Miracle-dz/UniFAR-FTUs huggingface dataset:
Ambient CO2, fish behaviour and altered GABAergic neurotransmission: exploring the mechanism of CO2-altered behaviour by taking a hypercapnia dweller down to low CO2 levels

ABSTRACT Recent studies suggest that projected rises of aquatic CO2 levels cause acid–base regulatory responses in fishes that lead to altered GABAergic neurotransmission and disrupted behaviour, threatening fitness and population survival. It is thought that changes in Cl− and HCO3− gradients across neural membranes interfere with the function of GABA-gated anion channels (GABAA receptors). So far, such alterations have been revealed experimentally by exposing species living in low-CO2 environments, like many oceanic habitats, to high levels of CO2 (hypercapnia). To examine the generality of this phenomenon, we set out to study the opposite situation, hypothesizing that fishes living in typically hypercapnic environments also display behavioural alterations if exposed to low CO2 levels. This would indicate that ion regulation in the fish brain is fine-tuned to the prevailing CO2 conditions. We quantified pH regulatory variables and behavioural responses of Pangasianodon hypophthalmus, a fish native to the hypercapnic Mekong River, acclimated to high-CO2 (3.1 kPa) or low-CO2 (0.04 kPa) water. We found that brain and blood pH was actively regulated and that the low-CO2 fish displayed significantly higher activity levels, which were reduced after treatment with gabazine, a GABAA receptor blocker. This indicates an involvement of the GABAA receptor and altered Cl− and HCO3− ion gradients. Indeed, Goldman calculations suggest that low levels of environmental CO2 may cause significant changes in neural ion gradients in P. hypophthalmus. Taken together, the results suggest that brain ion regulation in fishes is fine-tuned to the prevailing ambient CO2 conditions and is prone to disruption if these conditions change. Highlighted Article: Although high levels of CO2 have repeatedly been linked to behavioural disturbance in marine fish, reducing CO2 concentration alters behaviour in a hypercapnia-dwelling fish, suggesting that neural ion balance is fine-tuned to prevailing CO2 conditions.
Throughput Improvement of Molecular Dynamics Simulations Using Reconfigurable Computing

A number of grand-challenge scientific applications are unable to harness Terflops-scale computing capabilities of massively-parallel processing (MPP) systems due to their inherent scaling limits. For these applications, multi-paradigm computing systems that provide additional computing capability per processing node using accelerators are a viable solution. Among various generic and custom-designed accelerators that represent a data-parallel programming paradigm, FPGA devices provide a number of performance enhancing features including concurrency, deep-pipelining and streaming in a flexible manner. We demonstrate acceleration of a production-level biomolecular simulation, in which typical speedups are less than 20 on even the most powerful supercomputing systems, on an FPGA-enabled system with a high-level programming interface. Using accurate models of our FPGA implementation and parallel efficiency results obtained on the Cray XT3 system, we project that the time-to-solution is reduced significantly as compared to the microprocessor-only execution times. A further advantage of computing with FPGA-enabled systems over microprocessor-only implementations is performance sustainability for large-scale problems. The computational complexity of a biomolecular simulation is proportional to its problem sizes, hence the runtime on a microprocessor increases at a much faster rate as compared to FPGA-enabled systems which are capable of providing very high throughput for compute-intensive operations thereby sustaining performance for large-scale problems.
Chimerism of Buccal Membrane Cells in a Monochorionic Dizygotic Twin

No monochorionic dizygotic twins (MCDZTs) with cellular chimerism involving cells other than blood cells have been reported in the literature to date. Here we report a probable first case of MCDZTs with buccal cell chimerism. A 32-year-old woman conceived twins by in vitro fertilization by using 2 cryopreserved blastocysts that were transferred into her uterus. An ultrasound scan at 8 weeks’ gestation showed signs indicative of monochorionic twins. A healthy boy and a healthy girl were born, showing no sexual ambiguity. Cytogenetic analyses and microsatellite studies demonstrated chimerism in blood cells of both twins. Notably, repeated fluorescence in situ hybridization and microsatellite studies revealed chimerism in buccal cells obtained from 1 of the twins. Although the mechanism through which buccal cell chimerism was generated remains to be elucidated, ectopic differentiation of chimeric hematopoietic cells that migrated to the buccal membrane or the cellular transfer between the 2 embryos at the early stage of development might be responsible for the phenomenon. This hypothesis raises an interesting issue regarding embryonic development and cellular differentiation into organs during fetal development. Given the possibility of cryptic chimerism in various organs including gonadal tissues in MCDZTs, close observation will be required to determine whether complications develop in the course of the patients’ growth.
Overexpression of G-Protein-Coupled Receptor 40 Enhances the Mitogenic Response to Epoxyeicosatrienoic Acids

