bluuebunny/crossref_metadata_2025_split huggingface dataset:
Artificial intelligence in clinical and genomic diagnostics
Authors: Dias Raquel , Torkamani Ali 
Published: November 2019

AbstractArtificial intelligence (AI) is the development of computer systems that are able to perform tasks that normally require human intelligence. Advances in AI software and hardware, especially deep learning algorithms and the graphics processing units (GPUs) that power their training, have led to a recent and rapidly increasing interest in medical AI applications. In clinical diagnostics, AI-based computer vision approaches are poised to revolutionize image-based diagnostics, while other AI subtypes have begun to show similar promise in various diagnostic modalities. In some areas, such as clinical genomics, a specific type of AI algorithm known as deep learning is used to process large and complex genomic datasets. In this review, we first summarize the main classes of problems that AI systems are well suited to solve and describe the clinical diagnostic tasks that benefit from these solutions. Next, we focus on emerging methods for specific tasks in clinical genomics, including variant calling, genome annotation and variant classification, and phenotype-to-genotype correspondence. Finally, we end with a discussion on the future potential of AI in individualized medicine applications, especially for risk prediction in common complex diseases, and the challenges, limitations, and biases that must be carefully addressed for the successful deployment of AI in medical applications, particularly those utilizing human genetics and genomics data.
Nutritional deficiency and associated factors among new pulmonary tuberculosis patients of Bale Zone Hospitals, southeast Ethiopia
Authors: Hussien Bedru , Hussen Mohammedaman Mama , Seid Abdulwahab , Hussen Abduljewad 
Published: November 2019

Abstract
Objective
Tuberculosis remains deadliest communicable diseases accountable for health problem among various individuals annually and is related to malnutrition. Addressing nutritional deficiency in Tuberculosis patients is a crucial side of tuberculosis management programme. Therefore, the aim was to assess the magnitude of nutritional deficiency and associated factors among new pulmonary tuberculosis patients of Bale Zone Hospitals, south-east Ethiopia, 2018. Cross-sectional study design was utilized. Data collection was carried out using structured questionnaires and anthropometric measurements. Body mass index was calculated to see nutritional deficiency. Crude and adjusted odds ratios in conjunction with their corresponding 95% confidence intervals were computed. p-value < 0.05 was thought of to declare a result as statistically associated.

Results
Prevalence of nutritional deficiency was 63.2%. The mean Body mass index for all listed participants was 17.86 kg/m2. Employment status of the patients, p-value 0.012 (AOR = 1.82; 95% CI 1.14, 2.89) and Khat chewing, p-value 0.02 (AOR = 0.43; 95% CI 0.23, 0.85) were factors independently associated with nutritional deficiency. Prevalence of nutritional deficiency was found to be high. Nutritional support for the impoverished, regular nutritional assessment and dietary counseling are necessary for better treatment outcome and effective Tuberculosis management programme.
Determinants of underweight among 6–59 months old children in Berahle, Afar, North East Ethiopia: a case control study 2016
Authors: Hintsa Solomon , Gereziher Kiros 
Published: November 2019

Abstract
Objective
The objective of this study was to identify determinants of underweight among 6–59 months old children in Berahle Woreda, Afar, North East Ethiopia, in 2016.

Result
The median age (IQR) of cases and controls were 24 (34) and 18 (23) months respectively and 51.6% of the children were not exclusively breast-fed but 64.8% controls were exclusively breastfed. Age group of 48–59 months (AOR = 11.93; 95% CI 3.88–36.67), illiterate mothers (AOR = 2.32; 95% CI 1.19–4.55), low dietary diversity (AOR = 4.57; 95% CI 2.40–8.69), diarrhea in the past of 2 weeks (AOR = 2.93; 95% CI 1.46–5.85), birth interval (AOR = 5.17; 95% CI 2.37–11.26) and unprotected source of water (AOR = 2.62; 95% CI 1.42–4.85) were determinant factors of underweight.
Human mesenchymal stromal cells broadly modulate high glucose-induced inflammatory responses of renal proximal tubular cell monolayers
Authors: Islam Md Nahidul , Griffin Tomás P. , Sander Elizabeth , Rocks Stephanie , Qazi Junaid , Cabral Joana , McCaul Jasmin , McMorrow Tara , Griffin Matthew D. 
Published: November 2019

