1/BRCA2genes.

Conclusions

This study embodies the third report of a multi-gene analysis in the Brazilian population, and addresses the first report of many germline variants associated with HBOC in Brazil. Although further functional analyses are necessary to better characterize the contribution of those variants to the phenotype, these findings would improve the risk estimation and clinical follow-up of patients with HBOC clinical suspicion.
Acupoint application inhibits nerve growth factor and attenuates allergic inflammation in allergic rhinitis model rats
Authors: Tu Wenzhan , Chen Xiaolong , Wu Qiaoyun , Ying Xinwang , He Rong , Lou Xinfa , Yang Guanhu , Zhou Kecheng , Jiang Songhe
Published: February 2020

Background

Acupoint application therapy (AAT) has been widely used to treat allergic inflammation induced by allergic rhinitis (AR). The therapeutic effect of acupoint application is obvious. But the underlying therapeutic mechanism is still indistinct. Nerve growth factor (NGF) expression showed a dramatic rise in nasal mucosa tissue after AR, and allergic inflammation also increased significantly. To demonstrate how AAT can improve allergic inflammation by down-regulating the expression of NGF, AR rat models were established by intraperitoneal injection of ovalbumin (OVA) and nasal drops in SD rats. The number of nasal rubbing, sneezing and the degree of runny nose were observed and the symptoms were scored by behavioral symptom scoring method within 3 min. The expression levels of NGF and its downstream key proteins, such as IL-4, IL-5, IL-13, IgE and IFN-γ were determined by q-PCR, Western blot analysis, ELISA and immunofluorescence staining. Furthermore, H&E staining and toluidine blue staining were used to observe the pathological structure of nasal mucosa and mast cells in nasal mucosa, and the ultrastructure of nasal mucosa was observed by electron microscopy.

Results

Our data demonstrated that acupoint application significantly reduced the score of behavioral symptoms, and decreased the expression levels of NGF and its downstream key proteins, including IL-4, IL-5, IL-13, IgE, as well as promoting the expression level of IFN-γ in nasal mucosa tissue in AR rats. Thus, the activation of IgE and viability of mast cells was inhibited.

Conclusion

Our findings suggest that AAT can attenuate allergic inflammation by inhibiting the expression of NGF and its downstream pathway.
The value of MRI in management of endometrial hyperplasia with atypia
Authors: Natarajan Purushothaman , Vinturache Angela , Hutson Richard , Nugent David , Broadhead Timothy
Published: February 2020

Background

The value of the magnetic resonance imaging (MRI) in the assessment of women with endometrial hyperplasia and its role in diagnosis of myometrial invasion or coexistence of cancer is not known. This study aimed to evaluate the accuracy and usefulness of MRI in the management of patients diagnosed on endometrial biopsy with complex endometrial hyperplasia with atypia (CEHA).

Methods

A retrospective study of 86 cases diagnosed with endometrial hyperplasia with atypia on the initial endometrial biopsy in a tertiary university teaching hospital between 2010 and 2015 was carried out. The MRI accuracy in predicting malignant changes and influence the clinical management was compared among women who had either pelvic MRI, transvaginal ultrasound (TVUS), or no additional imagistic studies.

Results

MRI was performed in 24 (28%) and TVUS in 11 (13%)cases, while 51 (59%) women had no additional imagistic studies. In the group of women with no imaging studies, 26/51 (51%) were surgically treated and 8/26 (31%) were diagnosed with endometrial cancer (EEC) stage 1a. In the group of women who had TVUS, 5/11 (45%) were surgically treated and none was diagnosed with EEC. In the group of women who underwent an MRI examination, 20/24 (83%) were surgically treated. Among these, 11/20 (55%) were diagnosed with EEC, 7 had EEC stage 1a, and 4 had EEC stage 1b. Although MRI was able to identify malignant changes with a good sensitivity (91.7%), it had a low specificity in characterisation of malignant transformation (8%). MRI correctly identified 31% of the stage 1a and 33% of the stage 1b endometrial cancer.

