Miracle-dz/UniFAR-FTUs huggingface dataset:
Microarray screening for key genes and prognosis factors in interferon regulatory factor 1-silenced ovarian cancer SKOV-3 cells

Background: Ovarian cancer is a gynecological neoplastic disease with high mortality rate. Its early detection is difficult because of the lack of specific clinical symptoms. This study aimed to identify key genes and prognosis factors associated with ovarian cancer to provide new information and thus better understanding of ovarian cancer. Methods: Microarray data from the Gene Expression Omnibus (GEO) database (accession number GSE38551) were used for analysis. Differentially expressed genes (DEGs) were screened, and functional enrichment and protein-protein interaction (PPI) network analyses for DEGs were performed. A subnetwork was constructed to gain further information regarding DEGs scored in the PPI network. Finally, we performed survival analysis. Results: In total, 427 DEGs were obtained in interferon regulatory factor 1 ( IRF-1 )-silenced ovarian cancer SKOV-3 cell line samples compared to SKOV-3 samples without IRF-1 silencing. DEGs were mainly enriched in metabolic pathways and systemic lupus erythematosus. Tumor necrosis factor ( TNF ) and cadherin 1 ( CDH1 ; type 1, E-cadherin) were present in had higher degrees than others in both the PPI network and the subnetwork. The subnetwork results presented that CDH1 was enriched in the epithelium morphogenesis and cancer pathways, and TNF was enriched in response to lipids. The Mir-30 family served as a tumor suppressor in ovarian cancer. Survival analysis revealed that CDH1 was associated with ovarian cancer prognosis. Conclusions: TNF and CDH1 play important roles in ovarian cancer: CDH1 is an important prognosis factor for ovarian cancer and may be involved mainly via epithelial morphogenesis and cancer pathways. TNF may be involved via response to lipids.
L’épandage de matières fertilisantes d’origine résiduaire sur les prairies comporte-t-il des risques en termes de transfert de polluants organiques et inorganiques vers la chaîne alimentaire ?

L’objectif de cet article est d’identifier les points de vigilance relatifs aux transferts de polluants inorganiques ou organiques vers les animaux d’elevage via l’ingestion de sol, de plantes, d’eau ou encore de pedofaune, consecutivement a l’epandage de MAtieres Fertilisantes d’Origine Residuaire (MAFOR) sur les prairies. Cette identification consiste a prendre en compte simultanement les quantites de polluants ingerees (quantite de matrice ingeree × concentration du polluant dans cette matrice), la fraction biodisponible et le devenir des polluants au sein de l’organisme. Les etudes realisees en conditions de terrain et qui renseignent l’ensemble des donnees necessaires pour estimer l’impact des MAFOR epandues sur prairies sont rares et peu conclusives. Elles reposent principalement sur l’application des boues de stations d’epuration sur des prairies et ne permettent pas de comparer l’impact des autres formes de MAFOR. Cependant, en prenant en compte l’ensemble des connaissances sur les transferts de polluants vers les produits animaux, il apparait que les polluants organiques sont plus fortement absorbes que les Elements Traces Metalliques (ETM). Seuls les composes peu biotransformes s’accumulent significativement dans les produits animaux. In fine, les polluants organiques se concentrent generalement dans les tissus et produits gras alors que les ETM se retrouvent preferentiellement dans les abats. Cependant, un manque manifeste de connaissances sur le devenir de contaminants organiques emergents (bromes, perfluores, phtalates et paraffines) ou de certains ETM (vanadium et thallium) doit etre signale. De maniere globale, les transferts de polluants organiques et inorganiques vers les produits animaux, suite a l’epandage de MAFOR sur les prairies, ne peuvent etre exclus.
Management of Repeat Breeding Syndrome in Cows

