Miracle-dz/UniFAR-FTUs huggingface dataset:
EFFECTS OF FEEDING AND FOOD DEPRIVATION ON OXYGEN CONSUMPTION, MUSCLE PROTEIN CONCENTRATION AND ACTIVITIES OF ENERGY METABOLISM ENZYMES IN MUSCLE AND BRAIN OF SHALLOW-LIVING (SCORPAENA GUTTATA) AND DEEP-LIVING (SEBASTOLOBUS ALASCANUS) SCORPAENID FISHES

The effects of feeding and fasting were examined on the deep-living short-spine thornyhead (Sebastolobus alascanus) and the confamilial shallow-living spotted scorpionfish (Scorpaena guttata) to determine whether the low metabolic rate of the deeper-living species was in part a consequence of food deprivation in its habitat. Laboratory acclimation for periods of 90–115 days under either ad libitum feeding or complete fasting did not lead to similar rates of respiration in individuals of the two species held under identical conditions. Respiration of fish fed ad libitum was 52 % (S. guttata) or 68 % (S. alascanus) higher than for fasted fish of the same species. Furthermore, the metabolic rates of freshly collected specimens of S. alascanus resembled those of laboratory-fasted fish. In white skeletal muscle, both total protein concentration and the activities of four enzymes of ATP metabolism, lactate dehydrogenase (LDH) and pyruvate kinase (PK) of glycolysis, malate dehydrogenase (MDH) and citrate synthase (CS, a citric acid cycle indicator), were lower in S. alascanus than in S. guttata. Within a species, protein concentration and activities of the four enzymes in white muscle, but not in brain, were higher in fed than in starved fish, although these differences were greater in S. alascanus than in S. guttata. During fasting, LDH and PK activity in white muscle of S. alascanus decreased much more than MDH and CS activity; decreases in enzyme activities in red muscle were smaller than those in white muscle. Activities of enzymes in white skeletal muscle of field-collected S. alascanus generally resembled those of the fasted specimens. In contrast, red muscle of field- collected S. alascanus, compared with that of either fed or starved laboratory-held specimens, had a highly glycolytic poise (high LDH and PK activities relative to MDH and CS activities), which may suggest that muscle enzyme activities in the field-collected fish reflect adaptation to the low oxygen level in its adult habitat, the oxygen minimum layer. The strong correlations found between tissue biochemical properties and respiration rate allow us to develop a predictive index for metabolic rate from simple biochemical analyses, e.g. white muscle protein content or CS activity. We conclude that the low metabolic rate of S. alascanus is due to at least four depth-related factors: reduced abundance of food, low temperature, low ambient oxygen concentration and darkness, which may select for reduced locomotory activity.
On the evaluation of Polish definition extraction grammars

This paper presents the results of experiments in the automatic extraction of definitions (for semi-automatic glossary construction) from usually unstructured or only weakly structured e-learning texts in Polish. The extraction is performed by regular grammars over XMLencoded morphosyntactically-annotated documents. The results, although perhaps still not fully satisfactory, are carefully evaluated and compared to the inter-annotator agreement; they clearly improve on previous definition extraction attempts for Polish.
Human Immunodeficiency Virus Type 1 Tat Increases the Expression of Cleavage and Polyadenylation Specificity Factor 73-Kilodalton Subunit Modulating Cellular and Viral Expression

ABSTRACT The human immunodeficiency virus type 1 (HIV-1) Tat protein, which is essential for HIV gene expression and viral replication, is known to mediate pleiotropic effects on various cell functions. For instance, Tat protein is able to regulate the rate of transcription of host cellular genes and to interact with the signaling machinery, leading to cellular dysfunction. To study the effect that HIV-1 Tat exerts on the host cell, we identified several genes that were up- or down-regulated in tat-expressing cell lines by using the differential display method. HIV-1 Tat specifically increases the expression of the cleavage and polyadenylation specificity factor (CPSF) 73-kDa subunit (CPSF3) without affecting the expression of the 160- and 100-kDa subunits of the CPSF complex. This complex comprises four subunits and has a key function in the 3′-end processing of pre-mRNAs by a coordinated interaction with other factors. CPSF3 overexpression experiments and knockdown of the endogenous CPSF3 by mRNA interference have shown that this subunit of the complex is an important regulatory protein for both viral and cellular gene expression. In addition to the known CPSF3 function in RNA polyadenylation, we also present evidence that this protein exerts transcriptional activities by repressing the mdm2 gene promoter. Thus, HIV-1-Tat up-regulation of CPSF3 could represent a novel mechanism by which this virus increases mRNA processing, causing an increase in both cell and viral gene expression.
A Taxonomy for Denial-of-Service Attacks in Wireless Sensor Networks