Conclusion

In this study, we found a potential diagnostic value of MRI for identifying malignant transformation in patients with CEHA. However, pelvic MRI has a rather weak predictive value of myometrial invasion in women with CEHA and concurrent EEC. The diagnostic and therapeutic benefits of MRI assessment in patients with CEHA need further validation.
Exploring the evolution of engagement between academic public health researchers and decision-makers: from initiation to dissolution
Authors: Jessani Nasreen S. , Valmeekanathan Akshara , Babcock Carly , Ling Brenton , Davey-Rothwell Melissa A. , Holtgrave David R.
Published: February 2020

Context

Relationships between researchers and decision-makers have demonstrated positive potential to influence research, policy and practice. Over time, interest in better understanding the relationships between the two parties has grown as demonstrated by a plethora of studies globally. However, what remains elusive is the evolution of these vital relationships and what can be learned from them with respect to advancing evidence-informed decision-making. We therefore explored the nuances around the initiation, maintenance and dissolution of academic–government relationships.

Methods

We conducted in-depth interviews with 52 faculty at one school of public health and 24 government decision-makers at city, state, federal and global levels. Interviews were transcribed and coded deductively and inductively using Atlas.Ti. Responses across codes and respondents were extracted into an Excel matrix and compared in order to identify key themes.

Findings

Eight key drivers to engagement were identified, namely (1) decision-maker research needs, (2) learning, (3) access to resources, (4) student opportunities, (5) capacity strengthening, (6) strategic positioning, (7) institutional conditionalities, and (8) funder conditionalities. There were several elements that enabled initiation of relationships, including the role of faculty members in the decision-making process, individual attributes and reputation, institutional reputation, social capital, and the role of funders. Maintenance of partnerships was dependent on factors such as synergistic collaboration (i.e. both benefit), mutual trust, contractual issues and funding. Dissolution of relationships resulted from champions changing/leaving positions, engagement in transactional relationships, or limited mutual trust and respect.

Conclusions

As universities and government agencies establish relationships and utilise opportunities to share ideas, envision change together, and leverage their collaborations to use evidence to inform decision-making, a new modus operandi becomes possible. Embracing the individual, institutional, networked and systems dynamics of relationships can lead to new practices, alternate approaches and transformative change. Government agencies, schools of public health and higher education institutions more broadly, should pay deliberate attention to identifying and managing the various drivers, enablers and disablers for relationship initiation and resilience in order to promote more evidence-informed decision-making.
Comparing and assessing physical activity guidelines for children and adolescents: a systematic literature review and analysis
Authors: Parrish Anne-Maree , Tremblay Mark S. , Carson Stephanie , Veldman Sanne L. C. , Cliff Dylan , Vella Stewart , Chong Kar Hau , Nacher Maria , del Pozo Cruz Borja , Ellis Yvonne , Aubert Salome , Spaven Billie , Sameeha Mohd Jamil , Zhang Zhiguang , Okely Anthony D.
Published: February 2020

Background

The impact of declining physical activity and increased sedentary behaviour in children and adolescents globally prompted the development of national and international physical activity guidelines. This research aims to systematically identify and compare national and international physical activity guidelines for children and adolescents and appraise the quality of the guidelines to promote best practice in guideline development.

Methods

This systematic review was registered in the International Prospective Register of Systematic Reviews (PROSPERO) and reported using the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines. Only national, or international physical activity and/or sedentary behaviour guidelines were included in the review. Included guidelines targeted children and adolescents aged between 5 and 18 years. A grey literature search was undertaken incorporating electronic databases, custom Google search engines, targeted websites and international expert consultation. Guideline quality was assessed using the Appraisal of Guidelines for Research and Evaluation II Instrument (AGREE II).

Results

The search resulted in 50 national or international guidelines being identified. Twenty-five countries had a national guideline and there were three international guidelines (European Union, Nordic countries (used by Iceland, Norway and Sweden), World Health Organization (WHO)). Nineteen countries and the European Union adopted the WHO guidelines. Guidelines varied in relation to date of release (2008 to 2019), targeted age group, and guideline wording regarding: type, amount, duration, intensity, frequency and total amount of physical activity. Twenty-two countries included sedentary behaviour within the guidelines and three included sleep. Total scores for all domains of the AGREE II assessment for each guideline indicated considerable variability in guideline quality ranging from 25.8 to 95.3%, with similar variability in the six individual domains. Rigorous guideline development is essential to ensure appropriate guidance for population level initiatives.

