Miracle-dz/UniFAR-FTUs huggingface dataset:
Reduction of the concentration difference of proteins in biological liquids using a library of combinatorial ligands

The discovery of polypeptides and proteins with relevance to a particular biological state is complicated by their vast number and concentration range in most biological mixtures. Depletion methodologies are frequently used to remove the most abundant species; however, this removal not only fails significantly to enrich trace proteins, it may also nonspecifically deplete them due to their interactions with the removed high‐abundance proteins. Here we report a simple‐to‐use methodology that reduces the protein concentration range of a complex mixture like whole serum through the simultaneous dilution of high‐abundance proteins and the concentration of low‐abundance proteins. This methodology utilizes solid‐phase ligand libraries of immense diversity, generated by “split, couple, recombine” combinatorial chemistry, that are used for affinity‐based binding to the proteins of a given mixture. With a controlled sample‐to‐ligand ratio it is possible to modulate the relative concentration of proteins such that many peptides or proteins that are undetectable by classical analytical methods become easily accessible. The reduction in the dynamic range of unfractionated serum is specifically described along with treatment of other proteomes such as extracts from Escherichia coli, chicken egg white and cell culture supernatant. Mono‐ and bi‐dimensional electrophoresis (1‐DE and 2‐DE respectively) and surface‐enhanced laser desorption/ionization‐mass spectrometry (SELDI‐TOF‐MS) technology demonstrate the reduction in protein concentration range. Combining this approach with additional fractionation methods further increased the number of detectable species.
Peripheral Blood Mononuclear Cells Infiltration Downregulates Decidual FAAH Activity in an LPS‐Induced Embryo Resorption Model

Maternal infections with gram‐negative bacteria are associated with miscarriage and are one of the most common complications during pregnancy. Previous studies from our group have shown that lipopolysaccharide (LPS)‐activated infiltrating peripheral blood mononuclear cells (PBMC) into decidual tissue plays an important role in the establishment of a local inflammatory process that results in embryo cytotoxicity and early embryo resorption. Moreover, we have also shown that an increased endocannabinoid tone mediates LPS‐induced deleterious effects during early pregnancy loss. Here, we sought to investigate whether the infiltrating PBMC modulates the decidual endocannabinoid tone and the molecular mechanisms involved. PBMC isolated from 7‐day pregnant mice subjected to different treatments were co‐cultured in a transwell system with decidual tissue from control 7‐day pregnant mice. Decidual fatty acid amide hydrolase (FAAH) activity was measured by radioconvertion, total decidual protein nitration by Western blot (WB), and decidual FAAH nitration by immunoprecipitation followed by WB. We found that co‐culture of PBMC obtained from LPS‐treated mice increased the level of nitration of decidual FAAH, which resulted in a negative modulation of decidual FAAH activity. Interestingly, co‐treatment with progesterone or aminoguanidine prevented this effect. We found that LPS‐treated PBMC release high amounts of nitric oxide (NO) which causes tyrosine nitration of decidual FAAH, diminishing its enzymatic activity. Inactivation of FAAH, the main degrading enzyme of anandamide and similar endocannabinoids, could lead to an increased decidual endocannabinoid tone with embryotoxic effects. J. Cell. Physiol. 232: 1441–1447, 2017. © 2016 Wiley Periodicals, Inc.
Expression of mutant ubiquitin (UBB+1) and p62 in myotilinopathies and desminopathies

