Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of registered and published primary outcomes in randomized controlled trials.

CONTEXT As of 2005, the International Committee of Medical Journal Editors required investigators to register their trials prior to participant enrollment as a precondition for publishing the trial's findings in member journals. OBJECTIVE To assess the proportion of registered trials with results recently published in journals with high impact factors; to compare the primary outcomes specified in trial registries with those reported in the published articles; and to determine whether primary outcome reporting bias favored significant outcomes. DATA SOURCES AND STUDY SELECTION MEDLINE via PubMed was searched for reports of randomized controlled trials (RCTs) in 3 medical areas (cardiology, rheumatology, and gastroenterology) indexed in 2008 in the 10 general medical journals and specialty journals with the highest impact factors. DATA EXTRACTION For each included article, we obtained the trial registration information using a standardized data extraction form. RESULTS Of the 323 included trials, 147 (45.5%) were adequately registered (ie, registered before the end of the trial, with the primary outcome clearly specified). Trial registration was lacking for 89 published reports (27.6%), 45 trials (13.9%) were registered after the completion of the study, 39 (12%) were registered with no or an unclear description of the primary outcome, and 3 (0.9%) were registered after the completion of the study and had an unclear description of the primary outcome. Among articles with trials adequately registered, 31% (46 of 147) showed some evidence of discrepancies between the outcomes registered and the outcomes published. The influence of these discrepancies could be assessed in only half of them and in these statistically significant results were favored in 82.6% (19 of 23). CONCLUSION Comparison of the primary outcomes of RCTs registered with their subsequent publication indicated that selective outcome reporting is prevalent.
Fluoridated Elastomers: Effect on Disclosed Plaque

Objective To investigate the effect of fluoridated elastomers on the quantity of disclosed dental plaque surrounding an orthodontic bracket in vivo. Design A randomized, prospective, longitudinal clinical trial, employing a split mouth, crossover design. Setting The Orthodontic Departments of Liverpool and Sheffield Dental Hospitals. Subjects and methods The subjects were 30 individuals about to start fixed orthodontic treatment. The study consisted of two experimental periods of 6 weeks with a washout period between. Fluoridated elastomers were randomly assigned at the first visit to be placed around brackets on 12, 11, 33 or 22, 21, 43. Non-fluoridated elastomers were placed on the contra-lateral teeth. After 6 weeks (visit 2) the elastomers were removed, the teeth disclosed and a photograph taken. Non-fluoridated elastomers were placed on all brackets for one visit to allow for a washout period. At visit 3, fluoridated elastomers were placed on the contra-lateral teeth to visit 1. At visit 4, the procedures at visit 2 were repeated. The photographs were scanned, then the area and proportion of the buccal surface covered with disclosed plaque was measured using computerized image analysis. A mixed-effects ANOVA was carried out with the dependent variable being the area or percentage area of disclosed plaque. Results There was no evidence of a systematic error and substantial agreement for the repeat readings of the same images. The only significant independent variable for the area of disclosed plaque was the subject (p < 0.001). The significant independent variables for the proportion of disclosed plaque were the subject (p < 0.001) and the tooth type (p = 0.002). The independent variable describing the use of fluoridated or non-fluoridated elastomers was not significant for either the area or the proportion of disclosed plaque. Conclusion Fluoridated elastomers do not affect the quantity of disclosed plaque around an orthodontic bracket.
Localization to, and Effects of Pbp1, Pbp4, Lsm12, Dhh1, and Pab1 on Stress Granules in Saccharomyces cerevisiae