The aims of this study were to identify the status of repeat breeding syndrome (RBS) in a dairy farm, to establish the main cause of RBS and to reduce the number of RBS using the Ovsynch protocol. 20 cows were diagnosed with RBS using computer analysis of the herd and a specific diagnosis for the cause of RBS was attempted. Subsequently, they were divided into 2 groups: cows in group 1 (n=10) received no hormonal treatment while those in group 2 (n=10) were treated using the Ovsynch protocol. Artificial insemination and pregnancy diagnosis was performed in all cows. The 70% pregnancy rate obtained for Ovsynch showed that the hormonal effect as well as correct timing of insemination had a significant influence on RBS, pointing out towards the managerial factor as one of the main causes of RBS. The cow factor was also included, as endometritis, follicular cysts and anovulatory heats were diagnosed.
Accelerated 3D Left Atrial Late Gadolinium Enhancement in Patients with Atrial Fibrillation at 1.5 T: Technical Development.

Purpose To develop an accelerated three-dimensional (3D) late gadolinium enhancement (LGE) pulse sequence using balanced steady-state free precession readout with stack-of-stars k-space sampling and extra motion-state golden-angle radial sparse parallel (XD-GRASP) reconstruction and test the performance for detecting atrial scar and fibrosis in patients with atrial fibrillation (AF). Materials and Methods Twenty-five patients with AF (20 paroxysmal and five persistent; 65 years ± 7 [standard deviation]; 18 men) were imaged at 1.5 T using the proposed LGE sequence with 1.3 mm × 1.3 mm × 2-mm spatial resolution and predictable imaging time. The resulting images were compared with historic images of 25 patients with AF (18 paroxysmal and seven persistent; 67 years ± 10; 14 men) obtained using a reference 3D left atrial (LA) LGE sequence with 1.3 mm × 1.3 mm × 2.5-mm spatial resolution. Two readers visually graded the 3D LGE images (conspicuity, artifact, noise) on a five-point Likert scale (1 = worst, 3 = acceptable, 5 = best), in which the summed visual score (SVS) of 9 or greater was defined as clinically acceptable. Appropriate statistical analyses (Cohen κ coefficient, Mann-Whitney U test, t tests, and intraclass correlation) were performed, where a P value < . 05 was considered significant. Results Mean imaging time was significantly shorter (P < .01) for the proposed pulse sequence (5.9 minutes ± 1.3) than for the reference pulse sequence (10.6 minutes ± 2). Median SVS was significantly higher (P < .01) for the proposed (SVS = 11) than reference (SVS = 9.5) 3D LA LGE images. Interrater reproducibility in visual scores was higher for the proposed (κ = 0.78-1) than reference 3D LA LGE (κ = 0.44-0.75). Intrareader repeatability in fibrosis quantification was higher for the reference cohort (intraclass correlation coefficient [ICC] = 0.94) than the prospective cohort (ICC = 0.79). Conclusion The proposed 3D LA LGE method produced clinically acceptable image quality with 1.5 mm × 1.5 mm × 2-mm nominal spatial resolution and 6-minute predictable imaging time for quantification of LA scar and fibrosis in patients with AF. Supplemental material is available for this article. © RSNA, 2020.
SERVIÇOS COMPRADOS EM ESPECIALIDADES, EXAMES DE MÉDIA E ALTA COMPLEXIDADES: UM ESTUDO DOS GASTOS PÚBLICOS E DEMANDAS REPRIMIDAS NO MUNICÍPIO DE BENTO GONÇALVES – RS

O municipio de Bento Goncalves e responsavel financeiro e administrativo pela saude publica local, a comecar p atencao basica, media e alta complexidade, usufruindo de recursos do Ministerio da Saude, Governo do Estado e recursos proprios. O objetivo geral do estudo foi avaliar os gastos com especialidades e exames de media e alta complexidade oferecidos aos pacientes SUS, atraves de servicos comprados. Trata-se de um estudo descritivo, transversal, com abordagem quantitativa. A analise realizou-se no periodo de outubro de 2018 ate setembro de 2019, por meio da tabulacao de dados obtida do sistema G-MUS e demandas reprimidas no municipio. Os resultados evidenciaram que os gastos mensais com especialistas chegam a R$ 167.286. 24, sendo que deste valor, os exames que mais geram custos sao as ressonâncias magneticas em 30%, seguindo para ecocardiograma bidimensional em 11% e em terceiro lugar estao as colonoscopias e endoscopias em 10% do valor total. Atraves dos dados analisados, os gestores poderao utilizar os recursos com um melhor aproveitamento, reduzindo custos e demandas reprimidas.
A lab in the field: applications of real-time, in situ metagenomic sequencing

