Miracle-dz/UniFAR-FTUs huggingface dataset:
Identifying the topology of protein complexes from affinity purification assays

Motivation: Recent advances in high-throughput technologies have made it possible to investigate not only individual protein interactions, but also the association of these proteins in complexes. So far the focus has been on the prediction of complexes as sets of proteins from the experimental results. The modular substructure and the physical interactions within the protein complexes have been mostly ignored. Results: We present an approach for identifying the direct physical interactions and the subcomponent structure of protein complexes predicted from affinity purification assays. Our algorithm calculates the union of all maximum spanning trees from scoring networks for each protein complex to extract relevant interactions. In a subsequent step this network is extended to interactions which are not accounted for by alternative indirect paths. We show that the interactions identified with this approach are more accurate in predicting experimentally derived physical interactions than baseline approaches. Based on these networks, the subcomponent structure of the complexes can be resolved more satisfactorily and subcomplexes can be identified. The usefulness of our method is illustrated on the RNA polymerases for which the modular substructure can be successfully reconstructed. Availability: A Java implementation of the prediction methods and supplementary material are available at http://www.bio.ifi.lmu.de/Complexes/Substructures/. Contact: caroline.friedel@bio.ifi.lmu.de Supplementary information: Supplementary data are available at Bioinformatics online.
A Study on the Extrusion of Soy Protein Film Incorporated with Soy-Derived Cellulose Fibers

A STUDY ON THE EXTRUSION OF SOY PROTEIN FILM INCORPORATED WITH SOYDERIVED CELLULOSE FIBERS Roc Tsz-Pang Chan University of Guelph, 2012 Advisor: Dr. Loong-Tak Lim A biodegradable alternative to synthetic plastics was explored in this study through the extrusion of a soy-based protein/fiber composite film. Two fractions of fibers with different size distributions (nanoto micro-) were isolated from soy pods and stems using a chemi-mechanical method. Fibers through successive treatments were characterized via microscopy, x-ray diffraction, and Fourier Transform infrared analysis (FTIR). The continuous extrusion of homogenous SPI film (0.08 to 0.3 mm thick) was reported for the first time. Processing window was limited by protein sensitivity to moisture and heat. With the incorporation of extracted fibers, homogenous films were obtained with a concentration below 0.5% w/w fiber/SPI. Increasing fiber content resulted in the formation of aggregates. At the optimal concentration of 0.25% w/w fiber/SPI, films exhibited mild improvements in mechanical performance most noticeable at a high RH (84%). Film properties with and without fiber addition were negatively affected by relative humidity. Titanium dioxide addition suggested mild coupling effects for SPI and fiber.
Iridoids from Globularia dumulosa

Two new iridoids, 10-O-benzoylglobularigenin (1) and dumuloside (2) were isolated from the aerial parts of Globularia dumulosa together with seven known iridoid glucosides, davisioside (3), aucubin (4), melampyroside (5), catalpol (6), 10-O-benzoylcatalpol (7), alpinoside (8) and deacetylalpinoside (9). Three phenylethanoid glycosides, verbascoside, decaffeoylverbascoside, leucosceptoside A and three flavone glucosides, pectolinarigenin 7-O-β-ᴅ-glucopyranoside, nepetin 7-O-β-ᴅ-glucopyranoside, demethoxycentaureidin 7-O-β-ᴅ-glucopyranoside were also isolated and characterized. The structure elucidation of the isolated compounds was performed by spectroscopic (UV, IR, HR-MALDIMS, 1D- and 2D NMR) methods.
Transporters Involved in Root Nitrate Uptake and Sensing by Arabidopsis

Most plants use nitrate (NO3-) as their major nitrogen (N) source. The NO3- uptake capacity of a plant is determined by three interdependent factors that are sensitive to NO3- availability: (i) the functional properties of the transporters in roots that contribute to the acquisition of NO3- from the external medium, (ii) the density of functional transporters at the plasma membrane of root cells, and (iii) the surface and architecture of the root system. The identification of factors that regulate the NO3--sensing systems is important for both fundamental and applied science, because these factors control the capacity of plants to use the available NO3-, a process known as the “nitrate use efficiency. ” The molecular component of the transporters involved in uptake and sensing mechanism in Arabidopsis roots are presented and their relative contribution discussed.
A Joint Probability Data Association Filter Algorithm for Multiple Robot Tracking Problems