Protein aggregates in muscle cells are the morphological hallmark of myofibrillar myopathies, including myotilinopathies and desminopathies. The aim of the present study is to analyse the expression of mutant ubiquitin (UBB+1), an aberrant form of ubiquitin which accumulates in certain disorders characterized by intracellular aggregates of proteins, and p62, a multimeric signal protein which plays an active role in aggregate formation, in muscle biopsies from patients suffering from myotilinopathy and desminopathy in order to gain understanding of the mechanisms leading to protein aggregation in these disorders. Single immunohistochemistry, and single‐ and double‐labelling immunofluorescence and confocal microscopy for UBB+1 and p62, has been performed in muscle biopsies from patients suffering from myotilinopathy and desminopathy. Strong UBB+1 immunoreactivity, colocalizing with myotilin aggregates, was found in muscle fibres in myotilinopathies. UBB+1 accumulation, colocalizing with desmin aggregates, also occurs in desminopathies. In addition, strong p62 immunoreactivity colocalizing with myotilin aggregates was observed in myotilinopathies. Similarly, p62 immunoreactivity colocalizing with desmin aggregates was found in desminopathies. The present findings suggest that accumulation of protein aggregates in myotilinopathies and in desminopathies may be related with UBB+1/abnormal protein complexes which are resistant to proteasome degradation. Furthermore, these observations suggest a relationship between the presence of p62 and the formation of inclusions in different subtypes of myofibrillar myopathies.
State-feedback control design for continuous-time piecewise linear systems: An LMI approach

This paper studies the problem of state-feedback control design for a class of continuous-time piecewise linear systems. A new framework for the synthesis of piecewise linear control systems is given based on piecewise quadratic Lyapunov function and Reciprocal Projection Lemma. Under the new framework, Lyapunov variables and system dynamic matrices are separated by adding extra variables. And state-feedback control design for piecewise linear systems can be expressed in terms of linear matrix inequalities (LMIs). An example is given to illustrate the effectiveness of the proposed method.
Interleukin‐10 gene polymorphism influences the prognosis of T‐cell non‐Hodgkin lymphomas

Interleukin‐10 (IL‐10) is one of the cytokines implicated in the pathogenesis of diffuse large B‐cell lymphoma (DLBCL) in which it acts as auto/paracrine growth factor for lymphoma growth. T‐cell non‐Hodgkin lymphoma (NHL) is a heterogeneous disease, the biological basis of which is not fully understood. Some evidence suggests that IL‐10 might be associated with the progression of T‐cell NHLs and that IL‐10 may be involved in a rescue effect, protecting T cells from apoptotic cell death associated with upregulated bcl‐2 expression. The current study evaluated the impact of IL‐10 gene (IL10) polymorphism on the response to chemotherapy and survival in T‐cell NHL. IL10 polymorphisms were determined in 108 patients with T‐cell NHL. The response to chemotherapy was not dependent on IL10 polymorphism, while survival differed significantly according to IL10 polymorphism. The group with ATA haplotype showed superior overall survival (61·2 ± 5·9% vs. 21·2 ± 11·7%, P = 0·001) and failure‐free survival (35·0 ± 5·7% vs. 13·2 ± 8·7%, P = 0·001) compared to those without ATA haplotype. The ATA haplotype was identified as a favourable prognostic factor compared to non‐ATA haplotype (P = 0·037, hazard ratio 2·1), together with international prognostic index (IPI) in a multivariate model for overall survival. In conclusion, IL10 polymorphism may affect the survival of T‐cell NHL patients.
How accurately do adult sons and daughters report and perceive parental deaths from coronary disease ?

OBJECTIVES To describe how adult sons and daughters report and perceive parental deaths from heart disease DESIGN Two generation family study. SETTING West of Scotland. SUBJECTS 1040 sons and 1298 daughters aged 30–59 from 1477 families, whose fathers and mothers were aged 45–64 in 1972–76 and have been followed up for mortality over 20 years. OUTCOME Perception of a “family weakness” attributable to heart disease. RESULTS 26% of sons and daughters had a parent who had died of coronary heart disease (CHD). The proportion was higher in older offspring (+18% per 10 year age difference) and in manual compared with non-manual groups (+37%). Eighty nine per cent of parental deaths from CHD were correctly reported by offspring. Only 23% of sons and 34% of daughters with at least one parent who had died of CHD considered that they had a family weakness attributable to heart disease. Perceptions of a family weakness were higher when one or both parents had died of CHD, when parental deaths occurred at a younger age, in daughters compared with sons and in offspring in non-manual compared with manual occupations. CONCLUSIONS Only a minority of sons and daughters with experience of a parent having died from CHD perceive this in terms of a family weakness attributable to heart disease. Although men in manual occupations are most likely to develop CHD, they are least likely to interpret a parental death from CHD in terms of a family weakness. Health professionals giving advice to patients on their familial risks need to be aware of the difference between clinical definitions and lay perceptions of a family history of heart disease.
Primary anorectal malignant melanoma: rare but highly lethal malignancy

