Miracle-dz/UniFAR-FTUs huggingface dataset:
Exploration for Functional Nucleotide Sequence Candidates within Coding Regions of Mammalian Genes

The primary role of a protein coding gene is to encode amino acids. Therefore, synonymous sites of codons, which do not change the encoded amino acid, are regarded as evolving neutrally. However, if a certain region of a protein coding gene contains a functional nucleotide element (e.g. splicing signals), synonymous sites in the region may have selective pressure. The existence of such elements would be detected by searching regions of low nucleotide substitution. We explored invariant nucleotide sequences in 10 790 orthologous genes of six mammalian species (Homo sapiens, Macaca mulatta, Mus musculus, Rattus norvegicus, Bos taurus, and Canis familiaris), and extracted 4150 sequences whose conservation is significantly stronger than other regions of the gene and named them significantly conserved coding sequences (SCCSs). SCCSs are observed in 2273 genes. The genes are mainly involved with development, transcriptional regulation, and the neurons, and are expressed in the nervous system and the head and neck organs. No strong influence of conventional factors that affect synonymous substitution was observed in SCCSs. These results imply that SCCSs may have double function as nucleotide element and protein coding sequence and retained in the course of mammalian evolution.
Anti-inflammatory and antioxidant effect of Ceratonia siliqua L. methanol barks extract

Ceratonia siliqua L. has been used in Moroccan trad i ional medicine as antidiarrheal and diuretic. The infusion of carob leaves is used as an emetic for acute poisoni ng. The present investigation was designed to deter min the antiinflammatory potential of methanolic barks extract of Ceratonia siliqua in rodents using female Swiss mice (20-30 g) and Wistar male rats (150-250 g). The acute toxi city studies were carried out based on OECD 423 gui delines. The LD50 of Ceratonia siliqua was found to be more than 5 g /kg and did not produce mortality or changes in general behavior of the tested animals. Methanolic barks extract of Ceratonia siliqua was investigated for antiinflammatory properties by using carrageenan and ex perimental trauma-induced hind paw oedema in rodent s at the dose of 50, 100, 200 mg/kg p.o. respectively, Indom ethacin at 10 and 20 mg/kg was used as standard. Fr om the results obtained, the methanolic barks extract of C eratonia siliqua showed significant reduction (P ≤ 0.001) and inhibition of oedema comparable to the control and reference drug used in both models. This study show ed the justification of the use of Ceratonia siliqua in th e treatment of inflammatory disease conditions in M orocco.
Leveraging Linguistic Resources for Improving Neural Text Classification

This paper presents a deep linguistic attentional framework which incorporates word level concept information into neural clas-siﬁcation models. While learning neural classiﬁcation models often requires a large amount of labelled data, linguistic concept information can be obtained from exter-nal knowledge, such as pre-trained word embeddings, WordNet for common text and MetaMap for biomedical text. We explore two different ways of incorporating word level concept annotations, and show that leveraging concept annotations can boost the model performance and reduce the need for large amounts of labelled data. Experiments on various data sets validate the effectiveness of the proposed method.
An Environmental Perspective on Clothing Consumption: Consumer Segments and Their Behavioral Patterns

Efforts to decrease the environmental impact of today’s clothing industry across the entire process of production, purchase, maintenance, and disposal can be driven by either suppliers or consumers. Changing the behavior of the latter, however, requires an understanding of current clothing consumption patterns—a currently under-researched area. We therefore shed more light on these patterns in the purchase, use and maintenance, and discard phases by analyzing unique data on 4617 adult consumers (aged 18–65) from Germany, Poland, Sweden, and the U.S., who we divide into five segments based on clothing consumption behavior. At the low end of the spectrum is a consumer segment that earns the least, consumes mostly budget brand clothing, and is the least open to alternative more environmentally friendly business models such as fashion leasing or clothing libraries. At the other extreme lies a small segment that earns the most, engages in high consumption of medium or premium brand clothing, and is most open to alternative business models. Lying between these two is a primarily female segment that purchases an above average amount of clothing from budget brands. In addition to the segments’ different reported purchase behavior and a varying openness to alternative business models, we identify differences in willingness to pay for clothing made of material that is more environmentally friendly than conventional fabrics. These observations suggest several promising directions for environmental interventions tailored toward specific consumer segments.
Viterbi algorithm as an alternative to energy minimization for stereo image matching

