bluuebunny/crossref_metadata_2025_split huggingface dataset:
Targeted next generation sequencing assays using triplet samples of normal breast tissue, primary breast cancer, and recurrent/metastatic lesions
Authors: Akahane Toshiaki , Kanomata Naoki , Harada Oi , Yamashita Tetsumasa , Kurebayashi Junichi , Tanimoto Akihide , Moriya Takuya 
Published: May 2020

Abstract
Background: Next generation sequencing (NGS) has shown that recurrent/metastatic breast cancer lesions may have additional genetic changes compared with the primary tumour. These additional changes may be related to tumour progression and/or drug resistance. The breast cancer-targeted NGS, however, is not still widely used for comparing genomic profile of primary breast cancer and recurrent/metastatic lesions in clinical practice.Methods: Genomic DNA was extracted from normal breast tissue, primary breast cancer, and recurrent/metastatic lesion(s) from the same patient. A DNA library was constructed using the QIAseq Human Breast Cancer Panel (93 genes, Qiagen) and then sequenced by a MiSeq (Illumina). The Qiagen web portal was utilized for data analysis.Results: Of 35 breast cancer cases with recurrence/metastases, successful results for three or four samples (normal breast tissue, primary tumour, and at least one metastatic/recurrent lesion) were obtained for 11 patients (36 samples). We detected shared somatic mutations in all but one patient, who had germline mutation in TP53. Additional mutations were detected in recurrent/metastatic lesions compared with primary tumour in genes including TP53 (three patients) and one case each of ATR, BLM, CBFB, EP300, ERBB2, MUC16, PBRM1, and PIK3CA. Actionable mutations and/or copy number variations (CNVs) were detected in 82% (9/11) of recurrent/metastatic breast cancer cases.Conclusions: The QIAseq Human Breast Cancer Panel assay could identify driver mutations in both primary breast tumour tissue and recurrent/metastatic lesions in almost all patients. This method can assist in identifying drug-targetable mutation and CNV in metastatic breast cancers.
Perinatal Mood and Anxiety Disorders, Serious Mental Illness, and Delivery-Related Health Outcomes, United States, 2006-2015
Authors: McKee Kimberly Schmitt , Admon Lindsay K. , Winkelman Tyler N. A. , Muzik Maria , Hall Stephanie , Dalton Vanessa K. , Zivin Kara 
Published: May 2020

Abstract
Background: National estimates of perinatal mood and anxiety disorders (PMAD) and serious mental illness (SMI) among delivering women over time, as well as associated outcomes and costs, are lacking. The prevalence of perinatal mood and anxiety disorders and serious mental illness from 2006-2015 were estimated as well as associated risk of adverse obstetric outcomes, including severe maternal morbidity and mortality (SMMM), and delivery costs using a serial, cross-sectional analysis of National Inpatient Sample data. The prevalence of PMAD and SMI were estimated among delivering women as well as obstetric outcomes, healthcare utilization, and delivery costs using adjusted weighted logistic with predictive margins and generalized linear regression models, respectively. Results: The study included an estimated 39,025,974 delivery hospitalizations from 2006-2015 in the U.S. PMAD increased from 18.4 (95% CI 16.4-20.0) to 40.4 (95% CI 39.3-41.6) per 1,000 deliveries. SMI also increased among delivering women over time, from 4.2 (95% CI 3.9-4.6) to 8.1 (95% CI 7.9-8.4) per 1,000 deliveries. Medicaid covered 72% (95% CI 71.2-72.9) of deliveries complicated by SMI compared to 44% (95% CI 43.1-45.0) and 43.5% (95% CI 42.5-44.5) among PMAD and all other deliveries, respectively. Women with PMAD and SMI experienced higher incidence of SMMM, and increased hospital transfers, lengths of stay, and delivery-related costs compared to other deliveries (P<.001 for all). Conclusion: Over the past decade, the prevalence of both PMAD and SMI among delivering women increased substantially across the United States, and affected women had more adverse obstetric outcomes and delivery-related costs compared to other deliveries.
Patterns of human exposure to malaria vectors in Zanzibar and implications for malaria elimination efforts
Authors: Monroe April , Msaky Dickson , Kiware Samson , Tarimo Brian B. , Moore Sarah , Haji Khamis , Koenker Hannah , Harvey Steven , Finda Marceline , Ngowo Halfan , Mihayo Kimberly , Greer George , Ali Abdullah , Okumu Fredros 
Published: May 2020