AbstractBackgroundRenal proximal tubular epithelial cells (RPTEC) are dysfunctional in diabetic kidney disease (DKD). Mesenchymal stromal cells (MSC) may modulate DKD pathogenesis through anti-inflammatory mediators. This study aimed to investigate the pro-inflammatory effect of extended exposure to high glucose (HG) concentration on stable RPTEC monolayers and the influence of MSC on this response.MethodsMorphologically stable human RPTEC/TERT1 cell monolayers were exposed to 5 mM and 30 mM (HG)D-glucoseor to 5 mMD-glucose + 25 mMD-mannitol(MAN) for 5 days with sequential immunoassays of supernatants and end-point transcriptomic analysis by RNA sequencing. Under the same conditions, MSC-conditioned media (MSC-CM) or MSC-containing transwells were added for days 4–5. Effects of CM from HG- and MAN-exposed RPTEC/MSC co-cultures on cytokine secretion by monocyte-derived macrophages were determined.ResultsAfter 72–80 h, HG resulted in increased RPTEC/TERT1 release of interleukin (IL)-6, IL-8, monocyte chemoattractant protein (MCP)-1 and neutrophil gelatinase-associated lipocalin (NGAL). The HG pro-inflammatory effect was attenuated by concentrated (10×) MSC-CM and, to a greater extent, by MSC transwell co-culture. Bioinformatics analysis of RNA sequencing data confirmed a predominant effect of HG on inflammation-related mediators and biological processes/KEGG pathways in RPTEC/TERT1 stable monolayers as well as the non-contact-dependent anti-inflammatory effect of MSC. Finally, CM from HG-exposed RPTEC/MSC transwell co-cultures was associated with attenuated secretion of inflammatory mediators by macrophages compared to CM from HG-stimulated RPTEC alone.ConclusionsStable RPTEC monolayers demonstrate delayed pro-inflammatory response to HG that is attenuated by close proximity to human MSC. In DKD, this MSC effect has potential to modulate hyperglycemia-associated RPTEC/macrophage cross-talk.
ETV2/ER71 regulates the generation of FLK1+ cells from mouse embryonic stem cells through miR-126-MAPK signaling
Authors: Kim Ju Young , Lee Dong Hun , Kim Joo Kyung , Choi Hong Seo , Dwivedi Bhakti , Rupji Manali , Kowalski Jeanne , Green Stefan J. , Song Heesang , Park Won Jong , Chang Ji Young , Kim Tae Min , Park Changwon 
Published: November 2019

AbstractPrevious studies including ours have demonstrated a critical function of the transcription factor ETV2 (ets variant 2; also known as ER71) in determining the fate of cardiovascular lineage development. However, the underlying mechanisms of ETV2 function remain largely unknown. In this study, we demonstrated the novel function of the miR (micro RNA)-126-MAPK (mitogen-activated protein kinase) pathway in ETV2-mediated FLK1 (fetal liver kinase 1; also known as VEGFR2)+cell generation from the mouse embryonic stem cells (mESCs). By performing a series of experiments including miRNA sequencing and ChIP (chromatin immunoprecipitation)-PCR, we found that miR-126 is directly induced by ETV2. Further, we identified that miR-126 can positively regulate the generation of FLK1+cells by activating the MAPK pathway through targeting SPRED1 (sprouty-related EVH1 domain containing 1). Further, we showed evidence that JUN/FOS activate the enhancer region of FLK1 through AP1 (activator protein 1) binding sequences. Our findings provide insight into the novel molecular mechanisms of ETV2 function in regulating cardiovascular lineage development from mESCs.
Knowledge and perception of small holding farmers on supplementation and feeding sweet potato vines to goats
Authors: Luthuli Cynthia Fikile , Fon Fabian Nde , Gunya Busisiwe 
Published: November 2019