Primary anorectal malignant melanoma (MM) is a rare but highly lethal malignancy. The aim of this study was to present an overview of the clinical features and treatment strategies in patients with anorectal MM. Materials and methods: Nine patients who were diagnosed with anorectal MM between 1998 and 2010 were reviewed retrospectively. Results: The median age of the patients was 51 years (range: 28-75). The sex ratio of male to female was 1:2. The main presenting symptom was rectal bleeding. At the time of diagnosis, 1 patient was stage IV and 8 patients were stage III. All of the patients underwent an abdominoperineal resection. Only 1 patient received adjuvant immunotherapy and 8 patients received palliative immunotherapy or dacarbazine and/or platinum-based chemotherapy. The median progression-free survival was 31 weeks (range: 6-211). Sites of metastasis were the lung, liver, and brain in order of frequency. The median overall survival was 81 weeks (range: 54-229). Conclusion: Clear guidelines for the therapy of anorectal MM have not been established. In the treatment plan of primary anorectal MM, multimodal treatment options involving surgery, radiotherapy, and systemic treatment with chemotherapeutics or biological agents should be considered.
A seamless transfer algorithm based on frequency detection and feedforward control method in distributed generation system

This paper proposes a control strategy for grid interactive Power Conditioning System (PCS) which has a feedforward voltage control based on grid frequency detection. The PCS should supply the power to the critical load, regardless of the grid condition. In order to provide the power to the critical load continuously, the PCS should operate two modes. One is Grid-Connected mode and the other is Stand-Alone mode. It is important to know the grid condition to decide operation modes. This paper proposes a control method based on the grid frequency to detect the grid condition and consists of a current controller and a feedforward voltage controller. The grid frequency detection is able to reduce the grid fault detection time and a feedforward voltage controller helps voltage regulation fast. This proposed control strategy is verified by the simulation and experimental results.
Vision-based real-time detection of objects with non-homogeneous color distributions using a fuzzy classifier

This paper proposes a real-time object detection method based on a fast feature extraction method and a fuzzy classifier. In particular, this paper considers the challenging task of detecting an object whose appearance is with multiple and non-uniform color distribution. The proposed detection method is implemented in a real-time object detection system using a pan-tilt-zoom camera. Color histogram obtained from distributions of the appearance of an object on a non-uniformly partitioned hue and saturation (HS) color space is used as a feature vector. An efficient method for histogram extraction during the image scanning process is proposed for real-time implementation. For each search window, only histograms of the non-overlapping parts between two successive windows are computed, which reduces detection time. The classifier used is a fuzzy classifier with support vector learning. Experimental results using a pan-tilt-zoom camera verify efficiency of the feature extraction method.
The effects of task demand and web information type on recognition of verbal emotional advertising

Studies report that users avoid looking at areas they consider to display advertising. The objective of the present study was to systematically investigate the influences of task demand, and web information type on recognition of verbal emotional advertising when people focus on a primary task. Our findings contribute important insights into preattentive procssing research. First, the empirical evidence implies that preattentive procssing can extract enough semantic information from nonfocal verbal stimuli to determine the emotional content of a nonfocal word. Second, the study suggests the driver of attentional interference effects may be impacted by the visual field. Finally, the comparison between text-based and picture-based webpage indicates that the recognition of positive emotional headlines outperforms the recognition of negative ones in the picture-based webpage. Headlines featuring high arousal words were recognized more often than headlines featuring low arousal words. These findings provide strategies of ad copy and placement for marketers.
Radial Modulation of Microbubbles for Ultrasound Contrast Imaging

