Miracle-dz/UniFAR-FTUs huggingface dataset:
Two-protein signature of novel serological markers apolipoprotein-A2 and serum amyloid alpha predicts prognosis in patients with metastatic renal cell cancer and improves the currently used prognostic survival models.

BACKGROUND In metastatic renal cell cancer (mRCC), the Memorial Sloan-Kettering Cancer Center (MSKCC) risk model is widely used for clinical trial design and patient management. To improve prognostication, we applied proteomics to identify novel serological proteins associated with overall survival (OS). PATIENTS AND METHODS Sera from 114 mRCC patients were screened by surface-enhanced laser desorption ionization time-of-flight mass spectrometry (SELDI-TOF MS). Identified proteins were related to OS. Three proteins were subsequently validated with enzyme-linked immunosorbent assays and immunoturbidimetry. Prognostic models were statistically bootstrapped to correct for overestimation. RESULTS SELDI-TOF MS detected 10 proteins associated with OS. Of these, apolipoprotein A2 (ApoA2), serum amyloid alpha (SAA) and transthyretin were validated for their association with OS (P = 5.5 x 10(-9), P = 1.1 x 10(-7) and P = 0.0004, respectively). Combining ApoA2 and SAA yielded a prognostic two-protein signature [Akaike's Information Criteria (AIC) = 732, P = 5.2 x 10(-7)]. Including previously identified prognostic factors, multivariable Cox regression analysis revealed ApoA2, SAA, lactate dehydrogenase, performance status and number of metastasis sites as independent factors for survival. Using these five factors, categorization of patients into three risk groups generated a novel protein-based model predicting patient prognosis (AIC = 713, P = 4.3 x 10(-11)) more robustly than the MSKCC model (AIC = 729, P = 1.3 x 10(-7)). Applying this protein-based model instead of the MSKCC model would have changed the risk group in 38% of the patients. CONCLUSIONS Proteomics and subsequent validation yielded two novel prognostic markers and survival models which improved prediction of OS in mRCC patients over commonly used risk models. Implementation of these models has the potential to improve current risk stratification, although prospective validation will still be necessary.
Levels of processing during non-conscious perception: a critical review of visual masking

Understanding the extent and limits of non-conscious processing is an important step on the road to a thorough understanding of the cognitive and cerebral correlates of conscious perception. In this article, we present a critical review of research on subliminal perception during masking and other related experimental conditions. Although initially controversial, the possibility that a broad variety of processes can be activated by a non-reportable stimulus is now well established. Behavioural findings of subliminal priming indicate that a masked word or digit can have an influence on perceptual, lexical and semantic levels, while neuroimaging directly visualizes the brain activation that it evokes in several cortical areas. This activation is often attenuated under subliminal presentation conditions compared to consciously reportable conditions, but there are sufficiently many exceptions, in paradigms such as the attentional blink, to indicate that high activation, per se, is not a sufficient condition for conscious access to occur. We conclude by arguing that for a stimulus to reach consciousness, two factors are jointly needed: (i) the input stimulus must have enough strength (which can be prevented by masking) and (ii) it must receive top-down attention (which can be prevented by drawing attention to another stimulus or task). This view leads to a distinction between two types of non-conscious processes, which we call subliminal and preconscious. According to us, maintaining this distinction is essential in order to make sense of the growing neuroimaging data on the neural correlates of consciousness.
Ovarian Cancer Cells Induce Peripheral Mature Dendritic Cells to Differentiate Into Macrophagelike Cells In Vitro

Aims: Precursors of dendritic cells (DCs) are able to differentiate into macrophages induced by some tumor-associated molecules; however, whether peripheral mature DCs could differentiate into macrophages remains unknown. This study was designed to find out whether ovarian cancer cells could induce peripheral mature DCs to differentiate into macrophages. Main Methods: Mature DCs were cultured from monocytes with granulocyte-macrophage colony-stimulating factor and interleukin 4 (IL-4) for 6 days and lipopolysaccharide for another 24 hours and then were cocultured for 48 hours with ovarian cancer ascites or cell-free supernatants of SKOV3 and CAOV3 cell lines. In some experiments, mature DCs were cultured in the absence or presence of IL-10 or leukemia inhibitory factor (LIF) for the same time. In neutralization experiments, neutralizing monoclonal antibodies to IL-10 or LIF were added to the cultures. Cell phenotypes and phagocytosis were analyzed using flow cytometry; allogeneic T-cell proliferation assay was used to examine stimulatory activity of cells. Results and Conclusions: Mature DCs cocultured with ovarian cancer ascites or supernatants of SKOV3 and CAOV3 differentiated into a group of macrophagelike cells that exhibited increased expression of surface marker CD14+CD1a−, decreased expression of CD83, poorer T-cell costimulatory properties, and greater endocytosis of fluorescein isothiocyanate-dextran in vitro. Interleukin 10 but not LIF mediated this differentiation pathway.
Factors influencing online auction repurchase intention

