Miracle-dz/UniFAR-FTUs huggingface dataset:
The Influence of DNA Extraction Procedure and Primer Set on the Bacterial Community Analysis by Pyrosequencing of Barcoded 16S rRNA Gene Amplicons

In this study, the effect of different DNA extraction procedures and primer sets on pyrosequencing results regarding the composition of bacterial communities in the ileum of piglets was investigated. Ileal chyme from piglets fed a diet containing different amounts of zinc oxide was used to evaluate a pyrosequencing study with barcoded 16S rRNA PCR products. Two DNA extraction methods (bead beating versus silica gel columns) and two primer sets targeting variable regions of bacterial 16S rRNA genes (8f-534r versus 968f-1401r) were considered. The SEED viewer software of the MG-RAST server was used for automated sequence analysis. A total of 5.2 × 105 sequences were used for analysis after processing for read length (150 bp), minimum sequence occurrence (5), and exclusion of eukaryotic and unclassified/uncultured sequences. DNA extraction procedures and primer sets differed significantly in total sequence yield. The distribution of bacterial order and main bacterial genera was influenced significantly by both parameters. However, this study has shown that the results of pyrosequencing studies using barcoded PCR amplicons of bacterial 16S rRNA genes depend on DNA extraction and primer choice, as well as on the manner of downstream sequence analysis.
Causes of Death among Commercially Insured Multiple Sclerosis Patients in the United States

Background Information on causes of death (CODs) for patients with multiple sclerosis (MS) in the United States is sparse and limited by standard categorizations of underlying and immediate CODs on death certificates. Prior research indicated that excess mortality among MS patients was largely due to greater mortality from infectious, cardiovascular, or pulmonary causes. Objective To analyze disease categories in order to gain insight to pathways, which lead directly to death in MS patients. Methods Commercially insured MS patients enrolled in the OptumInsight Research database between 1996 and 2009 were matched to non-MS comparators on age/residence at index year and sex. The cause most-directly leading to death from the death certificate, referred to as the “principal” COD, was determined using an algorithm to minimize the selection of either MS or cardiac/pulmonary arrest as the COD. Principal CODs were categorized into MS, cancer, cardiovascular, infectious, suicide, accidental, pulmonary, other, or unknown. Infectious, cardiovascular, and pulmonary CODs were further subcategorized. Results 30,402 MS patients were matched to 89,818 controls, with mortality rates of 899 and 446 deaths/100,000 person-years, respectively. Excluding MS, differences in mortality rate between MS patients and non-MS comparators were largely attributable to infections, cardiovascular causes, and pulmonary problems. Of the 95 excessive deaths (per 100,000 person-years) related to infectious causes, 41 (43.2%) were due to pulmonary infections and 45 (47.4%) were attributed to sepsis. Of the 46 excessive deaths (per 100,000 person-years) related to pulmonary causes, 27 (58.7%) were due to aspiration. No single diagnostic entity predominated for the 60 excessive deaths (per 100,000 person-years) attributable to cardiac CODs. Conclusions The principal COD algorithm improved on other methods of determining COD in MS patients from death certificates. A greater awareness of the common CODs in MS patients will allow physicians to anticipate potential problems and, thereby, improve the care that they provide.
Supramaximal stimulation during intraoperative facial nerve monitoring as a simple parameter to predict early functional outcome after parotidectomy

