bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metastatic breast cancer patient perception of somatic tumor genomic testing
Authors: Adams Elizabeth J. , Asad Sarah , Reinbolt Raquel E. , Collier Katharine A. , Abdel-Rasoul Mahmoud , Gillespie Susan , Chen James L. , Cherian Mathew A. , Noonan Anne M. , Sardesai Sagar , VanDeusen Jeffrey , Wesolowski Robert , Williams Nicole , Shapiro Charles L. , Macrae Erin R. , Toland Amanda E. , Senter Leigha , Ramaswamy Bhuvaneswari , Lee Clara N. , Lustberg Maryam B. , Stover Daniel 
Published: October 2019

Abstract
Purpose: To assess metastatic breast cancer (MBC) patient perceptions and comprehension of tumor genomic testing and to evaluate associations with psychological wellbeing. Methods: In a prospective, single institution, single-arm trial, patients with MBC underwent next-generation sequencing at study entry, with sequencing results released at progression. Patients who completed surveys before undergoing sequencing were included in the study (n=58). We administered four validated psychosocial measures: Center for Epidemiologic Studies Depression Scale, Beck Anxiety Inventory, Trust in Physician Scale, and Communication and Attitudinal Self-Efficacy scale for Cancer. Genetic comprehension was assessed using 7-question objective and 6-question subjective measures. Longitudinal data were assessed using paired Wilcoxon signed rank and McNemar’s test of agreement. Results: There were no significant differences between the beginning and end of study in depression, anxiety, physician trust, or self-efficacy (median time on study: 7.6 months). Depression and anxiety were positively associated with each other and both negatively associated with self-efficacy. Self-efficacy decreased from pre- to post-genomic testing (p=0.05). There was a wide range of objective genetics comprehension and comprehension was significantly lower in non-white patients (p=0.02) and patients with lower income (p=0.04). Patients expressed increased confidence in their ability to teach others about genetics at end of study. Conclusions: This is the only study, to our knowledge, to longitudinally evaluate multiple psychological metrics in MBC as patients undergo tumor genomic testing. Among patients with MBC, depression and anxiety metrics were negatively correlated with patient self-efficacy. Patients undergoing somatic genomic testing had limited genomic knowledge, which varied by demographic groups.
Transcriptomic profiling revealed key signaling pathways for cold tolerance and acclimation of two carp species
Authors: Ge Guodong , Long Yong , Shi Lianyu , Ren Jing , Yan Junjun , Li Chitao , Li Qing , Cui Zongbin 
Published: October 2019

Abstract
Background Closely related species of the carp family ( Cyprinidae ) have evolved distinctive abilities to survive under cold stress, but molecular mechanisms underlying the generation of cold resistance remain largely unknow. In this study, we compared transcriptomic profiles of two carp species to identify key factors and pathways for cold tolerance and acclimation. Results Larvae of Songpu mirror carp and Barbless carp that were pretreated at 18°C for 24 hours significantly improved their survival rates under lethal cold temperature at 8°C or 10°C, indicating that two carp species possess the ability of cold acclimation. However, Songpu mirror carp exhibited stronger abilities of cold tolerance and acclimation than Barbless carp. Transcriptomic profiles of Songpu mirror carp and Barbless carp larvae at 28°C and 18°C were compared during cold acclimation through RNA-seq. Differentially expressed genes that are closely associated with the differences in cold acclimation between two carp species were identified through bioinformatics and Venn's diagram analysis. GO enrichment analysis of these genes indicated that cellular component assembly involved in morphogenesis, secondary alcohol metabolism and drug transport were the most up-regulated biological processes during cold acclimation of Songpu mirror carp. Conversely, positive regulation of macroautophagy, intracellular protein transport, and organonitrogen compound catabolism were the most down-regulated biological processes during cold acclimation of Barbless carp. KEGG enrichment analysis revealed that factors in the FoxO-related signaling pathways are mainly responsible for the development of differences in cold tolerance and acclimation between two carp species since altering the phosphorylation of key proteins in the FoxO-related signaling pathways with inhibitors or an activator significantly decreased the cold tolerance and acclimation of Songpu mirror carp. These data provided key clues for dissection of molecular mechanisms underlying the development of cold tolerance and acclimation in carps. Conclusions These findings indicate that larvae of two carp species possess different abilities of cold tolerance and can build cold acclimation under mild low temperature. Multiple biological processes and FoxO-related signaling pathways are closely associated with the development of differences in cold tolerance and acclimation between two carp species. Keywords: Carp; cold tolerance; cold acclimation; RNA-Seq; biological process; signaling pathways
Evolution of PHAS Loci in the Young Spike of Allohexaploid Wheat
Authors: Zhang Rongzhi , Huang Siyuan , Li Shiming , Song Guoqi , Li Yulian , Li Wei , Li Jihu , Gao Jie , Gu Tiantian , Li Dandan , Zhang Shujuan , Li Genying 
Published: October 2019

