Miracle-dz/UniFAR-FTUs huggingface dataset:
Learning to rank for censored survival data

Survival analysis is a type of semi-supervised ranking task where the target output (the survival time) is often right-censored. Utilizing this information is a challenge because it is not obvious how to correctly incorporate these censored examples into a model. We study how three categories of loss functions, namely partial likelihood methods, rank methods, and our classification method based on a Wasserstein metric (WM) and the non-parametric Kaplan Meier estimate of the probability density to impute the labels of censored examples, can take advantage of this information. The proposed method allows us to have a model that predict the probability distribution of an event. If a clinician had access to the detailed probability of an event over time this would help in treatment planning. For example, determining if the risk of kidney graft rejection is constant or peaked after some time. Also, we demonstrate that this approach directly optimizes the expected C-index which is the most common evaluation metric for ranking survival models.
Disrupting Industries with Blockchain: The Industry, Venture Capital Funding, and Regional Distribution of Blockchain Ventures

The blockchain (i.e., a decentralized and encrypted digital ledger) has the potential to disrupt many traditional business models. This study investigates the emerging blockchain business-application landscape by analyzing its industry, venture capital funding, and regional distribution. We do so by matching four venture databases on blockchain-based startups. First, our results show that blockchain startups are most prominently represented in the Finance & Insurance and Information & Communication industries. A fine-grained analysis of financial services yields increasing novel applications in existing service offerings – especially in payment networks and processing. Second, consistent with the first result, we find that mainly Finance & Insurance and Information & Communication industries are funded by venture capital. Third, our regional distribution analysis of the emerging ventures identifies two leading geographical blockchain clusters (i.e., the US and UK). Overall, our study contributes to the literature by providing one of the first analyses of blockchain-based business applications.
Profiles of Motor Laterality in Young Athletes' Performance of Complex Movements: Merging the MOTORLAT and PATHoops Tools

Laterality is a key aspect of the analysis of basic and specific motor skills. It is relevant to sports because it involves motor laterality profiles beyond left-right preference and spatial orientation of the body. The aim of this study was to obtain the laterality profiles of young athletes, taking into account the synergies between the support and precision functions of limbs and body parts in the performance of complex motor skills. We applied two instruments: (a) MOTORLAT, a motor laterality inventory comprising 30 items of basic, specific, and combined motor skills, and (b) the Precision and Agility Tapping over Hoops (PATHoops) task, in which participants had to perform a path by stepping in each of 14 hoops arranged on the floor, allowing the observation of their feet, left-right preference and spatial orientation. A total of 96 young athletes performed the PATHoops task and the 30 MOTORLAT items, allowing us to obtain data about limb dominance and spatial orientation of the body in the performance of complex motor skills. Laterality profiles were obtained by means of a cluster analysis and a correlational analysis and a contingency analysis were applied between the motor skills and spatial orientation actions performed. The results obtained using MOTORLAT show that the combined motor skills criterion (for example, turning while jumping) differentiates athletes' uses of laterality, showing a clear tendency toward mixed laterality profiles in the performance of complex movements. In the PATHoops task, the best spatial orientation strategy was “same way” (same foot and spatial wing) followed by “opposite way” (opposite foot and spatial wing), in keeping with the research assumption that actions unfolding in a horizontal direction in front of an observer's eyes are common in a variety of sports.
Microscopic Isthmuses and Fibrosis Within the Border Zone of Infarcted Hearts Promote Calcium-Mediated Ectopy and Conduction Block