Abstract Conclusion: A supramaximal stimulation at 2 mA during intraoperative electromyographic (EMG) facial nerve monitoring appears to be a simple and effective parameter to predict immediate postoperative injury. Objectives: To assess the role of systematic intraoperative facial nerve monitoring in predicting the early functional outcomes obtained after parotidectomy. Methods: Data were collected from patients who underwent parotidectomy. Intraoperative EMG monitoring of the facial nerve was performed by registering two parameters, event intensity (>100 μV) and amplitude of response after a supramaximal stimulation at 2 mA, at the beginning and end of gland removal. Early postoperative clinical functional facial nerve disorder was assessed at day 2. Results: Overall, 50 patients were included and an early facial dysfunction was detected in 27 cases (54%). The maximal response amplitude after supramaximal stimulation at the trunk of the facial nerve was higher in patients with normal facial function compared with those with poor outcomes at the end of surgery (p < 0.01). The postdissection to predissection ratios of maximal response amplitude, but not the stimulation thresholds, were indicative of a nerve conduction block and were significantly lower in the patient group with a poor outcome compared with the group with a normal facial outcome (p < 0.02).
The effect that touching a projection augmented model has on object-presence

A projection augmented model (PA model) is a type of projection based haptic augmented reality display. It consists of a real physical model, onto which a computer image is projected to create a realistic looking object. Users can physically touch the surface of a PA model with their bare hands, which has clear experiential value for the types of applications for which they are being developed. However, the majority of PA models are front-projected and do not provide haptic feedback for material properties (e.g. temperature and physical texture), which suggests a user's sense of object-presence will be reduced when this type of PA model is touched. (object-presence measures the subjective feeling that the object the PA model represents exists in a person's environment, as opposed to a white physical model and a projected computer image.) Alternatively, if people consider PA models to be essentially computer generated objects (i. e. it is the projected image that gives the 'dummy' physical model meaning), then the act of being able to touch computer generated information may increase object-presence. The empirical investigation reported in this paper found that object-presence was lower when this type of PA model was touched. The implications these results have for both PA models and other types of displays, are discussed.
Adolescent health concerns, problems, and patterns of utilization in a triethnic urban population.

All aspects of health (concerns, perceived adequacy of knowledge, problems, sources of care, and utilization of health care resources) were significantly influenced by the ethnic background, grade level, or sex of the 3,255 high school students surveyed in an urban triethnic community of 65,000. Variation in needs was not consistent for any one ethnic group, sex, or age group. The highest ranked concerns and problems were school, drugs, sex, getting along with parents and adults, acne, depression, and overweight. Ninety-one percent reported they often or sometimes worry about their health. Sources of medical care were family physician (56.8%) and hospital emergency room (15.9%). Reported visits in the past year were none (27.5%); one (24.1%); two to three (32.2%); and four or more (14.7%). In analyzing responses according to sex, grade, and ethnic background, several implications are apparent: (1) many of the concerns and problems identified require educational as well as health care services; (2) the diverse perceived health needs of an entire high school population indicate that the traditional one-semester general health course for all is grossly inadequate; and (3) students' concerns and problems are not limited to the areas of drugs, venereal disease, and unwanted pregnancy. The study is presented as a model for the needs assessment phase of planning and delivering adolescent health care and health education services for a community.
On the feasibility of water calorimetry with scanned proton radiation

Water calorimetry is considered to be the most direct primary method to realize the physical quantity gray for absorbed dose to water. The Swiss Federal Office of Metrology and Accreditation (METAS) has routinely operated a water calorimeter as primary standard for photon radiation since 2001. Nowadays, cancer therapy with proton radiation has become increasingly important and is a well established method. In the framework of the ProScan project conducted by the Paul Scherrer Institute (PSI), the spot-scanning technique is prepared for the subsequent application in hospitals, and adjusted to the recent findings of clinical research. In the absence of primary standards for proton radiation, the metrological traceability is assured by calibrating secondary standards in 60Co radiation and correcting with calculated beam quality correction factors. It is internationally recognized that the development of primary standards for proton radiation is highly desirable. In a common project of PSI and METAS, it is investigated whether a modified version of the water calorimeter in operation at METAS is suitable as primary standard for scanned proton radiation. A feasibility study has been conducted to investigate the linear energy transfer (LET) dependence of the heat defect and the influence of the time and space structure of the scanned beam on the homogeneity and stability of the temperature field in the water calorimeter. Simulations are validated against experimental data of the existing calorimeter used with photon radiation and extended to scanned proton radiation.
The performance of work stealing in multiprogrammed environments (extended abstract)

