Miracle-dz/UniFAR-FTUs huggingface dataset:
Towards Functional Proteomics of Membrane Protein Complexes in Synechocystis sp. PCC 68031

The composition and dynamics of membrane protein complexes were studied in the cyanobacterium Synechocystis sp. PCC 6803 by two-dimensional blue native/SDS-PAGE followed by matrix-assisted laser-desorption ionization time of flight mass spectrometry. Approximately 20 distinct membrane protein complexes could be resolved from photoautotrophically grown wild-type cells. Besides the protein complexes involved in linear photosynthetic electron flow and ATP synthesis (photosystem [PS] I, PSII, cytochrome b6f, and ATP synthase), four distinct complexes containing type I NAD(P)H dehydrogenase (NDH-1) subunits were identified, as well as several novel, still uncharacterized protein complexes. The dynamics of the protein complexes was studied by culturing the wild type and several mutant strains under various growth modes (photoautotrophic, mixotrophic, or photoheterotrophic) or in the presence of different concentrations of CO2, iron, or salt. The most distinct modulation observed in PSs occurred in iron-depleted conditions, which induced an accumulation of CP43′ protein associated with PSI trimers. The NDH-1 complexes, on the other hand, responded readily to changes in the CO2 concentration and the growth mode of the cells and represented an extremely dynamic group of membrane protein complexes. Our results give the first direct evidence, to our knowledge, that the NdhF3, NdhD3, and CupA proteins assemble together to form a small low CO2-induced protein complex and further demonstrate the presence of a fourth subunit, Sll1735, in this complex. The two bigger NDH-1 complexes contained a different set of NDH-1 polypeptides and are likely to function in respiratory and cyclic electron transfer. Pulse labeling experiments demonstrated the requirement of PSII activity for de novo synthesis of the NDH-1 complexes.
Optical remote sensing applications in viticulture - a review

The emergence of precision agriculture technologies and an increasing demand for higher quality grape products have led to a growing interest in the practice of precision viticulture; monitoring and managing spatial variations in productivity-related variables within single vineyard blocks. Potentially, one of the most powerful tools in precision viticulture is the use of remote sensing, which has the ability to rapidly provide a description of grapevine shape, size and vigour over entire vineyards. Its potential for improving viticultural practice will rely on being able to define useful relationships between these canopy descriptors and grape quality and yield. This paper introduces the reader to remote sensing and reviews its recent, and potential, applications in viticulture.
Fgf-Dependent Glial Cell Bridges Facilitate Spinal Cord Regeneration in Zebrafish

Adult zebrafish show a remarkable capacity to regenerate their spinal column after injury, an ability that stands in stark contrast to the limited repair that occurs within the mammalian CNS post-injury. The reasons for this interspecies difference in regenerative capacity remain unclear. Here we demonstrate a novel role for Fgf signaling during glial cell morphogenesis in promoting axonal regeneration after spinal cord injury. Zebrafish glia are induced by Fgf signaling, to form an elongated bipolar morphology that forms a bridge between the two sides of the resected spinal cord, over which regenerating axons actively migrate. Loss of Fgf function inhibits formation of this “glial bridge” and prevents axon regeneration. Despite the poor potential for mammalian axonal regeneration, primate astrocytes activated by Fgf signaling adopt a similar morphology to that induced in zebrafish glia. This suggests that differential Fgf regulation, rather than intrinsic cell differences, underlie the distinct responses of mammalian and zebrafish glia to injury.
Black Like Me: How Idealized Images of Caucasian Women Affect Body Esteem and Mood States of African-American Females.

