Miracle-dz/UniFAR-FTUs huggingface dataset:
Skeletogenic Fate of Zebrafish Cranial and Trunk Neural Crest

The neural crest (NC) is a major contributor to the vertebrate craniofacial skeleton, detailed in model organisms through embryological and genetic approaches, most notably in chick and mouse. Despite many similarities between these rather distant species, there are also distinct differences in the contribution of the NC, particularly to the calvariae of the skull. Lack of information about other vertebrate groups precludes an understanding of the evolutionary significance of these differences. Study of zebrafish craniofacial development has contributed substantially to understanding of cartilage and bone formation in teleosts, but there is currently little information on NC contribution to the zebrafish skeleton. Here, we employ a two–transgene system based on Cre recombinase to genetically label NC in the zebrafish. We demonstrate NC contribution to cells in the cranial ganglia and peripheral nervous system known to be NC–derived, as well as to a subset of myocardial cells. The indelible labeling also enables us to determine NC contribution to late–forming bones, including the calvariae. We confirm suspected NC origin of cartilage and bones of the viscerocranium, including cartilages such as the hyosymplectic and its replacement bones (hymandibula and symplectic) and membranous bones such as the opercle. The cleithrum develops at the border of NC and mesoderm, and as an ancestral component of the pectoral girdle was predicted to be a hybrid bone composed of both NC and mesoderm tissues. However, we find no evidence of a NC contribution to the cleithrum. Similarly, in the vault of the skull, the parietal bones and the caudal portion of the frontal bones show no evidence of NC contribution. We also determine a NC origin for caudal fin lepidotrichia; the presumption is that these are derived from trunk NC, demonstrating that these cells have the ability to form bone during normal vertebrate development.
Involvement of a P2X7 Receptor in the Acrosome Reaction Induced by ATP in Rat Spermatozoa

The acrosome reaction (AR) is the exocytosis of the acrosomal vesicle in response to different physiological and non‐physiological stimuli. Particularly in mammals, the AR is needed for sperm to fuse with the oocyte plasma membrane, and it occurs only in capacitated sperm. Previous evidence in the literature indicates that extracellular ATP induces the AR in capacitated human and bovine spermatozoa, but its receptor has not yet been identified. The aim of this work was to define a putative ATP receptor in rat spermatozoa using pharmacological and biochemical approaches. We found that ATP induced the AR only in capacitated rat spermatozoa, which was inhibited in the presence of two general inhibitors of ATP receptors (P2 receptors), Suramin, and oxidized ATP (oATP), and one inhibitor of P2X receptor (pyridoxalphosphate‐6‐azophenyl‐2′,4′‐disulfonic acid [PPADS]). In addition, the AR induced by ATP in capacitated rat spermatozoa was inhibited by brilliant blue‐G (BB‐G) and 17‐β‐oestradiol, two blockers of P2X7 receptors. Moreover, the ATP analog 2′(3′)‐O‐(4‐benzoylbenzoyl) ATP (BzATP) was almost 500 times more potent than ATP to induce the AR, which agrees with the pharmacology of a P2X7 receptor. Here, we show the presence of P2X7 receptor by Western blot and its localization in the tail and acrosome by indirect immunofluorescence. Finally, we quantify the presence of ATP in the rat oviduct during the estrous cycle. We found that the ATP concentration within the lumen of the oviduct is similar to those required to induce acrosome reaction, which agree with its role during in vivo fertilization. Therefore, our results strongly suggest that ATP induces the AR in capacitated rat spermatozoa through a P2X7 receptor, which may be functional during in vivo fertilization. J. Cell. Physiol. 230: 3068–3075, 2015. © 2015 Wiley Periodicals, Inc.
Validation of Fecal-based Methods for Monitoring Nutrition and Reproduction of Moose in the Greater Yellowstone Ecosystem