Abstract High-throughput metagenomic sequencing is considered one of the main technologies fostering the development of microbial ecology. Widely used second-generation sequencers have enabled the analysis of extremely diverse microbial communities, the discovery of novel gene functions, and the comprehension of the metabolic interconnections established among microbial consortia. However, the high cost of the sequencers and the complexity of library preparation and sequencing protocols still hamper the application of metagenomic sequencing in a vast range of real-life applications. In this context, the emergence of portable, third-generation sequencers is becoming a popular alternative for the rapid analysis of microbial communities in particular scenarios, due to their low cost, simplicity of operation, and rapid yield of results. This review discusses the main applications of real-time, in situ metagenomic sequencing developed to date, highlighting the relevance of this technology in current challenges (such as the management of global pathogen outbreaks) and in the next future of industry and clinical diagnosis.
Early Diagnosis of Mild Cognitive Impairment with 2-Dimensional Convolutional Neural Network Classification of Magnetic Resonance Images

We motivate and implement an Artificial Intelligence (AI) Computer Aided Diagnosis (CAD) framework, to assist clinicians in the early diagnosis of Mild Cognitive Impairment (MCI) and Alzheimer’s Disease (AD). Our framework is based on a Convolutional Neural Network (CNN) trained and tested on functional Magnetic Resonance Images datasets. We contribute to the literature on AI-CAD frameworks for AD by using a 2D CNN for early diagnosis of MCI. Contrary to current efforts, we do not attempt to provide an AI-CAD framework that will replace clinicians, but one that can work in synergy with them. Our framework is cheaper and faster as it relies on small datasets without the need of high-performance computing infrastructures. Our work contributes to the literature on digital transformation of healthcare, health Information Systems, and NeuroIS, while it opens novel avenues for further research on the topic.
Taking Context More Seriously: Managerial Networking and Performance in American and Korean Hospitals

Abstract While extensive literature on public management has suggested that management matters for performance, the role of national context in this mechanism has been significantly understudied. This article examines whether and how the impact of management on performance varies across national settings by conducting a comparative analysis of U.S. and Korean hospitals. Based on a parallel hospital manager survey and archival database in the two countries, we find that managerial networking contributes to performance in both U.S. and Korean hospitals, but its functional form varies between the two countries. These findings imply that management is the key to enhancing performance, but the effective strategy can vary depending on the national context. This study highlights the role of national context and advances the field of comparative public administration.
Management of legacy nutrient stores through nitrogen and phosphorus fertilization, catch crops, and gypsum treatment

We develop a modeling framework, based on discrete‐time dynamic optimization, to study the effect of legacy nutrient stores and soil nutrient dynamics on optimal nutrient management and agri‐environmental policy in crop production. Three alternative measures are studied to reduce nutrient loss: reduced fertilization, nonlegume catch crop cultivation and gypsum amendment. According to our results, landowner can bring down excessively high phosphorus stocks causing environmental damage within decades, by simultaneous optimization of the nitrogen and phosphorus fertilizers on the economic basis of profit maximization. Our results suggest that nitrogen loss abatement with catch crops is socially optimal, whereas the use of gypsum is well justified as a temporary measure on soils with high soil phosphorus levels. A dynamic tax‐subsidy‐scheme, which takes into account the current soil nutrient levels and field attributes such as soil texture, can enforce the socially optimal outcome. The welfare losses of the static steady‐state‐based tax‐subsidy‐schemes are increasing functions of the legacy nutrient stores and soil's ability to hold nutrients.
Effects of structural and trait competitiveness stimulated by points and leaderboards on user engagement and performance growth: A natural experiment with gamification in an informal learning environment