The cytochrome P450 epoxygenase-dependent arachidonic acid metabolites, epoxyeicosatrienoic acids (EETs), are potent survival factors and mitogens for renal epithelial cells, but the molecular identity in the cells that initiates the mitogenic signaling of EETs has remained elusive. We screened kidney cell lines for the expression of G-protein-coupled receptor 40 (GPR40) and found that the porcine renal tubular epithelial cell line LLCPKcl4, which has been previously demonstrated to be sensitive to the mitogenic effect of EETs, expresses higher levels of GPR40 mRNA and protein than the human embryonic kidney cell line HEK293. EETs induced only a weak mitogenic EGFR signaling and mild cell proliferation in HEK293 cells. To determine whether GPR40 expression level is what mediates the mitogenic sensitivity of cells to EETs, we created a human GPR40 (hGPR40) cDNA construct and transfected it into HEK293 cells and picked up a number of stable transfectants. We found that GPR40 overexpression in HEK293 cells indeed significantly enhanced EET-induced cell proliferation and markedly augmented EGFR phosphorylation ERK activation, which were inhibited by the EGFR tyrosine kinase inhibitor, AG1478, or the HB-EGF inhibitor, CRM197. EETs significantly enhanced release of soluble HB-EGF, a natural ligand of EGFR, into the culture medium of hGPR40-transfected HEK293 cells, compared to empty vector-transfected cells. In mouse kidneys, markedly higher level of GPR40 protein was found in the cortex and outer stripe of outer medulla compared to the inner stripe of outer medulla and inner medulla. In situ hybridization confirmed that GPR40 mRNA was localized to a subset of renal tubules in the kidney, including the cortical collecting duct. Thus, this study provides the first demonstration that upregulation of GPR40 expression enhances the mitogenic response to EETs and a relatively high expression level of GPR40 is detected in a subset of tubules including cortical collecting ducts in the mammalian kidney.
Bidirectionally Coupled Network and Road Traffic Simulation for Improved IVC Analysis

Recently, many efforts have been made to develop more efficient Inter-Vehicle Communication (IVC) protocols for on-demand route planning according to observed traffic congestion or incidents, as well as for safety applications. Because practical experiments are often not feasible, simulation of network protocol behavior in Vehicular Ad Hoc Network (VANET) scenarios is strongly demanded for evaluating the applicability of developed network protocols. In this work, we discuss the need for bidirectional coupling of network simulation and road traffic microsimulation for evaluating IVC protocols. As the selection of a mobility model influences the outcome of simulations to a great extent, the use of a representative model is necessary for producing meaningful evaluation results. Based on these observations, we developed the hybrid simulation framework Veins (Vehicles in Network Simulation), composed of the network simulator OMNeT++ and the road traffic simulator SUMO. In a proof-of-concept study, we demonstrate its advantages and the need for bidirectionally coupled simulation based on the evaluation of two protocols for incident warning over VANETs. With our developed methodology, we can advance the state-of-the-art in performance evaluation of IVC and provide means to evaluate developed protocols more accurately.
A SCUBA Map in the Spitzer First Look Survey: Source Catalog and Number Counts

