Miracle-dz/UniFAR-FTUs huggingface dataset:
Origins of Glutamatergic Terminals in the Inferior Colliculus Identified by Retrograde Transport and Expression of VGLUT1 and VGLUT2 Genes

Terminals containing vesicular glutamate transporter (VGLUT) 2 make dense axosomatic synapses on tectothalamic GABAergic neurons. These are one of the three types of glutamatergic synapses in the inferior colliculus (IC) identified by one of three combinations of transporter protein: VGLUT1 only, VGLUT2 only, or both VGLUT1 and 2. To identify the source(s) of these three classes of glutamatergic terminals, we employed the injection of Fluorogold (FG) into the IC and retrograde transport in combination with in situ hybridization for VGLUT1 and VGLUT2 mRNA. The distribution of FG-positive soma was consistent with previous reports. In the auditory cortex, all FG-positive cells expressed only VGLUT1. In the IC, the majority of FG-positive cells expressed only VGLUT2. In the intermediate nucleus of the lateral lemniscus, most FG-positive cells expressed VGLUT2, and a few FG-positive cells expressed both VGLUT1 and 2. In the superior olivary complex (SOC), the majority of FG-positive cells expressing VGLUT2 were in the lateral superior olive, medial superior olive, and some periolivary nuclei. Fewer FG-positive cells expressed VGLUT1&2. In the ventral cochlear nucleus, almost all FG-positive cells expressed VGLUT1&2. On the other hand in the dorsal cochlear nucleus, the vast majority of FG-positive cells expressed only VGLUT2. Our data suggest that (1) the most likely sources of VGLUT2 terminals in the IC are the intermediate nucleus of the lateral lemniscus, the dorsal cochlear nucleus, the medial and lateral superior olive, and the IC itself, (2) VGLUT1 terminals in the IC originate only in the ipsilateral auditory cortex, and (3) VGLUT1&2 terminals in IC originate mainly from the VCN with minor contributions from the SOC and the lateral lemniscal nuclei.
Incidence and multivariable correlates of long-term mortality in patients treated with surgical or percutaneous revascularization in the synergy between percutaneous coronary intervention with taxus and cardiac surgery (SYNTAX) trial.

AIMS The aim of this investigation was to determine the incidence and multivariable correlates of long-term (4-year) mortality in patients treated with surgical or percutaneous revascularization in the synergy between percutaneous coronary intervention (PCI) with TAXUS Express and Cardiac Surgery (SYNTAX) trial. METHODS AND RESULTS A total of 1800 patients were randomized to undergo coronary artery bypass graft (CABG) surgery (n = 897) or PCI (n = 903). Prospectively collected baseline and peri- and post-procedural data were used to determine independent correlates of 4-year all-cause death in the CABG and the PCI arms (Cox proportional hazards model). Four-year mortality rates in the CABG and the PCI arms were 9.0% [74 deaths (12 in-hospital)] and 11.8% [104 deaths (16 in-hospital)], respectively (log-rank P-value = 0.063). Censored data comprised 78 patients (8.7%) in the CABG arm, and 24 patients (2.7%) in the PCI arm (log-rank P-value < 0.001). Within the CABG arm, the strongest independent correlates of 4-year mortality were lack of discharge aspirin [hazard ratio (HR) 3.56; 95% CI: 2.04, 6.21; P < 0.001], peripheral vascular disease (PVD) (HR: 2.65; 95% CI: 1.49, 4.72; P = 0.001), chronic obstructive pulmonary disease, age, and serum creatinine. Within the PCI arm, the strongest independent correlate of 4-year mortality was lack of post-procedural anti-platelet therapy (HR: 152.16; 95% CI: 53.57, 432.22; P < 0.001), with 10 reported early (within 45 days) in-hospital deaths secondary to multifactorial causes precluding administration of anti-platelet therapy. Other independent correlates of mortality in the PCI arm included amiodarone therapy on discharge, pre-procedural poor left ventricular ejection fraction, a 'history of gastrointestinal bleeding or peptic ulcer disease', PVD (HR: 2.13; 95% CI: 1.26, 3.60; P = 0.005), age, female gender (HR: 1.60; 95% CI: 1.01, 2.56; P = 0.048), and the SYNTAX score (Per increase in 10 points: HR: 1.25; 95% CI: 1.06, 1.47; P = 0.007). CONCLUSION Independent correlates of 4-year mortality in the SYNTAX trial were multifactorial. Lack of discharge aspirin and lack of post-procedural anti-platelet therapy were the strongest independent correlates of mortality in the CABG and the PCI arms, respectively. Peripheral vascular disease is a common independent correlate of 4-year mortality and may be a marker of the severity of baseline coronary disease and risk of future native coronary disease (and extra-cardiac disease) progression.
The Banff 2007 Working Classification of Skin‐Containing Composite Tissue Allograft Pathology

