Miracle-dz/UniFAR-FTUs huggingface dataset:
Detection of Driver Modules with Rarely Mutated Genes in Cancers

Identifying driver modules or pathways is a key challenge to interpret the molecular mechanisms and pathogenesis underlying cancer. An increasing number of studies suggest that rarely mutated genes are important for the development of cancer. However, the driver modules consisting of mutated genes with low-frequency driver mutations are not well characterized. To identify driver modules with rarely mutated genes, we propose a functional similarity index to quantify the functional relationship between rarely mutated genes and other ones in the same module. Then, we develop a method to detect Driver Modules with Rarely mutated Genes (DMRG) by incorporating the functional similarity, coverage and mutual exclusivity. By applying DMRG on TCGA cancer dataset on three networks: HINT+HI2012, iRefIndex and MultiNet, we detect driver modules intersecting with the well-known signalling pathways and protein complexes, such as the cell cycle pathway and the mediator complex. DMRG can also detect driver modules effectively with 20, 40, 60 and 80 percent of samples by random selection. When compared with HotNet2, DMRG detects more rarely mutated cancer genes and has higher pathway enrichment. Overall, DMRG provides an effective method for the identification of driver modules with rarely mutated genes.
Patient and Public Involvement in the Coproduction of Knowledge

Patient and public involvement in health research is increasingly well established internationally, but the impacts of involvement on the research process are hard to evaluate. We describe a process of qualitative data analysis in a mental health research project with a high level of mental health service user and carer involvement, and reflect critically on how we produced our findings. Team members not from research backgrounds sometimes challenged academic conventions, leading to complex findings that would otherwise have been missing. An essential component of how we coproduced knowledge involved retaining methodological flexibility so that nonconventional research voices in the team could situate and critique what was conventionally known. Deliberate and transparent reflection on how “who we are” informed the knowledge we produced was integral to our inquiry. We conclude that reflecting on knowledge (co)production is a useful tool for evaluating the impact of patient and public involvement on health research.
Introduction to the IEEE Transactions on Cloud Computing

The inaugural Editor-in-Cheif (EiC) shares some of the open opportunities and challenges in cloud computing and then introduces the transactions and its progress. Since its launch early this year, IEEE Transactions on Cloud Computing (TCC) has been accepting submission of papers that introduce original and innovative ideas. That means submission of "extended versions" of already published works (e.g., conference/workshop papers) is not encouraged unless they contain significant number of "new and original" ideas/contributions along with more than 49% "brand new" material. TCC has been attracting submissions from academic researchers, industrial practitioners, policy and standards developers, and application communities from all over the world. During the last five months, we have received more than 150 submissions. In addition, four special issues have been scheduled to focus on specific challenges in cloud computing. They are also encouraging submission of revised versions of papers that are recognized as best papers from associated conferences. Along with EB members, I have been managing the content of the transactions and the rigorous peer review process to ensure publication of original and high-quality papers. Based on the quality, focus, and scope of each submitted paper, it either gets assigned to a suitable Associate Editor or desk rejected with suitable suggestions. Each paper that advances to the full review phase is assigned to an appropriate Associate Editor, who seeks three or more review reports from peers and experts in the field and makes an appropriate recommendation. The EiC has been able to make the final decision on each paper based on peer review reports and the recommendation of AE. The IEEE Computer Society is managing the manuscripts workflow from their initial submission to the final publication. The papers accepted for the first issue of TCC cover hot topics in Cloud computing ranging from Cloud security to energy-efficient resource provisioning.
Patient Perceptions of the Path to Osteoporosis Care Following a Fragility Fracture

Coordinator-based osteoporosis (OP) screening programs for fragility-fracture patients in orthopedic environments improve rates of OP testing and care, but there are still gaps in care. The purpose of this study was to understand the process by which patients decided whether to proceed with OP testing or care within these programs. Twenty-four fragility-fracture patients in the OP screening program at a large, urban, university hospital in Canada participated in one of five focus groups. Focus group transcripts were sorted and coded. Links between themes were developed to generate a description of the process leading to successful initiation of OP care after a fragility fracture. To initiate OP testing and care, patients had to both comprehend the link between their fragility fracture and OP, and make an action-oriented appraisal of what action to take. Several modifiable facilitators and barriers influenced the process between screening and undergoing OP testing and initiating treatment.
Navigating Hardships in Old Age

