Miracle-dz/UniFAR-FTUs huggingface dataset:
Gene expression of tenascin is altered in normal scars and keloids

Tenascin is an extracellular matrix molecule with structural similarity to fibronectin. An increase in extracellular matrix content of both tenascin and fibronectin is associated with early wound healing and with various skin fibroses. However, the relationship of tenascin and fibronectin expression during scar remodeling and the formation of pathologic scars such as keloids is unknown. Expression of tenascin in normal and abnormal human scars was examined and compared with that of fibronectin by immunohistochemistry and in situ hybridization. Tenascin and fibronectin protein and messenger RNA contents were elevated in normal, mature scars relative to quiescent skin, similar to the situation during earlier stages of healing. Tenascin and fibronectin expression was further enhanced in keloids relative to normal skin and scar, and, as has been shown for fibronectin, tenascin expression in uninjured skin adjacent to keloids was indistinguishable from that in quiescent skin from unaffected individuals. These data suggest that tenascin and fibronectin gene expression are coordinated during later stages of normal wound healing and that a defect involving common regulatory elements for these genes is associated with the formation of keloids.
Development of Intelligent Digital Certificate Fuzzer Tool

Present day software testing demands effective ways to find software vulnerabilities through testing. This is especially true in case of network security that employ digital certificates for authentication. Digital certificates are the de-facto standard for verification of users and an integral part of public key infrastructure used to secure channels of communication within networks. An effective approach to testing digital certificates is to implement protocol based fuzzing. Fuzzing in general terms is the process of inserting high volume of invalid or random inputs into a program with the aim of obtaining unexpected results, thus identifying errors and potential vulnerabilities. This paper aims to introduce a protocol aware, user friendly graphical user interface (GUI) based digital certificate fuzzing tool. The tool aims to provide an effective means of black box testing through the use of mutation based fuzzing and OpenSSL to create digital certificates with user provided test-case specific fields. The fuzzed certificates are used as inputs in order to expose defects in digital certificate validation systems.
JunB Inhibits ER Stress and Apoptosis in Pancreatic Beta Cells

Cytokines contribute to pancreatic β-cell apoptosis in type 1 diabetes (T1D) by modulation of β-cell gene expression networks. The transcription factor Activator Protein-1 (AP-1) is a key regulator of inflammation and apoptosis. We presently evaluated the function of the AP-1 subunit JunB in cytokine-mediated β-cell dysfunction and death. The cytokines IL-1β+IFN-γ induced an early and transitory upregulation of JunB by NF-κB activation. Knockdown of JunB by RNA interference increased cytokine-mediated expression of inducible nitric oxide synthase (iNOS) and endoplasmic reticulum (ER) stress markers, leading to increased apoptosis in an insulin-producing cell line (INS-1E) and in purified rat primary β-cells. JunB knockdown β-cells and junB−/− fibroblasts were also more sensitive to the chemical ER stressor cyclopiazonic acid (CPA). Conversely, adenoviral-mediated overexpression of JunB diminished iNOS and ER markers expression and protected β-cells from cytokine-induced cell death. These findings demonstrate a novel and unexpected role for JunB as a regulator of defense mechanisms against cytokine- and ER stress-mediated apoptosis.
A calcium‐ and voltage‐dependent chloride current in developing chick skeletal muscle.

