Miracle-dz/UniFAR-FTUs huggingface dataset:
Apocrine Carcinoma, Adenopathies, and Raised TAG‐72 Serum Tumor Marker

BACKGROUND The detection of tumor-associated glycoprotein-72 in the serum of patients with carcinomas, basically of the colon, has proved to be of great use in the follow-up of these gastrointestinal adenocarcinomas. RESULTS We report the case of a male patient presenting adenopathies in the right axilla. The histologic study of an adjacent skin tumor enabled the diagnosis of a cutaneous apocrine carcinoma. Among the studies made, the increase in the serum antibody CA72.4 can be highlighted. The tumor marker was negative after the extirpation of the skin tumor and the axillary adenopathies. CONCLUSION To our best knowledge, this is the first case in which a tumor serum marker is associated with a cutaneous apocrine carcinoma, a fact that should be confirmed with further patients. Its use in the monitoring of this infrequent skin neoplasia is also noteworthy.
MAP6 interacts with Tctex1 and Cav2.2/N‐type calcium channels to regulate calcium signalling in neurons

MAP6 proteins were first described as microtubule‐stabilizing agents, whose properties were thought to be essential for neuronal development and maintenance of complex neuronal networks. However, deletion of all MAP6 isoforms in MAP6 KO mice does not lead to dramatic morphological aberrations of the brain but rather to alterations in multiple neurotransmissions and severe behavioural impairments. A search for protein partners of MAP6 proteins identified Tctex1 – a dynein light chain with multiple non‐microtubule‐related functions. The involvement of Tctex1 in calcium signalling led to investigate it in MAP6 KO neurons. In this study, we show that functional Cav2.2/N‐type calcium channels are deficient in MAP6 KO neurons, due to improper location. We also show that MAP6 proteins interact directly with both Tctex1 and the C‐terminus of Cav2.2/N‐type calcium channels. A balance of these two interactions seems to be crucial for MAP6 to modulate calcium signalling in neurons.
Early age of first sex: a risk factor for HIV infection among women in Zimbabwe

Objective: To explore the relationship between early age of coital debut (15 years of age or younger) and risk for HIV infection among sexually active urbanized Zimbabwean women. Design: Cross-sectional analysis of screening data from a cohort study. Methods: Sexually active women aged 18–35 years were recruited from public sector family planning clinics in and around Harare, Zimbabwe between November 1999 and September 2002. They received a brief behavioral interview and HIV testing. Of the 4675 women screened, 4393 (94%) had complete data on sexual behaviors and HIV serostatus, and were included in this analysis. Results: HIV prevalence in this sample was 40.1%. The median age of coital debut was 18 years and 11.8% of women reporting having experienced coital debut at age 15 or younger. Women with early coital debut had a significantly higher risk profile, including multiple lifetime partners and not completing high school. In binary generalized linear regression models HIV risk was increased for women reporting early age of coital debut (relative hazard, 1.30; 95% confidence interval, 1.13–1.50), controlling for duration of sexual activity and current age; this effect was attenuated somewhat after controlling for other factors such as number of sexual partners. Conclusions: Our results show that early coital debut is a significant predictor of prevalent HIV infection independent of other identified factors in this population. HIV prevention strategies should include delaying the age of first coitus and should address the barriers that may prevent young women from so doing.
Use of palm oil fuel ash to improve chloride and corrosion resistance of high-strength and high-work

This paper presents the use of palm oil fuel ash as a pozzolanic material in producing high-strength and high-workability concrete. Portland cement Type I (CT) was partially replaced with ground palm oil fuel ash (PA). PA with 2–5% by weight retained on a sieve No. 325 was used. The concrete mixtures were made with portland cement Type I containing 10, 20, and 30% of PA. Compressive strength, coefficient of water absorption, rapid chloride penetration and corrosion resistance of concretes were determined. Test results indicated that the high-strength high-workability concrete can be achieved by using PA to replace portland cement Type I up to 20%. The resistance to chloride-induced corrosion of concrete containing PA as measured by accelerated corrosion test with impressed voltage is significantly improved in comparison to that of CT concrete.
Outage probability of underlay cognitive relay networks with spatially random nodes