Over the past few years, extensive research has been carried out in the field of ultrasound contrast imaging. In addition to the development of new types of ultrasound contrast agents, various imaging methods dedicated to contrast agents have been introduced, and some of them are now commercially available. In this study, we present results of an imaging technique that is capable of detecting echoes from microbubbles and eliminating those emanating from nonoscillating structures (tissue), thereby enhancing contrast imaging. The method is based on mixing a low frequency (LF) modulator signal and a high frequency (HF) imaging signal to effectively modulate the size of the contrast microbubble through its volumetric oscillations using the LF signal and to probe the radial motion using the HF imaging signal. To evaluate the performances and limitations of the method, high-speed optical observations and acoustic measurements were carried out on soft-shelled microbubbles. The results showed that, by incorporating the modulator signal, the bubbles respond differently compared to the HF excitation alone. The decorrelation between the signals obtained at the compression and expansion phase of the modulator signal is significantly high to be used as a parameter to detect contrast microbubbles and discriminate them from tissue. The echo received from a solid reflector shows identical responses during the compression and rarefaction phase of the LF signal. In conclusion, these results demonstrate the feasibility of this fully linear approach for improving the contrast detection.
A linear-quadratic unsupervised hyperspectral unmixing method dealing with intra-class variability

In hyperspectral imagery, unmixing methods are often used to analyse the composition of the pixels. Such methods usually suppose that a unique spectral signature, called an endmember, can be associated with each pure material present in the scene. This assumption is no more valid for materials that exhibit spectral variability due to illumination conditions, weathering, slight variations of the composition, etc. Methods currently appear dealing with this spectral variability and based on linear mixing assumption. However, intra-class variability issues frequently appear in nonflat scenes, and particularly in urban scenes. For urban scenes, the linear-quadratic mixing models better depict the radiative transfer. In this paper, we propose a new unsupervised unmixing method based on the assumption of a linear-quadratic mixing model, that deals with intra-class spectral variability. A new formulation of linear-quadratic mixing is proposed. An unmixing method is presented to process this new model. The method is tested on a semi-synthetic data set built with spectra extracted from a real hyperspectral image and mixtures of these spectra. Based on the results of nonlinear and linear unmixing, we discuss the interest of considering the nonlinearity regarding the impact of intra-class variability.
An assessment of in vitro androgenic activity and the identification of environmental androgens in United Kingdom estuaries

Environmental androgens are a group of compounds that to date have received very little attention. In this study, a yeast‐based androgen screen (YAS) was used to determine the level of in vitro androgenic activity in seven United Kingdom estuaries. Surface water, sediment pore water, and sediment particulate material solvent extracts collected from Southampton Water, the Thames, Mersey, Tees, Tyne, Clyde, and Forth were tested for in vitro androgenic activity. Eleven of the 41 surface water samples collected displayed androgenic activity >2 ng dihydrotestosterone (DHT) equivalents/L (3–9 ng DHT/L), while eight of the 39 sediment pore waters collected showed activity >45 ng DHT/L (51–187 ng DHT/L). High levels of androgenic activity were determined in the solvent extracts of sediments, with 10 of 39 samples exhibiting a level of androgenic activity >454 ng DHT/kg (1,020‐15,300 ng DHT/kg). In vitro YAS testing of five selected sewage treatment works (STW) effluents entering these estuaries showed that measurable levels (34–635 ng DHT/L) of androgenic activity were observed in those receiving only primary treatment (Howdon STW and Irvine Valley Sewer) at the time of the survey. A toxicity identification evaluation (TIE) study of Irvine Valley Sewer effluent using the YAS assay was used to identify the natural steroids/steroid metabolites dehydrotestosterone, androstenedione, androstanedione, 5β‐androstane‐3α, 11β‐diol‐17‐one, androsterone, and epi‐androsterone as responsible for 99% of the in vitro activity determined in the effluent.
2015 Recommendations for the Management of Polymyalgia Rheumatica: A European League Against Rheumatism/American College of Rheumatology Collaborative Initiative