1. Depolarization of embryonic chick myotubes from negative potentials elicits a rapid spike followed by a long‐duration after‐potential. The ionic basis of the long‐duration after‐potential was examined by making intracellular recordings from cultured myotubes, and by making whole‐cell patch‐clamp recordings from myoblasts and myoballs. 2. The peak potential of the long‐duration after‐potential varied with the chloride gradient, suggesting that a conductance increase to chloride is involved in generating the after‐potential. However, a calcium current was also implicated, since lowering the extracellular calcium or replacing extracellular calcium with cobalt abolished the after‐potential. 3. When extracellular calcium was replaced with strontium or barium, short‐duration spikes similar to calcium spikes were observed, but only strontium was able to support activation of long‐duration after‐potentials. Intracellular injection of calcium or strontium into myotubes bathed in calcium‐free extracellular solutions restored the ability of depolarization to evoke an after‐potential. Intracellular injection of magnesium, barium, nickel or cobalt did not restore this ability. These experiments strongly suggested that the long‐duration after‐potential was due to a calcium‐ and voltage‐activated chloride current. 4. Whole‐cell voltage‐clamp recordings from myoballs and myoblasts showed that a large chloride conductance could be activated by depolarization when the internal free calcium concentration was buffered at levels greater than 10(‐7) M. At 2.5 x 10(‐7) M‐calcium, the voltage dependence of activation was steepest in the range of ‐30 to ‐20 mV and the activation kinetics varied with the membrane potential. The time to half‐maximal activation ranged from 0.1 s at positive potentials to greater than 1 s at more negative potentials. The time constant for deactivation was approximately 1 s at ‐50 mV. No inactivation was observed. 5. The selectivity of the chloride current was measured by substituting other anions for chloride. The following permeability series was found: I‐ greater than NO3‐ greater than Br‐ greater than Cl‐ greater than acetate greater than F‐ greater than SO4‐ = glucuronate. Thus anion permeability decreased as the hydration radius increased. 6. Measurements of the resting potential of developing myoblasts and myotubes under ‘physiological’ conditions (37 degrees C, bicarbonate buffer) suggest that the after‐potential acts to depolarize these cells 10‐20 mV above their resting potential (approximately ‐60 mV) for several seconds. 7. We discuss the possibility that the long‐duration after‐potential may be involved in triggering myoblast fusion and in the generation of bursts of spontaneous contractions in developing myotubes.
Recycling Terms into a Partial Parser

Both full-text information retrieval and large scale parsing require text preprocessing to identify strong lexical associations in textual databases. In order to associate linguistic felicity with computational efficiency, we have conceived FASTR a unification-based parser supporting large textual and grammatical databases. The grammar is composed of term rules obtained by tagging and lemmatizing term lists with an online dictionary. Through FASTR, large terminological data can be recycled for text processing purposes. Great stress is placed on the handling of term variations through metarules which relate basic terms to their semantically close morphosyntactic variants.The quality of terminological extraction and the computational efficiency of FASTR are evaluated through a joint experiment with an industrial documentation center. The processing of two large technical corpora shows that the application is scalable to such industrial data and that accounting for term variants results in an increase of recall by 20%. Although automatic indexing is the most straightforward application of FASTR, it can be extended fruitfully to terminological acquisition and compound interpretation.
BILATERAL DIRECTIONAL ASYMMETRY OF THE APPENDICULAR SKELETON OF THE

Directional asymmetry (DA) of the lengths, diameters, and masses of the scapula, humerus, radius, and ulna were analyzed on a sample of 213 harbor porpoises from Denmark and West Greenland. The levels of DA were consistent across yearlings and older animals, mature and immature animals, sexes, and populations. All investigated variables showed significant DA favoring the right side. For the pooled sample, DA of lengths ranged from 0.2% SE 0.1 (ulna) to 1.2% SE 0.1 (scapula). DAs of diameters were 1.5% SE 0.2 for the humerus, 0.6% SE 0.1 for the radius, and 1.3% SE 0.2 for the ulna. DA of mass ranged from 2.8% SE 0.5 (humerus) to 4.3% SE 0.7 (ulna). The humerus and ulna had significantly larger mean diameter/ length ratios on the right side than the left, making them more robust. The large DA of scapula length indicates larger muscle mass associated with the right flipper, while the generally more robust right humerii and ulnae may be designed for higher levels of mechanical stress. These DAs and the examples of lateralized behavior recorded in cetaceans, point to the existence of lateralized use of the flippers at the population level in harbor porpoises and possibly other cetacean species.
A 1.2V-to-0.4V 3.2GHz-to-14.3MHz Power-Efficient 3-Port Register File in 65-nm CMOS