Understanding the influence of habitat and climate on wildlife nutrition, reproduction and demography is a major goal for natural resource managers and ecologists alike. Although both topdown (i.e., predation and disease) and bottom-up (i.e. habitat and nutrition) forces impact demography, the nutritional condition of an animal is an integration of its environment (Parker et al. 2009) and influences reproduction and survival (Clutton-Brock et al. 1987, Keech et al. 2000, Cook et al. 2004), thus allowing for the identification of limiting factors. Researchers and managers must understand which factors limit population growth before mitigating actions can be taken. The demography of large herbivores is affected by juvenile survival (i.e., recruitment; Gaillard et al. 2000, Raithel et al. 2007), and natural resource managers often index recruitment by estimating juvenile-adult female ratios via ground or aerial surveys (Czaplewski et al. 1983). Although these ratios may be a robust characterization of recruitment, they are likely not a good measure of reproductive rate in populations where neonates and juveniles are frequently consumed by large carnivores. Additionally, because pregnancy and subsequent survival of juveniles is strongly influenced by maternal condition (Clutton-Brock et al. 1987, Keech et al. 2000, Cook et al. 2004), recruitment rates alone cannot provide inference regarding the mechanism (i.e. relative strengths of top-down vs. bottom-up limitation) driving variation in reproduction and survival of young. Figure 1.Map of study area within the GYE. Black lines delineate National Park boundaries. Yellow stars indicate sampling areas where ultrasound, GC (CORT), T3, PSPB and fecal progestogen (FP) data were collected. Red stars indicate sampling areas where only PSPB and FP data were collected.
Health behaviour mediates the relationship between Type D personality and subjective health in the general population

Type D personality is associated with unhealthy behaviour and poor subjective health in the general population. This study investigated whether health behaviour mediates the relationship between Type D and subjective health. There were 217 participants who completed measures of Type D, health-related behaviour, physical symptoms and quality of life. Type D individuals reported significantly less healthy behaviour and significantly poorer subjective health than non-Type Ds. In addition, it was found that health behaviour partially mediates these relationships. The study demonstrates that health behaviour may partly explain the relationship between Type D and poor health outcomes.
Semi-automatic Video Assessment System

This paper describes a system for semi-automatic quality assessment of user generated content (UGC) from large events. It uses image and video processing techniques1 combined with a computational quality model that takes in account aesthetics and how human visual perception and attention mechanisms discriminate visual interest. We describe the approach and show that the developed system allows to sort and filter a large stream of UGC in an efficient and timely manner.
Characterization of a head-only aerosol exposure system for nonhuman primates

A well-characterized exposure chamber is necessary to generate reproducible atmospheres for inhalation toxicology studies. The aim of the present study was to characterize a head-only exposure chamber for non-human primates. Aerosols containing bovine serum albumin (BSA) were used to characterize a 16-L dynamic airflow head-only exposure chamber. A 250-ml plastic bottle with a respirator attached located inside the chamber was used to simulate a breathing head. Chamber leak rate, mixing, and aerosol spatial distributions were quantified. The chamber concentration profile was measured at the chamber exhaust using an aerodynamic particle sizer. Aerosol spatial distribution was determined by collecting filter samples at several chamber locations. The particle size distribution was determined by collecting cascade impactor samples at several chamber locations. The estimated chamber leak rate was within standards suggested in the literature. The measured average aerosol residence time was similar to theoretical aerosol residence time, suggesting that the chamber was mixing well. Additionally, the average concentration measured at each of the sampling locations within the chamber was similar, and the within-run coefficients of variation (CV) across all sampling locations was similar to those reported in previously published studies, again suggesting that the aerosol concentration throughout the chamber was uniform. The particle size distribution was similar throughout the exposure chamber. Additionally, the BSA concentration and particle size distributions measured in the breathing zone of the simulated head were not significantly different from measurements made elsewhere in the chamber, suggesting that respiration does not affect the average aerosol concentration or particle size distribution at the mouth.
Clinical Presentation of Atopic Dermatitis by Filaggrin Gene Mutation Status during the First 7 Years of Life in a Prospective Cohort Study

