Miracle-dz/UniFAR-FTUs huggingface dataset:
Erythropoietin and Friend Virus gp55 Activate Different JAK/STAT Pathways through the Erythropoietin Receptor in Erythroid Cells

ABSTRACT Abnormal erythropoietin (EPO)-independent cell growth is induced after infection of erythroid progenitor cells with a polycythemic strain of Friend virus (FVp). Binding of its Env-related glycoprotein (gp55) to the EPO receptor (EPOR) mimics the activation of the EPOR with EPO. We investigated the gp55-EPOR signaling in erythroblastoid cells from mice infected with FVp and in cells of FVp-induced or gp55-transgenic-mouse-derived erythroleukemia cell lines, comparing it with the EPO-EPOR signaling in EPO-responsive erythroblastoid cells. While the Janus protein tyrosine kinase JAK2 and the transcription factor STAT5 became tyrosine phosphorylated with the EPO stimulation in EPO-responsive erythroblastoid cells from anemic mice, JAK1 and STAT5 were constitutively tyrosine phosphorylated in all of these FVpgp55-induced erythroblastoid or erythroleukemic cells. Moreover, this constitutively tyrosine-phosphorylated STAT5 was unable to bind to its specific DNA sequences and did not translocate to the nucleus. Nuclear translocation and DNA binding of this STAT5 species required EPO stimulation. These findings clearly indicate that the FVpgp55-EPOR signaling is distinct from the EPO-EPOR signaling and suggest that STAT5 may not play an essential role in the transmission of the cell growth signals in FVp gp55-induced erythroleukemia cells.
Effect of lower doses of conjugated equine estrogens with and without medroxyprogesterone acetate on bone in early postmenopausal women.

CONTEXT Lower-than-commonly-prescribed doses of conjugated equine estrogens (CEEs) with medroxyprogesterone acetate (MPA) improve vasomotor symptoms and vaginal atrophy, provide acceptable bleeding and lipid profiles, and afford endometrial protection. This lower-dose therapy's protection against loss of bone mineral density (BMD) associated with menopause has not been thoroughly investigated. OBJECTIVE To determine the effects of lower doses of CEEs only or CEEs-MPA on spine and hip BMD, total body bone mineral content (BMC), and biochemical markers of bone turnover in postmenopausal women. DESIGN AND SETTING Two-year randomized, double-blind, placebo-controlled substudy of the Women's Health, Osteoporosis, Progestin, Estrogen trial, conducted at 19 US centers between August 1995 and October 2000. PARTICIPANTS Eight hundred twenty-two healthy postmenopausal women aged 40 to 65 years who were within 4 years of their last menstrual period. INTERVENTIONS Patients were randomly assigned to receive CEEs, 0.625; CEEs, 0.625 and MPA, 2.5; CEEs, 0.45; CEEs, 0.45 and MPA, 2.5; CEEs, 0.45 and MPA, 1.5; CEEs, 0.3; CEEs 0.3 and MPA, 1.5 (all doses in mg/d); or placebo for 2 years. All participants also received elemental calcium at 600 mg/d. MAIN OUTCOME MEASURES Changes from baseline in spine and total hip BMD, total body BMC, and biochemical markers of bone turnover (serum osteocalcin and urinary cross-linked N-telopeptides of type I collagen), assessed at 6-month intervals and compared among treatment groups with a modified intention-to-treat approach. RESULTS At 24 months, women assigned to all of the active treatment groups had significant gains from baseline (P<.001) in spine and hip BMD and total body BMC (except total body BMC in the group receiving CEEs, 0.3 mg/d). These changes were significantly different from those in the placebo group, in which losses of bone mass in spine and total body were evident over the course of the study (P<.001). The loss in hip BMD from baseline in the placebo group was significant at 18 (P =.02) but not at 24 months (P =.06). Osteocalcin and N-telopeptides of type I collagen were significantly reduced from baseline (P<.001) for all active treatment groups at all time points; no changes were found for the placebo group. For women treated with CEEs alone, the gains in spine BMD for the group taking CEEs, 0.625 mg/d, were significantly higher than those of the group taking CEEs, 0.3 mg/d (P =.02), but not the group treated with CEEs, 0.45 mg/d (P =.48). CONCLUSIONS Doses of CEEs or CEEs-MPA lower than 0.625 mg/d effectively increase BMD and BMC in early postmenopausal women.
Estimation of the Aqueous Solubility of Organic Molecules by the Group Contribution Approach

