Miracle-dz/UniFAR-FTUs huggingface dataset:
Spatial Patterns in Herbivory on a Coral Reef Are Influenced by Structural Complexity but Not by Algal Traits

Background Patterns of herbivory can alter the spatial structure of ecosystems, with important consequences for ecosystem functions and biodiversity. While the factors that drive spatial patterns in herbivory in terrestrial systems are well established, comparatively less is known about what influences the distribution of herbivory in coral reefs. Methodology and Principal Findings We quantified spatial patterns of macroalgal consumption in a cross-section of Ningaloo Reef (Western Australia). We used a combination of descriptive and experimental approaches to assess the influence of multiple macroalgal traits and structural complexity in establishing the observed spatial patterns in macroalgal herbivory, and to identify potential feedback mechanisms between herbivory and macroalgal nutritional quality. Spatial patterns in macroalgal consumption were best explained by differences in structural complexity among habitats. The biomass of herbivorous fish, and rates of herbivory were always greater in the structurally-complex coral-dominated outer reef and reef flat habitats, which were also characterised by high biomass of herbivorous fish, low cover and biomass of macroalgae and the presence of unpalatable algae species. Macroalgal consumption decreased to undetectable levels within 75 m of structurally-complex reef habitat, and algae were most abundant in the structurally-simple lagoon habitats, which were also characterised by the presence of the most palatable algae species. In contrast to terrestrial ecosystems, herbivory patterns were not influenced by the distribution, productivity or nutritional quality of resources (macroalgae), and we found no evidence of a positive feedback between macroalgal consumption and the nitrogen content of algae. Significance This study highlights the importance of seascape-scale patterns in structural complexity in determining spatial patterns of macroalgal consumption by fish. Given the importance of herbivory in maintaining the ability of coral reefs to reorganise and retain ecosystem functions following disturbance, structural complexity emerges as a critical feature that is essential for the healthy functioning of these ecosystems.
Identification of a Major QTL That Alters Flowering Time at Elevated [CO2] in Arabidopsis thaliana

Background The transition from vegetative to reproductive stages marks a major milestone in plant development. It is clear that global change factors (e.g., increasing [CO2] and temperature) have already had and will continue to have a large impact on plant flowering times in the future. Increasing atmospheric [CO2] has recently been shown to affect flowering time, and may produce even greater responses than increasing temperature. Much is known about the genes influencing flowering time, although their relevance to changing [CO2] is not well understood. Thus, we present the first study to identify QTL (Quantitative Trait Loci) that affect flowering time at elevated [CO2] in Arabidopsis thaliana. Methodology/Principal Findings We developed our mapping population by crossing a genotype previously selected for high fitness at elevated [CO2] (SG, Selection Genotype) to a Cape Verde genotype (Cvi-0). SG exhibits delayed flowering at elevated [CO2], whereas Cvi-0 is non-responsive to elevated [CO2] for flowering time. We mapped one major QTL to the upper portion of chromosome 1 that explains 1/3 of the difference in flowering time between current and elevated [CO2] between the SG and Cvi-0 parents. This QTL also alters the stage at which flowering occurs, as determined from higher rosette leaf number at flowering in RILs (Recombinant Inbred Lines) harboring the SG allele. A follow-up study using Arabidopsis mutants for flowering time genes within the significant QTL suggests MOTHER OF FT AND TFL1 (MFT) as a potential candidate gene for altered flowering time at elevated [CO2]. Conclusion/Significance This work sheds light on the underlying genetic architecture that controls flowering time at elevated [CO2]. Prior to this work, very little to nothing was known about these mechanisms at the genomic level. Such a broader understanding will be key for better predicting shifts in plant phenology and for developing successful crops for future environments.
Human CHD1 is required for early DNA-damage signaling and is uniquely regulated by its N terminus