Background Filaggrin null mutations result in impaired skin barrier functions, increase the risk of early onset atopic dermatitis and lead to a more severe and chronic disease. We aimed to characterize the clinical presentation and course of atopic dermatitis associated with filaggrin mutations within the first 7 years of life. Method The COPSAC cohort is a prospective, clinical birth cohort study of 411 children born to mothers with a history of asthma followed during their first 7 years of life with scheduled visits every 6 months, as well as visits for acute exacerbations of dermatitis. Atopic dermatitis was defined in accordance with international guidelines and described at every visit using 35 predefined localizations and 10 different characteristics. Results A total of 170 (43%) of 397 Caucasian children developed atopic dermatitis. The R501X and/or 2282del4 filaggrin null mutations were present in 26 (15%) of children with atopic dermatitis and were primarily associated with predilection to exposed skin areas (especially the cheeks and back of the hands) and an up-regulation of both acute and chronic dermatitis. Furthermore, we found the filaggrin mutations to be associated with a higher number of unscheduled visits (3.6 vs. 2.7; p = 0.04) and more severe (moderate-severe SCORAD 44% vs. 31%; p = 0.14), and widespread dermatitis (10% vs. 6% of the body area, p<0.001) with an earlier age at onset (246 vs. 473 days, p<0.0001) compared to wild-type. Conclusion In children, filaggrin mutations seem to define a specific endotype of atopic dermatitis primarily characterized by predilection to exposed areas of the body, in particular hands and cheeks, and an up-regulation in both acute and chronic morphological markers. Secondary, this endotype is characterized by an early onset of dermatitis and a more severe course, with more generalized dermatitis resulting in more frequent medical consultations.
Distinct Turbulence Structures in Stably Stratified Boundary Layers With Weak and Strong Surface Shear

Turbulence structures and exchange of momentum and heat in the nocturnal stable boundary layer (SBL) show distinct features under different stability conditions prompting interest in their connection. Here eddy covariance data collected at four different heights on a 62‐m meteorological tower over a large open flat terrain are used to characterize different SBL states and associated turbulence structures. In a SBL characterized by strong near‐surface winds, turbulent eddy sizes scale with their observational heights and the SBL experiences enhanced turbulent mixing of momentum and heat throughout (a state hereafter referred to as a “coupled” state). Conversely, in a decoupled SBL, weak winds occur near the surface and turbulent eddies are depressed and detached from the boundary leading to suppressed vertical mixing and layered SBL profiles. Because the transport of momentum and heat to the surface across SBL layers is determined by turbulent eddies, cross‐layer correlation and the aforementioned SBL coupling states can be delineated by distinct turbulence structures.
Hysteresis modeling and inverse feedforward control of an AFM piezoelectric scanner based on nano images

Atomic force microscope(AFM) is a very important instrument with atomistic level resolution, which has been widely employed in the field of micro/nano technology. As a critical part of AFM system, the piezoelectric scanner exists many defects such as hysteresis, creep, and ease of vibration effects, which has become a bottleneck in its further development and application. In this paper, an image-based method by using polar coordinate is presented to model the piezoelectric scanner utilized in AFM, which can effectively avoid the troubles of data acquisition in AFM system. The parameters of its inverse model are identified by the Least-square method(LSM) and an inverse feedforward control strategy is developed. To verify the performance of this strategy, Being CSPM5500 AFM has been employed, the analysis and performance evaluation have been conducted in detail, which demonstrates that the novel hysteresis model and the image-based inverse feedforward control strategy presented in this paper possess a good performance for AFM nano imaging.
State-Aware Dynamic Frequency Selection Scheme for Energy-Harvesting Real-Time Systems