This paper presents a 44.2-mW 3.2-GHz 3-port register file (RF) that demonstrates measured operation from 1.2 V down to 0.4 V. The 32-entry<inline-formula> <tex-math notation="LaTeX">$\times \,32$ </tex-math></inline-formula>-bit/word 2-read/1-write RF is fabricated in TSMC 65-nm low-power low threshold voltage (low-<inline-formula> <tex-math notation="LaTeX">$\text {V}_{\mathrm {t}}$ </tex-math></inline-formula>) CMOS process. A four-transistor read port is presented that permits the design of low-capacitance dynamic local bitlines (LBLs). Switching power in the LBLs and the LBL precharge buffer is thereby reduced. Based on extensive simulation results, the proposed read port is recommended for use in wide-worded RFs, which employ a wide dynamic-OR structure at the LBL stage. The proposed RF outperforms the conventional design in terms of power consumption for frequencies exceeding 3-GHz. The read port exploits intrinsic capacitive coupling to achieve robust operation over a wide voltage range. The architecture of the read port simultaneously enhances robustness of the dynamic bitline by 58.8% as compared to the conventional low-<inline-formula> <tex-math notation="LaTeX">$\text {V}_{\mathrm {t}}$ </tex-math></inline-formula> bitline.
Acoustic Noise Induces Attention Shifts and Reduces Foraging Performance in Three-Spined Sticklebacks (Gasterosteus aculeatus)

Acoustic noise is known to have a variety of detrimental effects on many animals, including humans, but surprisingly little is known about its impacts on foraging behaviour, despite the obvious potential consequences for survival and reproductive success. We therefore exposed captive three-spined sticklebacks (Gasterosteus aculeatus) to brief and prolonged noise to investigate how foraging performance is affected by the addition of acoustic noise to an otherwise quiet environment. The addition of noise induced only mild fear-related behaviours - there was an increase in startle responses, but no change in the time spent freezing or hiding compared to a silent control - and thus had no significant impact on the total amount of food eaten. However, there was strong evidence that the addition of noise increased food-handling errors and reduced discrimination between food and non-food items, results that are consistent with a shift in attention. Consequently, noise resulted in decreased foraging efficiency, with more attacks needed to consume the same number of prey items. Our results suggest that acoustic noise has the potential to influence a whole host of everyday activities through effects on attention, and that even very brief noise exposure can cause functionally significant impacts, emphasising the threat posed by ever-increasing levels of anthropogenic noise in the environment.
Field-driven ultrafast sub-ns programming in W\Al2O3\Ti\CuTe-based 1T1R CBRAM system

We optimize a 90nm-wide CuTe-based 1T1R CBRAM cell for highly controlled and ultrafast programming by engineering Al2O3 electrolyte and Ti buffer layers of appropriate density and thickness resp. By means of electrical and ab initio modeling, we demonstrate that switching is mainly controlled by field-driven motion of Cu+ species. Sub-ns programming is allowed by strong ionic-hopping barrier reduction over short insulating gap. Complete picture of conductance and switching phenomenology is shown in the entire operation range.
Cyclone Activity in the Arctic From an Ensemble of Regional Climate Models (Arctic CORDEX)

