Miracle-dz/UniFAR-FTUs huggingface dataset:
HMGB1, a Novel Cytokine-Like Mediator Linking Acute Neuronal Death and Delayed Neuroinflammation in the Postischemic Brain

Cerebral ischemic injury proceeds with excitotoxicity-induced acute neuronal death in the ischemic core and with delayed damage processes in the penumbra. However, knowledge concerning the direct mediators that connect these two processes is limited. Here, we demonstrate that high-mobility group box 1 (HMGB1), a nonhistone DNA-binding protein, is massively released into the extracellular space immediately after ischemic insult and that it subsequently induces neuroinflammation in the postischemic brain. Short hairpin (sh)RNA-mediated HMGB1 downregulation in the postischemic brain suppressed infarct size, microglia activation, and proinflammatory marker induction, indicating that HMGB1 plays a crucial role in the inflammatory process. The proinflammatory cytokine-like function of extracellular HMGB1 was further verified in primary cortical cultures and microglial cultures. HMGB1 was found to accumulate in NMDA-treated primary cortical culture media, and supernatants collected from these cultures were found to trigger microglia activation, the hallmark of brain inflammation. Moreover, treatment with recombinant HMGB1 also induced microglial activation, but HMGB1-depleted supernatant produced by anti-HMGB1 antibody treatment or by HMGB1 shRNA expression did not, thus demonstrating the essential role of HMGB1 in microglial activation. Together, these results indicate that HMGB1 functions as a novel proinflammatory cytokine-like factor that connects excitotoxicity-induced acute damage processes and delayed inflammatory processes in the postischemic brain.
Polygon-assisted JPEG and MPEG compression of synthetic images

Recent advances in realtime image compression and decompression hardware make it possible for a high-performance graphics engine to operate as a rendering server in a networked environment. If the client is a low-end workstation or set-top box, then the rendering task can be split across the two devices. In this paper, we explore one strategy for doing this. For each frame, the server generates a high-quality rendering and a low-quality rendering, subtracts the two, and sends the difference in compressed form. The client generates a matching low quality rendering, adds the decompressed difference image, and displays the composite. Within this paradigm, there is wide latitude to choose what constitutes a high-quality versus low-quality rendering. We have experimented with textured versus untextured surfaces, fine versus coarse tessellation of curved surfaces, Phong versus Gouraud interpolated shading, and antialiased versus nonantialiased edges. In all cases, our polygon-assisted compression looks subjectively better for a fixed network bandwidth than compressing and sending the high-quality rendering. We describe a software simulation that uses JPEG and MPEG-1 compression, and we show results for a variety of scenes. CR Categories: I.4. 2 [Computer Graphics]: Compression — Approximate methods I.3. 2 [Computer Graphics]: Graphics Systems — Distributed/network graphics Additional keywords: client-server graphics, JPEG, MPEG, polygon-assisted compression
Computing Generalized Method of Moments and Generalized Empirical Likelihood with R

This paper shows how to estimate models by the generalized method of moments and the generalized empirical likelihood using the R package gmm. A brief discussion is oered on the theoretical aspects of both methods and the functionality of the package is presented through several examples in economics and nance. It is a modied version of Chauss e (2010) published in the Journal of Statistical Software. It has been adapted to the version 1.4-0.
What do we know about lipoprotein(a)?

ABNORMAL LIPOPROTEIN(A) LEVELS Lp(a) levels vary markedly between subjects and population. In the Copenhagen General Population Study, a typical skewed plasma Lp(a) level distribution was shown, with 80% of the population having levels below 50 mg/dL, and only 20% of the population having levels in the 50–200 mg/dL range [10]. Thus, Lp(a) levels > 50 mg/dL, corresponding to the > 80th percentile, are considered abnormal and a constitute a clinical biomarker of an increased CVD risk. Lowest Lp(a) levels are seen in non-Hispanic whites, higher in Hispanics, and highest in blacks [11]. Of note, however, most studies and metaanalyses indicate an increased CVD risk with Lp(a) levels as low as > 25–30 mg/dL [5].
Msn 2-and Msn 4-Like Transcription Factors Play No Obvious Roles in the Stress Responses of the Fungal Pathogen Candida albicans †