Abstract
Background PhasiRNAs (phased secondary siRNAs) play important regulatory roles in the development processes and biotic and abiotic stresses in plants. A class of phasiRNAs involve in the reproductive development in grasses. Reproductive-associated phasiRNAs include two categories, 21-nt (nucleotide) and 24-nt phasiRNAs, which are triggered by miR2118 and miR2275 in premeiotic and meiotic anthers, respectively, which had been reported in rice, maize and other grass species. However, there were still absence in Triticum The allohexaploid wheat ( Triticum aestivum ) genome consists of three closely related subgenomes (subA, subB and subD), which is a model of allopolyploid in plants. And the evolution of PHAS loci in polyploid plants is still unavailable.Results Here, using 261 small RNA expression datasets from various tissues, a batch of PHAS (phasiRNA precursors) loci were identified in the young spike of wheat, most of which were triggered by miR2118 and miR2275 in their target site regions. Dissection of PHAS and their trigger miRNAs among the diploid (AA and DD), tetraploid (AABB) and hexaploid (AABBDD) genomes of Triticum indicated that distribution of PHAS loci were dominant randomly in local chromosomes, while their trigger miR2118 was dominant only in the subB genome. The diversity of PHAS loci in the three subgenomes of wheat and their progenitor genomes (AA, DD and AABB) suggested that they originated or diverged before the occurrence of AABB. The positive relationship between the PHAS loci or the trigger miRNAs and the ploidy of genome indicated the expansion of genome was the major drive force for the increase of PHAS loci and their trigger miRNAs in Triticum . In addition, the PHAS transcripts responded to abiotic stresses such as cold stress in wheat.Conclusions Altogether, non-coding phasiRNAs are conserved transcriptional regulators that display quick plasticity in genome dominance and sequence diversity and are involved in reproductive development and abiotic stress in wheat. It could be referred to molecular research on male reproductive development in Triticum .
Reconstruction and analysis of genome-scale metabolic model of weak Crabtree positive yeast Lachancea kluyveri
Authors: Nanda Piyush , Patra Pradipta , Das Manali , Ghosh Amit 
Published: October 2019

Abstract
Background Lachancea kluyveri , a weak Crabtree positive yeast, has been extensively studied for the unique URC pyrimidine catabolism it harbours. It produces more biomass than Saccharomyces cerevisiae due to the underlying Crabtree effect and resorts to fermentation only in oxygen limiting conditions that makes it suitable host for industrial scale protein production. Ethyl acetate, an important industrial chemical, has been demonstrated to be a major overflow metabolite during aerobic batch cultivation with a specific rate of 0.12 g per g dry weight per hour. Here, we attempted to reconstruct the metabolism of the yeast from the genome to better explain the observed phenotypes and aid further hypothesis generation. Results We report the first genome-scale metabolic model, iPN730, using Build Fungal Model in KBase workspace. The inconsistencies in the model were manually corrected using literature and published datasets. The model comprises of 1235 reactions, 1179 metabolites and 730 genes distributed in 8 compartments. The in silico viability and the growth rates in various carbon sources show good agreement. The gene essentiality of the metabolic model also performs well in comparison to experimental data confirmed by statistical analysis. Dynamic flux balance analysis describes the growth dynamics, substrate utilization and product formation kinetics in various oxygen limited conditions. The URC pyrimidine degradation pathway incorporated into the model enables it to grow on uracil or urea as the sole nitrogen source. Conclusion The genome-scale metabolic construction of L. kluyveri provides better understanding of metabolism, particularly that of pyrimidine metabolism and ethyl acetate production. Metabolic flux analysis using the model will enable hypotheses generation to gain deeper understanding of metabolism in weakly Crabtree positive yeast.
Relationship between platelet count and hepatic failure and residual liver regeneration after hemihepatectomy in patients with hepatitis B-related primary hepatocellular carcinoma
Authors: Ye Chuhui , Xu Banghao , Lu Kaiyi , Lu Tingting , Zhang Ling , Zeng Jingjing , Guo Ya , Peng Minhao , Wen Zhang 
Published: October 2019

