Miracle-dz/UniFAR-FTUs huggingface dataset:
NLRC5/MHC class I transactivator is a target for immune evasion in cancer

Significance Tumor antigen presentation to CD8+ T cells by MHC class I molecules is crucial for immune responses against cancers, whereas the loss of MHC class I is a common immune evasion strategy used by cancers. However, the molecular mechanisms leading to MHC class I deficiency have remained poorly defined. We demonstrate here that MHC class I transactivator (CITA)/NOD-like receptor (NLR) family, caspase recruitment (CARD) domain containing 5 (NLRC5) is a major target for cancer immune evasion. Reduced expression of MHC class I and related genes in cancer is frequently associated with genetic and epigenetic changes in NLRC5. The reduced NLRC5 expression is linked to impaired CD8+ T-cell activation and poor patient prognosis. These data indicate that CITA/NLRC5 is a novel prognostic marker and potential therapeutic target of cancers. Cancer cells develop under immune surveillance, thus necessitating immune escape for successful growth. Loss of MHC class I expression provides a key immune evasion strategy in many cancers, although the molecular mechanisms remain elusive. MHC class I transactivator (CITA), known as “NLRC5” [NOD-like receptor (NLR) family, caspase recruitment (CARD) domain containing 5], has recently been identified as a critical transcriptional coactivator of MHC class I gene expression. Here we show that the MHC class I transactivation pathway mediated by CITA/NLRC5 constitutes a target for cancer immune evasion. In all the 21 tumor types we examined, NLRC5 expression was highly correlated with the expression of MHC class I, with cytotoxic T-cell markers, and with genes in the MHC class I antigen-presentation pathway, including LMP2/LMP7, TAP1, and β2-microglobulin. Epigenetic and genetic alterations in cancers, including promoter methylation, copy number loss, and somatic mutations, were most prevalent in NLRC5 among all MHC class I-related genes and were associated with the impaired expression of components of the MHC class I pathway. Strikingly, NLRC5 expression was significantly associated with the activation of CD8+ cytotoxic T cells and patient survival in multiple cancer types. Thus, NLRC5 constitutes a novel prognostic biomarker and potential therapeutic target of cancers.
The Illusion of Moral Superiority

Most people strongly believe they are just, virtuous, and moral; yet regard the average person as distinctly less so. This invites accusations of irrationality in moral judgment and perception—but direct evidence of irrationality is absent. Here, we quantify this irrationality and compare it against the irrationality in other domains of positive self-evaluation. Participants (N = 270) judged themselves and the average person on traits reflecting the core dimensions of social perception: morality, agency, and sociability. Adapting new methods, we reveal that virtually all individuals irrationally inflated their moral qualities, and the absolute and relative magnitude of this irrationality was greater than that in the other domains of positive self-evaluation. Inconsistent with prevailing theories of overly positive self-belief, irrational moral superiority was not associated with self-esteem. Taken together, these findings suggest that moral superiority is a uniquely strong and prevalent form of “positive illusion,” but the underlying function remains unknown.
Sensorless Control of Salient PMSM Drives in the Transition Region

This paper considers speed and position estimation of salient permanent-magnet synchronous machines (PMSMs). An estimator of phase-locked loop (PLL) type is considered. Signal injection techniques are used in the zero-speed and low-speed regions, while information found in the back electromotive force (EMF) is used for higher speeds. Particular focus is put on the transition region, i.e., the speed region where the estimator switches between signal-injection and back-EMF-based methods. It is shown that the estimator may become unstable for certain setups of machine parameters and operating conditions if the transition region is determined incorrectly. To avoid this instability, design rules for how the transition region should be determined, as well as recommended selections for all parameters introduced, are given. The results of the analysis are also supported with experimental results
Metabolic and functional profiling of the normal rat retina