The regulation of translation and mRNA degradation in eukaryotic cells involves the formation of cytoplasmic mRNP granules referred to as P-bodies and stress granules. The yeast Pbp1 protein and its mammalian ortholog, Ataxin-2, localize to stress granules and promote their formation. In Saccharomyces cerevisiae, Pbp1 also interacts with the Pab1, Lsm12, Pbp4, and Dhh1 proteins. In this work, we determined whether these Pbp1 interacting proteins also accumulated in stress granules and/or could affect their formation. These experiments revealed the following observations. First, the Lsm12, Pbp4, and Dhh1 proteins all accumulate in stress granules, whereas only the Dhh1 protein is a constitutive P-body component. Second, deletion or over-expression of the Pbp4 and Lsm12 proteins did not dramatically affect the formation of stress granules or P-bodies. In contrast, Pbp1 and Dhh1 over-expression inhibits cell growth, and for Dhh1, leads to the accumulation of stress granules. Finally, a strain lacking the Pab1 protein was reduced at forming stress granules, although they could still be detected. This indicates that Pab1 affects, but is not absolutely required for, stress granule formation. These observations offer new insight into the function of stress granule components with roles in stress granule assembly and mRNP regulation.
Occupational fitness standards for beach lifeguards. Phase 1: the physiological demands of beach lifeguarding.

BACKGROUND Although similar standards exist internationally to select beach lifeguards (BLGs), these are generally not based on a task analysis. To reduce the likelihood of drowning, a BLG should reach a casualty within 3.5 min (210 s). AIM To quantify the physical demands of the most critical generic tasks undertaken by BLGs. METHODS A survey of 91 BLGs identified sea swimming while towing a casualty, board paddling with a casualty, and casualty handling as the most demanding activities. Performance during beach running (200 m), swimming in the sea (200 m), board paddling in the sea (400 m), swimming in a pool (200 m freestyle and 25 m underwater with 25 m return) and simulated casualty handling were measured. RESULTS The median area at sea patrolled by paddling and swimming was 400 m. The mean 200-m sea swim time was 3.1 min or 188 s (SD = 46 s) and 95% of the BLGs were able to swim 200 m in 3.5 min (n = 22). The mean time to paddle 400 m was 3.8 min or 226 s (SD = 35 s) and 30% of the BLGs were able to paddle 400 m in 3.5 min (n = 23). The 5th percentile paddling speed was 1.38 m/s, therefore, 95% of the BLGs tested should be able to paddle 289 m in 3.5 min. CONCLUSIONS If only a rescue board is available, the area out to sea patrolled by a lifeguard should be reduced from 400 m to 300 m.
Putative stem cell markers in limbal epithelial cells cultured on intact & denuded human amniotic membrane.

BACKGROUND & OBJECTIVES The ocular surface is an ideal region to study the epithelial stem cell (SC) biology because of the unique spatial arrangement of stem cells and transient amplifying cells. A major challenge in corneal SC biology is the ability to identify SC in vitro and in situ, and one of the major controversies in the field relates to reliable SC markers. This study was carried out to evaluate and compare the expression of the stem cell associated marker: ABCG2, keratinocyte stem cell marker: p63 and corneal differentiation markers: Cnx43 and K3/K12 on limbal explants cultured on human amniotic membrane (HAM) with intact epithelium and HAM denuded of its epithelium. METHODS Human limbal biopsies obtained from the cadaveric donor eyes were used in this study. The cells were cultured over the HAM with intact and denuded epithelium. Reverse transcriptase PCR, immunohistochemistry, Western blotting for ABCG2, P63, Cnx43 and K3/K12 were done. RESULTS The limbal epithelial cells cultured over intact HAM expressed the stem cell associated markers (ABCG2, p63) and showed reduced expression of the differentiation markers (Cnx43 and K3/K12) when compared to limbal epithelial cells cultured over denuded HAM, which expressed more differentiation markers at the end of three weeks. BrdU label retaining cells were observed in the limbal epithelial cells cultured over HAM with epihelium only. INTERPRETATION & CONCLUSIONS Our results showed that the intact HAM supported the growth of limbal epithelial cells expressing stem cell associated markers, and allowing little differentiation of the limbal cells to cornea phenotype. Further studies are needed to understand the properties of the amniotic epithelium that retains the stemness in the cultured limbal stem cells.
Haemophilus influenzae: A Significant Pathogen in Acute Otitis Media

Haemophilus influenzae is a major pathogen in acute otitis media (AOM) causing disease that is not clinically distinguishable from that caused by Streptococcus pneumoniae. AOM caused by H. influenzae is particularly associated with older age and recurrent disease. Antibiotics differ in their ability to eradicate H. influenzae from the middle ear space. In the United States, widespread pneumococcal vaccination has increased the importance of H. influenzae as a major theraputic challenge in the treatment of AOM.
E3 Ubiquitin Ligase CHIP and NBR1-Mediated Selective Autophagy Protect Additively against Proteotoxicity in Plant Stress Responses