Msn2and Msn4-Like Transcription Factors Play No Obvious Roles in the Stress Responses of the Fungal Pathogen Candida albicans† Susan Nicholls, Melissa Straffon,‡ Brice Enjalbert, André Nantel, Susan Macaskill, Malcolm Whiteway, and Alistair J. P. Brown* Molecular and Cell Biology, Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom, and Eukaryotic Genetics Group, NRC Biotechnology Research Institute, Montreal, Quebec, Canada
Kinetic Model of Pulsed Discharge in Humid Air

This paper is devoted to analysis of humid air plasmas of pulsed discharge application possibilities for heating of thin layers over water surface where the concentration of water molecules in a layer over water surface contains ~0.5%-4% of water molecules in the temperature range 30 °C-110 °C. Main neutral and charged components have been calculated with the help of detailed plasma-chemical code. Considerable generation of ozone has been detected. This can explain the results of successful discharge sterilization experiment.
The Evaluation of Genomic Applications in Practice and Prevention (EGAPP) initiative: methods of the EGAPP Working Group

The Evaluation of Genomic Applications in Practice and Prevention (EGAPP) Initiative, established by the National Office of Public Health Genomics at the Centers for Disease Control and Prevention, supports the development and implementation of a rigorous, evidence-based process for evaluating genetic tests and other genomic applications for clinical and public health practice in the United States. An independent, non-federal EGAPP Working Group (EWG), a multidisciplinary expert panel selects topics, oversees the systematic review of evidence, and makes recommendations based on that evidence. This article describes the EGAPP processes and details the specific methods and approaches used by the EWG.
Experience-dependent plasticity of adult-born neuron connectivity

In contrast to most areas of the adult brain, the dentate gyrus (DG) of the hippocampus is endowed with the capability to generate new neurons life-long. While recent evidence suggests that these adult-born neurons exert specialized functions in information processing compared to pre-existing DG granule neurons, to which extent the establishment of their evolving connectivity may be regulated by experience has been elusive. We recently demonstrated that environmental enrichment (EE) induces a surprising input-specific reorganization of the presynaptic connectivity of adult-born neurons, and that this form of structural plasticity appears to large degree confined to a defined period of few weeks shortly after their generation. Here, I briefly discuss how these findings may uncover a previously unknown layer of complexity in the processes regulating the synaptic integration of adult-born neurons and propose that their circuit incorporation within the pre-existing hippocampal network is not prefigured but rather modulated by specific experiences.
Computational Modelling of Structural Priming in Dialogue

Syntactic priming effects, modelled as increase in repetition probability shortly after a use of a syntactic rule, have the potential to improve language processing components. We model priming of syntactic rules in annotated corpora of spoken dialogue, extending previous work that was confined to selected constructions. We find that speakers are more receptive to priming from their interlocutor in task-oriented dialogue than in spona-neous conversation. Low-frequency rules are more likely to show priming.
Characterizing the nature of embedded young stellar objects through silicate, ice and millimeter observations