The correspondence problem in image matching is an ill-defined one. It is difficult to match two stereo images to produce an accurate depth map without applying some sort of constraints to the matching process. Matching is made especially difficult near discontinuities and occlusions in the images. A popular method of applying constraints to image matching is energy minimisation. However, this technique is computationally expensive and is not guaranteed to finish at an optimal solution. This paper describes the use of a least cost path finding algorithm called the Viterbi algorithm as an alternative to energy minimisation. The Viterbi algorithm operates on individual horizontal scanlines and uses a cost function to find the optimum "path" of nodes through disparity space from one side of the image to the other. Constraints can be applied by restricting the possible movements of the path or by modifying the cost function. The Viterbi algorithm, unlike energy minimisation, is not an iterative process and is guaranteed to find the path that has the least possible cost. The implementation of the Viterbi algorithm described in this paper uses constraints that were developed to make the image matching robust in the presence of discontinuities and occlusions. Results are shown for both synthetic and real-world stereo pairs.
Compressed power spectrum, carrier and DOA estimation via PARAFAC decomposition

This paper considers the problem of joint wideband spectrum sensing and direction-of-arrival (DoA) estimation in a sub-Nyquist sampling framework. A new phased-array based sub-Nyquist receiver architecture, which requires only a single delay channel for each sensor output and thus can be implemented simply and efficiently, is proposed. We proposed a CANDECOMP/PARAFAC (CP) decomposition-based method for joint wideband spectrum sensing and DOA estimation through exploiting the cross-correlations between different sensor outputs. Simulation results under different numbers of antennas and signal to noise ratios (SNR) are provided to corroborate our proposed algorithm.
Impacts of Parasites in Early Life: Contrasting Effects on Juvenile Growth for Different Family Members

Parasitism experienced early in ontogeny can have a major impact on host growth, development and future fitness, but whether siblings are affected equally by parasitism is poorly understood. In birds, hatching asynchrony induced by hormonal or behavioural mechanisms largely under parental control might predispose young to respond to infection in different ways. Here we show that parasites can have different consequences for offspring depending on their position in the family hierarchy. We experimentally treated European Shag (Phalacrocorax aristoteli) nestlings with the broad-spectrum anti-parasite drug ivermectin and compared their growth rates with nestlings from control broods. Average growth rates measured over the period of linear growth (10 days to 30 days of age) and survival did not differ for nestlings from treated and control broods. However, when considering individuals within broods, parasite treatment reversed the patterns of growth for individual family members: last-hatched nestlings grew significantly slower than their siblings in control nests but grew faster in treated nests. This was at the expense of their earlier-hatched brood-mates, who showed an overall growth rate reduction relative to last-hatched nestlings in treated nests. These results highlight the importance of exploring individual variation in the costs of infection and suggest that parasites could be a key factor modulating within-family dynamics, sibling competition and developmental trajectories from an early age.
Impact of anemia and cardiovascular disease on frailty status of community-dwelling older women: the Women's Health and Aging Studies I and II.