Research suggests that spirituality is important to a large percentage of the older adult population and serves as a promoter of healthy aging. In this qualitative research I conducted and analyzed multiple interviews with 6 women aged 80 and older. Using multiple in-depth interviews I explored the interplay between spirituality and resilience over the life course. A grounded theory analysis of the 30 interviews was performed. The major finding is that participants used their spirituality as a tool to promote and maintain resilience in later life. I present the results as an interpretation of the participants’ perceptions of their spirituality, and indicate their reliance on spirituality to overcome hardship over the life course. In addition, I discuss the connections between spirituality and resilience. The roles these two constructs play in the lives of older adults are considered.
Disease and the Advancement of Basic Science

The idea of the "two cultures" deals with a schism which is real enough though artificial. It is fertilized by error and misconception. Division between clinical medicine and the sciences basic to medicine and the dividing line which separates the medical school faculty from the rest of the academic world are further divisions. To complete the picture the physician in practice feels hostility toward the professors occupying the ivory towers of our medical schools. A casual glance suggests that we are all enemies—or at least foreigners. Where there is so much smoke there must be fire in the embers. This fire, though to a large degree latent, may be fanned into flame. The times we live in are conducive to irritability, and for always and ever there have been enough irritations to go round. With the vectors pulling in different directions, and apart, it is encourageing to see an effort
Tissue engineering.

The loss or failure of an organ or tissue is one of the most frequent, devastating, and costly problems in human health care. A new field, tissue engineering, applies the principles of biology and engineering to the development of functional substitutes for damaged tissue. This article discusses the foundations and challenges of this interdisciplinary field and its attempts to provide solutions to tissue creation and repair.
Help Yourself

Self-management interventions are increasingly offered to people with chronic health conditions. However, there has been limited exploration of how applicable such an approach is in early stage dementia. In this study we explored the views of people with dementia and family caregivers on the use of self-management in dementia. We conducted semistructured interviews with 13 people with early stage dementia and 11 caregivers. We analyzed transcripts using thematic analysis. We found eight themes in the analysis, and they indicated that self-management occurs in the context of peoples’ family and social relationships as well as relationships with professional services. Six of the themes involved barriers to and facilitators of self-management. It is evident from these findings that people with dementia and caregivers use self-management techniques. Their use of such techniques could be enhanced by the development of interventions designed to help people with dementia to develop their self-management skills.
New efficient methods of image compression in digital cameras with color filter array

Many consumer digital color cameras use a single light sensitive sensor and a color filter array (CFA) with each pixel element recording intensity information of one color component. The captured data is interpolated into a full color image, which is then compressed in many applications. Carrying out color interpolation before compression introduces redundancy in the data. In this paper we discuss methods and issues involved in the compression of CFA data before full color interpretation. The compression methods described operate on the same number of pixels as the sensor data. To obtain improved image quality, median filtering is applied as post-processing. Furthermore, to assure low complexity, the CFA data is compressed by JPEG. Simulations have demonstrated that substantial improvement in image quality is achievable using these new schemes.
“I’m No Superman”

Exercise-based cardiac rehabilitation (CR) programs help patients with coronary heart disease (CHD) reduce their risk of recurrent cardiac illness, disability, and death. However, men with CHD and Type 2 diabetes mellitus (T2DM) demonstrate lower attendance and completion of CR despite having a poor prognosis. Drawing on gender and masculinity theory, we report on a qualitative study of 16 Canadian diabetic men recently enrolled in CR. Major findings reflect two discursive positions men assumed to regain a sense of competency lost in illness: (a) working with the experts, or (b) rejection of biomedical knowledge. These positions underscore the varied and sometimes contradictory responses of seriously ill men to health guidance. Findings emphasize the priority given to the rehabilitation of a positive masculine identity. The analysis argues that gender, age, and employment status are powerful mechanisms of variable CR participation.
A large scale simulation of excitation propagation in layer 2/3 of primary and secondary visual cortices of mice

Analyzing network architecture and spatio-temporal dynamics of the visual cortical areas can facilitate understanding visual information processing in the brain. Recently, several physiological experiments utilizing the fast in-vivo imaging technique have demonstrated that the primary visual cortex (V1) and the secondary visual cortex (V2) in mice exhibit complex properties of the responses to visual and electrical stimuli. In order to provide a tool for quantitatively analyzing such a complex dynamics of the cortices at the level of neurons and circuits, here, we constructed a physiologically plausible large-scale network model of the layers 2/3 of V1 and V2, composed of 14,056 multi-compartment neuron models. The Message-Passing-Interface-based parallel simulations of our network model were able to reproduce, at least quantitatively, the neural responses experimentally observed in mouse V1 and V2 with the voltage-sensitive dye imaging.
Design and performance study of rate staggering storage for scalable video in a disk-array-based video server