We established a metabolic and functional profile map of the normal rat retina, given the premise that: 1) amino acid neurochemistry reflects metabolic integrity and cellular identity, and 2) the permeation of a cation channel probe, agmatine (1‐amino‐4‐guanidobutane, AGB), reflects cation channel functionality. The purpose was to provide a unique method of simultaneously assessing the metabolic and functional characteristics of the normal retina, upon which a comparison can be made to disease models. Quantitative pattern recognition analysis of overlapping amino acid and AGB expression profiles was used to provide a statistically robust classification of all neural elements according to their metabolic and functional characteristics. This classification was spatially complete and with single‐cell resolution. The resulting classification demonstrated 28 statistically separable theme classes dominated by characteristic glutamate, GABA, glycine, and/or taurine profiles, with each of the neuronal theme classes containing further subtypes. The inclusion of a functional parameter (AGB mapping) in the classification process nearly doubled the number of neural elements that could be ascribed a neurochemical/cation profile, compared to when amino acid labeling was used alone. Strong endogenous glutamate gated AGB labeling was observed in horizontal cells, rod bipolar cells, cholinergic amacrine cells, and AII amacrine cells. The resulting amino acid and AGB profile matrix constitutes a nomogram for assessing cellular responses to experimental challenges in models of ocular disease. J. Comp. Neurol. 505:92–113, 2007. © 2007 Wiley‐Liss, Inc.
SYNTAX score predicts postoperative atrial fibrillation in patients undergoing on-pump isolated coronary artery bypass grafting surgery

Objective: Atrial fibrillation (AF) is the most common arrhythmia following coronary artery by-pass graft surgery (CABG). The value of SYNTAX score to predict postoperative atrial fibrillation (PoAF) has not been clearly addressed. We aimed to evaluate this relationship in patients undergoing isolated CABG. Methods: This study was designed as a single-center, non-randomized, observational, prospective study. Ninety-four patients undergoing isolated on-pump CABG, who had sinus rhythm and were older than 18 years, were enrolled. Demographic characteristics of the patients were recorded; SYNTAX score was calculated preoperatively for each patient. The univariate and multivariate logistic regression analysis were used to determine for predictors of PoAF. Results: The median SYNTAX score of the enrolled patients was 21, (56–5). PoAF was observed in 31 (33.3%) patients. Univariate logistic regression showed that age, chronic obstructive pulmonary disease (COPD), red blood cell distribution width (RDW), urea, initial troponin I, peak postoperative troponin I, interventricular septum, left atrial diameter, and SYNTAX score were significantly associated with the frequency of PoAF following CABG. An independent association was identified with age [b 0.088, p:0.023, OR: 1.092, 95% CI (1.012–1.179)], COPD [(b: 2.222, p:0.003, OR: 9.228, 95% CI (2.150–39.602)], and SYNTAX score [(b: 0.130, p:0.002, OR: 1.139, 95% CI (1.050–1.235)]. Conclusion: This study showed that a higher SYNTAX score was related to more frequent PoAF in patients undergoing isolated on-pump CABG.
Multimethod latent class analysis

Correct and, hence, valid classifications of individuals are of high importance in the social sciences as these classifications are the basis for diagnoses and/or the assignment to a treatment. The via regia to inspect the validity of psychological ratings is the multitrait-multimethod (MTMM) approach. First, a latent variable model for the analysis of rater agreement (latent rater agreement model) will be presented that allows for the analysis of convergent validity between different measurement approaches (e.g., raters). Models of rater agreement are transferred to the level of latent variables. Second, the latent rater agreement model will be extended to a more informative MTMM latent class model. This model allows for estimating (i) the convergence of ratings, (ii) method biases in terms of differential latent distributions of raters and differential associations of categorizations within raters (specific rater bias), and (iii) the distinguishability of categories indicating if categories are satisfyingly distinct from each other. Finally, an empirical application is presented to exemplify the interpretation of the MTMM latent class model.
Ocean Acidification Accelerates Reef Bioerosion

In the recent discussion how biotic systems may react to ocean acidification caused by the rapid rise in carbon dioxide partial pressure (pCO2) in the marine realm, substantial research is devoted to calcifiers such as stony corals. The antagonistic process – biologically induced carbonate dissolution via bioerosion – has largely been neglected. Unlike skeletal growth, we expect bioerosion by chemical means to be facilitated in a high-CO2 world. This study focuses on one of the most detrimental bioeroders, the sponge Cliona orientalis, which attacks and kills live corals on Australia’s Great Barrier Reef. Experimental exposure to lowered and elevated levels of pCO2 confirms a significant enforcement of the sponges’ bioerosion capacity with increasing pCO2 under more acidic conditions. Considering the substantial contribution of sponges to carbonate bioerosion, this finding implies that tropical reef ecosystems are facing the combined effects of weakened coral calcification and accelerated bioerosion, resulting in critical pressure on the dynamic balance between biogenic carbonate build-up and degradation.
Analysis of subforms of free prostate-specific antigen in serum by two-dimensional gel electrophoresis: potential to improve diagnosis of prostate cancer.

