Miracle-dz/UniFAR-FTUs huggingface dataset:
An Easily Dissociated 26 S Proteasome Catalyzes an Essential Ubiquitin-mediated Protein Degradation Pathway in Trypanosoma brucei * 210

The 26 S proteasome, a complex between the 20 S proteasome and 19 S regulatory units, catalyzes ATP-dependent degradation of unfolded and ubiquitinated proteins in eukaryotes. We have identified previously 20 S and activated 20 S proteasomes in Trypanosoma brucei, but not 26 S proteasome. However, the presence of 26 S proteasome in T. brucei was suggested by the hydrolysis of casein by cell lysate, a process that requires ATP but is inhibited by lactacystin, and the lactacystin-sensitive turnover of ubiquitinated proteins in the intact cells. T. brucei cDNAs encoding the six proteasome ATPase homologues (Rpt) were cloned and expressed. Five of the sixT. brucei Rpt cDNAs, except for Rpt2, were capable of functionally complementing the corresponding rpt deletion mutants of Saccharomyces cerevisiae. Immunoblots showed the presence in T. brucei lysate of the Rpt proteins, which co-fractionated with the yeast 19 S proteasome complex by gel filtration and localized in the 19 S fraction of a glycerol gradient. All the Rpt and putative 19 S non-ATPase (Rpn) proteins were co-immunoprecipitated from T. brucei lysate by individual anti-Rpt antibodies. Treatment of T. brucei cells with a chemical cross-linker resulted in co-immunoprecipitation of 20 S proteasome with all the Rpt and Rpn proteins that sedimented in a glycerol gradient to the position of 26 S proteasome. These data demonstrate the presence of 26 S proteasome in T. bruceicells, which apparently dissociate into 19 S and 20 S complexes upon cell lysis. RNA interference to block selectively the expression of proteasome 20 S core and Rpt subunits resulted in significant accumulation of ubiquitinated proteins accompanied by cessation of cell growth. Expression of yeast RPT2 gene in T. brucei Rpt2-deficient cells could not rescue the lethal phenotype, thus confirming the incompatibility between the two Rpt2s. The T. brucei 11 S regulator (PA26)-deficient RNA interference cells grew normally, suggesting the dispensability of activated 20 S proteasome in T. brucei.
MORINGA PLANT AND IT USE AS FEED IN AQUACULTURE DEVELOPMENT: A REVIEW

Aquaculture, an important source for animal protein utilizes a lot of fishmeal regarded as the best protein source in fish feeds. For making feeds, aquaculture sector alone consumed the equivalent of about 23.8 million metric tons (mmt) of fish or 87% of nonfood fish by 2006. By 2011, the non-food uses of world fisheries were 23.2 mmt out of a total fish production of 154 mmt. The use of fishmeal is therefore substantial; 15.0 mmt being used in 2010. In Nigeria for example, small forage pelagic fish used in fishmeal production contributes 51% of total fish supply. Because most of the conventional plant/animal feed sources are equally in great demand for human consumption, there is an urgent need to examine other products from little researched plants such as moringa ( Moringa oleifera Lam) as alternative source of protein in aquaculture feeds. There is a dearth of information on the use of moringa leaf or seed meals as fish feed ingredients. An extensive search and analyses of published data on moringa and any of its use in aquaculture were therefore carried out. It was reported to be hardy, high yielding and thrive in diverse ecological zones. Its leaves, the kernel and the fat-free kernel meals contain 26.4 %, 36.7 % and 61.4 % of crude protein, respectively. The kernel contains over 40 % of good quality oil comparable to olive oil. The leaves and pods are rich in vitamins and minerals. Moringa leaves are free from anti-nutritional factors except for saponins and phenols. Studies on the use of moringa in fish feed production are few and far between as is discovered in this review. Combination of seed and leaf meals in desired proportion might result in obtaining a plant-based protein source that could favourably replace fishmeal in fish feeds. Hence, this review on available information on M. oleifera used in fish feeds exposes the need for further research. Keywords: Fish feed ingredients, Fishmeal, Alternative protein sources, Moringa oleifera, Antinutritional factors
Employing Region Features for Searching an Image Database