Abstract CHD1 is a conserved chromatin remodeling enzyme required for development and linked to prostate cancer in adults, yet its role in human cells is poorly understood. Here, we show that targeted disruption of the CHD1 gene in human cells leads to a defect in early double-strand break (DSB) repair via homologous recombination (HR), resulting in hypersensitivity to ionizing radiation as well as PARP and PTEN inhibition. CHD1 knockout cells show reduced H2AX phosphorylation (γH2AX) and foci formation as well as impairments in CtIP recruitment to the damaged sites. Chromatin immunoprecipitation following a single DSB shows that the reduced levels of γH2AX accumulation at DSBs in CHD1-KO cells are due to both a global reduction in H2AX incorporation and poor retention of H2AX at the DSBs. We also identified a unique N-terminal region of CHD1 that inhibits the DNA binding, ATPase, and chromatin assembly and remodeling activities of CHD1. CHD1 lacking the N terminus was more active in rescuing the defects in γH2AX formation and CtIP recruitment in CHD1-KO cells than full-length CHD1, suggesting the N terminus is a negative regulator in cells. Our data point to a role for CHD1 in the DSB repair process and identify a novel regulatory region of the protein.
The Missing Link in Epstein-Barr Virus Immune Evasion: the BDLF3 Gene Induces Ubiquitination and Downregulation of Major Histocompatibility Complex Class I (MHC-I) and MHC-II

ABSTRACT The ability of Epstein-Barr virus (EBV) to spread and persist in human populations relies on a balance between host immune responses and EBV immune evasion. CD8+ cells specific for EBV late lytic cycle antigens show poor recognition of target cells compared to immediate early and early antigen-specific CD8+ cells. This phenomenon is due in part to the early EBV protein BILF1, whose immunosuppressive activity increases with lytic cycle progression. However, published data suggest the existence of a hitherto unidentified immune evasion protein further enhancing protection against late EBV antigen-specific CD8+ cells. We have now identified the late lytic BDLF3 gene as the missing link accounting for efficient evasion during the late lytic cycle. Interestingly, BDLF3 also contributes to evasion of CD4+ cell responses to EBV. We report that BDLF3 downregulates expression of surface major histocompatibility complex (MHC) class I and class II molecules in the absence of any effect upon other surface molecules screened, including CD54 (ICAM-1) and CD71 (transferrin receptor). BDLF3 both enhanced internalization of surface MHC molecules and reduced the rate of their appearance at the cell surface. The reduced expression of surface MHC molecules correlated with functional protection against CD8+ and CD4+ T cell recognition. The molecular mechanism was identified as BDLF3-induced ubiquitination of MHC molecules and their subsequent downregulation in a proteasome-dependent manner. IMPORTANCE Immune evasion is a necessary feature of viruses that establish lifelong persistent infections in the face of strong immune responses. EBV is an important human pathogen whose immune evasion mechanisms are only partly understood. Of the EBV immune evasion mechanisms identified to date, none could explain why CD8+ T cell responses to late lytic cycle genes are so infrequent and, when present, recognize lytically infected target cells so poorly relative to CD8+ T cells specific for early lytic cycle antigens. The present work identifies an additional immune evasion protein, BDLF3, that is expressed late in the lytic cycle and impairs CD8+ T cell recognition by targeting cell surface MHC class I molecules for ubiquitination and proteasome-dependent downregulation. Interestingly, BDLF3 also targets MHC class II molecules to impair CD4+ T cell recognition. BDLF3 is therefore a rare example of a viral protein that impairs both the MHC class I and class II antigen-presenting pathways.
Tissue-Specific Salmonella Typhimurium Gene Expression during Persistence in Pigs

