Miracle-dz/UniFAR-FTUs huggingface dataset:
Integrating Phylodynamics and Epidemiology to Estimate Transmission Diversity in Viral Epidemics

The epidemiology of chronic viral infections, such as those caused by Hepatitis C Virus (HCV) and Human Immunodeficiency Virus (HIV), is affected by the risk group structure of the infected population. Risk groups are defined by each of their members having acquired infection through a specific behavior. However, risk group definitions say little about the transmission potential of each infected individual. Variation in the number of secondary infections is extremely difficult to estimate for HCV and HIV but crucial in the design of efficient control interventions. Here we describe a novel method that combines epidemiological and population genetic approaches to estimate the variation in transmissibility of rapidly-evolving viral epidemics. We evaluate this method using a nationwide HCV epidemic and for the first time co-estimate viral generation times and superspreading events from a combination of molecular and epidemiological data. We anticipate that this integrated approach will form the basis of powerful tools for describing the transmission dynamics of chronic viral diseases, and for evaluating control strategies directed against them.
Effects of short-term estradiol and norethindrone acetate treatment on the breasts of normal postmenopausal women

ObjectiveThe aim of this study was to evaluate among postmenopausal women the effects of a 3-month treatment with estradiol (E2) alone or in combination with norethindrone acetate (NA) on expression of hormone receptors and proliferation in the breast as well as on lipids and climacteric symptoms. MethodsSixty healthy postmenopausal women were computer-randomized into two groups, with one group receiving 1 mg of E2 and the other group receiving 1 mg of E2 and 0.5 mg of NA daily for 12 weeks. Before and after treatment, middle-needle biopsies were obtained for histology and investigation of the expression levels of estrogen receptors (ERs; ER-&agr; and ER-&bgr;), progesterone receptors (PRs; PR-A and PR-B), androgen receptor (AR), the proliferation marker Ki67, and collagen. Climacteric symptoms were recorded, and serum was collected to measure lipoprotein levels. ResultsFifty-six women finished the 12-week study. Proliferating cells (Ki67-positive) were very rare in all but a few of the untreated women. There were proliferating cells in both E2- and E2/NA–treated groups; however, these were not widespread and limited to nests of cells that amounted to 2% of the total epithelial cells. Some of these nests were positive for human epithelial growth factor receptor 2. Treatments caused no marked changes in the expression of ER-&agr;, ER-&bgr;, or AR. However, both treatments resulted in an increase in PR-A and PR-B expressions. The presence of collagen was clearly associated with a mammographic diagnosis of dense breasts, but neither hormone treatment affected breast density. Both E2 and E2/NA treatments were effective in relieving hot flashes and sweating without adverse effects on blood pressure, weight, and liver, kidney, and thyroid functions. A decrease in cholesterol, high-density lipoprotein cholesterol, and low-density lipoprotein cholesterol was induced by E2/NA but not by E2. ConclusionsThis short-term prospective study shows that E2 and estrogen-progestogen treatment can up-regulate PRs but do not significantly affect ERs, AR, proliferation, or breast density.
I/O Deduplication: Utilizing content similarity to improve I/O performance

Duplication of data in storage systems is becoming increasingly common. We introduce I/O Deduplication, a storage optimization that utilizes content similarity for improving I/O performance by eliminating I/O operations and reducing the mechanical delays during I/O operations. I/O Deduplication consists of three main techniques: content-based caching, dynamic replica retrieval, and selective duplication. Each of these techniques is motivated by our observations with I/O workload traces obtained from actively-used production storage systems, all of which revealed surprisingly high levels of content similarity for both stored and accessed data. Evaluation of a prototype implementation using these workloads showed an overall improvement in disk I/O performance of 28 to 47% across these workloads. Further breakdown also showed that each of the three techniques contributed significantly to the overall performance improvement.
Power-spectrum condition for energy-efficient watermarking