BACKGROUND The physiological basis of the geriatric syndrome of frailty, a clinical state of increased vulnerability to adverse outcomes such as disability and mortality, remains to be better characterized. We examined the cross-sectional relationship between hemoglobin (Hb) and a recently-validated measure of frailty in community-dwelling older women, and whether this relationship was modified by cardiovascular disease (CVD) status. METHODS Data were pooled from women 70-80 years old participating in the Women's Health and Aging Studies I and II (Baltimore, MD, 1992-1996) with known frailty status and Hb > or = 10 g/dL (n = 670). Logistic regression was used to model the relationship between frailty and Hb, adjusting for demographics, major chronic diseases, and physiologic and functional impairments. RESULTS Prevalence of frailty was 14%. Frailty risk was highest at the lowest Hb levels, and lowest at mid-normal Hb levels (e.g., 13-14 g/dL). Mildly low and low-normal Hb concentrations were independently associated with frailty. Compared to an Hb concentration equal to 13.5 g/dL, the adjusted odds of being frail were 1.9 (95% confidence interval: 1.1-3.4) and 1.5 (95% confidence interval: 1.0-2.1) times higher for Hb concentrations equal to 11.5 g/dL and 12 g/dL, respectively. A statistically significant (p <.05) multiplicative interaction between Hb level and CVD status with respect to frailty risk was observed. CONCLUSION In community-dwelling older women, mildly low and low-normal Hb levels were independently associated with increased frailty risk. This risk was synergistically modified by the presence of CVD. These results suggest that mild anemia, and even low-normal Hb levels are independent, potentially modifiable risk factors for frailty in community-dwelling older adults.
Towards intra-operative diagnosis of tumours during breast conserving surgery by selective-sampling Raman micro-spectroscopy

Breast-conserving surgery (BCS) is increasingly employed for the treatment of early stage breast cancer. One of the key challenges in BCS is to ensure complete removal of the tumour while conserving as much healthy tissue as possible. In this study we have investigated the potential of Raman micro-spectroscopy (RMS) for automated intra-operative evaluation of tumour excision. First, a multivariate classification model based on Raman spectra of normal and malignant breast tissue samples was built and achieved diagnosis of mammary ductal carcinoma (DC) with 95.6% sensitivity and 96.2% specificity (5-fold cross-validation). The tumour regions were discriminated from the healthy tissue structures based on increased concentration of nucleic acids and reduced concentration of collagen and fat. The multivariate classification model was then applied to sections from fresh tissue of new patients to produce diagnosis images for DC. The diagnosis images obtained by raster scanning RMS were in agreement with the conventional histopathology diagnosis but were limited to long data acquisition times (typically 10 000 spectra mm−2, which is equivalent to ~5 h mm−2). Selective-sampling based on integrated auto-fluorescence imaging and Raman spectroscopy was used to reduce the number of Raman spectra to ~20 spectra mm−2, which is equivalent to an acquisition time of ~15 min for 5 × 5 mm2 tissue samples. This study suggests that selective-sampling Raman microscopy has the potential to provide a rapid and objective intra-operative method to detect mammary carcinoma in tissue and assess resection margins.
Language Brokering and Depressive Symptoms in Mexican-American Adolescents: Parent-Child Alienation and Resilience as Moderators.

This study aimed to untangle the mixed effects of language brokering by examining a contextual factor (i.e., parent-child alienation) and a personal attribute (i.e., resilience) that may relate to adolescents' feelings during translating (i.e., sense of burden and efficacy) and that may moderate the association between such feelings and adolescent depressive symptoms. Participants included 557 adolescent language brokers (Mage = 12.96) in Mexican-American families. Results showed that adolescents with a strong sense of alienation from parents or low resilience (a) experienced more burden or less efficacy in translating and (b) were more susceptible to the detrimental effects of feeling a sense of burden and the beneficial effects of experiencing a sense of efficacy, as measured by depressive symptoms.
Identification of Novel Ezrin Inhibitors Targeting Metastatic Osteosarcoma by Screening Open Access Malaria Box

