Miracle-dz/UniFAR-FTUs huggingface dataset:
Development of Specific Oligonucleotide Probes to Detect Vibrio Species

Many species of Vibrio are responsible for diseases in marine organisms and for economic losses to the aquaculture industry. The aim of this preliminary study was to obtain species‐specific DNA zones to be used as potential probes from a phylogenetic analysis of the 23S ribosomal RNA (rRNA) gene of different Vibrio species from marine and human organisms. Species‐specific probes were identified for V. parahaemolyticus, V. fortis, V. splendidus, and for two clusters of taxonomically related species, namely V. harveyi/campbelli and V. lentus/aestuarianus. A reverse line blot assay showed that the designed probes can specifically detect the different Vibrio species, thereby proving that these probes can be used to evaluate the presence of pathogenic and nonpathogenic Vibrio species in the sea and in marine organisms to assist in the investigation of environmental risks.
Unsupervised Mining of Lexical Variants from Noisy Text

The amount of data produced in user-generated content continues to grow at a staggering rate. However, the text found in these media can deviate wildly from the standard rules of orthography, syntax and even semantics and present significant problems to downstream applications which make use of this noisy data. In this paper we present a novel unsupervised method for extracting domain-specific lexical variants given a large volume of text. We demonstrate the utility of this method by applying it to normalize text messages found in the online social media service, Twitter, into their most likely standard English versions. Our method yields a 20% reduction in word error rate over an existing state-of-the-art approach.
Amyloid cascade and tau pathology cerebrospinal fluid markers in mild cognitive impairment with regards to Alzheimer's disease cerebral metabolic signature.

BACKGROUND Biomarker relationships in early stages of Alzheimer's disease (AD) are elusive. Cerebrospinal fluid (CSF) levels of amyloid-β 1-42 (Aβ42) and total tau (tTau) as well as 18F-fluorodeoxyglucose positron emission tomography (FDG-PET) contribute to help unravel AD pathology. Furthermore, peptides related to amyloid-β protein precursor (AβPP) processing [e.g., soluble AβPPα and β (sAβPPα and sAβPPβ, respectively); sortilin-related receptor with A-type repeats (SORL1, also called LR11 or SORLA)] are factors crucially implicated in the formation of pathological hallmarks of AD. OBJECTIVE To unveil differences in CSF concentrations of Aβ42, sAβPPα, sAβPPβ, tTau, and SORL1 between patients with mild cognitive impairment (MCI) who were categorized according to expert interpretation of FDG scans. METHODS PET results were classified as suggesting high likelihood for AD (MCI-AD high), intermediate likelihood for AD (MCI-AD intermediate), or little likelihood for AD (MCI-AD unlikely). An AD dementia group was also included. Differences between the groups were tested by Kruskal- Wallis test, Mann-Whitney test, or χ2. Provided statistically significant differences were detected, multiple linear regression models were employed. RESULTS Aβ42 levels in patients with MCI-AD high (n = 15) were lower compared to MCI-AD intermediate (n = 18) and MCI-AD unlikely patients (n = 25) (p = 0.002), while they did not differ from patients with AD dementia (n = 17). The regression model revealed a significant impact of the metabolic pattern on Aβ42 concentrations. SORL1, tTau, sAβPPα, and sAβPPβ concentrations did not differ between the groups. CONCLUSION These findings point to linkages between plaque pathology and glucose cerebral hypometabolism.
Characterization of the Lipid Profile in Dementia and Depression in the Elderly

The purpose of the study was to examine the association of plasma lipid concentrations with changes in cognitive function and depressive states in elderly Greek individuals. The study population consisted of 3 groups: A) 37 subjects with dementia, B) 33 subjects with depression, and C) 33 controls. All individuals were screened with the Mini-Mental State Examination (MMSE), the Geriatric Depression Scale (GDS), and an evaluation of their psychiatric state. Lipid profile was assessed in all subjects, and the results were statistically evaluated at P < . 05 level of significance. Groups A and B had significantly lower levels of total plasma cholesterol and HDL cholesterol than group C (P < .01). Triglyceride levels did not differ significantly between groups A and C, although they were significantly higher in group B. The results of this study suggest that an association does exist between the plasma concentration of cholesterol and HDL-C and depression and/or cognitive impairment. Further studies are required to explore the significance of these observations and establish if lipid levels could serve as markers for diagnostic and therapeutic purposes. (J Geriatr Psychiatry Neurol 2007;20:138-144)
Yeast Systems Biology: Our Best Shot at Modeling a Cell

