Miracle-dz/UniFAR-FTUs huggingface dataset:
Inter-individual differences in sleep response to shift work in novice police officers – A prospective study

ABSTRACT The aim of this longitudinal study on novice police officers was to investigate inter-individual differences in sleep response to shift work, and to identify potential baseline predictors thereof. A total of 42 subjects were assessed at baseline, prior to commencing shift work. They were re-assessed during three follow-up sessions within the first 2 years of shift work exposure after approximately 4, 12, and 20 months of rotating shift work. Wrist actigraphy and sleep logs were used to investigate nocturnal sleep at baseline and daytime sleep after night shifts during the follow-up sessions. Actigraphically estimated total sleep time and subjective sleep quality were analyzed as outcome variables, using mixed-effects analysis of variance. Systematic inter-individual differences were observed in the overall response of these outcome variables to shift work. In this sample, flexibility of sleeping habits and gender were found to be predictors of daytime total sleep time in the first 2 years of shift work exposure. Flexibility of sleeping habits and subjective quality of nighttime sleep prior to shift work were found to be predictors of subjective quality of daytime sleep. These results suggest that it may be possible to detect and even predict sleep deficiencies in response to shift work early on, which could be a basis for the development of individualized interventions to improve shift work tolerance.
Does the platform switching implant affect the crestal bone level? A systematic review and meta-analysis

Objectives: To assess the effects of platform switching in patients restored with implant supported fixed restorations on implant failure and patient satisfaction. Materials and methods: We searched the Cochrane Oral Health Group Trial register (04 February 2017), Cochrane Central Register of Controlled Trials (The Cochrane Library 2017, Issue 02), MEDLINE (January 1966 to 04 February 2017) and the WHO International Clinical Trial Registry Platform (04 February 2017). We hand searched citation lists of relevant publications. We did not apply any language or date restrictions. Randomised controlled trials (RCTs) comparing the effectiveness of platform switching versus platform matching in patients restored with implant supported fixed restorations were included. Two reviewers independently assessed trials for inclusion and risk of bias, extracted data and checked for accuracy. We have expressed results as risk ratio (RR) or mean differences (MD), together with their 95% confidence intervals (CI). The primary outcome measures were implant failure and patient satisfaction. Results: We included 12 studies (513 participants). There was no difference between platform switching and matching after 1-3 years of follow up in implant failures (RR 0.32, 95% CI 0.01 to 7.70; studies = 7) or patient satisfaction (MD 0.13, 95% CI -0.29 to 0.55; participants = 24; studies = 1). Regarding marginal bone loss, when we pooled down the data obtained from six trials, we identified substantial heterogeneity (I2 = 81%) with inconsistency in the direction of effect, which was unexplained by clinical or methodological differences between the studies, and accordingly we did not perform meta-analysis for this outcome. Conclusions: In patients restored with implant supported fixed restorations, there is insufficient evidence to support platform switching or platform matching implant-abutment connection design to improve implant survival and patient satisfaction.
Neural Mechanisms of Human Perceptual Choice Under Focused and Divided Attention

Perceptual decisions occur after the evaluation and integration of momentary sensory inputs, and dividing attention between spatially disparate sources of information impairs decision performance. However, it remains unknown whether dividing attention degrades the precision of sensory signals, precludes their conversion into decision signals, or dampens the integration of decision information toward an appropriate response. Here we recorded human electroencephalographic (EEG) activity while participants categorized one of two simultaneous and independent streams of visual gratings according to their average tilt. By analyzing trial-by-trial correlations between EEG activity and the information offered by each sample, we obtained converging behavioral and neural evidence that dividing attention between left and right visual fields does not dampen the encoding of sensory or decision information. Under divided attention, momentary decision information from both visual streams was encoded in slow parietal signals without interference but was lost downstream during their integration as reflected in motor mu- and beta-band (10–30 Hz) signals, resulting in a “leaky” accumulation process that conferred greater behavioral influence to more recent samples. By contrast, sensory inputs that were explicitly cued as irrelevant were not converted into decision signals. These findings reveal that a late cognitive bottleneck on information integration limits decision performance under divided attention, and places new capacity constraints on decision-theoretic models of information integration under cognitive load.
Impact of castration with or without alpha-tocopherol supplementation on the urethral sphincter of rats.