Abstract
Background Zanzibar provides a good case study for malaria elimination. The islands have experienced a dramatic reduction in malaria burden since the introduction of effective vector control interventions and case management. Malaria prevalence has now been maintained below 1% for the past decade and the islands can feasibly aim for elimination. Methods To better understand factors that may contribute to remaining low-level malaria transmission in Zanzibar, layered human behavioural and entomological research was conducted between December 2016 and December 2017 in 135 randomly selected households across six administrative wards. The study included: 1) household surveys, 2) structured household observations of nighttime activity and sleeping patterns, and 3) paired indoor and outdoor mosquito collections. Entomological and human behavioural data were integrated to provide weighted estimates of exposure to vector bites, accounting for proportions of people indoors or outdoors, and protected by insecticide-treated nets (ITNs) each hour of the night. Results Overall, 92% of female Anopheles mosquitoes were caught in the rainy season compared to 8% in the dry season and 72% were caught outdoors compared to 28% indoors. For individual ITN users, ITNs prevented an estimated two-thirds (66%) of exposure to vector bites and nearly three quarters (73%) of residual exposure was estimated to occur outdoors. Based on observed levels of ITN use in the study sites, the population-wide mean personal protection provided by ITNs was 42%. Discussion/Conclusions This study identified gaps in malaria prevention in Zanzibar with results directly applicable for improving ongoing programme activities. While overall biting risk was low, the most notable finding was that current levels of ITN use are estimated to prevent less than half of exposure to malaria vector bites. Variation in ITN use across sites and seasons suggests that additional gains could be made through targeted social and behaviour change interventions. However, even for ITN users, gaps in protection remain, with a majority of exposure to vector bites occurring outdoors before going to sleep. Supplemental interventions targeting outdoor exposure to malaria vectors, and groups that may be at increased risk of exposure to malaria vectors, should be explored.
Could age increase the strength of inverse association between ultraviolet B exposure and colorectal cancer?
Authors: Purushothaman Vidya Lakshmi , Cuomo Raphael E , Garland Cedric F , Mackey Tim Ken 
Published: May 2020

Abstract
Background: Vitamin D has been identified as a potential protective factor the development of colorectal cancer (CRC). We expect to see a stronger association of ultraviolet B (UVB) exposure and CRC crude rates with increasing age since chronic vitamin D deficiency leads to sustained molecular changes that increase cancer risk. The DINOMIT (disjunction, initiation, natural selection, overgrowth, metastasis, involution, and transition) model postulates various stages of cancer development due to vitamin D deficiency and the associated latency period. The purpose of this study is to examine this age-dependent inverse relationship globally.Methods: In this ecological study, a series of linear and polynomial regression tests were performed between country specific UVB estimates adjusted for cloud cover and crude incidence rates of CRC for different age groups. Multiple linear regression was used to investigate the association between crude incidence rates of colorectal cancer and UVB estimate adjusting for urbanization, skin pigmentation, smoking, animal consumption, per capita GDP, and life expectancy. Statistical analysis was followed by geospatial visualization by producing choropleth maps.Results: The inverse relationship between UVB exposure and CRC crude rates was stronger in older age groups at the country level. Quadratic curve fitting was preferred, and these models were statistically significant for all age groups. The inverse association between crude incidence rates of CRC and UVB exposure was statistically significant for age groups above 45 years, after controlling for covariates.Conclusion: The age-dependent inverse association between UVB exposure and incidence of colorectal cancer exhibits a greater effect size among older age groups in global analyses. Studying the effect of chronic vitamin D deficiency on colorectal cancer etiology will help in understanding the necessity for population wide screening programs for vitamin D deficiency, especially in regions with inadequate UVB exposure. Further studies are required to assess the need for adequate public health programs such as selective supplementation and food fortification.
Efficacy and safety of artesunate-amodiaquine and artemether-lumefantrine and prevalence of molecular markers associated with resistance, Guinea: an open-label two-arm randomized controlled trial
Authors: Beavogui Abdoul Habib , Camara Alioune , Delamou Alexandre , Doumbouya Abdoulaye , Kourouma Karifa , Bouedouno Patrice , Guilavogui Timothee , Santos Souza Samaly dos , Kelley Julia , Talundzic Eldin , Fofana Aissata , Plucinski Mateusz M , Diallo Mamadou Saliou 
Published: May 2020