Abstract
Objective A retrospective analysis of the influences of platelet (PLT) counts on liver failure and liver regeneration in patients with primary hepatocellular carcinoma (HCC) provides a treatment strategy for clinical prevention and treatment of postoperative liver failure and residual liver regeneration. Method The clinical data of 111 patients with a background of hepatitis B virus infection and who underwent (expanded) half liver resection at the First Affiliated Hospital of Guangxi Medical University from June 2012 to June 2017 were collected and statistically analyzed. Results　On the basis of the International Study Group of Liver Surgery liver failure-grading standards and Dino–Clavien postoperative complication criteria, the incidence of grade B and above liver failure was 55%, and complication II level and above was 47.5% in the PLT decline group after semihepatectomy. The incidence rates in the normal group were 26.8% and 23.9%. A statistically significant difference was determined in the two groups (P1=0.003, P2 = 0.011). The average volumes of liver hyperplasia (residual liver volume (RLV)80.4 days − RLV) in the PLT decline and normal groups were 132.09 ± 61.89 cm3 and 190.89 ± 91.98c cm3, respectively; the average rates of hyperplasia ((RLV80.4days−RLV)/RLV) were 16.59%± 7.36% and 24.78% ± 10.82%. The difference between the two groups was statistically significant (PProliferation = 0.001, PProliferation rate = 0.001). Univariable and multivariable logistic regression analyses of postoperative liver failure grade and proliferation rate in patients who underwent semihepatectomy suggested that the decrease in postoperative PLT count (PLT < 125 × 109/L) might be an independent risk factor of severe posthepatectomy liver failure (PHLF) (PHLF-B or above) and residual liver regeneration rate for patients with primary HCC after half liver resection. No death occurred. Conclusions A correlation existed between PLT count and postoperative PHLF or liver regeneration. Monitoring PLT counts after liver resection may help us predict the suffering from PHLF-B or above and severe postoperative complications.
The Influence of dietary diversity on the nutritional status of children between 6 and 23 months of age in Tanzania
Authors: Khamis Ahmed Gharib , Mwanri Akwilina Wendelin , Ntwenya Julius Edward , Kreppel Katharina 
Published: October 2019