This paper describes recent work on the use of regional data extracted from segmented images for use as search keys in an image database query system. The motivation for this work is the increasing availability and use of digital photography within the home and the lack of suitable search facilities based on the content of the images therein. The selection of images from the database is performed by Radial Basis Function networks, the placement of which is carried out by Kohonen's Learning Vector Quantisation approach. The work, which has been carried out in collaboration with Hewlett Packard Labs in Bristol, has shown that the use of features extracted on a local regional level, rather than a global scale can provide a high success rate when used as keys for a database query. A manual region classi cation was carried out on a test set of images in order to evaluate the performance of the system and it was found that, of the regions returned with a classi cation, an impressive 76.6% matched that used for the search key.
Draft Genome Sequences of Pandrug-Resistant Serratia marcescens Clinical Isolates Harboring blaNDM-1

ABSTRACT The draft genome sequences of two clonal, pandrug-resistant Serratia marcescens clinical isolates were determined. The resistance phenotype was plasmid driven, as 14 of 17 resistance genes were present on large IncFIB(K), IncHI2, and IncA/C2 plasmids indicating a large pool of transmissible antibiotic resistance genes.
On some applications of finite-state automata theory to natural language processing

We describe new applications of the theory of automata to natural language processing: the representation of very large scale dictionaries and the indexation of natural language texts. They are based on new algorithms that we introduce and describe in detail. In particular, we give pseudocodes for the determinisation of string to string transducers, the deterministic union of p-subsequential string to string transducers, and the indexation by automata. We report on several experiments illustrating the applications.
Millimeter-scale epileptiform spike propagation patterns and their relationship to seizures

Objective. Current mapping of epileptic networks in patients prior to epilepsy surgery utilizes electrode arrays with sparse spatial sampling (∼1.0 cm inter-electrode spacing). Recent research demonstrates that sub-millimeter, cortical-column-scale domains have a role in seizure generation that may be clinically significant. We use high-resolution, active, flexible surface electrode arrays with 500 μm inter-electrode spacing to explore epileptiform local field potential (LFP) spike propagation patterns in two dimensions recorded from subdural micro-electrocorticographic signals in vivo in cat. In this study, we aimed to develop methods to quantitatively characterize the spatiotemporal dynamics of epileptiform activity at high-resolution. Approach. We topically administered a GABA-antagonist, picrotoxin, to induce acute neocortical epileptiform activity leading up to discrete electrographic seizures. We extracted features from LFP spikes to characterize spatiotemporal patterns in these events. We then tested the hypothesis that two-dimensional spike patterns during seizures were different from those between seizures. Main results. We showed that spatially correlated events can be used to distinguish ictal versus interictal spikes. Significance. We conclude that sub-millimeter-scale spatiotemporal spike patterns reveal network dynamics that are invisible to standard clinical recordings and contain information related to seizure-state.
Acquisition et transfert de stratégies au sein d'une intervention métacognitive pour des élèves présentant des difficultés d'apprentissage

Ce travail de these porte sur l'evaluation d'une intervention metacognitive destinee a des eleves presentant des difficultes d'apprentissages. Plus specifiquement, elle s'interesse a l'acquisition de strategies cognitives et metacognitives au sein de cette intervention ainsi qu'a leur transfert dans un probleme de mathematiques. Seize eleves, âges de huit a douze ans, ont suivi individuellement une intervention metacognitive semi-standardisee de douze seances. Durant ces seances, les eleves sont amenes a decouvrir et perfectionner un certain nombre de strategies cognitives et metacognitives en resolvant des tâches non scolaires tirees de deux programmes metacognitifs, le DELF (Buchel & Buchel, 1990) et le PEI (Feuerstein, Rand, Hoffman, & Miller, 1980) ainsi que des tâches scolaires (resolution de probleme en mathematiques et comprehension de textes). Les resultats montrent que l'intervention metacognitive de douze semaines permet aux eleves d'acquerir des strategies mais egalement de transferer certaines des strategies apprises dans un exercice de resolution de probleme de mathematiques. Les resultats quantitatifs sont illustres par trois cas uniques. Ces descriptions permettent de mettre en avant differents facteurs qui favorisent l'acquisition et le transfert de strategies.
Underreporting of Chargeable Hours in Public Accounting: An Examination of Practitioner Attitudes and Attributes