Several group contribution methods to estimate the aqueous solubility of organic molecules are proposed and evaluated for their ability to predict the water solubility of new molecules. The learning set consisted of 1168 organic compounds with experimental data taken from the literature after critical evaluation. The best method, based on a new fragment atom scheme, leads to a squared correlation coefficient of 0.95 and an average absolute calculation error of 0.50 log unit, which is superior to other group contribution methods currently available. One of the advantages of this model is that it has upper and lower limits so that the predicted solubilities cannot be unrealistily high or low.
Super-resolution reconstruction: using non-local structure similarity and edge sharpness dictionary

Image super-resolution (SR) reconstruction, which gains high-pixel and multi-detail image from single or several low-pixel images, has attracted increasing interest in recent years. This study proposes a new SR method based on sparse representation, which made good use of the non-local (NL) structure similarity and edge sharpness dictionary. Firstly, all the training patches are classified into different clusters according to diverse edge sharpness of patches. Secondly, different dictionaries are trained for different training patches in each cluster. Thirdly, the NL structure similarity is added into the constraint of NL structure similarity model, and the suitable dictionary is selected for current patch to achieve the coefficients according to the value of edge sharpness of patch. Finally, the high-resolution (HR) image is obtained by integrating HR patches obtained by the product of HR dictionaries and coefficients. Moreover, by calculating edge sharpness, the different dictionaries which adapt to patches with different structure are obtained, and the NL similarity is well utilised and more details are added to HR patch. Compared to some classical and common methods, the proposed method possesses better reconstruction effects in numerical and visual aspects.
Relationship of Oxidant and Antioxidant Markers to Asthma Severity in Egyptian Asthmatic Children

BACKGROUND: Asthma is a chronic airway disease which is characterized by oxidant antioxidant imbalance with the generation of oxidative stress related mediators. AIM: The study aimed to evaluate the role of asymmetric dimethylarginine, and malondialdehyde as oxidant markers and serum paraoxonase activity as an antioxidant marker in asthma, and to determine their relationship to the asthma severity and lung function among asthmatic children in Egypt. PATIENTS AND METHODS: This case control study was conducted on sixty patients with asthma compared with sixty apparently healthy children of matched age and sex. RESULTS: Serum concentrations of oxidant markers as asymmetric dimethylarginine and malondialdehyde were significantly increased in asthmatic patients while anti-oxidant marker as paraoxonase activity was significantly decreased compared to healthy controls (P < 0.05). ANOVA test revealed highly significant elevation of the serum concentrations of oxidant markers while anti-oxidant marker was significantly decreased in severe asthmatic patients (P < 0.001) compared to the patients with moderate and mild asthma respectively. Serum malondialdehyde concentration was a strong predictor of asthma severity by multiple regression analysis (P < 0.05). CONCLUSION: The study revealed an imbalance between oxidative and antioxidant defence systems in asthmatic children. Serum concentration of malondialdehyde was the most predictive biomarker having a significant association with asthma severity.
Enzyme coupled immunoassay of insulin using a novel coupling reagent.

A novel coupling reagent, meta-maleimidobenzoyl N-hydroxysuccinimide ester was synthesized. Using this reagent, insulin was conjugated very easily with beta-D-galactosidase [EC 3.2. 1.23] in neutral, aqueous solution. No reduction of the enzyme activity was observed during the coupling procedure. The competitive bindings of the conjugate and insulin to anti-insulin serum were tested. The results indicated that the conjugate has enough immune reactivity for use in enzyme coupled immunoassay. Using this assay 20-800 pg of insulin were detectable.
Biphasic Ferrogels for Triggered Drug and Cell Delivery

Ferrogels are an attractive material for many biomedical applications due to their ability to deliver a wide variety of therapeutic drugs on‐demand. However, typical ferrogels have yet to be optimized for use in cell‐based therapies, as they possess limited ability to harbor and release viable cells. Previously, an active porous scaffold that exhibits large deformations and enhanced biological agent release under moderate magnetic fields has been demonstrated. Unfortunately, at small device sizes optimal for implantation (e.g., 2 mm thickness), these monophasic ferrogels no longer achieve significant deformation due to a reduced body force. A new biphasic ferrogel, containing an iron oxide gradient, capable of large deformations and triggered release even at small gel dimensions, is presented in this study. Biphasic ferrogels demonstrate increased porosity, enhanced mechanical properties, and potentially increased biocompatibility due to their reduced iron oxide content. With their ability to deliver drugs and cells on‐demand, it is expected that these ferrogels will have wide utility in the fields of tissue engineering and regenerative medicine.
An extended-release formulation of desferrioxamine for subcutaneous administration