Plant stress responses require both protective measures that reduce or restore stress-inflicted damage to cellular structures and mechanisms that efficiently remove damaged and toxic macromolecules, such as misfolded and damaged proteins. We have recently reported that NBR1, the first identified plant autophagy adaptor with a ubiquitin-association domain, plays a critical role in plant stress tolerance by targeting stress-induced, ubiquitinated protein aggregates for degradation by autophagy. Here we report a comprehensive genetic analysis of CHIP, a chaperone-associated E3 ubiquitin ligase from Arabidopsis thaliana implicated in mediating degradation of nonnative proteins by 26S proteasomes. We isolated two chip knockout mutants and discovered that they had the same phenotypes as the nbr1 mutants with compromised tolerance to heat, oxidative and salt stresses and increased accumulation of insoluble proteins under heat stress. To determine their functional interactions, we generated chip nbr1 double mutants and found them to be further compromised in stress tolerance and in clearance of stress-induced protein aggregates, indicating additive roles of CHIP and NBR1. Furthermore, stress-induced protein aggregates were still ubiquitinated in the chip mutants. Through proteomic profiling, we systemically identified heat-induced protein aggregates in the chip and nbr1 single and double mutants. These experiments revealed that highly aggregate-prone proteins such as Rubisco activase and catalases preferentially accumulated in the nbr1 mutant while a number of light-harvesting complex proteins accumulated at high levels in the chip mutant after a relatively short period of heat stress. With extended heat stress, aggregates for a large number of intracellular proteins accumulated in both chip and nbr1 mutants and, to a greater extent, in the chip nbr1 double mutant. Based on these results, we propose that CHIP and NBR1 mediate two distinct but complementary anti-proteotoxic pathways and protein's propensity to aggregate under stress conditions is one of the critical factors for pathway selection of protein degradation.
Postdiagnosis Diet Quality Is Inversely Related to a Biomarker of Inflammation among Breast Cancer Survivors

Background: Inflammation and immune response have potential prognostic implications for breast cancer survivors. We examined how postdiagnosis diet quality is cross-sectionally related to biomarkers of inflammation and adipose-derived hormones among breast cancer survivors and determined whether physical activity or body size modified any observed associations. Methods: Participants included 746 women diagnosed with stage 0 to IIIA breast cancer. Thirty months after diagnosis, the women completed food frequency questionnaires. We scored diet quality with the Healthy Eating Index (HEI)-2005. Serum concentrations of C-reactive protein (CRP), serum amyloid A, leptin, and adiponectin were measured in fasting 30 mL blood samples. Log biomarker values were regressed on quartiles of HEI-2005 scores in multivariate models, and β scores were exponentiated and expressed as geometric means within quartiles of HEI-2005 scores. Results: Women with better versus poor quality postdiagnosis diets, as defined by higher HEI-2005 scores (Q4 versus Q1), had lower concentrations of CRP (1.6 mg/L versus 2.5 mg/L), but no significant difference in concentrations of serum amyloid A, leptin, or adiponectin. Among women not engaging in recreational physical activity after diagnosis, better diet quality was associated with lower CRP concentrations (2.5 mg/L versus 5.0 mg/L), but no association was observed among women engaging in any recreational physical activity (1.4 mg/L versus 1.6 mg/L; P heterogeneity = 0.03). Conclusions: Among breast cancer survivors, a better-quality diet seems to be associated with lower levels of chronic inflammation. Impact: Lower levels of chronic inflammation have been associated with improved survival after breast cancer. Cancer Epidemiol Biomarkers Prev; 19(9); 2220–8. ©2010 AACR.
A community detection algorithm using network topologies and rule-based hierarchical arc-merging strategies