The ability of state‐of‐the‐art regional climate models to simulate cyclone activity in the Arctic is assessed based on an ensemble of 13 simulations from 11 models from the Arctic‐CORDEX initiative. Some models employ large‐scale spectral nudging techniques. Cyclone characteristics simulated by the ensemble are compared with the results forced by four reanalyses (ERA‐Interim, National Centers for Environmental Prediction‐Climate Forecast System Reanalysis, National Aeronautics and Space Administration‐Modern‐Era Retrospective analysis for Research and Applications Version 2, and Japan Meteorological Agency‐Japanese 55‐year reanalysis) in winter and summer for 1981–2010 period. In addition, we compare cyclone statistics between ERA‐Interim and the Arctic System Reanalysis reanalyses for 2000–2010. Biases in cyclone frequency, intensity, and size over the Arctic are also quantified. Variations in cyclone frequency across the models are partly attributed to the differences in cyclone frequency over land. The variations across the models are largest for small and shallow cyclones for both seasons. A connection between biases in the zonal wind at 200 hPa and cyclone characteristics is found for both seasons. Most models underestimate zonal wind speed in both seasons, which likely leads to underestimation of cyclone mean depth and deep cyclone frequency in the Arctic. In general, the regional climate models are able to represent the spatial distribution of cyclone characteristics in the Arctic but models that employ large‐scale spectral nudging show a better agreement with ERA‐Interim reanalysis than the rest of the models. Trends also exhibit the benefits of nudging. Models with spectral nudging are able to reproduce the cyclone trends, whereas most of the nonnudged models fail to do so. However, the cyclone characteristics and trends are sensitive to the choice of nudged variables.
Adenylyl Cyclase Activation Modulates Activity-Dependent Changes in Synaptic Strength and Ca2+/Calmodulin-Dependent Kinase II Autophosphorylation

Activation of the Ca2+- and calmodulin-dependent protein kinase II (CaMKII) and its conversion into a persistently activated form by autophosphorylation are thought to be crucial events underlying the induction of long-term potentiation (LTP) by increases in postsynaptic Ca2+. Because increases in Ca2+ can also activate protein phosphatases that oppose persistent CaMKII activation, LTP induction may also require activation of signaling pathways that suppress protein phosphatase activation. Because the adenylyl cyclase (AC)–protein kinase A signaling pathway may provide a mechanism for suppressing protein phosphatase activation, we investigated the effects of AC activators on activity-dependent changes in synaptic strength and on levels of autophosphorylated αCaMKII (Thr286). In the CA1 region of hippocampal slices, briefly elevating extracellular Ca2+ induced an activity-dependent, transient potentiation of synaptic transmission that could be converted into a persistent potentiation by the addition of phosphatase inhibitors or AC activators. To examine activity-dependent changes in αCaMKII autophosphorylation, we replaced electrical presynaptic fiber stimulation with an increase in extracellular K+ to achieve a more global synaptic activation during perfusion of high Ca2+ solutions. In the presence of the AC activator forskolin or the protein phosphatase inhibitor calyculin A, this treatment induced a LTP-like synaptic potentiation and a persistent increase in autophosphorylated αCaMKII levels. In the absence of forskolin or calyculin A, it had no lasting effect on synaptic strength and induced a persistent decrease in autophosphorylated αCaMKII levels. Our results suggest that AC activation facilitates LTP induction by suppressing protein phosphatases and enabling a persistent increase in the levels of autophosphorylated CaMKII.
Aposn Performance Under the Man and Wan Environments

The all-photonic overlaid star network (APOSN) provides a simple architecture for high-speed backbone networks using available optical technologies. We consider in this paper a distributed signaling and scheduling protocol to enable prompt responding and flexible control of traffic demands. A contention-based approach is used for bandwidth allocation, and there is no coordination among the edge switches and the edge switches transmit traffic to the egress switches via the core switch at any time. Two schemes are considered here: the optical burst switching (OBS) operation that is random, as opposed to the more orderly scheduled distributed TDM (DTDM). By studying the operation ranges of various typical parameters for these two schemes as well as their variants, we are able to provide performance tradeoffs and insights into the effect of system parameter settings
Intravenous administration of follistatin: Delivery to the liver and effect on liver regeneration after partial hepatectomy