THE Genetics Society of America’s Edward Novitski Prize recognizes an extraordinary level of creativity and intellectual ingenuity in the solution of significant problems in genetics research. The 2014 recipient, Charles Boone, has risen to the top of the emergent discipline of postgenome systems biology by focusing on the global mapping of genetic interaction networks. Boone invented the synthetic genetic array (SGA) technology, which provides an automated method to cross thousands of strains carrying precise mutations and map large-scale yeast genetic interactions. These network maps offer researchers a functional wiring diagram of the cell, which clusters genes into specific pathways and reveals functional connections.
Facial expression recognition based on Gabor and conditional random fields

In this paper, a facial expression recognition algorithm based on Gabor and conditional random fields is proposed. Firstly, owing to the fact that in the existing databases, the number of people and images are relatively small, we established our own facial expression database, and some preprocessing methods are performed thereon. Secondly, Gabor features are extracted in five scales and eight directions from the facial expression images, which are performed dimensionality reduction via PCA and the feature information with less dimension is acquired. Finally, facial expression is recognized and classified by using Conditional Random Fields (CRFs). In the experiments based on the facial database we established, the overall average recognition rate of the proposed algorithm is up to 91.62%, which shows the effectiveness of the proposed algorithm.
"Vivir con vitalidad -M": an european multimedia programme.

During recent decades Successful Ageing has emerged as a new paradigm in Gerontology. National, European and International organizations have recommended the introduction of programs to promote active ageing. The present study examines the effectiveness of a psychosocial multimedia program called "Vivir con Vitalidad-M" (Vital Ageing-M), developed to promote Successful Ageing. A quasi-experimental pre-post with control group design was carried out, which included the application of a questionnaire on opinions, activities, physical exercise, nutrition, health, social relationships and life satisfaction. The "Vivir con Vitalidad-M" program produces behavioural changes in the expected direction in older persons attending the program. The program appears to be effective with regard to changes in life styles (diet and physical exercise), in perceptions about successful ageing and in self-efficacy for ageing, with regard to an increase in the number of physical, cultural, intellectual and social activities carried out, finally, in life-satisfaction.
Virtual active touch: Perceived roughness through a pointing-stick-type tactile interface

For realizing a tactile display for a handheld device, active touch movement should be represented on a small interface. We propose the addition of a tactile feedback mechanism for a pointing-stick-type (PS) input device. In this study, we describe a method for enabling virtual active touch with a cursor on the screen operated by the PS-type tactile interface without actual touch movement. First, to validate our concept, we compared tactile detection capabilities of roughness information represented by the PS-type tactile interface and the interface with actual touch movement. The experimental results showed that the PS-type tactile interface exhibited almost the same ability as the interface involving actual touch movement. We also found that the force-to-velocity scaling factor of the cursor movement had a significant influence on the roughness detection capability of the interface. In addition, to apply our method to devices having small screens, such as mobile phones, we tried to restrict the cursor velocity in proportion to the object size that appears on the screen. The experimental results showed that the PS-type tactile interface can represent almost the same roughness information as the original object size.
High levels of erythropoietin are associated with protection against neurological sequelae in African children with cerebral malaria