Ventricular tachycardia (VT) secondary to myocardial infarction (MI) remain a major cause of sudden death in adults. Premature ventricular complexes (PVCs), the first initiating beats of a portion of these arrhythmias, arise from triggered activity in the infarct border zone (BZ). At the cellular scale, spontaneous calcium release (SCR) events are a known cause of triggered activity and have been reported in cells that survive MI. At the tissue scale, fibrosis has been shown to play an important role in creating the substrate for VT. However, the interplay between SCR-mediated triggered activity and fibrosis upon VT formation in infarcted hearts has not been fully investigated. Here, we conduct in-silico experiments to assess how macroscopic and microscopic anatomical properties of the BZ can create a substrate for SCR-mediated VT formation. To study this question, we employ a stochastic subcellular-scale model of SCR events and action potential to simulate different cardiac preparations. Within 2D sheet models with idealized infarct scars and BZ we show that the probability of PVCs is higher, 55%, in preparations with thin conducting isthmuses (0.2 mm) transcending the scar. In an anatomically-detailed model of the rabbit ventricles with a realistic representation of intramural scars, we show that the heart’s protective source-sink mismatch prevents ectopy. Furthermore, we demonstrate that fibrosis disrupts this antiarrhythmic mechanism making PVCs more likely. PVC probability is highest (≥ 25%) when fibrosis accounts for 60% and 90% of the BZ in the 2D sheet and the 3D anatomical model, respectively. Above these thresholds, PVC occurrence decreases because of: 1) the reduced number of myocytes in the BZ; 2) conduction block. Block is caused either by disconnection of BZ cells from the myocardium or due to source-sink mismatches at regions of rapid tissue expansion. Moreover, while outward propagation to healthy tissue may fail, PVCs traveling inward through the scar might encounter more favorable loading conditions. These PVCs may exit to the myocardium and reenter back at the region of block. Overall, our findings indicate that thin isthmuses and strands of myocytes interspersed with fibrosis can be arrhythmogenic. Ablation of these microscopic structures may prevent VT formation.
Transmembrane Domain 1 of Human Organic Anion Transporting Polypeptide 2B1 Is Essential for Transporter Function and Stability

Organic anion transporting polypeptides (OATPs, gene symbol SLCO) are important membrane transporter proteins that mediate the uptake of wide ranges of endogenous and exogenous compounds. OATP2B1 has been found in multiple organs and tissues, including the liver, small intestine, kidney, brain, placenta, heart, skin, as well as skeletal muscle, and is proposed to be involved in the uptake of orally administered drugs. Quite a few reports have demonstrated that transmembrane domains (TMs) are crucial for proper functions of OATP family members. Comparative modeling proposed that TM1, along with TM2, 4, and 5 of the N-terminal half of OATP2B1, may be localized within the substrate interaction pocket and are important for uptake function of the transporter. Alanine scanning of the putative transmembrane domain 1 of OATP2B1 revealed that substitution of L58 with alanine dramatically altered the Km value, and mutation of V52, H55, Q59, and L69 resulted in significantly reduced substrate turnover number, whereas A61V, Q62A, and S66A exhibited significant change in both Km and Vmax values. In addition, phenylalanine at position 51 seems to play an important role in maintaining proper folding of OATP2B1 because alanine replacement of F51 caused accelerated degradation of the transporter protein. Although proteasome and lysosome inhibitors could partially recover protein level, the mutant transporter remained nonfunctional. Taken together, the identification of nine essential amino acid residues within TM1 of OATP2B1 suggested that the transmembrane domain is important for maintaining proper function of the transporter.
Time to build on good design: Resolving the temporal dynamics of gene regulatory networks