ABSTRACT Rooted in theories of competitiveness and social comparison, we model the effects of users’ structural and trait competitiveness on their engagement and performance growth in an informal learning environment. We hypothesise that game elements of points and leaderboards stimulate users’ structural competitiveness, which affects users’ engagement and has an inverted-U effect on performance growth. We further hypothesise that these effects are stronger among individuals with higher trait competitiveness. We tested our hypotheses using data from a natural experiment conducted over 300 days on 88,310 unique users who made 215,920 game interactions within the Cyber Detectives exhibit at the Tech Interactive museum in California. Our results are based on two objective measures of trait-competitiveness as both behaviour and outcome (percentile ranking on total time spent and number of badges earned, respectively), multiple objective measures of user engagement (time spent per attempt, number of reattempts, and daily user attempts), and an objective measure of performance growth (points). Results provide overall support to our hypotheses. We contribute to the gamification literature by providing strong causal evidence of points and leaderboards triggering structural and trait competitiveness, which interact to affect both engagement and performance growth in informal learning contexts.
Killer whales are attracted to herring fishing vessels

Marine mammals and fisheries often target the same resources, which can lead to operational interactions. Potential consequences of operational interaction include entanglements and damaged or reduced catches but also enhanced foraging opportunities, which can attract marine mammals to fishing vessels. Responsible fisheries management therefore requires detailed knowledge of the impact of these interactions. In northern Norway, killer whales Orcinus orca are frequently observed in association with large herring aggregations during the winter. We use a combination of biotelemetry and fisheries data to study if, to what extent and at what distances killer whales are attracted to fishing activity. Twenty-five satellite transmitters were deployed on killer whales at herring overwintering and spawning grounds, often near fishing vessels. Over 50% of the killer whale core areas of high usage overlapped with the fisheries core areas, and individual whales spent up to 34% of their time close to active fishing. We used a 3-state hidden Markov model to assess whether killer whale movements were biased towards fishing activities. Of the overall whale movements, 15% (CI = 11-21%) were biased towards fishing activities, with marked heterogeneity among individuals (0-57%). During periods of active fishing, whale movements were biased towards fishing events 44% (CI = 24-66%) of the time, with individual percentages ranging from 0 to 79%. Whales were more likely to be attracted when they were within 20 km. This information can be used in fishery management to consider potential consequences for fishers and whales.
Extended Spectrum Pleuromutilins: Potent Translation Inhibitors with Broad-Spectrum Antibacterial Activity In Vitro and In Vivo

Background: Extended spectrum pleuromutilins (ESP) are a new generation of pleuromutilin (PM) antibiotics with chemical modifications at the C-14 side chain and the tricyclic PM core resulting in extending the antibacterial spectrum of conventional PMs to include a wide range of Gram-negative bacterial pathogens including Enterobacteriaceae in addition to staphylococci, streptococci, and fastidious Gram-negative bacteria. A series of ESP (BC-7634, BC-9539, BC-9545 and BC-9543) were investigated for their 1) ability to inhibit bacterial transcription/translation (TT) of E. coli and S. aureus; 2) in vitro antibacterial activity; and 3) in vivo efficacy in a murine sepsis model induced by E. coli and S. aureus.
Correlation between Shanghai crude oil futures, stock, foreign exchange, and gold markets: a GARCH-vine-copula method

ABSTRACT The relationship between markets has always been a topic of heated debate among scholars from various countries. One of the most important concerns is the need to model the relationships between the crude oil market and other markets. Based on daily return observations from 2018 to 2019, we apply a GARCH-vine-copula approach to probe the linkage between Shanghai crude oil futures, stock, foreign exchange, and gold markets. We find that obvious tail dependencies do exist between these markets. And the crude oil futures market occupies a dominant position. Moreover, when the Shanghai crude oil futures market is taken as the known condition, the links between different markets reduce to some extent. Finally, value at risk results denote that the risk of the Shanghai crude oil futures market is relatively high, but portfolio investment can effectively reduce the risk. Moreover, the model fitting results at different confidence levels have passed the Kupiec backtest, indicating that the model in this paper fits the relationship between these markets well.
Role of mineral filler in asphalt mixture

