Miracle-dz/UniFAR-FTUs huggingface dataset:
Over- and under-diagnosis in asthma

Asthma is extremely common with a prevalence of approximately 10% in Europe. It presents with symptoms which have a broad differential diagnosis and examination can be entirely normal. There is no agreed gold standard to diagnose asthma, and the objective tests that can aid diagnosis are often poorly available to primary care physicians. There is evidence that asthma is widely misdiagnosed. Overdiagnosis leads to unnecessary treatment and a delay in making an alternative diagnosis. Underdiagnosis risks daily symptoms, (potentially serious) exacerbations and long-term airway remodelling. An agreed standardised approach to diagnosis, with inclusion of objective measurements prior to treatment, is required to reduce misdiagnosis of asthma. Key points Asthma presents with common respiratory symptoms and physical examination is often normal; in addition, the most widely available tests (peak flow and spirometry) can be normal unless the patient is exacerbating. Treating asthma prior to carrying out objective tests decreases their sensitivity and can make confirmation of the diagnosis difficult. There is no single gold standard test to diagnose asthma, and there are significant differences between the suggested algorithms in commonly used guidelines. Both under- and over-diagnosis are widespread and lead to significant risks to patients. Asthma is frequently misdiagnosed. Both over- and under-diagnosis are associated with inappropriate treatment and potential patient harm. Although no gold standard diagnostic test is available, objective testing can improve diagnostic accuracy. http://ow.ly/Ej3830ohfxJ
E-commerce of Islamic fashion product: usability and user acceptance

HU is an e-commerce of Islamic fashion product with online mall concept using website and mobile application as its medium. The number of HU visitors increased from year to year along with improvements created by HU. However, data from HU shows that the canceled order rate is still high. Also, website and mobile application visitor conversion rate from visitor to buyer at HU website and mobile application’s conversion funnel is about 11%. In addition, preliminary study results indicate that there are problems experienced by users while using HU’s website and mobile application. Therefore, this research aims to evaluate HU’s website and mobile application with usability and user acceptance approach to provide suggestions for improvements to HU website and mobile application user interface. The study involved 120 participants who were categorized into four groups of participants. Usability evaluation is done by measuring the effectiveness, efficiency, and user satisfaction. While the user acceptance evaluation is measured by using a questionnaire. Research shows that HU website and mobile application has good effectiveness but has poor efficiency seen from the criterion of time completion and frequency of error. It is also found that there are some low ratings of user satisfaction questionnaires and user acceptance questionnaires. The results of the study are eight proposed improvements to the website user interface and nine proposed improvements to the mobile application user interface.
Kidney Function and Arterial Calcification in Major Vascular Beds

Background The purpose of this study was to investigate the association between kidney function and arterial calcification in major vascular beds and to establish whether arterial calcification mediates the relation between kidney function measures and cardiovascular disease (CVD) incidence. Methods and Results In 2241 participants from the Rotterdam Study (mean age 69 years, 52% female), kidney function was assessed using the estimated glomerular filtration rate and urine albumin‐to‐creatinine ratio. All participants underwent noncontrast computed tomography to quantify the amount of arterial calcification in the coronary arteries, aortic arch, extracranial, and intracranial internal carotid arteries. We used linear regression models, adjusted for age, sex, and cardiovascular risk factors, to evaluate the association between kidney function and arterial calcification volume in the 4 vessel beds. Incidence rate of CVD was calculated in 3 groups of participants based on their kidney function and presence of arterial calcification. We conducted mediation analysis to evaluate whether arterial calcification mediates this association. We found that in age‐ and sex‐adjusted models, lower estimated glomerular filtration rate and higher albumin‐to‐creatinine ratio were associated with larger calcification volumes in all 4 vascular beds. Adjusting for cardiovascular risk factors attenuated the effect estimates. CVD incidence was higher in participants with estimated glomerular filtration rate <60 mL/min per 1.73 m2 and presence of arterial calcification compared with individuals with estimated glomerular filtration rate >60 and no calcification. After adjusting for cardiovascular risk factors, arterial calcification did not mediate the association between kidney function measures and CVD incidence. Conclusions The association of impaired kidney function and larger volumes of arterial calcification is partly explained by cardiovascular risk factors. Arterial calcification does not mediate the association between kidney function and CVD beyond cardiovascular risk factors.
Long noncoding RNA CHRF exacerbates IL‐6‐induced inflammatory damages by downregulating microRNA‐146a in ATDC5 cells