AbstractGoats in rural communities are often raised in conditions which do not allow them to achieve their maximum performance nor express their genetic potentials. For goats to perform to their full potential, they require high nutritious feed especially in the winter season when there is food shortage or during high milk-producing periods. However, supplementation can be done using fresh green feeds, protein blocks or vitamins which are often expensive, hence the need to source for indigenous crop residues. This study assessed the knowledge and perceptions of farmers on feeding sweet potato vines to their goats. The data were gathered by administering a total of 105 structured questionnaires using face-to-face interviews. The results showed that the majority of farmers (71.4%) were aware and practise some sort of supplementary feeding. Most farmers (72.4%) cultivated sweet potatoes, and they used them for different purposes such as income generation (53.3%), consumption (27.5%) or both (8%). Sweet potato vines were being discarded as waste or burnt (32.4%), left on the field as manure (25.7%), conserved as propagation material (8.6%) or randomly fed to livestock (7.6%). Nevertheless, most of the farmers (78.1%) rejected the use of sweet potato vines as feed to livestock. In conclusion, more intervention measures are required for developing farmers’ knowledge and perception on feeding sweet potatoe vines to livestock. Farmers may be assisted through training and workshops on the use of sweet potato vines and other indigenous forage supplementation as feed.
Transcriptome analysis reveals an important candidate gene involved in both nodal metastasis and prognosis in lung adenocarcinoma
Authors: Zhu Xiao , Luo Hui , Xu Ying 
Published: November 2019

AbstractLymph node metastasis of lung cancer is a serious problem. Therefore, there is a need for a detailed transcriptome study of metastatic lung adenocarcinoma. The lung adenocarcinoma RNA-seq data and the corresponding clinical information available from TCGA were analyzed. Differential expression, gradient changes, and biological pathways were carried out. Potential gene(s) associated with tumor metastasis and survival were validated by Cox regression. A total of 406 and 439 differentially expressed genes were identified for lymph node metastasis and TNM stages, respectively. Of the 296 intersection genes, 112 were associated with nodal metastasis and/or staging. Only 25 of these 112 genes with gradient changes were involved in nodal metastasis, and 13 were involved in staging. Only one gene, RN7SL494P, might be involved in lung adenocarcinoma development and poor outcome. Finally, Cox regression results verified that age, pathology classification, radiotherapy and chemotherapy are all the independent prognostic factors. In particular, RN7SL494P was further verified to be an independent factor affecting lymph node metastasis and patient survival. Furthermore, we verified the RN7SL494P function using simulation data generated by mixing cell lines of the Cancer Cell Line Encyclopedia (CCLE) and obtained consistent results. Our findings suggest a potential clinical application of the RN7SL494P as a promising marker in the evaluation of patients with primary lung adenocarcinoma, not only for predicting nodal metastasis, but also for the prognosis of the outcome.
Periodic pulse control of Hopf bifurcation in a fractional-order delay predator–prey model incorporating a prey refuge
Authors: Liu Xiuduo , Fang Hui 
Published: November 2019

AbstractThis paper is concerned with periodic pulse control of Hopf bifurcation for a fractional-order delay predator–prey model incorporating a prey refuge. The existence and uniqueness of a solution for such system is studied. Taking the time delay as the bifurcation parameter, critical values of the time delay for the emergence of Hopf bifurcation are determined. A novel periodic pulse delay feedback controller is introduced into the first equation of an uncontrolled system to successfully control the delay-deduced Hopf bifurcation of such a system. Since the stability theory is not well-developed for nonlinear fractional-order non-autonomous systems with delays, we investigate the periodic pulse control problem of the original system by a semi-analytical and semi-numerical method. Specifically, the stability of the linearized averaging system of the controlled system is first investigated, and then it is shown by numerical simulations that the controlled system has the same stability characteristics as its linearized averaging system. The proposed periodic pulse delay feedback controller has more flexibility than a classical linear delay feedback controller guaranteeing the control effect, due to the fact that the pulse width in each control period can be flexibly selected.
Clinical significance of stromal ER and PR expression in periampullary adenocarcinoma
Authors: Andersson Gustav , Lundgren Sebastian , Heby Margareta , Nodin Björn , Elebro Jacob , Jirström Karin 
Published: November 2019

Abstract
Background
Tamoxifen treatment has previously been reported to confer life-prolonging effects in patients with advanced pancreatic cancer, and most evidently so in women. None of these trials did however include biomarkers, and the relevance of female hormone signaling in pancreatic or other periampullary adenocarcinoma remains largely unexplored. The aim of this study was to examine the extent and potential clinical significance of estrogen receptor-α (ER) and progesterone receptor (PR) expression in pancreatic and other periampullary cancers.

