Miracle-dz/UniFAR-FTUs huggingface dataset:
Systematic enrichment analysis of microRNA expression profiling studies in endometriosis

Objective(s): The purpose of this study was to conduct a meta-analysis on human microRNAs (miRNAs) expression data of endometriosis tissue profiles versus those of normal controls and to identify novel putative diagnostic markers. Materials and Methods: PubMed, Embase, Web of Science, Ovid Medline were used to search for endometriosis miRNA expression profiling studies of endometriosis. The miRNAs expression data were extracted, and study quality of each article was assessed. The frequently reported miRNAs with consistent regulation were screened out by a meta-profiling algorithm. The putative targets of consistently expressed miRNAs were predicted by using four target prediction tools (TargetScan, PicTar, miRanda, miRDB), and gene ontology pathway enrichment analysis (KEGG and Panther pathways) of the miRNA targets were carried out with GeneCodis web tool. Results: A total of 194 related literatures were retrieved in four databases. One hundred and thirty four differentially expressed miRNAs were found in the 12 microRNA expression profiling studies that compared endometriosis tissues with normal tissues, with 28 miRNAs reported in at least two studies, and 9882 candidate genes retrieved for 13 consistently expressed miRNAs. Kyoto encyclopedia of genes and genomes (KEGG) and Panther pathways enrichment analysis showed that endometriosis related differently expressed miRNA targets were mainly enriched in cancer, endocytosis, Wnt signalling pathway, and angiogenesis. It showed that these differently expressed miRNAs and gene are potential biomarkers of endometriosis. Conclusion: miRNAs appear to be potent regulators of gene expression in endometriosis and its associated reproductive disorders, raising the prospect of using miRNAs as biomarkers and therapeutic agent in endometriosis.
Combinations of penoxsulam and diquat as foliar applications for control of waterhyacinth and common salvinia: evidence of herbicide antagonism.

Waterhyacinth ( Eichhornia crassipes [Mart.] Solms) and common salvinia ( Salvinia minima Baker) are two floating aquatic plants that can cause wide-spread problems in the southern United States. These species can cause reductions in ecosystem function as well as the abundance of native plant species. Herbicides are often used in an attempt to control both species; however, few recommendations exist for common salvinia. Penoxsulam (2-(2,2-difluoroethoxy)N (5,8 dimethoxy [1,2,4] triazolo [1,5c ] pyrimidin-2-yl)-6 (trifluoromethyl) benzenesulfonamide) is newly registered for use in aquatic environments and is efficacious on floating plants as a submersed application; however, foliar application rates are largely undefined. The objectives of these studies were to determine the effect of foliar application rates of penoxsulam for waterhyacinth and common salvinia, and to evaluate the effectiveness of combinations of penoxsulam with diquat against these same plants species. A mesocosm study was conducted using foliar rates of penoxsulam (24.5, 49.1, and 98.2 g ai ha -1 ) alone and in combination with diquat (130.8 g ai ha -1 ). At six weeks after treatment (WAT), penoxsulam alone at all rates resulted in 100% control of waterhyacinth, and at 10 WAT control remained ≥ 90%. Penoxsulam was not as effective at controlling common salvinia. The combination of herbicides did not increase efficacy, and there was evidence of antagonism at the rates tested. Future studies should assess lower rates for waterhyacinth control and influences of salvinia mat thickness on application timing and herbicide efficacy.
Multi-task Curriculum Transfer Deep Learning of Clothing Attributes