Wireless sensor networks (WSNs) are transitioning to real-world applications, where they face attacks already experienced by the Internet and wireless ad hoc networks. One such attack is that of denial-of-service ( DOS), which we believe will only become more prevalent as sensor networks become more pervasive and accessible. With the inherent resource limitations of WSN devices, they are particularly susceptible to the consumption and destruction of these scarce resources. We present a DOS attack taxonomy to identify the attacker, his capabilities, the target of the attack, vulnerabilities used, and the end result. We survey vulnerabilities in WSNs and give possible defenses. Protecting WSNs against DOS attacks—while remaining low-cost and flexible—is a primary research challenge that bears further exploration.
A More Precise Latency Bound of Deficit Round-Robin Scheduler

Delay is an important Quality of Service (QoS) parameter. A significant pa rt of an end-to-end delay of a data flow is latency - the delay induced by scheduling algorithms in network devices. In this paper we present a latency analysis of a Deficit Round-Robin (DRR) scheduler. We correc t inaccuracies and deficiencies of the DRR latency analysis detected in works of other authors. We derive a new and more precise latency bound of the DRR scheduler and show that, contrary to the latency bounds derived by other authors, our bound is mathematically correct. Finally we give a comparative analysis of the DRR latency bounds discussed in the paper.
Expanding the Repertoire of Biomarkers for Alzheimer’s Disease: Targeted and Non-targeted Approaches

The first biofluid markers developed for Alzheimer’s disease (AD) used targeted approaches for discovery. These initial biomarkers were directed at key protein constituents of the hallmark brain lesions in AD. Biomarkers for plaques targeted the amyloid beta protein (Aβ) and for tangles, the microtubule-associated protein tau. Cerebrospinal fluid levels of Aβ and tau have excellent diagnostic utility and can be used to monitor aspects of therapeutic development. Recent research has extended our current concepts of AD, which now include a slow buildup of pathology during a long pre-symptomatic period, a complex cascade of pathological pathways in the brain that may accelerate once symptoms develop, the potential of aggregated proteins to spread across brain pathways, and interactions with vascular and other age-associated brain pathologies. There are many potential roles for biomarkers within this landscape. A more diverse set of biomarkers would provide a better picture of the staging and state of pathological events in the brain across the stages of AD. The aim of this review is to focus on methods of biomarker discovery that may help to expand the currently accepted biomarkers. Opportunities and approaches for targeted and non-targeted (or −omic) biomarker discovery are highlighted, with examples from recent studies. How biomarker discoveries can be developed and integrated to become useful tools in diagnostic and therapeutic efforts is discussed.
The LIM Homeodomain Protein Lhx6 Regulates Maturation of Interneurons and Network Excitability in the Mammalian Cortex

Deletion of LIM homeodomain transcription factor-encoding Lhx6 gene in mice results in defective tangential migration of cortical interneurons and failure of differentiation of the somatostatin (Sst)- and parvalbumin (Pva)-expressing subtypes. Here, we characterize a novel hypomorphic allele of Lhx6 and demonstrate that reduced activity of this locus leads to widespread differentiation defects in Sst+ interneurons, but relatively minor and localized changes in Pva+ interneurons. The reduction in the number of Sst-expressing cells was not associated with a loss of interneurons, because the migration and number of Lhx6-expressing interneurons and expression of characteristic molecular markers, such as calretinin or Neuropeptide Y, were not affected in Lhx6 hypomorphic mice. Consistent with a selective deficit in the differentiation of Sst+ interneurons in the CA1 subfield of the hippocampus, we observed reduced expression of metabotropic Glutamate Receptor 1 in the stratum oriens and characteristic changes in dendritic inhibition, but normal inhibitory input onto the somatic compartment of CA1 pyramidal cells. Moreover, Lhx6 hypomorphs show behavioral, histological, and electroencephalographic signs of recurrent seizure activity, starting from early adulthood. These results demonstrate that Lhx6 plays an important role in the maturation of cortical interneurons and the formation of inhibitory circuits in the mammalian cortex.
Driving vision by topology