Osteoarthritis (OA) is a frequent chronic musculoskeletal disorder which lacks applicably effective therapeutic strategy. In this study, we attempted to investigate whether long noncoding RNA (lncRNA) cardiac hypertrophy‐related factor (CHRF) participated in mediating interleukin‐6 (IL‐6)‐induced in vitro inflammatory damages as well as the regulatory mechanisms. ATDC5 cells were stimulated with IL‐6, and then cellular damages were evaluated on the basis of cell viability by CCK‐8, apoptotic cells by observation with flow cytometry, apoptosis‐associated proteins by western blot analysis, and accumulation of inflammatory factors by quantitative reverse transcription polymerase chain reaction (RT‐qPCR), enzyme‐linked immunosorbent assay (ELISA), and western blot analysis. Then, effects of lncRNA CHRF on IL‐6‐treated cells were evaluated. We further explored the downstream factor of lncRNA CHRF and demonstrated whether lncRNA CHRF functioned through the downstream factor. Afterwards, crucial signaling cascades were anatomized. We found that IL‐6 reduced cell viability, elevated apoptosis, induced upregulation of inflammatory factors, as well as upregulated lncRNA CHRF and down‐regulated miR‐146a expression. Then, we found lncRNA CHRF overexpression aggravated IL‐6‐induced alterations, and lncRNA CHRF knockdown showed the opposite effects. Furthermore, miR‐146a was identified to be negatively regulated by lncRNA CHRF, and its overexpression abrogated the roles of lncRNA CHRF in IL‐6‐treated cells. IL‐6‐induced the accumulation of IκBα, p65, JAK1, and STAT3 at phosphorylated level was further facilitated by lncRNA CHRF whereas repressed by miR‐146a. In conclusion, lncRNA CHRF aggravated the IL‐6‐induced inflammatory damages in ATDC5 cells. We further outlined a possible mechanism that through downregulating miR‐146a, lncRNA CHRF evoked the activation of NF‐κB and JAK1/STAT3 signaling cascades.
Applying hydrodynamic pressure to efficiently generate induced pluripotent stem cells via reprogramming of centenarian skin fibroblasts

Induced pluripotent stem cell (iPSC)-technology is an important platform in medicine and disease modeling. Physiological degeneration and disease onset are common occurrences in the aging population. iPSCs could offer regenerative medical options for age-related degeneration and disease in the elderly. However, reprogramming somatic cells from the elderly is inefficient when successful at all. Perhaps due to their low rates of replication in culture, traditional transduction and reprogramming approaches with centenarian fibroblasts met with little success. A simple and reproducible reprogramming process is reported here which enhances interactions of the cells with the viral vectors that leads to improved iPSC generation. The improved methods efficiently generates fully reprogrammed iPSC lines from 105–107 years old subjects in feeder-free conditions using an episomal, Sendai-Virus (SeV) reprogramming vector expressing four reprogramming factors. In conclusion, dermal fibroblasts from human subjects older than 100 years can be efficiently and reproducibly reprogrammed to fully pluripotent cells with minor modifications to the standard reprogramming procedures. Efficient generation of iPSCs from the elderly may provide a source of cells for the regeneration of tissues and organs with autologous cells as well as cellular models for the study of aging, longevity and age-related diseases.
Draft Genome Sequences of 64 Type Strains of 50 Species and 25 Subspecies of the Genus Staphylococcus Rosenbach 1884

