Miracle-dz/UniFAR-FTUs huggingface dataset:
Subjective measures of health and all-cause mortality – the Rotterdam Study

Background Subjectively assessed health is related to mortality. Various subjective indicators of health have been studied, but it is unclear whether perceived physical functioning or mental health best accounts for the relation with mortality. Method We studied the relation of subjective measures of health with all-cause mortality in 5538 participants of age 55 to 96 years at baseline from the Rotterdam Study. Various instruments of subjectively assessed health were used, that included basic activities of daily living (BADL), instrumental activities of daily living (IADL), quality of life (QoL), positive affect, somatic symptoms and negative affect. All participants completed questionnaires for each subjective measure of health and were followed for mortality for a mean of 12.2 (s.e. = 0.09) years. Cox regression analysis was conducted in the total sample. Results In this cohort, 2021 persons died during 48 534 person-years of follow-up. All measures of subjective health were related to mortality after adjusting for age, gender, education, cognition, prevalent chronic diseases and cardiovascular risk [BADL hazard ratio (HR, calculated per Z-score) = 1.35, 95% confidence interval (CI) 1.29–1.41; IADL HR = 1.27, 95% CI 1.22–1.32; QoL HR = 0.85, 95% CI 0.81–0.89; positive affect HR = 0.92, 95% CI 0.88–0.96; somatic symptoms HR = 1.11, 95% CI 1.06–1.16; and negative affect HR = 1.05, 95% CI 1.01–1.10]. In the mutually adjusted model, only BADL (HR = 1.24, 95% CI 1.16–1.32) and IADL (HR = 1.10, 95% CI 1.04–1.17) remained independently associated with mortality. Conclusions Measures of subjectively assessed health are important indicators of mortality. Our study shows that of the different measures of subjective health, perceived physical health predicts mortality over and above mental health. Conversely, the association between mental health and mortality may partly be explained by poor perceived physical health.
Light-Modulated Responses of Growth and Photosynthetic Performance to Ocean Acidification in the Model Diatom Phaeodactylum tricornutum

Ocean acidification (OA) due to atmospheric CO2 rise is expected to influence marine primary productivity. In order to investigate the interactive effects of OA and light changes on diatoms, we grew Phaeodactylum tricornutum, under ambient (390 ppmv; LC) and elevated CO2 (1000 ppmv; HC) conditions for 80 generations, and measured its physiological performance under different light levels (60 µmol m−2 s−1, LL; 200 µmol m−2 s−1, ML; 460 µmol m−2 s−1, HL) for another 25 generations. The specific growth rate of the HC-grown cells was higher (about 12–18%) than that of the LC-grown ones, with the highest under the ML level. With increasing light levels, the effective photochemical yield of PSII (Fv′/Fm′) decreased, but was enhanced by the elevated CO2, especially under the HL level. The cells acclimated to the HC condition showed a higher recovery rate of their photochemical yield of PSII compared to the LC-grown cells. For the HC-grown cells, dissolved inorganic carbon or CO2 levels for half saturation of photosynthesis (K1/2 DIC or K1/2 CO2) increased by 11, 55 and 32%, under the LL, ML and HL levels, reflecting a light dependent down-regulation of carbon concentrating mechanisms (CCMs). The linkage between higher level of the CCMs down-regulation and higher growth rate at ML under OA supports the theory that the saved energy from CCMs down-regulation adds on to enhance the growth of the diatom.
Role of the innate immunity in female reproductive tract

The mucosal immune system in the female reproductive tract (FRT) is well equipped to meet the sexually transmitted pathogens, allogeneic sperm, and the immunologically distinct fetus. Analysis of the FRT indicates that epithelial cells provide a physical barrier against pathogens and microbial infections as well as secretions containing anti-microbial peptides, cytokines, and chemokines which recruit and activate immune cells. Epithelial and immune cells confer protection in part through Toll-like receptors. The aim of this literature is to review the diverse components of the innate immune system, contributing to an exclusive protection system throughout the FRT.
Operational Experiment of Seamless Handover of a Mobile Router using Multiple Care-of Address Registration