Composite tissue allotransplantation (CTA) is a recently introduced option for limb replacement and reconstruction of tissue defects. As with other allografts, CTA can undergo immune‐mediated rejection; therefore standardized criteria are required for characterizing and reporting severity and types of rejection. This article documents the conclusions of a symposium on CTA rejection held at the Ninth Banff Conference on Allograft Pathology in La‐Coruňa, Spain, on 26 June 2007, and proposes a working classification, the Banff CTA‐07, for the categorization of CTA rejection. This classification was derived from a consensus discussion session attended by the first authors of three published classification systems, pathologists and researchers from international centers where clinical CTA has been performed. It was open to all attendees to the Banff conference. To the extent possible, the format followed the established National Institutes of Health (NIH) guidelines on Consensus Development Programs. By consensus, the defining features to diagnose acute skin rejection include inflammatory cell infiltration with involvement of epidermis and/or adnexal structures, epithelial apoptosis, dyskeratosis and necrosis. Five grades of severity of rejection are defined. This classification refines proposed schemas, represents international consensus on this topic, and establishes a working collective classification system for CTA reporting of rejection in skin‐containing CTAs.
The effect of study arm on prostate cancer treatment in the large screening trial ERSPC

Prostate cancer (PC) mortality is the most valid end‐point in screening trials, but could be influenced by the choice of initial treatment if treatment has an effect on mortality. In this study, PC treatment was compared between the screening and control arms in a screening trial. Data were collected from the European Randomized Study of Screening for Prostate Cancer (ERSPC). The characteristics and initial treatment of PC cases detected in the screening and the control arm were compared. Polytomous logistic regression analysis was used to assess the influence of study arm on treatment, adjusting for potential confounders and with statistical imputation of missing values. A total of 8,389 PC cases were detected, 5,422 in the screening arm and 3,145 in the control arm. Polytomous regression showed that trial arm was associated with treatment choice after correction for missing values, especially in men with high‐risk PC. A control subject with high‐risk PC was more likely than a screen subject to receive radiotherapy (OR: 1.43, 95% CI: 1.01–2.05, p = 0.047), expectant management (OR: 2.92, 95% CI: 1.33–6.42, p = 0.007) or hormonal treatment (OR: 1.77, 95% CI: 1.07–2.94, p = 0.026) instead of radical prostatectomy. However, trial arm had only a minor role in treatment choice compared to other variables. In conclusion, a small effect of trial arm on treatment choice was seen, particularly in men with high‐risk PC. Therefore, differences in treatment between arms are unlikely to play a major role in the interpretation of the results of the ERSPC.
Brief Communication HUMAN SCALP RECORDED SIGMA ACTIVITY IS MODULATED BY SLOW EEG OSCILLATIONS DURING DEEP SLEEP