Abstract
Background Undernutrition poses a serious health challenge in developing countries. Tanzania has the highest undernutrition burdens in East and Southern Africa. Poor infant and young child feeding practices including consumption of undiversified diet are the main cause for undernutrition. There is limited information regarding the association between dietary diversity and undernutrition in Tanzania. The objective of this paper was to examine to what extent the dietary diversity is associated with undernutrition of children of 6 to 23 months in Tanzania.Methods This is a secondary data analysis from data collected by the Tanzania Demographic and Health Survey of 2015-2016. Stunting, wasting and underweight were calculated from Z-scores based on 2006 WHO standards. A dietary diversity score was created by summing the number of food groups reported for each child by the mother ranging from 0 to 7. Then, a Minimum Dietary Diversity (MDD) indicator was used to assess the diversity of the diet given to children. Bivariate and multivariate logistic regression techniques were used to assess the odds ratios of becoming undernourished.Results A total of 2,960 children were enrolled in this study. The majority (73.9%) of children did not reach the recommended Minimum Dietary Diversity (MDD). The most commonly consumed types of foods were grains, roots and tubers (91%), and Vitamin A containing fruits and vegetables (65%). Consumption of a diverse diet was significantly associated with a reduction of stunting, wasting and being underweight in children. The likelihood of being stunted, wasted and underweight was found to decrease as the number of food group consumed increased. Children who did not received an MDD diet had a significantly higher likelihood of being stunted (AOR=1.37, 95% CI; 1.13-1.65) and underweight (AOR=1.49, 95% CI; 1.15-1.92), but this was not the case for wasting. Consumption of animal source foods has been found to be associated with reduced stunting among children.Conclusion Consumption of a diverse diet was associated with a reduction in undernutrition among children of 6 to 23 months in Tanzania. Measures to improve the type of complementary foods in order to meet the energy and nutritional demands of children should be considered in Tanzania.
Seniors’ Campus Continuums: Local Solutions for Broad Spectrum Seniors Care
Authors: Morton-Chang Frances Margaret , Majumder Shilpi , Berta Whitney 
Published: October 2019

Abstract
Background As demand and desire to “age-in-place” grows within an aging population, challenges exist to realizing this wish. Changing demographics and new areas of need have governments nationally and internationally calling for more focused attention on integrative approaches to health and well-being. Seniors’ Campus Continuums seek bridge the “divide” between health and social care for residents and local community. This paper investigates factors that influence Campus evolution, ongoing functioning, and ability to offer wrap around care for older adults wishing remain in their own home and community. Methods This research uses a comparative case study approach across multiple bounded cases to explore how Seniors’ Campus Continuums operating in various contexts integrate health, housing and social care around older adults living on the campus and in the local community. Six seniors’ campuses from across Ontario offering four physically co-located components – mixed independent housing options, internal community supports to residents, external community supports to the broader community, and a long-term care home – were studied and compared. Results Eight factors that promote or impede Seniors’ Campus Continuum evolution, design and function, and ability to provide wrap-around care to older adults with progressive needs are identified including: i. historical legacies; ii. windows of opportunity; iii. organizational structure and capacity; iv. intentional physical and social design; v. campus services mix, amenities and partnerships; vi. policy rigidities and enablers; vii. human resources shortages and innovation; viii. funding limitations and opportunities. Together these factors describe opportunities to optimize care on many levels. Conclusion Seniors’ Campus Continuums offer creative boundary-spanning approaches to address a variety of needs while taking into account local contexts. At an individual level, campuses increase access to a range of care supports and housing options to benefit seniors’ health and wellbeing. At an organizational level, they offer consistency and coordination of care, improved economies of scale, and rich environments for training/research, education and volunteering. At a system level, they offer potential to help people avoid ending up in the “wrong places.” This study fills a gap in evidence-based research around understanding of this integrative model and offers lessons learned for future development.
Different arrhythmic prognosis in high-risk arrhythmogenic right ventricular cardiomyopathy according to the indication of the defibrillator
Authors: Ruiz-Salas Amalio , Navarro-Arce Isabel , Medina-Palomo Carmen , Barrera-Cordero Alberto , Jiménez-Navarro Manuel , Rueda-Calle Eloy , García-Pinilla José Manuel , Cabrera-Bueno Fernando , Morcillo-Hidalgo Luis , Gómez-Doblas Juan José , Alzueta Javier 
Published: October 2019

