Miracle-dz/UniFAR-FTUs huggingface dataset:
L-carnitine improved bovine blastocyst rate and quality when supplemented at different preimplantation stages

The present study investigated the effect ofL-carnitine supplementation during different pre-implantation stages on bovine embryo development rate and quality. Good morphologically cumulus-oocyte complexes (n=2126) recovered from slaughterhouse ovaries were matured, fertilized in vitro and presumed zygotes were further cultured in vitro (IVC) in CR1-aa media till day 8. For the setup of the study, L-carnitine (1.5 mM) was added at different technological steps (IVM, IVF, IVC and all stages) and different developmental stages (early IVC: 1to 4-cell vs. late IVC: 8-cellembryos). Moreover, untreated (control) group was also included in this experiment.Quality of embryos developed from all experimental groupswere evaluated usingterminal deoxynucleotidy ltransferased UTP nick end labeling (TUNEL) assay which assesses total normal and apoptotic cell numbers ofembryos. Real-time PCR was used to profile 5 embryo marker genes (SOD2, CDX2, IFNt, Glut8 and TFAM) in addition; GAPDH was used as housekeeping gene. Results of the current study showed a significant increase in blastocyst rate at day 8 of culture when Lcarnitine was added at IVM (34.1±2.6), early IVC (34.6±1.7), late IVC (38.4±2.8), and all stages (36.4±3.5) compared to control (22.5±1.4) and IVF (26.0±1.1) groups.The blastocyst total number of cells was greater (P < 0.05) in groups that L-carnitine was added at IVM (134.1±4.9), IVF (125.7±2.8), early IVC (133.8±5.7), late IVC (139.2±3.5) and all stages (137.0±4.1) compared to control (115.3±3.6). On the other hand, control embryo group has more apoptotic cells (10.4±1.9) than L-carnitine treated groups at IVM (4.1±1.2), IVF (5.5±1.6), early IVC (3.9±1.4), late IVC (4.0±1.7) and all stages (2.8±2.0). The expression profile of SOD2, IFNt, Glut8 and TFAM genes was increased in embryos treated with L-carnitine at IVM, early IVC, late IVC and all stages compared to IVF and control groups. In addition, CDX2 transcript was more abundant in IVM, late IVC and all stages treated groups than in any other embryo group. Overall, the findings of the present study support the notion that L-carnitinecould be a potential antioxidant substance that has a positive effect on embryo development rate and quality when supplemented to all culture media throughout bovine preimplantation.
Diagnosing Parkinson's Diseases Using Fuzzy Neural System

This study presents the design of the recognition system that will discriminate between healthy people and people with Parkinson's disease. A diagnosing of Parkinson's diseases is performed using fusion of the fuzzy system and neural networks. The structure and learning algorithms of the proposed fuzzy neural system (FNS) are presented. The approach described in this paper allows enhancing the capability of the designed system and efficiently distinguishing healthy individuals. It was proved through simulation of the system that has been performed using data obtained from UCI machine learning repository. A comparative study was carried out and the simulation results demonstrated that the proposed fuzzy neural system improves the recognition rate of the designed system.
Determination of trichothecenes in cereals and cereal-based products by liquid chromatography–tandem mass spectrometry