Recognising detailed clothing characteristics (finegrained attributes) in unconstrained images of people inthe-wild is a challenging task for computer vision, especially when there is only limited training data from the wild whilst most data available for model learning are captured in well-controlled environments using fashion models (well lit, no background clutter, frontal view, high-resolution). In this work, we develop a deep learning framework capable of model transfer learning from well-controlled shop clothing images collected from web retailers to in-the-wild images from the street. Specifically, we formulate a novel Multi-Task Curriculum Transfer (MTCT) deep learning method to explore multiple sources of different types of web annotations with multi-labelled fine-grained attributes. Our multi-task loss function is designed to extract more discriminative representations in training by jointly learning all attributes, and our curriculum strategy exploits the staged easy-to-hard transfer learning motivated by cognitive studies. We demonstrate the advantages of the MTCT model over the state-of-the-art methods on the X-Domain benchmark, a large scale clothing attribute dataset. Moreover, we show that the MTCT model has a notable advantage over contemporary models when the training data size is small.
Voice Onset Time and the Perception of Japanese Voicing Contrasts (清水克正教授退職記念号)

Much crosslinguistic research exists on the production and perception of voice onset time (VOT). However, most research on the perception of VOT uses synthetic stimuli instead of natural speech stimuli. Effects of synthetic speech on the perception of VOT are not known, but more research needs to be done to see if there are differences between perception using synthetic speech and perception using natural speech. This pilot study uses natural speech to investigate perception of Japanese VOT by Japanese listeners. Results clearly show that not just VOT, but other phonetic factors too must be responsible for differences in perception of the voicedvoiceless distinction in Japanese word-initial stop consonants.
Complement-Mediated Enhancement of Antibody Function for Neutralization of Pseudotype Virus Containing Hepatitis C Virus E2 Chimeric Glycoprotein

ABSTRACT We previously reported a number of features of hepatitis C virus (HCV) chimeric glycoproteins related to pseudotype virus entry into mammalian cells. In this study, pseudotype virus was neutralized by HCV E2 glycoprotein-specific antibodies and infected human sera. Neutralization (50% reduction of pseudotype virus plaque formation) was observed with two human immunoglobulin G1 monoclonal antibodies (MAbs) at concentrations of between 2.5 and 10 μg/ml. A hyperimmune rabbit antiserum to an E2 hypervariable region 1 (HVR1) mimotope also exhibited an HCV E2 pseudotype virus neutralization titer of ∼1/50. An E1 pseudotype virus used as a negative control was not neutralized to a significant level (<1/10) by these MAbs or rabbit antiserum to E2 HVR1. Since HCV probably has a lipid envelope, the role of complement in antibody-mediated virus neutralization was examined. Significant increases in the neutralization titers of the human MAbs (∼60- to 160-fold higher) and rabbit antiserum to HVR1 mimotopes (∼10-fold higher) were observed upon addition of guinea pig complement. Further, these studies suggested that complement activation occured primarily by the classical pathway, since a deficiency in the C4 component led to a significant decrease in the level of virus neutralization. This same decrease was not observed with factor B-deficient complement. We also determined that 9 of 56 HCV-infected patient sera (16%) had detectable pseudotype virus neutralization activity at serum dilutions of between 1/20 and 1/50 and that complement addition enhanced the neutralization activity of some of the HCV-infected human sera. Taken together, these results suggest that during infection, HCV E2 glycoprotein induces a weak neutralizing antibody response, that those antibodies can be measured in vitro by the surrogate pseudotype virus plaque reduction assay, and that neutralization function can be augmented by complement.
Temporal Variation in Photosynthetic Pigments and UV-Absorbing Compounds in Shallow Populations of Two Hawaiian Reef Corals1

