Miracle-dz/UniFAR-FTUs huggingface dataset:
The Study of the Aggregated Pattern of TX100 Micelle by Using Solvent Paramagnetic Relaxation Enhancements

TX100 (Triton X-100) is a typical nonionic surfactant that is widely used in biology. However, the detailed aggregated conformation of TX100, such as the boundary between the polar region and the nonpolar region, and the arrangement of hydrophobic chains in micelles, are still controversial. In the manuscript, the aggregation pattern of TX100 has been studied using sPREs (solvent Paramagnetic Relaxation Enhancements)-based NMR (Nuclear Magnetic Resonance spectroscopy). It was found that the average positions of the protons in the TX100 micelle are consistent with those in the multilayer staggered spherical micelle model with the p-tertoctylphenyl groups dispersing in the different layers.
Failed dental implants: diagnosis, removal and survival of reimplantations.

BACKGROUND Over time, the percentage of dental implants that fail increases because of biological and technical issues. Inevitably, clinicians will dedicate more time to dealing with ailing and failing dental implants. METHODS The authors searched the literature for articles that addressed diagnostic manifestations of failed implants and reasons for their demise, as well as survival rates of dental implant reimplantations. RESULTS The authors found that there is no precise cut point (besides 100 percent) with regard to the amount of bone loss in the absence of mobility that indicates an implant has failed. The decision to treat or explant an ailing implant is a judgment call by the treating clinician. Survival rates found in the literature after first and second reimplantations ranged from 71 percent to 100 percent and 50 percent to 100 percent, respectively. The 100 percent findings were based on small groups of implants, and there were scant data addressing implant survival after second reimplantations. CONCLUSIONS The decision to remove an implant needs to be based on clinical assessments, radiographic evaluations or both. If the implant is deemed hopeless, there are devices that facilitate their removal. Furthermore, reimplantations can be performed successfully, but their survival rate appears to be lower than that of implants placed at sites from which they were not lost formerly. PRACTICAL IMPLICATIONS Ailing dental implants should not be condemned prematurely, because patients often respond to treatment of peri-implantitis. Many patients desire reimplantations in sites in which implants have failed. This procedure is valuable, especially if it makes possible the fabrication of an implant-supported fixed or removable prosthesis.
Contribution of Basophils to Cutaneous Immune Reactions and Th2-Mediated Allergic Responses

Basophils are potent effector cells of innate immunity and also play a role in T helper 2 (Th2)-mediated allergic responses. But, although their in vitro functions are well studied, their in vivo functions remain largely unknown. However, several mouse models of basophil depletion have recently been developed and used to investigate basophil functions. For example, in a croton oil-induced model of irritant contact dermatitis in conditionally basophil-depleted transgenic mice, we found that basophils rapidly infiltrate inflamed skin and subsequently induce infiltration of eosinophils. We also showed that basophils induce Th2 skewing upon epicutaneous sensitization with various haptens and peptide antigens. Intriguingly, basophils also promoted Th2 polarization upon protein antigen exposure in the presence of dendritic cells (DCs). The dermal DC subset associated with Th2 skewing was recently identified as CD301b+ DC. Such studies with basophil-deficient mouse models have significantly improved our understanding of the mechanisms involved in human immune-related diseases. In this review, we will focus on the relative contribution of basophils and DCs to Th2-mediated allergic responses.
Plasma from pre‐eclamptic patients induces the expression of the anti‐angiogenic miR‐195‐5p in endothelial cells

We examined the effect of plasma incubation from preeclampsia pregnant on the antiangiogenic miR‐195‐5p expression. Higher miR‐195‐5p expression was found in cultures incubated with preeclampsia plasma compared to those incubated with healthy pregnant plasma. Next, as VEGF is a target of miR‐195‐5p we have quantified its expression by real‐time qPCR and ELISA. We found reduced VEGF levels in culture incubated with preeclampsia plasma. Therefore, we have concluded that the higher expression of miR‐195‐5p in endothelial cell cultures incubated with preeclampsia plasma may contribute to decreased expression of VEGFA (gene and protein) and increased antiangiogenic status in preeclampsia. Therefore, this miR may be an important target in preeclampsia.
Coronary veins determine the pattern of sympathetic innervation in the developing heart