The increasing availability of -omics data is driving the development of computational methods for integrating these datasets to connect the underlying molecular mechanisms to phenotypes. Building gene regulatory networks (GRNs) from transcriptomic studies often results in a static view of gene expression, which can make it difficult to disentangle pathway structure. Increasing the temporal resolution of any experimental design provides the opportunity to model the dynamic nature of a regulatory pathway response to a stimulus. Many transient intermediate states can separate the initial prestimulus state from the final poststimulus state; time-series analyses permit the detection and integration of these intermediate steps into the pathway. The difficulty is to incorporate these time-dependent changes to determine causal relationships within the GRN, such as which transcription factor (TF) regulates which target genes. In PNAS, Varala et al. (1) address this challenge by integrating time into their GRN to unravel the temporal cascade of nitrogen signaling. Their time-based analysis offers a potent and general approach to uncover the temporal transcriptional logic for any plant or animal response system. Nitrogen (N) commonly limits plant production and the widespread application of mineral N fertilizer has greatly increased crop yields (2). Unfortunately, the production of mineral N fertilizer is expensive in terms of fossil energy. Furthermore, plant assimilation of applied N is inefficient; for example, cereals such as maize, rice, and wheat take up less than 40% of the applied N (3). The remaining N is lost to the environment through processes including denitrification and volatilization, releasing greenhouse gases, leaching, contaminating groundwater, and surface runoff, causing eutrophication of fresh and estuarine waters (4). Therefore, the excessive use of N fertilizer both increases the cost of crop production and causes environmental pollution. One might expect that, consequently, plant N use efficiency (NUE) would represent a major target for … [↵][1]1To whom correspondence should be addressed. Email: c.robertson. mcclung{at}Dartmouth.edu. [1]: #xref-corresp-1-1
A Protocol for Systematic Literature Review on Methods to handle Multiple Concerns in Architecture-Based Self-Adaptive Systems

In this study we aim to identify, and summarize current methods handling multiple concerns in self-adaptive systems. Thus, we conduct a systematic literature review, which is a well-defined method to identify and evaluate studies in a specific domain regarding a particular set of research questions (Kitchenham & Charters, 2007). By performing a systematic literature review, we obtain a fair and unbiased evaluation of selected topic using a rigorous and reliable method.
Outpatient physiotherapists’ attitudes and beliefs toward patients with chronic pain: A qualitative study

ABSTRACT Purpose: To conduct a knowledge translation exercise by sharing knowledge from a scoping review, describing physiotherapists’ attitudes toward and beliefs about chronic pain, and to gain perspectives on these findings from physiotherapists working with this clientele. Method: We conducted three focus groups with a total of 14 outpatient physiotherapists working in public hospitals. We first showed a video (reflecting an encounter between a clinician and a person living with chronic pain) created based on themes that emerged from a scoping review we conducted, followed by a discussion about attitudes and beliefs toward chronic pain. The sessions were audio-taped and transcripts were analyzed through descriptive and thematic analysis. Results: The consultations reinforced three core themes related to physiotherapists’ attitudes toward and beliefs about chronic pain: 1) the development of chronic pain; 2) the relationship to disability and the legitimacy of chronic pain; and 3) physiotherapists’ ability to manage psychological aspects of their patient’s pain. Conclusion: Physiotherapists in our sample appear unsure of how to interpret severe pain within the context of minimal objective findings. Physiotherapists may benefit from training on how to assess and treat psychosocial factors associated with pain.
A Systematic Analysis of Patient Portals Adoption, Acceptance and Usage: The Trajectory for Triple Aim?

Personal Health Records (PHR), often known as patient portal, are consumer-centric tools that can strengthen consumers’ ability to actively manage their own health and healthcare. The incorporation of patient portals provides the promise to assist with Triple Aim and population health goals. Patient portals encourage patients to play a more active role in their healthcare by giving them more responsibility for maintaining a healthy lifestyle and managing chronic diseases and thus may provide a costeffective way to improve quality of care. In this study, we extend the existing literature by using a data analytic approach to provide more insights in adopting mobile patient portals. Specifically, we aim to use topic modeling approach, LDA algorithm, to systematically analyze users’ feedback (i.e., online users’ reviews) from the actual use of a common mobile patient portal, Epic’s MyChart. To validate the extracted topics, we compared the results of LDA analysis with that of human analysis. Overall, the extracted topics revealed opportunities for improvement and to enhance the design of current basic portals to improve usage. Improved portal usage will move toward effective population health management and achievement of the triple aim goals.
Portable imaging polarimeters