The authors use four criteria to examine a novel community detection algorithm: (a) effectiveness in terms of producing high values of normalized mutual information (NMI) and modularity, using well-known social networks for testing; (b) examination, meaning the ability to examine mitigating resolution limit problems using NMI values and synthetic networks; (c) correctness, meaning the ability to identify useful community structure results in terms of NMI values and Lancichinetti-Fortunato-Radicchi (LFR) benchmark networks; and (d) scalability, or the ability to produce comparable modularity values with fast execution times when working with large-scale real-world networks. In addition to describing a simple hierarchical arc-merging (HAM) algorithm that uses network topology information, we introduce rule-based arc-merging strategies for identifying community structures. Five well-studied social network datasets and eight sets of LFR benchmark networks were employed to validate the correctness of a ground-truth community, eight large-scale real-world complex networks were used to measure its efficiency, and two synthetic networks were used to determine its susceptibility to two resolution limit problems. Our experimental results indicate that the proposed HAM algorithm exhibited satisfactory performance efficiency, and that HAM-identified and ground-truth communities were comparable in terms of social and LFR benchmark networks, while mitigating resolution limit problems.
Carbon Monoxide-Releasing Molecules: Characterization of Biochemical and Vascular Activities

Carbon monoxide (CO) is generated in living organisms during the degradation of heme by the enzyme heme oxygenase, which exists in constitutive (HO-2 and HO-3) and inducible (HO-1) isoforms. Carbon monoxide gas is known to dilate blood vessels in a manner similar to nitric oxide and has been recently shown to possess antiinflammatory and antiapoptotic properties. We report that a series of transition metal carbonyls, termed here carbon monoxide-releasing molecules (CO-RMs), liberate CO to elicit direct biological activities. Specifically, spectrophotometric and NMR analysis revealed that dimanganese decacarbonyl and tricarbonyldichlororuthenium (II) dimer release CO in a concentration-dependent manner. Moreover, CO-RMs caused sustained vasodilation in precontracted rat aortic rings, attenuated coronary vasoconstriction in hearts ex vivo, and significantly reduced acute hypertension in vivo. These vascular effects were mimicked by induction of HO-1 after treatment of animals with hemin, which increases endogenously generated CO. Thus, we have identified a novel class of compounds that are useful as prototypes for studying the bioactivity of CO. In the long term, transition metal carbonyls could be utilized for the therapeutic delivery of CO to alleviate vascular- and immuno-related dysfunctions. The full text of this article is available at http://www.circresaha. org.
In Vitro Effects of Polyphosphate against Prevotella intermedia in Planktonic Phase and Biofilm

ABSTRACT Polyphosphate (polyP) has gained a wide interest in the food industry due to its potential as a decontaminating agent. In this study, we examined the effect of sodium tripolyphosphate (polyP3; Na5P3O10) against planktonic and biofilm cells of Prevotella intermedia, a major oral pathogen. The MIC of polyP3 against P. intermedia ATCC 49046 determined by agar dilution method was 0.075%, while 0.05% polyP3 was bactericidal against P. intermedia in time-kill analysis performed using liquid medium. A crystal violet binding assay for the assessment of biofilm formation by P. intermedia showed that sub-MICs of polyP3 significantly decreased biofilm formation. Under the scanning electron microscope, decreased numbers of P. intermedia cells forming the biofilms were observed when the bacterial cells were incubated with 0.025% or higher concentrations of polyP3. Assessment of biofilm viability with LIVE/DEAD staining and viable cell count methods showed that 0.05% or higher concentrations of polyP3 significantly decreased the viability of the preformed biofilms in a concentration-dependent manner. The zone sizes of alpha-hemolysis formed on horse blood agar produced by P. intermedia were decreased in the presence of polyP3. The expression of the genes encoding hemolysins and the genes of the hemin uptake (hmu) locus was downregulated by polyP3. Collectively, our results show that polyP is an effective antimicrobial agent against P. intermedia in biofilms as well as planktonic phase, interfering with the process of hemin acquisition by the bacterium.
Utilizing Device Slack for Energy-Efficient I/O Device Scheduling in Hard Real-Time Systems with Non-preemptible Resources