A sensitive, accurate and precise method for the simultaneous determination of nivalenol (NIV), deoxynivalenol (DON), T-2 toxin (T-2) and HT-2 toxin (HT-2) in different food matrices, including wheat, maize, barley, cereal-based infant foods, snacks, biscuits and wafers, has been developed. The method, using liquid chromatography coupled with atmospheric pressure chemical ionization triple quadrupole mass spectrometry (LC–APCI–MS/MS), allowed unambiguous identification of the selected trichothecenes at low µg per kg levels in such complex food matrices. A clean-up procedure, based on reversed phase SPE Oasis® HLB columns, was used, allowing good recoveries for all studied trichothecenes. In particular, NIV recoveries significantly improved compared to those obtained by using Mycosep® #227 columns for clean-up of the extracts. Limits of detection in the various investigated matrices ranged 2.5–4.0 µg kg−1 for NIV, 2.8–5.3 µg kg−1 for DON, 0.4–1.7 µg kg−1 for HT-2 and 0.4–1.0 µg kg−1 for T-2. Mean recovery values, obtained from cereals and cereal products spiked with NIV, DON, HT-2 and T-2 toxins at levels from 10 to 1000 µg kg−1, ranged from 72 to 110% with mean relative standard deviation lower than 10%. A systematic investigation of matrix effects in different cereals and cereal products was also carried out by statistically comparing the slopes of standard calibration curve with matrix-matched calibration curve for each of the four toxins and the eight matrices tested. For seven of the eight matrices tested, statistically significant matrix effects were observed, indicating that, for accurate quantitative analysis, matrix-matched calibration was necessary. The method was applied to the analysis of 57 samples of ground wheat originated from South Italy and nine cereal food samples collected from retail markets.
Dynamic Elbow Flexion Force Estimation Through a Muscle Twitch Model and sEMG in a Fatigue Condition

We propose a joint force estimation method to compute elbow flexion force using surface electromyogram (sEMG) considering time-varying effects in a fatigue condition. Muscle fatigue is a major cause inducing sEMG changes with respect to time over long periods and repetitive contractions. The proposed method composed the muscle-twitch model representing the force generated by a single spike and the spikes extracted from sEMG. In this study, isometric contractions at six different joint angles (10 subjects) and dynamic contractions with constant velocity (six subjects) were performed under non-fatigue and fatigue conditions. Performance of the proposed method was evaluated and compared with that of previous methods using mean absolute value (MAV). The proposed method achieved average 6.7 ± 2.8 %RMSE for isometric contraction and 15.6 ± 24.7%RMSE for isokinetic contraction under fatigue condition with more accurate results than the previous methods.
Diversity and population structure of a near–shore marine–sediment viral community

Viruses, most of which are phage, are extremely abundant in marine sediments, yet almost nothing is known about their identity or diversity. We present the metagenomic analysis of an uncultured near–shore marine–sediment viral community. Three–quarters of the sequences in the sample were not related to anything previously reported. Among the sequences that could be identified, the majority belonged to double–stranded DNA phage. Temperate phage were more common than lytic phage, suggesting that lysogeny may be an important lifestyle for sediment viruses. Comparisons between the sediment sample and previously sequenced seawater viral communities showed that certain phage phylogenetic groups were abundant in all marine viral communities, while other phage groups were under–represented or absent. This ‘marineness’ suggests that marine phage are derived from a common set of ancestors. Several independent mathematical models, based on the distribution of overlapping shotgun sequence fragments from the library, were used to show that the diversity of the viral community was extremely high, with at least 104 viral genotypes per kilogram of sediment and a Shannon index greater than 9 nats. Based on these observations we propose that marine–sediment viral communities are one of the largest unexplored reservoirs of sequence space on the planet.
Simplifying mixture Models through Function Approximation Simplifying Mixture Models through Function Approximation

The finite mixture model is widely used in various statistical learning problems. However, the model obtained may contain a large number of components, making it inefficient in practical applications. In this paper, we propose to simplify the mixture model by first grouping similar components together and then performing local fitting through function approximation. By using the squared loss to measure the distance between mixture models, our algorithm naturally combines the two different tasks of component clustering and model simplification. The proposed method can be used to speed up various algorithms that use mixture models during training (e.g., Bayesian filtering, belief propagation) or testing (e.g., kernel density estimation, SVM testing). Encouraging results are observed in the experiments on density estimation, clustering-based image segmentation and simplification of SVM decision functions.
From photographs to findings: visual meaning-making and interpretive engagement in the analysis of participant-generated images

