Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular Evolution of Sterol-Sensing Domain in Eukaryotes

The sterol-sensing domain (SSD) is a ∼180 amino acid long region that is conserved in six families of proteins such as hydroxymethylglutaryl-CoA reductase (HMDH), SREBP (sterol regulatory element binding protein) cleavage activating protein (SCAP), Niemann-Pick C-1 type protein (NPC1), Patched, Patched-related and Dispatched [1]. This domain encompasses five transmembrane helices and is involved in sterol-level sensing in the cell. All these classes of proteins thus have functions related to sterols. HMDH is a cholesterol biosynthetic enzyme that is degraded when sterol levels are high. SCAP is responsible for regulating SREBP, a transcription factor of cholesterol biosynthetic genes. NPC1 is responsible for intracellular transport of cholesterol. Patched plays a role in cell differentiation during development and morphogenesis. It is a receptor of hedgehog, a ligand that is bound to cholesterol. Dispatched is involved in releasing the cholesterol-bound hedgehog. The importance of SSD in proper functioning of these proteins has been shown by various mutation experiments. For example, mutations in the SSD region of NPC1 disrupt normal transportation of cholesterol in the cells [2]. Mutation in SSD can be lethal to cells and cause various diseases due to the abruption of cholesterol homeostasis in cells. The role of SSD in sterol homeostasis in cells makes it an important target for bio-medical research in understanding and curing cholesterol-related diseases. Despite its importance, SSD has not been thoroughly studied in its own entirety. In order to elucidate the molecular evolution of SSD and related protein families, in this study we examined SSDs in various eukaryotic species as well as in different protein families. Existence of HMDH proteins with and without SSDs, for example, provided us with an excellent opportunity to study how their functions and domains have been acquired during the evolution of this protein family.
Cellular Redistribution of Protein Tyrosine Phosphatases LAR and PTPσ by Inducible Proteolytic Processing

Most receptor-like protein tyrosine phosphatases (PTPases) display a high degree of homology with cell adhesion molecules in their extracellular domains. We studied the functional significance of processing for the receptor-like PTPases LAR and PTPσ. PTPσ biosynthesis and intracellular processing resembled that of the related PTPase LAR and was expressed on the cell surface as a two-subunit complex. Both LAR and PTPσ underwent further proteolytical processing upon treatment of cells with either calcium ionophore A23187 or phorbol ester TPA. Induction of LAR processing by TPA in 293 cells did require overexpression of PKCα. Induced proteolysis resulted in shedding of the extracellular domains of both PTPases. This was in agreement with the identification of a specific PTPσ cleavage site between amino acids Pro821 and Ile822. Confocal microscopy studies identified adherens junctions and desmosomes as the preferential subcellular localization for both PTPases matching that of plakoglobin. Consistent with this observation, we found direct association of plakoglobin and β-catenin with the intracellular domain of LAR in vitro. Taken together, these data suggested an involvement of LAR and PTPσ in the regulation of cell contacts in concert with cell adhesion molecules of the cadherin/catenin family. After processing and shedding of the extracellular domain, the catalytically active intracellular portions of both PTPases were internalized and redistributed away from the sites of cell–cell contact, suggesting a mechanism that regulates the activity and target specificity of these PTPases. Calcium withdrawal, which led to cell contact disruption, also resulted in internalization but was not associated with prior proteolytic cleavage and shedding of the extracellular domain. We conclude that the subcellular localization of LAR and PTPσ is regulated by at least two independent mechanisms, one of which requires the presence of their extracellular domains and one of which involves the presence of intact cell–cell contacts.
A novel fuzzy clustering method based on chaos small-world algorithm for image edge detection

