Miracle-dz/UniFAR-FTUs huggingface dataset:
Modulation of Neural Circuit Operation by Prior Environmental Stress1

Abstract Many organisms are exposed to harsh environmental conditions that may impair the operation of vital neuronal circuits and imperil the animal before these conditions directly cause cell and tissue death. Prior exposure to extreme but sub-lethal stress has long-term effects on neural circuit function enabling motor pattern generators to operate under previously non-permissive conditions. Using several model systems we have been investigating the mechanisms underlying stress-mediated neuroprotection, particularly thermotolerance imparted by a prior heat shock. Prior anoxia and cold shock also impart thermotolerance of motor pattern generation suggesting that different stressors activate common protective pathways. Synaptic transmission, action potential generation and neuronal potassium conductance are modulated by prior heat shock. Pharmacological block of potassium channels, which increases the duration of action potentials and the amplitude of postsynaptic potentials, mimics the thermoprotective effect of a prior heat shock. A universal consequence of heat shock and other stresses is the increased expression of a suite of heat shock proteins of which HSP70 is most closely linked to organismal thermotolerance. Increased levels of HSP70 are sufficient, but not necessary for synaptic thermoprotection. Accumulating evidence suggests the existence of multiple, overlapping pathways for protection and that these mechanisms may be neuron specific depending on their functional roles.
Traveling pulses in a stochastic neural field model of direction selectivity

We analyze the effects of extrinsic noise on traveling pulses in a neural field model of direction selectivity. The model consists of a one-dimensional scalar neural field with an asymmetric weight distribution consisting of an offset Mexican hat function. We first show how, in the absence of any noise, the system supports spontaneously propagating traveling pulses that can lock to externally moving stimuli. Using a separation of time-scales and perturbation methods previously developed for stochastic reaction-diffusion equations, we then show how extrinsic noise in the activity variables leads to a diffusive-like displacement (wandering) of the wave from its uniformly translating position at long time-scales, and fluctuations in the wave profile around its instantaneous position at short time-scales. In the case of freely propagating pulses, the wandering is characterized by pure Brownian motion, whereas in the case of stimulus-locked pulses, it is given by an Ornstein–Uhlenbeck process. This establishes that stimulus-locked pulses are more robust to noise.
Innovation through MIDI : Developing Windows MIDI Applications

Worlds MIDI can be used to investigate the sounds formed by data and relationships that exist in various real and abstract worlds. These worlds include descriptive data or organisational relationships that occur within chemistry, mathematics, artificial life and biology. Descriptive data or data from any process can be converted into MIDI data and performed in real-time. The sounds of cellular automata have been explored by the author (Eales, 1996), and the sounds of protein synthesis is described by Dunn (1997). Analysis of the sound of complex systems may lead to new insights regarding the organisation of such systems.
Alternative end-joining catalyzes class switch recombination in the absence of both Ku70 and DNA ligase 4

The classical nonhomologous end-joining (C-NHEJ) DNA double-strand break (DSB) repair pathway employs the Ku70/80 complex (Ku) for DSB recognition and the XRCC4/DNA ligase 4 (Lig4) complex for ligation. During IgH class switch recombination (CSR) in B lymphocytes, switch (S) region DSBs are joined by C-NHEJ to form junctions either with short microhomologies (MHs; “MH-mediated” joins) or no homologies (“direct” joins). In the absence of XRCC4 or Lig4, substantial CSR occurs via “alternative” end-joining (A-EJ) that generates largely MH-mediated joins. Because upstream C-NHEJ components remain in XRCC4- or Lig4-deficient B cells, residual CSR might be catalyzed by C-NHEJ using a different ligase. To address this, we have assayed for CSR in B cells deficient for Ku70, Ku80, or both Ku70 and Lig4. Ku70- or Ku80-deficient B cells have reduced, but still substantial, CSR. Strikingly, B cells deficient for both Ku plus Lig4 undergo CSR similarly to Ku-deficient B cells, firmly demonstrating that an A-EJ pathway distinct from C-NHEJ can catalyze CSR end-joining. Ku-deficient or Ku- plus Lig4-deficient B cells are also biased toward MH-mediated CSR joins; but, in contrast to XRCC4- or Lig4-deficient B cells, generate substantial numbers of direct CSR joins. Our findings suggest that more than one form of A-EJ can function in CSR.
COOLING OF NEUTRON STARS WITH COLOR SUPERCONDUCTING QUARK CORES

