Miracle-dz/UniFAR-FTUs huggingface dataset:
A comparison of the association between large haplotype blocks under selection and the presence/absence of inversions

Abstract Inversions may contribute to ecological adaptation and phenotypic diversity, and with the advent of “second” and “third” generation sequencing technologies, the ability to detect inversion polymorphisms has been enhanced dramatically. A key molecular consequence of an inversion is the suppression of recombination allowing independent accumulation of genetic changes between alleles over time. This may lead to the development of divergent haplotype blocks maintained by balancing selection. Thus, divergent haplotype blocks are often considered as indicating the presence of an inversion. In this paper, we first review the features of a 7.7 Mb inversion causing the Rose‐comb phenotype in chicken, as a model for how inversions evolve and directly affect phenotypes. Second, we compare the genetic basis for alternative mating strategies in ruff and timing of reproduction in Atlantic herring, both associated with divergent haplotype blocks. Alternative male mating strategies in ruff are associated with a 4.5 Mb inversion that occurred about 4 million years ago. In fact, the ruff inversion shares some striking features with the Rose‐comb inversion such as disruption of a gene at one of the inversion breakpoints and generation of a new allele by recombination between the inverted and noninverted alleles. In contrast, inversions do not appear to be a major reason for the fairly large haplotype blocks (range 10–200 kb) associated with ecological adaptation in the herring. Thus, it is important to note that divergent haplotypes may also be maintained by natural selection in the absence of structural variation.
A probabilistic switch model of information flow in social networks: application of virtual circuits to organisational design

Network building and exchange of information by people within networks is crucial to the innovation process. Contrary to older models, in social networks the flow of information is noncontinuous and nonlinear. There are critical barriers to information flow that operate in a probabilistic manner. New models and new analytic tools are needed for these systems. This paper introduces the concept of virtual circuits and draws on recent concepts of network modelling and design to introduce a probabilistic switch theory that can be described using matrices. It can be used to model multistep information flow between people within organisational networks, to provide formal definitions of efficient and balanced networks and to describe distortion of information as it passes along human communication channels. The concept of multi-dimensional information space arises naturally from the use of matrices. The theory and the use of serial diagonal matrices have applications to organisational design and to the modelling of other systems. It is hypothesised that opinion leaders or creative individuals are more likely to emerge at information-rich nodes in networks. A mathematical definition of such nodes is developed and it does not invariably correspond with centrality as defined by early work on networks.
Lean design improves both health-care facilities and processes: a literature review

This article presents a literature review of the challenges and possibilities for Lean design in modern health-care facilities. Many of today's health-care facilities are in dire need of renovation since limited financial resources among health-care demand improved work process efficiency, safety and employee well-being. Lean philosophy has been successfully implemented into hospitals with up-and-running hospital processes, but has not been thoroughly tested as a design methodology. The principles of Lean do not contradict with user-centric, participatory or ergonomic design approaches and thus the possibilities of using Lean as a complementary design methodology to the aforementioned approaches are discussed in this article. Lean fundamentals are also useful when dealing with change management issues. Lean offers a fundamentally solid ideology and a wide range of tools – many of which seem fitting to solve several urgent design problems in today's health-care design.
Effect of aspirin versus cilostazol for inhibition of antiplatelet aggregation in type 2 diabetes mellitus patients (ESCORT-DM Study)

BackgroundThe role of aspirin in primary prevention of cardiovascular disease in patients with diabetes is controversial. In contrast, some studies have suggested beneficial effects of cilostazol on cardiovascular disease in patients with diabetes. Here we prospectively investigated the antiplatelet effects of cilostazol compared with aspirin in patients with diabetes and cardiovascular risk factors.MethodsWe randomly assigned 116 patients with type 2 diabetes and cardiovascular risk factors but no evident cardiovascular disease to receive aspirin at a dose of 100 mg or cilostazol at a dose of 200 mg daily for 14 days. The primary efficacy outcome was antiplatelet effects of aspirin and cilostazol assessed with the VerifyNow system (aspirin response units; ARU) and PFA-100 (closure time; CT). Secondary outcomes were changes of clinical laboratory data.ResultsThe decrease of ARU (-0.4 ± 7.1% vs. -28.9 ± 9.9%, p < 0.001) and the increase of CT (25.7 ± 54.1% vs. 99.6 ± 63.5%, p < 0.001) were significantly greater in aspirin compared cilostazol. The prevalence of aspirin resistance was 7.5% according to VerifyNow (defined by ARU ≥ 550) and 18.9% according to PFA-100 (CT < 192 s). Compared with aspirin, cilostazol treatment was associated with increased HDL cholesterol (7.1 ± 12.7% vs. 4.2 ± 18.0%, p = 0.006) and decreased triglycerides (-9.4 ± 33.7% vs. 4.4 ± 17.57%, p = 0.016). However, there were no significant changes in total and LDL cholesterol, CRP level, and CD40 ligand between cilostazol and aspirin groups.ConclusionsAspirin showed better antiplatelet effects assessed with VerifyNow and PFA-100 compared with cilostazol. However, there were favorable changes in atherogenic dyslipidemia only in the cilostazol treatment group.Trial registrationNCT02933788, dated october 14, 2016
Integrated analysis reveals the prognostic significance of pyrimidine metabolic rate limiting enzymes in patients with lung adenocarcinoma