The EEG during deep sleep exhibits a distinct cortically generated slow oscillation of around and below 1 Hz which can be distinguished from other delta (0.5 3.5 Hz) activity. Intracranial studies showed that this slow oscillation triggers and groups cortical network firing. In the present study, we examined whether the phases of the slow oscillation during sleep stage 4 are correlated with the magnitude of sigma (12 16 Hz) and gamma (>20 Hz) scalp activity. For this purpose, 10-min segments of uninterrupted stage 4 sleep EEG from 9 subjects were analyzed by applying wavelet techniques. We found that scalp recorded sigma, but not gamma, activity is modulated by the phases of the slow oscillation during deep sleep. Enhancement of sigma activity was observed to be triggered by the peak of the surface positive slow wave component, whereas reduction of sigma activity started around the peak of the negative component.
Induced polymerization of mammalian acetyl-CoA carboxylase by MIG12 provides a tertiary level of regulation of fatty acid synthesis

Acetyl-CoA carboxylase (ACC), the first committed enzyme in fatty acid (FA) synthesis, is regulated by phosphorylation/dephosphorylation, transcription, and an unusual mechanism of protein polymerization. Polymerization of ACC increases enzymatic activity and is induced in vitro by supraphysiological concentrations of citrate (> 5 mM). Here, we show that MIG12, a 22 kDa cytosolic protein of previously unknown function, binds to ACC and lowers the threshold for citrate activation into the physiological range (< 1 mM). In vitro, recombinant MIG12 induced polymerization of ACC (as determined by nondenaturing gels, FPLC, and electron microscopy) and increased ACC activity by > 50-fold in the presence of 1 mM citrate. In vivo, overexpression of MIG12 in liver induced ACC polymerization, increased FA synthesis, and produced triglyceride accumulation and fatty liver. Thus, in addition to its regulation by phosphorylation and transcription, ACC is regulated at a tertiary level by MIG12, which facilitates ACC polymerization and enhances enzymatic activity.
H11 Kinase/Heat Shock Protein 22 Deletion Impairs Both Nuclear and Mitochondrial Functions of STAT3 and Accelerates the Transition Into Heart Failure on Cardiac Overload

Background— Cardiac overload, a major cause of heart failure, induces the expression of the heat shock protein H11 kinase/Hsp22 (Hsp22). Methods and Results— To determine the specific function of Hsp22 in that context, a knockout mouse model of Hsp22 deletion was generated. Although comparable to wild-type mice in basal conditions, knockout mice exposed to pressure overload developed less hypertrophy and showed ventricular dilation, impaired contractile function, increased myocyte length and accumulation of interstitial collagen, faster transition into heart failure, and increased mortality. Microarrays revealed that hearts from knockout mice failed to transactivate genes regulated by the transcription factor STAT3. Accordingly, nuclear STAT3 tyrosine phosphorylation was decreased in knockout mice. Silencing and overexpression experiments in isolated neonatal rat cardiomyocytes showed that Hsp22 activates STAT3 via production of interleukin-6 by the transcription factor nuclear factor-&kgr;B. In addition to its transcriptional function, STAT3 translocates to the mitochondria where it increases oxidative phosphorylation. Both mitochondrial STAT3 translocation and respiration were also significantly decreased in knockout mice. Conclusions— This study found that Hsp22 represents a previously undescribed activator of both nuclear and mitochondrial functions of STAT3, and its deletion in the context of pressure overload in vivo accelerates the transition into heart failure and increases mortality.
Rare copy number variations in congenital heart disease patients identify unique genes in left-right patterning