Recently, vision research has centred on the extraction and organization of geometric features, and on geometric relations. It is largely assumed that topological structure, that is linked edgel chains and junctions, cannot be extracted reliably from image intensity data. In this paper we demonstrate that this view is overly pessimistic and that visual tasks, such as perceptual grouping, can be carried out much more efficiently and reliably if well-formed topological structures are available. Towards this end, we describe an edge detection algorithm designed to recover much better scene topology than previously considered possible. In doing this we need make no sacrifice to geometric accuracy of the edge description.
A cellular genetics approach identifies gene-drug interactions and pinpoints drug toxicity pathway nodes

New approaches to toxicity testing have incorporated high-throughput screening across a broad-range of in vitro assays to identify potential key events in response to chemical or drug treatment. To date, these approaches have primarily utilized repurposed drug discovery assays. In this study, we describe an approach that combines in vitro screening with genetic approaches for the experimental identification of genes and pathways involved in chemical or drug toxicity. Primary embryonic fibroblasts isolated from 32 genetically-characterized inbred mouse strains were treated in concentration-response format with 65 compounds, including pharmaceutical drugs, environmental chemicals, and compounds with known modes-of-action. Integrated cellular responses were measured at 24 and 72 h using high-content imaging and included cell loss, membrane permeability, mitochondrial function, and apoptosis. Genetic association analysis of cross-strain differences in the cellular responses resulted in a collection of candidate loci potentially underlying the variable strain response to each chemical. As a demonstration of the approach, one candidate gene involved in rotenone sensitivity, Cybb, was experimentally validated in vitro and in vivo. Pathway analysis on the combined list of candidate loci across all chemicals identified a number of over-connected nodes that may serve as core regulatory points in toxicity pathways.
Economics of Organic Vs Inorganic Carrot Production in Nepal

During February-April 2008, a study was conducted to compare the yield and economics of organic and inorganic carrot production and its profit volume in Chitwan district of Nepal. Face to face interview method was used to collect the primary information from randomly selected organic and inorganic carrot producers. Among the cost components, per unit cost on female labor and organic fertilizer were found to be higher in organic production system where as higher per unit cost on seed, tillage operation and male labor were found in inorganic production system. Higher cost and higher revenue was found in inorganic production system but higher benefit cost ratio was found in organic production system. This revealed that adoption of organic carrot production system was economically profitable than inorganic production system. Key words: Benefit cost ratio; Carrot; Cost; Gross margin; Organic agriculture The Journal of Agriculture and Environment Vol:10, Jun.2009 Page: 27-33
Plasma miR-10a: A Potential Biomarker for Coronary Artery Disease

Aims. MicroRNAs (miRNAs) are involved in the pathogenesis of coronary artery disease (CAD). The objective of this study is to determine plasma levels of miR-10a in CAD and analyze its association with the severity of CAD. Materials and Methods. Plasma miR-10a levels in 60 CAD patients including stable angina pectoris (SAP) (n = 29), unstable angina pectoris (UAP) or non-ST elevation myocardial infarction (MI) (NSTEMI) (n = 17), or ST elevation MI (STEMI) (n = 14) and 20 non-CAD subjects were assessed by real-time polymerase chain reaction (qRT-PCR), and associations of miR-10a levels with risk factors of CAD and its severity were analyzed. Results. The qRT-PCR results showed that plasma miR-10a levels were decreased in CAD patients, and CAD with high SYNTAX scores or STEMI was significantly associated with lower miR-10a levels. Conclusions. Lower plasma miR-10a levels were negatively associated with the presence as well as severity of CAD, and plasma miR-10a can act as a potential biomarker for estimating the presence and severity of CAD.
Cooperative Communication Aware Link Scheduling for Cognitive Vehicular Ad-hoc Networks