NEMO Basic Support (NEMO BS) adds a mobility function to IPv6 routers, such a router is called as a mobile router. The network behind the mobile router (mobile network) becomes logically static. This function is considered useful when a network has a lot of nodes that do not have a mobility function but move with the network. The typical usage of this technology is the network provided in a transportation system like a bus or airplane. In the base specification of NEMO BS, a mobile router can use one IPv6 address as its attachment point at one time. Therefore, the mobile router and its mobile network will face service disruption of network connectivity while the mobile router is moving from one network to other network. In this paper, we explain two operational experiments of network mobility. One is an experiment using only the base NEMO BS function. The other is an experiment of seamless handover using multiple network interfaces to solve the problem. In these experiments, the mobile networks were actual conference networks which held a few hundred people. The result shows that the multiple interfaces usage provides one-third to one-tenth of the packet loss rate compared to the case that is not using the technology. Also most attendees of the conference did not notice the movement, which means the technology can be used for the realistic solution for the seamless handover.
Smartphones for Smarter Delivery of Mental Health Programs: A Systematic Review

Background The rapid growth in the use of mobile phone applications (apps) provides the opportunity to increase access to evidence-based mental health care. Objective Our goal was to systematically review the research evidence supporting the efficacy of mental health apps for mobile devices (such as smartphones and tablets) for all ages. Methods A comprehensive literature search (2008-2013) in MEDLINE, Embase, the Cochrane Central Register of Controlled Trials, PsycINFO, PsycTESTS, Compendex, and Inspec was conducted. We included trials that examined the effects of mental health apps (for depression, anxiety, substance use, sleep disturbances, suicidal behavior, self-harm, psychotic disorders, eating disorders, stress, and gambling) delivered on mobile devices with a pre- to posttest design or compared with a control group. The control group could consist of wait list, treatment-as-usual, or another recognized treatment. Results In total, 5464 abstracts were identified. Of those, 8 papers describing 5 apps targeting depression, anxiety, and substance abuse met the inclusion criteria. Four apps provided support from a mental health professional. Results showed significant reductions in depression, stress, and substance use. Within-group and between-group intention-to-treat effect sizes ranged from 0.29-2.28 and 0.01-0.48 at posttest and follow-up, respectively. Conclusions Mental health apps have the potential to be effective and may significantly improve treatment accessibility. However, the majority of apps that are currently available lack scientific evidence about their efficacy. The public needs to be educated on how to identify the few evidence-based mental health apps available in the public domain to date. Further rigorous research is required to develop and test evidence-based programs. Given the small number of studies and participants included in this review, the high risk of bias, and unknown efficacy of long-term follow-up, current findings should be interpreted with caution, pending replication. Two of the 5 evidence-based mental health apps are currently commercially available in app stores.
Paraoxonase-1 (PON1) induces metastatic potential and apoptosis escape via its antioxidative function in lung cancer cells

Paraoxonase-1 (PON1) gene polymorphisms have been closely associated with the development of advanced cancers while PON1 secretion to the serum is linked with inhibition of oxidized high-density lipoprotein by its antioxidative function. Our group previously demonstrated that post-translational modification of serum PON1 in form of fucosylated PON1 is a potential biomarker of small cell lung cancer. Here, we interrogated the role of PON1 in the pathobiology of lung cancer (LC) by addressing cell-autonomous mechanisms using gain-of-function and loss-of-function approaches and protein expression profiling of tissue samples in our clinical biobank. PON1 expression in LC patient tissues varied between overexpression in squamous cell carcinoma and minimal loss in adenocarcinoma sub-types. Simultaneous overexpression of PON1 both at the gene and protein stability levels induced pro-oncogenic characteristics in LC cells and xenografts. PON1 overexpression supported metastatic progression of LC by decreasing G1/S ratio and LC cell senescence involving p21Waf1/Cip1. PON1 suppressed drug- and ligand-induced cell death and protected LC cells from genotoxic damages with maintained ATP levels, requiring p53-directed signals. PON1 promoted ROS deregulation protecting the mitochondria from dysregulation. PON1 knockdown resulted in the blockage of its antioxidant function in LC cells through Akt signaling with reduced invasive signature as a consequence of scant expression. Targeted glycolysis stimulated PON1 antioxidant activity regulating phosphorylation of AMPK-α. The functional data imply that exploitation of the antioxidative function of PON1 is consequential in driving LC pathogenesis at the cell-autonomous mechanistic level with consequences on tumor growth.
6-1-2013 Schizophrenia : Causes , Crime , and Implications for Criminology and Criminal Justice