Purpose – The purpose of this study is to integrate expectancy disconfirmation theory (EDT) to explore cognitive beliefs and affect influencing an individual's intention to repurchase in online marketplaces.Design/methodology/approach – The paper used EDT to conduct an empirical study and data were collected from a total of 303 bidders of online auctions. A structural equation modeling (SEM) was used to assess the relationships of the research model.Findings – The findings show that bidders' disconfirmation of online auctions is positively associated with their satisfaction, which in turn is positively associated with their repurchase intentions.Practical implications – Both bidders' expectation of policy and auctioneers' performance of policy are important determinants of disconfirmation. Auctioneers need to recognize the distinctive roles of information policy in selling and bidding rules. Besides, neither bidders' expectation of sellers' reputation nor their expectation of service quality has a signifi.
Decreased CYP3A Expression and Activity in Guinea Pig Models of Diet-Induced Metabolic Syndrome: Is Fatty Liver Infiltration Involved?

Background: In humans, CYP3A drug-metabolizing enzyme subfamily is the most important. Numerous pathophysiological factors, such as diabetes and obesity, were shown to affect CYP3A activity. Often considered a precursor state for type II diabetes, metabolic syndrome exerts a modulating role on CYP3A, in our hypothesis. Objective: To evaluate the effect of metabolic syndrome on CYP3A drug-metabolizing activity/expression in guinea pigs. Methods: Hepatic microsomes were prepared from male Hartley guinea pigs fed with a control, a high-fat high sucrose (HFHS) or a high-fat high fructose diet (HFHF). Domperidone was selected as a probe substrate of CYP3A and formation of four of its metabolites was evaluated using high-performance liquid chromatography. CYP3A protein and mRNA expression were assessed by Western blot and reverse-transcription quantitative polymerase chain reaction, respectively. Hepatic fatty infiltration was evaluated using standard Oil Red O staining. Triglyceride and free fatty acid liver content were also quantified. Results: Microsomal CYP3A activity was significantly decreased in both HFHS and HFHF diet groups versus the control diet group. Significant decreases of CYP3A mRNA and protein expression were observed in both HFHS and HFHF diet groups. Oil Red O staining showed a massive liver fatty infiltration in the HFHS and HFHF diet groups, which was not observed in the control diet group. Both triglyceride and free fatty acid liver content were significantly increased in the HFHS and HFHF diet groups. Conclusion: Diet-induced metabolic syndrome decreases CYP3A expression/activity in guinea pigs. This may ultimately lead to variability in drug response, ranging from lack of effect to life-threatening toxicity.
Prediction of Recanalization Trumps Prediction of Tissue Fate: The Penumbra A Dual-edged Sword

Background and Purpose— To determine whether infarct core or penumbra is the more significant predictor of outcome in acute ischemic stroke, and whether the results are affected by the statistical method used. Methods— Clinical and imaging data were collected in 165 patients with acute ischemic stroke. We reviewed the noncontrast head computed tomography (CT) to determine the Alberta Score Program Early CT score and assess for hyperdense middle cerebral artery. We reviewed CT-angiogram for site of occlusion and collateral flow score. From perfusion-CT, we calculated the volumes of infarct core and ischemic penumbra. Recanalization status was assessed on early follow-up imaging. Clinical data included age, several time points, National Institutes of Health Stroke Scale at admission, treatment type, and modified Rankin score at 90 days. Two multivariate regression analyses were conducted to determine which variables predicted outcome best. In the first analysis, we did not include recanalization status among the potential predicting variables. In the second, we included recanalization status and its interaction between perfusion-CT variables. Results— Among the 165 study patients, 76 had a good outcome (modified Rankin score ⩽2) and 89 had a poor outcome (modified Rankin score >2). In our first analysis, the most important predictors were age (P<0.001) and National Institutes of Health Stroke Scale at admission (P=0.001). The imaging variables were not important predictors of outcome (P>0.05). In the second analysis, when the recanalization status and its interaction with perfusion-CT variables were included, recanalization status and perfusion-CT penumbra volume became the significant predictors (P<0.001). Conclusions— Imaging prediction of tissue fate, more specifically imaging of the ischemic penumbra, matters only if recanalization can also be predicted.
Psychiatric advance directives and reduction of coercive crisis interventions