Using the Submillimetre Common-User Bolometer Array (SCUBA) instrument on the James Clerk Maxwell Telescope, we have made a submillimeter mosaic at 850 μm of a subarea of the Spitzer First Look Survey (FLS). Our image covers the central 151 arcmin2 of the northern extragalactic continuous viewing zone field of the FLS to a median 3 σ depth of 8.4 mJy. The image contains six 850 μm sources detected at 3.0 σ or higher significance. We make the catalog of these SCUBA-selected FLS sources available to the community. After correcting for incompleteness and flux bias, we find that the density of sources brighter than 7 mJy in our field is 2.2 × 102 deg-2 (95% Poisson confidence limits), which is consistent with other surveys that probe the bright end of the submillimeter population.
A Novel Wind Power Forecast Model: Statistical Hybrid Wind Power Forecast Technique (SHWIP)

As the result of increasing population and growing technological activities, nonrenewable energy sources, which are the main energy providers, are diminishing day by day. Due to this factor, efforts on efficient utilization of renewable energy sources have increased all over the world. Wind is one of the most significant alternative energy resources. However, in comparison with other renewable energy sources, it is so variable that there is a need for estimating and planning of wind power generation. In this paper, a new statistical short-term (up to 48 h) wind power forecast model, namely statistical hybrid wind power forecast technique (SHWIP), is presented. In the proposed model, weather events are clustered with respect to the most important weather forecast parameters. It also combines the power forecasts obtained from three different numerical weather prediction (NWP) sources and produces a hybridized final forecast. The proposed model has been in operation at the Wind Power Monitoring and Forecast System for Turkey (RITM), and the results of the new model are compared with well-known statistical models and physical models in the literature. The most important characteristics of the proposed model is the need for a lesser amount of historical data while constructing the mathematical model compared with the other statistical models such as artificial neural networks (ANN) and support vector machine (SVM). To produce a reliable forecast, ANN and SVM need at least 1 year of historical data; on the other hand, the proposed SHWIP method's results are applicable even under 1 month of training data, and this is an important feature for the forecast of the newly established wind power plants (WPPs).
Video structuring: From pixels to visual entities

In this paper we propose a method for automatic structuring of video documents. The video is firstly segmented into shots based on a scale space filtering graph partition method. For each detected shot the associated static summary is developed using a leap key-frame extraction method. Based on the representative images obtained, we introduce next a combined spatial and temporal video attention model that is able to recognize moving salient objects. The proposed approach extends the state-of-the-art image region based contrast saliency with a temporal attention model. Different types of motion presented in the current shot are determined using a set of homographic transforms, estimated by recursively applying the RANSAC algorithm on the interest point correspondence. Finally, a decision is taken based on the combined spatial and temporal attention models. The experimental results validate the proposed framework and demonstrate that our approach is effective for various types of videos, including noisy and low resolution data.
SAR raw signal simulation of oil slicks in ocean environments

Synthetic aperture radar (SAR) raw signal simulation is a powerful tool for design of oil slick detection and interpretation systems. In this paper, the ocean simulation issues are presented, and the main problems relating to the oil presence on the sea surface are treated. Attention is focused on the electromagnetic side of the problem, taking account of the sensor signatures, the dielectric, physical-chemical, and geometric nature of the oil slick, and the environmental conditions. The presented SAR simulator is based on an ocean model and an oil slick model. The former makes use of multiscale description of the ocean surface: the distributed surface model for the SAR-ocean interaction is considered by taking into account the nonlinear hydrodynamic effect for the water particle movement. The latter model implements a modification of the ocean spectrum, based on the Marangoni theory and accounting for the nonlinear wave interaction mechanism. However, the proposed SAR raw signal simulator is modular and flexible, thus allowing other possible physical models for modeling the oil slick effect over the ocean spectrum. Meaningful SAR simulation experiments are presented and discussed, elucidating the role of difference on pollutants, oil thickness, wind speed and direction, incident wavelength and angle and other radar parameters. Validation of the simulator is also presented by comparison with experimental data. A striking conclusion of the paper is that higher order moments (from the second on) of oil slick SAR image statistics are quite different compared to those pertinent to an equivalent wind speed decrease on the imaged area. This suggests a convenient way to define new appropriate oil slick signatures.
Activation of PKCβII by PMA Facilitates Enhanced Epithelial Wound Repair through Increased Cell Spreading and Migration