Salmonellosis caused by Salmonella Typhimurium is one of the most important bacterial zoonotic diseases. The bacterium persists in pigs resulting in asymptomatic ‘carrier pigs’, generating a major source for Salmonella contamination of pork. Until now, very little is known concerning the mechanisms used by Salmonella Typhimurium during persistence in pigs. Using in vivo expression technology (IVET), a promoter-trap method based on ΔpurA attenuation of the parent strain, we identified 37 Salmonella Typhimurium genes that were expressed 3 weeks post oral inoculation in the tonsils, ileum and ileocaecal lymph nodes of pigs. Several genes were expressed in all three analyzed organs, while other genes were only expressed in one or two organs. Subsequently, the identified IVET transformants were pooled and reintroduced in pigs to detect tissue-specific gene expression patterns. We found that efp and rpoZ were specifically expressed in the ileocaecal lymph nodes during Salmonella peristence in pigs. Furthermore, we compared the persistence ability of substitution mutants for the IVET-identified genes sifB and STM4067 to that of the wild type in a mixed infection model. The ΔSTM4067::kanR was significantly attenuated in the ileum contents, caecum and caecum contents and faeces of pigs 3 weeks post inoculation, while deletion of the SPI-2 effector gene sifB did not affect Salmonella Typhimurium persistence. Although our list of identified genes is not exhaustive, we found that efp and rpoZ were specifically expressed in the ileocaecal lymph nodes of pigs and we identified STM4067 as a factor involved in Salmonella persistence in pigs. To our knowledge, our study is the first to identify Salmonella Typhimurium genes expressed during persistence in pigs.
Properties of Aluminum Filled Polypropylene Composites

Polymers and metals have a long history of use in diverse applications. Metal filled polymer composites are nothing new, as the first attempt to combine these two classes of materials was made in the earlier years of the 20th century. The composites made by incorporation of powdery metal fillers into thermoplastic polymers combine the advantageous properties of metals and plastics. They offer light weight, resistance to corrosion, rapid fabrication rates and a wide range of moduli etc. In the present study, aluminum filled polypropylene (PP) composites with different filler particle shapes and filler loadings varying from 0% to 55% by volume were prepared. The effect of filler loadings and filler particle shapes on the properties of the composites was identified. The percolation concentrations were between 15% and 30% by volume for flaky aluminium filled PP composites, whereas with spherical aluminium particles the percolation concentrations were between 30% and 45% by volume. A steep decrease in electrical resistivity and a pronounced decrease in tensile strength and elongation at break on addition of the metal filler occurred for all investigated systems. Thermal characterization studies showed that the addition of aluminium reduced the crystallinity of the polypropylene and slightly retarded its thermal degradation. High void levels must be taken into account in evaluating the results.
Own Song Selectivity in the Songbird Auditory Pathway: Suppression by Norepinephrine

Background Like human speech, birdsong is a learned behavior that supports species and individual recognition. Norepinephrine is a catecholamine suspected to play a role in song learning. The goal of this study was to investigate the role of norepinephrine in bird's own song selectivity, a property thought to be important for auditory feedback processes required for song learning and maintenance. Methodology/Principal Findings Using functional magnetic resonance imaging, we show that injection of DSP-4, a specific noradrenergic toxin, unmasks own song selectivity in the dorsal part of NCM, a secondary auditory region. Conclusions/Significance The level of norepinephrine throughout the telencephalon is known to be high in alert birds and low in sleeping birds. Our results suggest that norepinephrine activity can be further decreased, giving rise to a strong own song selective signal in dorsal NCM. This latent own song selective signal, which is only revealed under conditions of very low noradrenergic activity, might play a role in the auditory feedback and/or the integration of this feedback with the motor circuitry for vocal learning and maintenance.
Fault Detection and Diagnosis System for a Three-Phase Inverter Using a DWT-Based Artificial Neural Network

Inverters are considered the basic building blocks of industrial electrical drive systems that are widely used for various applications; however, the failure of electronic switches mainly affects the constancy of these inverters. For safe and reliable operation of an electrical drive system, faults in power electronic switches must be detected by an efficient system that is capable of identifying the type of faults. In this paper, an open switch fault identification technique for a three-phase inverter is presented. Single, double, and triple switching faults can be diagnosed using this method. The detection mechanism is based on stator current analysis. Discrete wavelet transform (DWT) using Daubechies is performed on the Clarke transformed (-) stator current and features are extracted from the wavelets. An artificial neural network is then used for the detection and identification of faults. To prove the feasibility of this method, a Simulink model of the DWT-based feature extraction scheme using a neural network for the proposed fault detection system in a three-phase inverter with an induction motor is briefly discussed with simulation results. The simulation results show that the designed system can detect faults quite efficiently, with the ability to differentiate between single and multiple switching faults.
The relationship of school breakfast to psychosocial and academic functioning: cross-sectional and longitudinal observations in an inner-city school sample.