We consider an underlay cognitive relay network coexisting with a primary multicast network (e.g. digital television (TV) broadcasting network), in which secondary user (SU) transmissions are power constrained to limit the interference on any primary receiver in the network. The primary receivers and SU relays are randomly located due to irregular deployments and/or mobility and thus, their spatial distributions are modeled by two independent Poisson point processes (PPPs). In this paper, we analyze an opportunistic relaying scenario and develop a relay-selection scheme by considering the interference constraints on all the primary receivers in the network. We then analytically evaluate the relaying performance in terms of outage probability by using tools from stochastic geometry and point process theory, and finally compare the performance against that of direct communication. Closed-form expressions are derived for the outage probabilities of both the relay and direct links, along with their high-signal-to-noise ratio (SNR) asymptotics.
Acoustic, Morphological, and Functional Aspects of `yeah/ja' in Dutch, English and German

We explore different forms and functions of one of the most common feedback expressions in Dutch, English, and German, namely `yeah/ja' which is known for its multi-functionality and ambiguous usage in dialog. For example, it can be used as a yes-answer, or as a pure continuer, or as a way to show agreement. In addition, `yeah/ja' can be used in its single form, but it can also be combined with other particles, forming multi-word expressions, especially in Dutch and German. We have found substantial differences on the morpho-lexical level between the three related languages which enhances the ambiguous character of `yeah/ja'. An explorative analysis of the prosodic features of `yeah/ja' has shown that mainly a higher intensity is used to signal speaker incipiency across the inspected languages.
Parkinsonism in GTP cyclohydrolase 1 mutation carriers.

Sir, We read with great interest the article by Mencacci and colleagues (2014) reporting a significantly higher frequency of GTP cyclohydrolase 1 ( GCH1 ) variants in patients with Parkinson’s disease compared to controls. Whole-exome sequencing of a large case-control cohort showed that rare GCH1 coding variants are associated with a 7-fold increased risk of Parkinson’s disease. Heterozygous loss-of-function mutations in GCH1 , a crucial enzyme for dopamine production in nigrostriatal neurons (Kaufman, 1959; Nagatsu et al. , 1964), are the most common cause of DOPA-responsive dystonia (DRD) (Ichinose et al. , 1994). DRD is a rare hereditary disease characterized by childhood-onset, generalized dystonia and a dramatic long-lasting response to levodopa (Segawa et al. , 1976). The disease may also manifest in adulthood with parkinsonism as the sole or dominant clinical feature (Hjermind et al. , 2006; Momma et al. , 2009). GCH1 mutations have been shown to segregate in pedigrees with multiple individuals affected by isolated parkinsonism, a phenotype …
CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems

Central to Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-Cas systems are repeated RNA sequences that serve as Cas-protein–binding templates. Classification is based on the architectural composition of associated Cas proteins, considering repeat evolution is essential to complete the picture. We compiled the largest data set of CRISPRs to date, performed comprehensive, independent clustering analyses and identified a novel set of 40 conserved sequence families and 33 potential structure motifs for Cas-endoribonucleases with some distinct conservation patterns. Evolutionary relationships are presented as a hierarchical map of sequence and structure similarities for both a quick and detailed insight into the diversity of CRISPR-Cas systems. In a comparison with Cas-subtypes, I-C, I-E, I-F and type II were strongly coupled and the remaining type I and type III subtypes were loosely coupled to repeat and Cas1 evolution, respectively. Subtypes with a strong link to CRISPR evolution were almost exclusive to bacteria; nevertheless, we identified rare examples of potential horizontal transfer of I-C and I-E systems into archaeal organisms. Our easy-to-use web server provides an automated assignment of newly sequenced CRISPRs to our classification system and enables more informed choices on future hypotheses in CRISPR-Cas research: http://rna.informatik. uni-freiburg.de/CRISPRmap.
Transcriptome Analysis of Indole-3-Butyric Acid-Induced Adventitious Root Formation in Nodal Cuttings of Camellia sinensis (L.)