Ezrin is a member of the ERM (ezrin, radixin, moesin) family of proteins and functions as a linker between the plasma membrane and the actin cytoskeleton. Ezrin is a key driver of tumor progression and metastatic spread of osteosarcoma. We discovered a quinoline-based small molecule, NSC305787, that directly binds to ezrin and inhibits its functions in promoting invasive phenotype. NSC305787 possesses a very close structural similarity to commonly used quinoline-containing antimalarial drugs. On the basis of this similarity and of recent findings that ezrin has a likely role in the pathogenesis of malaria infection, we screened antimalarial compounds in an attempt to identify novel ezrin inhibitors with better efficacy and drug properties. Screening of Medicines for Malaria Venture (MMV) Malaria Box compounds for their ability to bind to recombinant ezrin protein yielded 12 primary hits with high selective binding activity. The specificity of the hits on ezrin function was confirmed by inhibition of the ezrin-mediated cell motility of osteosarcoma cells. Compounds were further tested for phenocopying the morphologic defects associated with ezrin suppression in zebrafish embryos as well as for inhibiting the lung metastasis of high ezrin-expressing osteosarcoma cells. The compound MMV667492 exhibited potent anti-ezrin activity in all biologic assays and had better physicochemical properties for drug-likeness than NSC305787. The drug-like compounds MMV020549 and MMV666069 also showed promising activities in functional assays. Thus, our study suggests further evaluation of antimalarial compounds as a novel class of antimetastatic agents for the treatment of metastatic osteosarcoma. Mol Cancer Ther; 14(11); 2497–507. ©2015 AACR.
Antral ulcers induced by alendronate, a nitrogen-containing biphophonate, in rat stomachs - prophylactic effect of rebamipide.

We demonstrated the development of antral ulcers induced in rats by alendronate and investigated the pathogenic factors involved in this model. Animals fasted for 18 h were given alendronate p.o. , and then re-fed normally and killed on various days up to 7 days later. Alendronate caused non-hemorrhagic damage in both the corpus and antrum of fasted rats, but after refeeding for 3 days the lesions in the corpus healed completely, while those in the antrum developed into large ulcers with increased vascular permeability. The development of antral ulcers was accompanied by an increase in MPO activity and lipid peroxidation as well as a decrease in SOD activity and GSH content in the mucosa. Histologically, the damage did not penetrate the muscularis mucosa, yet severe edema and neutrophil infiltration were observed in the submucosa. Neither omeprazole nor indomethacin had any effect, while allopurinol and SOD reduced the severity of these ulcers. Rebamipide dose-dependently suppressed the ulcerogenic response to alendronate, with a concomitant reversal of the increased vascular permeability, MPO activity and lipid peroxidation as well as the reduced SOD activity and GSH content. These results suggest that alendronate did not cause gross damage in the stomach of fasted rats, yet produced large ulcers in the antrum with severe edema after refeeding. The pathogenesis of these ulcers may be explained by impairment of the mucosal antioxidative system and does not involve acid/peptic digestion and deficiency of prostaglandins. Rebamipide prevents the antral ulcers, probably due to its anti-oxidative as well as anti-inflammatory actions.
City Research Online

The present study provides the ﬁrst direct molecular genetics support for Gray’s Reinforcement Sensitivity Theory (RST), which is one of the most inﬂuential biologically oriented personality theories. It was investigated whether the DRD2 Taq IA and the COMT polymorphisms were related to the dimensions of Gray’s personality theory, as measured by the Carver and White BIS/BAS scales. In a sample of 295 healthy subjects results revealed signiﬁcant DRD2 r COMT interactions (i.e. epistasis) for the total BAS scale (related to positive emotionality) and for the subscales Drive (D) and Fun Seeking (FS). High BAS scores were observed if the catabolic enzyme activity and the D 2 receptor density as indicated by the two polymorphisms were in disequilibrium, i.e. in the presence of the Val x /A1 x (low enzyme activity/ high receptor density) or the Val + /A1 + (high enzyme activity/low receptor density) alleles. In a random subsample ( n = 48), it could be demonstrated that those allele combinations of COMT and DRD2 associated with high BAS scores also had signiﬁcantly lower prolactin levels under resting conditions, indicating high dopamine activity, compared to those allele combinations with low BAS scores. Further-more, two-way interactions of DRD2 Taq IA r smoking status and of the Met allele of COMT r smoking status on FS and Met r gender on BIS could be shown.
Intelligent Data Reduction Algorithm for Sensor Network based Fault Diagnostic System