This paper is aimed at criminologists and criminal justicians seeking to understand their role in educating law enforcement and correctional personnel who must deal with the mentally ill. It is motivated by William Johnson’s (2011) recent call for rethinking the interface between mental illness, criminal justice, and academia, and his call for advocacy. We concur with his concerns, and insist that this rethinking must necessarily include grounding in the etiology of mental illness (specifically, with schizophrenia) as it is currently understood by researchers in the area. Advocacy must go hand in hand with a thorough knowledge of the condition of the people for whom we are advocating. We first examine major etiological models of schizophrenia, emphasizing the neurodevelopmental model that incorporates genetics, neurological functioning, and immunological factors guided by the assumption that the typical criminologist/criminal justician has minimal acquaintance with such material. We then address the link between schizophrenia and criminal behavior, and conclude with a discussion of the implications for criminology and criminal justice.
High levels of segregation distortion in the molecular linkage map of bread wheat representing the West Asia and North Africa region

The Fertile Crescent is a primary center of wheat domestication and diversity. Despite its importance for bread wheat breeding, few efforts have been made to fully understand the genetic structure of the Anatolian bread wheat. A lack of information regarding the genetic structure of the bread wheat from this region is evident. Therefore, this study aimed to provide new insights into the genetic structure of bread wheat from Anatolia. A genetic linkage map was constructed based on recombinant inbred lines derived from a cross between the Turkish cultivar Gerek-79 and the Moroccan cultivar Arrehane, by using DArT markers anchored with simple sequence repeat markers. This map consisted of 54 linkage groups belonging to 21 bread wheat chromosomes, spanning a total of 935.629 cM. The total number of mapped markers varied from 5 to 87, depending on the chromosome. Seventy-seven DArT markers with unpublished chromosomal locations were mapped on different chromosomes, whereas 23 were mapped onto chromosomes that deviated from those detailed in the literature. This linkage map represents a key starting point towards our understanding of the genome structure of Anatolian bread wheat, which would, in turn, permit us to genetically dissect important agromorphological and quality characteristics. This linkage map will be useful for the identification of QTL for biotic and abiotic stresses, and for important agronomic traits that are valuable for Anatolian wheat.
Evaluation of a silver-impregnated coating to inhibit colonization of orthopaedic implants by biofilm forming methicillin-resistant Staphylococcus pseudintermedius

Summary Objectives: To evaluate the in vitro anti -bacterial activity of a silver-impregnated coating against a biofilm-forming strain of methicillin-resistant Staphylococcus pseud -intermedius (MRSP). Methods: A clinical MRSP isolate sourced from a failed canine knee implant was evaluated for biofilm production and used in the present study. Using a standard test method and a clinically approved titanium substrate, the antimicrobial activity of a novel silver plasma coating was determined at two times: five minutes after inoculation of the specimens (T0) and after 24 hours of incubation (T24). Scanning electron microscopy was used to evaluate the biofilm formation on specimens. Results: The tested clinical MRSP isolate was classified as a strong biofilm producer. The silver coating significantly reduced the MRSP growth more than four log steps compared to the non-coated specimens and showed more than 99.98% reduction in the number of colony forming units after 24 hours. Scanning electron microscopy images revealed that silver-coated surfaces did not manifest detectable biofilm, while biofilm formation was readily observed on the control specimens. Clinical significance: The silver coating exhibited excellent activity against the multi-drug resistant biofilm-forming MRSP isolate. The next stage of this work will involve testing in an animal model of orthopaedic infection. Positive results from animal studies would support the introduction of the silver plasma coating as a new strategy for preventing implant contamination, biofilm formation, and surgical infection in dogs undergoing orthopaedic surgery. Supplementary Material for this paper is available online at: http://dx.doi. org/10.3415/VCOT-15-08-0134
What Factors Are Associated with Good Performance in Children with Cochlear Implants? From the Outcome of Various Language Development Tests, Research on Sensory and Communicative Disorders Project in Japan: Nagasaki Experience