To solve the fuzzy edge detection problems in image processing, a novel fuzzy clustering method based on chaos small-world algorithm (CSWFCM) is presented. The traditional fuzzy clustering method (FCM) is good at local searching capability, but it is sensitive to the initial value and easy to trap into local minimum value. The small-world algorithm (SWA), inspired by the mechanism of small-world phenomenon, is a novel global searching algorithm, which enables to enhance the diversity of the population and avoid trapping into local minimum value. However, the further capability of solving complicated problems is limited for its low efficiency of local short-range searching operator. In this paper, the chaos disturbance is utilized to improve the searching efficiency of SWA after local short-range search, and the chaos small-world algorithm (CSWA) is used to optimize the FCM in image edge detection. The simulation results show that the proposed algorithm can correctly detect the fuzzy and exiguous edges with higher convergence speed.
Fossil Remnants of Reionization in the Halo of the Milky Way

Our recently completed one billion particle Via Lactea II simulation of a Milky Way-sized dark matter halo resolves over 50,000 gravitationally bound clumps orbiting today within the virialized region of the main host. About 2300 of these subhalos have one or more “progenitors” with M > 106 M☉ at redshift z = 11, i.e., massive enough for their gas to have cooled via excitation of H2 and fragmented prior to the epoch of cosmic reionization. We count 4500 such progenitors: if these were able to convert a fraction of their gas content into very metal-poor stars with a Salpeter initial mass function (IMF), they would be shining today with a visual magnitude MV = 6.7 per solar mass in stars. Assuming a universal baryon fraction, we show that mean star formation efficiencies as low as 0.1% in progenitors ≪108 M☉ would overproduce the abundance of the faint Galactic dwarf spheroidals observed by the Sloan Digital Sky Survey. Star formation at first light must either have occurred with an IMF lacking stars below 0.9 M☉, or was intrinsically very inefficient in small dark matter halos. If the latter, our results may be viewed as another hint that there is a minimum scale in galaxy formation.
Wind blows, traffic flows: Green Internet routing under renewable energy

We present a study on minimizing non-renewable energy for the Internet. The classification of renewable and non-renewable energy brings in several challenges. First, it is necessary to understand how the routing system can distinguish the two types of energy in the power supply. Second, the routing problem changes due to renewable energy; and so do the algorithm designs and analysis. We first clarify the model of how routers can distinguish renewable and non-renewable energy supporting their power supply. This cannot be determined by the routing system alone, and involves modeling the energy generation and supply of the grid. We then present the router power consumption model, which has a fixed startup power and a dynamic traffic-dependent power. We formulate a minimum non-renewable energy routing problem, and two special cases representing either the startup power dominates or the traffic-dependent power dominates. We analyze the complexity of these problems, develop optimal and sub-optimal algorithms, and jointly consider QoS requirements such as path stretch. We evaluate our algorithms using real data from both National and European centers. As compared to the algorithms minimizing the total energy, our algorithms can reduce the non-renewable energy consumption for more than 20% under realistic assumptions.
Comparison of Edge Partitioners for Graph Processing

Deploying graph on a cluster requires its partitioning into a number of subgraphs, and assigning them to different machines. Two partitioning approaches have been proposed: vertex partitioning and edge partitioning. In the edge partitioning approach edges are allocated to partitions. Recent studies show that, for power-law graphs, edge partitioning is more effective than vertex partitioning. In this paper we provide an overview of existing edge partitioning algorithms. However, based only on published work, we cannot draw a clear conclusion about the relative performances of these partitioners. For this reason, we compare all the edge partitioners currently available for GraphX. Our preliminary results suggest that Hybrid-Cut partitioner provides the best performance.
Advancedwireless Multiuser Video Streaming using the Scalable Video Coding Extensions of H.264/MPEG4-AVC

We propose a dynamic sharing of radio resources in a wireless multiuser system by combining a flexible video coding scheme, namely the currently developed scalable video coding (SVC) extension of H.264/AVC with appropriate radio link buffer management for multiuser streaming services. The paper introduces the components of the proposed system and the used cross-layer interface. Simulation results verify the benefits of our approach
The Effect of Acute Rhodiola rosea Ingestion on Exercise Heart Rate, Substrate Utilisation, Mood State, and Perceptions of Exertion, Arousal, and Pleasure/Displeasure in Active Men