Although the use of visual research is gaining increased acceptance, there remains a lack of attention directed to how to rigorously analyse visual images. A framework of ‘interpretive engagement’ is proposed to describe analytic processes for meaning-making of participant-generated visual images. The ‘interpretive engagement’ framework comprises three stages of meaning-making; these are meaning-making through participant engagement (Stage 1), through researcher-driven engagement (Stage 2), and through re-contextualising (Stage 3). These three stages on their own are limited, but in combination provide rich and comprehensive visual analysis. The ‘interpretive engagement’ framework involves five key elements, namely, the researcher, the participant, the image and the context of its production and the audience/s. Each plays a significant role, contributing to the overall analysis. To illustrate the framework, a research example using participant-generated photographs from young people with chronic illness is used. This enables the visual analytic work we advocate to be evident and tangible for the reader, illustrating how interpretive engagement can support the development of substantive findings. Although multifaceted, we argue this analytic framework is predominantly researcher-driven with an emphasis on close inspection and engaging with the details of each image to determine overarching elements of the images as a collection. It involves systematically and deliberately interpreting the material followed by articulation of an analytic story which accommodates participant intentions, researcher interpretations, theoretical underpinnings and emerging knowledge claims. Implementation of this interpretive framework offers the potential for rich and thorough visual analysis and interpretations.
Susceptibility of Primary HTLV-1 Isolates from Patients with HTLV-1-Associated Myelopathy to Reverse Transcriptase Inhibitors

Since human T-lymphotropic virus type 1 (HTLV-1)-associated diseases are associated with a high HTLV-1 load, reducing this load may treat or prevent disease. However, despite in vitro evidence that certain nucleoside/nucleotide analogue reverse transcriptase inhibitors (NRTIs) are active against HTLV-1, in vivo results have been disappointing. We therefore assayed the sensitivity of HTLV-1 primary isolates to a panel of RT inhibitors. HTLV-1 primary isolates were obtained, pre- and post- NRTI treatment, from patients with HTLV-1-associated myelopathy. Sensitivity to azidothymidine (AZT), lamivudine (3TC), tenofovir (TDF) and three phosphonated carbocyclic 2’-oxa-3’aza nucleosides (PCOANs) was assessed in a RT inhibitor assay. With the exception of 3TC, HTLV RT from primary isolates was less sensitive to all tested inhibitors than HTLV-1 RT from MT-2 cells. HTLV-1 RT from primary isolates and from chronically infected, transformed MT-2 cells was insensitive to 3TC. Sensitivity of primary isolates to RT inhibitors was not reduced following up to 12 months of patient treatment with AZT plus 3TC. The sensitivity of HTLV-1 primary isolates to NRTIs differs from that of cell lines and may vary among patients. Failure of NRTIs to reduce HTLV-1 viral load in vivo was not due to the development of phenotypic NRTI resistance. AZT and the three PCOANs assayed all consistently inhibited primary isolate HTLV-1 RT.
Organizational Socialization: A Field Study into Socialization Success and Rate

The last decade has witnessed a resurgence of organizational socialization research. However, a critical question has been neglected: Is there a common underlying pattern to organizational socialization? We investigated newcomer learning, job satisfaction and intent to quit as common indicators of socialization, in research with 222 newcomers at two organizations during the crucial post-entry period. The results support a learning-dependent model of newcomer adjustment, with learning in specific domains related to improved attitudinal outcomes. Some aspects of organizational socialization were not uniform across the two organizations, suggesting a need for further development of socialization models and greater accounting for this in organizational socialization research.
Incidental Scene Text Understanding: Recent Progresses on ICDAR 2015 Robust Reading Competition Challenge 4

Different from focused texts present in natural images, which are captured with user's intention and intervention, incidental texts usually exhibit much more diversity, variability and complexity, thus posing significant difficulties and challenges for scene text detection and recognition algorithms. The ICDAR 2015 Robust Reading Competition Challenge 4 was launched to assess the performance of existing scene text detection and recognition methods on incidental texts as well as to stimulate novel ideas and solutions. This report is dedicated to briefly introduce our strategies for this challenging problem and compare them with prior arts in this field.
Larger female fish contribute disproportionately more to self-replenishment