OBJECTIVE To determine if a relationship exists between participation in a school breakfast program and measures of psychosocial and academic functioning in school-aged children. METHODS Information on participation in a school breakfast program, school record data, and in-depth interviews with parents and children were collected in 1 public school in Philadelphia, Pa, and 2 public schools in Baltimore, Md, prior to the implementation of a universally free (UF) breakfast program and again after the program had been in place for 4 months. One hundred thirty-three low-income students had complete data before and after the UF breakfast program on school breakfast participation and school-recorded measures, and 85 of these students had complete psychosocial interview data before and after the UF breakfast program. Teacher ratings of behavior before and after the UF breakfast program were available for 76 of these students. RESULTS Schoolwide data showed that prior to the UF breakfast program, 240 (15%) of the 1627 students in the 3 schools were eating a school-supplied breakfast each day. Of the 133 students in the interview sample, 24 (18%) of the students ate a school-supplied breakfast often, 26 (20%) ate a school-supplied breakfast sometimes, and 83 (62%) ate a school-supplied breakfast rarely or never. Prior to the UF breakfast program, students who ate a school-supplied breakfast often or sometimes had significantly higher math scores and significantly lower scores on child-, parent-, and teacher-reported symptom questionnaires than children who ate a school-supplied breakfast rarely or never. At the end of the school term 4 months after the implementation of the UF breakfast program, school-supplied breakfast participation had nearly doubled and 429 (27%) of the 1612 children in the 3 schools were participating in the school breakfast program each day. In the interview sample, almost half of the children had increased their participation. Students who increased their participation in the school breakfast program had significantly greater increases in their math grades and significantly greater decreases in the rates of school absence and tardiness than children whose participation remained the same or decreased. Child and teacher ratings of psychosocial problems also decreased to a significantly greater degree for children with increased participation in the school breakfast program. CONCLUSION Both cross-sectional and longitudinal data from this study provide strong evidence that higher rates of participation in school breakfast programs are associated in the short-term with improved student functioning on a broad range of psychosocial and academic measures.
Population Pharmacokinetics and Exposure–Response Analyses of Eslicarbazepine Acetate Efficacy and Safety in Monotherapy of Partial‐Onset Seizures

Eslicarbazepine acetate (ESL) is a once‐daily oral antiepileptic drug (AED) indicated for partial‐onset seizures (POS). ESL pharmacokinetics (PK) and exposure–response analyses were supported by 2 phase 3 conversion to ESL (1200, 1600 mg) monotherapy studies. The PK model development included 10 phase 1–2 studies (ESL 600–1200 mg daily). Seizure diaries were completed daily; subjects exited if seizures worsened. Exposure–response models were developed for time to study exit, probability of seizure freedom, time to first occurrence of dizziness, headache, and nausea; serum sodium levels were explored. A 1‐compartment model with first‐order absorption/elimination described ESL PK. Clearance and distribution volume were significantly related to body weight and sex. Higher eslicarbazepine minimum concentration (Cmin) and use of 1 baseline AED were associated with significantly lower risk of study exit, whereas eslicarbazepine Cmin was a significant predictor of seizure freedom during the last 4 weeks of monotherapy. Eslicarbazepine exposure and the time to first occurrence of adverse events were not related. A shallow negative relationship described the relationship between change from baseline in serum sodium level and eslicarbazepine exposure. Eslicarbazepine apparent clearance and distribution volume estimates were similar to those reported for ESL adjunctive therapy. Dose adjustment based on body weight was not required. The time to study exit and probability of seizure freedom during the last 4 weeks of monotherapy were weakly related to eslicarbazepine exposure. Because the first occurrence of adverse events or hyponatremia were also not significantly related to eslicarbazepine exposure, dose adjustment using plasma eslicarbazepine concentrations is not supported.
Translational Research Principles of an Effectiveness Trial for Diabetes Care in an Urban African American Population

