Miracle-dz/UniFAR-FTUs huggingface dataset:
Improving the Quality of Diagnostic Studies Evaluating Point of Care Tests for Acute HIV Infections: Problems and Recommendations

The diagnosis of acute human immunodeficiency virus (HIV) infection (AHI) plays a unique role in preventing the spread of HIV and ending the epidemic. Acutely infected individuals are thought to contribute substantially to forward transmissions of HIV; however, diagnosing AHI in resource-limited settings has proven to be a challenge. While fourth generation antigen-antibody combination assays have been successful in high-resource settings, rapid point of care (POC) versions of these assays have yet to demonstrate high sensitivity to detect AHI. Newer RNA/DNA based POC technologies are being validated, but the challenge to understand the additional value of these devices depends on the quality of study evaluations, in particular choice of study designs and case mix of included populations. In this commentary, we aimed to review the quality of studies evaluating a new fourth generation rapid test for detecting AHI, to identify general methodological limitations and biases in diagnostic accuracy studies, and to recommend strategies for avoiding them in future evaluations. The new studies that were evaluated continued to report the same weaknesses and biases that were seen in previous evaluations of fourth generation rapid tests. We recommend that investigators design future studies carefully, keeping in mind how diagnostic performance may be influenced by prevalence, population, patient case mixes, and reference standards. Care must be taken to avoid biases specific to diagnostic accuracy studies (spectrum, verification, incorporation and reference standard biases). To improve on quality, reporting checklists and guidelines such as Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) and Standards for Reporting Diagnostic accuracy studies (STARD) should be reviewed prior to conducting studies.
VISUALIZATION AND ANIMATION OF MOUNT EVEREST

In the year 1988 a new topographical map 1:50’000 of the Mount Everest region was published by the National Geographical Society. The full map content was derived from aerial images of scale 1:35’000, acquired in a 1984 photogrammetric flight. This highly acclaimed topographical map, produced with Swiss photogrammetric and cartographic know-how, serves until nowadays as an important work of reference. We took the analogue data (images, contours), converted them into digital form through scanning, and produced a texture-mapped 3D computer model. With a DTM of 10 m grid size and natural texture pixel size of 1 m this model is currently the best dataset available for an area of 25 by 25 km around the summit of Mount Everest. The basic data has been used for diverse scientific purposes and in a number of TV specials and Magazine reports.This paper reports briefly about the production procedure of the model and discusses some issues related to the interactive real-time visualization of such an extended high resolution photorealistic dataset.
Design of very deep pipelined multipliers for FPGAs

This work investigates the use of very deep pipelines for implementing circuits in FPGAs, where each pipeline stage is limited to a single FPGA logic element (LE). The architecture and VHDL design of a parameterized integer array multiplier is presented and also an IEEE 754 compliant 32-bit floating-point multiplier. We show how to write VHDL cells that implement such approach, and how the array multiplier architecture was adapted. Synthesis and simulation were performed for Altera Apex20KE devices, although the VHDL code should be portable to other devices. For this family, a 16 bit integer multiplier achieves a frequency of 266 MHz, while the floating point unit reaches 235 MHz, performing 235 MFLOPS in an FPGA. Additional cells are inserted to synchronize data, what imposes significant area penalties. This and other considerations to apply the technique in real designs are also addressed.
Active Cytotoxic Necrotizing Factor 1 Associated with Outer Membrane Vesicles from Uropathogenic Escherichia coli

ABSTRACT Cytotoxic necrotizing factor type 1 (CNF1) is one of the virulence factors produced by uropathogenic Escherichia coli (UPEC). How this toxin is translocated from the bacterial cytoplasm to the surrounding environment is not well understood. Our data suggest that CNF1 may be regarded as a secreted protein, since it could be detected in culture supernatants. Furthermore, we found that CNF1 was tightly associated to outer membrane vesicles, suggesting that such vesicles play a role in the secretion of this protein. Interestingly, vesicle samples containing CNF1 could exert the effects known for this protein on HeLa cell cultures, showing that CNF1 is transported by vesicles in its active form. Taken together, our results strongly suggest that outer membrane vesicles could be a means for the bacteria to deliver CNF1 to the environment and to the infected tissue. In addition, our results indicate that the histone-like nucleoid structuring protein H-NS has a role in the downregulation of CNF1 production and that it affects the outer membrane vesicle release in UPEC strain J96.
Successive radiations, not stasis, in the South American primate fauna