Conclusions

This review revealed considerable variability between national/international physical activity guideline quality, development and recommendations, highlighting the need for rigorous and transparent guideline development methodologies to ensure appropriate guidance for population-based approaches. Where countries do not have the resources to ensure this level of quality, the adoption or adolopment (framework to review and update guidelines) of the WHO guidelines or guidelines of similar quality is recommended.

Trial registration

Review registration: PROSPERO 2017 CRD42017072558.
The new child food package is associated with reduced obesity risk among formula fed infants participating in the Special Supplemental Nutrition Program for Women, Infants and Children (WIC) in Los Angeles County, California, 2003–2016
Authors: Chaparro M. Pia , Anderson Christopher E. , Crespi Catherine M. , Wang May C. , Whaley Shannon E.
Published: February 2020

Background

The Special Supplemental Nutrition Program for Women, Infants and Children (WIC) changed the food packages provided to its participants in 2009, to better align them with the Dietary Guidelines for Americans. Previous research found that the 2009 WIC food package change was associated with reduced obesity risk, particularly among breastfed infants but also among those who were never breastfed. The objective of this study was to determine if the new child food package introduced in 2009, including more produce and whole grains for 1–4-year old children, was associated with healthier growth trajectories and reduced obesity risk at age 4 years among children who were exclusively formula fed during infancy.

Methods

Administrative data on WIC-participating children in Los Angeles County, 2003–2016, were used (N = 74,871), including repeated measures of weight and length (or height); child’s age, gender, and race/ethnicity; maternal education and language; and family poverty. Gender-stratified spline mixed models were used to examine weight-for-height z-score (WHZ) growth trajectories from 0 to 4 years and Poisson regression models were used to assess obesity (BMI-for-age > 95th percentile) at age 4. The main independent variable was duration of receipt (dose) of the new child package, categorized as 0, > 0 to < 1, 1 to < 2, 2 to < 3, 3 to < 4, and 4 years.

Results

WHZ growth trajectories were similar for children across new child package dose groups. Boys and girls who were fully formula fed during infancy but received the new child food package for 4 years had a 7% (RR = 0.93; 95%CI = 0.89–0.98) and a 6% (RR = 0.94; 95%CI = 0.89–0.99) lower obesity risk, respectively, compared to children who received the new child food package for 0 years. There were no differences in obesity risk for children receiving < 4 years of the new child package vs. 0 years.

Conclusions

Providing healthy foods during childhood to children who were exclusively formula fed as infants was associated with modest improvements in obesity outcomes. While breastfeeding promotion should still be prioritized among WIC participants, providing healthy foods during childhood may provide health benefits to formula fed children, who comprise a sizeable proportion of children served by WIC.
Overexpression of a panel of cancer stem cell markers enhances the predictive capability of the progression and recurrence in the early stage cholangiocarcinoma
Authors: Padthaisong Sureerat , Thanee Malinee , Namwat Nisana , Phetcharaburanin Jutarop , Klanrit Poramate , Khuntikeo Narong , Titapun Attapol , Sungkhamanon Sakkarn , Saya Hideyuki , Loilome Watcharin
Published: February 2020

Background

Cancer recurrence is the important problem of cholangiocarcinoma (CCA) patients, lead to a very high mortality rate. Therefore, the identification of candidate markers to predict CCA recurrence is needed in order to effectively manage the disease. This study aims to examine the predictive value of cancer stem cell (CSC) markers on the progression and recurrence of CCA patients.

Methods

The expression of 6 putative CSC markers, cluster of differentiation 44 (CD44), CD44 variant 6 (CD44v6), CD44 variants 8-10 (CD44v8-10), cluster of differentiation 133 (CD133), epithelial cell adhesion molecule (EpCAM), and aldehyde dehydrogenase 1A1 (ALDH1A1), was investigated in 178 CCA tissue samples using immunohistochemistry (IHC) and analyzed with respect to clinicopathological data and patient outcome including recurrence-free survival (RFS) and overall survival (OS). The candidate CSC markers were also investigated in serum from CCA patients, and explored for their predictive ability on CCA recurrence.

Results

Elevated protein level of CD44 and positive expression of CD44v6 and CD44v8-10 were significantly associated with short RFS and OS, while high levels of ALDH1A1 were correlated with a favorable prognosis patient. The elevated CD44v6 level was also correlated with higher tumor staging, whereas a decreasing level of ALDH1A1 was correlated with lower tumor staging. The levels of CD44, CD44v6 and CD44v8-10 were also correlated and were associated with a poor outcome. Furthermore, soluble CD44, CD44v6, CD44v8-10 and EpCAM were significantly increased in the recurrence group for early stage CCA; they also correlated with high levels of the tumor marker CA19-9. Elevated levels of CD44, CD44v6, CD44v8-10 or EpCAM alone or in combination has the potential to predict CCA recurrence.