OBJECTIVE To analyze the impact of low levels of testosterone induced by orchiectomy and the effect of alpha-tocopherol supplementation on oxidative stress in the urethral sphincter. MATERIALS AND METHODS Forty male Wistar rats weighing 250-300 g were divided into four groups with 10 each: Sham group; Orchiectomy group: bilateral orchiectomy; Orchiectomy-pre-Tocopherol group: bilateral orchiectomy preceded by alpha-tocopherol supplementation for four weeks; Orchiectomy-full-Tocopherol group: bilateral orchiectomy with alpha-tocopherol supplementation for four weeks preceding the procedure and for eight weeks afterwards. At the protocol end, animals were euthanized and had the sphincter analyzed stereologically focusing on collagen and muscle fibers percentage. Oxidative stress levels were determined using 8-epi-PGF2. RESULTS The 8-epi-PGF2 levels were statistically higher (p < 0.0003) in the Orchiectomy group compared to others groups while Sham and Orchiectomy-full-Tocopherol groups presented statistically similar values (p = 0.52). Collagen volumetric densities were significantly lower in Sham and Orchiectomy-full-Tocopherol groups (p < 0.022). Sham group presented statistically greater muscle fiber percent. CONCLUSION Castration caused oxidative stress in the urethral sphincter complex, with increased collagen deposition. Alpha-tocopherol had a protective effect and its supplementation for twelve weeks provided the greatest protection.
Fault detection in power transformers using random neural networks

This paper discuss the application of artificial neural network-based algorithms to identify different types of faults in a power transformer, particularly using DGA (Dissolved Gas Analysis) test. The analysis of Random Neural Network (RNN) using Levenberg-Marquardt (LM) and Broyden-Fletcher-Goldfarb-Shanno (BFGS) algorithms has been done using the data of dissolved gases of power transformers collected from Punjab State Transmission Corporation Ltd.(PSTCL), Ludhiana, India. Sorting of the preprocessed data have been done using dimensionality reduction technique, i.e., principal component analysis. The sorted data is used as inputs to the Random Neural Networks (RNN) classifier. It has been seen from the results obtained that BFGS has better performance for the diagnosis of fault in transformer as compared to LM.
EVALUATION OF AUTOMATIC ROAD EXTRACTION

Internal self-diagnosis and external evaluation of the obtained results are essential for any automatic system. In the long run these factors are of major importance for the relevance of the system for practical applications. Obviously, this statement is also true for image analysis in photogrammetry and remote sensing. However, so far only relatively little work has been carried out in this area. This paper deals with the external evaluation of automatic road extraction algorithms by means of comparison to manually plotted linear road axis used as reference data. The comparison is performed in two steps: (1) Matching of the extracted primitives to the reference network; (2) Calculation of quality measures. Each part depends on the other: the less tolerant is matching, the less exhaustive the extraction is considered to be, but the more accurate it looks. Therefore, the matching process is an important part of the evaluation process. The quality measures proposed for the automatically extracted road data comprise completeness, correctness, quality, redundancy, planimetric RMS differences and gap statistics. They aim at evaluating exhaustivity as well as assessing geometrical accuracy. The evaluation methodology is presented and discussed in detail. Results of a comparative evaluation of three different automatic road extraction approaches are presented. They show the overall status of the road extractors, as well as the individual strengths and weaknesses of each individual approach. Thus, the applicability of the evaluation method is proven.
A Corpus-based Method for Extracting Paraphrases of Emotion Terms

Since paraphrasing is one of the crucial tasks in natural language understanding and generation, this paper introduces a novel technique to extract paraphrases for emotion terms, from non-parallel corpora. We present a bootstrapping technique for identifying paraphrases, starting with a small number of seeds. WordNet Affect emotion words are used as seeds. The bootstrapping approach learns extraction patterns for six classes of emotions. We use annotated blogs and other datasets as texts from which to extract paraphrases, based on the highest-scoring extraction patterns. The results include lexical and morpho-syntactic paraphrases, that we evaluate with human judges.
Postinoculation Protozoan Establishment and Association Patterns of Methanogenic Archaea in the Ovine Rumen