Methods
ER and PR expression was examined using immunohistochemistry on tissue microarrays with primary tumors from a retrospective consecutive cohort of 175 patients with resected periampullary adenocarcinoma, with long-term clinical follow-up. Non-parametric and Chi square tests were applied to examine the associations of stromal ER and PR expression with patient and tumor characteristics. Kaplan-Meier analysis and log rank test were applied to illustrate survival differences in relation to ER and PR expression. Cox regression proportional hazards models were applied to examine the associations between investigative factors and risk of death and recurrence, and to test for interactions between KRAS mutation status and hormone receptor expression in relation to survival.

Results
Expression of both ER and PR was more frequent in the tumor-associated stroma than in the epithelium. A significant prognostic interaction, independent of tumor morphology, was found between stromal PR expression and KRAS mutation status in relation to both overall and recurrence-free survival (pinteraction = 0.026 and pinteraction = 0.005), in particular in women (pinteraction = 0.002 and pinteraction = 0.005). Specifically, stromal PR expression was associated with a prolonged survival in patients with KRAS-mutated tumors, whereas the opposite was seen for KRAS wild-type tumors. The prognostic value of ER positivity was limited to the subgroup of women with tumors of pancreatic origin.

Conclusions
These results demonstrate that stromal PR rather than ER expression, together with KRAS mutation status, provides long-term prognostic information in patients with periampullary adenocarcinoma. Further study into the mechanistic basis for these observations may unveil important clues to the pathogenesis of these cancers and open up for the discovery of novel treatment options.
Exosome release and neuropathology induced by α-synuclein: new insights into protective mechanisms of Drp1 inhibition
Authors: Fan Rebecca Z. , Guo Min , Luo Shouqing , Cui Mei , Tieu Kim 
Published: November 2019

AbstractTargeting alpha-synuclein (α-syn) as a therapeutic strategy for Parkinson’s disease (PD) has been intensively pursued largely due to its well-recognized pathogenic role. Since its discovery as the first familial link to PD over two decades ago, this protein has been associated with multiple neurotoxic mechanisms, such as mitochondrial dysfunction and impaired autophagic flux. We report here that blocking dynamin-related protein 1 (Drp1) improved both mitochondrial function and autophagic flux in experimental models of α-syn. Using rat dopaminergic neuronal cells with inducible wild-type human α-syn, we observed excessive mitochondrial fragmentation and increased Drp1 levels 48 h after gene induction. Functionally, these cells exhibited lower mitochondrial membrane potential, reduced ATP production rate and mitochondrial spare respiratory capacity, as well as increased levels of mitochondrial reactive oxygen species. To evaluate the protective role of Drp1 inhibition, we used three complementary approaches: gene silencing mediated by siRNA, overexpression of Drp1-dominant negative and the small molecule mitochondrial division inhibitor-1 (mdivi-1). Both morphological and functional defects induced by α-syn were attenuated by these strategies. Importantly, Drp1 inhibition reduced proteinase K-resistant α-syn aggregates. Based on that observation, we investigated the involvement of autophagy. Through a combination of stable autophagy reporter cells and immunoreactivity for LC3 and p62 in neuronal cells with either α-syn overexpression or treatment of human α-syn preformed fibrils (PFF), we observed that Drp1 inhibition abolished autophagic impairment induced by α-syn. Consistent with its role in improving autophagy function, Drp1 inhibition reduced exosome release and spread of α-syn pathology from neurons to neurons and from microglia to neurons. In summary, this study highlights new insights that Drp1 inhibition confers neuroprotection through both mitochondrial and autophagy-lysosomal pathways, further strengthening the therapeutic potential of targeting Drp1.
Bioactivity of Citrus essential oils (CEOs) against microorganisms associated with spoilage of some fruits
Authors: Ajayi-Moses Oluwatayo Benjamin , Ogidi Clement Olusola , Akinyele Bamidele Juliet 
Published: November 2019

Abstract
Background
This study evaluated the antimicrobial potentials of Citrus essential oils (CEOs) against spoilage microorganisms isolated from selected fruits. The fruits were randomly purchased from different markets in Akure, Nigeria.

Methods
The microorganisms were isolated and identified using molecular tools. In vitro antimicrobial efficacies of CEOs and their synergistic potentials were tested against spoilage microorganisms using agar well diffusion. The bioactive compounds in CEOs were identified using gas chromatography–mass spectrometry (GC–MS).