Dominant human genetic diseases that impair reproductive fitness and have high locus heterogeneity constitute a problem for gene discovery because the usual criterion of finding more mutations in specific genes than expected by chance may require extremely large populations. Heterotaxy (Htx), a congenital heart disease resulting from abnormalities in left-right (LR) body patterning, has features suggesting that many cases fall into this category. In this setting, appropriate model systems may provide a means to support implication of specific genes. By high-resolution genotyping of 262 Htx subjects and 991 controls, we identify a twofold excess of subjects with rare genic copy number variations in Htx (14.5% vs. 7.4%, P = 1.5 × 10−4). Although 7 of 45 Htx copy number variations were large chromosomal abnormalities, 38 smaller copy number variations altered a total of 61 genes, 22 of which had Xenopus orthologs. In situ hybridization identified 7 of these 22 genes with expression in the ciliated LR organizer (gastrocoel roof plate), a marked enrichment compared with 40 of 845 previously studied genes (sevenfold enrichment, P < 10−6). Morpholino knockdown in Xenopus of Htx candidates demonstrated that five (NEK2, ROCK2, TGFBR2, GALNT11, and NUP188) strongly disrupted both morphological LR development and expression of pitx2, a molecular marker of LR patterning. These effects were specific, because 0 of 13 control genes from rare Htx or control copy number variations produced significant LR abnormalities (P = 0.001). These findings identify genes not previously implicated in LR patterning.
Short-range Impact of Damage on Object Recognition in a Trained Neuronal Network

We investigate the impact of damage on a neuronal network trained to recognise objects. A neuronal network is formed by a set of nodes that represent neurons, and edges that represent the connections between the neurons. To set the stage, we review some existing models that describe the dynamics of individual neurons. We then focus on Integrate-and-Fire (IF) models that we use for this project. We then discuss the numerical method that we use for our model of interacting IF neurons. We then construct our network using a multilayer-network formalism. We consider a simple multilayer network architecture that represents the interactions between the retina and the primal visual cortex (V1) in the brain. We train the system to recognise objects and di erentiate between them using the "continuous transformation learning rule", which is based on relative spike times of pre-synaptic and post-synaptic neurons. To highlight the robustness and stability of the trained neuronal network, we simulate damage a ecting the connections in the network and measure the performance of the deteriorated systems. A network has good performances if the neurons in the V1 representation di erentiate successfully between di erent objects. In this situation, a subset of the neurons responds strongly to the stimuli corresponding to one object and weakly to the other. Our study provides preliminary insights on the impact of damage on connections between two neuronal subsystems.
Simulation of z-dependent dispersion coefficients in tapered photonic crystal fibers

Photonic crystal fibers (PCFs) with a periodic structure of air holes in the cladding are typically made of single material such as silica glass. Various characteristics of solid-core PCFs such as their dispersion coefficients can be tailored by control of their structural parameters like the core and the air-hole diameters as well as the pitch (the hole-to-hole distance) of the cladding. In tapered PCFs, such structural parameters change along the fiber length resulting in z-dependent dispersion coefficients which is in contrast with the un-tapered or ordinary PCFs where their dispersion coefficients are constant with the fiber length. In this paper, we simulate the exact behavior of dispersion coefficients with different orders, ß2 to ß8, as a function of tapering length z in tapered PCFs. The results of this work which have not been reported before are important for many applications in nonlinear optics such as ultra-short pulse propagation and supercontinuum generation in tapered PCFs.
Expression Profiling without Genome Sequence Information in a Non-Model Species, Pandalid Shrimp (Pandalus latirostris), by Next-Generation Sequencing

While the study of phenotypic variation is a central theme in evolutionary biology, the genetic approaches available to understanding this variation are usually limited because of a lack of genomic information in non-model organisms. This study explored the utility of next-generation sequencing (NGS) technologies for studying phenotypic variations between 2 populations of a non-model species, the Hokkai shrimp (Pandalus latirostris; Decapoda, Pandalidae). Before we performed transcriptome analyses using NGS, we examined the genetic and phenotypic differentiation between the populations. Analyses using microsatellite DNA markers suggested that these populations genetically differed from one another and that gene flow is restricted between them. Moreover, the results of our 4-year field observations indicated that the egg traits varied genetically between the populations. Using mRNA extracted from the ovaries of 5 females in each population of Hokkai shrimp, we then performed a transcriptome analysis of the 2 populations. A total of 13.66 gigabases (Gb) of 75-bp reads was obtained. Further, 58,804 and 33,548 contigs for the first and second population, respectively, and 47,467 contigs for both populations were produced by de novo assembly. We detected 552 sequences with the former approach and 702 sequences with the later one; both sets of sequences showed greater than twofold differences in the expression levels between the 2 populations. Twenty-nine sequences were found in both approaches and were considered to be differentially expressed genes. Among them, 9 sequences showed significant similarity to functional genes. The present study showed a de novo assembly approach for the transcriptome of a non-model species using only short-read sequence data, and provides a strategy for identifying sequences showing significantly different expression levels between populations.
Review: protein secondary structure prediction continues to rise.