When 1 μg 125I‐follistatin was administered into a rat intravenously, radioactivity levels in serum decreased rapidly. Analysis with a biexponential equation showed that the initial half‐ life and the terminal half‐life were 4.0 and 130.8 minutes, respectively. After 2 hours of infusion, approximately 9% of the follistatin infused remained in the liver, which was much more than that in kidney, spleen, pancreas, intestine, or lung. Autoradiography of the liver obtained at 24 hours of infusion revealed that numerous grains were located in parenchymal cells. Radioactivity of 125I‐ follistatin in the liver remained elevated until 72 hours and declined markedly thereafter. When a booster shot of 125I‐follistatin was administered at 72 hours, radioactivity in the liver at 120 hours was markedly increased compared with that in rats that received a single shot of 125I‐follistatin. We then examined the effect of intravenous infusion of follistatin on liver regeneration after hepatectomy of 70%. Immediately after the hepatectomy, either 1 microgram follistatin or saline was infused intravenously. In some rats, a booster shot was infused at 72 hours. After 120 hours of hepatectomy of 70%, remnant liver weight, liver regeneration rate, and DNA content were significantly (P < .05) higher in rats that received a booster shot of follistatin at 72 hours than those in control rats. These results indicate that follistatin administered intravenously accumulates in the liver and promotes liver regeneration after partial hepatectomy.
AAA+ ATPases in the Initiation of DNA Replication

All cellular organisms and many viruses rely on large, multi-subunit molecular machines, termed replisomes, to ensure that genetic material is accurately duplicated for transmission from one generation to the next. Replisome assembly is facilitated by dedicated initiator proteins, which serve to both recognize replication origins and recruit requisite replisomal components to the DNA in a cell-cycle coordinated manner. Exactly how imitators accomplish this task, and the extent to which initiator mechanisms are conserved among different organisms have remained outstanding issues. Recent structural and biochemical findings have revealed that all cellular initiators, as well as the initiators of certain classes of double-stranded DNA viruses, possess a common adenine nucleotide-binding fold belonging to the ATPases Associated with various cellular Activities (AAA+) family. This review focuses on how the AAA+ domain has been recruited and adapted to control the initiation of DNA replication, and how the use of this ATPase module underlies a common set of initiator assembly states and functions. How biochemical and structural properties correlate with initiator activity, and how species-specific modifications give rise to unique initiator functions, are also discussed.
High Frequencies of Polyfunctional CD8+ NK Cells in Chronic HIV-1 Infection Are Associated with Slower Disease Progression

ABSTRACT Natural killer (NK) cells are effector and regulatory innate immune cells and play a critical role in the first line of defense against various viral infections. Although previous reports have indicated the vital contributions of NK cells to HIV-1 immune control, nongenetic NK cell parameters directly associated with slower disease progression have not been defined yet. In a longitudinal, retrospective study of 117 untreated HIV-infected subjects, we show that higher frequencies as well as the absolute numbers of CD8+ CD3− lymphocytes are linked to delayed HIV-1 disease progression. We show that the majority of these cells are well-described blood NK cells. In a subsequent cross-sectional study, we demonstrate a significant loss of CD8+ NK cells in untreated HIV-infected individuals, which correlated with HIV loads and inversely correlated with CD4+ T cell counts. CD8+ NK cells had modestly higher frequencies of CD57-expressing cells than CD8− cells, but CD8+ and CD8− NK cells showed no differences in the expression of a number of activating and inhibiting NK cell receptors. However, CD8+ NK cells exhibited a more functional profile, as detected by cytokine production and degranulation. IMPORTANCE We demonstrate that the frequency of highly functional CD8+ NK cells is inversely associated with HIV-related disease markers and linked with delayed disease progression. These results thus indicate that CD8+ NK cells represent a novel NK cell-derived, innate immune correlate with an improved clinical outcome in HIV infection.
Statistics of Chaotic Impedance and Scattering Matrices : The Random Coupling Model

We propose a model to study the statistical properties of the impedance (Z) and scattering (S) matrices of open electromagnetic cavities with several transmission lines or waveguides connected to the cavity. The model is based on assumed properties of chaotic eigenfunctions for the closed system. Analysis of the model successfully reproduces features of the random matrix model believed to be universal, while at the same time incorporating features which are specific to individual systems. Statistical properties of the cavity impedance Z are obtained in terms of the radiation impedance (i.e., the impedance seen at a port with the cavity walls moved to infinity). Effects of wall absorption and nonreciprocal media (e.g., magnetized ferrite) are discussed. Theoretical predictions are tested by direct comparison with numerical solutions for a specific system.