Using the theory of social comparison, the present research explores how exposure to idealized images of physically attractive Caucasian women affects and changes the self-reported esteem levels of African-American women. Though research reveals that the number of portrayals of African-Americans in ads is growing, little if any research has explored how images and advertisements influence behaviors and attitudes toward advertising images and messages. A sample of African-American females was surveyed on body esteem and other self-perception variables. The sample was then later exposed to 18 images of physically attractive females after which a second measure of body esteem was assessed. Unlike Caucasian females, data show that self-esteem levels for this African-American sample of females were relatively unaffected and changed after exposure to idealized images of physical attractive, thin, beautiful Caucasian models. Theoretical implications are discussed with respect to future research in the area of racial issues and mass media effects. Idealized images and women of color HOW IDEALIZED IMAGES IN PRINT ADS AFFECT WOMEN OF COLOR The purpose of this research is to examine the effects of idealized images of Caucasian women in print ads on women of color (the terms "African-American," "women of color," "black," are and will be used interchangeably throughout this paper). Academic research has continued to explore and examine the frequency and portrayal of African-Americans in advertising (see for example, Taylor and Stern, 1997; Taylor, Lee, & Stern, 1995; Zinkhan, Qualls, and Biswas, 1990). Yet, there has been little to no analysis on the effects of Caucasian or African-American images used in ads on the attitudes and purchase behaviors of members of various ethnic groups. From a strategic standpoint, advertisers know that in order to ensure that audiences are effectively responding to advertisements, black models may be more effective than white models when communicating with (and persuading) a black target audience (Bush, Hair, & Solomon, 1979; Choudhury & Schmid, 1974; Green, 2000; Wheatley, 1971; Whittler, 1991). Despite this evidence, it is not commonplace, but more a rare occurrence to find "ethnic" ads with African-American images as main characters in advertisements placed in mainstream media (e.g., Bowen & Schmid, 1997).
A real-time adaptive oxygen transfer rate estimator for metabolism tracking in escherichia coli cultures

Oxygen transfer rate (OTR) is the most significant signal for aerobic bioprocess control, since most microbic metabolic activity relies on oxygen consumption. However, accurate estimation of OTR is challenging due to the difficulty of determining uncertain oxygen transfer parameters and system dynamics. This paper presents an adaptive estimator, which incorporates exhaust gas, stir speed and dissolved oxygen measurements, to predict the real-time OTR. The design of this estimator takes into account the headspace dilution effect, off-gas sensor dynamics and uncertain oxygen transfer parameters. Through simulation the estimated real-time OTR is shown to accurately track quick changes of oxygen demand in the culture. Thus, it can be applied to a variety of controls and estimation purposes, such as determining when the culture is in oxidative or overflow metabolism.
Genetic Disease and Mouse Models Potassium Ion Movement in the Inner Ear : Insights from

Physiological Society. ESSN: 1548-9221. Visit our website at http://www.the-aps.org/. American Physiological Society, 9650 Rockville Pike, Bethesda MD 20814-3991. Copyright © 2009 the American the physiological developments. It is published bimonthly in February, April, June, August, October, and December by (formerly published as News in Physiological Science) publishes brief review articles on major Physiology by gest on N ovem er 7, 2016 http://physioline.physiology. org/ D ow nladed fom
Incremental training of Restricted Boltzmann Machines using information driven saccades

In the context of developmental robotics, a robot has to cope with complex sensorimotor spaces by reducing their dimensionality. In the case of sensor space reduction, classical approaches for pattern recognition use either hardcoded feature detection or supervised learning. We believe supervised learning and hard-coded feature extraction must be extended with unsupervised learning of feature representations. In this paper, we present an approach to learn representations using space-variant images and saccades. The saccades are driven by a measure of quantity of information in the visual scene, emerging from the activations of Restricted Boltzmann Machines (RBMs). The RBM, a generative model, is trained incrementally on locations where the system saccades. Our approach is implemented using real data captured by a NAO robot in indoor conditions.
Neuropathology and pathogenesis of HIV encephalopathies.