The earliest Neotropical primate fossils complete enough for taxonomic assessment, Dolichocebus, Tremacebus, and Chilecebus, date to approximately 20 Ma. These have been interpreted as either closely related to extant forms or as extinct stem lineages. The former hypothesis of morphological stasis requires most living platyrrhine genera to have diverged before 20 Ma. To test this hypothesis, we collected new complete mitochondrial genomes from Aotus lemurinus, Saimiri sciureus, Saguinus oedipus, Ateles belzebuth, and Callicebus donacophilus. We combined these with published sequences from Cebus albifrons and other primates to infer the mitochondrial phylogeny. We found support for a cebid/atelid clade to the exclusion of the pitheciids. Then, using Bayesian methods and well-supported fossil calibration constraints, we estimated that the platyrrhine most recent common ancestor (MRCA) dates to 19.5 Ma, with all major lineages diverging by 14.3 Ma. Next, we estimated catarrhine divergence dates on the basis of platyrrhine divergence scenarios and found that only a platyrrhine MRCA less than 21 Ma is concordant with the catarrhine fossil record. Finally, we calculated that 33% more change in the rate of evolution is required for platyrrhine divergences consistent with the morphologic stasis hypothesis than for a more recent radiation. We conclude that Dolichocebus, Tremacebus, and Chilecebus are likely too old to be crown platyrrhines, suggesting they were part of an extinct early radiation. We note that the crown platyrrhine radiation was concomitant with the radiation of 2 South American xenarthran lineages and follows a global temperature peak and tectonic activity in the Andes.
Exercise training prior to myocardial infarction attenuates cardiac deterioration and cardiomyocyte dysfunction in rats

OBJECTIVES: The present study was performed to investigate 1) whether aerobic exercise training prior to myocardial infarction would prevent cardiac dysfunction and structural deterioration and 2) whether the potential cardiac benefits of aerobic exercise training would be associated with preserved morphological and contractile properties of cardiomyocytes in post-infarct remodeled myocardium. METHODS: Male Wistar rats underwent an aerobic exercise training protocol for eight weeks. The rats were then assigned to sham surgery (SHAM), sedentary lifestyle and myocardial infarction or exercise training and myocardial infarction groups and were evaluated 15 days after the surgery. Left ventricular tissue was analyzed histologically, and the contractile function of isolated myocytes was measured. Student's t-test was used to analyze infarct size and ventricular wall thickness, and the other parameters were analyzed by the Kruskal-Wallis test followed by Dunn's test or a one-way analysis of variance followed by Tukey's test (p<0.05). RESULTS: Myocardial infarctions in exercise-trained animals resulted in a smaller myocardial infarction extension, a thicker infarcted wall and less collagen accumulation as compared to myocardial infarctions in sedentary animals. Myocardial infarction-induced left ventricular dilation and cardiac dysfunction, as evaluated by +dP/dt and -dP/dt, were both prevented by previous aerobic exercise training. Moreover, aerobic exercise training preserved cardiac myocyte shortening, improved the maximum shortening and relengthening velocities in infarcted hearts and enhanced responsiveness to calcium. CONCLUSION: Previous aerobic exercise training attenuated the cardiac dysfunction and structural deterioration promoted by myocardial infarction, and such benefits were associated with preserved cardiomyocyte morphological and contractile properties.
EVALUATION OF THE ANTI BACTERIAL EFFECTS OF NICKEL NANOPARTICLES ON BIOFILM PRODUCTION OF MUPIROCIN RESISTANT ISOLATES OF S.AUREUS