We show that within a recently developed nonlocal chiral quark model the critical density for a phase transition to color superconducting quark matter under neutron star conditions can be low enough for these phases to occur in compact star configurations with masses below 1.3 M ⊙ . We study the cooling of these objects in isolation for different values of the gravitational mass and argue that, if the quark matter phase would allow unpaired quarks, the corresponding hybrid stars would cool too fast. The comparison with observational data puts tight constraints on possible color superconducting quark matter phases. Possible candidates with diquark gaps of the order of 10 keV - 1 MeV such as the "2SC+X" and the color spin locking (CSL) phase are presented.
Characterization of Calcium Oxalates Generated as Biominerals in Cacti1

The chemical composition and morphology of solid material isolated from various Cactaceae species have been analyzed. All of the tested specimens deposited high-purity calcium oxalate crystals in their succulent modified stems. These deposits occurred most frequently as round-shaped druses that sometimes coexist with abundant crystal sand in the tissue. The biominerals were identified either as CaC2O4.2H2O (weddellite) or as CaC2O4.H2O (whewellite). Seven different species from the Opuntioideae subfamily showed the presence of whewellite, and an equal number of species from the Cereoideae subfamily showed the deposition of weddellite. The chemical nature of these deposits was assessed by infrared spectroscopy. The crystal morphology of the crystals was visualized by both conventional light and scanning electron microscopy. Weddellite druses were made up of tetragonal crystallites, whereas those from whewellite were most often recognized by their acute points and general star-like shape. These studies clearly demonstrated that members from the main traditional subfamilies of the Cactaceae family could synthesize different chemical forms of calcium oxalate, suggesting a definite but different genetic control. The direct relationship established between a given Cactaceae species and a definite calcium oxalate biomineral seems to be a useful tool for plant identification and chemotaxonomy.
Chinese hamster ovary cell lysosomes retain pinocytized horseradish peroxidase and in situ-radioiodinated proteins

We used Chinese hamster ovary cells, a cell line of fibroblastic origin, to investigate whether lysosomes are an exocytic compartment. To label lysosomal contents, Chinese hamster ovary cells were incubated with the solute marker horseradish peroxidase. After an 18-h uptake period, horseradish peroxidase was found in lysosomes by cell fractionation in Percoll gradients and by electron microscope cytochemistry. Over a 24-h period, lysosomal horseradish peroxidase was quantitatively retained by Chinese hamster ovary cells and inactivated with a t 1/2 of 6 to 8 h. Lysosomes were radioiodinated in situ by soluble lactoperoxidase internalized over an 18-h uptake period. About 70% of the radioiodine incorporation was pelleted at 100,000 X g under conditions in which greater than 80% of the lysosomal marker enzyme beta-hexosaminidase was released into the supernatant. By one-dimensional electrophoresis, about 18 protein species were present in the lysosomal membrane fraction, with radioiodine incorporation being most pronounced into species of 70,000 to 75,000 daltons. After a 30-min or 2-h chase at 37 degrees C, radioiodine that was incorporated into lysosomal membranes and contents was retained in lysosomes. These observations indicate that lysosomes labeled by fluid-phase pinocytosis are a terminal component of endocytic pathways in fibroblasts.
Endoscopic Instruments and Electrosurgical Unit for Colonoscopic Polypectomy