With the increasing deployment of battery-powered embedded systems such as sensor nodes in extreme environments, harvesting renewable energy from ambient environments to achieve near perpetual operation of a system has attracted considerable research efforts in the recent past. In this paper, the authors propose a dynamic frequency selection scheme for energy-harvesting real-time systems. The proposed scheme characterizes the state of a system from the perspectives of system utilization and harvested energy with respect to a certain period of time. A portion of the battery energy is allocated to a group of tasks in the period of time by jointly considering the system utilization and energy state, and the operating frequency is selected based on the allocated energy. The derived operating frequency is fine tuned to further enhance energy efficiency when overflow occurs. Simulation results demonstrate the effectiveness of the proposed scheme. Compared with the state-of-the-art scheme that decouples the energy and timing design constraints, the proposed scheme achieves comparable deadline miss rate when the battery capacity is lower than 5000 J and achieves about 11.5% lower deadline miss rate when the battery capacity is greater than 30 000 J. The proposed scheme also outperforms the benchmarking scheme in energy efficiency. When the battery is near a full charge or overflow occurs, the proposed scheme incurs less energy waste when compared with the benchmarking algorithm, which is favorable for autonomous operation of the system. Furthermore, the time complexity of the proposed scheme is one order of magnitude lower than that of the benchmarking scheme, which makes the proposed scheme well suited for dynamic scheduling.
Pancreas-Specific Sirt1-Deficiency in Mice Compromises Beta-Cell Function without Development of Hyperglycemia

Aims/Hypothesis Sirtuin 1 (Sirt1) has been reported to be a critical positive regulator of glucose-stimulated insulin secretion in pancreatic beta-cells. The effects on islet cells and blood glucose levels when Sirt1 is deleted specifically in the pancreas are still unclear. Methods This study examined islet glucose responsiveness, blood glucose levels, pancreatic islet histology and gene expression in Pdx1Cre; Sirt1ex4F/F mice that have loss of function and loss of expression of Sirt1 specifically in the pancreas. Results We found that in the Pdx1Cre; Sirt1ex4F/F mice, the relative insulin positive area and the islet size distribution were unchanged. However, beta-cells were functionally impaired, presenting with lower glucose-stimulated insulin secretion. This defect was not due to a reduced expression of insulin but was associated with a decreased expression of the glucose transporter Slc2a2/Glut2 and of the Glucagon like peptide-1 receptor (Glp1r) as well as a marked down regulation of endoplasmic reticulum (ER) chaperones that participate in the Unfolded Protein Response (UPR) pathway. Counter intuitively, the Sirt1-deficient mice did not develop hyperglycemia. Pancreatic polypeptide (PP) cells were the only other islet cells affected, with reduced numbers in the Sirt1-deficient pancreas. Conclusions/Interpretation This study provides new mechanistic insights showing that beta-cell function in Sirt1-deficient pancreas is affected due to altered glucose sensing and deregulation of the UPR pathway. Interestingly, we uncovered a context in which impaired beta-cell function is not accompanied by increased glycemia. This points to a unique compensatory mechanism. Given the reduction in PP, investigation of its role in the control of blood glucose is warranted.
Projection structure at 8 Å resolution of the melibiose permease, an Na–sugar co‐transporter from Escherichia coli

The ion‐coupled sugar membrane symporter or co‐transporter melibiose permease (MelB), responsible for α‐galactoside accumulation in Escherichia coli, is a representative member of the glycoside–pentoside–hexuronide family of the vast class of electrochemical potential‐driven porters. Pure solubilized preparations of a MelB recombinant protein were subjected to two‐dimensional crystallization trials and several crystal forms were observed. Two of these appeared as large wide tubes suitable for analysis by electron crystallography. Flattened tubes on carbon support film, embedded in amorphous ice prior to electron cryomicroscopy, showed two‐sided plane group symmetries P121 or P2221, with unit cell dimensions a = 89.9 Å, b = 51.6 Å, γ = 91.9° and a = 188.9 Å, b = 48.8 Å, γ = 90°, respectively. The projection map from the P2221 crystals at 8 Å resolution displayed an asymmetric protein unit consisting of two domains lining a central and curve‐shaped cleft. Together, the MelB monomer could host the 12 predicted transmembrane α‐helices. Overall, the MelB helix packing arrangement compared more favorably with that of the Na+/H+ antiporter NhaA than that of the oxalate antiporter.
Ieee Transactions on Intelligent Transportation Systems 1 Integrating Off-board Cameras and Vehicle On-board Localization for Pedestrian Safety