Estimating the position of a mobile robot in a real environment is taken into account as one of the most challenging topics in the recent literature (Fox et al., 2000). This problem can be usually explored in two ways. Firstly, a mobile robot should be able to have knowledge about its current position. The Dead-reckoning of a mobile robot may be used to update the position of the robot assuming the initial position is known. However, the encoders of a robot cannot provide precise measurements and, therefore, the position obtained by this way is not reliable. To achieve more accurate approximation of a robot’s position, measurements obtained by sensors set on a robot are used to correct the information provided by the encoders. If the mapping of a physical environment is known, the abovementioned procedure can be easily accomplished by using some well-known approaches such as Kalman filtering (Kalman & Bucy, 1961) to localize the exact position of a mobile robot (Siegwart & Nourbakhsh, 2004). However, when there is not any knowledge about the map, mapping and localization should be conducted simultaneously. The aforementioned topic is known as Simultaneous Localization and Mapping (SLAM) in the literature (Howard, 2005). In many applications, one may intend to localize other robots’ position via a reference robot. Robot soccer problems or people tracking scenarios can be fallen in the pre-mentioned category. Although this problem appears similar to the common localization algorithms, the traditional approaches can not be used because the reference robot does not access to the odometry data of each mobile robot used in localization algorithms to predict the future position of the robot. This issue may be completely perceivable in the people tracking scenario because there is not any information about the movement of people. In this case, some models should be proposed to represent the movement of each object. By defining a suitable motion model for each target and using measurements provided by a reference robot about the current position of the moving object, a linear/nonlinear state space model is constructed representing the movement of each object. The above-discussed topic can be fallen in the category of target tracking problems where the final aim is defined as tracking the position of a mobile object by a reference sensor. Because of inaccurate data obtained by sensors and uncertain motion models which may not provide reliable prediction of an object’s movement, filtering algorithms are used to extract
Hydrogen bonds in rubredoxins from mesophilic and hyperthermophilic organisms.

The extent and strength of the hydrogen bond networks in rubredoxins from the hyperthermophile Pyrococcus furiosus (PfRd), and its mesophilic analogue Clostridium pasteurianum (CpRd), are examined and compared using NMR spectroscopy. NMR parameters examined in this study include through-hydrogen bond (h3)J(NC)(') scalar couplings and (1)H, (13)C, and (15)N chemical shifts, as well as covalent (1)J(NH) and (1)J(NC)(') scalar couplings. These parameters have allowed the characterization in solution of 12 hydrogen bonds in each protein. Despite a 83% sequence homology and a low RMSD for the backbone heavy atoms (0.648 A) in the crystalline state, subtle, but definite, changes have been identified in the detailed hydrogen-bonding patterns. CpRd shows an increased number of hydrogen bonds in the triple-stranded beta-sheet and an additional hydrogen bond in the multiple-turn segment including residues 14-32. On the other hand, PfRd exhibits an overall strengthening of N-H.O=C hydrogen bonds in the loops involved at the metal binding site as well as evidence for an additional NH.S(Cys) hydrogen bond involving the alanine residue 44. These data, as well as temperature dependence of the NMR parameters, suggest that the particular NMR hydrogen bond pattern found in the hyperthermophile rubredoxin leads to an increased stabilization at the metal binding pocket. It seems to result from a subtle redistribution of hydrogen-bonding interactions between the triple-stranded beta-sheet and the actual metal binding site.
Izalpinin from fruits of Alpinia oxyphylla with antagonistic activity against the rat bladder contractility.