Anatomical congruence of peripheral nerves and blood vessels is well recognized in a variety of tissues. Their physical proximity and similar branching patterns suggest that the development of these networks might be a coordinated process. Here we show that large diameter coronary veins serve as an intermediate template for distal sympathetic axon extension in the subepicardial layer of the dorsal ventricular wall of the developing mouse heart. Vascular smooth muscle cells (VSMCs) associate with large diameter veins during angiogenesis. In vivo and in vitro experiments demonstrate that these cells mediate extension of sympathetic axons via nerve growth factor (NGF). This association enables topological targeting of axons to final targets such as large diameter coronary arteries in the deeper myocardial layer. As axons extend along veins, arterial VSMCs begin to secrete NGF, which allows axons to reach target cells. We propose a sequential mechanism in which initial axon extension in the subepicardium is governed by transient NGF expression by VSMCs as they are recruited to coronary veins; subsequently, VSMCs in the myocardium begin to express NGF as they are recruited by remodeling arteries, attracting axons toward their final targets. The proposed mechanism underlies a distinct, stereotypical pattern of autonomic innervation that is adapted to the complex tissue structure and physiology of the heart.
Molecular characterization of neoplastic and normal “sister” lymphoblastoid B-cell lines from chronic lymphocytic leukemia

Abstract Chronic lymphocytic leukemia (CLL) B-cells resemble self-renewing CD5 + B-cells carrying auto/xeno-antigen-reactive B-cell receptors (BCRs) and multiple innate pattern-recognition receptors, such as Toll-like receptors and scavenger receptors. Integration of signals from BCRs with multiple surface membrane receptors determines whether the cells will be proliferating, anergic or apoptotic. To better understand the role of antigen in leukemogenesis, CLL cell lines producing monoclonal antibodies (mAbs) will facilitate structural analysis of antigens and supply DNA for genetic studies. We present here a comprehensive genotypic and phenotypic characterization of available CLL and normal B-cell-derived lymphoblastoid cell lines (LCLs) from the same individuals (n = 17). Authenticity and verification studies of CLL-patient origin were done by IGHV sequencing, fluorescence in situ hybridization (FISH) and DNA/short tandem repeat (STR) fingerprinting. Innate B-cell features, i.e. natural Ab production and CD5 receptors, were present in most CLL cell lines, but in none of the normal LCLs. This panel of immortalized CLL-derived cell lines is a valuable reference representing a renewable source of authentic Abs and DNA.
RELIABILITY OF THE DETECTION OF THE BARYON ACOUSTIC PEAK

The correlation function of the distribution of matter in the universe shows, at large scales, baryon acoustic oscillations, which were imprinted prior to recombination. This feature was first detected in the correlation function of the luminous red galaxies of the Sloan Digital Sky Survey (SDSS). Recently, the final release (DR7) of the SDSS has been made available, and the useful volume is about two times bigger than in the old sample. We present here, for the first time, the redshift–space correlation function of this sample at large scales together with that for one shallower, but denser volume-limited subsample drawn from the Two-Degree Field Redshift Survey. We test the reliability of the detection of the acoustic peak at about 100 h−1 Mpc and the behavior of the correlation function at larger scales by means of careful estimation of errors. We confirm the presence of the peak in the latest data although broader than in previous detections.
Influence of diet and obesity on COPD development and outcomes