BACKGROUND The aim of this study was to develop a method to separate and quantify subforms of free prostate-specific antigen (fPSA) in serum by two-dimensional electrophoresis and to assess the diagnostic accuracy of these subforms for prostate cancer (PCa) diagnosis in comparison with total PSA (tPSA) and the ratio of fPSA to tPSA (%fPSA). METHODS Sera from 50 patients with and without PCa, respectively, were studied. PSA was isolated by immunoadsorption on streptavidin-coated magnetic beads with biotinylated anti-PSA antibodies and separated by two-dimensional electrophoresis. After semidry blotting, the intensities of the fPSA spots were quantified by chemiluminescence using an imager analyzer. RESULTS The method detected subforms to a concentration of 0.1 mug/L fPSA with an imprecision (CV) <16%. We detected 15 immunoreactive fPSA spots of different intensities. Spots F2 and F3 were present in all samples. F2 was lower in samples from non-PCa patients (median, 23%) than in samples from PCa patients (49%), whereas F3 behaved inversely (non-PCa, 73%; PCa, 45%). Ratios of F2 to F3 and F2/F3 to %fPSA, respectively, showed improved diagnostic accuracy compared with tPSA and %fPSA. Better differentiation by F2/F3 or by F2/F3 to %fPSA was particularly evident in patients with %fPSA values >15%. There were no associations between the PCa grading scale and fPSA subforms. CONCLUSIONS fPSA subforms separated by two-dimensional electrophoresis may improve both sensitivity and specificity in prostate cancer diagnostics compared with tPSA and %fPSA. The development of a practicable assay based on the immunologic properties of these different fPSA subforms seems to be promising.
Size Effect in Double-Punch Tests on Concrete Cylinders

Results of two series of experiments with a total of 42 double-punch tests on plain concrete cylinders are reported. The specimen size, which was the only tests variable, ranged from 8 to 128 times the maximum aggregate size. The observed size effect is in good agreement with Bazant's nonlinear fracture mechanics approach.
Comparison of fatty meal and intravenous cholecystokinin infusion for gallbladder ejection fraction.

UNLABELLED Gallbladder ejection fraction (GBEF) measured with a fatty meal (half-and-half milk) was compared with that measured with 2 equal sequential intravenous infusions of cholecystokinin (CCK-8) in a paired study of healthy subjects. METHODS GBEF was measured by (99m)Tc-hepatic iminodiacetic acid cholescintigraphy in 13 healthy subjects. Each subject received 2 sequential doses of CCK-8 (3 ng/kg/min for 10 min) on day 1, followed by, on day 2, a 240-mL (8 oz) fatty meal (half-and-half milk) per 70 kg of body weight. RESULTS The mean +/- SD GBEF of 53.6% +/- 20.2% with fatty meal was significantly lower than the mean of 75.8% +/- 16.3% (P < 0.01) with the first dose of CCK-8 and 71.3% +/- 17.4% (P < 0.05) with the second dose. Fatty meal GBEF varied widely, from 23.5% to 91.8%. Percentile rankings of the fatty meal GBEF were determined as the preferred methodology for reporting results. Latent and ejection periods were significantly longer with fatty meal than with either dose of CCK-8. CONCLUSION GBEF measured with fatty meal can serve as an alternative method to intravenous injection of CCK-8 when the hormone is no longer available for clinical use. The measurement of GBEF with fatty meal requires careful attention to the details of the meal and the measurement time sequence.
Comprehensive performance and robustness analysis of 2D turn models for network-on-chips