The antimicrobial effects of nickel nanoparticles on some bacterial strains such as S. aureus and E.coli have been shown in limited studies. The aim of this study was to investigate the inhibitory effects of nickel nanoparticles on biofilm formation by mupirocin resistant S. aureus isolates. Materials & Methods: In this study, 150 S. aureus isolates were collected from educational hospitals in Urmia city. The sensitivity of isolates to mupirocin and other commonly used antibiotics was investigated by agar disk diffusion method. Microtiter dish biofilm formation assay method was used to determine the amounts of biofilm formation in the presence/absence of nickel nanoparticles. Results: From 150 isolates, 30 ones were resistant to mupirocin. The highest levels of resistance to other antibiotics in Mupirocin resistant isolates were seen to penicillin and Trimetoprim/sulfametoxazol respectively, and the least amounts of resistance were seen to ticoplanin and linezolid, respectively. 33.3% of investigated isolates were biofilm producers. The inhibitory effect of nickel nanoparticles on biofilm formation by mupirocin resistant S.aureus isolates was significant (P = 0.039). Conclusion: Considering the inhibitory effects of nickel nanoparticles on biofilm of mupirocin resistant S. aureus isolates and the safety of nickel usage in dental materials which allow its administration in the nose and mouth mucosa, after further studies it may be useful for prevention of biofilm formation and removal of the carriers from mupirocin resistant S. aureus.
Understanding the spatio-temporal characteristics of Twitter data with geotagged and non-geotagged content: two case studies with the topic of flu and Ted (movie)

ABSTRACT The dynamic characteristics of geotagged Twitter messages provide researchers with vast potential for analysing the spatial diffusion of events such as disease outbreaks, environmental changes and social movements. The percentage of geotagged data, however, is extremely small compared to non-geotagged data, whereas non-geotagged tweets often contain noises generated by automated robots, location spoofing and human-made mistakes. Given these challenges, this study aims to understand the difference in Twitter diffusion characteristics between geotagged and non-geotagged. Tweets were collected using two keywords ‘flu’ and movie Ted from four targeted cities (San Diego, Los Angeles, Denver, New York) to represent different topics and geographical areas in the United States. This study presents methodological and analytical frameworks to filter out noises, analyse the internal structure of the diffusion process, and investigate the spatial distribution of geotagged tweets and their associations with land-use types. Results indicate that geotagged tweets demonstrated less noise and stronger correlations to events, filtered non-geotagged tweets were effective in the trend and content analyses, and the topic choice in Twitter was associated with the correlation between geotagged and non-geotagged tweets. Further, geotagged tweets of multiple topics showed significant spatial variation related to the land-use distribution and the city structure.
Laboratory diagnosis for dengue.

Effective epidemiological surveillance for dengue fever must include the ability of routine laboratory confirmation and monitoring of circulating serotypes. Laboratory surveillance is essential so that differential diagnosis could be performed between dengue fever and other acute febrile diseases, due to clinical similarities exhibited. In general, the dengue´s laboratory diagnosis aims: 1) laboratory, serologic and/or virologic infection´s confirmation; 2) identification of circulating serotypes; 3) laboratory confirmation of severe and fatal cases; 4) support for epidemiological investigations to determine the levels of disease transmission and 5) performance of molecular studies in order to identify existing genotypes in the region (VORNDAM & KUNO, 1997). For adequate effectiveness of the laboratory diagnosis, it is required to take into account the appropriate time for blood sampling and to what type of test it is designated. This information is of great importance when interpreting the results.
Reducing the area overhead of TMR-systems by protecting specific signals