Tea (Camellia sinensis L.) is a popular world beverage, and propagation of tea plants chiefly depends on the formation of adventitious roots in cuttings. To better understand potential mechanisms involved in adventitious root formation, we performed transcriptome analysis of single nodal cuttings of C. sinensis treated with or without indole-3-butyric acid (IBA) using the Illumina sequencing method. Totally 42.5 million RNA-Seq reads were obtained and these were assembled into 59,931 unigenes, with an average length of 732 bp and an N50 of 1292 bp. In addition, 1091 differentially expressed unigenes were identified in the tea cuttings treated with IBA compared to controls, including 656 up- and 435 down-regulated genes. Further real time RT-PCR analysis confirmed RNA-Seq data. Functional annotation analysis showed that many genes were involved in plant hormone signal transduction, secondary metabolism, cell wall organization and glutathione metabolism, indicating potential contributions to adventitious rooting. Our study presents a global view of transcriptome profiles of tea cuttings in response to IBA treatment and provides new insights into the fundamental mechanisms associated with auxin-induced adventitious rooting. Our data will be a valuable resource for genomic research about adventitious root formation in tea cuttings, which can be used to improve rooting for difficult-to-root varieties.
Host-Symbiont Specificity Expressed during Early Adsorption of Rhizobium meliloti to the Root Surface of Alfalfa

Early (4 h) adsorption of Rhizobium meliloti L5-30 in low numbers to alfalfa roots in mineral solution was examined for competition with other bacterial strains. All tested competitor strains decreased the adsorption of L5-30 by extents which depended on the strain and its concentration. The decrease of adsorption by R. meliloti competitors (all of them infective in alfalfa) was nearly complete at saturation (97 to 99% decrease). All other heterologous rhizobia and Agrobacterium tumefaciens at saturating concentrations (106 to 107 per ml) decreased adsorption of L5-30 only partially, less than 60%. The differential effects of homologous and heterologous competitors indicate that initial adsorption of R. meliloti to the root surface of its host occurs in symbiont-specific as well as nonspecific modes and suggest the existence of binding sites on roots which are highly selective for the specific microsymbiont in the presence of other heterologous bacteria even in very unfavorable (less than 10−4) symbiont-competitor concentration ratios.
Two Periplasmic Disulfide Oxidoreductases, DsbA and SrgA, Target Outer Membrane Protein SpiA, a Component of the Salmonella Pathogenicity Island 2 Type III Secretion System*

The formation of disulfide is essential for the folding, activity, and stability of many proteins secreted by Gram-negative bacteria. The disulfide oxidoreductase, DsbA, introduces disulfide bonds into proteins exported from the cytoplasm to periplasm. In pathogenic bacteria, DsbA is required to process virulence determinants for their folding and assembly. In this study, we examined the role of the Dsb enzymes in Salmonella pathogenesis, and we demonstrated that DsbA, but not DsbC, is required for the full expression of virulence in a mouse infection model of Salmonella enterica serovar Typhimurium. Salmonella strains carrying a dsbA mutation showed reduced function mediated by type III secretion systems (TTSSs) encoded on Salmonella pathogenicity islands 1 and 2 (SPI-1 and SPI-2). To obtain a more detailed understanding of the contribution of DsbA to both SPI-1 and SPI-2 TTSS function, we identified a protein component of the SPI-2 TTSS apparatus affected by DsbA. Although we found no substrate protein for DsbA in the SPI-1 TTSS apparatus, we identified SpiA (SsaC), an outer membrane protein of SPI-2 TTSS, as a DsbA substrate. Site-directed mutagenesis of the two cysteine residues present in the SpiA protein resulted in the loss of SPI-2 function in vitro and in vivo. Furthermore, we provided evidence that a second disulfide oxidoreductase, SrgA, also oxidizes SpiA. Analysis of in vivo mixed infections demonstrated that a Salmonella dsbA srgA double mutant strain was more attenuated than either single mutant, suggesting that DsbA acts in concert with SrgA in vivo.
Stability of Oculomotor Fixation as a Function of Target Contrast and Blur