This paper provides a data placement method based on rate staggering to store scalable video data in a disk-array-based video server. Scalable video means a video which is coded in such a way that subsets of the full video bit stream can be decoded to create low quality/resolution videos. Supporting layered multiple resolutions from a video server is very desirable in many applications. Note that in a disk array the video data corresponding to different rates of the same video clip are not required to reside in the same disk. In view of this, we propose and explore in this paper the approach of rate staggering, i.e., staggering video data in the disk array based on data rates, it is shown that the advantages of the proposed rate staggering method include: (1) minimizing the intermediate buffer space required by the server, (2) achieving better load balancing due to finer scheduling granularity, and (3) alleviating the disk bandwidth fragmentation. These advantages enable a video server using the rate staggering method to provide feasible solutions to some video stream requests which cannot be met otherwise. The system throughput can thus be increased. We also conduct several simulations for various applications. These experimental results show that the rate staggering method can significantly improve the performance of a VOD system.
A 2K/8K mode small-area FFT processor for OFDM demodulation of DVB-T receivers

We present a novel implementation for 2K/8K dual-mode small-area FFT for the OFDM demodulator of DVB-T receivers. Besides pipelining the FFT to reduce the area and enhance the data throughput, SDF butterfly units for radix-2 and radix-4 processing are adopted to resolve the power consumption difficulty and the P&R (place and route) problem. SRAM is used in the butterfly units to relax the auto-refreshing requirement if DRAM is used.
“Protect Your Loved Ones From Fataki”

The Fataki campaign aired in Tanzania via radio from 2008 to 2011 to address cross-generational sex, a major driver of HIV in the region. The campaign sought to incite social disapproval of men who engage in such relationships, generate dialogue around the issue, and encourage community interventions in these relationships through social learning. Using qualitative methods, we explored campaign reactions, use of the term Fataki to describe men in relationships with much younger women, and the nature of discussions spurred by the campaign. We conducted focus group discussions and individual interviews in Iringa and Pwani regions with young women, older men, and community leaders. Results showed that the Fataki term was widely used and had negative connotations reflecting social disapproval of men who participate in such relationships. Dialogue spurred by the campaign, primarily directed toward young women, focused on reasons for avoiding these relationships. We conclude with suggestions for relevant future interventions.
Classification of awake, REM, and NREM from EEG via singular spectrum analysis

In this study, a single-channel electroencephalography (EEG) analysis method has been proposed for automated 3-state-sleep classification to discriminate Awake, NREM (non-rapid eye movement) and REM (rapid eye movement). For this purpose, singular spectrum analysis (SSA) is applied to automatically extract four brain rhythms: delta, theta, alpha, and beta. These subbands are then used to generate the appropriate features for sleep classification using a multi class support vector machine (M-SVM). The proposed method provided 0.79 agreement between the manual and automatic scores.
Serostatus Disclosure, Stigma Resistance, and Identity Management Among HIV-Positive Gay Men in Ireland

In this study, we examined how non-infectiousness due to antiretroviral therapy has affected HIV-positive gay men’s experience of serostatus disclosure to casual sex partners. Interviews were conducted with 15 seropositive gay men living in Ireland. Using grounded theory, three constructions of non-disclosure were proposed—as self-protection, as a morally permissible act, and as a rejection of the HIV-positive identity. Each construction entailed an aspect related to the sexual exclusion of those living with HIV, and an aspect related to their social exclusion. The extent to which the lives of those interviewed were affected by stigma was starkly revealed, as was the extent to which they stigmatized others living with HIV and rejected the HIV-positive identity. The research highlights the failure to socially normalize HIV and that interventions are needed to reduce the distress associated with seropositivity.
OFDM performance analysis in the phase noise arising from the hot-carrier effect

Phase noise can be regarded as the most severe cause of performance degradation in the orthogonal frequency multiplexing division (OFDM) systems. The hot-carriers (HCs), found in the CMOS synchronization circuits, are the high-energy charge carriers that degrade the MOSFET devices performance by increasing the threshold voltage required to operate the MOSFETs. The HC effect manifests itself as the phase noise whose level increases with the continued MOSFET operation and results in the performance degradation of the voltage-controlled oscillator (VCO) built on the MOSFETs. Nowadays, the HC effect is particularly evident in the short-channel MOSFET devices. Consequently, the MOSFET instability due to this effect leads to the OFDM system performance degradation. In this paper, we analyze the OFDM performance in the presence of synchronization errors induced by the hot-carrier effect. We derive the relationship between the OFDM system performance and the hot-carrier effect in terms of a crucial parameter, the MOSFET threshold voltage. We also present a new general phase noise model for the OFDM systems influenced by the hot-carrier effect, which is based on our new phase noise mask function. According to our simulations, we show that the OFDM bit-error-rate evaluation using our new phase noise model in the presence of the HC effect can be different in three orders-of-magnitude from the existing models independent of the HC
Brazil's Soy Moratorium