Cerebral malaria (CM) in children is associated with a high mortality and long-term neurocognitive sequelae. Both erythropoietin (Epo) and vascular endothelial growth factor (VEGF) have been shown to be neuroprotective. We hypothesized that high plasma and cerebrospinal fluid (CSF) levels of these cytokines would prevent neurological sequelae in children with CM. We measured Epo, VEGF, and tumor necrosis factor in paired samples of plasma and CSF of Kenyan children admitted with CM. Logistic regression models were used to identify risk and protective factors associated with the development of neurological sequelae. Children with CM (n = 124) were categorized into three groups: 76 without sequelae, 32 with sequelae, and 16 who died. Conditional logistic regression analysis matching the 32 patients with CM and neurological sequelae to 64 patients with CM without sequelae stratified for hemoglobin level estimated that plasma Epo (>200 units/liter) was associated with >80% reduction in the risk of developing neurological sequelae [adjusted odds ratio (OR) 0.18; 95% C.I. 0.05–0.93; P = 0.041]. Admission with profound coma (adjusted OR 5.47; 95% C.I. 1.45–20.67; P = 0.012) and convulsions after admission (adjusted OR 16.35; 95% C.I. 2.94–90.79; P = 0.001) were also independently associated with neurological sequelae. High levels of Epo were associated with reduced risk of neurological sequelae in children with CM. The age-dependent Epo response to anemia and the age-dependent protective effect may influence the clinical epidemiology of CM. These data support further study of Epo as an adjuvant therapy in CM.
The probiotic mixture VSL#3 mediates both pro- and anti-inflammatory responses in bone marrow-derived dendritic cells from C57BL/6 and BALB/c mice

Probiotic bacteria express a wide range of molecular structures that bind to receptors on innate immune cells and mediate health-promoting effects in the host. We have recently demonstrated in a colitis model that favourable effects of the probiotic mixture VSL#3 may in part be due to the suppression of intestinal chemokine expression. To obtain more insights into the underlying mechanisms, in the present study, we analysed the modulation of bone marrow-derived dendritic cells (BM-DC) from BALB/c (T helper (Th)2 biased) v. C57BL/6 (Th1 biased) mice. Our findings showed that VSL#3 differed from pure Toll-like receptor (TLR) ligands by inducing the production of various cytokines, including IL-12 p70 subunit (IL-12p70), IL-23 and IL-10. Dedicated TLR arrays were employed to profile mRNA from BM-DC cultured with lipopolysaccharide (LPS), VSL#3, or a combination of both. This approach led to the identification of (1) a cluster of genes that were up- or down-regulated, irrespective of the stimulus, (2) a cluster of genes that were synergistically up-regulated by LPS and VSL#3 in BM-DC from C57BL/6 mice, but not in those from BALB/c mice, and (3) a cluster of LPS-induced genes that were suppressed by VSL#3, in particular chemokine genes. These data show that this probiotic mixture has both pro- and anti-inflammatory effects on BM-DC and suggest that their immune-modulating properties in vivo may depend on the genetic background of the host.
Experimental and numerical studies of the vortex-induced vibration behavior of an asymmetrical composite beam bridge

The vortex-induced vibration behavior and mechanism of an asymmetrical composite beam cable-stayed bridge is investigated by means of aerodynamic sectional tests and computational fluid dynamics methods. Tests are performed for the bridge deck under five wind attack angles (0°, ±2.5°, and ±5°) and two wind directions (0° and 180°) during the completion and construction stages. The influence of damping ratios, wind barriers, and vehicles on the vortex-induced vibration behaviors of the bridge deck is examined. The test and simulation results show that the properties of the vortex-induced vibrations vary with the wind direction as a result of the asymmetry of the main girder. The vertical maximum vortex-induced vibration amplitude of the bridge deck was found to occur at the wind attack angle of −5° and wind direction of 180°, while the torsional maximum was found at the wind attack angle of −5° and wind direction of 0°. Both vehicles and wind barriers have amplification effects on the vortex-induced vibrations of the bridge deck when the wind direction is 180°. The vortex-induced vibration of the bridge deck can be effectively mitigated when the damping ratio increases from 0.5% to 1.5%. The vortex-induced vibration mechanism of the bridge deck under different wind directions can be attributed to the same vortex shedding mode (the Kelvin–Helmholtz vortex and the Kármán vortex street). While, the location of the vortex generation and direction of the vortex shedding at the wake are strongly influenced by the wind directions, resulting in the variation of the vortex-induced vibration properties of the bridge deck with the wind direction. This study provides a guideline for the design of bridges with asymmetrical main girders to suppress the VIV.
A Novel Circular Array Structure and Particle Swarm Optimization in Aperture Synthesis Radiometers