In the modern life, machines are used for various areas in industries as the advance of science and industrial development has proceeded. In many machines, the rotating machines play an important role in many processes. Therefore, the development of fault diagnosis and monitoring system for rotating machines is required. An ubiquitous sensor network (USN) is a combination of the key computer science and engineering area technology including the wireless network, embedded system hardware and software, communication, real-time system, etc. It collects environmental information to realize a variety of functions. In this work, a data reduction algorithm for USN based remote fault diagnostic system which can be easily applied to previously built factories is proposed. To verify the feasibility of the proposed scheme, some simulations and experiments are executed.
The Hepatitis E Virus ORF3 Protein Regulates the Expression of Liver-Specific Genes by Modulating Localization of Hepatocyte Nuclear Factor 4

The hepatitis E virus (HEV) is a small RNA virus and the cause of acute viral hepatitis E. The open reading frame 3 protein (pORF3) of HEV appears to be a pleiotropic regulatory protein that helps in the establishment, propagation and progression of viral infection. However, the global cellular effects of this protein remain to be explored. In the absence of traditional in vitro viral infection systems or efficient replicon systems, we made an adenovirus based ORF3 protein expression system to study its effects on host cell gene expression. We infected Huh7 hepatoma cells with recombinant adenoviruses expressing pORF3 and performed microarray-based gene expression analyses. Several genes down regulated in pORF3-expressing cells were found to be under regulation of the liver-enriched hepatocyte nuclear factor 4 (HNF4), which regulates hepatocyte-specific gene expression. While HNF4 localizes to the nucleus, its phosphorylation results in impaired nuclear localization of HNF4. Here we report that pORF3 increases HNF4 phosphorylation through the ERK and Akt kinases, which results in impaired nuclear translocation of HNF4 and subsequently the down modulation of HNF4-responsive genes in pORF3-expressing cells. We propose that modulation of several hepatocyte specific genes by pORF3 will create an environment favorable for viral replication and pathogenesis.
Semistatic Cell Differentiation and Integration With Dynamic BBU-RRH Mapping in Cloud Radio Access Network

In this paper, a self-organizing cloud radio access network (C-RAN) is proposed, which dynamically adapt to varying network capacity demands. A load prediction model is considered for provisioning and allocation of base band units (BBUs) and remote radio heads (RRHs). The density of active BBUs and RRHs is scaled based on the concept of cell differentiation and integration (CDI) aiming efficient resource utilisation without sacrificing the overall quality of service (QoS). A CDI algorithm is proposed in which a semi-static CDI and dynamic BBU-RRH mapping for load balancing are performed jointly. Network load balance is formulated as a linear integer-based optimization problem with constraints. The semistatic part of CDI algorithm selects proper BBUs and RRHs for activation/deactivation after a fixed CDI cycle, and the dynamic part performs proper BBU to RRH mapping for network load balancing aiming maximum QoS with minimum possible handovers. A discrete particle swarm optimization (DPSO) is developed as an evolutionary algorithm to solve network load balancing optimization problem. The performance of DPSO is tested based on two problem scenarios and compared to genetic algorithm (GA) and the exhaustive search (ES) algorithm. The DPSO is observed to deliver optimum performance for small-scale networks and near optimum performance for large-scale networks. The DPSO has less complexity and is much faster than GA and ES algorithms. Computational results of a CDI-enabled C-RAN demonstrate significant throughput improvement compared to a fixed C-RAN, i.e., an average throughput increase of 45.53% and 42.102%, and an average blocked users reduction of 23.149%, and 20.903% is experienced for proportional fair and round Robin schedulers, respectively.