Rapid repair of epithelial wounds is essential for intestinal homeostasis, and involves cell proliferation and migration, which in turn are mediated by multiple cellular signaling events including PKC activation. PKC isoforms have been implicated in regulating cell proliferation and migration, however, the role of PKCs in intestinal epithelial cell (IEC) wound healing is still not completely understood. In the current work we used phorbol 12-myristate 13-acetate (PMA), a well recognized agonist of classical and non-conventional PKC subfamilies to investigate the effect of PKC activation on IEC wound healing. We found that PMA treatment of wounded IEC monolayers resulted in 5.8±0.7-fold increase in wound closure after 24 hours. The PMA effect was specifically mediated by PKCβII, as its inhibition significantly diminished the PMA-induced increase in wound closure. Furthermore, we show that the PKCβII-mediated increase in IEC wound closure after PMA stimulation was mediated by increased cell spreading/cell migration but not proliferation. Cell migration was mediated by PKCβII dependent actin cytoskeleton reorganization, enhanced formation of lamellipodial extrusions at the leading edge and increased activation of the focal adhesion protein, paxillin. These findings support a role for PKCβII in IEC wound repair and further demonstrate the ability of epithelial cells to migrate as a sheet thereby efficiently covering denuded surfaces to recover the intestinal epithelial barrier.
Expressed Sequence Tag Analysis of the Erythrocytic Stage of Plasmodium berghei

Rodent malaria parasites, such as Plasmodium berghei, are practical and useful model organisms for human malaria research because of their analogies to the human malaria in terms of structure, physiology, and life cycle. Exploiting the available genetic sequence information, we constructed a cDNA library from the erythrocytic stages of P. berghei and analyzed the expressed sequence tag (EST). A total of 10,040 ESTs were generated and assembled into 2,462 clusters. These EST clusters were compared against public protein databases and 48 putative new transcripts, most of which were hypothetical proteins with unknown function, were identified. Genes encoding ribosomal or membrane proteins and purine nucleotide phosphorylases were highly abundant clusters in P. berghei. Protein domain analyses and the Gene Ontology functional categorization revealed translation/protein folding, metabolism, protein degradation, and multiple family of variant antigens to be mainly prevalent. The presently-collected ESTs and its bioinformatic analysis will be useful resources to identify for drug target and vaccine candidates and validate gene predictions of P. berghei.
3D Object Retrieval Using Reflective Symmetry

This paper proposes a retrieval system for three dimensional objects using reflective symmetry. For the retrieval method, a reflective symmetric axis with a projector is used. The symmetric plane is calculated by the reflection symmetry, and the depth buffer is calculated for the symmetric plane. Then, by applying the Fourier transform to the depth buffer, the feature vector for the object is generated and retrieved. Considering that most of the objects have symmetrical characteristics, the proposed method of retrieving three dimensional objects using a reflective symmetric surface is an outstanding retrieval system.
Organization and dynamics of human mitochondrial DNA

Heteroplasmic mutations of mitochondrial DNA (mtDNA) are an important source of human diseases. The mechanisms governing transmission, segregation and complementation of heteroplasmic mtDNA-mutations are unknown but depend on the nature and dynamics of the mitochondrial compartment as well as on the intramitochondrial organization and mobility of mtDNA. We show that mtDNA of human primary and immortal cells is organized in several hundreds of nucleoids that contain a mean of 2-8 mtDNA-molecules each. Nucleoids are enriched in mitochondrial transcription factor A and distributed throughout the entire mitochondrial compartment. Using cell fusion experiments, we demonstrate that nucleoids and respiratory complexes are mobile and diffuse efficiently into mitochondria previously devoid of mtDNA. In contrast, nucleoid-mobility was lower within mitochondria of mtDNA-containing cells, as differently labeled mtDNA-molecules remained spatially segregated in a significant fraction (37%) of the polykaryons. These results show that fusion-mediated exchange and intramitochondrial mobility of endogenous mitochondrial components are not rate-limiting for intermitochondrial complementation but can contribute to the segregation of mtDNA molecules and of mtDNA mutations during cell growth and division.
Why is it so difficult to compare treebanks? TIGER and TüBa-D/Z revisited