Objectives We conducted multi-directional language development tests as a part of the Research on Sensory and Communicative Disorders (RSVD) in Japan. This report discusses findings as well as factors that led to better results in children with severe-profound hearing loss. Methods We evaluated multiple language development tests in 33 Japanese children with cochlear implants (32 patients) and hearing aid (1 patient), including 1) Test for question and answer interaction development, 2) Word fluency test, 3) Japanese version of the Peabody picture vocabulary test-revised, 4) The standardized comprehension test of abstract words, 5) The screening test of reading and writing for Japanese primary school children, 6) The syntactic processing test of aphasia, 7) Criterion-referenced testing (CRT) for Japanese language and mathematics, 8) Pervasive development disorders ASJ rating scales, and 9) Raven's colored progressive matrices. Furthermore, we investigated the factors believed to account for the better performances in these tests. The first group, group A, consisted of 14 children with higher scores in all tests than the national average for children with hearing difficulty. The second group, group B, included 19 children that scored below the national average in any of the tests. Results Overall, the results show that 76.2% of the scores obtained by the children in these tests exceeded the national average scores of children with hearing difficulty. The children who finished above average on all tests had undergone a longer period of regular habilitation in our rehabilitation center, had their implants earlier in life, were exposed to more auditory verbal/oral communication in their education at affiliated institutions, and were more likely to have been integrated in a regular kindergarten before moving on to elementary school. Conclusion In this study, we suggest that taking the above four factors into consideration will have an affect on the language development of children with severe-profound hearing loss.
Author ' s response to reviews Title : SDHA Loss of Function Mutations in a Subset of Young Adult Wild-type Gastrointestinal

Background: KIT/PDGFRA wild-type gastrointestinal stromal tumors (WT GIST) have been associated with alteration of the succinate dehydrogenase (SDH) complex II function. A recent report identified, in two cases of young adults WT GIST, a germline mutation in SDHA encoding the main subunit of the SDH complex II. Methods: Next generation sequencing was applied on five pediatric and one young adult WT GIST, by whole exome capture and SOLiD 3-plus system sequencing. The putative mutations were first confirmed by Sanger sequencing and then screened on a larger panel of 11 pediatric and young adult WT GIST, including 5 in the context of Carney triad. Results: A germline p.Arg31X nonsense SDHA mutation was identified in one of the six cases tested by SOLiD platform. An additional somatic p.D38V missense mutation in SDHA exon 2 was identified by Sanger sequencing in the extended WT GIST patients cohort. Western blotting showed loss of SDHA expression in the two cases harboring SDHA mutations, while expression being retained in the other WT GIST tumors. Results were further confirmed by immunohistochemistry for both SDHA and SDHB, which showed a concurrent loss of expression of both proteins in SDHA-mutant lesions, while the remaining WT tumors showed only loss of SDHB expression. Conclusion: Germline and/or somatic aberrations of SDHA occur in a small subset of WT GISTs, outside the Carney’s triad and are associated with loss of both SDHA and SDHB protein expression. Mutations of the SDH complex II are more particularly associated with WT GIST occurring in young adults. Although pediatric GIST consistently display alterations of SDHB protein expression, further molecular studies are needed to identify the crucial genes involved in their tumorigenesis.
The Chthonomonas calidirosea Genome Is Highly Conserved across Geographic Locations and Distinct Chemical and Microbial Environments in New Zealand's Taupō Volcanic Zone