Recent literature on the underreporting of chargeable hours indicates that it may have undesirable effects on business operations and lead to other activities affecting work quality. Accounting practitioners were surveyed to provide data for the study. Results from an analysis of covariance indicate that underreporting activity is significantly affected by the level of time budget pressure present, the length of time an accountant has spent in public practice, his/her ethical attitudes, and the existence of organizational sanctions.
XMM-Newton Observations of the Red Type 1.8 Quasar 2M1049+5837: Reflection from Cold and Warm (Ionized) Matter

Chandra observations of the type 1.8, low-redshift (z = 0.115), red (J − KS ∼ 2) quasar 2MASSJ 104943+583750 (2M1049+5837) indicated an unusually hard X-ray spectrum (HR ∼ 0.6), suggesting obscuration of NH ∼ 4 × 1022 cm−2 and a flat Γ ∼ 0.4 power-law slope. A higher signal-to-noise ratio XMM-Newton observation reported here reveals a more complex spectrum, being extremely hard above ~2 keV, Γ ∼ − 0.6, with a well-defined soft excess similar to the bright, nearby Seyfert 2 galaxy Mrk 3. Such extremely hard quasar spectra cannot be a dominant contributor to the cosmic X-ray background (CXRB; Γ ∼ 1.4). Modeling of 2M1049+5837 shows the observed 2-10 keV spectrum to be the sum of a strongly absorbed “normal” Γ ∼ 1.8 underlying quasar X-ray continuum, and a cold reflection component (R ∼ 2). The strong attenuation of the intrinsic X-ray continuum by a sub-Compton-thick line-of-sight column, NH ∼ 3.4 × 1023 cm−2, reveals a soft X-ray emission component whose spectrum indicates reprocessing/emission from, possibly extended, photoionized gas. The luminosity of the soft X-ray component is similar to Seyfert 2 galaxies, an order of magnitude less than comparable type 1 AGNs, suggesting partial obscuration of core-bright emission. The optical emission is complex, with distinct red and blue scattered light components believed to originate in two extended regions visible in HST imaging data. The unusual combination of properties: optical and X-ray obscuration of the nuclear emission, partially obscured broad but unobscured narrow emission lines, and partially obscured soft X-ray excess, implies an intermediate viewing angle, over or through the edge of an obscuring disk + wind or torus. 2M1049+5837 again demonstrates both the ambiguity of low signal-to-noise X-ray spectra/hardness ratios and the potential of 2MASS-selected red sources for exploring the complex obscuration and geometry of the nuclear regions in AGNs.
A Realistic Large-Scale Model of the Cerebellum Granular Layer Predicts Circuit Spatio-Temporal Filtering Properties

The way the cerebellar granular layer transforms incoming mossy fiber signals into new spike patterns to be related to Purkinje cells is not yet clear. Here, a realistic computational model of the granular layer was developed and used to address four main functional hypotheses: center-surround organization, time-windowing, high-pass filtering in responses to spike bursts and coherent oscillations in response to diffuse random activity. The model network was activated using patterns inspired by those recorded in vivo. Burst stimulation of a small mossy fiber bundle resulted in granule cell bursts delimited in time (time windowing) and space (center-surround) by network inhibition. This burst–burst transmission showed marked frequency-dependence configuring a high-pass filter with cut-off frequency around 100 Hz. The contrast between center and surround properties was regulated by the excitatory–inhibitory balance. The stronger excitation made the center more responsive to 10–50 Hz input frequencies and enhanced the granule cell output (with spikes occurring earlier and with higher frequency and number) compared to the surround. Finally, over a certain level of mossy fiber background activity, the circuit generated coherent oscillations in the theta-frequency band. All these processes were fine-tuned by NMDA and GABA-A receptor activation and neurotransmitter vesicle cycling in the cerebellar glomeruli. This model shows that available knowledge on cellular mechanisms is sufficient to unify the main functional hypotheses on the cerebellum granular layer and suggests that this network can behave as an adaptable spatio-temporal filter coordinated by theta-frequency oscillations.
Tree model reconstruction innovization using multi-objective differential evolution