We study the performance of user-level thread schedulers in multiprogrammed environments. Our goal is a user-level thread scheduler that delivers efficient performance under multiprogramming without any need for kernel-level resource management, such as coscheduling or process control. We show that a non-blocking implementation of the work-stealing algorithm achieves this goal. With this implementation, the execution time of a computation running with arbitrarily many processes on arbitrarily many processors can be modeled as a simple function of work and critical-path length. This model holds even when the processes run on a set of processors that arbitrarily grows and shrinks over time. We observe linear speedup whenever the number of processes is small relative to the average parallelism.
Iterative Energy-Efficient Stable Matching Approach for Context-Aware Resource Allocation in D2D Communications

Energy efficiency (EE) is critical to fully achieve the huge potentials of device-to-device (D2D) communications with limited battery capacity. In this paper, we consider the two-stage EE optimization problem, which consists of a joint spectrum and power allocation problem in the first stage, and a context-aware D2D peer selection problem in the second stage. We provide a general tractable framework for solving the combinatorial problem, which is NP-hard due to the binary and continuous optimization variables. In each stage, user equipments (UEs) from two finite and disjoint sets are matched in a two-sided stable way based on the mutual preferences. First, the preferences of UEs are defined as the maximum achievable EE. An iterative power allocation algorithm is proposed to optimize EE under a specific match, which is developed by exploiting nonlinear fractional programming and Lagrange dual decomposition. Second, we propose an iterative matching algorithm, which first produces a stable match based on the fixed preferences, and then dynamically updates the preferences according to the latest matching results in each iteration. Finally, the properties of the proposed algorithm, including stability, optimality, complexity, and scalability, are analyzed in detail. Numerical results validate the efficiency and superiority of the proposed algorithm under various simulation scenarios.
Long-Term Multivitamin Supplementation and Cognitive Function in Men

BACKGROUND Despite widespread use of multivitamin supplements, their effect on cognitive health-a critical issue with aging-remains inconclusive. To date, no long-term clinical trials have studied multivitamin use and cognitive decline in older persons. OBJECTIVE To evaluate whether long-term multivitamin supplementation affects cognitive health in later life. DESIGN Randomized, double-blind, placebo-controlled trial of a multivitamin from 1997 to 1 June 2011. The cognitive function substudy began in 1998. Up to 4 repeated cognitive assessments by telephone interview were completed over 12 years. (ClinicalTrials.gov: NCT00270647) SETTING: The Physicians' Health Study II. PATIENTS 5947 male physicians aged 65 years or older. INTERVENTION Daily multivitamin or placebo. MEASUREMENTS A global composite score averaging 5 tests of global cognition, verbal memory, and category fluency. The secondary end point was a verbal memory score combining 4 tests of verbal memory, which is a strong predictor of Alzheimer disease. RESULTS No difference was found in mean cognitive change over time between the multivitamin and placebo groups or in the mean level of cognition at any of the 4 assessments. Specifically, for the global composite score, the mean difference in cognitive change over follow-up was -0.01 SU (95% CI, -0.04 to 0.02 SU) when treatment was compared with placebo. Similarly, cognitive performance did not differ between the multivitamin and placebo groups on the secondary outcome, verbal memory (mean difference in cognitive change over follow-up, -0.005 SU [CI, -0.04 to 0.03 SU]). LIMITATION Doses of vitamins may be too low or the population may be too well-nourished to benefit from a multivitamin. CONCLUSION In male physicians aged 65 years or older, long-term use of a daily multivitamin did not provide cognitive benefits. PRIMARY FUNDING SOURCE National Institutes of Health, BASF, Pfizer, and DSM Nutritional Products.
Terrestrial isopod community as indicator of succession in a peat bog