Desferrioxamine mesylate (DFO) remains the first line iron chelating agent. Since it has a short half-life and poor absorption through the gastrointestinal tract, DFO must be administered parenterally, usually by daily subcutaneous infusion administered over 8–12 h. The objective of this paper was the development of multivesicular liposome (depofoam) for the extended-release of DFO and study of iron excretion efficiency compared to the free form of DFO. Depofoam particles were characterized by their morphology, particle size, capture volume, and in vitro release. Also, in vivo activity of this formulation in iron overload rats was studied. The in vitro studies in 0.9% sodium chloride at 37°C showed that the multivesicular liposomes released DFO slowly over several days without a rapid initial release, and 57% of DFO was released in 9 days. Administration of a single dose of 100 mg/kg of an optimized Depo-DFO formulation in an iron overload rats, as a single bolus subcutaneous injection, led to significant elevation of urinary iron excretion at the first day that were maintained at levels of more than 110 μg/kg for 3 days. Administration of the unencapsulated DFO at the same dose resulted in elevation of urinary iron excretion in the first day (~73% amount of iron excretion by Depo-DFO) followed by a quick decline to base line levels in the second day. The total urinary iron excreted by Depo-DFO is 3-times greater than that elicited by DFO. In conclusion, Depo-DFO appears to have potential usefulness as an extended-release formulation of DFO.
GSK3β reduces risk of sporadic Parkinson's disease in ethnic Chinese

Genetic variability of glycogen synthase kinase‐3β (GSK3β) may be linked to Parkinson's disease (PD). Its role in ethnic Chinese population is still unclear. We examined the association between GSK3β variation and PD in a Han Chinese population from mainland China. Using a case–control methodology, we genotyped the single nucleotide polymorphism (SNP) in GSK3β (rs334558) to investigate the association with risk of PD. A total of 1,280 ethnic Han Chinese study subjects comprising 761 sporadic PD patients and 519 controls were recruited. The T allele of a promoter SNP rs334558 was found to reduce the risk of PD (OR = 0.82, 95% CI: 0.696–0.960, P = 0.014). Patients with CT + TT genotypes have a reduced risk of PD compared to those with CC genotype (OR = 0.61, 95% CI: 0.477–0.776, P = 6.09E−5). In addition, we demonstrated that CT + TT subjects cannot be distinguished from CC subjects based on their clinical features. Our data suggest that rs334558 variant in GSK3β reduces the risk of PD in a Han Chinese population from mainland China. Further studies of large series of subjects are necessary to fully elucidate the true role of GSK3β in PD. © 2012 Wiley Periodicals, Inc.
Systematic Mapping of Posttranslational Modifications in Human Estrogen Receptor-α with Emphasis on Novel Phosphorylation Sites*S

A systematic study of posttranslational modifications of the estrogen receptor isolated from the MCF-7 human breast cancer cell line is reported. Proteolysis with multiple enzymes, mass spectrometry, and tandem mass spectrometry achieved very high sequence coverage for the full-length 66-kDa endogenous protein from estradiol-treated cell cultures. Nine phosphorylated serine residues were identified, three of which were previously unreported and none of which were previously observed by mass spectrometry by any other laboratory. Two additional modified serine residues were identified in recombinant protein, one previously reported but not observed here in endogenous protein and the other previously unknown. Although major emphasis was placed on identifying new phosphorylation sites, N-terminal loss of methionine accompanied by amino acetylation and a lysine side chain acetylation (or possibly trimethylation) were also detected. The use of both HPLC-ESI and MALDI interfaced to different mass analyzers gave higher sequence coverage and identified more sites than could be achieved by either method alone. The estrogen receptor is critical in the development and progression of breast cancer. One previously unreported phosphorylation site identified here was shown to be strongly dependent on estradiol, confirming its potential significance to breast cancer. Greater knowledge of this array of posttranslational modifications of estrogen receptor, particularly phosphorylation, will increase our understanding of the processes that lead to estradiol-induced activation of this protein and may aid the development of therapeutic strategies for management of hormone-dependent breast cancer.
Mortality and serum insulin-like growth factor (IGF)-I and IGF binding protein 3 concentrations.