Members of the genus Staphylococcus have been isolated from humans, animals, and the environment. Accurate identification with whole-genome sequencing requires access to data derived from type strains. ABSTRACT Members of the genus Staphylococcus have been isolated from humans, animals, and the environment. Accurate identification with whole-genome sequencing requires access to data derived from type strains. We provide sequence data for type strains of 64 taxa in the genus that at the time of this writing have standing in the nomenclature.
Whole-Genome Sequence of an Isogenic Haploid Strain, Saccharomyces cerevisiae IR-2idA30(MATa), Established from the Industrial Diploid Strain IR-2

We present the draft genome sequence of an isogenic haploid strain, IR-2idA30(MATa), established from Saccharomyces cerevisiae IR-2. Assembly of long reads and previously obtained contigs from the genome of diploid IR-2 resulted in 50 contigs, and the variations and sequencing errors were corrected by short reads. ABSTRACT We present the draft genome sequence of an isogenic haploid strain, IR-2idA30(MATa), established from Saccharomyces cerevisiae IR-2. Assembly of long reads and previously obtained contigs from the genome of diploid IR-2 resulted in 50 contigs, and the variations and sequencing errors were corrected by short reads.
Joint and Direct Optimization for Dictionary Learning in Convolutional Sparse Representation

Convolutional sparse coding (CSC) is a useful tool in many image and audio applications. Maximizing the performance of CSC requires that the dictionary used to store the features of signals can be learned from real data. The so-called convolutional dictionary learning (CDL) problem is formulated within a nonconvex, nonsmooth optimization framework. Most existing CDL solvers alternately update the coefficients and dictionary in an iterative manner. However, these approaches are prone to running redundant iterations, and their convergence properties are difficult to analyze. Moreover, most of those methods approximate the original nonconvex sparse inducing function using a convex regularizer to promote computational efficiency. This approach to approximation may result in nonsparse representations and, thereby, hinder the performance of the applications. In this paper, we deal with the nonconvex, nonsmooth constraints of the original CDL directly using the modified forward–backward splitting approach, in which the coefficients and dictionary are simultaneously updated in each iteration. We also propose a novel parameter adaption scheme to increase the speed of the algorithm used to obtain a usable dictionary and in so doing prove convergence. We also show that the proposed approach is applicable to parallel processing to reduce the computing time required by the algorithm to achieve convergence. The experimental results demonstrate that our method requires less time than the existing methods to achieve the convergence point while using a smaller final functional value. We also applied the dictionaries learned using the proposed and existing methods to an application involving signal separation. The dictionary learned using the proposed approach provides performance superior to that of comparable methods.
Universal Plug and Play (UPnP) Internet Gateway Device (IGD)-Port Control Protocol (PCP) Interworking Function

This document specifies the behavior of the UPnP IGD (Internet Gateway Device)/PCP interworking function. An UPnP IGD-PCP Interworking function is required to be embedded in CP routers to allow for transparent NAT control in environments where UPnP is used in the LAN side and PCP in the external side of the CP router.
Learning Recurrent Neural Networks with Hessian-Free Optimization : Supplementary Materials

2 Details of the pathological synthetic problems 3 2.1 The addition, multiplication, and XOR problem . 3 2.2 The temporal order problem . 4 2.3 The 3-bit temporal order problem . 4 2.4 The random permutation problem . 4 2.5 Noiseless memorization . 5
Highlights and Perspectives on Evolutionary Neuroscience