The challenge in conserving energy in embedded real-time systems is to reduce power consumption while preserving temporal correctness. Much research has focused on power conservation for the processor, while power conservation for I/O devices has received little attention. In this paper, we analyze the problem of online energy-aware I/O scheduling for hard real-time systems based on the preemptive periodic task model with non-preemptible shared resources. We extend the concept of device slack proposed in [2] to support non-preemptible shared resources; and propose an online energy-aware I/O scheduling algorithm: Energy-efficient Device Scheduling with Non-preemptible Resources (EEDS NR). The EEDS NR algorithm utilizes device slack to perform device power state transitions to save energy, without jeopardizing temporal correctness. An evaluation of the approach shows that it yields significant energy savings.
Adjustments in the Forcing-Feedback Framework for Understanding Climate Change

AbstractThe traditional forcing–feedback framework has provided an indispensable basis for discussing global climate changes. However, as analysis of model behavior has become more detailed, shortcomings and ambiguities in the framework have become more evident, and physical effects unaccounted for by the traditional framework have become interesting. In particular, the new concept of adjustments, which are responses to forcings that are not mediated by the global-mean temperature, has emerged. This concept, related to the older ones of climate efficacy and stratospheric adjustment, is a more physical way of capturing unique responses to specific forcings. We present a pedagogical review of the adjustment concept, why it is important, and how it can be used. The concept is particularly useful for aerosols, where it helps to organize what has become a complex array of forcing mechanisms. It also helps clarify issues around cloud and hydrological response, transient versus equilibrium climate change, and ge.
ALTERNATIVE FREQUENCY AND TIME DOMAIN VERSIONS OF FRACTIONAL BROWNIAN MOTION

This paper compares models of fractional processes and associated weak convergence results based on moving average representations in the time domain with spectral representations. Both approaches have been applied in the literature on fractional processes. We point out that the conventional forms of these models are not equivalent, as is commonly assumed, even under a Gaussianity assumption. We show that it is necessary to distinguish between “two-sided” processes depending on both leads and lags from one-sided or “causal” processes, because in the case of fractional processes these models yield different limiting properties. We derive new representations of fractional Brownian motion and show how different results are obtained for, in particular, the distribution of stochastic integrals in the multivariate context. Our results have implications for valid statistical inference in fractional integration and cointegration models.We thank F. Hashimzade and two anonymous referees for their valuable comments.
Incorporating Uncertainty in Unexploded Ordnance Discrimination

We examine representations of feature vector uncertainty in the context of unexploded ordnance (UXO) discrimination with electromagnetic data. We compare a local uncertainty estimate derived from the curvature of the misfit function with global estimates of the model posterior probability density (PPD) obtained with Markov chain sampling. For well-posed experiments (i.e., with high SNR and adequate spatial coverage), the two methods of uncertainty appraisal agree. However, when the inverse problem is ill posed, we find out that the PPD can be multimodal. To incorporate these uncertainties in discrimination, we first develop an extension of discriminant analysis which integrates over the posterior distribution of the model. When dealing with multimodal PPDs, we show that an effective solution is to input all modes of the PPD-corresponding to all models at local minima of the misfit-into discrimination and, then, to classify on the basis of the model which is most likely a UXO.
An Architecture for Compiling UDF-centric Workflows

Data analytics has recently grown to include increasingly sophisticated techniques, such as machine learning and advanced statistics. Users frequently express these complex analytics tasks as workflows of user-defined functions (UDFs) that specify each algorithmic step. However, given typical hardware configurations and dataset sizes, the core challenge of complex analytics is no longer sheer data volume but rather the computation itself, and the next generation of analytics frameworks must focus on optimizing for this computation bottleneck. While query compilation has gained widespread popularity as a way to tackle the computation bottleneck for traditional SQL workloads, relatively little work addresses UDF-centric workflows in the domain of complex analytics. In this paper, we describe a novel architecture for automatically compiling workflows of UDFs. We also propose several optimizations that consider properties of the data, UDFs, and hardware together in order to generate different code on a case-by-case basis. To evaluate our approach, we implemented these techniques in Tupleware, a new high-performance distributed analytics system, and our benchmarks show performance improvements of up to three orders of magnitude compared to alternative systems.