Routing algorithms play an important role in Network-on-Chip (NoC) based System-on-Chips. Turn model based routing disallows some of the turns in order to avoid deadlock, while providing partial adaptivity. In this paper, all 2D uniform turn models are examined for deadlock freeness and connectivity; 50 deadlock free turn models are extracted that provide full connectivity in the network. An extended adaptivity metric is introduced to classify the turn models; all extracted turn models are compared in terms of adaptivity, robustness and latency. Experimental results identify the most robust turn models and the most efficient ones in terms of latency.
Trout Use of Woody Debris and Habitat in Appalachian Wilderness Streams of North Carolina

Abstract Wilderness areas in the Appalachian Mountains of North Carolina are set aside to preserve characteristics of both old-growth and second-growth forests and associated streams. Woody debris loadings, trout habitat, and trout were inventoried in three southern Appalachian wilderness streams in North Carolina by the basin-wide visual estimation technique. Two streams in old-growth wilderness areas contained more large woody debris (LWD, diameter >10 cm) and more and smaller pools and riffles than did a stream in a second-growth area managed as wilderness. Furthermore, the size distribution of woody debris in the second-growth stream was skewed to smaller size-classes than that in the old-growth streams. Brook trout Salvelinus fontinalis, rainbow trout Oncorhynchus mykiss, and brown trout Salmo trutta in the three streams were always found in habitat units that had large amounts of LWD but were present in only 70–90% of the large number of units with little or no LWD. In the absence of high fishing pr.
The intelligibility of noise-vocoded speech: spectral information available from across-channel comparison of amplitude envelopes

Noise-vocoded (NV) speech is often regarded as conveying phonetic information primarily through temporal-envelope cues rather than spectral cues. However, listeners may infer the formant frequencies in the vocal-tract output—a key source of phonetic detail—from across-band differences in amplitude when speech is processed through a small number of channels. The potential utility of this spectral information was assessed for NV speech created by filtering sentences into six frequency bands, and using the amplitude envelope of each band (≤30 Hz) to modulate a matched noise-band carrier (N). Bands were paired, corresponding to F1 (≈N1 + N2), F2 (≈N3 + N4) and the higher formants (F3′ ≈ N5 + N6), such that the frequency contour of each formant was implied by variations in relative amplitude between bands within the corresponding pair. Three-formant analogues (F0 = 150 Hz) of the NV stimuli were synthesized using frame-by-frame reconstruction of the frequency and amplitude of each formant. These analogues were less intelligible than the NV stimuli or analogues created using contours extracted from spectrograms of the original sentences, but more intelligible than when the frequency contours were replaced with constant (mean) values. Across-band comparisons of amplitude envelopes in NV speech can provide phonetically important information about the frequency contours of the underlying formants.
Analytical Solutions for the Viscoelastic Response of Composite Beams Including Partial Interaction

This paper addresses the issue of the deformations that occur in composite steel-concrete beams caused by the quasi-viscoelastic effects of creep and shrinkage of the concrete slab, and in which the effects of partial shear interaction (PI) at the interface between the slab and the steel joist are included in the analysis. By making recourse to an algebraic representation of the viscoelastic response of the concrete, the formulation in this paper leads to a unique and useful solution of the problem in closed form, which follows from the establishment of a second order linear differential equation. The solution therefore does not require a discretisation along the beam as is usually required for numerical techniques, but only one discretisation in the time domain, and furthermore the resulting solution is generic in the sense that it may be applied for a variety of loading and restraint conditions. Specific solutions, which are validated against a numerical technique reported elsewhere, are presented for the cases of a simply supported beam, an encastré beam and for a propped cantilever.
Advanced Fatigue Damage Development in Graphite Epoxy Laminates.

Abstract : Results of an experimental investigation of damage development in T300/5208 graphite epoxy laminates subjected to tension-tension cyclic loading are reported. The concept of laminate stiffness reduction as a damage analogue is shown to be a valuable means of test control and damage interpretation. The relationship between stiffness and number of cycles is shown to be unique for each laminate type studied, each possessing three distinct stages, but markedly different among the laminate types. By using two complementary nondestructive evaluation (NDE) techniques, edge replication and penetrant-enhanced stereo X- ray radiography along with a method for deploying fatigue-damaged specimens, the stages of stiffness reduction were found to correspond variously to the predominance of matrix cracking or delamination or interactions of these matrix damage modes. A number of subordinate matrix damage modes including interior delamination, microcracking, and longitudinal splitting are identified with the matrix cracks which produce them. (Author)
Incrimination of Aedes (Stegomyia) hensilli Farner as an Epidemic Vector of Chikungunya Virus on Yap Island, Federated States of Micronesia, 2013