Purpose Large-scale effectiveness trials designed to translate evidence-based diabetes care to community settings are few. Studies describing these methods among high-risk minority populations are particularly limited. Methods The authors describe Project Sugar, a randomized controlled trial conducted in 2 phases: Project Sugar 1 (1994-1999), which piloted a 4-arm clinic and homebased intervention using nurse case management and community health workers in 186 urban African Americans with type 2 diabetes, and Project Sugar 2 (2000-2005), which examined effectiveness of this intervention among 542 diabetic, urban African Americans. Results and Conclusions Project Sugar had success with regard to recruitment and retention, both in phase 1 (80% rate at 24 months) and phase 2 (>90% at 24 months). Using the RE-AIM framework, planning and research design for Project Sugar 2 is described in detail for elements that contributed to the reach, effectiveness, adoption, implementation, and maintenance of this study within a minority community setting. In addition to successful strategies, challenges to conducting effectiveness trials in an inner-city African American community are identified.
The complete mitochondrial genome of large flying fox, Pteropus vampyrus (Pteropus, Pteropodidae)

Abstract The large flying fox (Pteropus vampyrus) is named after its fox-like face and noted for being one of the largest bats. Here, we reported the complete mitogenome sequence of P. vampyrus, which was 16,554 bp and composed of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one control region, with a base composition of lower G+C content (41.5%). Like other bats, all genes were located on H-strand except for eight tRNA and ND6 genes. Most protein-coding genes started with an ATG codon except for ND2, ND3, and ND5, which initiated with ATA or ATT instead, and terminated with the typical stop codon (TAA/TAG) or a single T or an unexpected codon of AGG. Within the control region, 6 bp repeat (TACGCA) was appeared only nine times, much lower than other published Pteropus species. These results provided basic information for researching Pteropus vampyrus on genetics, phylogeny, and adaptive evolution.
Automatic Segmentation of Anatomical Structures using Deformable Models and Bio-Inspired/Soft Computing

This PhD dissertation is focused on the development of algorithms for the automatic segmentation of anatomical structures in biomedical images, usually the hippocampus in histological images from the mouse brain. Such algorithms are based on computer vision techniques and artificial intelligence methods. More precisely, on the one hand, we take advantage of deformable models to segment the anatomical structure under consideration, using prior knowledge from different sources, and to embed the segmentation into an optimization framework. On the other hand, metaheuristics and classifiers can be used to perform the optimization of the target function defined by the shape model (as well as to automatically tune the system parameters), and to refine the results obtained by the segmentation process, respectively. Three new different methods, with their corresponding advantages and disadvantages, are described and tested. A broad theoretical discussion, together with an extensive introduction to the state of the art, has also been included to provide an overview necessary for understanding the developed methods.
Real-time 3D mapping using a 2D laser scanner and IMU-aided visual SLAM

In this paper, we present a solution to 3D mapping using a 2D laser scanner with pose estimates from an IMU-aided visual SLAM system. Accurate motion estimation of a robot is achieved by visual-inertial fusion based on an extended Kalman filter (EKF). Range measurements scanned on the vertical plane are received constantly by a 2D laser scanner mounted on the robot, which are re-organized as point clouds in Cartesian space. With the pose estimates of the robot, the point clouds can be transformed into the world frame in real time. Furthermore, these point clouds received between two consecutive keyframes of the visual SLAM system are accumulated together into a unit relative to a keyframe, which can be corrected later by loop closing in visual SLAM. The 3D globally consistent map is built simultaneously by gathering these units of point clouds. The proposed approach and its performance are demonstrated and evaluated by our indoor experiments using a Turtlebot mounted with a Kinect camera, an IMU and a 2D laser scanner.