Abstract
​ Background: Antimalarial resistance is a threat to recent gains in malaria control. This study aimed to assess the efficacy and safety of artesunate-amodiaquine (ASAQ) and artemether-lumefantrine (AL) in the management of uncomplicated malaria and to measure the prevalence of molecular markers of resistance of Plasmodium falciparum in sentinel sites in Maferinyah and Labé Health Districts in Guinea in 2016. Methods: This was a two-arm randomized controlled trial of the efficacy of AL and ASAQ among children aged 6-59 months with uncomplicated P. falciparum malaria in two sites. Children were followed for 28 days to assess clinical and parasitological response. The primary outcome was the Kaplan-Meier estimate of Day 28 (D28) efficacy after correction by microsatellite-genotyping. Pre-treatment (D0) and day of failure samples were assayed for molecular markers of resistance in the pfk13 and pfmdr1 genes. Results: A total of 421 participants were included with 211 participants in the Maferinyah site and 210 in Labé. No early treatment failure was observed in any study arms. However, 22 (5.3%) participants developed a late treatment failure (8 in the ASAQ arm and 14 in the AL arm), which were further classified as 2 recrudescences and 20 reinfections. The Kaplan-Meier estimate of the corrected efficacy at D28 was 100% for both AL and ASAQ in Maferinyah site and 99% (95% Confidence Interval: 97.2-100%) for ASAQ and 99% (97.1-100%) for AL in Labé. The majority of successfully analyzed D0 (98%, 380/389) and all day of failure (100%, 22/22) samples were wild type for pfk13 . All 9 observed pfk13 mutations were polymorphisms not associated with artemisinin resistance. The NFD haplotype was the predominant haplotype in both D0 (197/362, 54%) and day of failure samples (11/18, 61%) successfully analyzed for pfmdr1 . Vomiting was the most common observed side effect (14%) across all arms. Conclusions: This study observed high efficacy and safety of both ASAQ and AL in Guinea, providing evidence for their continued use to treat uncomplicated malaria. Continued monitoring of ACT efficacy and safety and molecular makers of resistance in Guinea is important to detect emergence of parasite resistance and to inform evidence-based malaria treatment policies.
Identification and genetic analysis of qCL1.2 , a novel allele of the “green revolution” gene SD1 from wild rice ( Oryza rufipogon ) that enhances plant height
Authors: Zhang Lizhen , Huang Jingfen , Wang Yanyan , Xu Rui , Yang Ziyi , Zhao Zigang , Liu Shijia , Tian Yunlu , Zheng Xiaoming , Li Fei , Wang Junrui , Song Yue , Li Jiaqi , Cui Yongxia , Zhang Lifang , Cheng Yunlian , Lan Jinhao , qiao weihua , Yang Qingwen 
Published: May 2020

Abstract
Background: The exploitation of novel alleles from wild rice that were lost during rice cultivation could be very important for rice breeding and evolutionary studies. Plant height (PH) was a target of artificial selection during rice domestication and is still a target of modern breeding. The “green revolution” gene semi-dwarf 1 (SD1) were well documented and used in the past decades, allele from wild rice could provide new insights into the functions and evolution of this gene.Results: We identified a PH-related quantitative trait locus, qCL1.2, from wild rice using a set of chromosome segment substitution lines. qCL1.2 encodes a novel allele of SD1 gene. The wild allele of SD1 is a dominant locus that can significantly promote rice internode length by regulating the expression levels of genes involved in gibberellin biosynthesis and signal transduction. Nucleotide diversity and haplotype network analyses of the SD1 gene were performed using 2,822 rice landraces. Two previously reported functional nucleotide polymorphisms clearly differentiated japonica and indica rice; however, they were not associated with PH selection. Other new functional nucleotide polymorphisms in the coding, but not promoter, regions were involved in PH selection during rice domestication. Our study increases understanding of the rice SD1 gene and provides additional evidence of this gene’s selection during rice domestication.Conclusions: Our findings provide evidence that SD1 gene from wild rice enhances plant height and new functional nucleotide polymorphisms of this gene were artificially selected during cultivated rice differentiation.
The Correlation between Follow-up MRI Findings and Laboratory Results in Pyogenic Spondylodiscitis
Authors: Ahn Kyung-Sik , Kang Chang Ho , Hong Suk-Joo , Kim Baek Hyun , Shim Euddeum 
Published: May 2020