A simple but powerful theoretical model for watermarking and attacks is presented. The attack consists of Wiener estimation of the watermark, followed by weighted feedback of the estimate to reduce the detector's correlation value. The Wiener attack is provably optimal, and it leads to the notion of energy-efficient watermarking, the generation of watermarks that resist Wiener estimation. It also leads to a meaningful way to measure watermark robustness. Designing watermarks to resist the attack produces a power-spectrum condition (PSC): the watermark's power spectrum should be a scaled version of the original document's. Experiments with signal models demonstrate the importance of the PSC and show that watermarks that fail to meet the PSC may be vulnerable to attack. These analytic predictions are confirmed with experiments on natural images. The paper provides a theoretical basis for the popular heuristic argument that a watermark should be embedded in the "perceptually significant frequency components" of the original document and discourages the use of watermarks whose power spectra are not closely matched to the original document's power spectrum.
Near-Optimal Precoding Design for MIMO Gaussian Wiretap Channel under Power Constraint

We consider the optimal precoding design under power constraint for the Gaussian MIMO wiretap channel with a transmitter, a legitimate receiver, and an eavesdropper, each equipped with arbitrary number of antennas. The transmitter has access to full channel state information (CSI) of the legitimate link and eavesdropper link. Such an optimization problem is non-convex and an analytical optimal solution is difficult to obtain. In this paper, by resorting to the majorization theory, we develop a theoretical upper bound on the secrecy capacity which is proved useful in evaluating existing sub-optimal methods. Our analysis shows that, given that the number of antennas at the eavesdropper is no less than that of the transmitter, the generalized singular value decomposition (GSVD)-based method proposed in [1], albeit generally non-optimal, provides a near-optimal solution to the MIMO wiretap precoding design in the high signal-to-noise ratio (SNR) regime. Numerical results are provided to corroborate our theoretical results.
Protein-protein interaction network topology as a measure of bacterial plasmid-chromosome co-evolution

In this work, we investigate the evolvability of plasmids by examining the topology of plasmid-chromosome gene interactions in Escherichia coli ST131. We discover a convergence of the ratio of non-trivial loops per protein-protein interaction, which allows us to introduce a new invariant of bacterial PPINs: the indirect connectivity value.
Subjective health complaints and psychosocial work environment among university personnel.

BACKGROUND Questionnaires are often used to study health problems in working populations. An association between self-reported symptoms and psychosocial strain has been suggested, but results from such studies are difficult to interpret, as a gender difference might be present. The knowledge in this area is not clear. AIMS To compare the prevalence of subjective health symptoms and their relation to psychosocial work strain among men and women in different age groups, all working as university staff. METHODS A cross-sectional survey was carried out among university personnel. The questionnaire included a subjective health complaint inventory consisting of 29 items about subjective somatic and psychological symptoms experienced during the last 30 days and psychosocial work factors. Regression analyses were performed. RESULTS In total, 172 (86%) of 201 eligible employees participated. Women had a higher prevalence of musculoskeletal symptoms than men. Significant differences were found between the genders for headaches, neck pain and arm pain. There was a significant relationship between musculoskeletal symptoms and work strain for both genders. This was found for both men and women below 40 years and among men above the age of 40. No significant difference was found between genders regarding pseudoneurological, gastrointestinal, allergic and flu-like symptoms. CONCLUSIONS More female than male university personnel reported musculoskeletal symptoms. The musculoskeletal symptoms were associated with high work strain in both genders, but, for women, this was limited to employees under the age of 40. The cause of this gender difference is unknown.
Adrenomedullin messenger ribonucleic acid expression in the placentae of normal and preeclamptic pregnancies.