Colorectal polypectomy is an effective method for prevention of colorectal cancer. Many endoscopic instruments have been used for colorectal polypectomy, such as snares, forceps, endoscopic clips, a Coagrasper, retrieval net, injector, and electrosurgery generator unit (ESU). Understanding the characteristics of endoscopic instruments and their proper use according to morphology and size of the colorectal polyp will enable endoscopists to perform effective polypectomy. I reviewed the characteristics of endoscopic instruments for colorectal polypectomy and their appropriate use, as well as the basic principles and settings of the ESU.
Entropy Minimization SLAM Using Stereo Vision

In this paper we present an information-based approach to solve the SLAM problem using stereo vision. This approach results for an improvement, in terms of both efficiency and robustness, of our early multi-view ICP randomized algorithm. Instead of minimizing an ICP-based cost, we propose the minimization of the entropy of the 2D distribution induced by the projection of the 3D point cloud. In addition we embed both the egomotion/action estimation algorithm which precedes global rectification and the new global rectification algorithm in an autonomous exploration schema. We assume plane-parallel environments and, for the sake of efficiency, we also assume a flat floor and a fixed stereo camera mounted on the robot. We show successful experiments both under tele-operating the robot and under autonomous navigation.
Setting up a STAR Tier 2 Site at Golias/Prague Farm

High Energy Nuclear Physics (HENP) collaborations' experience show that the computing resources available at a single site are often neither sufficient nor satisfy the need of remote collaborators eager to carry their analysis in the fastest and most convenient way. From latencies in the network connectivity to the lack of interactivity, work at distant computing centers is often inefficient. Having fully functional software stack on local resources is a strong enabler of science opportunities for any local group who can afford the time investment. The situation becomes more complex as vast amount of data are often needed to perform meaningful analysis. Prague's heavy-ions group participating in STAR experiment at RHIC has been a strong advocate of local computing as the most efficient means of data processing and physics analyses. To create an environment where science can freely thrive, a Tier 2 computing center was set up at a Regional Computing Center for Particle Physics called "Golias". It is the biggest farm in the Czech Republic fully dedicated for particle physics experiments. We report on our experience in setting up a fully functional Tier 2 center leveraging the minimal locally available human and financial resources. We discuss the solutions chosen to address storage space and analysis issues and the impact on the farms overall functionality. This includes a locally built STAR analysis framework, integration with a local DPM system (a cost effective storage solution), the influence of the availability and quality of the network connection to Tier 0 via a dedicated CESNET/ESnet link and the development of light-weight yet fully automated data transfer tools allowing the movement of entire datasets from BNL (Tier 0) to Golias (Tier 2). We will summarize the impact of the gained computing performance on the efficiency of the local physics group at offline physics analysis and show the feasibility of such a solution that can used by other groups as well.
Reachability Logic

This paper introduces reachability logic , a language-independent seven-rule proof system for deriving reachability properties of systems. The key ingredients of reachability logic are its sentences, which are called reachability rules and generalize the transitions of operational semantics and the Hoare triples of axiomatic semantics, and the Circularity proof rule, which generalizes invariant proof rules for iterative and recursive constructs in axiomatic semantics. The target transition system is described as a set of reachability rules, which are taken as axioms in a reachability logic proof. Typical deﬁ-nition styles which can be read as collections of reachability rules include conventional small-step and big-step operational semantics. The reachability logic proof system is shown sound (in the sense of partial correctness) and relatively complete. The soundness result has also been formalized in Coq, allowing to convert reachability logic proofs into proof certiﬁcates depending only on the operational semantics and the unavoidable domain reasoning. Reachability logic thus eliminates the need to independently deﬁne an axiomatic and an operational semantics for each language, and the non-negligible e ﬀ ort to prove the former sound and complete w.r. t the latter.
Withdrawal of skeletal muscle cells from cell cycle progression triggers differentiation of Toxoplasma gondii towards the bradyzoite stage