The natural light field has long been known to be partly linearly polarized, and it has been suggested that various objects reflect light that is polarized at a specific orientation. Although humans use polarized light, our inability to see it limits our study and understanding of its distribution in nature and of the information it carries. By placing two twisted nematic liquid crystals and a fixed polarizing filter in series in front of a CCD camera, we constructed a portable polarimeter that analyses the linear polarization characteristics of a full image on a single pixel basis. Two configurations are presented: an autonomous sensor that uses a small camcorder for recording images that are analyzed at a later stage; and an online sensor that uses a digital camera connected to a personal computer which controls and analyses the information. Field measurements reveal possible usage for analyzing spatial orientation of objects or breaking color camouflage. Our new polarimeters provide an opportunity to inspect and understand an aspect of the visual world, currently obscure to our eyes.
Effect of a mitochondrial‐targeted coenzyme Q analog on pancreatic β‐cell function and energetics in high fat fed obese mice

We recently reported that mitoquinone (mitoQ, 500 μmol/L) added to drinking water of C57BL/6J mice attenuated weight gain and reduced oxidative stress when administered to high‐fat (HF) fed mice. Here, we examined the effects of mitoQ administered to HF fed mice on pancreatic islet morphology, dynamics of insulin secretion, and islet mitochondrial metabolism. C57BL/6J mice were fed HF for 130 days while we administered vehicle (cyclodextrin [CD]) or mitoQ added to the drinking water at up to 500 μmol/L. MitoQ‐treated mice vs vehicle gained significantly less weight, expended significantly more energy as determined by indirect calorimetry, and trended to consume less (nonsignificant) food. As we and others reported before, mitoQ‐treated mice drank less water but showed no difference in percent body fluid by nuclear magnetic resonance. Circulating insulin and glucose‐stimulated insulin secretion by isolated islets were decreased in mitoQ‐treated mice while insulin sensitivity (plasma insulin x glucose) was greater. Islet respiration as basal oxygen consumption (OCR), OCR directed at ATP synthesis, and maximal uncoupled OCR were also reduced in mitoQ‐treated mice. Quantitative morphologic studies revealed that islet size was reduced in the mitoQ‐treated mice while visual inspection of histochemically stained sections suggested that mitoQ reduced islet lipid peroxides. MitoQ markedly improved liver function as determined by plasma alanine aminotransferase. In summary, mitoQ treatment reduced the demand for insulin and reduced islet size, likely consequent to the action of mitoQ to mitigate weight gain and improve liver function.
SIMULATION: A powerful tool for prototyping telecommunications networks

Simulation models of telecomunication networks are valuable tools for evaluating network performance during the design, development, and operational phases of network life. This paper relates the concepts of discrete event simulation to the context of application to the telecommunication field. A range of software, useful to this enterprise, is discussed, the range extending from general-purpose to very problem-oriented languages. Finally, a primitive network simulation model, using the GPSS simulation language, is presented to illustrate the technique. A basic bibliography, categorized by simulation subject, is included.
Harimaru: a new potato variety for a local specialty

‘Harimaru’ is a new potato variety bred from a cross between ‘Saikai 35’ as a female parent and ‘Pike’ as a male parent. Marker selection was performed for 1,647 seedlings to combine resistance genes to late blight (R1), Potato virus Y (Rychc), Potato virus X (Rx1), and golden cyst nematode (H1). In total, 194 selected clones were evaluated in the field, among which the best clone was officially released as ‘Harimaru’. Its yield was slightly lower than the local standard variety, ‘May Queen’. However, it produces tasty potatoes, that do not become mushy with long boiling times despite its high starch content. ‘Harimaru’ may become a local specialty potato and its multiple resistance to potato viruses may allow cultivation using homemade seed tubers from the previous season’s crop.
A systematic approach for identifying shared mechanisms in epilepsy and its comorbidities