A novel array configuration, circular lattice array (CLA), to generate uniform rectangular grid u-v coverage for aperture synthesis radiometers is introduced. Particle swarm optimization (PSO) algorithm is applied to finding optimal CLA configurations. To evaluate the advantages of the CLA over previously proposed circular arrays, a comparative study is carried out by analyzing the performance of the CLA in terms of both the number of samples in u-v coverage and the computation cost of the fitness function in optimization algorithm. The obtained optimization results for 5-30 elements are also presented.
An Intrinsic Robust Transient Fault-Tolerant Developmental Model for Digital Systems

A biologically inspired developmental model targeted at hardware implementation (off-shelf FPGA) is proposed which exhibits extremely robust transient fault-tolerant capability: in the software simulation of the experimental application. In a 6x6 cell French Flag, some individuals were discovered using evolution that have the ability to “recover” themselves from almost any kinds of transient faults, even in the worst case of only one “live” cell remaining. All cells in this model have identical genotype (physical structures), and only differ in internal states.
Sequence and structure-based prediction of eukaryotic protein phosphorylation sites.

Protein phosphorylation at serine, threonine or tyrosine residues affects a multitude of cellular signaling processes. How is specificity in substrate recognition and phosphorylation by protein kinases achieved? Here, we present an artificial neural network method that predicts phosphorylation sites in independent sequences with a sensitivity in the range from 69 % to 96 %. As an example, we predict novel phosphorylation sites in the p300/CBP protein that may regulate interaction with transcription factors and histone acetyltransferase activity. In addition, serine and threonine residues in p300/CBP that can be modified by O-linked glycosylation with N-acetylglucosamine are identified. Glycosylation may prevent phosphorylation at these sites, a mechanism named yin-yang regulation. The prediction server is available on the Internet at http://www.cbs. dtu.dk/services/NetPhos/or via e-mail to NetPhos@cbs. dtu.dk.
Draft genome sequences and description of Lactobacillus rhamnosus strains L31, L34, and L35

Lactobacillus rhamnosus is a facultative, lactic acid bacterium in the phylum Firmicutes. Lactobacillus spp. are generally considered beneficial, and specific strains of L. rhamnosus are validated probiotics. We describe the draft genomes of three L. rhamnosus strains (L31, L34, and L35) isolated from the feces of Thai breastfed infants, which exhibit anti-inflammatory properties in vitro. The three genomes range between 2.8–2.9 Mb, and contain approximately 2,700 protein coding genes.
Teaching To and Through Cultural Diversity

Abstract This discussion examines some of the major issues and attributes of culturally responsive teaching. It begins with explaining my views of culturally responsive teaching and how I incorporate cultural responsiveness in my writing to teach readers what it means. These general conceptual frameworks are followed by a discussion of some specific actions essential to its implementation. They are restructuring teacher attitudes and beliefs about cultural, ethnic, and racial diversity; resisting resistance to cultural diversity in teacher education and classroom instruction; centering culture and difference in the teaching process; and establishing pedagogical connections between culturally responsive teaching and subjects and skills routinely taught in schools. Excerpts from samples of my own and others’ scholarship are woven throughout to exemplify general patterns, themes, and principles of culturally responsive teaching.
Distribution of Computed Tomographic Features of Stroke in Relation to Cardiac Source of Embolism Risk Groups Feature Bilateral anterior circulation cortical infarct