This paper presents a new method of fault-tolerant design for combinational circuits. For an arbitrary chosen subset X1 of inputs the designed system is fault-tolerant, but not necessarily for the other inputs. For all the inputs from X1 the same level of fault tolerance as for Triple Modular Redundancy (TMR) is achieved. Compared to TMR the necessary area can be significantly reduced. Since the subset X1 of inputs, for which the system is fault-tolerant, can be chosen by the designer, the proposed fault-tolerant design method is optimally adapted to the real requirements of fault tolerance.
Multi-resolution spatial simulation for molecular crowding

Spatial phenomena attract increasingly interest in computational biology. Molecular crowding, i.e. a dense population of macromolecules, is known to have a significant impact on the kinetics of molecules. However, an in-detail inspection of cell behavior in time and space is extremely costly. To balance between cost and accuracy, multi-resolution approaches offer one solution. Particularly, a combination of individual and lattice-population based algorithms promise an adequate treatment of phenomena like macromolecular crowding. In realizing such an approach, central questions are how to specify and synchronize the interaction between population and individual spatial level, and to decide what is best treated at a specific level, respectively. Based on an algorithm which combines the next subvolume method and a simple, individual-based spatial approach, we will present possible answers to these questions, and will discuss first experimental results.
Violence and self-reported health: does individual socioeconomic position matter?

Abstract: Background: Violence is a major public health problem. Both clinical and population based studies shows that violence against men and women has physical and psychological health consequences. However, elsewhere and in Sweden little is known of the effect of individual socioeconomic position (SEP) on the relation between violence and health outcomes. Objective: This study aimed to assess the effect of individual SEP on the relation between violence and three health outcomes (general health, pain and anxiety) among women in Stockholm County. Methods: The study used data from the Stockholm Public Health Survey, a cross-sectional survey carried out in 2006 for the Stockholm County Council by Statistic Sweden. 34 704 respondents answered the survey, the response rate was sixth one percent. Analyses were carried out using descriptive statistics and logistic regression analysis in SPSS v.17. 0. Results: Individual SEP increased the odds of reporting poor health outcomes among victimized women in Stockholm County. Regarding self-reported health women in low-SEP who reported victimization in the past twelve months had odds of 2,36 (95% CI 1.48-3.77) for the age group 18-29 years and 3.78 (95% CI 2.53-5.64) for the age group 30-44 years compared with women in high-SEP and non-victim. For pain the odds was 2,41 (95% CI 1,56-3,73) for the age group 18-29 years and 2,98 (95% CI 1,99-4,46) for women aged 30-44 years. Regarding anxiety the age group 18-29 years had odds of 2,53 (95% CI 1,58-4,03) and for the age group 30-44 years had odds of 3,87 (95% CI 2,55-5,87). Conclusion: Results showed that individual SEP (measured by occupation) matters to the relationship between violence and health outcomes such as general self-reported health, pain and anxiety. Women in lower SEP and experienced victimization in the past twelve months had increased odds of reporting poorer self-rated health, pain and anxiety compared to those in higher SEP with no experience of victimization. However, further exploration of the relationship between poverty, individual SEP is needed using other Swedish population samples.
Extra pair paternity in birds: a review of interspecific variation and adaptive function

The application of molecular genetic techniques has revolutionized our view of avian mating systems. Contrary to prior expectations, birds are only very rarely sexually monogamous, with ‘extra‐pair offspring’ found in approximately 90% of species. Even among socially monogamous species, over 11% of offspring are, on average, the result of extra‐pair paternity (EPP). Based on over 150 molecular genetic studies of EPP in birds, we review two topical areas: (i) ecological explanations for interspecific variation in the rate of EPP; and (ii) evidence bearing on the adaptive function of EPP. We highlight the remaining challenges of understanding the relative roles of genes and ecology in determining variation between taxa in the rate of extra paternity, and testing for differences between extra‐pair offspring and those sired within‐pair.
Disentangling the Complexity of HGF Signaling by Combining Qualitative and Quantitative Modeling