Much research points to important and diverse effects of sleep on neural and cognitive functioning, suggesting that the relationship between sleep and the brain holds the key [Hobson, 2005]. Sleep is associated with distinctive patterns of neural activity which differ between rapid-eye movement (REM) sleep and non-REM sleep [Staunton, 2005]. Sleep is thought to play a role in synaptic remodelling [Jha et al., 2005], and sleep deprivation negatively impacts on a variety of aspects of cognitive function, including learning, reaction times and attention [Hobson, 2005; Staunton, 2005]. The biology and functions of sleep have mostly been tackled using experiments. By carefully manipulating certain variables and holding others constant, researchers have attempted to isolate effects that are specific to sleep and to particular aspects of sleep (notably REM vs. nonREM). Complementing experimental approaches are cross-species comparisons, which potentially provide important evidence about biological function and evolution. It has been known for many years that the amount of time spent sleeping is highly variable across mammal species, from about 3 h to about 20 h per day [Siegel, 2009]. In principle, any hypothesis for the function of sleep should be capable of explaining this variation, but pinWhy do we sleep? In a sense, it is equally valid to ask why we wake, except that the functions of the things we do while awake – eating and reproducing, for example – are quite obvious, whereas the same is not true for the things that we do while asleep – such as rapid eye movements and dreaming. This is why the function of sleep has exercised the minds of scientists, writers and philosophers since Aristotle. Sleep appears to be biologically necessary: sleep deprivation in mammals is followed by a tiredness-induced ‘rebound’ and, if chronic, leads to impaired physiological and mental functioning, or, in the extreme, even death [Allada and Siegel, 2008]. Yet despite its apparent necessity, a consensus on the function of sleep remains elusive: prominent hypotheses include conservation of energy when activities are unprofitable or impossible [Siegel, 2009], memory consolidation [Stickgold and Walker, 2007] or some physiological function, such as maintenance of the immune system [Opp and Krueger, 2015]. So many different hypotheses have been proposed that some have even suggested that sleep has no specific biological function [Rial et al., 2007], although, as Rechtschaffen [1971] asserted, in that case sleep must be ‘the biggest mistake the evolutionary process ever made’. Published online: February 12, 2016
Scalable Atomic Visibility with RAMP Transactions

Databases can provide scalability by partitioning data across several servers. However, multipartition, multioperation transactional access is often expensive, employing coordination-intensive locking, validation, or scheduling mechanisms. Accordingly, many real-world systems avoid mechanisms that provide useful semantics for multipartition operations. This leads to incorrect behavior for a large class of applications including secondary indexing, foreign key enforcement, and materialized view maintenance. In this work, we identify a new isolation model—Read Atomic (RA) isolation—that matches the requirements of these use cases by ensuring atomic visibility: either all or none of each transaction’s updates are observed by other transactions. We present algorithms for Read Atomic Multipartition (RAMP) transactions that enforce atomic visibility while offering excellent scalability, guaranteed commit despite partial failures (via coordination-free execution), and minimized communication between servers (via partition independence). These RAMP transactions correctly mediate atomic visibility of updates and provide readers with snapshot access to database state by using limited multiversioning and by allowing clients to independently resolve nonatomic reads. We demonstrate that, in contrast with existing algorithms, RAMP transactions incur limited overhead—even under high contention—and scale linearly to 100 servers.
A CURA : A Framework for Quality-retaining Power Saving on Mobile OLED

Organic light-emitting diode (OLED) technology is regarded as a promising alternative to mobile displays. In this paper, we introduce the design, algorithm, and implementation of a novel framework called CURA for quality-retaining power saving on mobile OLED displays. First, we link human visual attention to OLED power saving and model the OLED image scaling optimization problem. The objective is to minimize the power required to display an image without adversely impacting the user’s visual experience. Then, we present the algorithm used to solve the modeled problem, and prove its optimality even without an accurate power model. Finally, based on the framework, we implement two practical applications on a commercial OLED mobile tablet. The results of experiments conducted on the tablet with real images demonstrate that CURA can reduce significant OLED power consumption while retaining the visual quality of images.
Frankenstein ’ s PSO : A Composite Particle Swarm Optimization Algorithm

During the last decade, many modifications of the original particle swarm optimization (PSO) algorithm have been proposed. In many cases, it is claimed that the modified variant is superior to some reference variant in some way. The differences between two variants can often be seen as an algorithmic component being present in one variant but not in the other. From this perspective, the question arises as to whether it is possible to integrate different algorithmic components into a single PSO variant that performs better than the variants from which its components are taken. In this paper, we take this perspective to design a new PSO algorithm whose components were selected after a careful evaluation of their impact on optimization speed and reliability. We call this composite algorithm Frankenstein’s PSO in an analogy to the popular character of Mary Shelley’s novel. The evaluation of Frankenstein’s PSO performance suggests that the answer to the driving question is positive. We present the process that guided us in selecting and adapting the algorithmic components included in Frankenstein’s PSO. The performance of the composite algorithm is validated via a comparison with the variants from which the components were taken on a number of well-known benchmark problems.
2-3-2014 Improving the Estimation of Word Importance for News Multi-Document Summarization-Extended Technical Report