ABSTRACT As we seek to understand the physiological mechanisms of coral bleaching, it is important to understand the background temporal variation in photosynthetic pigments and photoprotective compounds that corals exhibit. In this study, reef flat populations of two hermatypic coral species, Montipora capitata (Dana, 1846) and Porites compressa Dana, 1846, were sampled monthly in Kāne‘ohe Bay, Hawai‘i, from January 1998 to March 1999. Surface ultraviolet radiation (UVR) was measured continually during this time period at the same location. High-performance liquid chromatography (HPLC) analysis of photo-synthetic pigments and mycosporine-like amino acids (MAAs) revealed temporal changes in concentrations and proportions of these compounds in tissues of both species of coral. Chlorophyll a (chl a), chlorophyll c2 (chl c2), peridinin, and diadinoxanthin concentrations changed on a skeletal weight (M. capitata) or surface area (P. compressa) basis, significantly correlating with seasonal changes in solar input (number of days from the winter solstice). In P. compressa, diadinoxanthin increased in proportion to the total pigment pool during summer months, suggesting an up-regulation of a xanthophyll cycle. In M. capitata, the ratio of chl a: chl c2 decreased during winter months, suggesting photoacclimation to lower light levels. It is surprising that there was not a clear seasonal pattern in total MAA concentration for either species, with the exception of shinorine in P. compressa. The relative stability of MAA concentrations over the course of the year despite a pronounced seasonal trend in UVR suggests either that MAAs are not performing a photoprotective role in these species or that concentrations are kept at a threshold level in the presence of a dynamic light environment.
A Comparison of Mothers’ Quality of Life after Normal Vaginal, Cesarean, and Water Birth Deliveries

Background Assessment of quality of life (QOL) is of paramount importance for improving postpartum QOL which will in turn enhance QOL of mothers, children, individuals, and the community. The present study aimed to evaluate and compare postpartum QOL after Cesarean Section (CS), Normal Vaginal Delivery (NVD), and water birth delivery. Methods This descriptive analytical, cross-sectional study was conducted on postpartum women referred to urban health centers and two public hospitals in 2012-13 in Shiraz, Iran. Overall, 59 women with NVD, 39 with CS, and 39 with water birth, all at 2 months postpartum, were recruited into the study through multi-stage sampling. Postpartum QOL was measured using Short Form Health Survey (SF-36) which hadbeen adapted previously in Iran. Then, the data were analyzed using descriptive statistics and one-way analysis of variance (ANOVA) in SPSS, version 18. Results The results showed that the NVD group had the highest mean score in physical health domains; the women with water birth had the highest mean score in mental health domains and total QOL. Regarding postpartum QOL the results of one-way ANOVA showed no statistically significant differences between the three modes of delivery. Conclusion Women with water birth and NVD had the highest and second highest total QOL mean scores, respectively; women with NVD and water birth experienced better physical health. Thus, providing more information to pregnant women to encourage them to use NVD and water birth is suggested.
Expanding Maps of an Interval with Holes

We study a class of open chaotic dynamical systems. Consider an expanding map of an interval from which a few small open subintervals are removed (thus creating \holes"). Almost every point of the original interval then eventually escapes through the holes, so there can be no absolutely continuous invariant measures. We construct a so called conditionally invariant measure that is equivalent to the Lebesgue measure. Our measure is unique and naturally generates another measure, which is singular but invariant. By this, we generalize early results by Pianigiani, Yorke, Collet, Martinez and Schmidt, who studied similar maps under an additional Markov assumption. We do not assume any Markov property here and use \bounded variation" techniques rather than Markov coding.
Anthropogenic sound and marine mammal health: measures of the nervous and immune systems before and after intense sound exposure

Anthropogenic sound is a potential stressor for marine mammals that may affect health, as has been demonstrated in other mammals. Therefore, we have initiated investigations on the effects of intense underwater sounds on nervous system activation and immune function in marine mammals. Blood samples were obtained before and after sound exposures (single underwater impulsive sounds (up to 200 kPa) produced from a seismic water gun and (or) single pure tones (up to 201 dB re 1 µPa) resembling sonar "pings" from a white whale, Delphinapterus leucas, and a bottlenose dolphin, Tursiops truncatus, to measure neural-immune parameters. Norepinephrine, epinephrine, and dopamine levels increased with increasing sound levels and were significantly higher after high-level sound exposures (>100 kPa) compared with low-level sound exposures ( 100 kPa) qu'apres une exposition a un son de basse intensite (<100 kPa) et plus elevees que chez les temoins (P = 0,003, 0,006 et 0,020). La concentration de phosphatase alcaline a decru pendant la duree de l'experience (P < 0,001), alors que celle de la gamma glutamyl transferase a augmente (P < 0,001). Parmi les mesures significatives de changements neurologiques et immunitaires chez le grand dauphin apres une exposition a des sons impulsifs, signalons une augmentation de l'aldosterone (P = 0,003) et une diminution des monocytes (P = 0,006). Les changements neurologiques et immunitaires lors d'expositions a des sons tonals sont minimaux, bien qu'on observe des changements de plusieurs parametres neurologiques et immunologiques sur une periode temps plus longue.
NF1 regulation of RAS/ERK signaling is required for appropriate granule neuron progenitor expansion and migration in cerebellar development