Abstract Terrestrial isopods were studied in the Dubravica peat bog and surrounding forest in the northwestern Croatia. Sampling was conducted using pitfall traps over a two year period. Studied peat bog has a history of drastically decrease in area during the last five decades mainly due to the process of natural succession and changes in the water level. A total of 389 isopod individuals belonging to 8 species were captured. Species richness did not significantly differ between bog, edge and surrounding forest. High species richness at the bog is most likely the result of progressive vegetation succession, small size of the bog and interspecific relationships, such as predation. With spreading of Molinia grass on the peat bog, upper layers of Sphagnum mosses become less humid and probably more suitable for forest species that slowly colonise bog area. The highest diversity was found at the edge mainly due to the edge effect and seasonal immigration, but also possibly due to high abundance and predator pressure of the Myrmica ants and lycosid spiders at the bog site. The most abundant species were Trachelipus rathkii and Protracheoniscus politus, in the bog area and in the forest, respectively. Bog specific species were not recorded and the majority of the species collected belong to the group of tyrphoneutral species. However, Hyloniscus adonis could be considered as a tyrphoxenous species regarding its habitat preferences. Most of collected isopod species are widespread eurytopic species that usually inhabit various habitats and therefore indicate negative successive changes or degradation processes in the peat bog.
Will Posttranslational Modifications of Brain Proteins Provide Novel Serological Markers for Dementias?

Drug development for dementias is significantly hampered by the lack of easily accessible biomarkers. Fluid biomarkers of dementias provide indications of disease stage, but have little prognostic value, cannot detect early pathological changes, and can only be measured in CSF (cerebrospinal fluid) which significantly limits their applicability. In contrast, imaging based biomarkers can provide indications of probability of disease progression, yet are limited in applicability due to cost, radiation and radio-tracers. These aspects highlight the need for other approaches to the development of biomarkers of dementia, which should focus on not only providing information about pathological changes, but also on being measured easily and reproducibly. For other diseases, focus on development of assays monitoring highly specific protease-generated cleavage fragments of proteins has provided assays, which in serum or plasma have the ability to predict early pathological changes. Proteolytic processing of brain proteins, such as tau, APP, and α-synuclein, is a key pathological event in dementias. Here, we speculate that aiming biomarker development for dementias at detecting small brain protein degradation fragments of generated by brain-derived proteases specifically in blood samples could lead to the development of novel markers of disease progression, stage and importantly of treatment efficacy.
Synergistic induction of apoptosis by combination of BTK and dual mTORC1/2 inhibitors in diffuse large B cell lymphoma

Diffuse large B cell lymphoma is generally treated by chemotherapy and there is an unmet medical need for novel targeted therapies or combination therapies. Using in vitro screening, we have identified the combination of ibrutinib, an inhibitor of the tyrosine kinase BTK, and AZD2014, an mTOR catalytic inhibitor, as being highly synergistic in killing ABC-subtype DLBCL cell lines. Simultaneous inhibition of BTK and mTOR causes apoptosis both in vitro and in vivo and results in tumor regression in a xenograft model. We identify two parallel mechanisms that underlie apoptosis in this setting: cooperative inhibition of cap-dependent translation, and the inhibition of an NF-κB/IL10/STAT3 autocrine loop. Combined disruption of these pathways is required for apoptosis. These data represent a rational basis for the dual inhibition of BTK and mTOR as a potential treatment for ABC-subtype DLBCL.
Demonstrating the safety and performance of a velocity sourced series elastic actuator

Actuators with deliberately added compliant elements in the transmission system are often described as improving the safety of the actuator at the detriment of the performance. We show that our variant of the series elastic actuator topology, the velocity sourced series elastic actuator, has well defined performance characteristics that make for improvements in safety and performance over conventional high impedance actuators. The improvement in performance was principally achieved by having tight velocity control of the DC motor that acts as the mechanical power source for the actuator. Results for performance are given for point to point transition times, while results for safety are based on empirical assessment of the head injury criterion during collisions.
Optimal selection of individuals for BRCA mutation testing: a comparison of available methods.