This paper presents an innovization design principle for procedural tree model of woody plants (trees) reconstruction by multi-objective optimization. Reconstruction of a parameterized procedural model from imagery is addressed by a multi-objective differential evolution algorithm, which evolves a parametrized procedural model by fitting a set of its rendered images to a set of given projected images using bi-objective comparisons made on a pixel level of the images. The use of multi-objective approach gives the decision maker a chance to select the final resulting model, and helps determine the optimization criteria tradeoff weights for later production.
Antipermeability function of PEDF involves blockade of the MAP kinase/GSK/beta-catenin signaling pathway and uPAR expression.

PURPOSE Pigment epithelium-derived factor (PEDF) is a potent inhibitor of vascular endothelial growth factor (VEGF)-induced endothelial permeability. The goal of this study was to understand the mechanism by which PEDF blocks VEGF-induced increases in vascular permeability. METHODS The paracellular permeability of bovine retinal endothelial (BRE) cells was measured by assaying transendothelial cell electrical resistance and tracer flux. Western blot analysis was used to show phosphorylation of VEGFR2, MAP kinases, and glycogen synthase kinase 3 (GSK3)-beta. Confocal imaging and Western blot analysis were used to determine subcellular distribution of beta-catenin. Real-time RT-PCR and Western blot analysis were used to quantify urokinase plasminogen activator receptor (uPAR) expression. RESULTS PEDF blocked VEGF-induced phosphorylation of extracellular signal-regulated kinase (ERK), p38 MAP kinase, the p38 substrate MAP kinase-activated protein kinase-2 (MAPKAPK-2), and GSK3-beta, but it had no effect on the phosphorylation of VEGFR2. In addition, the VEGF-induced transcriptional activation of beta-catenin and uPAR expression were blocked by PEDF and by inhibitors of p38 and MEK. Finally, the VEGF-induced increase in permeability was blocked by both PEDF and the same kinase inhibitors. CONCLUSIONS The data suggest that p38 MAP kinase and ERK act upstream of GSK/beta-catenin in VEGF-induced activation of the uPA/uPAR system and that PEDF-mediated inhibition of the VEGF-induced increase in vascular permeability involves blockade of this pathway. These findings are important for developing precise and potent therapies for treatment of diseases characterized by vascular barrier dysfunction.
The Human Serum Metabolome

Continuing improvements in analytical technology along with an increased interest in performing comprehensive, quantitative metabolic profiling, is leading to increased interest pressures within the metabolomics community to develop centralized metabolite reference resources for certain clinically important biofluids, such as cerebrospinal fluid, urine and blood. As part of an ongoing effort to systematically characterize the human metabolome through the Human Metabolome Project, we have undertaken the task of characterizing the human serum metabolome. In doing so, we have combined targeted and non-targeted NMR, GC-MS and LC-MS methods with computer-aided literature mining to identify and quantify a comprehensive, if not absolutely complete, set of metabolites commonly detected and quantified (with today's technology) in the human serum metabolome. Our use of multiple metabolomics platforms and technologies allowed us to substantially enhance the level of metabolome coverage while critically assessing the relative strengths and weaknesses of these platforms or technologies. Tables containing the complete set of 4229 confirmed and highly probable human serum compounds, their concentrations, related literature references and links to their known disease associations are freely available at http://www.serummetabolome. ca.
Effects of random temperature and pressure influence on the single-channel optical transmission system

In this article we focus on the numerical investigation of random temperature changes in different sections of the optical fibers and their influence on material properties of the fibers. The important issue is to determine whether these temperature changes affect the dispersion and nonlinear effects in the fiber and consequently the transmitted pulse. Moreover, the effects of pressure are also investigated. We found out that the pressure and temperature changes influence dispersion effects in single-channel optical transmission system.
Comparative depth distribution of corallimorpharians and scleractinians (Cnidaria: Anthozoa)