Background and Purpose: The lack of valid criteria for the clinical diagnosis of cardiogenic embolism is a major problem in both patient care and research. The aim of this study was to identify features on the initial computed tomogram of the brain that discriminate between patient groups with and without a cardiac source of embolism. To gain insight into the neuroradiological features relevant to the diagnosis of cardiac embolic stroke, we studied the initial computed tomogram of the 1,267 patients with ischemic stroke and such a scan in the National Institute of Neurological Disorders and Stroke (NINDS) Stroke Data Bank. Methods: We analyzed the initial computed tomographic data from 1,267 patients with ischemic stroke in the NINDS Stroke Data Bank. Based solely on the presence of cardiac sources of embolism, we defined groups with high (n=244), medium (n=165), and low (n=858) risk for cardiogenic embolism and compared the features on the initial computed tomogram among these three groups. Results: Patients in the high-risk group were significantly more likely (p< 0.001) to have infarcts involving one half lobe or larger or infarcts involving both superficial and deep structures than patients in the mediumor low-risk groups. In contrast, deep small infarcts had a negative association (p=0.004) with the presence of a cardiac source of embolism. There was no significant trend across risk groups in the percent with hemorrhagic infarction, regardless of whether patients with anticoagulant use at the time of the stroke were excluded. Conclusion: Although some features of the initial computed tomogram had highly significant associations with the presence of a cardiac source of embolism, the predictive value of these features for an embolic source was low. (Stroke 1992;23:1748-1751)
A Distributed Localization Scheme for Wireless Sensor Networks with Improved Grid-Scan and Vector-Based Refinement

Localization is a fundamental and essential issue for wireless sensor networks (WSNs). Existing localization algorithms can be categorized as either range-based or range-free schemes. Range-based schemes are not suitable for WSNs because of their irregularity of radio propagation and their cost of additional devices. In contrast, range-free schemes do not need to use received signal strength to estimate distances and only need simple and cheap hardware, and are thus more suitable for WSNs. However, existing range-free schemes are too costly and not accurate enough or are not scalable. To improve previous work, we present a fully distributed range-free localization scheme for WSNs. We assume that only a few sensor nodes, called anchors, know their locations, and the remaining (normal) nodes need to estimate their own locations by gathering nearby neighboring information. We propose an improved grid-scan algorithm to find the estimated locations of the normal nodes. Furthermore, we derive a vector-based refinement scheme to improve the accuracy of the estimated locations. Analysis, simulation, and experiment results show that our scheme outperforms the other range-free schemes even when the communication radius is irregular.
Towards periodicity based anomaly detection in SCADA networks

Supervisory Control and Data Acquisition (SCADA) networks are commonly deployed to aid the operation of large industrial facilities. The polling mechanism used to retrieve data from field devices causes the data transmission to be highly periodic. In this paper, we propose an approach that exploits traffic periodicity to detect traffic anomalies, which represent potential intrusion attempts. We present a proof of concept to show the feasibility of our approach.
The Risk Implications of Mergers and Acquisitions with Information Technology Firms

Abstract We address the dynamics of post-merger risks for a firm acquiring an information technology (IT) company over a long-term horizon, and examine the impact of mergers and acquisitions (M&A) motives on its post-merger risks after controlling for its self-selection into the specific motives the acquiring firm seeks. We find that a strong run-up in risk occurs before M&A transactions are initiated, but this risk begins to decline over the post-merger period. However, post-merger risks tend to persist for firms seeking M&A transactions with a customer-side motive, whereas this does not occur with a production-side motive. While greater post-merger risks are associated with M&As with a customer-side motive, our results suggest that its association with post-merger risks is moderated by industry dynamism. Overall, our study sheds new light on the post-merger risk by addressing its dynamic nature and uncovering the potential interplay between M&A motives and industry dynamism when IT firms are acquired.
A nonsynonymous substitution of cystatin A, a cysteine protease inhibitor of house dust mite protease, leads to decreased mRNA stability and shows a significant association with atopic dermatitis

Background: Cystatin A (CSTA) is a strong candidate for atopic dermatitis (AD) because it maps to AD susceptibility locus on chromosome 3q21 and it does inhibit Der p 1 and Der f 1, major house dust mite cysteine proteases and environmental triggers for AD and asthma.