The nervous system is frequently affected in patients with the acquired immune deficiency syndrome (AIDS). In addition to opportunistic CNS infections and cerebral lymphomas, approx. 20% of the patients develop HIV-associated encephalopathies. Two major histopathological manifestations are observed. HIV leukoencephalopathy (progressive diffuse leukoencephalopathy) is characterized by a diffuse loss of myelin in the deep white matter of the cerebral and cerebellar hemispheres, with scattered multinucleated giant cells and microglia but scarce or absent inflammatory reaction. HIV encephalitis (multinucleated giant cell encephalitis) is associated with accumulations of multinucleated giant cells, inflammatory reaction and often focal necroses. In some patients, both patterns may overlap. In order to identify the HIV genome in the CNS, brain tissue from 27 patients was analyzed for the presence of HIV gag sequences using the polymerase chain reaction (PCR) and primers encoding a 109 base pair segment of the gag gene. Amplification of HIV gag succeeded in all 5 patients with clinical and histopathological evidence for HIV encephalopathy but was negative in the 20 AIDS patients with opportunistic bacterial, parasitic and/or viral infections or with cerebral lymphomas. These results strongly suggest that the evolution of histopathologically recognizable HIV-encephalopathies closely correlates with the presence and/or tissue concentration of HIV. Since there were no cases with amplified HIV DNA in the absence of HIV-associated tissue lesions, we conclude that harboring and replication of HIV in the CNS rapidly causes corresponding clinical and morphological changes of HIV-associated encephalopathies. In two children with severe HIV encephalomyelitis, large amounts of HIV gag and env transcripts were detected in affected areas of the brain and spinal cord by in situ hybridization. (ABSTRACT TRUNCATED AT 250 WORDS)
On Automated Hyperonym Hierarchy Construction Using an Internet Search Engine

In this paper we propose an approach for automatic construction of concept hier- archies from the snippets returned by Internet search engines using a number of well known techniques. We use surface lexical patterns to construct a set of candidate hypernyms of a given term and additional filtering that is based on both lexical patterns and distributional analysis. Preliminary experimental results for real life English examples are presented.
THREE-STEP ITERATION PROCESS FOR A FINITE FAMILY OF ASYMPTOTICALLY QUASI-NONEXPANSIVE MAPPINGS IN THE INTERMEDIATE SENSE IN CONVEX METRIC SPACES

The purpose of this paper is to establish some strong convergence theorems of three-step iteration process with errors for approximating common fixed points for a finite family of asymptotically quasi-nonexpansive mappings in the intermediate sense in the setting of convex metric spaces. The results obtained in this paper generalize, improve and unify some main results of [1]-[7], [9]-[11], [13]-[17], [19] and [21].
Cancer esearch cular and Cellular Pathobiology ermal Growth Factor Receptor Expression Identifies ctionally and Molecularly Distinct Tumor-Initiating Cells uman Glioblastoma Multiforme and Is Required R Gliomagenesis

r Res; 70( ermal growth factor receptor (EGFR) is a known diagnostic and, although controversial, prognostic r of human glioblastoma multiforme (GBM). However, its functional role and biological significance M remain elusive. Here, we show that multiple GBM cell subpopulations could be purified from the ens of patients with GBM and from cancer stem cell (CSC) lines based on the expression of EGFR f other putative CSC markers. All these subpopulations are molecularly and functionally distinct, are igenic, and need to express EGFR to promote experimental tumorigenesis. Among them, EGFRsing tumor-initiating cells (TIC) display the most malignant functional and molecular phenotype. ingly, modulation of EGFR expression by gain-of-function and loss-of-function strategies in GBM nes enhances and reduces their tumorigenic ability, respectively, suggesting that EGFR plays a funtal role in gliomagenesis. These findings open up the possibility of new therapeutically relevant damen scenarios, as the presence of functionally heterogeneous EGFR and EGFR TIC subpopulations within the same tumor might affect clinical response to treatment. Cancer Res; 70(19); 7500–13. ©2010 AACR.
PRECLINICAL STUDY: Mechanisms of respiratory insufficiency induced by methadone overdose in rats