Toxoplasma gondii is a widespread intracellular parasite of mammals and birds and an important opportunistic pathogen of humans. Following primary infection, fast‐replicating tachyzoites disseminate within the host and either are subsequently eliminated by the immune system or transform to latent bradyzoites which preferentially persist in brain and muscle tissues. The factors which determine the parasites' tissue distribution during chronic toxoplasmosis are unknown. Here we show that mouse skeletal muscle cells (SkMCs) after differentiation to mature, myosin heavy chain‐positive, polynucleated myotubes, significantly restrict tachyzoite replication and facilitate expression of bradyzoite‐specific antigens and tissue cyst formation. In contrast, proliferating mononuclear myoblasts and control fibroblasts enable vigorous T. gondii replication but do not sustain bradyzoite or tissue cyst formation. Bradyzoite formation correlates with upregulation of testis‐specific Y‐encoded‐like protein‐2 gene expression (Tspyl2) and p21Waf1/Cip1 as well as downregulation of cyclin B1 and absence of DNA synthesis, i.e. a cell cycle arrest of syncytial myotubes. Following infection with T. gondii, myotubes but not myoblasts or fibroblasts further upregulate the negative cell cycle regulator Tspyl2. Importantly, RNA interference‐mediated knock‐down of Tspyl2 abrogates differentiation of SkMCs to myotubes and enables T. gondii to replicate vigorously but abolishes bradyzoite‐specific gene expression and tissue cyst formation. Together, these data indicate that Tspyl2‐mediated host cell cycle withdrawal is a physiological trigger of Toxoplasma stage conversion in mature SkMCs. This finding might explain the preferred distribution of T. gondii tissue cysts in vivo.
Distributed Multiple Description Video Transmission via Noncooperative Games With Opportunistic Players

Recent works have shown how multiple description coding proves to be an effective solution for multimedia streaming over peer-to-peer (P2P) and content delivery networks (CDNs). However, the presence of losses and congestions throughout the network affects the visual quality of the reconstructed sequence at the end terminal. These inconveniences can be mitigated by specifying different levels of Quality of Service, but an optimal packet classification is hard to obtain since P2P and CDN protocols operate at higher protocol layers (ignoring network conditions of the lowest stages), the network can be quite distributed and little information can be available regarding other network segments involved in the transmission. The peculiarities of the transmission scenario require a distributed and robust packet classification strategy that grants both intra-stream and inter-stream diversities among the loss patterns for the different streams. The classification approach presented here is characterized via a noncooperative game, where the different uploading nodes are players/descriptions competing for the allocation of the available network resources. Each player may switch from a selfish strategy to a more cooperative strategy according to its convenience (opportunistic players). Experimental results show that the proposed solution proves to be quite effective under different network scenarios.
Cell-free plasma human immunodeficiency virus type 1 titer assessed by culture and immunocapture-reverse transcription-polymerase chain reaction

The relationship between plasma human immunodeficiency virus type 1 (HIV-1) infectious titer, determined by quantitative fivefold end-point dilution culture, and the detection of genomic HIV-1 RNA by immunocapture-cDNA-polymerase chain reaction was determined. The optimal plasma specimen collection and storage conditions for the use of such virologic markers for clinical trials were also determined. The variabilities in the measurement of infectious HIVLAI titer associated with intra- and interdonor peripheral blood mononuclear cells were 1.2 and 0.86 log10 50% tissue culture infective doses (TCID50)/ml (95% confidence interval range), respectively. Plasma HIV-1 titers did not change significantly after storing whole blood for 6 h either at 4 degrees C or ambient temperature or plasma for a median of 267 days (range, 259 to 482) at -70 degrees C. The detection of genomic HIV-1 RNA encapsulated in viral particles was very consistent, reproducible, and unaffected by either heparin or acid citrate or by multiple freeze-thawing. The HIV-1 RNA titers also appeared to generally correlate with the biologic titer obtained by the microculture assay. The consistency in infectious HIV-1 titer was evaluated by using 27 unfrozen plasma specimens collected from five subjects over 1 to 9 days. The median change in HIV-1 titer relative to baseline was -0.5 log10 TCID50/ml (interquartile range, -1.03 to 0.175 log10). In contrast, no significant change in HIV-1 RNA for the same frozen plasma specimens was noted. As such, immunocapture-cDNA-polymerase chain reaction may be a useful measure of plasma viremia for studying the natural history of HIV disease and assessing response to therapy.
A role for Synapsin in associative learning: the Drosophila larva as a study case.