BACKGROUND Alpinia oxyphylla (Zingiberaceae), an herbaceous perennial plant, its capsular fruit is commonly used in traditional Chinese medicine for the treatment of different urinary incontinence symptoms including frequency, urgency and nocturia. These symptoms are similar to the overactive bladder syndrome. In our lab, we found that the 95% ethanol extract of the capsular fruits exhibited significant anti-muscarinic activity. Some constituents in capsular fruits including flavonoids (e.g., izalpinin and tectochrysin), diarylheptanoids (e.g., yakuchinone A and yakuchinone B) and sesquiterpenes (e.g., nootkatone), are regarded as representative chemicals with putative pharmacological activities. OBJECTIVE This study aimed to evaluate the in vitro antagonistic actions of izalpinin on carbachol-induced contraction of the rat detrusor muscle. MATERIALS AND METHODS In vitro inhibition of rat detrusor contractile response to carbachol was used to study the functional activity of izalpinin. The isolated detrusor strips of rats were mounted in organ baths containing oxygenated Krebs' solution. The cumulative consecutive concentration-response curves to carbachol-evoked contractions in strips of rat bladder were obtained. RESULTS Carbachol induced concentration-dependent contractions of isolated rat bladder detrusor strips. The vehicle DMSO had no impact on the contraction response. The contraction effects were concentration-dependently antagonized by izalpinin, with a mean EC50 value of 0.35 µM. The corresponding cumulative agonist concentration-response curves shifted right-ward. CONCLUSIONS Izalpinin exhibits inhibitory role of muscarinic receptor-related detrusor contractile activity, and it may be a promising lead compound to treat overactive bladder.
The AT&t speech API: a study on practical challenges for customized speech to text service

AT&T has recently opened its extensive portfolio of state-ofthe-art Speech Technology to external end-developers as a platform called “The AT&T Speech API”. This study discusses a series of practical challenges found in an industrial deployment of speech to text services, particularly, we examine different strategies for customizing the speech to text process by considering intrinsic factors, inherent to the audio signal, or extrinsic factors, available from other sources, in an industry-grade implementation.
Accuracy evaluation of a 3D ultrasound-based neuronavigation system.

We have investigated the 3D navigation accuracy of a frameless ultrasound-based neuronavigation system (SonoWand) for surgical planning and intraoperative image guidance. In addition, we present a detailed description and review of the error sources associated with surgical neuronavigation based on preoperative MRI data and intraoperative ultrasound. A phantom with 27 precisely defined points was scanned with ultrasound by various translation and tilt movements of the ultrasound probe (180 3D scans in total), and the 27 image points in each volume were located using an automatic detection algorithm. These locations were compared to the physically measured locations of the same 27 points. The accuracy of the neuronavigation system and the effect of varying acquisition conditions were found through a thorough statistical analysis of the differences between the two point sets. The accuracy was found to be 1.40 +/- 0.45 mm (arithmetic mean) for the ultrasound-based neuronavigation system in our laboratory setting. Improper probe calibration was the major contributor to this figure. Based on our extensive data set and thorough evaluation, the accuracy found in the laboratory setting is expected to be close to the overall clinical accuracy for ultrasound-based neuronavigation. Our analysis indicates that the overall clinical accuracy may be as low as 2 mm when using intraoperative imaging to compensate for brain shift.
Effect of (cid:1) -Blocking Therapy on Outcome in the Multicenter UnSustained Tachycardia Trial (MUSTT)

Background — (cid:1) -Blockers are known to reduce total mortality and sudden death in survivors of recent myocardial infarction. The effects of these agents in patients at high risk for sudden death with remote infarction are not clear. Methods and Results —We analyzed the effect of (cid:1) -blockers on outcomes in 2096 patients with coronary artery disease, ejection fraction (cid:2) 40%, and spontaneous nonsustained ventricular tachycardia enrolled in the Multicenter UnSustained Tachycardia Trial (MUSTT). Forty-five percent of 702 patients with inducible sustained ventricular tachyarrhythmia and 35% of 1394 patients without inducible tachycardia were discharged from hospital receiving (cid:1) -blockers. Patients treated with (cid:1) -blockers were younger and had higher ejection fractions, higher rates of recent angina, and more recent infarction. (cid:1) -Blockers were associated with decreased total mortality for the entire study population (5-year mortality 50% with (cid:1) -blockers versus 66% without (cid:1) -blockers; adjusted P (cid:1) 0.0001). The mortality benefit associated with (cid:1) -blockers was present in patients with and without inducible tachycardia, except those treated with implantable defibrillators. There was no significant effect of (cid:1) -blocker therapy on the rate of arrhythmic death or cardiac arrest (adjusted P (cid:1) 0.2344). Conclusions — (cid:1) -Blocking agents have beneficial effects on survival of patients having characteristics of those enrolled in the MUSTT trial. These effects do not appear to be due to a specific antiarrhythmic effect of (cid:1) -blockers. The beneficial effects of (cid:1) -blockers were demonstrable in all patients except those treated with implantable defibrillators. ( Circulation . 2002;106:2694-2699.) of (cid:1) (cid:1) with a reduced risk of for of
The role of the viral genome in oncogenesis.