Methadone may cause respiratory depression. We aimed to understand methadone‐related effects on ventilation as well as each opioid‐receptor (OR) role. We studied the respiratory effects of intraperitoneal methadone at 1.5, 5, and 15 mg/kg (corresponding to 80% of the lethal dose‐50%) in rats using arterial blood gases and plethysmography. OR antagonists, including intravenous 10 mg/kg‐naloxonazine at 5 minutes (mu‐OR antagonist), subcutaneous 30 mg/kg‐naloxonazine at 24 hours (mu1‐OR antagonist), 3 mg/kg‐naltrindole at 45 minutes (delta‐OR antagonist) and 5 mg/kg‐Nor‐binaltorphimine at 6 hours (kappa‐OR antagonist) were pre‐administered. Plasma concentrations of methadone enantiomers were measured using high‐performance liquid chromatography coupled to mass‐spectrometry. Methadone dose‐dependent inspiratory time (TI) increase tended to be linear. Respiratory depression was observed only at 15 mg/kg and characterized by an increase in expiratory time (TE) resulting in hypoxemia and respiratory acidosis. Intravenous naloxonazine completely reversed all methadone‐related effects on ventilation, while subcutaneous naloxonazine reduced its effects on pH (P < 0.05), PaCO2 (P < 0.01) and TE (P < 0.001) but only partially on TI (P < 0.001). Naltrindole reduced methadone‐related effects on TE (P < 0.001). Nor‐binaltorphimine increased methadone‐related effects on pH and PaO2 (P < 0.05) Respiratory effects as a function of plasma R‐methadone concentrations showed a decrease in PaO2 (EC50: 1.14 µg/ml) at lower concentrations than those necessary for PaCO2 increase (EC50: 3.35 µg/ml). Similarly, increased TI (EC50: 0.501 µg/ml) was obtained at lower concentrations than those for TE (EC50: 4.83 µg/ml). Methadone‐induced hypoxemia is caused by mu‐ORs and modulated by kappa‐ORs. Additionally, methadone‐induced increase in TE is caused by mu1‐ and delta‐opioid receptors while increase in TI is caused by mu‐ORs.
The Helicobacter pylori Urease B Subunit Binds to CD74 on Gastric Epithelial Cells and Induces NF-κB Activation and Interleukin-8 Production

ABSTRACT The pathogenesis associated with Helicobacter pylori infection is the result of both bacterial factors and the host response. We have previously shown that H. pylori binds to CD74 on gastric epithelial cells. In this study, we sought to identify the bacterial protein responsible for this interaction. H. pylori urease from a pool of bacterial surface proteins was found to coprecipitate with CD74. To determine how urease binds to CD74, we used recombinant urease A and B subunits. Recombinant urease B was found to bind directly to CD74 in immunoprecipitation and flow cytometry studies. By utilizing both recombinant urease subunits and urease B knockout bacteria, the urease B-CD74 interaction was shown to induce NF-κB activation and interleukin-8 (IL-8) production. This response was decreased by blocking CD74 with monoclonal antibodies. Further confirmation of the interaction of urease B with CD74 was obtained using a fibroblast cell line transfected with CD74 that also responded with NF-κB activation and IL-8 production. The binding of the H. pylori urease B subunit to CD74 expressed on gastric epithelial cells presents a novel insight into a previously unrecognized H. pylori interaction that may contribute to the proinflammatory immune response seen during infection.
Hand and arm coordination during reach to grasp after stroke

The research explores kinematic impairments of reach to grasp in patients with lesions involving the parietal cortex and cerebellum; brain areas considered important for controlling hand and arm coordination. The effectiveness of current targeted interventions is reviewed and a novel intervention tested in a proof of concept pilot study. The first study demonstrates that even though movements of people with parietal lobe and cerebellar lesions are characterised by prolonged duration and longer trajectories, coordination, expressed by correlation between kinematic features of transport and grasp, is comparable to controls. Coordination is also largely preserved after perturbations to the transport component. Slower movements, potentially controlled by other brain areas may compensate for latent impairments in hand and arm coordination. A systematic review identifies functional therapy, electrical stimulation and robot training as potential interventions for improving hand and arm coordination after stroke. However, insufficient evidence and heterogeneity in terms of the stroke population prevents definitive conclusions regarding effectiveness. A second empirical study examines a novel treatment approach by way of treatment targeted towards patients with these specific lesions. The study shows that high intensity, repetitive practice of reach to grasp with auditory rhythmic cueing is well tolerated by a sample of stroke patients with moderate upper limb impairments. Findings such as shorter wrist path trajectories provide early indications for improved motor control during reach to grasp. Results suggest a need for more challenging practice with higher dosage particularly as reach to grasp movements remain prolonged, despite training that emphasizes progression of speed.
Some Bounds on the Size of Codes