This paper is a contribution to the ongoing discussion on treebank annotation schemes and their impact on PCFG parsing results. We provide a thorough comparison of two German treebanks: the TIGER treebank and the TuBa-D/Z. We use simple statistics on sentence length and vocabulary size, and more refined methods such as perplexity and its correlation with PCFG parsing results, as well as a Principal Components Analysis. Finally we present a qualitative evaluation of a set of 100 sentences from the TuBa- D/Z, manually annotated in the TIGER as well as in the TuBa-D/Z annotation scheme, and show that even the existence of a parallel subcorpus does not support a straightforward and easy comparison of both annotation schemes.
Survey and analysis of the design issues of a low cost micro power DC-DC step up converter for indoor light energy harvesting applications

This paper discusses the pertinent issues in designing and developing a DC-DC converter for a low cost, micro power indoor light harvesting system using CMOS technology. The different issues associated to this problem are studied and the relevant literature is analysed. The paper surveys and analyses the design options available for the PV cells, step-up voltage converter circuit architecture, maximum power point tracking (MPPT) methods and energy storage devices. From this analysis a possible solution is discussed.
Six DoF Decentralised SLAM

This paper presents a decentralised multivehicle application of simultaneous localisation and mapping (SLAM) for unmanned aerial vehicles (UAVs). The UAVs are equipped with inertial measurement units (IMU), to determine the vehicles position, velocity and attitude, and vision cameras to detect features in the environment. This paper describes an algorithm that enables multiple vehicles to acquire a joint 3D map which can cope with arbitrary latency. The key idea behind this application is to represent the maps in information form (negative log-likelihood) for communication. Experimental results are provided using computer simulation to illustrate the effectiveness of our approach.
Change detection for nonlinear systems; a particle filtering approach

We present a change detection method for nonlinear stochastic systems based on projection particle filtering. The statistic for this method is chosen in such a way that it can be calculated recursively while the computational complexity of the method remains constant with respect to time. We present some simulation results that show the advantages of this method compared to linearization techniques.
Phase I Study of a Bispeci fi c Ligand-Directed Toxin Targeting CD 22 and CD 19 ( DT 2219 ) for Refractory B-cell Malignancies

Purpose: The novel bispecific ligand-directed toxin (BLT) DT2219 consists of a recombinant fusion between the catalytic and translocation enhancing domain of diphtheria toxin (DT) and bispecific single-chain variable fragments (scFV) of antibodies targeting human CD19 and CD22. We conducted a phase I dose-escalation study to assess the safety, maximum tolerated dose, and preliminary efficacy of DT2219 in patients with relapsed/refractory B-cell lymphoma or leukemia. Experimental Design:DT2219 was administered intravenously over 2 hours every other day for 4 total doses. Dose was escalated from0.5mg/kg/day to 80mg/kg/day in nine dose cohorts until a dose-limiting toxicity (DLT) was observed. Results: Twenty-five patients with mature or precursor B-cell lymphoid malignancies expressing CD19 and/or CD22 enrolled to the study. Patients received median 3 prior lines of chemotherapy and 8 failed hematopoietic transplantation. All patients received a single course of DT2219; one patient was retreated. The most common adverse events, including weight gain, low albumin, transaminitis, and fever were transient grade 1–2 and occurred in patients in higher dose cohorts ( 40 mg/kg/day). Two subjects experienced DLT at dose levels 40 and 60 mg/kg. Durable objective responses occurred in 2 patients; one was complete remission after 2 cycles. Correlative studies showed a surprisingly low incidence of neutralizing antibody (30%). Conclusions:We have determined the safety of a novel immunotoxin DT2219 and established its biologically active dose between 40 and 80 mg/kg/day 4. A phase II study exploring repetitive courses of DT2219 is planned. Clin Cancer Res; 21(6);
Dynamic scaling of an adsorption-diffusion process on fractals

We study numerically a dynamic scaling of a diffusion process involving the Langmuir type adsorption. We find dynamic scaling functions in one and two dimensions and compare them with direct numerical simulations. We study further the dynamic scaling law on fractal surfaces. The adsorption–diffusion process obeys the slow fracton dynamics on the fractal surfaces.