Synapsins are evolutionarily conserved, highly abundant vesicular phosphoproteins in presynaptic terminals. They are thought to regulate the recruitment of synaptic vesicles from the reserve pool to the readily-releasable pool, in particular when vesicle release is to be maintained at high spiking rates. As regulation of transmitter release is a prerequisite for synaptic plasticity, we use the fruit fly Drosophila to ask whether Synapsin has a role in behavioral plasticity as well; in fruit flies, Synapsin is encoded by a single gene (syn). We tackled this question for associative olfactory learning in larval Drosophila by using the deletion mutant syn(97CS), which had been backcrossed to the Canton-S wild-type strain (CS) for 13 generations. We provide a molecular account of the genomic status of syn(97CS) by PCR and show the absence of gene product on Western blots and nerve-muscle preparations. We found that olfactory associative learning in syn(97CS) larvae is reduced to approximately 50% of wild-type CS levels; however, responsiveness to the to-be-associated stimuli and motor performance in untrained animals are normal. In addition, we introduce two novel behavioral control procedures to test stimulus responsiveness and motor performance after "sham training. " Wild-type CS and syn(97CS) perform indistinguishably also in these tests. Thus, larval Drosophila can be used as a case study for a role of Synapsin in associative learning.
Chapter 10. Peeling of Tomatoes Using Infrared Heating Technology

Chemical peeling of tomatoes is a common industrial practice worldwide. Peeling tomatoes using heat from infrared (IR) radiation presents an emerging chemical-free process, where the IR thermal energy eliminates chemicals used for separating the tomato peel from the flesh. IR peeling eliminates water usage and reduces energy consumption during peeling while improving the quality of the finished product. Because it requires neither chemicals nor a heating medium, such as hot water or steam, IR peeling is categorized as a ‘dry-peeling’ method. This chapter reviews the development of the IR peeling technique, including the IR heating principle, tomato peeling properties, peeling performance, the peeled product quality, the mechanism underlying IR dry-peeling, different types of IR emitters, the design of dry-peeling equipment, and computer simulations of the IR peeling process.
Combining bosentan and sildenafil in pulmonary arterial hypertension patients failing monotherapy: real-world insights

Pulmonary arterial hypertension is a severe disease with a complex pathogenesis, for which combination therapy is an attractive option. This study aimed to assess the impact of sequential combination therapy on both short-term responses and long-term outcomes in a real-world setting. Patients with idiopathic/heritable pulmonary arterial hypertension, or pulmonary arterial hypertension associated with congenital heart disease or connective tissue disease and who were not meeting treatment goals on either first-line bosentan or sildenafil monotherapy, were given additional sildenafil or bosentan and assessed after 3–4 months. Double combination therapy significantly improved clinical and haemodynamic parameters, independent of aetiology or the order of drug administration. Significant improvements in functional class were observed in patients with idiopathic/heritable pulmonary arterial hypertension. The 1-, 3- and 5-year overall survival estimates were 91%, 69% and 59%, respectively. Patients with pulmonary arterial hypertension associated with connective tissue disease had significantly poorer survival rates compared to other aetiologies (p<0.003). The favourable short-term haemodynamic results and good survival rates, observed in patients receiving both bosentan and sildenafil, supports the use of sequential combination therapy in patients failing on monotherapy in a real-world setting. Bosentan and sildenafil combination therapy improved haemodynamics and exercise in PAH patients failing monotherapy http://ow.ly/LGrPm