The aim of this study was to examine the effect of acute Rhodiola rosea (R. rosea) ingestion on substrate utilisation, mood state, RPE, and exercise affect. Ten males (mean age ± S.D. = 26 ± 6 years) completed two 30-minute cycling trials at an intensity of 70% of V˙O2max⁡ following ingestion of either 3 mg·kg−1 body mass of R. rosea or placebo using a double-blind, crossover design. During exercise, heart rate and RPE were recorded. Participants completed measures of mood state and exercise affect before and after exercise. Expired air samples were taken during exercise to determine substrate utilisation. Repeated measures analysis of variance indicated that RPE was significantly lower at 30 minutes into exercise versus placebo (P = 0.003). Perceptions of arousal (P = 0.05) and pleasure were significantly higher after exercise with R. rosea compared to placebo (P = 0.003). Mood state scores for vigor were also higher in R. rosea condition compared to placebo (P = 0.008). There were no significant differences in energy expenditure, carbohydrate, or fat oxidation between conditions (P > 0.05). Ingestion of R. rosea favourably influenced RPE and exercise affect without changes in energy expenditure or substrate utilization during 30-minute submaximal cycling performance.
How does surgery compare to sham surgery or physiotherapy as a treatment for tendinopathy? A systematic review of randomised trials

Purpose To assess the effectiveness of surgery on all tendinopathies by comparing it to no treatment, sham surgery and exercise-based therapies for both mid-term (12 months) and long-term (> 12 months) outcomes. Methods Our literature search included EMBASE, Medline, CINAHL and Scopus. A combined assessment of internal validity, external validity and precision of each eligible study yielded its overall study quality. Results were considered significant if they were based on strong (Level 1) or moderate (Level 2) evidence. Results 12 studies were eligible. Participants had the following types of tendinopathy: shoulder in seven studies, lateral elbow in three, patellar in one and Achilles in one. Two studies were of good, four of moderate and six of poor overall quality. Surgery was superior to no treatment or placebo, for the outcomes of pain, function, range of movement (ROM) and treatment success in the short and midterm. Surgery had similar effects to sham surgery on pain, function and range of motion in the midterm. Physiotherapy was as effective as surgery both in the midterm and long term for pain, function, ROM and tendon force, and pain, treatment success and quality of life, respectively. Conclusion We recommend that healthcare professionals who treat tendinopathy encourage patients to comply with loading exercise treatment for at least 12 months before the option of surgery is seriously entertained.
Genetic and Environmental Control of Neurodevelopmental Robustness in Drosophila

Interindividual differences in neuronal wiring may contribute to behavioral individuality and affect susceptibility to neurological disorders. To investigate the causes and potential consequences of wiring variation in Drosophila melanogaster, we focused on a hemilineage of ventral nerve cord interneurons that exhibits morphological variability. We find that late-born subclasses of the 12A hemilineage are highly sensitive to genetic and environmental variation. Neurons in the second thoracic segment are particularly variable with regard to two developmental decisions, whereas its segmental homologs are more robust. This variability “hotspot” depends on Ultrabithorax expression in the 12A neurons, indicating variability is cell-intrinsic and under genetic control. 12A development is more variable and sensitive to temperature in long-established laboratory strains than in strains recently derived from the wild. Strains with a high frequency of one of the 12A variants also showed a high frequency of animals with delayed spontaneous flight initiation, whereas other wing-related behaviors did not show such a correlation and were thus not overtly affected by 12A variation. These results show that neurodevelopmental robustness is variable and under genetic control in Drosophila and suggest that the fly may serve as a model for identifying conserved gene pathways that stabilize wiring in stressful developmental environments. Moreover, some neuronal lineages are variation hotspots and thus may be more amenable to evolutionary change.
The Simulation Study of Shanghai and Shenzhen 300 Index By Garch Models