Two species of Aedes (Stegomyia) were collected in response to the first chikungunya virus (CHIKV) outbreak on Yap Island: the native species Ae. hensilli Farner and the introduced species Ae. aegypti (L.). Fourteen CHIKV-positive mosquito pools were detected. Six pools were composed of female Ae. hensilli, six pools were composed of female Ae. aegypti, one pool was composed of male Ae. hensilli, and one pool contained female specimens identified as Ae. (Stg.) spp. Infection rates were not significantly different between female Ae. hensilli and Ae. aegypti. The occurrence of human cases in all areas of Yap Island and the greater number of sites that yielded virus from Ae. hensilli combined with the ubiquitous distribution of this species incriminate Ae. hensilli as the most important vector of CHIKV during the outbreak. Phylogenic analysis shows that virus strains on Yap are members of the Asia lineage and closely related to strains currently circulating in the Caribbean.
Isoperimetric Sequences for Infinite Complete Binary Trees, Meta-Fibonacci Sequences and Signed Almost Binary Partitions

In this paper we demonstrate connections between three seemingly unrelated concepts. (1) The discrete isoperimetric problem in the infinite binary tree with all the leaves at the same level, $ {\mathcal T}_{\infty}$: The $n$-th edge isoperimetric number $\delta(n)$ is defined to be $\min_{|S|=n, S \subset V({\mathcal T}_{\infty})} |(S,\bar{S})|$, where $(S,\bar{S})$ is the set of edges in the cut defined by $S$. (2) Signed almost binary partitions: This is the special case of the coin-changing problem where the coins are drawn from the set ${\pm (2^d - 1): $d$ is a positive integer}$. The quantity of interest is $\tau(n)$, the minimum number of coins necessary to make change for $n$ cents. (3) Certain Meta-Fibonacci sequences: The Tanny sequence is defined by $T(n)=T(n{-}1{-}T(n{-}1))+T(n{-}2{-}T(n{-}2))$ and the Conolly sequence is defined by $C(n)=C(n{-}C(n{-}1))+C(n{-}1{-}C(n{-}2))$, where the initial conditions are $T(1) = C(1) = T(2) = C(2) = 1$. These are well-known "meta-Fibonacci" sequences. The main result that ties these three together is the following: $$ \delta(n) = \tau(n) = n+ 2 + 2 \min_{1 \le k \le n} (C(k) - T(n-k) - k). $$ Apart from this, we prove several other results which bring out the interconnections between the above three concepts.
Subcellular distribution and immunocytochemical localization of Na,K-ATPase subunit isoforms in human skeletal muscle.

The expression of Na,K-ATPase isoforms was investigated in human skeletal muscle membranes isolated by subcellular fractionation. The alpha 1, alpha 2, alpha 3 and beta 1 subunits were detectable in membranes prepared from the human soleus muscle. The alpha 1 subunit was largely detected in a fraction enriched with plasma membranes (PM), its abundance in an intracellular membrane fraction (IM) accounted for only 4% of that in the PM fraction. No alpha 1 subunits were detected in membranes of sarcoplasmic reticulum (SR) origin. The PM and IM fractions were enriched with alpha 2 subunits which were less abundant in the SR-enriched fraction. The abundance of alpha 2 molecules within the IM fraction was about 75% of that in the PM fraction when the total protein content for the two fractions was taken into account. Immunocytochemical studies confirmed the localization of the alpha 1 subunit to the muscle cell surface. The alpha 2 subunit was also found to be present in the cell surface but the observation that alpha 2 immunofluorescence was diffusely dispersed throughout the muscle fibre indicated that it was also present intracellularly, consistent with its biochemical localization in the PM and IM membrane fractions. The alpha 3 subunit was detected largely in the PM fraction but the lack of good antibodies to this isoform precluded an analysis of its immunocytochemical localization. The beta 1 subunit was enriched in the PM fraction but was also detected to a modest extent in the IM. (ABSTRACT TRUNCATED AT 250 WORDS)