Cross-sectional epidemiological studies have shown that the incidence of several nervous system diseases is more frequent in epilepsy patients than in the general population. Some comorbidities (e.g., Alzheimer’s disease and Parkinson’s disease) are also risk factors for the development of seizures; suggesting they may share pathophysiological mechanisms with epilepsy. A literature-based approach was used to identify gene overlap between epilepsy and its comorbidities as a proxy for a shared genetic basis for disease, or genetic pleiotropy, as a first effort to identify shared mechanisms. While the results identified neurological disorders as the group of diseases with the highest gene overlap, this analysis was insufficient for identifying putative common mechanisms shared across epilepsy and its comorbidities. This motivated the use of a dedicated literature mining and knowledge assembly approach in which a cause-and-effect model of epilepsy was captured with Biological Expression Language. After enriching the knowledge assembly with information surrounding epilepsy, its risk factors, its comorbidities, and antiepileptic drugs, a novel comparative mechanism enrichment approach was used to propose several downstream effectors (including the GABA receptor, GABAergic pathways, etc.) that could explain the therapeutic effects carbamazepine in both the contexts of epilepsy and AD. We have made the Epilepsy Knowledge Assembly available at https://www.scai. fraunhofer.de/content/dam/scai/de/downloads/bioinformatik/epilepsy.bel and queryable through NeuroMMSig at http://neurommsig.scai. fraunhofer.de. The source code used for analysis and tutorials for reproduction are available on GitHub at https://github.com/cthoyt/epicom.
Proof of Concept for a Visual Analytics Dashboard for Transportation Network Analysis

This paper discusses the latest developments in the field of visual analytics, and the role of network analysis for transportation systems. Multilayer and multiplex based visualizations are considered reliable solutions for handling the information overload the decision makers are facing in the addressed domain. The existing tools matching these requirements are briefly reviewed. Then, a proof of concept for a dashboard is presented focusing on a transportation network analysis with multiple network measures and indices in a multiplex visualization. Visual Analytics Dashboard; Transportation Network Analysis; Multilayer and Multiplex Visualization.
Japanese Society of Medical Oncology Clinical Guidelines: Molecular Testing for Colorectal Cancer Treatment, Third Edition

The Japanese Society of Medical Oncology (JSMO) previously published 2 editions of the clinical guidelines: “Japanese guidelines for testing of KRAS gene mutation in colorectal cancer” in 2008 and “Japanese Society of Medical Oncology Clinical Guidelines: RAS (KRAS/NRAS) mutation testing in colorectal cancer patients” in 2014. These guidelines have contributed to the proper use of KRAS and RAS mutation testing, respectively. Recently, clinical utility, particularly for colorectal cancer (CRC) patients with BRAF V600E mutation or DNA mismatch‐repair (MMR) deficiency, has been established. Therefore, the guideline members decided these genetic alterations should also be involved. The aim of this revision is to properly carry out testing for BRAF V600E mutation and MMR deficiency in addition to RAS mutation. The revised guidelines include the basic requirements for testing for these genetic alterations based on recent scientific evidence. Furthermore, because clinical utility of comprehensive genetic testing using next‐generation sequencing and somatic gene testing of analyzing circulating tumor DNA has increasingly evolved with recent advancements in testing technology, we noted the current situation and prospects for these testing technologies and their clinical implementation in the revised guidelines.
Social Network Sites in Businesses: Combating Technostress

This survey research examined social networking sites (SNS) internal to the company to determine how SNS use affects attitudes, and ultimately turnover intentions. We hypothesize that due to social capital, emotional dissonance, and conservation of resource theories, work SNS use will decrease work isolation, which will decrease work-related attitudes and increase turnover intentions. Due to social capital theory, we propose that work SNS use will decrease work isolation. Due to emotional dissonance theory, we hypothesize that work isolation will decrease positive emotions and job satisfaction, and increase job tensions, such as work stress. All three of these factors will increase turnover intentions. These findings suggest that technology has the potential of reducing technostress symptoms at work. We found that incorporating internal SNS in businesses improves attitudes and behaviors, which is important for managers to consider as ways to save costs due to employee turnover.