Conclusions

The overexpression of CD44, CD44v6, CD44v8-10 and EpCAM increases predictability of post-operative CCA recurrence. Moreover, the overexpression of the panel of CSC markers combined with CA19-9 could improve our predictive ability for tumor recurrence in early stage CCA patients. This result may be beneficial for the patients in order to predict the outcome after treatment and may be useful for clinical intervention in order to improve patient survival.
Primary pulmonary myxoid sarcoma with EWSR1-CREB1 fusion: a case report and review of the literature
Authors: Chen Zhenwei , Yang Yihui , Chen Rongming , Ng Chi Sing , Shi Hongqi
Published: February 2020

Background

Primary pulmonary myxoid sarcoma (PPMS) is an extremely rare lung sarcoma that is characterized in most cases by recurrent balanced chromosomal translocation t(2;22)(q33;q12) leading to the oncogenic fusion gene EWSR1-CREB1.

Case presentation

We report a case of PPMS with molecular confirmation using fluorescence in situ hybridization (FISH) and DNA sequencing in a 45-year-old female patient. Computer tomography (CT) scanning revealed a peripheral circumscribed solid mass of 2.1 × 2 cm in the right lung superior lobe. Histologically, the tumor cells ranged from stellate, polygonal to chondrocyte-like or physaliferous-like, forming reticular network of delicate lace-like cellular strands and cords in abundant myxoid stroma. The tumor cell immunophenotype was positive for vimentin, EMA and negative for CK-pan, TTF-1, CAM5.2, S-100, calponin, SMA, desmin, ALK, CD31 and CD34. Molecular analysis demonstrated EWSR1-CREB1 gene fusion in this tumor. During 38 months of follow-up, the patient was alive with no clinical or radiological evidence of recurrence or metastasis.

Conclusion

PPMS is a rare low-grade sarcoma with distinct histological and genetic features. We add another case to the literature of this rare tumor and report for the first time occurrence of chondrocyte-like and physaliferous-like tumor cells in this tumor, thus enriching its morphologic and cytologic spectrum.
Wild edible ectomycorrhizal fungi: an underutilized food resource from the rainforests of Tshopo province (Democratic Republic of the Congo)
Authors: Milenge Kamalebo Héritier , De Kesel André
Published: February 2020

Background

Ectomycorrhizal (EcM) fungi constitute a source of income as well as proper food with considerable nutritional value. Although edible EcM fungi are highly diverse and expected to host considerable nutritional attributes, only few studies focus on their use and promotion in the province of Tshopo (DR Congo). This study provides original ethnomycological and diversity data on edible ectomycorrhizal rainforest fungi from the Man-and-Biosphere reserve of Yangambi and the reserve of Yoko.

Methods

The list of edible fungi follows the current taxonomy. Taxa were collected in plots situated in different types of rainforests. Each taxon is supported by herbarium reference specimens. Ethnomycological data on locally consumed EcM fungi were collected from randomly selected people living near the Man-and-Biosphere reserve of Yangambi and the Yoko reserve. People were interviewed using a semi-structured questionnaire. The interview campaign involved 160 informants, all randomly selected from 6 different ethnic communities.

Results

The results reveal that rainforests from the Yangambi Biosphere reserve and Yoko forest reserve provide a relatively high number of edible fungi, more than local people actually use. Mixed forest stands hold the highest diversity in saprotrophic edible fungi (pvalue < 0.001) while no significant difference (pvalue > 0.05) was observed in the number of saprotrophic and EcM fungi within monodominant forests. In spite of being accessible, this renewable natural resource is underexploited. Although a wide array of EcM fungi is available in primary forests dominated by ectomycorrhizal trees, local people’s major interest goes to the saprotrophic fungi from areas with degraded mixed forests.

Conclusion

The lack of local interest for EcM fungi is probably related to the considerable distance people have to cover to collect them. As a result, the edible EcM fungi from the Tshopo area represent a potentially interesting but underutilized resource.