In pathological pregnancies, alterations in circulating maternal and fetal adrenomedullin (ADM) concentrations may mediate compensatory vascular responses in the fetal or placental circulation. To address whether ADM is a potential paracrine vasoactive factor within the placenta, the regional distribution and cellular localization of ADM mRNA expression were determined by Northern blot and in situ hybridization of different regions of the placenta and fetal membranes from pregnancies complicated by severe preeclampsia [<28 wk (n = 7) and >28 wk (n = 13)] and from normotensive pregnancies [<28 wk (n = 6) and >28 wk (n = 15)]. Northern blotting revealed that ADM mRNA (1.3 kb) was expressed in chorionic villi and basal plate regions, but was most abundantly expressed in the choriodecidua. By in situ hybridization, ADM mRNA was localized to the syncytiotrophoblasts and the extravillous cytotrophoblasts in the basal plate and choriodecidua regions. ADM mRNA expression was increased in the choriodecidua, syncytial knots, and cytotrophoblasts in peri-infarct regions in preeclampsia. In chorionic villous explant studies maintained at reduced oxygen tension, ADM mRNA abundance was increased at 12, 24, and 48 h. ADM mRNA expressed in syncytiotrophoblasts and cytotrophoblasts in the basal plate decidua and choriodecidua may contribute to the maternal and fetal plasma levels. In preeclampsia, regional increases in ADM mRNA may be induced by hypoxia and mediate local fetal/placental adaptive responses to reduced placental perfusion.
Detecting single file movement

We study the problem of detecting a single file behavior in a set of trajectories. A group of entities is moving in single file if they are following each other, one behind the other. This movement pattern occurs often, among animals, humans, and vehicles. It is challenging to detect because it does not have a fixed layout. In this paper we first model the notion of following behind, on which we base our definition of single file. We present efficient algorithms for detecting following behind and single file behaviors. We test and evaluate these algorithms on real and generated test data.
The Obese Brain Athlete: Self-Regulation of the Anterior Insula in Adiposity

The anterior insular cortex (AIC) is involved in emotional processes and gustatory functions which can be examined by imaging techniques. Such imaging studies showed increased activation in the insula in response to food stimuli as well as a differential activation in lean and obese people. Additionally, studies investigating lean subjects established the voluntary regulation of the insula by a real-time functional magnetic resonance imaging-brain computer interface (rtfMRI-BCI) approach. In this exploratory study, 11 lean and 10 obese healthy, male participants were investigated in a rtfMRI-BCI protocol. During the training sessions, all obese participants were able to regulate the activity of the AIC voluntarily, while four lean participants were not able to regulate at all. In successful regulators, functional connectivity during regulation vs. relaxation between the AIC and all other regions of the brain was determined by a seed voxel approach. Lean in comparison to obese regulators showed stronger connectivity in cingular and temporal cortices during regulation. We conclude, that obese people possess an improved capacity to self-regulate the anterior insula, a brain system tightly related to bodily awareness and gustatory functions.
IN VITRO SAFETY TESTING STRATEGY FOR SKIN IRRITATION USING THE 3D RECONSTRUCTED HUMAN EPIDERMIS

One of the most recent trends in skin irritation safety testing of personal care and cosmetic products, discussed in detail in this review, is the use of reconstructed human epidermis models. Some of the commercially-available models have undergone a series of validation trials, which successfully advanced them as valuable tools for industry use. On a broader perspective, the 3D models are now part of the integrated decision-tree testing strategies used in regulatory settings for skin irritation and/or corrosion registration and labeling of newly designed formulations. Furthermore, the reconstructed human epidermis models are also widely used by industry for product development, safety testing, and ranking of personal care and cosmetic products’ irritation potential. Although the specific protocols used for meeting either legislation-driven regulatory safety testing or nonregulatory, industrial safety screening may differ considerably, the in vitro tissue systems and approaches are aligned to meet the newest legislation or corporate policies prohibiting the use of animals for safety testing.
Cloud computing: An emerging trend for small and medium enterprises