Abstract
Background Although MRI is the gold-standard imaging method in the diagnosis of spondylodiscitis, role of follow-up imaging is debated and there can be discrepancies with regard to the significance of bony or soft tissue responses to treatment. Purpose of our study is to test whether the MRI changes on follow-up imaging correlate with laboratory findings of treatment response. Methods A total of 48 patients with pyogenic spondylodiscitis who underwent baseline and follow-up MRI were retrospectively reviewed. The extent of bone marrow edema, paravertebral soft tissue inflammation, and disc height were compared on baseline and follow-up MRIs with the C-reactive protein (CRP) and erythrocyte sedimentation rate (ESR) levels obtained from the medical records at baseline and on follow-up. Relationships between the MRI and laboratory changes were analyzed using the Spearmann correlation test. Results The mean MRI follow-up period was 42.25 days. Based on the CRP (resolved: n=19, resolving: n=19, and aggravated: n=10), there was significant correlation between the laboratory results and the changes in the bone and soft tissues (p < 0.01, both). The correlation was best with soft tissue changes (rho: 0.48) followed by bony changes (rho: 0.41). Based on the ESR (resolved: n=8, resolving: n=22, and worsened: n=18), the correlation was stronger with bone changes (rho: 0.45, p < 0.01) than it was with soft tissue changes (rho: 0.39, p = 0.01). Conclusion Follow-up MRI findings of pyogenic spondylodiscitis show variable tissue responses. CRP was best correlated with soft tissue changes, while ESR showed the best association with bony changes.
WITHDRAWN: Role of Organizations in Preparedness and Emergency Response to Flood Disaster in Bangladesh
Authors: Hossain Babul 
Published: May 2020

Abstract
The present study is to know the role of organizations and make an assessment on their performances regarding preparedness and emergency response of flood disaster affected people. This study has used a mixed-method approach. Flood-affected people were the respondents to evaluate the organizational role. The study reveals that before the flood in 2017 to minimize the loss and damages, the GOs play a very effective role concerning the arrangement of preparatory meetings and preparing shelter centers, and NGOs play a very useful role in making arrangements for awareness-building training. During the emergency period, the GOs played a comparatively better role in providing CI sheets and cash money as relief for establishing housing facilities and emergency support. The NGOs played relatively a better role in providing food, water, clothes, medicine, etc. This study put forward complications such as limited sanctions, disruption of communication, lack of awareness of sufferers, and overlapping. The findings of this study would be a significant for the disaster policymakers, and civil societies.
Eating disorders among patients with borderline personality disorder: understanding the prevalence and psychopathology
Authors: Khosravi Mohsen 
Published: May 2020

Abstract
Background: Treatment protocols can be bolstered and etiological and maintenance factors can be recognized more easily by a superior understanding of emotions and emotion regulation in the comorbidity of borderline personality disorder (BPD) and feeding and eating disorders (FEDs). Therefore, the present study aimed at investigating the prevalence and psychopathology of FEDs in patients with BPD.Methods: In this cross-sectional study, 220 participants were examined in three groups, namely BPD (n = 38), BPD+FEDs (n = 72), and the healthy control (n = 110), from August 2018 to November 2019. The participants were selected by systematic random sampling among the patients who referred to Baharan psychiatric hospital in Zahedan, Iran, with the sampling interval of 3. The subjects were evaluated by borderline personality inventory (BPI), structured clinical interview for DSM-5 personality disorders (SCID-5-PD), structured clinical interviews for DSM-5: research version (SCID-5-RV), the 26-item eating attitudes test (EAT-26), 20-item Toronto alexithymia scale (TAS-20), Beck anxiety disorder (BAI), and Beck depression inventory-II (BDI-II). Results: The results showed a 65.4% (n = 72) prevalence of FEDs in patients with BPD. Also, the highest and lowest prevalence rates were reported for “other specified feeding and eating disorders” (51.3%) and “bulimia nervosa” (6.9%), respectively. Although the highest mean score of TAS-20 was related to anorexia nervosa, there was no significant difference between the scores of various types of FEDs. The mediation analysis showed that anxiety and depression would play a mediating role in the relationship between alexithymia and eating-disordered behaviors. Conclusions: The results have suggested that alexithymia, anxiety, and depression should receive clinical attention as potential therapeutic targets in the comorbidity of BPD and FEDs. The clinical implications of the research have been conducted to date, and directions for future research have been discussed.
Neuroprotective effect of Indobufen against pyroptosis following cerebral ischemia-reperfusion injury both in vivo and in vitro
Authors: Zhang Tian , Xu Dan , Li Fengyang , Liu Rui , Hou Kai , Gou Xue , Liu Jia , Fang Weirong , Li Yunman 
Published: May 2020