the empirical analysis of Shanghai and Shenzhen 300 Index, using Garch family models, shows that the fluctuation of Shanghai and Shenzhen 300 Index has an outstanding Garch effects, the fluctuation of stock market has constancy and weak leverage effect. The conditional variance of stock returns series is stationary and the stock market has predictability. We can predict the volatility of stock market based on EGRACH-M (1, 1) models.
Joint Scheduling and Flow Control for Multi-hop Cognitive Radio Network with Spectrum Underlay

In this paper, we introduce a joint flow control and scheduling algorithm for multi-hop cognitive radio networks with spectrum underlay. Our proposed algorithm maximizes the total utility of secondary users while stabilizing the cognitive radio network and still satisfies the total interference from secondary users to primary network is less than an accepted level. Based on Lyapunov optimization technique, we show that our scheme is arbitrarily close to the optimal.
"Blind" speech segmentation: automatic segmentation of speech without linguistic knowledge

A new automatic speech segmentation procedure, called the "Blind" speech segmentation, is presented. This procedure allows a speech sample to be segmented into sub-word units without the knowledge of any linguistic information (such as, orthographic or phonetic transcription). Hence, this procedure involves finding the optimal number of sub-word segments in the given speech sample, before locating the sub-word segment boundaries.
Social bookmark data mining using extended graph kernel

In this study, we present a social bookmark data community and propose a method to extract the rules of community changes. The transaction data collected from a data stream is considered a graph representing change in structure and sequence data for each relevant time period, while analyzing changes in the sequence graph of the community. The algorithm proposed in this paper is the hierarchical clustering method combined with convolution graph kernels weighted in time. We use this algorithm on the entire community to analyze the relationship among graph sequences and show that it occasionally appears (disappearing in the middle of the sequences) and changes the extracted community rules. Experimental results obtained using synthetic data sets and real social bookmark data show that changes in the community captured the occasional occurrence of the proposed algorithm. The proposed method can detect and analyze social bookmark data including large-scale time-series graph.
DIETARY SURVEYS AND NUTRITIONAL EPIDEMIOLOGY Gluten intake in 6 – 36-month-old Danish infants and children based on a national survey

Coeliac disease (CD) affects about 1 % of the general population. Information concerning gluten intake in the general population is scarce. In particular, variation in gluten intake during the complementary feeding period may be an independent risk factor in CD pathogenesis. We determined the intake of gluten from wheat, barley, rye and oats in a cross-sectional National Danish Survey of Dietary Habits among Infants and Young Children (2006 – 2007). The study population comprised a random sample of 1743 children aged 6 – 36 months, recruited from the National Danish Civil Registry. The protein contents from wheat,rye,barleyandoats werefound inthe NationalDanish FoodComposition Table, andmultiplied with the amounts in the recipes. The amounts ofgluten were calculated as the amount of cereal protein × 0 · 80 for wheat and oats, ×0 · 65 for rye and ×0 · 50 for barley. Dietary intake was recorded daily for seven consecutive days in pre-coded food records supplemented with open-answer possibilities. Gluten intake increased with age ( P < 0 · 0001). Oats were introduced ﬁ rst, rapidly outpaced by wheat, the intake of which continued to increase with age, whereas oats started to decrease at 12 months. Boys had a higher intake of energy ( P ≤ 0 · 0001) and all types of gluten, except for barley ( P ≤ 0 · 87). In 8 – 10-month-old ( P < 0 · 0001) and 10 – 12-month-old ( P = 0 · 007), but not in 6 – 8-month-old infants ( P = 0 · 331), non-breast-fed infants had higher total gluten intake than partially breast-fed infants. In conclusion, this study presents representative population-based data on gluten intake in Danish infants and young children.
Peduncle Detection of Sweet Pepper for Autonomous Crop Harvesting—Combined Color and 3-D Information