The impact of Information and Communication Technology, particularly the Internet, has transformed small and large organizations. Cloud Computing is emerging as one of the major IT trends of the 21st Century offering utility oriented services to organizations. This study was conducted to investigate how Small and Medium Enterprises in ECBD can utilize Cloud Computing as a business management tool to enhance networking, productivity and efficiency. The study uses qualitative approach for data collection and analysis. The findings are expected to help SMEs understand how Cloud Computing can overcome constraints, such as lack of access, use and sharing of reliable and comprehensive information amongst other social barriers. Amidst the hype surrounding this modern trend, the study reveals various challenges that hinder the utilization of Cloud Computing such as ignorance, limited infrastructure and security concerns. The study provides recommendations for SMEs to remain focused and relevant in the modern business world.
Pemphigus treatment with azathioprine. Clinical and immunologic correlation.

A prospective study of ten patients with early pemphigus, who were treated with azathioprine, is described. The dosage of azathioprine was 50 to 250 mg/day. Nine of the ten patients had good to excellent results. Seven of the ten patients were either never given corticosteroids or had the corticosteroids completely withdrawn. There was good clinical and immunologic correlation in eight of the ten patients. There were no significant side-effects and no wound-healing problems. High-dose corticosteroid therapy is still the treatment of choice for severe, generalized, toxic pemphigus, but in early pemphigus azathioprine alone may control the disease.
Video Analysis of the Mechanisms for Ankle Injuries in Football

Background Although ankle sprains are frequent in football, little is known about their mechanisms. Purpose To describe the injury mechanisms for ankle injuries in male elite football. Study Design Prospective cohort study. Methods Videotapes and injury information were collected for 313 of 409 matches from Norwegian and Icelandic elite football during the 1999 to 2000 seasons. Video recordings of incidents that resulted in ankle injuries were analyzed and cross-referenced with injury reports from the team medical staff. Results A total 46 acute ankle injuries were reported to have occurred, that is, 4.5 injuries per 1000 match hours. Of these, 26 (57%) were identified on the videotapes. Two mechanisms thought to be specific to football were found: 1) player-to-player contact with impact by an opponent on the medial aspect of the leg just before or at foot strike, resulting in a laterally directed force causing the player to land with the ankle in a vulnerable, inverted position; and 2) forced plantar flexion where the injured player hit the opponent's foot when attempting to shoot or clear the ball. Conclusions Systematic video analysis provides detailed information on the mechanisms for ankle injuries in football—for lateral ligament sprains and for the condition dubbed “OpenCurlyDoubleQuote;footballer's ankle. ”
Verification of Java Card Applets

This work covers a methodology to develop a behavioral interface specification based on an informal documentation for a given Java Card applet and to check and to verify the applet w.r. t. this specification. A combination of a static checking tool (ESC/Java) and an interactive program verification tool (JIVE) is used in this task. This work is part of the project VerifiCard which is supported by the European Union. An approach to interactively create and to check an initial interface specification with ESC/Java is presented and discussed. This specification is afterwards translated into JIVE’s specification language and the results from a check with ESC/Java are verified using JIVE’s approach. Errors detected by an application of the methodology to a real-world Java Card applet are presented and discussed.
Psychological distress in asthma and allergy: the Västerbotten Environmental Health Study

With the aim to better understand the association between asthma/allergy and psychological distress, it was hypothesized that levels of stress, exhaustion, anxiety, depression, and health worries for environmental pollution would be higher in allergic asthma, allergic rhinitis, and atopic dermatitis than in non-allergic asthma and in referents without asthma or allergy. Taking part in the population-based Västerbotten Environmental Health Study (aged 18–79 years), 76 respondents reported a physician-based diagnosis of allergic asthma, 86 reported non-allergic asthma, 190 reported allergic rhinitis, and 46 reported atopic dermatitis as the only form of asthma/allergy. A group of 2876 respondents without an asthma/allergy diagnosis constituted as referents. The participants responded to the Perceived Stress Scale, the Shirom-Melamed Burnout Questionnaire, the Hospital Anxiety and Depression Scale, and the Environmental Pollution subscale of the Modern Health Worries Scale. Levels of stress, exhaustion, and anxiety were higher in allergic asthma and atopic dermatitis than in non-allergic asthma, allergic rhinitis, and among referents, and there was a strong tendency of such group differences for depression and health worries. The results imply that stress reduction and treatment of negative affect may in certain cases be fruitful interventions in patients with atopy.
Detection of Real-world Fights in Surveillance Videos