In this paper, we propose a supervised model for ranking word importance that incorporates a rich set of features. Our model is superior to prior approaches for identifying words used in human summaries. Moreover we show that an extractive summarizer which includes our estimation of word importance results in summaries comparable with the state-of-the-art by automatic evaluation. Disciplines Computer Engineering | Computer Sciences Comments University of Pennsylvania Department of Computer and Information Science Technical Report No. MSCIS-14-02. This technical report is available at ScholarlyCommons: http://repository.upenn. edu/cis_reports/989 Improving the Estimation of Word Importance for News Multi-Document Summarization Extended Technical Report Kai Hong University of Pennsylvania Philadelphia, PA, 19104 hongkai1@seas.upenn. edu Ani Nenkova University of Pennsylvania Philadelphia, PA, 19104 nenkova@seas.upenn. edu
Improving the Estimation of Word Importance for News Multi-Document Summarization - Extended Technical Report

In this paper, we propose a supervised model for ranking word importance that incorporates a rich set of features. Our model is superior to prior approaches for identifying words used in human summaries. Moreover we show that an extractive summarizer which includes our estimation of word importance results in summaries comparable with the state-of-the-art by automatic evaluation.
Edinburgh Research Explorer High-resolution 3D imaging of osteocytes and computational modelling in mechanobiology

Osteocytes are involved in mechanosensation and mechanotransduction in bone and hence, are key to bone adaptation in response to development, ageing and disease. Thus, detailed knowledge of the three-dimensional (3D) structure of the osteocyte network (ON) and the surrounding lacuno-canalicular network (LCN) is essential. Enhanced understanding of the ON&LCN will contribute to a better understanding of bone mechanics on cellular and sub-cellular scales, for instance through improved computational models of bone mechanotransduction. Until now, the location of the ON within the hard bone matrix and the sub-µm dimensions of the ON&LCN have posed significant challenges for 3D imaging. This review identifies relevant microstructural phenotypes of the ON&LCN in health and disease and summarises how light microscopy, electron microscopy and X-ray imaging techniques have been used in studies of osteocyte anatomy, pathology and mechanobiology to date. In this review, we assess the requirements for ON&LCN imaging and examine the state of the art in the fields of imaging and computational modelling as well as recent advances in high-resolution 3D imaging. Suggestions for future investigations using volume electron microscopy are indicated and we present new data on the ON&LCN using serial block-face scanning electron microscopy. A correlative approach using these high-resolution 3D imaging techniques in conjunction with in silico modelling in bone mechanobiology will increase understanding of osteocyte function and, ultimately, lead to improved pathways for diagnosis and treatment of bone diseases such as osteoporosis.
Sniffing the mood for cooperation: Personality and odor induced affective states effects

The paper explores situational and dispositional underpinnings of cooperative behavior. According to psychological research, cooperation is strongly related to affective states (Forgas, 1998) and personality dimensions (Volk, Thöni, & Ruigrok, 2011). In an experimental study we examined the conditions under which people cooperate with each other. The dispositional traits of co-workers (personality), the contribution to a collaborative effort, and a situational factor – ambient odor condition were taken into consideration. A one-way ANOVA revealed that compared to a malodorous condition, both the pleasant odor condition and the natural odor condition showed higher rates of cooperation. Further analysis indicated that only malodors influenced affective states which in turn determined social decisions. Although we found effects for the participants’ agreeableness and the coworker’s contribution to a joint work, they appeared to play a less critical role than affective states induced by the experimental odor conditions tested here.