Germline mutation in the NF1 tumor suppressor gene underlies Neurofibromatosis type 1. The NF1 gene encodes for neurofibromin, a Ras GTPase-activating protein, and thus negatively regulates the RAS signaling pathway. Here, Sanchez-Ortiz et al. show that neurofibromin is required for appropriate development of cerebellar folia layering and structure. Neonatal administration of inhibitors of the Erk pathway reversed the morphological defects. This work provides a basis for using neonatal Erk inhibitor-based therapies to treat NF1-induced cerebellar disorders.
Examining the Relationships between Capital, Risk and Efficiency in European Banking

This paper analyses the relationship between capital, risk and efficiency for a large sample of European banks between 1992 and 2000. In contrast to the established US evidence we do not find a positive relationship between inefficiency and bank risk-taking. Inefficient European banks appear to hold more capital and take on less risk. Empirical evidence is found showing the positive relationship between risk on the level of capital (and liquidity), possibly indicating regulators' preference for capital as a mean of restricting risk-taking activities. We also find evidence that the financial strength of the corporate sector has a positive influence in reducing bank risk-taking and capital levels. There are no major differences in the relationships between capital, risk and efficiency for commercial and savings banks although there are for co-operative banks. In the case of co-operative banks we do find that capital levels are inversely related to risks and we find that inefficient banks hold lower levels of capital. Some of these relationships also vary depending on whether banks are among the most or least efficient operators.
Robust Intrapulmonary CD8 T Cell Responses and Protection with an Attenuated N1L Deleted Vaccinia Virus

Background Vaccinia viruses have been used as a model for viral disease and as a protective live vaccine. Methodology and Principal Findings We investigated the immunogenicity of an attenuated strain of vaccinia virus engineered to inactivate the N1L gene (vGK5). Using the intranasal route, this recombinant virus was 2 logs less virulent compared to the wildtype VACV-WR. Infection by the intranasal, intraperitoneal, and tail scarification routes resulted in the robust induction of cytolytic virus-specific CD8 T cells in the spleens and the lungs. VACV-specific antibodies were also detected in the sera of mice infected 3–5 months prior with the attenuated vGK5 virus. Finally, mice immunized with vGK5 were significantly protected when challenged with a lethal dose of VACV-WR. Conclusions These results indicate that the attenuated vGK5 virus protects against subsequent infection and suggest that the N1L protein limits the strength of the early antiviral CD8 T cell response following respiratory infection.
Accelerometry combined with heart rate telemetry in the assessment of total energy expenditure

The aim of the present study was: (1) to develop a new method for total energy expenditure (TEE) assessment, using accelerometry (ACC) and heart rate (HR) telemetry in combination; (2) to validate the new method against the criterion measure (DLW) and to compare with two of the most common methods, FLEX-HR and ACC alone. In the first part of the study VO2, HR and ACC counts were measured in twenty-seven subjects during walking and running on a treadmill. Considering the advantages and disadvantages of the HR and ACC methods an analysis model was developed, using ACC at intensities of low and medium levels and HR at higher intensities. During periods of inactivity, RMR is used. A formula for determining TEE from ACC, HR and RMR was developed: TEE =1·1×(EQHR×TTHR+EQACC1×TTACC1+EQACC2×TTACC2+RMR×TTRMR). In the validation part of the study a sub-sample of eight subjects wore an accelerometer, HR was logged and TEE was measured for 14d with the DLW method. Analysis of the Bland–Altman plots with 95% CI indicates that there are no significant differences in TEE estimated with HR–ACC and ACC alone compared with TEE measured with DLW. It is concluded that the HR–ACC combination as well as ACC alone has potential as a method for assessment of TEE during free-living activities as compared with DLW
Natural Allelic Variation in the Temperature-Compensation Mechanisms of the Arabidopsis thaliana Circadian Clock Sequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession nos. AY685131 and AY685132.