ABSTRACT Chthonomonas calidirosea T49T is a low-abundance, carbohydrate-scavenging, and thermophilic soil bacterium with a seemingly disorganized genome. We hypothesized that the C. calidirosea genome would be highly responsive to local selection pressure, resulting in the divergence of its genomic content, genome organization, and carbohydrate utilization phenotype across environments. We tested this hypothesis by sequencing the genomes of four C. calidirosea isolates obtained from four separate geothermal fields in the Taupō Volcanic Zone, New Zealand. For each isolation site, we measured physicochemical attributes and defined the associated microbial community by 16S rRNA gene sequencing. Despite their ecological and geographical isolation, the genome sequences showed low divergence (maximum, 1.17%). Isolate-specific variations included single-nucleotide polymorphisms (SNPs), restriction-modification systems, and mobile elements but few major deletions and no major rearrangements. The 50-fold variation in C. calidirosea relative abundance among the four sites correlated with site environmental characteristics but not with differences in genomic content. Conversely, the carbohydrate utilization profiles of the C. calidirosea isolates corresponded to the inferred isolate phylogenies, which only partially paralleled the geographical relationships among the sample sites. Genomic sequence conservation does not entirely parallel geographic distance, suggesting that stochastic dispersal and localized extinction, which allow for rapid population homogenization with little restriction by geographical barriers, are possible mechanisms of C. calidirosea distribution. This dispersal and extinction mechanism is likely not limited to C. calidirosea but may shape the populations and genomes of many other low-abundance free-living taxa. IMPORTANCE This study compares the genomic sequence variations and metabolisms of four strains of Chthonomonas calidirosea, a rare thermophilic bacterium from the phylum Armatimonadetes. It additionally compares the microbial communities and chemistry of each of the geographically distinct sites from which the four C. calidirosea strains were isolated. C. calidirosea was previously reported to possess a highly disorganized genome, but it was unclear whether this reflected rapid evolution. Here, we show that each isolation site has a distinct chemistry and microbial community, but despite this, the C. calidirosea genome is highly conserved across all isolation sites. Furthermore, genomic sequence differences only partially paralleled geographic distance, suggesting that C. calidirosea genotypes are not primarily determined by adaptive evolution. Instead, the presence of C. calidirosea may be driven by stochastic dispersal and localized extinction. This ecological mechanism may apply to many other low-abundance taxa.
On Gaussian comparison inequality and its application to spectral analysis of large random matrices

Recently, Chernozhukov, Chetverikov, and Kato [Ann. Statist. 42 (2014) 1564--1597] developed a new Gaussian comparison inequality for approximating the suprema of empirical processes. This paper exploits this technique to devise sharp inference on spectra of large random matrices. In particular, we show that two long-standing problems in random matrix theory can be solved: (i) simple bootstrap inference on sample eigenvalues when true eigenvalues are tied; (ii) conducting two-sample Roy's covariance test in high dimensions. To establish the asymptotic results, a generalized $\epsilon$-net argument regarding the matrix rescaled spectral norm and several new empirical process bounds are developed and of independent interest.
The pixel rectangle index used in object based building extraction from high resolution images

An improved high resolution object-based building extraction method based on Pixel Rectangle Index is presented in this paper. We use Minimum Span Tree optimal theory to realize object-based high resolution image segmentation. First, we proposed a rotation invariant Pixel Rectangle Index by introducing the principal direction of homogeneous area. Second, we improved the calculation of edge-weight by introducing the band-weight and Pixel Rectangle Index. The QuickBird high resolution images were used to do the building extraction experiment. The experiment result proved that this method can obtain high extraction accuracy and this algorithm can be efficiently used in remote sensing images.