BACKGROUND Previous studies provided conflicting results regarding the association of serum IGF-I or IGF-binding protein-3 (IGFBP-3) and mortality. The aim of this study was to assess the relation of IGF-I and IGFBP-3 levels with mortality from all causes, cardiovascular disease (CVD), and cancer in a prospective population-based study. METHODS From the Study of Health in Pomerania (SHIP) 1988 men and 2069 women aged 20-79 yr were followed up on average 8.5 yr. Causes of deaths were coded according to the International Classification of Diseases, 10th revision. Serum IGF-I and IGFBP-3 levels were determined by chemiluminescence immunoassays and categorized into three groups (low, normal, high) according to the sex- and age-specific 10th and 90th percentiles. RESULTS Adjusted analyses revealed that men with low but not high IGF-I levels had an almost 2-fold higher risk of all-cause mortality [hazard ratio (HR) 1.92 (95% confidence interval [CI] 1.35; 2.73)], CVD mortality [HR 1.92 (95% CI 1.00; 3.71)], and cancer mortality [HR 1.85 (95% CI 1.00; 3.45)] compared with men with normal IGF-I levels. In women, no association between IGF-I and mortality was found. Moreover, low IGFBP-3 levels were associated with higher all-cause mortality in men [HR 1.87 (95% CI 1.31; 2.64)] and women [HR 1.63 (95% CI 0.96; 2.76)]. CONCLUSIONS The present study found inverse associations between IGF-I or IGFBP-3 levels and mortality from all causes, CVD, or cancer in men and between IGFBP-3 and all-cause mortality in women.
Supply Chain Contracts Coordination with Consumer's Strategic Returns Policies under the Service Level Constraint

Consider a kind of supply chain system consisting of one manufacturer,one retailer and a group of consumers.A consumer strategic returns model involving in consumer individual decisions is formulated,in which the optimal price,ordering quantities as well as returns policies are given under the service-level constraint.Next,since the two-sides-marginalization exists in the decentralized supply chain,three contracts,that is,traditional buy-back contract,differentiated buyback contract and sale-rebate contract are designed to coordinate the supply chain and their coordination mechanisms are further discussed.Results show that the traditional buy-back contract and sale-rebate contract cannot attain the supply chain coordination,while the rest can realize the supply chain coordination.Finally,the impacts of the service-level constraint on supply chain's profits and the effect of differentiated buy-back contract were analyzed by numerical analysis.
Simultaneous Analysis of Hundreds of Y‐Chromosomal SNPs for High‐Resolution Paternal Lineage Classification using Targeted Semiconductor Sequencing

SNPs from the non‐recombining part of the human Y chromosome (Y‐SNPs) are informative to classify paternal lineages in forensic, genealogical, anthropological, and evolutionary studies. Although thousands of Y‐SNPs were identified thus far, previous Y‐SNP multiplex tools target only dozens of markers simultaneously, thereby restricting the provided Y‐haplogroup resolution and limiting their applications. Here, we overcome this shortcoming by introducing a high‐resolution multiplex tool for parallel genotyping‐by‐sequencing of 530 Y‐SNPs using the Ion Torrent PGM platform, which allows classification of 432 worldwide Y haplogroups. Contrary to previous Y‐SNP multiplex tools, our approach covers branches of the entire Y tree, thereby maximizing the paternal lineage classification obtainable. We used a default DNA input amount of 10 ng per reaction but preliminary sensitivity testing revealed positive results from as little as 100 pg input DNA. Furthermore, we demonstrate that sample pooling using barcodes is feasible, allowing increased throughput for lower per‐sample costs. In addition to the wetlab protocol, we provide a software tool for automated data quality control and haplogroup classification. The unique combination of ultra‐high marker density and high sensitivity achievable from low amounts of potentially degraded DNA makes this new multiplex tool suitable for a wide range of Y‐chromosome applications.
Cognitively Inspired Real-Time Vision Core