ABSTRACT Association patterns between archaea and rumen protozoa were evaluated by analyzing archaeal 16S rRNA gene clone libraries from ovine rumen inoculated with different protozoa. Five protozoan inoculation treatments, fauna free (negative control), holotrich and cellulolytic protozoa, Isotricha and Dasytricha spp. , Entodinium spp. , and total fauna (type A) were tested. We used denaturing gradient gel electrophoresis, quantitative PCR, and phylogenetic analysis to evaluate the impact of the protozoan inoculants on the respective archaeal communities. Protozoan 18S ribosomal DNA clone libraries were also evaluated to monitor the protozoal population that was established by the inoculation. Phylogenetic analysis suggested that archaeal clones associated with the fauna-free, the Entodinium, and the type A inoculations clustered primarily with uncultured phylotypes. Polyplastron multivesiculatum was the predominant protozoan strain established by the holotrich and cellulolytic protozoan treatment, and this resulted predominantly in archaeal clones affiliated with uncultured and cultured methanogenic phylotypes (Methanosphaera stadtmanae, Methanobrevibacter ruminantium, and Methanobacterium bryantii). Furthermore, the Isotricha and Dasytricha inoculation treatment resulted primarily in archaeal clones affiliated with Methanobrevibacter smithii. This report provides the first assessment of the influence of protozoa on archaea within the rumen microbial community and provides evidence to suggest that different archaeal phylotypes associate with specific groups of protozoa. The observed patterns may be linked to the evolution of commensal and symbiotic relationships between archaea and protozoa in the ovine rumen environment. This report further underscores the prevalence and potential importance of a rather large group of uncultivated archaea in the ovine rumen, probably unrelated to known methanogens and undocumented in the bovine rumen.
Quantifying β-catenin subcellular dynamics and cyclin D1 mRNA transcription during Wnt signaling in single living cells

Signal propagation from the cell membrane to a promoter can induce gene expression. To examine signal transmission through sub-cellular compartments and its effect on transcription levels in individual cells within a population, we used the Wnt/β-catenin signaling pathway as a model system. Wnt signaling orchestrates a response through nuclear accumulation of β-catenin in the cell population. However, quantitative live-cell measurements in individual cells showed variability in nuclear β-catenin accumulation, which could occur in two waves, followed by slow clearance. Nuclear accumulation dynamics were initially rapid, cell cycle independent and differed substantially from LiCl stimulation, presumed to mimic Wnt signaling. β-catenin levels increased simultaneously at adherens junctions and the centrosome, and a membrane-centrosome transport system was revealed. Correlating β-catenin nuclear dynamics to cyclin D1 transcriptional activation showed that the nuclear accumulation rate of change of the signaling factor, and not actual protein levels, correlated with the transcriptional output of the pathway. DOI: http://dx.doi. org/10.7554/eLife.16748. 001
Effective DNA/RNA Co-Extraction for Analysis of MicroRNAs, mRNAs, and Genomic DNA from Formalin-Fixed Paraffin-Embedded Specimens