Background: Reprogramming of metabolism is illustrated in many types of cancer and is associated with the clinical outcomes of cancer patients. However, the prognostic significance of pyrimidine metabolism signaling pathway in patients with lung adenocarcinoma (LUAD) is unclear.Methods: Using the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) datasets, we determined the prognostic significance of pyrimidine metabolic rate limiting enzymes in patients with lung cancer. The enrichment of pyrimidine metabolism signaling pathway was analyzed by gene set enrichment analysis (GSEA). The expression profiles of pyrimidine metabolic rate limiting enzymes were identified from Affymetrix gene expression data and RNA-seq data. The Kaplan-Meier Plotter was used to identify the prognostic significance of the pyrimidine metabolic rate limiting enzymes. Spearman’s correlation and multivariate cox regression were used to determine the correlation efficiency of pyrimidine metabolic rate limiting enzymes.Results: The pyrimidine metabolism signaling pathway is significantly enriched in LUAD tissues, but not in lung squamous cell carcinoma (LUSC) tissues. Compared with normal lung tissues, the pyrimidine metabolic rate limiting enzymes are highly expressed in lung tumor tissues. Furthermore, the high expression levels of pyrimidine metabolic rate limiting enzymes are associated with unfavorable prognosis in patients with LUAD. Moreover, we demonstrate that the hypo-DNA methylation, DNA amplification and TP53 mutation are contributing to the high expression levels of pyrimidine metabolic rate limiting enzymes in cancer cells. Finally, we reveal the significant connections between the pyrimidine metabolic rate limiting enzymes. Comprehensively, the pyrimidine metabolic rate limiting enzymes are highly expressed in patients with bladder cancer, breast cancer, colon cancer, liver cancer and stomach cancer. And the high expression levels of pyrimidine metabolic rate limiting enzymes are associated with unfavorable prognosis in patients with liver cancer. Conclusions: Pyrimidine metabolism signaling pathway is associated with the development of lung adenocarcinoma. Pyrimidine metabolic rate limiting enzymes CAD, DTYMK, RRM1, RRM2, TK1, TYMS, UCK2, NR5C2 and TK2 have significant prognostic effects in patients with lung adenocarcinoma.
Flicker Noise of Phase in RF Amplifiers and Frequency Multipliers: Characterization, Cause, and Cure

The high phase stability of atomic frequency standards has called for the development of associated electronic equipment of equivalent or superior stability. We have surveyed the performance of existing high quality frequency multipliers and R F amplifiers which operate in the range of 5 MHz to microwave frequencies. We were most interested in the phase noise in the range of Fourier frequencies, f , of about Hz to l o t 3 Hz, since most electronic servo systems in existing atomic frequency standards use modulation frequencies which fall within this range. This range also includes the passive linewidths of existing atomic frequency standards.
Creating and Sustaining Genres in Cultural Products: Co-Evolution of Technology, Organisation and Markets in the Video Games Industry

Genres in cultural or ‘creative’ industries are important heuristics for innovation: they offer both directions and structure for advance, yet also constrain choices in a path-dependent fashion. The constraining forces may lead to risk-averse conservatism, which is sometimes accused of the increasing phenomenon of sequels and franchises of movies, television programmes, books and video games. This paper analyses patterns of innovation in an established genre and a newly-created genre in video games, namely First Person Shooter (FPS), and Social Games. It draws on case studies of four leading organisations developing games in the two genres. While the study shows significant creative behaviour and thinking in the early stages of the new genre of social games, it also finds tendencies to limit choices rapidly following early success, in order to close and stabilise the path. Conversely, in the mature genre of FPS there is considerable creative thinking and innovation introduced to rejuvenate and sustain interest in mature paths. The paper analyses the types of organisational initiatives, objects, tools and processes that either sustain paths or disembed from them. It integrates the notion of cultural product genre into our understanding of co-evolutionary development of technology, organisation and markets.
Multivariate machine learning models for prediction of postoperative intestinal obstruction in patients underwent laparoscopic colorectal surgery: A retrospective observational study