The global increase in the prevalence and incidence of obesity has called serious attention to this issue as a major public health concern. Obesity is associated with many chronic diseases, including cardiovascular disease and diabetes, and recently the role of overweight and obesity in lung disease has received new interest. Independently of obesity, diet also plays a role as a risk factor for many chronic diseases, and evidence is accumulating to support a role for diet in the prevention and management of several lung diseases. Chronic obstructive lung disease is the third-leading cause of death globally, and both obesity and diet appear to play roles in its pathophysiology. Obesity has been associated with decreased lung-function measures in population-based studies, with increased prevalence of several lung diseases and with compromised pulmonary function. In contrast, obesity has a protective effect against mortality in severe chronic obstructive pulmonary disease (COPD). Nutrient intake and dietary patterns have also been associated with lung-function measures and the development and progression of COPD. Taken together, this suggests that a focus on obesity and diet should be part of public health campaigns to reduce the burden of lung disease, and could have important implications for clinicians in the management of their patients. Future research should also focus on elucidating these relationships in diverse populations and age-groups, and on understanding the complex interaction between behavior, environment, and genetics in the development and progression of COPD. The goal of this article is to review current evidence regarding the role that obesity and diet play in the development of COPD, and in COPD-related outcomes.
Early Inflammation Mainly Affects Normally and Poorly Aerated Lung in Experimental Ventilator-Induced Lung Injury*

Objective:The common denominator in most forms of ventilator-induced lung injury is an intense inflammatory response mediated by neutrophils. PET with [18F]fluoro-2-deoxy-D-glucose can be used to image cellular metabolism, which, during lung inflammatory processes, mainly reflects neutrophil activity, allowing the study of regional lung inflammation in vivo. The aim of this study was to assess the location and magnitude of lung inflammation using PET imaging of [18F]fluoro-2-deoxy-D-glucose in a porcine experimental model of early acute respiratory distress syndrome. Design:Prospective laboratory investigation. Setting:A university animal research laboratory. Subjects:Seven piglets submitted to experimental ventilator-induced lung injury and five healthy controls. Interventions:Lung injury was induced by lung lavages and 210 minutes of injurious mechanical ventilation using low positive end-expiratory pressure and high inspiratory pressures. All animals were subsequently studied with dynamic PET imaging of [18F]fluoro-2-deoxy-D-glucose. CT scans were acquired at end expiration and end inspiration. Measurements and Main Results:[18F]fluoro-2-deoxy-D-glucose uptake rate was computed for the whole lung, four isogravitational regions, and regions grouping voxels with similar density. Global and intermediate gravitational zones [18F]fluoro-2-deoxy-D-glucose uptakes were higher in ventilator-induced lung injury piglets compared with controls animals. Uptake of normally and poorly aerated regions was also higher in ventilator-induced lung injury piglets compared with control piglets, whereas regions suffering tidal recruitment or tidal hyperinflation had [18F]fluoro-2-deoxy-D-glucose uptakes similar to controls. Conclusions:The present findings suggest that normally and poorly aerated regions—corresponding to intermediate gravitational zones—are the primary targets of the inflammatory process accompanying early experimental ventilator-induced lung injury. This may be attributed to the small volume of the aerated lung, which receives most of ventilation.
An Efficient Robust Eye Localization by Learning the Convolution Distribution Using Eye Template

Eye localization is a fundamental process in many facial analyses. In practical use, it is often challenged by illumination, head pose, facial expression, occlusion, and other factors. It remains great difficulty to achieve high accuracy with short prediction time and low training cost at the same time. This paper presents a novel eye localization approach which explores only one-layer convolution map by eye template using a BP network. Results showed that the proposed method is robust to handle many difficult situations. In experiments, accuracy of 98% and 96%, respectively, on the BioID and LFPW test sets could be achieved in 10 fps prediction rate with only 15-minute training cost. In comparison with other robust models, the proposed method could obtain similar best results with greatly reduced training time and high prediction speed.
Weighted Joint Sparse Representation for Removing Mixed Noise in Image