Previous studies have shown that changes in target parameters, such as luminance, color, size, and shape exert little effect on the stability of fixation, measured as the standard deviation of eye positions over several seconds of fixation. In this study, we investigated the effect of target contrast and dioptric blur on the stability of fixation in five normal subjects. The horizontal positions of both eyes were assessed by infrared limbal tracking while the subjects fixated binocularly for 20-s intervals on a cross-shaped target at 2 m. Across subjects, the mean stability of fixation on a high contrast target worsened significantly from 8.9 to 12.0 min arc with fixation through increasing amounts (0 to 4 D) of dioptric blur. However, without blur there was no statistically significant effect on fixation stability of varying the target contrast from 7 to 84%. The variability of vergence was not significantly influenced in either condition. Like other target parameters investigated in previous studies, dioptric blur and contrast have relatively inconsequential effects on fixation stability, indicating that the signals used to control fixation are largely independent of stimulus parameters. Practically, the findings suggest that when patients' eye movements are recorded for clinical reasons, the results are unlikely to be affected seriously by the presence of residual refractive error.
Moving Object Detection by Detecting Contiguous Outliers in the Low-Rank Representation

Object detection is a fundamental step for automated video analysis in many vision applications. Object detection in a video is usually performed by object detectors or background subtraction techniques. Often, an object detector requires manually labeled examples to train a binary classifier, while background subtraction needs a training sequence that contains no objects to build a background model. To automate the analysis, object detection without a separate training phase becomes a critical task. People have tried to tackle this task by using motion information. But existing motion-based methods are usually limited when coping with complex scenarios such as nonrigid motion and dynamic background. In this paper, we show that the above challenges can be addressed in a unified framework named DEtecting Contiguous Outliers in the LOw-rank Representation (DECOLOR). This formulation integrates object detection and background learning into a single process of optimization, which can be solved by an alternating algorithm efficiently. We explain the relations between DECOLOR and other sparsity-based methods. Experiments on both simulated data and real sequences demonstrate that DECOLOR outperforms the state-of-the-art approaches and it can work effectively on a wide range of complex scenarios.
Genome-Enabled Estimates of Additive and Nonadditive Genetic Variances and Prediction of Apple Phenotypes Across Environments

The nonadditive genetic effects may have an important contribution to total genetic variation of phenotypes, so estimates of both the additive and nonadditive effects are desirable for breeding and selection purposes. Our main objectives were to: estimate additive, dominance and epistatic variances of apple (Malus × domestica Borkh.) phenotypes using relationship matrices constructed from genome-wide dense single nucleotide polymorphism (SNP) markers; and compare the accuracy of genomic predictions using genomic best linear unbiased prediction models with or without including nonadditive genetic effects. A set of 247 clonally replicated individuals was assessed for six fruit quality traits at two sites, and also genotyped using an Illumina 8K SNP array. Across several fruit quality traits, the additive, dominance, and epistatic effects contributed about 30%, 16%, and 19%, respectively, to the total phenotypic variance. Models ignoring nonadditive components yielded upwardly biased estimates of additive variance (heritability) for all traits in this study. The accuracy of genomic predicted genetic values (GEGV) varied from about 0.15 to 0.35 for various traits, and these were almost identical for models with or without including nonadditive effects. However, models including nonadditive genetic effects further reduced the bias of GEGV. Between-site genotypic correlations were high (>0.85) for all traits, and genotype-site interaction accounted for <10% of the phenotypic variability. The accuracy of prediction, when the validation set was present only at one site, was generally similar for both sites, and varied from about 0.50 to 0.85. The prediction accuracies were strongly influenced by trait heritability, and genetic relatedness between the training and validation families.
Effect of Discontinuation of Fluoride Intake from Water and Toothpaste on Urinary Excretion in Young Children