While chance events, oceanography and selective pressures inject stochasticity into the replenishment of marine populations with dispersing life stages, some determinism may arise as a result of characteristics of breeding individuals. It is well known that larger females have higher fecundity, and recent laboratory studies have shown that maternal traits such as age and size can be positively associated with offspring growth, size and survival. Whether such fecundity and maternal effects translate into higher recruitment in marine populations remains largely unanswered. We studied a population of Amphiprion chrysopterus (orange-fin anemonefish) in Moorea, French Polynesia, to test whether maternal size influenced the degree of self-recruitment on the island through body size–fecundity and/or additional size-related maternal effects of offspring. We non-lethally sampled 378 adult and young juveniles at Moorea, and, through parentage analysis, identified the mothers of 27 self-recruits (SRs) out of 101 recruits sampled. We also identified the sites occupied by each mother of an SR and, taking into account variation in maternal size among sites, we found that females that produced SRs were significantly larger than those that did not (approx. 7% greater total length, approx. 20% greater biomass). Our analyses further reveal that the contribution of larger females to self-recruitment was significantly greater than expected on the basis of the relationship between body size and fecundity, indicating that there were important maternal effects of female size on traits of their offspring. These results show, for the first time in a natural population, that larger female fish contribute more to local replenishment (self-recruitment) and, more importantly, that size-specific fecundity alone could not explain the disparity.
IRate: Initial Video Bitrate Selection System for HTTP Streaming

Many HTTP streaming video systems have been developed and widely deployed in recent years. Previous efforts were mainly spent on improving the caching of videos or proposing mid-stream measurement methods to update the best bitrate. However, since the video length is often short, the mid-stream measurement may not even converge to the best bitrate due to insufficient bandwidth estimates. On the other hand, because of diversified Web infrastructure, estimating the actual network quality at the pre-stream stage is increasingly challenging for video service providers. In this paper, we propose IRate, which enables video service providers to proactively profile clients' streaming performance by carrying out pre-stream measurement in the Content Delivery Network (CDN). With the measurement results, the video stream can start at the best video quality at the onset of streaming. This is especially beneficial to short video clips, which are very popular in the Internet today. IRate is composed of a probe kit and a quality oracle. The probe kit utilizes the pre-stream time window (e.g., user's think time and pre-roll advertisement) for measuring network quality by running a lightweight measurement script on the Web page to induce probe packets from the IRate middlebox on the server side. With the measurement results, the quality oracle estimates the clients' streaming performance by determining the highest initial bitrate with a pre-trained decision tree. Our testbed results show that IRate is able to achieve 80% accuracy in determining the bitrate within 10s. By having a better estimate of the best initial bitrate, the buffering time and rebuffering events are significantly reduced in HTTP streaming. Furthermore, the stability and the efficiency in dynamic adaptive streaming over HTTP streaming are also improved by about 40% and 36%, respectively. Our user quality of experience (QoE) experiment further validates that IRate can improve the QoE by more than 6% and the perceived quality of initial quality by 24% in the actual Internet environment.
Some thoughts on English for Research Publication Purposes (ERPP) and related issues

Academic writing for research publication takes place around the globe, involving, according to a recent account, 5.5 million scholars, 2,000 publishers and 17,500 research/higher education institutions (Lillis & Curry 2010: 1). Because so many scholars whose first language is not English are now using English for publication purposes and because of the research interest that has developed in the field, a specialist term has been coined, English for Research Publication Purposes (ERPP). This paper presents an overview of some issues relating to ERPP.
ERK 1 / 2-mediated phosphorylation of myometrial caldesmon during pregnancy and labor