Therapy for polymyalgia rheumatica (PMR) varies widely in clinical practice as international recommendations for PMR treatment are not currently available. In this paper, we report the 2015 European League Against Rheumatism (EULAR)/American College of Rheumatology (ACR) recommendations for the management of PMR. We used the Grading of Recommendations, Assessment, Development and Evaluation (GRADE) methodology as a framework for the project. Accordingly, the direction and strength of the recommendations are based on the quality of evidence, the balance between desirable and undesirable effects, patients’ and clinicians’ values and preferences, and resource use. Eight overarching principles and nine specific recommendations were developed covering several aspects of PMR, including basic and follow‐up investigations of patients under treatment, risk factor assessment, medical access for patients and specialist referral, treatment strategies such as initial glucocorticoid (GC) doses and subsequent tapering regimens, use of intramuscular GCs and disease modifying anti‐rheumatic drugs (DMARDs), as well as the roles of non‐steroidal anti‐rheumatic drugs and non‐pharmacological interventions. These recommendations will inform primary, secondary and tertiary care physicians about an international consensus on the management of PMR. These recommendations should serve to inform clinicians about best practices in the care of patients with PMR.
Perfusion estimation using subharmonic contrast microbubble signals

Contrast enhanced subharmonic imaging (SHI) may facilitate estimation of quantifiable flow parameters such as perfusion. A modified Logiq 9 scanner operating in grayscale SHI mode was used to measure SHI time intensity curves in a flow phantom. Different concentrations (1 and 2% by volume) of the contrast agent Optison and flow rates (9.8 and 19.6 ml/min) were evaluated. In vivo, 4 dogs received intravenous contrast injections (dose: 0.1 ml/kg) and renal SHI was performed. Low perfusion states were induced by ligating surgically exposed segmental renal arteries. Following 3 contrast injections a microvascular staining technique based on stable (non-radioactive), isotope labeled microspheres was employed to quantify the degree of perfusion in 8 sections of each kidney. Digital clips were transferred to a PC: and SHI time intensity curves acquired in each section using Image-Pro Plus software. SHI fractional blood volumes (FBV) were calculated and the perfusion estimated from the initial slope of the FBV uptake. In vitro, SHI intensity increased approximately linearly with time as the bubbles flowed in. The slopes of the uptake curves were estimated to 0.0074, 0.016 and 0.015 s/sup -1/, respectively. The slope approximately doubled when either concentration or flow rate doubled. In vivo, 270 SHI time intensity curves were acquired. SHI perfusion estimates correlated significantly with microsphere results (r = 0.57; p < 0.0001). The best SHI perfusion estimates occurred for high perfusion states in the anterior of the kidneys (r = 0.73; p = 0.0001). In conclusion, SHI perfusion estimates have been obtained in vitro and in vivo. The perfusion estimates were in reasonable agreement with a microvascular staining technique.
Genetic variants in surfactant, pulmonary‐associated protein D (SFTPD) and Japanese susceptibility to ulcerative colitis

Background: Identifying culprit genes for a complex trait in a homogeneous population such as the Japanese remains challenging. We aimed to use previous achievements of genome‐wide association studies to identify precise susceptibility loci for inflammatory bowel disease in Japanese people and to simultaneously investigate the replication of recently identified susceptibility loci. Methods: An unrelated Japanese population of 174 Crohn's disease patients, 296 ulcerative colitis (UC) patients, and 394 healthy controls was consecutively enrolled in this study. Genotype and haplotype analyses focusing on susceptibility to inflammatory bowel disease were performed using 7 single nucleotide polymorphisms (SNPs) including 5 HapMap tag SNPs within surfactant, pulmonary‐associated protein D (SFTPD) along with the 2 Caucasian susceptibility loci. We performed fine‐scale mapping of trait‐associated loci with the extension of a shattered coalescent process in a Bayesian framework. Epistasis on disease phenotypes was statistically explored with the interaction dendrogram. Results: A minor allele G of rs911887 reached statistical significance for susceptibility to UC. The 2‐allele haplotype GG comprising rs911887 and rs2243639 (Ala160Thr) within SFTPD was significantly associated with susceptibility to UC. A posterior density plot shows that trait‐associated variants in the vicinity of rs911887 are likely to exist. An association between NKX2‐3 and UC susceptibility was replicated and diverse evidence of epistasis in Japan was suggested. Conclusions: This preliminary study suggests that SFTPD is both a susceptibility gene and a disease‐modifying gene for UC in Japanese. Replication of the causality and functional analyses of SFTPD is urgently warranted. (Inflamm Bowel Dis 2009;)