This letter presents a three-dimensional (3-D) visual detection method for the challenging task of detecting peduncles of sweet peppers (Capsicum annuum) in the field. Cutting the peduncle cleanly is one of the most difficult stages of the harvesting process, where the peduncle is the part of the crop that attaches it to the main stem of the plant. Accurate peduncle detection in 3-D space is, therefore, a vital step in reliable autonomous harvesting of sweet peppers, as this can lead to precise cutting while avoiding damage to the surrounding plant. This letter makes use of both color and geometry information acquired from an RGB-D sensor and utilizes a supervised-learning approach for the peduncle detection task. The performance of the proposed method is demonstrated and evaluated by using qualitative and quantitative results [the area-under-the-curve (AUC) of the detection precision-recall curve]. We are able to achieve an AUC of 0.71 for peduncle detection on field-grown sweet peppers. We release a set of manually annotated 3-D sweet pepper and peduncle images to assist the research community in performing further research on this topic.
DAFOE: a Platform for Building Ontologies from Texts

Although text-based ontology engineering gained much popularity in the last 10 years, very few ontology engineering platforms exploit the full potential of the connection between texts and ontologies. We propose DAFOE, a new platform for building ontologies with a terminological component using diff erent types of linguistic entries (text corpora, results of natural language processing tools, terminologies or thesauri). DAFOE supports knowledge structuring and conceptual modelling from these linguistic entries as well as ontology formalization. DAFOE outputs models with two main original features: an ontology articulated with a lexical component and a connection with the text or linguistic entry that motivated their defi nition.
A Comparative Study on the Effectiveness of Positive Psychotherapy and Group Cognitive-Behavioral Therapy for the Patients Suffering From Major Depressive Disorder

Objective: Aim of this experimental study is evaluating the effectiveness of two different approaches towards the treatment of major depressive disorder (MDD): Positive-oriented psychotherapy and group cognitive-behavior therapy. Methods: Eighteen out-patients suffering from major depression were randomly divided into two groups to be treated according to either of these two approaches. Both groups undertook the treatments for 12 weeks. All the subjects were tested by Beck Depression Inventory, Subjective Wellbeing Scale, Oxford test of Happiness, and the scale of Subjective Units of Distress before and after the treatments. Results: The results show significant differences between the two groups in terms of the variables of happiness and mental distress, suggesting that effectiveness of positive psychotherapy is more than cognitive-behavioral therapy in increasing happiness. These two approaches were significantly different in neither decreasing the acuteness of depression symptoms nor increasing subjective wellbeing. Conclusion: As a whole, the results of this comparative study indicate that positive psychotherapy is more effective in increasing happiness among MDD patients.
Parallel Exploitation of Diverse Host Nutrients Enhances Salmonella Virulence

Pathogen access to host nutrients in infected tissues is fundamental for pathogen growth and virulence, disease progression, and infection control. However, our understanding of this crucial process is still rather limited because of experimental and conceptual challenges. Here, we used proteomics, microbial genetics, competitive infections, and computational approaches to obtain a comprehensive overview of Salmonella nutrition and growth in a mouse typhoid fever model. The data revealed that Salmonella accessed an unexpectedly diverse set of at least 31 different host nutrients in infected tissues but the individual nutrients were available in only scarce amounts. Salmonella adapted to this situation by expressing versatile catabolic pathways to simultaneously exploit multiple host nutrients. A genome-scale computational model of Salmonella in vivo metabolism based on these data was fully consistent with independent large-scale experimental data on Salmonella enzyme quantities, and correctly predicted 92% of 738 reported experimental mutant virulence phenotypes, suggesting that our analysis provided a comprehensive overview of host nutrient supply, Salmonella metabolism, and Salmonella growth during infection. Comparison of metabolic networks of other pathogens suggested that complex host/pathogen nutritional interfaces are a common feature underlying many infectious diseases.