Background: Psychiatric advance directives are intended to enable self-determined treatment for patients who lose decisional capacity, and thus reduce the need for coercive interventions such as police transport, involuntary commitment, seclusion and restraints, and involuntary medications during mental health crises; whether PADs can help prevent the use of these interventions in practice is unknown. Aims: This study examined whether completion of a Facilitated Psychiatric Advance Directive (F-PAD) was associated with reduced frequency of coercive crisis interventions. Method: The study prospectively compared a sample of PAD completers (n = 147) to non-completers (n = 92) on the frequency of any coercive interventions, with follow-up assessments at 6, 12, and 24 months. Repeated-measures multiple regression analysis was used to estimate the effect of PADs. Models controlled for relevant covariates including a propensity score for initial selection to PADs, baseline history of coercive interventions, concurrent global functioning and crisis episodes with decisional incapacity. Results: F-PAD completion was associated with lower odds of coercive interventions (adjusted OR = 0.50; 95% CI = 0.26–0.96; p < 0.05). Conclusions: PADs may be an effective tool for reducing coercive interventions around incapacitating mental health crises. Less coercion should lead to greater autonomy and self-determination for people with severe mental illness.
When Too Much Usage is Too Much: Exploring the Process of IT Addiction

Although IT usage is generally known as a desirable behavior, addictive IT usage is likely to have some adverse consequences for individuals, organizations and even societies. This paper investigates IT addiction and aims to identify the mechanisms behind its development. Based on a thorough review of the literature, we conceptualize IT addiction as a psychological dependency on IT that involves excessive use of technology. Furthermore, we identify the elements that are associated with the formation of addiction. Based on the analysis of 12 in-depth interviews and 182 qualitative surveys, we developed a process theory of IT addiction that explains how these behaviors progress through time. The model highlights the key elements that are associated with IT-related addictive behaviors and shows how they relate to the technology, the user and the environment. It also highlights the problematic consequences of such behaviors on the well-being of addicted users.
Acid Susceptibility at Various Depths of pH-Cycled Enamel and Dentine Specimens

pH-cycling and in situ studies have shown that fluctuations in de-/remineralisation conditions or in fluoride usage can lead to laminations inside enamel or dentine lesions. Layers with different mineral content are thought to reflect the history of fluoride administrations. Studying the dissolution properties of such lesions at various depths – using bulk specimens – is presumably hampered by limited diffusion of acids through the lesion pores. Therefore, in this study the acid susceptibility of enamel and dentine lesions and the underlying sound tissues was studied by exposing sections to acid buffers from the cut rather than from the external surface. Specimens were obtained from a previous study of the effects of high-fluoride (0, 1,000, 2,000, 3,000/5,000 ppm F) toothpastes on enamel and dentine de-/remineralisation. Sections were subjected to acid buffers for 3 and 7 days and the changes in mineral content were monitored by contact microradiography. For enamel lesions a significant difference in dissolution over depth was observed between the groups subjected to the different fluoride schemes. At 7 days a dose response was found between the different fluoride groups and the lesion parameters. In the no-fluoride group dissolution in the original lesion and the sound tissue were similar. All dentine lesions which had been treated with fluoride showed inhibition of dissolution, but the inhibition did not increase with higher fluoride concentrations. Deeper into the dentine tissue there was some protection, but it was not statistically significant. We conclude that penetration of fluoride through the lesion pores determines the dissolution pattern of a lesion at various depths.
Activity of Lower Limb Muscles During Squat With and Without Abdominal Drawing-in and Pilates Breathing