We introduce a cognitively inspired novel binary image representation and utilize it for real-time operating computer vision core, which is capable of simultaneously detecting a specific object in an image, classifying an image region provided by an algorithm such as motion detection, and tracking multiple objects in a video. In this framework, hidden layer representations of binary receptive field neural networks are utilized to generate compact image representations for various classification based functionalities. Object detection is implemented by learning a classifier on hidden layer activities and performing sliding window based search on the image. Morever, a classification based object tracking algorithm is introduced that uses the proposed framework, whose tracking performance in standard datasets is shown to be comparable to the state of the art Email addresses: ozyilmaz@turgutozal.edu. tr (Ozgur Yilmaz), iozsarac@aselsan.com. tr (Ismail Ozsarac), ogunay@aselsan.com. tr (Omer Gunay), huozkan@aselsan.com. tr (Huseyin Ozkan) 1Corresponding author Preprint submitted to Journal of LTEX Templates May 7, 2015 techniques. We further propose several additional functionalities on the same core, such as sparse interest point extraction, salient motion detection, scene recognition. These set of capabilities in the arsenal, artificial vision is expected to perform the necessary fundamental operations in real time, paving a way for more complex inferences, such as geometric computations and cross-modal information fusion.
Protein microarray analysis identifies cyclic nucleotide phosphodiesterase as an interactor of Nogo‐A

Nogo‐A, a neurite outgrowth inhibitor, is expressed exclusively on oligodendrocytes and neurons in the CNS. The central domain of Amino‐Nogo spanning amino acids 567–748 in the human Nogo‐A designated NIG, mediates persistent inhibition of axonal outgrowth and induces growth cone collapse by signaling through an as yet unidentified NIG receptor. We identified 82 NIG‐interacting proteins by screening a high‐density human protein microarray composed of 5000 proteins with a recombinant NIG protein as a probe. Following an intensive database search, we selected 12 neuron/oligodendrocyte‐associated NIG interactors. Among them, we verified the molecular interaction of NIG with 2′, 3′‐cyclic nucleotide 3′‐phosphodiesterase (CNP), a cell type‐specific marker of oligodendrocytes, by immunoprecipitation and cell imaging analysis. Although CNP located chiefly in the cytoplasm of oligodendrocytes might not serve as a cell‐surface NIG receptor, it could act as a conformational stabilizer for the intrinsically unstructured large segment of Amino‐Nogo.
Ultra-Wideband Radar Diffraction Approximation for Dielectric Edges

In this paper, a diffraction simulation for dielectric edges is introduced. The simulation is based on geometrical theory of diffraction (GTD) and is implemented as an improvement of the millimeter-wave surface characterization. This material characterization technique has been introduced in [1] and uses the microwave ellipsometry. The subject of current investigations is the usage of autonomous security robots for the detection of hot spots, the localization and characterization of objects. These robots should support fire brigades or disaster relief teams by millimeter-wave surface characterization. The developed technique was inspired by the established optical ellipsometry. The optical characterization technique does not consider the effect diffraction at the edges of the surface. Hence, the ellipsometry is limited to large surfaces where the diffraction effects can be neglected, but for the supposed application it is necessary to compensate these effects.
A silencer element from the alpha-globin gene inhibits expression of beta-like genes

We have studied the cis and trans interactions of the alpha- and beta-globin genes in a transient expression system. We found that the alpha-globin gene inhibited beta-globin expression in cis but not in trans. The silencer element responsible for this inhibition was localized to a 259-base-pair fragment at the 5' end of the alpha-globin gene.
Non-Local Estimation of Speech Signal for Vowel Onset Point Detection in Varied Environments

Vowel onset point (VOP) is an important information extensively employed in speech analysis and synthesis. Detecting the VOPs in a given speech sequence, independent of the text contexts and recording environments, is a challenging area of research. Performance of existing VOP detection methods have not yet been extensively studied in varied environmental conditions. In this paper, we have exploited the non-local means estimation to detect those regions in the speech sequence which are of high signal-to-noise ratio and exhibit periodicity. Mostly, those regions happen to be the vowel regions. This helps in overcoming the ill-effects of environmental degradations. Next, for each short-time frame of estimated speech sequence, we cumulatively sum the magnitude of the corresponding Fourier transform spectrum. The cumulative sum is then used as the feature to detect the VOPs. The experiments conducted on TIMIT database show that the proposed approach provides better results in terms of detection and spurious rate when compared to a few existing methods under clean and noisy test conditions.