CCTVs have since long been used to enforce security, e.g. to detect fights arising from many different situations. But their effectiveness is questionable, because they rely on continuous and specialized human supervision, demanding automated solutions. Previous work are either too superficial (classification of short-clips) or unrealistic (movies, sports, fake fights). None performed detection of actual fights on long duration CCTV recordings. In this work, we tackle this problem by firstly proposing CCTV-Fights1, a novel and challenging dataset containing 1,000 videos of real fights, with more than 8 hours of annotated CCTV footage. Then we propose a pipeline, on which we assess the impact of different feature extractors, through Two-stream CNN, 3D CNN and a local interest point descriptor, as well as different classifiers, such as end-to-end CNN, LSTM and SVM. Results confirm how challenging the problem is, and highlight the importance of explicit motion information to improve performance.
A vehicular wireless sensor network for CO2 monitoring

Micro-climate monitoring usually requires deploying a large number of measurement tools. By adopting vehicular wireless sensor networks (VSNs), we can use fewer tools to achieve fine-grained monitoring. This work proposes a VSN architecture to realize micro-climate monitoring based on GSM short messages and availability of GPS receivers on vehicles. We demonstrate our prototype of a ZigBee-based car network to monitor the concentration of carbon dioxide (CO2) gas in areas of interest. The reported data are sent to a server, which is integrated with Google Maps as our user interface. Since mobility of these vehicles is not controllable and sending short messages incurs charges, we also design an on-demand approach to adjust vehicles' reporting rates to balance between the micro-climate accuracy and the communication cost.
Constitutive over expression of IL-1β, IL-6, NF-κB, and Stat3 is a potential cause of lung tumorgenesis in urethane (ethyl carbamate) induced Balb/c mice

Background: Lung cancer is a leading cause of cancer death. There has been found a substantial gap in the understanding of lung cancer genesis at the molecular level. We developed urethane (ethyl carbamate) induced lung tumor mice model to understand the mechanism and molecules involved in the cancer genesis. There might be many molecules involved, but we subsequently emphasized here the study of alternation in the expression of NF-κB, Stat3, and inflammatory cytokines interleukin-1β and interleukin-6 to hypothesize that the microenvironment created by these molecules is promoting tumor formation. Materials and Methods: 7–8 week old Balb/c mice of either sex were given intraperitoneal (i.p.) injection of urethane (1g/kgbw) for eight consecutive weeks. Histopathological analysis was done to detect abnormality or invasions occurred in the lung tissues. Automated cell counter was used to count the number of inflammatory cells. The expression of NF-κB, Stat3, and IL-1β was observed at translational level by western blot, while the expression of IL-1β and IL-6 was observed at transcriptional level by semiquantitative reverse transcriptase polymerase chain reaction (RT-PCR) method. Secretion of IL-1β and IL-6 in the blood was measured by enzyme-linked immunosorbent assay (ELISA) method at different time intervals. Results: Histopathological analysis showed various lung cancer stages hyperplasia, atypical adenomatous hyperplasia, and adenocarcinoma. Increased population of inflammatory cells, persistant expression of NF-κB, Stat3, pStat3, and IL-1β at translational level, while at transcriptional level constitutive enhanced expression of IL-1β and IL-6 followed by increased secretion of IL-1β and IL-6 in the blood were observed in urethane-injected mice in comparison to phosphate buffer saline (PBS) injected mice at 12, 24, and 36 weeks Conclusions: Overexpression of key molecules such as NF-κB, Stat3, pStat3, IL-1β, and IL-6 might have caused chronic inflammation, leading to the progression of lung cancer.