We present some upper bounds on the size of nonlinear codes and their restriction to systematic codes and linear codes. These bounds are independent of other known theoretical bounds, e.g., the Griesmer bound, the Johnson bound, the Plotkin bound, and of linear programming bounds. One of the new bound is actually an improvement of a bound by Zinoviev, Litsyn, and Laihonen. Our experiments show that in the linear case our bounds provide the best value in a wide range, compared with all other closed-formula upper bounds. In the nonlinear case, we also compare our bound with the linear programming bound and with some improvements on it, show that there are cases where we beat these bounds. In particular, we obtain a new bound in Brouwer's table for A3(16,3).
Age at Onset and the Risk of Proliferative Retinopathy in Type 1 Diabetes

OBJECTIVE Age at onset of type 1 diabetes influences the risk of microvascular complications. However, the long-term risk of proliferative retinopathy within the wide spectrum of age at onset of type 1 diabetes is less well known. RESEARCH DESIGN AND METHODS A sample of 1,117 consecutively recruited patients was drawn from the FinnDiane Study population (4,800 patients). Type 1 diabetes was defi ned as age at onset ≤40 years, insulin treatment initiated within 1 year, and C-peptide ≤0.3 nmol/1. Retinopathy status was graded based on ophthalmic records and/or fundus photographs. The risk of proliferative retinopathy was studied in age-at-onset groups 0–4, 5–14, and 15–40 years. RESULTS The mean durations to proliferative retinopathy were 24.3 (22.7–25.9) years in the 0–4 years group, 20.1 (19.2–21.1) years in the 5–14 years group, and 21.6 (19.8–23.3) years in the 15–40 years group (P < 0.001). In a Cox regression model, with A1C, blood pressure, sex, and BMI as covariates, the highest risk of proliferative retinopathy was observed in the 5–14 years group (hazard ratio 1.90 [95% CI 1.45–2.48], P < 0.001). Diabetes onset 0–4 vs. 5–14 years made no difference in the long-term risk of proliferative retinopathy (P = 0.2). When split into two groups, age at onset < 15 years was associated with a higher long-term risk than age at onset >15 years (1.82 [1.40–2.36], P < 0.001). CONCLUSIONS Age at onset significantly modifies the long-term risk of proliferative retinopathy. The highest risk is in age-at-onset group 5–14 years, whereas the lowest risk is in age-at-onset group 15–40 years.
Web and Social Media Analytics towards Enhancing Urban Transportations: A Case for Bangalore

Cities today are typically plagued by multiple issues such as âĂŞ traffic jams, garbage, transit overload, public safety, drainage etc. Citizens today tend to discuss these issues in public forums, social media, web blogs, in a widespread manner. Given that issues related to public transportation are most actively reported across web-based sources, we present a holistic framework for collection, categorization, aggregation and visualization of urban public transportation issues. The primary challenges in deriving useful insights from web-based sources, stem from: (a) the number of reports; (b) incomplete or implicit spatio-temporal context; and the (c) unstructured nature of text in these reports. This paper provides the text categorization techniques that can be adopted to address specifically these challenges. The work initiates with the formal complaint data from the largest public transportation agency in Bangalore, complemented by complaint reports from web-based and social media sources. An easy to navigate and well-organized dashboard is developed for efficient visualization. The dashboard is currently being piloted with the largest transportation agency in Bangalore.
Systematic Study on the Self-Assembled Hexagonal Au Voids, Nano-Clusters and Nanoparticles on GaN (0001)

Au nano-clusters and nanoparticles (NPs) have been widely utilized in various electronic, optoelectronic, and bio-medical applications due to their great potentials. The size, density and configuration of Au NPs play a vital role in the performance of these devices. In this paper, we present a systematic study on the self-assembled hexagonal Au voids, nano-clusters and NPs fabricated on GaN (0001) by the variation of annealing temperature and deposition amount. At relatively low annealing temperatures between 400 and 600°C, the fabrication of hexagonal shaped Au voids and Au nano-clusters are observed and discussed based on the diffusion limited aggregation model. The size and density of voids and nano-clusters can systematically be controlled. The self-assembled Au NPs are fabricated at comparatively high temperatures from 650 to 800°C based on the Volmer-Weber growth model and also the size and density can be tuned accordingly. The results are symmetrically analyzed and discussed in conjunction with the diffusion theory and thermodynamics by utilizing AFM and SEM images, EDS maps and spectra, FFT power spectra, cross-sectional line-profiles and size and density plots.