Background Machine learning may predict postoperative intestinal obstruction (POI) in patients underwent laparoscopic colorectal surgery for malignant lesions.Methods We used five machine learning algorithms (Logistic regression, Decision Tree, Forest, Gradient Boosting and gbm), analyzed by 28 explanatory variables, to predict POI. The total samples were randomly divided into training and testing groups, with a ratio of 8:2. The model was evaluated by the area operation characteristic curve (AUC), F1-Measure, accuracy, recall, and MSE under the receiver.Results A total of 637 patients were enrolled in this study, 122 (19.15%) of them had POI. Gradient Boosting and gbm had the most accurate in training group and testing group respectively.The f1_score of Gradient Boosting was the highest in the training group (f1_score =0.710526), and the f1_score of gbm was the highest in the testing group (f1_score =0.500000). In addition, the results of the importance matrix of Gbdt algorithm model showed that the important variables that account for the weight of intestinal obstruction after the first five operations are time to pass flatus or passage of stool, cumulative dose of rescue opioids used in postoperative days 3 (POD 3), duration of surgery, height and weight.Conclusions Machine learning algorithms may predict the occurrence of POI in patients underwent laparoscopic colorectal surgery for malignant lesions, especially Gradient Boosting and GBM algorithms. Moreover, time to pass flatus or passage of stool, cumulative dose of rescue opioids used during POD 3, duration of surgery, height and weight play an important role in the development of POI.
A Warning and Intervention System to Prevent Road-Departure Accidents

SUMMARY A driver assistance system is described which provides an automatic road-departure warning and intervention function. The system is intended for drivers who are drifting off the roadway at a shallow angle of departure due to inattention, drowsiness, intoxication, or other causes. An integrated set of model-based estimation algorithms serves to anticipate imminent road departures. Interventions are achieved using differential braking -- the application of unequal brake torques at the right and left wheels. The driver remains in the loop, always able to provide the primary steering commands. A driver state assessment module is being developed to further adapt to individual driven and to identify changes in driver behavior. We describe the algorithms, present simulation results, and include preliminary experimental data from a prototype vehicle.
Zur Verformungsentwicklung von Böden unter zyklischer Beanspruchung

Im vorliegenden Bericht werden zyklische Elementversuche (Triaxial‐, Rahmenscherversuche) sowie Modellversuche mit zyklischen Belastungen an Flachfundamenten und Pfählen vorgestellt. Im Triaxialversuch werden bindige und nichtbindige Proben mit bis zu 5 mal 10 hoch 6 Lastwechseln, im Rahmenscherversuch werden Sandproben mit 10 hoch 4 Lastwechseln, zyklisch belastet. Die Modellversuche mit bis zu 10 hoch 5 Lastwechseln werden in nichtbindigem Boden durchgeführt.
Konkurrensyta land–sjö för svenska godstransporter

This project aims to investigate the competition between road and rail transports on one hand and the sea transports on the other. Shippers choose different unimodal or multimodal transport chains to carry various types of goods in, to and from Sweden. Transport prices are a key factor when choosing the transport chain. Sea transport prices are set on the world market and fluctuate more than prices for road and rail transports. Imbalances in transport flows also affect the intermodal competition, in particular for transports to/from mainland Europe. According to the statistics the modal split, measured in tonne-kilometers on Swedish territory (including a stretch along the coast) has been relatively constant since 1990. Nearly 40 percent of the tonne-kilometers are carried out by road, nearly 40 per cent by sea and a bit more than 20 per cent by rail. Sweden had so far by definition not inland waterway transports. Simulations with the national Swedish freight model Samgods with ten percent lower on-route costs for vessels indicate different adaptations for different commodity groups. The tonne-kilometers by sea performed on the Swedish territory are expected to increase by about two per cent if all 33 commodities are included. However, for Cement, lime and building materials and Pulp, paper and paper waste increases of almost ten percent are computed. On the other hand, no significant changes in demand are calculated for i.e. Crude oil, which is carried exclusively by sea today. As expected, more competition between the land-based modes and sea transports is calculated for international transports than for domestic transports. If all commodities are included, the largest increases for sea transports are calculated along the Eastern coast (southern part), the Southern coast and through the Kiel Canal. Sea transports are also calculated to increase along the coast in the North of Sweden and to/from Gothenburg on the Western coast. Reductions are expected to occur for both road and rail. The authors emphasize that the results should be seen as indicative.
Needs analysis for task-based language teaching: A case study of Indigenous vocational education and training students who speak EAL/EAD