Results
The highest bacterial count (5.84 × 105 cfu/g) was recorded in tomatoes, while African star apple had the highest fungal count of 3.04 × 105 sfu/g. Microorganisms isolated from fruits were Bacillus spp., Micrococcus luteus, Serratia marcescens, Aspergillus spp., Mucor piriformis, Fusarium oxysporum, Penicillium spp., Rhizopus spp., Alternaria alternata and others. Phytochemicals in the CEOs were anthraquinones, cardiac glycosides, tannins, alkaloids, terpenoids, saponins, steroids, flavonoids and phenol. The diameter zones of inhibition displayed by CEOs against tested microorganisms at 100 mg/ml ranged from 3.3 mm to 26.8 mm with B. muralis being the most susceptible bacteria. The minimum inhibitory concentration (MIC) against all the tested isolates ranged from 12.5 to 100 mg/ml, while the minimum bactericidal and fungicidal concentrations ranged from 25 to ≥ 100 mg/ml. The synergism between lime and lemon at ratio 1:1 had better antimicrobial activity than each essential oil when used singly. GC–MS revealed the presence of limonene, beta-pinene, alpha-phellandrene, terpinen-4-ol, alpha-terpineol and geraniol in EOs of lime and lemon.

Conclusion
The inhibitory potential of CEOs could be attributed to their bioactive compounds, which can be exploited and used as preservatives by food industries.
Neoplastic cells parasitized by Mycobacterium leprae: report of two cases of melanocytic nevus and one of basal cell carcinoma
Authors: Teixeira Cleverson Soares , Montalvão Patricia Pinheiro , de Oliveira Isabella Tostes , Wachholz Patrick Alexander 
Published: November 2019

AbstractBackgroundLeprosy is a major public health concern in many developing countries. Mycobacterium leprae (M. leprae), the causative agent of leprosy, has the ability to parasitize different types of human cells and tissues. In this article, the uncommon parasitism of nevus and neoplastic and epithelial cells byM. lepraeare described using histological sections doubly stained by Fite-Faraco (FF) and immunohistochemistry (IHC), respectively.Case presentationThree patients with borderline-lepromatous and lepromatous leprosy underwent excision of melanocytic nevi (cases 1–2) and basal cell carcinoma (case 3). Histological sections confirmed the clinical diagnosis of melanocytic nevus and basal cell carcinoma, but leprosy lesions were evident in adjacent tissues. FF staining and IHC (CD68, Melan A, and 34βE12) demonstrated the presence of bacilli within the nevus cells and also in the epithelial cells of the basal cell carcinoma.ConclusionsM. lepraehas the ability to parasitize different types of cells, including neoplastic cells. Pathologists working in settings where leprosy is endemic should be aware that some cutaneous biopsy specimens may also present with leprosy findings.
The comparative study of geographically and demographically of the of animal protein consumption from livestock source
Authors: Novra Ardi , Fatati Fatati , Mulawarman Mulawarman 
Published: November 2019

Livestock is one of the important sources for protein in Jambi Province. However, the information on the consumption behavior of animal protein by local people was not available . Hence, the study aimed to analyze the behavior of consumption of protein sources from livestock between geographically and demographically separate regions.The researchsurveyconductedfor sixmonthsusingcross-section datawith the unitof analysisis the household. The multistage cluster random sampling(CRS) technique was used to selectthreetypes sub-districts(urban, migrantandnativerural) inthreedistrictsrepresentingthe western,central and eastern. The selected numbers of 150 householdswhere are allocatedequally with50electedforeach district. Simultaneous equationsmodel ofAIDS(Almost Ideal Demand System) was usedtoanalyze the difference inthe proportion ofconsumer spendingforfood material sources ofanimal protein from livestock. The AIDS model estimated bySeeminglyUnrelatedEquation (SUR) technique usingthe SAS/ETS9.12. The result showed that geographically, the household expenditure for eggs significantdifferencesamong the others and the highestoccur ineastern regions; while demographically, the household expenditure formeatin rural areas was significantly higher thanin the urban, but fordairysignificantly higher than in urban areas. The household expenditure for eggs more responsive to the other prices, but the meat more responsive to own and dairy prices. The same non-price factor was significantly influenced to all commodities for livestock products, and the relationship between eggandmeatcommodities weresubstituted, but with dairywascomplementary. It is concluded that demographic factors are more influential than geographic factors on the behavior of animal protein consumption from livestockKeywords: Geographically, Demographically, Livestock, Protein, AIDS