Abstract
Background: Arrhythmogenic right ventricular cardiomyopathy (ARVC/D) is an inherited cardiomyopathy characterized by ventricular arrhythmias and heart failure. The aim of our study was to analyze the impact of the ICD indication in the prognosis of patients with high-risk ARVC/D according to the consensus document. Methods The high-risk category includes patients who experienced cardiac arrest due to sustained ventricular tachycardia or ventricular fibrillation and patients with severe right or left ventricular dysfunction. We included 41 patients with high-risk ARVC/D: 33 in secondary prevention and 8 in primary prevention. Results We followed 41 patients during 6.37 ± 4.88 years. Twenty-six patients (63.4%) had at least one appropriate arrhythmic event: 24 p (72.7%) in secondary prevention and 2 p (25%) in primary prevention; p=0.02. Twenty-four patients (72.7%) in secondary prevention and five (62.5%) in primary prevention had a cardiovascular event such as arrhythmias, admission due to heart failure, heart transplantation or cardiovascular death. Conclusions High-risk ARVC/D patients had a high number of cardiovascular events, but their nature and treatment were different. Arrhythmic prognosis was worse in secondary prevention and most of the events found in primary prevention were related to heart failure and, therefore, without benefit of the ICD.
Tumour Content Ratio Matters for Detecting Epidermal Growth Factor Receptor Mutation by Cobas Test in Small Biopsies; a Retrospective Study
Authors: Kogo Mariko , Fujimoto Daichi , Hosoya Kazutaka , Nagata Kazuma , Nakagawa Atsushi , Tachikawa Ryo , Yamashita Daisuke , Kitamura Yuka , Imai Yukihiro , Tomii Keisuke 
Published: October 2019

Abstract
Background
Recent studies indicate the benefit of treatment with osimertinib over that with conventional epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKI) for untreated EGFR -mutated non-small cell lung cancer (NSCLC). Cobas ver2 is the only companion diagnostic method for detecting EGFR mutations with osimertinib treatment. We clinically experience false negative cases with this test, but its actual sensitivity is unknown. Moreover, no study has suggested the importance of tumour dissection, and most facilities do not routinely perform them on small biopsies. The purpose of this study was to evaluate the sensitivity of cobas in clinical practice and clarify the role of dissection as a component of the cobas testing

Materials and Methods
We examined 132 patients with EGFR -mutated NSCLC diagnosed by bronchoscopy and confirmed with PCR clamp. Patients were tested with cobas and the EGFR -positive rate was calculated. Samples with undetected EGFR mutations were retested after tumour dissection and the rate of samples whose EGFR mutation was corrected to positive was assessed. To evaluate tumour cellularity, the tumour content ratio was assessed by calculating tumour cell count over the total cell count on the slide.

Results
The positive rate of EGFR mutation identification was 76% with cobas, although EGFR mutation-negative patients retained responses to TKI therapy equivalent to positive patients did; however, the tumour content ratio of negative samples was significantly lower than that of positive samples. Twenty-nine negative samples underwent dissection and 24% were corrected to positive. Moreover, 53% of the samples with a tumour content ratio below 10% was negative for cobas, but 33% of these turned positive after dissection.

Conclusion
Cobas had a high false negative rate in clinical practice, and tumour content ratio might be associated with this rate. Dissection could improve the sensitivity of cobas, especially in samples with low tumour cellularity.
A prospective study of erectile dysfunction in men after pelvic surgical procedures and its association with non - modifiable risk factors
Authors: Artemi Sofia , Vassiliu Panteleimon , Arkadopoulos Nikolaos , Smyrnioti Maria - Eleni , Sarafis Pavlos , Smyrniotis Vasileios 
Published: October 2019

Abstract
Objective: Erectile dysfunction can be caused iatrogenically, due to pelvic surgery. The purpose of this study was to evaluate sexual function at various times after pelvic surgery in male patients and to investigate the non-modifiable risk factors associated with the presence and intensity of sexuality in these patients.
Results: The mean age of the participants was 66.16 ± 13.07 years old. Regarding comorbidity, 47.2% reported various cardiovascular problems, 20.8% hypertension, 9.4% diabetes mellitus and 5.7% depression. A history of colectomy was present in 36.8%, 18.9% had undergone sigmoidectomy, and 33% inguinal hernia repair. The percentage of severe erectile function increased from 38.7% before surgery to 48.1% (25% increase) after surgery, at the end of the follow-up period (p <0.05). In the multivariate analysis model, age emerged as an independent predictor of erectile function ( p <0.001). Age was the most important determinant of the IIEF score, which was aggravated by 25% from the first to the last assessment of patients.