that suitable technics will detect differences between the trans formed cells and cells of the parental type. Markers often used to follow such transformation are changes in karyotype, in morphology, in antigenic makeup, and in the acquisition of tumorigenic potential. Although it is known that at least a portion of the virus genome persists following virus transfor mation of cells, little is known of the state in which the genome of DNA-containing viruses exists in the tranformcd cell, and much more experimentation will be required to delineate the information added to the cells during transformation and the viral genes required to effect and to maintain the transformed state.
Cerebellar neurodegeneration in the absence of microRNAs

Genome-encoded microRNAs (miRNAs) are potent regulators of gene expression. The significance of miRNAs in various biological processes has been suggested by studies showing an important role of these small RNAs in regulation of cell differentiation. However, the role of miRNAs in regulation of differentiated cell physiology is not well established. Mature neurons express a large number of distinct miRNAs, but the role of miRNAs in postmitotic neurons has not been examined. Here, we provide evidence for an essential role of miRNAs in survival of differentiated neurons. We show that conditional Purkinje cell–specific ablation of the key miRNA-generating enzyme Dicer leads to Purkinje cell death. Deficiency in Dicer is associated with progressive loss of miRNAs, followed by cerebellar degeneration and development of ataxia. The progressive neurodegeneration in the absence of Dicer raises the possibility of an involvement of miRNAs in neurodegenerative disorders.
A listening power-saving Mechanism in MAC layer for the DCF of 802.11n

In this article, we propose a listening power-saving Mechanism (LPSM) which consists of an intelligent scheme for intelligent idle listening [16], a Network Allocation Vector (NAV) scheme to reduce the energy consumed in listening to the transmissions from other active stations, and a sleeping technique for an idle station to reduce the energy consumed in idle listening regardless of whether the station is busy or not. Our analysis and simulation results show that our schemes can reduce the total power consumption of a busy station by about 80% through shortening the time in listening to the idle channel and to the transmission of other busy stations effectively. In particular, energy consumption is significantly reduced when the number of active stations is very large. The power consumption for an idle station applying the sleeping technique in Listening Power-Saving Mechanism (LPSM) can be reduced by 33.7% if the maximal beacon interval is set to 320ms. An important characteristic of our scheme is that it is fully compatible with the legacy Distributed Coordination Function (DCF) and that there will be no throughput reduction if this power saving mechanism is applied to the DCF of 802.11.
DBC based Face Recognition using DWT

The applications using face biometric has proved its reliability in last decade. In this paper, we propose DBC based Face Recognition using DWT (DBC- FR) model. The Poly-U Near Infra Red (NIR) database images are scanned and cropped to get only the face part in pre-processing. The face part is resized to 100*100 and DWT is applied to derive LL, LH, HL and HH subbands. The LL subband of size 50*50 is converted into 100 cells with 5*5 dimention of each cell. The Directional Binary Code (DBC) is applied on each 5*5 cell to derive 100 features. The Euclidian distance measure is used to compare the features of test image and database images. The proposed algorithm render better percentage recognition rate compared to the existing algorithm.
NogoA restricts synaptic plasticity in the adult hippocampus on a fast time scale

Whereas the role of NogoA in limiting axonal fiber growth and regeneration following an injury of the mammalian central nervous system (CNS) is well known, its physiological functions in the mature uninjured CNS are less well characterized. NogoA is mainly expressed by oligodendrocytes, but also by subpopulations of neurons, in particular in plastic regions of the CNS, e.g., in the hippocampus where it is found at synaptic sites. We analyzed synaptic transmission as well as long-term synaptic plasticity (long-term potentiation, LTP) in the presence of function blocking anti-NogoA or anti-Nogo receptor (NgR) antibodies and in NogoA KO mice. Whereas baseline synaptic transmission, short-term plasticity and long-term depression were not affected by either approach, long-term potentiation was significantly increased following NogoA or NgR1 neutralization. Synaptic potentiation thus seems to be restricted by NogoA. Surprisingly, synaptic weakening was not affected by interfering with NogoA signaling. Mechanistically of interest is the observation that by blockade of the GABAA receptors normal synaptic strengthening reoccurred in the absence of NogoA signaling. The present results show a unique role of NogoA expressed in the adult hippocampus in restricting physiological synaptic plasticity on a very fast time scale. NogoA could thus serve as an important negative regulator of functional and structural plasticity in mature neuronal networks.
Adiponectin: more than just another fat cell hormone?