Methods predicting protein secondary structure improved substantially in the 1990s through the use of evolutionary information taken from the divergence of proteins in the same structural family. Recently, the evolutionary information resulting from improved searches and larger databases has again boosted prediction accuracy by more than four percentage points to its current height of around 76% of all residues predicted correctly in one of the three states, helix, strand, and other. The past year also brought successful new concepts to the field. These new methods may be particularly interesting in light of the improvements achieved through simple combining of existing methods. Divergent evolutionary profiles contain enough information not only to substantially improve prediction accuracy, but also to correctly predict long stretches of identical residues observed in alternative secondary structure states depending on nonlocal conditions. An example is a method automatically identifying structural switches and thus finding a remarkable connection between predicted secondary structure and aspects of function. Secondary structure predictions are increasingly becoming the work horse for numerous methods aimed at predicting protein structure and function. Is the recent increase in accuracy significant enough to make predictions even more useful? Because the recent improvement yields a better prediction of segments, and in particular of beta strands, I believe the answer is affirmative. What is the limit of prediction accuracy? We shall see.
A Comparison of Afghanistan, Yuma, Az, and Manufactured Sands Melted on EB-PVD Thermal Barrier Coatings

Abstract : Sand ingestion into military aircraft turbine engines from desert environments have tested the performance and life of the engine. In particular, turbine section blades and nozzles are coated with a molten glass when the sand is heated to melting temperatures. This molten glass attacks protective coatings on the surface of these parts. Further research is needed to understand the sands behavior on thermal barrier coatings (TBC) when heated to melting temperatures. Also, further research is needed with manufactured sand used in current engine testing to understand the sand ingestion discrepancies between test engines and operational engines. In this study natural sands from Yuma, Arizona, and Afghanistan will be heated to melting temperatures side-by-side with the manufactured sands specifically created for engine testing. All sands will be heated on EB-PVD TBC buttons provided by two companies who produce TBC coated turbine blades for current military engines. The results of manufactured sand should theoretically behave like natural sand and CMAS melted on a thermal barrier coating in order to substantiate past, current, and future testing. Additionally, the two EB-PVD TBCs behavior with the molten and cooled sand will be compared in this study.
Construct Validity of the Violence Risk Scale—Sexual Offender Version for Measuring Sexual Deviance

Previous studies have identified sexual deviance as a particularly strong predictor of sexual recidivism in sex offenders. The present study examined the construct validity (i.e., convergent and discriminant validity) of the three dynamic factor domains (Sexual Deviance, Criminality, Treatment Responsivity) of the Violence Risk Scale— Sexual Offender version (VRS-SO) as well as the Screening Scale for Pedophilic Interests (SSPI; for comparison purposes) with respect to phallometric measures of sexual deviance. VRS-SO and phallometric data were collected from 124 federally incarcerated sex offenders from a maximum security forensic psychiatric facility. The Sexual Deviance factor and SSPI were positively correlated to varying degrees with computed arousal indexes (Percent Full Erection, difference scores) for child stimuli but were not significantly correlated with nondeviant arousal, supporting the convergent and discriminant validity of these measures, respectively. Convergent validity also appeared stronger for sex offender subtypes with child victims. Criminality and Treatment Responsivity did not correlate with male stimuli, although they were positively correlated with arousal to female profiles. The VRS-SO Sexual Deviance factor and some phallometric indexes of deviant arousal (e.g., female children) were predictive of sexual recidivism whereas the SSPI was not. The pattern of findings across analyses broadly supports the construct validity of the VRS-SO in assessing sexual deviance.