— Situational awareness for industrial vehicles is crucial to ensure safety of personnel and equipment. While human drivers and onboard sensors are able to detect obstacles and pedestrians within line-of-sight, in complex environments initially occluded or obscured dynamic objects can unpredictably enter the path of a vehicle. We propose a system which integrates a vision-based offboard pedestrian tracking subsystem with an onboard localization and navigation subsystem. This combination enables warnings to be communicated and effectively extends the vehicle controller's field of view to include areas that would otherwise be blind spots. A simple flashing light interface in the vehicle cabin provides a clear and intuitive interface to alert drivers of potential collisions. Alternatively, the system is also be applied to vehicles that have autonomous navigation capabilities, in which case, instead of alert lights, the vehicle is halted or redirected. We implemented and tested the proposed solution on an automated industrial vehicle under autonomous operation and on a human driven vehicle in a full-scale production facility, for a period of four months.
Mmm1p Spans Both the Outer and Inner Mitochondrial Membranes and Contains Distinct Domains for Targeting and Foci Formation*

In the yeast Saccharomyces cerevisiae, the integral membrane protein Mmm1p is required for maintenance of mitochondrial morphology and retention of mitochondrial DNA (mtDNA). Mmm1p localizes to discrete foci on mitochondria that are adjacent to mtDNA nucleoids in the matrix, raising the possibility that this protein plays a direct role in organizing, replicating, or segregating mtDNA. Although Mmm1p has been shown to cross the outer membrane with its C terminus facing the cytoplasm, the location of the N terminus has not been resolved. Here we show that Mmm1p spans both the outer and inner mitochondrial membranes, exposing its N terminus to the matrix. Surprisingly, deletion of the N-terminal extension decreased steady-state levels of the Mmm1 protein but did not affect mitochondrial morphology or mtDNA maintenance. Moreover, expression of Neurospora crassa MMM1, which naturally lacks a long N-terminal extension, substituted for loss of Mmm1p in budding yeast. These results indicate that the matrix-exposed portion of Mmm1p is not essential for mtDNA nucleoid maintenance. Additional studies revealed that the transmembrane segment and C-terminal domain of Mmm1p are required for foci formation and mitochondrial targeting, respectively. Our data suggest that the double membrane-spanning topology of Mmm1p at the membrane contact site is critical for formation of tubular mitochondria.
The L60V Variation in Hepatitis B Virus Core Protein Elicits New Epitope-Specific Cytotoxic T Lymphocytes and Enhances Viral Replication

ABSTRACT Mutations in the core protein (HBc) of hepatitis B virus (HBV) are associated with aggressive hepatitis and advanced liver diseases in chronic hepatitis B (CHB). In this study, we identified the L60V variation in HBc that generates a new HLA-A2-restricted CD8+ T cell epitope by screening an overlapping 9-mer peptide pool covering HBc and its variants. The nonameric epitope V60 was determined by structural and immunogenic analysis. The HBc L60V variation is correlated with hepatic necroinflammation and higher viral levels, and it may be associated with a poor prognosis in CHB patients. Immunization with the defined HBV epitope V60 peptide elicited specific cytotoxic T lymphocyte (CTL)-induced liver injury in HLA-A2+ HBV transgenic mice. In addition, in vitro and in vivo experiments both demonstrated that the HBc L60V variation facilitates viral capsid assembly and increases HBV replication. These data suggest that the HBc L60V variation can impact both HBV replication and HBV-specific T cell responses. Therefore, our work provides further dissection of the impact of the HBc L60V variation, which orchestrates HBV replication, viral persistence, and immunopathogenesis during chronic viral infection.
Minimum Error Rate Training by Sampling the Translation Lattice

Minimum Error Rate Training is the algorithm for log-linear model parameter training most used in state-of-the-art Statistical Machine Translation systems. In its original formulation, the algorithm uses N-best lists output by the decoder to grow the Translation Pool that shapes the surface on which the actual optimization is performed. Recent work has been done to extend the algorithm to use the entire translation lattice built by the decoder, instead of N-best lists. We propose here a third, intermediate way, consisting in growing the translation pool using samples randomly drawn from the translation lattice. We empirically measure a systematic improvement in the BLEU scores compared to training using N-best lists, without suffering the increase in computational complexity associated with operating with the whole lattice.