Signaling pathways are characterized by crosstalk, feedback and feedforward mechanisms giving rise to highly complex and cell-context specific signaling networks. Dissecting the underlying relations is crucial to predict the impact of targeted perturbations. However, a major challenge in identifying cell-context specific signaling networks is the enormous number of potentially possible interactions. Here, we report a novel hybrid mathematical modeling strategy to systematically unravel hepatocyte growth factor (HGF) stimulated phosphoinositide-3-kinase (PI3K) and mitogen activated protein kinase (MAPK) signaling, which critically contribute to liver regeneration. By combining time-resolved quantitative experimental data generated in primary mouse hepatocytes with interaction graph and ordinary differential equation modeling, we identify and experimentally validate a network structure that represents the experimental data best and indicates specific crosstalk mechanisms. Whereas the identified network is robust against single perturbations, combinatorial inhibition strategies are predicted that result in strong reduction of Akt and ERK activation. Thus, by capitalizing on the advantages of the two modeling approaches, we reduce the high combinatorial complexity and identify cell-context specific signaling networks.
Sharing Big Buck Bunny in

The Internet has evolved rapidly over the last twenty years, flowing away from early Telnet designs to a more content-oriented nature. Researchers developed XIA to redesign the underpinnings of the Internet to accommodate not only today’s Internet traffic, but allow future innovators to add principals as technology changes. Within this architecture we sought to create a video streaming application using the foundation that XIA provides. We present a novel approach to using DAGs in order to facilitate network-level failover for content chunk delivery. We capitalize on the connectionless nature of XIA’s chunking protocol by creating content servers that simply host content without any need for connectionhandling. We also use a centralized directory to foster the lookup of CIDs based on video name. Our streaming video application is publicly available and should help guide future XIA application developers.
Impact of a quasi-stochastic cellular automaton backscatter scheme on the systematic error and seasonal prediction skill of a global climate model

The impact of a nonlinear dynamic cellular automaton (CA) model, as a representation of the partially stochastic aspects of unresolved scales in global climate models, is studied in the European Centre for Medium Range Weather Forecasts coupled ocean–atmosphere model. Two separate aspects are discussed: impact on the systematic error of the model, and impact on the skill of seasonal forecasts. Significant reductions of systematic error are found both in the tropics and in the extratropics. Such reductions can be understood in terms of the inherently nonlinear nature of climate, in particular how energy injected by the CA at the near-grid scale can backscatter nonlinearly to larger scales. In addition, significant improvements in the probabilistic skill of seasonal forecasts are found in terms of a number of different variables such as temperature, precipitation and sea-level pressure. Such increases in skill can be understood both in terms of the reduction of systematic error as mentioned above, and in terms of the impact on ensemble spread of the CA's representation of inherent model uncertainty.
Modification chimique de la cellulose nanofibrillée par les alcoxysilanes : application à l'élaboration de composites et mousses

In this thesis, nanofibrillated cellulse (NFC) has been isolated from oat straw and chemically modified by alkoxysilanes in water medium. Silylated NFC has been subsequently used to elaborate novel biobased composite materials and foamsChapter I presents some general aspects about nanocelluloses – in particular Nanofibrillated Cellulose (NFC) - and their use in composite materials and foams.Chapter II is dedicated to the functionalization of NFC by methyltrimethoxysilane - chosen as a model silane - and to the comprehensive examination of the silylated material. Reaction conditions such as pH, reaction time and initial silane concentration have been particularly in-vestigated and optimized using two distinct experimental protocols. The modifications have been characterized at the molecular level by various physicochemical techniques. The proper-ties of the silylated nanofibrils i.e. the morphology, crystallinity, wettability, hygroscopicity and thermal stability, have been subsequently examined. Chapter III investigates the impact of silylation on the mechanical and hygroscopic properties of NFC-reinforced composites prepared with two distinct polymeric matrices: poly(lactic acid) (PLA) and polydimethylsiloxane (PDMS). Chapter IV examines the impact of silylation on the properties of NFC-foams prepared by freeze drying, in particular on the porosity, compressive properties, thermal conductivity, wet-tability, hygroscopicity and oleophilicity.