Joint sparse representation (JSR) has shown great potential in various image processing and computer vision tasks. Nevertheless, the conventional JSR is fragile to outliers. In this paper, we propose a weighted JSR (WJSR) model to simultaneously encode a set of data samples that are drawn from the same subspace but corrupted with noise and outliers. Our model is desirable to exploit the common information shared by these data samples while reducing the influence of outliers. To solve the WJSR model, we further introduce a greedy algorithm called weighted simultaneous orthogonal matching pursuit to efficiently approximate the global optimal solution. Then, we apply the WJSR for mixed noise removal by jointly coding the grouped nonlocal similar image patches. The denoising performance is further improved by incorporating it with the global prior and the sparse errors into a unified framework. Experimental results show that our denoising method is superior to several state-of-the-art mixed noise removal methods.
Labile plasma iron, more practical and more sensitive to iron overload in myelodysplastic syndromes

Objectives: In order to gain an insight into labile plasma iron (LPI) in iron metabolism microenvironment in MDS. Methods: We performed ELISA, quantitative real-time polymerase chain reaction, flow cytometry, MRI T2* assays to test LPI, iron biochemical parameters, and liver iron concentration (LIC) among 22 MDS patients. Results: LPI has a statistical difference (P < 0.001 by analysis of variance (ANOVA)), which decreased gradually, among three groups, while no difference was found in adjusted serum ferritin (ASF) (P = 0.086 by ANOVA). After DFO treatment, serum hepcidin expression increased from 301.26 ± 59.78 to 340.33 ± 49.78 µg/l (P = 0.032), while hepcidin/ASF was upregulated gradually from 0.16 ± 0.08 to 0.22 ± 0.03 (P = 0.045). APAF-1 expression (P = 0.047) and erythroid apoptosis rate (P = 0.009) decreased significantly, respectively. No statistical difference was found in EPO (P = 0.247) and GDF15 expression (P = 0.172). LIC dropped from 9.83 ± 4.84 to 6.28 ± 4.01 mg/g dry weight (P < 0.001). No significant difference was found in cardiac T2* (P = 0.594). LPI has a closer connection to LIC than ASF (r = 0.739, P < 0.001 vs. r = 0.321, P = 0.034). Discussion: LPI seems to be a real-time indicator which reflects body iron loading status instantaneously. Despite the limited knowledge available on LPI speciation in different types and degrees of IO, LPI measurements can be and are in fact used for identifying systemic IO and for initiating/adjusting chelation regimens.
Food waste conversion to microbial polyhydroxyalkanoates

Polyhydroxyalkanoates (PHAs) are biopolymers with desirable material properties similar to petrochemically derived plastics. PHAs are naturally produced by a wide range of microorganisms as a carbon storage mechanism and can accumulate to significantly high levels. PHAs are an environmentally friendly alternative to their petroleum counterparts because they can be easily degraded, potentially reducing the burden on municipal waste systems. Nevertheless, widespread use of PHAs is not currently realistic due to a variety of factors. One of the major constraints of large‐scale PHA production is the cost of carbon substrate for PHA‐producing microbes. The cost of production could potentially be reduced with the use of waste carbon from food‐related processes. Food wastage is a global issue and therefore harbours immense potential to create valuable bioproducts. This article's main focus is to examine the state of the art of converting food‐derived waste into carbon substrates for microbial metabolism and subsequent conversion into PHAs.
Miro proteins coordinate microtubule‐ and actin‐dependent mitochondrial transport and distribution

In the current model of mitochondrial trafficking, Miro1 and Miro2 Rho‐GTPases regulate mitochondrial transport along microtubules by linking mitochondria to kinesin and dynein motors. By generating Miro1/2 double‐knockout mouse embryos and single‐ and double‐knockout embryonic fibroblasts, we demonstrate the essential and non‐redundant roles of Miro proteins for embryonic development and subcellular mitochondrial distribution. Unexpectedly, the TRAK1 and TRAK2 motor protein adaptors can still localise to the outer mitochondrial membrane to drive anterograde mitochondrial motility in Miro1/2 double‐knockout cells. In contrast, we show that TRAK2‐mediated retrograde mitochondrial transport is Miro1‐dependent. Interestingly, we find that Miro is critical for recruiting and stabilising the mitochondrial myosin Myo19 on the mitochondria for coupling mitochondria to the actin cytoskeleton. Moreover, Miro depletion during PINK1/Parkin‐dependent mitophagy can also drive a loss of mitochondrial Myo19 upon mitochondrial damage. Finally, aberrant positioning of mitochondria in Miro1/2 double‐knockout cells leads to disruption of correct mitochondrial segregation during mitosis. Thus, Miro proteins can fine‐tune actin‐ and tubulin‐dependent mitochondrial motility and positioning, to regulate key cellular functions such as cell proliferation.
Gallager codes for CDMA applications .I. Generalizations, constructions, and performance bounds