Background Retrospective studies of archived human specimens, with known clinical follow-up, are used to identify predictive and prognostic molecular markers of disease. Due to biochemical differences, however, formalin-fixed paraffin-embedded (FFPE) DNA and RNA have generally been extracted separately from either different tissue sections or from the same section by dividing the digested tissue. The former limits accurate correlation whilst the latter is impractical when utilizing rare or limited archived specimens. Principal Findings For effective recovery of genomic DNA and total RNA from a single FFPE specimen, without splitting the proteinase-K digested tissue solution, we optimized a co-extraction method by using TRIzol and purifying DNA from the lower aqueous and RNA from the upper organic phases. Using a series of seven different archived specimens, we evaluated the total amounts of genomic DNA and total RNA recovered by our TRIzol-based co-extraction method and compared our results with those from two commercial kits, the Qiagen AllPrep DNA/RNA FFPE kit, for co-extraction, and the Ambion RecoverAll™ Total Nucleic Acid Isolation kit, for separate extraction of FFPE-DNA and -RNA. Then, to accurately assess the quality of DNA and RNA co-extracted from a single FFPE specimen, we used qRT-PCR, gene expression profiling and methylation assays to analyze microRNAs, mRNAs, and genomic DNA recovered from matched fresh and FFPE MCF10A cells. These experiments show that the TRIzol-based co-extraction method provides larger amounts of FFPE-DNA and –RNA than the two other methods, and particularly provides higher quality microRNAs and genomic DNA for subsequent molecular analyses. Significance We determined that co-extraction of genomic DNA and total RNA from a single FFPE specimen is an effective recovery approach to obtain high-quality material for parallel molecular and high-throughput analyses. Our optimized approach provides the option of collecting DNA, which would otherwise be discarded or degraded, for additional or subsequent studies.
Sustained Attention and Executive Functioning Performance in Attention-Deficit/Hyperactivity Disorder

The aim of this study was to further refine the cognitive phenotype of attention-deficit/hyperactivity disorder (ADHD), with respect to the ability to sustain attention and executive functioning. Participants were 34 boys with ADHD (combined type) and 28 normal controls. The groups were closely matched for age and IQ. All participants were 12 years of age. Both groups performed a computerized sustained attention task and a response interference task. Measures related to speed, accuracy, and time on task were collected. We found that children with ADHD performed slower, less accurately, more impulsively, and with less stability than controls. Both groups produced more errors with increasing time on task, reflecting reduced vigilance. Importantly, no interaction with time on task was found. The overall pattern of results suggests that measures related to accuracy are more informative than measures related to speed of responding in refining the cognitive phenotype of ADHD.
Bottom trawl catch comparison in the Mediterranean Sea: Flexible Turtle Excluder Device (TED) vs traditional gear

The Mediterranean Sea is a hotspot of biodiversity, but the high fishing pressure results in high bycatch rates of protected (sea turtles and cetaceans) and top predator species (sharks). The reduction of bycatch is challenging for fishery scientists, as conservation of these species has become a priority. Among the animals threatened by fishing activities, the loggerhead (Caretta caretta) represents a charismatic species considered as “vulnerable” at the global scale by IUCN. In the Mediterranean Sea, trawl nets show the highest probabilities of bycatch of protected species, with high rates of mortality. A new flexible Turtle Excluder Device (TED) has been tested for the first time on a commercial scale in the Mediterranean Sea to assess its effectiveness in reducing bycatch. The results did not show any significant (α = 0.05) loss in terms of commercial weight, but a significant reduction of debris in the codend of the nets mounting the TED respect to traditional nets. The catch comparison of the main commercial species showed similar rates without any significant loss of sizes, with the only exception of anglerfishes (Lophius spp.) that showed a loss of the largest individuals by TED. In terms of bycatch, the traditional nets captured mostly rays and sharks, while no turtles were captured, at all. In this regard, the authors were informed by other vessels operating in the same areas at the time of the trials about some accidental catches of loggerhead turtles. Our results demonstrated that the flexible TED represents a practical and effective solution to reduce the bycatch of endangered species in coastal Mediterranean demersal multispecies fisheries, as demonstrated experimentally also in other areas of the world. The measures involving technical modifications of fishing gears require significant investments but are technically feasible and could guarantee the success of the conservation.
Topical Herpes Simplex Virus 2 (HSV-2) Vaccination with Human Papillomavirus Vectors Expressing gB/gD Ectodomains Induces Genital-Tissue-Resident Memory CD8+ T Cells and Reduces Genital Disease and Viral Shedding after HSV-2 Challenge