Throughput maximization is a key challenge for wireless applications in cognitive Vehicular Ad-hoc Networks (CVANETs). As a potential solution, cooperative communications, which may increase link capacity by exploiting spatial diversity, has attracted a lot of attention in recent years. However, if link scheduling is considered, this transmission mode may perform worse than direct transmission in terms of end-to-end throughput. In this paper, we propose a cooperative communication aware link scheduling scheme and investigate the throughput maximization problem in C-VANETs. Regarding the features of cooperative communications and the availability of licensed spectrum, we extend the links into cooperative links/general links, define extended link-band pairs, and form a 3-dimensional (3-D) cooperative conflict graph to characterize the conflict relationship among those pairs. Given all cooperative independent sets in this graph, we mathematically formulate an endto-end throughput maximization problem and near-optimally solve it by linear programming. Due to the NP-completeness of finding all independent sets, we also develop a heuristic pruning algorithm for cooperative communication aware link scheduling. Our simulation results show that the proposed scheme is effective in increasing end-to-end throughput for the session in C-VANETs.
Not More than Three Tissue Kallikreins Identified from Organs of the Guinea Pig

Abstract The large and varied multigene families of tissue kallikreins of rat and mouse are considered to selectively release as many bioactive peptides. In order to determine whether a similar family of enzymes is expressed in the organs of the guinea pig purification studies were performed. Tissue kallikreins from the submandibular gland, coagulating gland/prostate complex and the pancreas were separated by affinity chromatography on benzamidine-Sepharose. Amino-terminal sequences, the patterns of hydrolysis rates of a number of peptide p-nitroanilides, inactivation rates by active site-directed irreversible inhibitors, specific kininogenase activities and types of kinin released were used to probe the identity of the isolated enzymes. Guinea pig tissue kallikreins 1 and 2 have been reported previously. In the present study we have identified a third type, designated tissue kallikrein 1a because of its sequence similarity to kallikrein 1, which differs from the latter in the catalytic properties. The inferred occurrence of not more than two or three independent tissue kallikrein genes in the guinea pig contrasts with the varied family of enzymes expressed by the large number of such genes present in rats and mice. Expression in the guinea pig (and also in humans) of only a small number of tissue kallikreins makes specific processing of a multitude of biologically active peptides by such enzymes unlikely.
A model of inflation with variable time lags

Variable time lags are a possible source of randomness in relationships between economic time series. They are modelled here by means of variable regression coefficients. The model entails heteroscedastic residuals with a negative serial correlation and can be estimated by the Kalman filter. This extension of the traditional regression model is highly significant for the relationship between quarterly values of wages and prices in Iceland.
Impact of Wheat Row Planting on Yield of Smallholders in Arsi Zone of Ethiopia

Promotion and scaling up of wheat row planting is seen as best farming practice for increasing wheat yield in Ethiopia. Farmers have been practicing wheat row planting manually for the last three to five years. However, there is lack of empirical study on the impact of row planting on wheat yield compared to the conventional broadcast planting method. To fill this gap, this study estimates the impact of row planting on wheat yield of farmers. Cross-sectional survey data collected from randomly selected 133 farmers, logit model, and propensity score matching methods were used to achieve the objective of the study. The study obtained that wheat row planting has significant impact on wheat yield of farmers. The mean yield of row planted wheat was higher by 14.6 percent when compared to the mean yield of conventional broadcast planting method. It is recommended that other agronomic practices along with the row planting method need to be considered for increasing wheat yield as well as for the successful promotion, adoption and scaling up of wheat row planting practices.
RelateAdmix: a software tool for estimating relatedness between admixed individuals

MOTIVATION Pairwise relatedness plays an important role in a range of genetic research fields. However, currently only few estimators exist for individuals that are admixed, i.e. have ancestry from more than one population, and these estimators fail in some situations. RESULTS We present a new software tool, RelateAdmix, for obtaining maximum likelihood estimates of pairwise relatedness from genetic data between admixed individuals. We show using simulated data that it gives rise to better estimates than three state-of-the-art software tools, REAP, KING and Plink, while still being fast enough to be applicable to large datasets. AVAILABILITY AND IMPLEMENTATION The software tool, implemented in C and R, is freely available from www.popgen. dk/software.
F-SVM: Combination of Feature Transformation and SVM Learning via Convex Relaxation