Context. Determining the evolutionary stage of a Young Stellar Object (YSO) is of fundamental importance to test star formation theories. Classification schemes for YSOs are based on evaluating the degree of dissipation of the surrounding envelope, whose main effects are the extinction of the optical radiation from the central YSO and re-emission in the far-infrared to millimeter part of the electromagnetic spectrum. Since extinction is a property of column density along the line of sight, the presence of a protoplanetary disk may lead to a misclassification of pre-main sequence stars with disks when viewed edge-on. Aims. We performed radiative transfer calculations to show the effects of different geometries on the main indicators of YSO evolutionary stage. In particular we tested not only the effects on the infrared colors, like the slope α of the flux between 2.2 and 24 μ m, but also on other popular indicators of YSO evolutionary stage, such as the bolometric temperature and the optical depth of silicates and ices. Methods. We used the axisymmetric 3D radiative transfer codes RADMC and RADICAL to calculate the spectral energy distribution including silicates and ice features in a grid of models covering the range of physical properties typical of embedded and pre-main sequence sources. Results. Our set of models compares well with existing observations, supporting the assumed density parametrization and the adopted dust opacities. We show that for systems viewed at intermediate angles (25°-70°) the “classical” indicators of evolution are able to classify the degree of evolution of young stellar objects since they accurately trace the envelope column density, and they all agree with each other. On the other hand, edge-on system are misclassified for inclinations larger than ~65° ± 5°, where the spread is mostly due to the range of mass and the flaring degree of the disk. In particular, silicate emission, typical of pre-main sequence stars with disks, turns into silicate absorption when the disk column density along the line of sight reaches 1 $\times$ 10 22 cm -2 , corresponding e.g. to a 5 $\times$ 10 -3 $M_\odot$ flaring disk viewed at 64°. A similar effect is noticed in all the other classification indicators studied: α , T bol , and the H 2 O and CO 2 ice absorption strengths. This misclassification has a large impact on the nature of the flat-spectrum sources $(\alpha \simeq 0)$, whose number can be explained by simple geometrical arguments without invoking evolution. A reliable classification scheme using a minimal number of observations is constituted by observations of the millimeter flux with both a single dish and an interferometer.
Magnifying Endoscopy with Narrow Band Imaging of Early Gastric Cancer: Correlation with Histopathology and Mucin Phenotype

Background/Aims Magnifying endoscopy with narrow band imaging (ME-NBI) is a useful modality for the detailed visualization of microsurface (MS) and microvascular (MV) structures in the gastrointestinal tract. This study aimed to determine whether the MS and MV patterns in ME-NBI differ according to the histologic type, invasion depth, and mucin phenotype of early gastric cancers (EGCs). Methods The MS and MV patterns of 160 lesions in 160 patients with EGC who underwent ME-NBI before endoscopic or surgical resection were prospectively collected and analyzed. EGCs were categorized as either differentiated or undifferentiated and as either mucosal or submucosal, and their mucin phenotypes were determined via immunohistochemistry of the tumor specimens. Results Differentiated tumors mainly displayed an oval and/or tubular MS pattern and a fine network or loop MV pattern, whereas undifferentiated tumors mainly displayed an absent MS pattern and a corkscrew MV pattern. The destructive MS pattern was associated with submucosal invasion, and this association was more prominent in the differentiated tumors than in the undifferentiated tumors. MUC5AC expression was increased in lesions with either a papillary or absent MS pattern and a corkscrew MV pattern, whereas MUC6 expression was increased in lesions with a papillary MS pattern and a loop MV pattern. CD10 expression was more frequent in lesions with a fine network MV pattern. Conclusions ME-NBI can be useful for predicting the histopathology and mucin phenotype of EGCs.
Admission Hyperglycemia in Critically Ill Sepsis Patients: Association With Outcome and Host Response*

Objectives: To investigate whether admission hyperglycemia is associated with the presentation and/or outcome of sepsis, what the influence of hyperglycemia is on key host responses to sepsis, and whether hyperglycemia differentially affects patients with diabetes mellitus. Design and Setting: A substudy of a prospective observational cohort study was conducted in the intensive care of two tertiary hospitals between January 2011 and July 2013. Patients: Of all consecutive critically ill sepsis patients, admission glucose was used to stratify patients in euglycemia (71–140 mg/dL), mild hyperglycemia (141–199 mg/dL), and severe hyperglycemia (≥ 200 mg/dL), and patients with hypoglycemia were excluded. Fifteen plasma biomarkers providing insight in key host responses implicated in sepsis pathogenesis were measured on admission. Measurements and Main Results: Of 987 sepsis patients with admission glucose levels greater than 70 mg/dL, 519 (52.6%) had normal glucose levels, 267 (27.1%) had mild, and 201 (20.4%) severe hyperglycemia. Admission hyperglycemia was accompanied by mitigated alterations in plasma host response biomarker levels indicative of activation of the cytokine network, the vascular endothelium, and the coagulation system in patients without a history of diabetes. Severe, but not mild, admission hyperglycemia was associated with increased 30-day mortality (adjusted hazard ratio, 1.66 [95% CI, 1.24–2.23]), in both patients without diabetes (adjusted hazard ratio, 1.65 [95% CI, 1.12–2.42]) and with diabetes (adjusted hazard ratio, 1.91 [95% CI, 1.01–3.62]). Conclusion: Admission hyperglycemia is associated with adverse outcome of sepsis irrespective of the presence or absence of preexisting diabetes by a mechanism unrelated to exaggerated inflammation or coagulation.
Evolutive equilibrium selection I: symmetric two player binary choice games