Supply-chain governance is needed to avoid deforestation Brazil's Soy Moratorium (SoyM) was the first voluntary zero-deforestation agreement implemented in the tropics and set the stage for supply-chain governance of other commodities, such as beef and palm oil [supplementary material (SM)]. In response to pressure from retailers and nongovernmental organizations (NGOs), major soybean traders signed the SoyM, agreeing not to purchase soy grown on lands deforested after July 2006 in the Brazilian Amazon. The soy industry recently extended the SoyM to May 2016, by which time they assert that Brazil's environmental governance, such as the increased enforcement and national implementation of the Rural Environmental Registry of private properties (Portuguese acronym CAR) mandated by the Forest Code (FC) (1), will be robust enough to justify ending the agreement (2). We argue that a longer-term commitment is needed to help maintain deforestation-free soy supply chains, as full compliance and enforcement of these regulations is likely years away. Ending the SoyM prematurely would risk a return to deforestation for soy expansion at a time when companies are committing to zero-deforestation supply chains (3).
LeCramFS: an efficient compressed file system for flash-based portable consumer devices

Cost-effectiveness is one of the most critical factors in the development of portable consumer devices. The use of compression techniques is a simple but effective solution for achieving such cost-effectiveness. This paper gives a comprehensive analysis of file system level compression techniques for portable consumer devices. Since conventional compressed file systems are optimized for disk like devices and relatively abundant computing resources, they are not suitable for portable devices with small amount of memory and weak processing power. This paper presents the design and implementation of LeCramFS, which is a new read-only compressed file system designed for small portable devices and flash memory. Experiments by implementation show that the proposed file system outperforms conventional ones in terms of memory-efficiency and I/O performance.
MICROBIOLOGY OF LUNG INFECTIONS IN CYSTIC FIBROSIS PATIENTS

Hoiby, N. (Statens Seruminstitut, Department of Clinical Microbiology, Rigshospitalet and the Paediatric Department TG, Copenhagen, Denmark). Microbiology of lung infections in cystic fibrosis patients. Acta Paediatr Scand 1982; suppl 301: 33-54. — Recurrent and chronic pulmonary infection is the major cause of morbidity and mortality in cystic fibrosis. Most of the exacerbations of the respiratory symptoms are due to bacterial infections, but infections caused by virus, chlamydia and mycoplasma may also contribute to the progression of the lung disease. A possible synergism between RS-virus infection and chronic P. aeruginosa infection has been found. Allergic aspergillosis occurs in a few patients. Since the first description of the disease nearly 5O years ago, S. aureus has been recognized as a serious pathogen in CF, but due to efficient antibiotics, the importance of these bacteria to the mortality of CF patients has continued to decrease and is now minimal. During the last 20 years chronic P. aeruginosa infections caused by peculiar mucoid strains have replaced S. aureus as the main infectious problem in CF. The chronic P. aeruginosa infections are characterized by a pronounced antibody response, and the selected pressure of these antibodies in concert with other defense mechanisms in the CF lungs probably favour mucoid strains compared to non-mucoid strains. Epidemiological typing of P. aeruginosa from CF patients and from their environments indicate that cross-infection occurs between these patients; thus suitable prevention in hygiene measures should, therefore, be undertaken.
Integration of nomadic devices with automotive user interfaces

The number of nomadic devices such as PDAs, MP3 players and especially cell phones has largely grown in the last years; Indeed, cell phones are becoming powerful, always-connected computers that store a lot of personal information (contacts, calendar, personal videos and pictures). The small size of their keyboards and screens is a major limitation of nomadic devices, hampering their utilization in vehicles. Handling them while driving may distract the user and increases the risk of accident, and it is illegal in some countries. According to the Web 2.0 vision, the Internet is a platform rather than a mere source of information. The interfaces of Ajax-based applications are user friendly, and they allow storing personal information and preferences. Google Maps is a good example of this philosophy. Nowadays, it is a familiar tool in desktop computers to locate destinations and to plan routes at home. In this paper we propose a new model of Web 2.0 information migration to nomadic devices that facilitates is access to cars.