Mineral filler, fine-grained mineral particles naturally present in or manufactured and added to aggregates play a significant role on the performance of asphalt mastic and asphalt mixtures. A clear understanding of effects of filler on the properties of asphalt paving mixtures is critical to ensure a good asphalt mixture design and its field performance. In this study, the basic properties of mineral filler, mainly including physical and chemical properties, were first reviewed and followed by the effects on mastic and mixture performances. This review finds that particle size distribution and specific surface area are the two most important physical characteristics for fillers in terms of its impact on mastic performances. Fillers, including diatomite, hydrated lime and cement, can improve the high temperature and durability performances of mastic and mixture. However, fillers, like glass powder, steel slag and bentonite, have a detrimental effect on the low-temperature performances. It can be concluded that it is important to carefully select the mineral filler type and proportion in order to improve the asphalt mixture performances.
Short-term starvation in silver pomfret (Pampus argenteus): molecular effects on lipid mobilization and utilization

To investigate the effects of short-term starvation on lipid metabolism, juvenile silver pomfret (Pampus argenteus) with an initial weight of 18.1 ± 1.53 g were starved for 6 days. Fish were sampled on days 0, 2, 4 and 6 of starvation (S0, S2, S4 and S6, respectively) and then analysed. The results showed that short-term starvation induced a significant decrease in visceral index, hepatosomatic index. The crude lipid content was also significantly decreased by 42.22% and 82.96% on S2 and S6 respectively. In addition, short-term starvation significantly decreased the plasma triacylglycerol, non-esterified fatty acid and low-density lipoprotein cholesterol. Moreover, short-term starvation significantly increased the expressions of hormone-sensitive lipase (HSL) and adipose triglyceride lipase (ATGL) at the mRNA and protein levels in the muscle and the ATGL expression at the protein level in the liver. The expressions of fatty acid translocase (CD36) and plasma membrane fatty acid-binding protein (FABPpm) at the protein level in the muscle were significantly increased by short-term starvation, while the expressions of fatty acid transport protein 1 (FATP1), FABPpm and lipoprotein lipase (LPL) at the protein level in the liver were significantly increased by short-term starvation. Furthermore, the expressions of peroxisome proliferator activated receptor (PPAR) α and PPARγ at the mRNA and protein levels in the muscle were significantly elevated by short-term starvation. These findings suggested that short-term starvation increased lipid mobilization and utilization possibly through activation of lipolysis-related genes (HSL and ATGL), lipid uptake-related genes (LPL, CD36, FATP1 and FABPpm) and PPARs.
TAG.ME: Taxonomic Assignment of Genetic Markers for Ecology

Background Sequencing of amplified genetic markers, such as the 16S rRNA gene, have been extensively used to characterize microbial community composition. Recent studies suggested that Amplicon Sequences Variants (ASV) should replace the Operational Taxonomic Units (OTU), given the arbitrary definition of sequence identity thresholds used to define units. Alignment-free methods are an interesting alternative for the taxonomic classification of the ASVs, preventing the introduction of biases from sequence identity thresholds. Results Here we present TAG.ME, a novel alignment-independent and amplicon-specific method for taxonomic assignment based on genetic markers. TAG.ME uses a multilevel supervised learning approach to create predictive models based on user-defined genetic marker genes. The predictive method can assign taxonomy to sequenced amplicons efficiently and effectively. We applied our method to assess gut and soil sample classification, and it outperformed alternative approaches, identifying a substantially larger proportion of species. Benchmark tests performed using the RDP database, and Mock communities reinforced the precise classification into deep taxonomic levels. Conclusion TAG.ME presents a new approach to assign taxonomy to amplicon sequences accurately. Our classification model, trained with amplicon specific sequences, can address resolution issues not solved by other methods and approaches that use the whole 16S rRNA gene sequence. TAG.ME is implemented as an R package and is freely available at http://gabrielrfernandes.github. io/tagme/