The aim of the paper is the construction of a distributional model which enables the study of the evolutionary dynamics that arise for symmetric games, and the equilibrium selection mechanisms that originate from such processes. The evolution of probability distributions over the state variables is studied using the Fokker-Planck diffusion equation. Equilibrium selection using the ��basin of attraction�� approach, and a selection process suggested by Pontryagin are contrasted. Examples are provided for all generic 2-person symmetric binary choice games.
A novel discharge risk model for patients hospitalised for acute decompensated heart failure incorporating N-terminal pro-B-type natriuretic peptide levels: a European coLlaboration on Acute decompeNsated Heart Failure: ÉLAN-HF Score

Background Models to stratify risk for patients hospitalised for acute decompensated heart failure (ADHF) do not include the change in N-terminal pro-B-type natriuretic peptide (NT-proBNP) levels during hospitalisation. Objective The aim of our study was to develop a simple yet robust discharge prognostication score including NT-proBNP for this notorious high-risk population. Design Individual patient data meta-analyses of prospective cohort studies. Setting Seven prospective cohorts with in total 1301 patients. Patients Our study population was assembled from the seven studies by selecting those patients admitted because of clinically validated ADHF, discharged alive, and NT-proBNP measurements available at admission and at discharge. Main outcome measures The endpoints studied were all-cause mortality and a composite of all-cause mortality and/or first readmission for cardiovascular reason within 180 days after discharge. Results The model that incorporated NT-proBNP levels at discharge as well as the changes in NT-proBNP during hospitalisation in addition to age ≥75 years, peripheral oedema, systolic blood pressure ≤115 mm Hg, hyponatremia at admission, serum urea of ≥15 mmol/L and New York Heart Association (NYHA) class at discharge, yielded the best C-statistic (area under the curve, 0.78, 95% CI 0.74 to 0.82). The addition of NT-proBNP to a reference model significantly improved prediction of mortality as shown by the net reclassification improvement (62%, p<0.001). A simplified model was obtained from the final Cox regression model by assigning weights to individual risk markers proportional to their relative risks. The risk score we designed identified four clinically significant subgroups. The pattern of increasing event rates with increasing score was confirmed in the validation group (BOT-AcuteHF, n=325, p<0.001). Conclusions In patients hospitalised for ADHF, the addition of the discharge NT-proBNP values as well as the change in NT-proBNP to known risk markers, generates a relatively simple yet robust discharge risk score that importantly improves the prediction of adverse events.
Mod-$p$ cohomology growth in $p$-adic analytic towers of 3-manifolds

Let M be a compact 3-manifold with infinite fundamental group . Given a homomorphism from to a p-adic analytic group G with dense image, we describe the possible mod-p homology growth of covers Mn of M determined by the congruence subgroups Gn. If d D dim.G/ > 3, this growth is always non-trivial, growing at least as fast as Vol.Mn/ 1/=d . Mathematics Subject Classification (2010). 22E40.
Contribution of electrophysiological remodelling to generation of anatomical re-entries around the right pulmonary veins in human atrium: a simulation study

Atrial arrhythmias are characterised by rapid and irregular activation of atrium. In this study, the effects of remodelling on ionic currents were incorporated in a model of human atrial action potential and were integrated in a two-dimensional (2D) model of human left atrium tissue including orifices for right pulmonary veins. We examined the effects of atrial remodelling on atrial arrhythmias when ectopic beats between pulmonary veins were applied. Under normal tissue conditions, no re-entry phenomenon was induced. In atrial remodelling, action potential duration (APD), effective refractory period (ERP) and conduction velocity (CV) were decremented and stable re-entries around the right pulmonary veins were produced. Our study suggests that the electrical remodelling is a key factor to generate anatomical re-entries around the pulmonary veins.
The Action of N-terminal Acetyltransferases on Yeast Ribosomal Proteins*