Li, Yunping, Hyun-Dong Je, Sabah Malek, and Kathleen G. Morgan. ERK1/2-mediated phosphorylation of myometrial caldesmon during pregnancy and labor. Am J Physiol Regul Integr Comp Physiol 284: R192–R199, 2003. First published October 3, 2002; 10.1152/ajpregu.00290. 2002. — We used a timed-pregnant rat model to track changes in myometrial contractility during pregnancy and labor and to correlate these changes with upstream signaling events. Myometrium was harvested from CO2-euthanized rats. Although contraction amplitudes increased at 16 and 20 days of pregnancy, contraction incidence and area under the force curve were inhibited, consistent with the myometrial quiescence of pregnancy. The Ca2 sensitivity of contraction was decreased at 20 days of pregnancy and this was partially reversed in labor. The protein content of h-caldesmon (hCaD) was increased in pregnancy. A 40-fold increase in the signal from a phospho-CaD antibody specific for phosphorylation at an ERK1/2 site occurred during labor. ERK1/2 activation increased significantly at the onset of labor. Myosin light chain phosphorylation (LC20-P) increased significantly in labor compared with the nonpregnant state. Thus we conclude that the increase in CaD protein content during pregnancy may contribute to a suppression of the contractility of pregnant myometrium. Conversely, CaD phosphorylation, through an ERK1/2-mediated signaling pathway, as well as an increase in basal LC20-P, is suggested to contribute to the reversal of inhibition and promote contraction of the uterus during labor.
Democratic Governance Beyond the Nation-State:

International institutions not only increase system effectiveness or output legitimacy, but are also a normatively plausible response to the problems for democracy that are caused by globalization. In this way, international institutions also increase input legitimacy. It is therefore a false approach to pin down the problem of democracy beyond the nation-state as a choice between `effective problem-solving through international institutions' and `democratic political processes'. At the same time, it is indisputable that the actual functioning of these international institutions does not meet democratic standards. By correctly pointing to the deficits of current international institutions, sceptics too quickly conclude that most deficits in the working of international institutions cannot be remedied. The sceptical argument is founded on two more or less explicit background hypotheses that can be empirically challenged. The first background hypothesis states that a demos cannot exist at the transnational level. I will modify this statement in theoretical terms and offer some conceptual distinctions that may prepare the ground for further empirical investigation. The second background hypothesis of the sceptics postulates a zero-sum relationship between national sovereignty and supranationality. I will put forward some concrete institutional proposals that undermine the zero-sum logic of the sceptics, concluding that in a denationalized society, democratic legitimacy can only be achieved by a mixed constitution comprising majority procedures and negotiation mechanisms.
Colombia a Source of Cacao Genetic Diversity As Revealed by the Population Structure Analysis of Germplasm Bank of Theobroma cacao L.

Beans of the species Theobroma cacao L. , also known as cacao, are the raw material to produce chocolate. Colombian cacao has been classified as a fine flavor cacao that represents the 5% of cacao world’s production. Colombian genetic resources from this species are conserved in ex situ and in-field germplasm banks, since T. cacao has recalcitrant seeds to desication and long-term storage. Currently, the collection of T. cacao of the Colombian Corporation of Agricultural Research (CORPOICA) has approximately 700 germplasm accessions. We conducted a molecular analysis of Corpoica’s cacao collection and a morphological characterization of some accessions with the goal to study its genetic diversity and population structure and, to select interesting accessions for the cacao’s breeding program. Phenotypic evaluation was performed based on 18 morphological traits and 4 biochemical traits. PCA analysis of morphological traits explained 60.6% of the total variation in seven components and 100% of the total variation of biochemical traits in four components, grouping the collection in 4 clusters for both variables. We explored 565 accessions from Corpoica’s germplasm and 252 accessions from reference populations using 96 single nucleotide polymorphism (SNP) molecular markers. Molecular patterns of cacao Corpoica’s collection were obtained amplifying specific alleles in a Fluidigm platform that used integrated circuits of fluids. Corpoica’s collection showed highest genetic diversity [Expected Heterozygosity (HE = 0.314), Observed Heterozygosity (HO = 0.353)] that is reduced when reference populations were included in the dataset (HE = 0.294, HO = 0.261). The collection was divided into four clusters based on population structure analysis. Cacao accessions from distinct groups showed some taxonomic concordance and reflected their geographic origins. For instance, accessions classified as Criollo were clearly differentiated in one group and we identified two new Colombian genetic groups. Using a number of allelic variations based on 87 SNP markers and 22 different morphological/biochemical traits, a core collection with a total of 232 accessions was selected as a primary genetic resource for cacao breeders.