PURPOSE Several methods have been described that estimate the likelihood that a family history of cancer is a result of a mutation in the BRCA1 or BRCA2 genes. We examined the performance of six different methods with the aim of identifying an optimal strategy for selecting individuals for mutation testing in clinical practice. PATIENTS AND METHODS Two hundred fifty-seven families who had completed BRCA1 and BRCA2 mutation screening were assessed by six models representing the major methodologies used to assess the likelihood of a pathogenic mutation. The performance of each method as a selection criterion was compared with the result of mutation testing to produce sensitivity, specificity, and receiver operating curve data. The impact of incorporating breast cancer pathology data in the assessment was also analyzed. RESULTS The highest accuracy was achieved by the Bayesian probabilistic model (BRCAPRO). The formal probabilistic methods were significantly more accurate than clinical scoring methods. The methods were further improved by the incorporation of information on breast cancer pathology (tumor grade and estrogen receptor/progesterone receptor status). The resulting combined probability figure was highly accurate when selecting individuals for BRCA1 testing. Some BRCA2 mutation carriers were missed by all of the models examined. CONCLUSION Formal probabilistic models provide significantly greater accuracy in the selection of families for gene testing than the use of clinical criteria or scoring methods. The accuracy is further enhanced by incorporating information on the pathology of breast cancers occurring in the families.
Ontogeny of water transport in rat brain: postnatal expression of the aquaporin‐4 water channel

Brain water transport is poorly understood at the molecular level, and marked changes occur during brain development. As the aquaporin‐4 (AQP4) water channel protein is abundant in brain, the expression levels and subcellular distribution of this protein were examined during postnatal development. This study focused on the cerebellum, which showed the same pattern of AQP4 development as the rest of the brain. Semiquantitative immunoblotting revealed very low levels of AQP4 in the first postnatal week. A pronounced increase was noted in the second week, from 2% of adult level at postnatal day 7 (PN7) to 25% at PN14. At PN1 and PN3 immunofluorescence microscopy revealed weak labelling, mainly in radial processes (Bergmann fibres) and at the pial surface. Between PN7 and PN14 the labelling underneath the pia showed a strong increase, and immunoreactivity also appeared around blood vessels throughout the cerebellum. High‐resolution immunogold electron microscopy revealed that the subpial and perivascular labelling was restricted to glial end feet, notably to those plasma membrane domains that were apposed to the basal laminae. At no stage was there any evidence of neuronal AQP4 labelling, and AQP1, −2, −3 and −5 proteins were not detected in the neuropil. Riboprobes to AQP4 mRNA produced a particularly strong in situ hybridization signal in glial cells between PN7 and PN14, corresponding to the stage of the most rapid increase of AQP4 protein. The time course and pattern of AQP4 expression suggests that this aquaporin plays an important role in brain water and K+ homeostasis from the second week of development.
Towards Constraint-based High Performance Cloud System in the Process of Cloud Computing Adoption in an Organization

Cloud computing is penetrating into various domains and environments, from theoretical computer science to economy, from marketing hype to educational curriculum and from R&D lab to enterprise IT infrastructure. Yet, the currently developing state of cloud computing leaves several issues to address and also affects cloud computing adoption by organizations. In this paper, we explain how the transition into the cloud can occur in an organization and describe the mechanism for transforming legacy infrastructure into a virtual infrastructure-based cloud. We describe the state of the art of infrastructural cloud, which is essential in the decision making on cloud adoption, and highlight the challenges that can limit the scale and speed of the adoption. We then suggest a strategic framework for designing a high performance cloud system. This framework is applicable when transformation cloudbased deployment model collides with some constraints. We give an example of the implementation of the framework in a design of a budget-constrained high availability cloud system.