We assessed whether CaCO3 concentration of seawater may be relevant to the occur- rence of members of Corallimorpharia and Scleractinia, which are very similar except for the posses- sion by scleractinians of a calcareous skeleton. In collections of both the Challenger Deep-sea Expe- dition 1872-1876 and the US Antarctic (Research) Program, average depth of occurrence was significantly greater for corallimorpharians than for scleractinians. We also compared depth of occur- rence relative to the position of the aragonite saturation horizon (ASH) at many localities from which specimens were collected. Nearly 25 and 50% of stations at which scleractinians were collected were below the ASH for the Antarctic and Challenger stations, respectively; 50 and 100% of the Antarctic and Challenger stations at which corallimorpharians were collected were below the ASH, respec- tively. Statistical analyses of these data to test whether there is a difference in the depth, relative to the ASH, at which scleractinians and corallimorpharians occur indicate a difference for the Chal- lenger but not the Antarctic stations; more data are needed. The scleractinians that tolerate living below the ASH belong to a minority of the genera recorded in the surveys, and do not include spe- cies considered important in forming bioherms; those that occur deepest are solitary. Some deep-sea scleractinians may be unaffected by shoaling of the ASH that is predicted across all ocean basins in the near future, some may be confined to water shallower than is now the case, and others may cease producing a skeleton, becoming morphologically indistinguishable from corallimorpharians.
Scout-explorer multi-agent framework for terrain coverage

Multi-Agent systems enable us to simulate swarm behaviour wherein intelligence emerges from the collective instead of the individual. The problem of terrain coverage forms a prominent field of research in multi-agent systems with wide-ranging real-life applications. We propose a new multi-agent framework called the Scout-Explorer framework which utilizes global terrain knowledge to cover a previously unknown terrain while being energy effective. The paper demonstrates results obtained via simulations over multiple metrics comparing standard terrain coverage algorithms with a spatiotemporal implementation of the proposed framework.
The Effect of Age on Improvements in Vestibulo-Ocular Reflexes and Balance Control after Acute Unilateral Peripheral Vestibular Loss

Background An acute unilateral peripheral vestibular loss (aUVL) initially causes severe gaze and balance control problems. However, vestibulo-ocular reflexes (VOR) and balance control are nearly normal 3 months later as a result of peripheral recovery and/or central compensation. As pre-existing vestibular sensory loss is assumed to be greater in the healthy elderly, this study investigated whether improvements in VOR and balance function over time after aUVL are different for the elderly than for the young. Methods Thirty aUVL patients divided into three age-groups were studied (8 age range 23–35, 10 with range 43–58, and 12 with range 60–74 years). To measure VOR function eye movements were recorded during caloric irrigation, rotating chair (ROT), and head impulse tests. Balance control during stance and gait was recorded as lower trunk angular velocity in the pitch and roll planes. Measurements were taken at deficit onset, and 3, 6, and 13 weeks later. Results There was one difference in VOR improvements over time between the age-groups: Low acceleration ROT responses were less at onset in the elderly group. Deficit side VOR responses and asymmetries in each group improved to within ranges of healthy controls at 13 weeks. Trunk sway of the elderly was greater for stance and gait at onset when compared to healthy age-matched controls and the young and greater than that of the young and controls during gait tasks at 13 weeks. The sway of the young was not different from controls at either time point. Balance control for the elderly improved slower than for the young. Conclusion These results indicate that VOR improvement after an aUVL does not differ with age, except for low accelerations. Recovery rates are different between age-groups for balance control tests. Balance control in the elderly is more abnormal at aUVL onset for stance and gait tasks with the gait abnormalities remaining after 13 weeks. Thus, we conclude that balance control in the elderly is more affected by the UVL than for the young, and the young overcome balance deficits more rapidly. These differences with age should be taken into account when planning rehabilitation.