Abstract
Background: Indobufen is a new generation of antiplatelet agents and has been shown to have antithrombotic effects in animal models. However, the efficacy of Indobufen on cerebral ischemia/reperfusion (I/R) injury and its mechanisms remain to be investigated. Methods: In this study, the efficacy of Indobufen with both pre- and post-treatment on rats suffering middle cerebral artery occlusion/reperfusion (MCAO/R) was investigated. Furthermore, human umbilical vein endothelial cells (HUVECs) were cultured and underwent oxygen glucose deprivation/reoxygenation (OGD/R) injury for in vitro studies. Relationship between Indobufen and pyroptosis associated NF-κB/Caspase-1/GSDMD pathway was preliminarily discussed. Results: The pharmacodynamic tests revealed that Indobufen ameliorated I/R injury by decreasing the platelet aggregation, infarct size, brain edema and neurologic impairment in rats and rescuing cell apoptosis/pyroptosis in HUVECs. The underlying mechanisms were probably related to pyroptosis suppression by regulating the NF-κB/Caspase-1/GSDMD pathway. Conclusion: Overall, these studies indicates that Indobufen exerts protective and therapeutic effects against I/R injury by pyroptosis suppression via downregulating NF-κB/Caspase-1/GSDMD pathway.
Current Status of Scientific Research Accomplishments of Senior Eight-year-program Medical Students in China: A Multicenter Cross-sectional Questionnaire-based Study
Authors: Wan Mengyao , Liu Shuang , Zhu Jiawei , Xiao Sulong , Yuan Lei , Lei Xiaokang , Lei Hao , Shi Xiaomeng , You Wen , Ruan Gechong , Li Ji , Qian Jiaming 
Published: May 2020

Abstract
Backgrounds: Among the distinct medical education systems in China, the eight-year program is an elite program dedicated to cultivating physician scientists. Although the research ability of senior students in eight-year medical programs is a pivotal quality, it remains unclear. This study aimed to clarify the current status and challenges of students’ research experience, abilities and outputs.Methods: A multicenter cross-sectional study was conducted in five medical schools in northern China. Electronic questionnaires were sent to 235 randomly chosen fifth-grade or sixth-grade eight-year-program medical students. A total of 211 responses were collected and analyzed using SPSS 22.0.Results: Only 13.3% of participants chose research as their future career goal. Students generally felt that conducting research was stressful and difficult. The greatest obstacle was a lack of time due to heavy workloads. The two major motivations for research were graduation and future employment (75.8%) and research interest (24.2%). More than half of the students (142, 67.3%) had research experience by the time of the survey, among whom 84 students already had research outputs. A higher proportion of students with outputs was motivated by the requirements for graduation or employment compared to students without outputs (71.4% vs. 55.2%, P = 0.046).Conclusions: Senior eight-year-program medical students in China generally had high pressure to conduct research and devoted their efforts to overcome these challenges. More guidance and novel encouragement to enhance students’ initiative and interest in research could be provided by medical schools and educators in the future.
Comparative Study OCT versus MRI T2 in Diagnosis of Degenerative Cartilage Lesions
Authors: Faur Cosmin Ioan , Abu-Awwad Ahmed , Tudoran Mariana , Ungureanu Ana Maria , Tudoran Cristina , Patrascu Jenel Marian , Sinescu Cosmin 
Published: May 2020

Abstract
BackgroundWhen diagnosed early, degenerative cartilage lesions are reversible if the appropriate therapeutical measures are applied. Currently available diagnostic methods (radiography, MRI and arthroscopic examination) do not provide the accuracy needed in the early diagnosis of these lesions.MethodsThe aim of the study is to analyse, in an ex vivo study on osteochondral fragments taken from patients undergoing total knee arthroplasty, weather the OCT technique is effective in detecting these lesions. The results will be compared to the preoperative MRI images (especially T2 mapping technique).ResultsThe percentage of the agreement between the two reviewers was 89% (8 out of 9 cases) during the OCT examination process.ConclusionOCT is a new technique potentially useful in the diagnosis of cartilage lesions. The possibility of performing it through minimally invasive techniques currently (arthroscopic surgery) further increases the value of this technique. OCT is a non-destructive diagnosing technique in degenerative cartilage lesions whose efficiency is comparable to MRI T2 technique and superior to conventional MRI.