ABSTRACT No herpes simplex virus 2 (HSV-2) vaccine has been licensed for use in humans. HSV-2 glycoproteins B (gB) and D (gD) are targets of neutralizing antibodies and T cells, but clinical trials involving intramuscular (i.m.) injection of HSV-2 gB and gD in adjuvants have not been effective. Here we evaluated intravaginal (ivag) genetic immunization of C57BL/6 mice with a replication-defective human papillomavirus pseudovirus (HPV PsV) expressing HSV-2 gB (HPV-gB) or gD (HPV-gD) constructs to target different subcellular compartments. HPV PsV expressing a secreted ectodomain of gB (gBsec) or gD (gDsec), but not PsV expressing a cytoplasmic or membrane-bound form, induced circulating and intravaginal-tissue-resident memory CD8+ T cells that were able to secrete gamma interferon (IFN-γ) and tumor necrosis factor alpha (TNF-α) as well as moderate levels of serum HSV neutralizing antibodies. Combined immunization with HPV-gBsec and HPV-gDsec (HPV-gBsec/gDsec) vaccines conferred longer survival after vaginal challenge with HSV-2 than immunization with HPV-gBsec or HPV-gDsec alone. HPV-gBsec/gDsec ivag vaccination was associated with a reduced severity of genital lesions and lower levels of viral shedding in the genital tract after HSV-2 challenge. In contrast, intramuscular vaccination with a soluble truncated gD protein (gD2t) in alum and monophosphoryl lipid A (MPL) elicited high neutralizing antibody titers and improved survival but did not reduce genital lesions and viral shedding. Vaccination combining ivag HPV-gBsec/gDsec and i.m. gD2t-alum-MPL improved survival and reduced genital lesions and viral shedding. Finally, high levels of circulating HSV-2-specific CD8+ T cells, but not serum antibodies, correlated with reduced viral shedding. Taken together, our data underscore the potential of HPV PsV as a platform for a topical mucosal vaccine to control local manifestations of primary HSV-2 infection. IMPORTANCE Genital herpes is a highly prevalent chronic disease caused by HSV infection. To date, there is no licensed vaccine against HSV infection. This study describes intravaginal vaccination with a nonreplicating HPV-based vector expressing HSV glycoprotein antigens. The data presented in this study underscore the potential of HPV-based vectors as a platform for the induction of genital-tissue-resident memory T cell responses and the control of local manifestations of primary HSV infection.
Promoter Methylation of CDKN2A, RARβ, and RASSF1A in Non-Small Cell Lung Carcinoma: Quantitative Evaluation Using Pyrosequencing

Background While qualitative analysis of methylation has been reviewed, the quantitative analysis of methylation has rarely been studied. We evaluated the methylation status of CDKN2A, RARβ, and RASSF1A promoter regions in non-small cell lung carcinomas (NSCLCs) by using pyrosequencing. Then, we evaluated the association between methylation at the promoter regions of these tumor suppressor genes and the clinicopathological parameters of the NSCLCs. Methods We collected tumor tissues from a total of 53 patients with NSCLCs and analyzed the methylation level of the CDKN2A, RARβ, and RASSF1A promoter regions by using pyrosequencing. In addition, we investigated the correlation between the hypermethylation of CDKN2A and the loss of p16INK4A immunoexpression. Results Hypermethylation of CDKN2A, RARβ, and RASSF1A promoter regions were 16 (30.2%), 22 (41.5%), and 21 tumors (39.6%), respectively. The incidence of hypermethylation at the CDKN2A promoter in the tumors was higher in undifferentiated large cell carcinomas than in other subtypes (p=0.002). Hyperrmethylation of CDKN2A was significantly associated with p16INK4A immunoexpression loss (p=0.045). With regard to the clinicopathological characteristics of NSCLC, certain histopathological subtypes were found to be strongly associated with the loss of p16INK4A immunoexpression (p=0.016). Squamous cell carcinoma and undifferentiated large cell carcinoma showed p16INK4A immunoexpression loss more frequently. The Kaplan-Meier survival curves analysis showed that methylation level and patient survival were barely related to one another. Conclusion We quantitatively analyzed the promoter methylation status by using pyrosequencing. We showed a significant correlation between CDKN2A hypermethylation and p16INK4A immunoexpression loss.