As there is no homeostatic mechanism for maintaining circulating fluoride (F) in the human body, the concentration may decrease and increase again when intake is interrupted and re-started. The present study prospectively evaluated this process in children exposed to F intake from water and toothpaste, using F in urine as a biomarker. Eleven children from Ibiá, Brazil (with sub-optimally fluoridated water supply) aged two to four years who regularly used fluoridated toothpaste (1,100 ppm F) took part in the study. Twenty-four-hour urine was collected at baseline (Day 0, F exposure from water and toothpaste) as well as after the interruption of fluoride intake from water and dentifrice (Days 1 to 28) (F interruption) and after fluoride intake from these sources had been re-established (Days 29 to 34) (F re-exposure). Urinary volume was measured, fluoride concentration was determined and the amount of fluoride excreted was calculated and expressed in mg F/day. Urinary fluoride excretion (UFE) during the periods of fluoride exposure, interruption and re-exposure was analyzed using the Wilcoxon test. Mean UFE was 0.25 mg F/day (SD: 0.15) at baseline, dropped to a mean of 0.14 mg F/day during F interruption (SD: 0.07; range: 0.11 to 0.17 mg F/day) and rose to 0.21 (SD: 0.09) and 0.19 (SD: 0.08) following F re-exposure. The difference between baseline UFE and the period of F interruption was statistically significant (p < 0.05), while the difference between baseline and the period of F re-exposure was non-significant (p > 0.05). The findings suggest that circulating F in the body of young children rapidly decreases in the first 24 hours and again increases very fast after discontinuation and re-exposure of F from water and toothpaste.
The dynamical approach to speech perception: From fine phonetic detail to abstract phonological categories

phonological units, in a way that leads variations in how a given word is produced to be factored out at an early stage of processing (e.g., Fitzpatrick and Wheeldon, 2000; Lahiri and Reetz, 2002; Stevens, 2002). It is often hypothesized that inter-individual variations are removed prior to building up this abstract representation by means of a speaker normalization procedure (see Johnson, 2005b, for a recent review). A clear demarcation is established in that framework between the surface phonetic form of a word and the underlying phonological representation associated with that word. The abstractionist approach contends that the phonological representation for each word is both unique and permanently stored in memory. Readers are referred to Cutler et al. (2007), Eulitz and Lahiri (2004), Lahiri and Reetz (2002), Pallier et al. (2001), and Stevens (2002), for recent important papers in the abstractionist framework. In the terminology employed by Pitt and Johnson (2003), abstractionist models such as Lahiri and Reetz’s (2002) FUL model offer a representationbased solution to the speech variability problem. According to the FUL (Featurally Underspecified Lexicon) model, phonological representations in the lexicon are underspecified for certain features such as [coronal], and it is assumed that this makes listeners insensitive to surface variations shown by words for these features. For example, assimilation of word-final coronals to the place of articulation of the following consonant is considered to remain consistent with the underspecified phonological representation of the carrier word and, because of this so-called no-mismatch relationship between the word’s surface and underlying forms, assimilation is expected to have no disruptive effect on the identification of the word. As opposed to representationbased models, processing-based models rely on the assumption that recognizing the assimilated variant of a word entails recovering the word’s unassimilated shape through a phonological inference process. In spite of the fact that they too are representation-oriented, exemplar models stand, in their most prototypical form at least, in sharp opposition to abstractionist models like FUL along many dimensions. A major difference with the abstractionist stance relates to the fact that each exemplar is viewed as corresponding to a language chunk that is stored in memory with all the details specific to the particular circumstances in which it has been produced or encountered. This includes sensory-motor, semantic and pragmatic characteristics, but also indexical information about the speaker’s identity and the situation of occurrence, to mention but a few properties. Exemplars are therefore deeply anchored into their context of occurrence in the largest possible Roles of fine phonetic detail and abstract phonological categories in speech
L-functions and Automorphic Representations

Our goal is to formulate a theorem that is part of a recent classification of automorphic representations of orthogonal and symplectic groups. To place it in perspective, we devote much of the paper to a historical introduction to the Langlands program. In our attempt to make the article accessible to a general mathematical audience, we have centred it around the theory of L-functions, and its implicit foundation, Langlands’ principle of functoriality. Mathematics Subject Classification (2010). Primary 11F66, 11F70, 11R37, 11F57, 22F55.