The generalization error bound of support vector machine (SVM) depends on the ratio of radius and margin, while standard SVM only considers the maximization of the margin but ignores the minimization of the radius. Several approaches have been proposed to integrate radius and margin for joint learning of feature transformation and SVM classifier. However, most of them either require the form of the transformation matrix to be diagonal, or are non-convex and computationally expensive. In this paper, we suggest a novel approximation for the radius of minimum enclosing ball (MEB) in feature space, and then propose a convex radius-margin based SVM model for joint learning of feature transformation and SVM classifier, i.e., F-SVM. An alternating minimization method is adopted to solve the F-SVM model, where the feature transformation is updatedvia gradient descent and the classifier is updated by employing the existing SVM solver. By incorporating with kernel principal component analysis, F-SVM is further extended for joint learning of nonlinear transformation and classifier. Experimental results on the UCI machine learning datasets and the LFW face datasets show that F-SVM outperforms the standard SVM and the existing radius-margin based SVMs, e.g., RMM, R-SVM+ and R-SVM+{\mu}.
Cold surge activity over the Gulf of Mexico in a warmer climate1

Cold surges are a dominant feature of midlatitude tropical interaction. During the North Hemisphere (NH) winter, midlatitude waves propagating from the Rocky Mountains into the Gulf of Mexico result in cold surges, also known as Nortes or Tehuantepecers, associated with severe weather over the southern part of Mexico. The magnitude of their intense surface winds, precipitation and drops in surface temperature depends on the characteristics of the midlatitude wave propagating into the tropics. The high spatial resolution (20km X 20km) version of the TL959L60-AGC Model of the Meteorological Research Institute of Japan is used to examine changes in cold surge activity under the A1B greenhouse gas emission scenario for the 2080 - 2099 period. The model realistically reproduces the spatial and temporal characteristics of cold surges for the 1980 - 1989 control period. The effect of changes in baroclinicity, static stability and mean flow over North America suggest that in a warmer climate, increased cold surge activity over the Gulf of Mexico would occur. However, these systems would have shorter wavelength (higher phase speeds) and shorter lifespans that could reduce the total amount of winter precipitation. The increased frequency of cold surges over the Gulf of Mexico would be a consequence of weaker baroclinicity and static stability in the lower troposphere over the cold surge genesis region, along with more dominant westerly winds, resulting from ENSO-like conditions in the atmospheric circulations over North America.
Side Chain Hydrophobicity Modulates Therapeutic Activity and Membrane Selectivity of Antimicrobial Peptide Mastoparan-X

The discovery of new anti-infective compounds is stagnating and multi-resistant bacteria continue to emerge, threatening to end the “antibiotic era”. Antimicrobial peptides (AMPs) and lipo-peptides such as daptomycin offer themselves as a new potential class of antibiotics; however, further optimization is needed if AMPs are to find broad use as antibiotics. In the present work, eight analogues of mastoparan-X (MPX) were investigated, having side chain modifications in position 1, 8 and 14 to modulate peptide hydrophobicity. The self-association properties of the peptides were characterized, and the peptide-membrane interactions in model membranes were compared with the bactericidal and haemolytic properties. Alanine substitution at position 1 and 14 resulted in higher target selectivity (red blood cells versus bacteria), but also decreased bactericidal potency. For these analogues, the gain in target selectivity correlated to biophysical parameters showing an increased effective charge and reduction in the partitioning coefficient for membrane insertion. Introduction of an unnatural amino acid, with an octyl side chain by amino acid substitution, at positions 1, 8 and 14 resulted in increased bactericidal potency at the expense of radically reduced membrane target selectivity. Overall, optimized membrane selectivity or bactericidal potency was achieved by changes in side chain hydrophobicity of MPX. However, enhanced potency was achieved at the expense of selectivity and vice versa in all cases.