Recent research has shown that adipose tissue is not simply an inert storage depot for lipids but is also an important endocrine organ that plays a key role in the integration of endocrine, metabolic, and inflammatory signals for the control of energy homeostasis. The adipocyte has been shown to secrete a variety of bioactive proteins into the circulation. These secretory proteins, which have been collectively named adipocytokines (1), include leptin (2), tumor necrosis factor (TNF)-α (3), plasminogen-activator inhibitor type 1 (PAI-1) (4), adipsin (5), resistin (6), and adiponectin (7). Adiponectin, the gene product of the adipose most abundant gene transcript 1 (apM1) (7), is a novel and important member of the adipocytokine family. Adiponectin cDNA was first isolated by large-scale random sequencing of the human adipose tissue cDNA library (7). It is a collagen-like protein that is exclusively synthesized in white adipose tissue, is induced during adipocyte differentiation, and circulates at relatively high (microgram/milliliter) concentrations in the serum. Both murine and human forms of adiponectin have been isolated independently by several groups, and various descriptive names have been given to the same compound by different investigators: adipocyte complement-related protein of 30 kilodalton (Acrp30) (8), Adipo Q (9), and gelatin binding protein of 28 kilodalton (GBP28) (10). The former two are murine analogs and the latter the human counterpart. Throughout this review, we will be referring to the protein by its most commonly used name, adiponectin. Adiponectin has been postulated to play an important role in the modulation of glucose and lipid metabolism in insulin-sensitive tissues in both humans and animals. Decreased circulating adiponectin levels have been demonstrated in genetic and diet-induced murine models of obesity (11), as well as in diet-induced forms of human obesity (12). Low adiponectin levels have also been strongly implicated in the development of insulin resistance …
The Sec7 Guanine Nucleotide Exchange Factor GBF1 Regulates Membrane Recruitment of BIG1 and BIG2 Guanine Nucleotide Exchange Factors to the Trans-Golgi Network (TGN)*

Background: GBF1, BIG1, and BIG2 are guanine nucleotide exchange factors (GEFs) that activate ARFs to regulate secretory traffic. Results: GBF1 activity promotes subsequent recruitment of BIG1/2. Conclusion: The three GEFs are functionally coupled in a GEF/ARF/GEF cascade. Significance: Coupling integrates all coating events within the pathway to simultaneously regulate passage of cargo through multiple compartments. Three Sec7 guanine nucleotide exchange factors (GEFs) activate ADP-ribosylation factors (ARFs) to facilitate coating of transport vesicles within the secretory and endosomal pathways. GBF1 recruits COPI to pre-Golgi and Golgi compartments, whereas BIG1 and BIG2 recruit AP1 and GGA clathrin adaptors to the trans-Golgi network (TGN) and endosomes. Here, we report a functional cascade between these GEFs by showing that GBF1-activated ARFs (ARF4 and ARF5, but not ARF3) facilitate BIG1 and BIG2 recruitment to the TGN. We localize GBF1 ultrastructurally to the pre-Golgi, the Golgi, and also the TGN. Our findings suggest a model in which GBF1 localized within pre-Golgi and Golgi compartments mediates ARF activation to facilitate recruitment of COPI to membranes, whereas GBF1 localized at the TGN mediates ARF activation that leads to the recruitment of BIG1 and BIG2 to the TGN. Membrane-associated BIG1/2 then activates ARFs that recruit clathrin adaptors. In this cascade, an early acting GEF (GBF1) activates ARFs that mediate recruitment of late acting GEFs (BIG1/2) to coordinate coating events within the pre-Golgi/Golgi/TGN continuum. Such coordination may optimize the efficiency and/or selectivity of cargo trafficking through the compartments of the secretory pathway.