Indigenous students enrol in vocational education and training (VET) programs because they provide a viable pathway into the workplace or further education. However, most high school VET programs use mainstream teaching methodologies which already assume that students speak the Standard Australian English required for the workplace. This approach can disadvantage Indigenous students, particularly those from remote communities who speak a traditional Aboriginal language as a home language. This paper describes a case study of a second language Task-Based Needs Analysis (TBNA) undertaken at a residential high school specialising in VET for Indigenous students, most of whom come from Western Australia's remote communities and speak English as an Additional Language (EAL). The study used naturalistic data collection methods (non-participant observation, unstructured interviews and document collection) to identify the actual language and literacy tasks that students are likely to encounter in various workplace settings. The main findings are presented in relation to work-oriented tasks, work-life tasks and cross-cultural interactions. The research described here provides a potential guide for undertaking a TBNA as the starting point for designing and implementing task-based language teaching programs, especially for Indigenous VET students (and others from non-Western cultures) who speak EAL.
Comparison between EVM and RSM turbulence models in predicting flow and heat transfer in rib-roughened channels

A 3D analysis of two-equation eddy viscosity (EVMs) and Reynolds stress (RSM) turbulence models and their application to solve flow and heat transfer in rotating rib-roughened internal cooling channels is the main focus of this study. The flow in these channels is affected by ribs, rotation, buoyancy, bends and boundary conditions. The EVMs considered are the standard k–ϵ model of Launder and Spalding [1], the renormalization group k–ϵ model of Yakhot and Orszag [2], the realizable k–ϵ model of Shih et al. [3], the standard k–ω model of Wilcox [4] and the shear–stress transport (SST) k–ω model of Menter [5]. The viscosity-affected near-wall region is resolved by enhanced near-wall treatment using combined two-layer model with enhanced wall functions. The results for both stationary and rotating channels showed the advantages of Reynolds stress model (RSM), Gibson and Launder [6], Launder [7] and Launder et al. [8] in predicting the flow field and heat transfer compared to two-equation EVMs that need corrections to account for streamline curvature, buoyancy and rotation.
PESTICIDE EXPOSURE LEVELS ON SURFACES WITHIN SPRAYER CABS

Surface levels of pesticides and herbicides were measured at various interior and exterior locations on five tractors (four with cabs using carbon–bed air–filtering systems and one without) and three commercial spray rigs. All equipment was used on farms or by commercial spray contractors for both fruit orchard and vegetable crop applications in central New York State. Sampling was conducted at the end of the growing season in October 2000. The highest chemical concentration levels were found on steering wheels and gauges, and in dust collected from the fabric seats. Contamination of the steering wheel and seat areas could result in operator exposure to pesticides if the tractor is used for other farm purposes such as baling hay or mowing grass where the operator may not be using personal protective equipment. Pesticide residues on the outlet louvers from the air filtering systems of the enclosed cabs often included more compounds and at higher levels than samples from the inlet louvers. A carbon bed once saturated may release compounds back into the tractor cab environment at a later point in time. Information on carbon bed efficiency and specificity of chemical removal in relation to bed size and chemical break through trends is not generally available from the manufacturer, but would be important in future studies to optimize carbon bed replacement schedules.
MRI Evaluation of Suspected Pathologic Fracture at the Extremities from Metastasis: Diagnostic Value of Added Diffusion-Weighted Imaging

Objective To assess the diagnostic value of combining diffusion-weighted imaging (DWI) with conventional magnetic resonance imaging (MRI) for differentiating between pathologic and traumatic fractures at extremities from metastasis. Materials and Methods Institutional Review Board approved this retrospective study and informed consent was waived. This study included 49 patients each with pathologic and traumatic fractures at extremities. The patients underwent conventional MRI combined with DWI. For qualitative analysis, two radiologists (R1 and R2) independently reviewed three imaging sets with a crossover design using a 5-point scale and a 3-scale confidence level: DWI plus non-enhanced MRI (NEMR; DW set), NEMR plus contrast-enhanced fat-saturated T1-weighted imaging (CEFST1; CE set), and DWI plus NEMR plus CEFST1 (combined set). McNemar's test was used to compare the diagnostic performances among three sets and perform subgroup analyses (single vs. multiple bone abnormality, absence/presence of extra-osseous mass, and bone enhancement at fracture margin). Results Compared to the CE set, the combined set showed improved diagnostic accuracy (R1, 84.7 vs. 95.9%; R2, 91.8 vs. 95.9%, p < 0.05) and specificity (R1, 71.4% vs. 93.9%, p < 0.005; R2, 85.7% vs. 98%, p = 0.07), with no difference in sensitivities (p > 0.05). In cases of absent extra-osseous soft tissue mass and present fracture site enhancement, the combined set showed improved accuracy (R1, 82.9–84.4% vs. 95.6–96.3%, p < 0.05; R2, 90.2–91.1% vs. 95.1–95.6%, p < 0.05) and specificity (R1, 68.3–72.9% vs. 92.7–95.8%, p < 0.005; R2, 83.0–85.4% vs. 97.6–98.0%, p = 0.07). Conclusion Combining DWI with conventional MRI improved the diagnostic accuracy and specificity while retaining sensitivity for differentiating between pathologic and traumatic fractures from metastasis at extremities.