We focus on applications of low-rate Gallager (1963) (low-density parity-check) codes in code-division multiple-access schemes. The codes that we present here achieve good performance with relatively short frame-lengths in additive white Gaussian noise channels and, perhaps more importantly, in fading channels. These codes can be decoded with low complexity by using iterative decoding procedures. We present a construction that yields good short frame-length Gallager codes. Bounds on the frame-error probability for a maximum-likelihood decoder are obtained.
Review of methods for handling confounding by cluster and informative cluster size in clustered data

Clustered data are common in medical research. Typically, one is interested in a regression model for the association between an outcome and covariates. Two complications that can arise when analysing clustered data are informative cluster size (ICS) and confounding by cluster (CBC). ICS and CBC mean that the outcome of a member given its covariates is associated with, respectively, the number of members in the cluster and the covariate values of other members in the cluster. Standard generalised linear mixed models for cluster‐specific inference and standard generalised estimating equations for population‐average inference assume, in general, the absence of ICS and CBC. Modifications of these approaches have been proposed to account for CBC or ICS. This article is a review of these methods. We express their assumptions in a common format, thus providing greater clarity about the assumptions that methods proposed for handling CBC make about ICS and vice versa, and about when different methods can be used in practice. We report relative efficiencies of methods where available, describe how methods are related, identify a previously unreported equivalence between two key methods, and propose some simple additional methods. Unnecessarily using a method that allows for ICS/CBC has an efficiency cost when ICS and CBC are absent. We review tools for identifying ICS/CBC. A strategy for analysis when CBC and ICS are suspected is demonstrated by examining the association between socio‐economic deprivation and preterm neonatal death in Scotland. © 2014 The Authors. Statistics in Medicine published by John Wiley & Sons, Ltd.
MYSTIQ: a system for finding more answers by using probabilities

MystiQ is a system that uses probabilistic query semantics [3] to find answers in large numbers of data sources of less than perfect quality. There are many reasons why the data originating from many different sources may be of poor quality, and therefore difficult to query: the same data item may have different representation in different sources; the schema alignments needed by a query system are imperfect and noisy; different sources may contain contradictory information, and, in particular, their combined data may violate some global integrity constraints; fuzzy matches between objects from different sources may return false positives or negatives. Even in such environment, users some-times want to ask complex, structurally rich queries, using query constructs typically found in SQL queries: joins, subqueries, existential/universal quantifiers, aggregate and group-by queries: for example scientists may use such queries to query multiple scientific data sources, or a law enforcement agency may use it in order to find rare associations from multiple data sources. If standard query semantics were applied to such queries, all but the most trivial queries will return an empty answer.
Immunohistochemistry for Pathologists: Protocols, Pitfalls, and Tips

Immunohistochemistry (IHC) is an important auxiliary method for pathologists in routine diagnostic work as well as in basic and clinical research including exploration of biomarkers, as IHC allows confirmation of target molecule expressions in the context of microenvironment. Although there has been a considerable progress in automation and standardization of IHC, there are still many things to be considered in proper optimization and appropriate interpretation. In this review, we aim to provide possible pitfalls and useful tips for practicing pathologists and residents in pathology training. First, general procedure of IHC is summarized, followed by pitfalls and tips in each step and a summary of troubleshooting. Second, ways to an accurate interpretation of IHC are discussed, with introduction to general quantification and analysis methods. This review is not intended to provide complete information on IHC, but to be used as a basic reference for practice and publication.