Abstract Barbosa, AC, Martins, FM, Silva, AF, Coelho, AC, Intelangelo, L, and Vieira, ER. Activity of lower limb muscles during squat with and without abdominal drawing-in and Pilates breathing. J Strength Cond Res 31(11): 3018–3023, 2017—The purpose of this study was to assess the effects of abdominal drawing-in and Pilates breathing on the activity of lower limb muscles during squats. Adults (n = 13, 22 ± 3 years old) with some Pilates experience performed three 60° squats under each of the following conditions in a random order: (I) normal breathing, (II) drawing-in maneuver with normal breathing, and (III) drawing-in maneuver with Pilates breathing. Peak-normalized surface electromyography of the rectus femoris, biceps femoris, gastrocnemius medialis, and tibialis anterior during the knee flexion and extension phases of squat exercises was analyzed. There were significant differences among the conditions during the knee flexion phase for the rectus femoris (p = 0.001), biceps femoris (p = 0.038), and tibialis anterior (p = 0.001), with increasing activation from conditions I to III. For the gastrocnemius medialis, there were significant differences among the conditions during the knee extension phase (p = 0.023), with increased activity under condition I. The rectus and biceps femoris activity was higher during the extension vs. flexion phase under conditions I and II. The tibialis anterior activity was higher during the flexion compared with the extension phase under all conditions, and the medial gastrocnemius activity was higher during the extension phase under condition I. Doing squats with abdominal drawing-in and Pilates breathing resulted in increased rectus, biceps femoris, and tibialis anterior activity during the flexion phase, increasing movement stability during squat exercises.
Isolated IgA Anti-β2 Glycoprotein I Antibodies in Patients with Clinical Criteria for Antiphospholipid Syndrome

Seronegative antiphospholipid syndrome (SNAPS) is an autoimmune disease present in patients with clinical manifestations highly suggestive of Antiphospholipid Syndrome (APS) but with persistently negative consensus antiphospholipid antibodies (a-PL). IgA anti-β2 Glycoprotein I (aB2-GPI) antibodies are associated with APS. However, they are not currently considered to be laboratory criteria due to the heterogeneity of published works and the use of poor standardized diagnostic systems. We have aimed to assess aPL antibodies in a group of patients with clinical manifestations of APS (C-APS) to evaluate the importance of the presence of IgA aB2GPI antibodies in APS and its relation with other aPL antibodies. Only 14% of patients with C-APS were positive for any consensus antibody, whereas the presence of isolated IgA aB2GPI antibodies was found in 22% of C-APS patients. In patients with arterial thrombosis IgA aB2GPI, antibodies were the only aPL antibodies present. Serologic profile in primary APS (PAPS) is different from systemic autoimmune disorders associated APS (SAD-APS). IgA aB2GPI antibodies are more prevalent in PAPS and IgG aB2GPI antibodies are predominant in SAD-APS. The analysis of IgA aB2GPI antibodies in patients with clinical manifestations of PAPS might avoid underdiagnosed patients and provide a better diagnosis in patients with SAD-APS. Laboratory consensus criteria might consider including analysis of IgA aB2GPI for APS diagnosis.
A developmental basis for stochasticity in floral organ numbers

Stochasticity ubiquitously inevitably appears at all levels from molecular traits to multicellular, morphological traits. Intrinsic stochasticity in biochemical reactions underlies the typical intercellular distributions of chemical concentrations, e.g., morphogen gradients, which can give rise to stochastic morphogenesis. While the universal statistics and mechanisms underlying the stochasticity at the biochemical level have been widely analyzed, those at the morphological level have not. Such morphological stochasticity is found in foral organ numbers. Although the floral organ number is a hallmark of floral species, it can distribute stochastically even within an individual plant. The probability distribution of the floral organ number within a population is usually asymmetric, i.e., it is more likely to increase rather than decrease from the modal value, or vice versa. We combined field observations, statistical analysis, and mathematical modeling to study the developmental basis of the variation in floral organ numbers among 50 species mainly from Ranunculaceae and several other families from core eudicots. We compared six hypothetical mechanisms and found that a modified error function reproduced much of the asymmetric variation found in eudicot floral organ numbers. The error function is derived from mathematical modeling of floral organ positioning, and its parameters represent measurable distances in the floral bud morphologies. The model predicts two developmental sources of the organ-number distributions: stochastic shifts in the expression boundaries of homeotic genes and a semi-concentric (whorled-type) organ arrangement. Other models species- or organ-specifically reproduced different types of distributions that reflect different developmental processes. The organ-number variation could be an indicator of stochasticity in organ fate determination and organ positioning.
Constant-approximation algorithms for highly connected multi-dominating sets in unit disk graphs