Temperature compensation is a defining feature of circadian oscillators, yet no components contributing to the phenomenon have been identified in plants. We tested 27 accessions of Arabidopsis thaliana for circadian leaf movement at a range of constant temperatures. The accessions showed varying patterns of temperature compensation, but no clear associations to the geographic origin of the accessions could be made. Quantitative trait loci (QTL) were mapped for period and amplitude of leaf movement in the Columbia by Landsberg erecta (CoL) and Cape Verde Islands by Landsberg erecta (CvL) recombinant inbred lines (RILs) at 12°, 22°, and 27°. Six CvL and three CoL QTL were located for circadian period. All of the period QTL were temperature specific, suggesting that they may be involved in temperature compensation. The flowering-time gene GIGANTEA and F-box protein ZEITLUPE were identified as strong candidates for two of the QTL on the basis of mapping in near isogenic lines (NILs) and sequence comparison. The identity of these and other candidates suggests that temperature compensation is not wholly determined by the intrinsic properties of the central clock proteins in Arabidopsis, but rather by other genes that act in trans to alter the regulation of these core proteins.
Comparison of the UDP-N-Acetylmuramate:l-Alanine Ligase Enzymes from Mycobacterium tuberculosis andMycobacterium leprae

ABSTRACT In the peptidoglycan of Mycobacterium leprae,l-alanine of the side chain is replaced by glycine. When expressed in Escherichia coli, MurC (UDP-N-acetyl-muramate:l-alanine ligase) ofM. leprae showed Km andVmax for l-alanine and glycine similar to those of Mycobacterium tuberculosis MurC, suggesting that another explanation should be sought for the presence of glycine.
The development of the ProMAS: a Probabilistic Medication Adherence Scale

Current self-report medication adherence measures often provide heavily skewed results with limited variance, suggesting that most participants are highly adherent. This contrasts with findings from objective adherence measures. We argue that one of the main limitations of these self-report measures is the limited range covered by the behaviors assessed. That is, the items do not match the adherence behaviors that people perform, resulting in a ceiling effect. In this paper, we present a new self-reported medication adherence scale based on the Rasch model approach (the ProMAS), which covers a wide range of adherence behaviors. The ProMAS was tested with 370 elderly receiving medication for chronic conditions. The results indicated that the ProMAS provided adherence scores with sufficient fit to the Rasch model. Furthermore, the ProMAS covered a wider range of adherence behaviors compared to the widely used Medication Adherence Report Scale (MARS) instrument, resulting in more variance and less skewness in adherence scores. We conclude that the ProMAS is more capable of discriminating between people with different adherence rates than the MARS.
Nutritional Control of Reproductive Status in Honeybees via DNA Methylation

Fertile queens and sterile workers are alternative forms of the adult female honeybee that develop from genetically identical larvae following differential feeding with royal jelly. We show that silencing the expression of DNA methyltransferase Dnmt3, a key driver of epigenetic global reprogramming, in newly hatched larvae led to a royal jelly–like effect on the larval developmental trajectory; the majority of Dnmt3 small interfering RNA–treated individuals emerged as queens with fully developed ovaries. Our results suggest that DNA methylation in Apis is used for storing epigenetic information, that the use of that information can be differentially altered by nutritional input, and that the flexibility of epigenetic modifications underpins, profound shifts in developmental fates, with massive implications for reproductive and behavioral status.