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry was used to determine the state of N-terminal acetylation of 68 ribosomal proteins from a normal strain ofSaccharomyces cerevisiae and from the ard1-Δ,nat3-Δ, and mak3-Δ mutants (4), each lacking a catalytic subunit of three different N-terminal acetyltransferases. A total 30 of the of 68 ribosomal proteins were N-terminal-acetylated, and 24 of these (80%) were NatA substrates, unacetylated in solely the ard1-Δ mutant and having mainly Ac-Ser- termini and a few with Ac-Ala- or Ac-Thr- termini. Only 4 (13%) were NatB substrates, unacetylated in solely thenat3-Δ mutant, and having Ac-Met-Asp- or Ac-Met-Glu- termini. No NatC substrates were uncovered, e.g.unacetylated in solely mak3-Δ mutants, consistent with finding that none of the ribosomal proteins had Ac-Met-Ile-, Ac-Met-Leu-, or Ac-Met-Phe- termini. Interestingly, two new types of the unusual NatD substrates were uncovered, having either Ac-Ser-Asp-Phe- or Ac-Ser-Asp-Ala- termini that were unacetylated in the ard1-Δ mutant, and only partially acetylated in themak3-Δ mutant and, for one case, also only partially in the nat3-Δ mutant. We suggest that the acetylation of NatD substrates requires not only Ard1p and Nat1p, but also auxiliary factors that are acetylated by the Mak3p and Nat3p N-terminal acetyltransferases.
Approaches to disambiguating toponyms

Many approaches have been proposed in recent years in the context of Geographic Information Retrieval (GIR), mostly in order to deal with geographically constrained information in un-structured texts. Most of these approaches share a common scheme: in order to disambiguate a toponym t with n possible referents in a document d, they find a certain number of context toponyms c0,. ,ck that are contained in d. A score for each referent is calculated according to the context toponyms, and the referent with the highest score is selected. According to the method used to calculate the score, Toponym Disambiguation (TD) methods may be grouped into three main categories, as proposed by [7]: • map-based: methods that use an explicit representation of toponyms on a map, for instance to calculate the average distance of unambiguous context toponyms from referents; • knowledge-based: methods that exploit external knowledge sources such as gazetteers, Wikipedia or ontologies to find disambiguation clues; • data-driven or supervised: methods based on machine learning techniques.
On the cyclostationary properties of the 1/f noise of microwave semiconductor devices

This paper addresses, from an experimental perspective, the long-standing question on whether the 1/f noise of microwave semiconductor devices should be considered cyclostationary in compact models. By using a simple instrumentation setup and basic mixer concepts, it will be shown that the external equivalent current noise sources of such devices simply CANNOT be stationary. To demonstrate our ideas, a through experimental analysis was carried out on purely-resistive bridge circuits made up of microwave varactors and transistors under large-signal operation whose DC current component is kept constant. When computing the voltage noise power of specific circuit arrangements, errors in excess of 20dB may be induced if the stationary concept is adopted. The difference between the stationary or cyclostationary concepts will be simulated with the aid of the simulator ADS from Agilent.
Cognitive Radio and Networking Research at Virginia Tech

More than a dozen Wireless @ Virginia Tech faculty are working to address the broad research agenda of cognitive radio and cognitive networks. Our core research team spans the protocol stack from radio and reconfigurable hardware to communications theory to the networking layer. Our work includes new analysis methods and the development of new software architectures and applications, in addition to work on the core concepts and architectures underlying cognitive radios and cognitive networks. This paper describes these contributions and points towards critical future work that remains to fulfill the promise of cognitive radio. We briefly describe the history of work on cognitive radios and networks at Virginia Tech and then discuss our contributions to the core cognitive processing underlying these systems, focusing on our cognitive engine. We also describe developments that support the cognitive engine and advances in radio technology that provide the flexibility desired in a cognitive radio node. We consider securing and verifying cognitive systems and examine the challenges of expanding the cognitive paradigm up the protocol stack to optimize end-to-end network performance. Lastly, we consider the analysis of cognitive systems using game theory and the application of cognitive techniques to problems in dynamic spectrum sharing and control of multiple-input multiple-output radios.