Given an undirected graph on a node set $V$ and positive integers $k$ and $m$, a $k$-connected $m$-dominating set ($(k,m)$-CDS) is defined as a subset $S$ of $V$ such that each node in $V \setminus S$ has at least $m$ neighbors in $S$, and a $k$-connected subgraph is induced by $S$. The weighted $(k,m)$-CDS problem is to find a minimum weight $(k,m)$-CDS in a given node-weighted graph. The problem is called the unweighted $(k,m)$-CDS problem if the objective is to minimize the cardinality of a $(k,m)$-CDS. These problems have been actively studied for unit disk graphs, motivated by the application of constructing a virtual backbone in a wireless ad hoc network. However, constant-approximation algorithms are known only for $k \leq 3$ in the unweighted $(k,m)$-CDS problem, and for $(k,m)=(1,1)$ in the weighted $(k,m)$-CDS problem. In this paper, we consider the case in which $m \geq k$, and we present a simple $O(5^k k! )$-approximation algorithm for the unweighted $(k,m)$-CDS problem, and a primal-dual $O(k^2 \log k)$-approximation algorithm for the weighted $(k,m)$-CDS problem. Both algorithms achieve constant approximation factors when $k$ is a fixed constant.
ndnSIM 2 . 0 : A new version of the NDN simulator for NS-3

The fundamental departure of the Named-Data Networking (NDN) communication paradigm from the IP principles requires extensive evaluation through experimentation, and simulation is a necessary tool to enable the experimentation at scale. We released the first version of ndnSIM, an open source NS-3-based NDN simulator, back in June 2012. Since then, ndnSIM has undergone substantial development resulting in ndnSIM 2.0, which was released in January 2015. This paper reports the design and features of this new simulator version. The goal of the new release is to match the simulation platform to the latest advancements of NDN research. Therefore, it uses the ndn-cxx library (NDN C++ library with eXperimental eXtensions) and the NDN Forwarding Daemon (NFD) to enable experiments with real code in a simulation environment.
Bacterial keratitis: a prospective clinical and microbiological study

AIM To define the clinical and microbiological profile of bacterial keratitis at the Jules Gonin Eye Hospital and to test the in vitro bacterial resistance. METHODS Patients presenting with bacterial keratitis were prospectively followed; clinical features (age, risk factors, visual acuity) and response to therapy were analysed. Bacteriological profile was determined and the sensitivity/resistance of isolated strains were tested towards 12 ocular antibiotics (NCCLS disc diffusion test). RESULTS 85 consecutive patients (mean age 44.3 (SD 20.7) years) were prospectively enrolled from 1 March 1997 to 30 November 1998. The following risk factors were identified: contact lens wear, 36%; blepharitis, 21%; trauma, 20%; xerophthalmia, 15%; keratopathies, 8%; and eyelid abnormalities, 6%. The most commonly isolated bacteria wereStaphylococcus epidermidis, 40%;Staphylococcus aureus, 22%;Streptococcus pneumoniae, 8%; othersStreptococcus species, 5%;Pseudomonas, 9%;Moraxella andSerratia marcescens, 5% each;Bacillus,Corynebacterium, Alcaligenes xyloxidans, Morganella morganii, andHaemophilus influenza, 1% each. 1–15% of strains were resistant to fluoroquinolones, 13–22% to aminoglycosides, 37% to cefazolin, 18% to chloramphenicol, 54% to polymyxin B, 51% to fusidic acid, and 45% to bacitracin. Five of the 85 patients (5.8%) had a poor clinical outcome with a visual loss of one or more lines of visual acuity. CONCLUSION Fluoroquinolones appear to be the therapy of choice for bacterial keratitis, but, based upon these in vitro studies, some strains may be resistant.