Miracle-dz/UniFAR-FTUs huggingface dataset:
The Complete Campylobacter jejuni Transcriptome during Colonization of a Natural Host Determined by RNAseq

Campylobacter jejuni is a major human pathogen and a leading cause of bacterial derived gastroenteritis worldwide. C. jejuni regulates gene expression under various environmental conditions and stresses, indicative of its ability to survive in diverse niches. Despite this ability to highly regulate gene transcription, C. jejuni encodes few transcription factors and its genome lacks many canonical transcriptional regulators. High throughput deep sequencing of mRNA transcripts (termed RNAseq) has been used to study the transcriptome of many different organisms, including C. jejuni; however, this technology has yet to be applied to defining the transcriptome of C. jejuni during in vivo colonization of its natural host, the chicken. In addition to its use in profiling the abundance of annotated genes, RNAseq is a powerful tool for identifying and quantifying, as-of-yet, unknown transcripts including non-coding regulatory RNAs, 5’ untranslated regulatory elements, and anti-sense transcripts. Here we report the complete transcriptome of C. jejuni during colonization of the chicken cecum and in two different in vitro growth phases using strand-specific RNAseq. Through this study, we identified over 250 genes differentially expressed in vivo in addition to numerous putative regulatory RNAs, including trans-acting non-coding RNAs and anti-sense transcripts. These latter potential regulatory elements were not identified in two prior studies using ORF-based microarrays, highlighting the power and value of the RNAseq approach. Our results provide new insights into how C. jejuni responds and adapts to the cecal environment and reveals new functions involved in colonization of its natural host.
PLS-Based Gene Selection and Identification of Tumor-Specific Genes

In view of the characteristics of high-dimensional small sample, strong relevance, and high noise of the identification of tumor-specific genes on microarray, a novel partial least squares (PLS) based gene-selection method, which synthesizes genetic relatedness and is suitable for multicategory classification, is presented. Using the explanation difference of independent variables on dependent variable (class), we define three indicators for global gene selection, which takes into accounts the combined effects of all the genes and the correlation among the genes. Integrated with the linear kernel support vector classifier (SVC), the proposed method is tested by MIT acute myeloid leukemia/acute lymphoblastic leukemia (AML/ALL) and small round blue cell tumors (SRBCT) data sets. A subset of specific genes with small numbers and high identification are obtained. The results indicate that our proposed PLS-based method for tumor-specific genes selection is highly efficient. Compared to the literature, the selected specific genes from both two-category dataset AML/ALL and multicategory dataset SRBCT are credible. Further investigation shows that the proposed gene-selection method is robust. Overall, the proposed method can effectively solve feature-selection problem on high-dimensional small sample. At the same time, it has good performance for multicategory classification as well.
Towards living long and being healthy--the challenge for liaison psychiatric services for older adults.

The ultimate goal of our generation is to live long and be healthy. Despite prolonged life expectancy (the second half of the last century added 20 years to the average life span, and this will increase by another 10 years by 2050) [1], the health problems we face remain similar to those of the last century. Furthermore, the number of 'unhealthy' days (in terms of physical or mental ill health as well as activity limitation days) over the last 8 years seems to be on the increase, especially in the older population [2], and worsening health appears to affect equally both institutionalised and community based elderly adults [3]. During the last four to five decades, we have witnessed a dramatic epidemiological transition in the leading causes of death from infectious and acute diseases to chronic and degenerative illnesses including cardiovascular diseases and cancer, respiratory diseases and injuries, diabetes and Alzhe-imer's disease [4]. These conditions also cause severe disability , which when measured via limitations in activities of daily living is a common factor leading to the need for long-term care [5]. These physical problems are usually accompanied by a worsening of mental function in the elderly: (i) depression following cerebrovascular accidents, heart problems and hip injury; (ii) delirium due to various physical problems; and, above all, (iii) cognitive impairment underlying many sustained injuries and predisposing the elderly to delirium. In many frail elderly adults, many highly prevalent symptoms due to multiple diseases and risk factors (e.g. immobil-ity, instability, impaired cognition and incontinence) are frequently reported. The concept of these geriatric syndromes can be a useful theoretical framework to guide diagnostic analysis and education in medical practice and teaching and also needs to include the diagnosis, treatment, teaching and awareness of mental health problems associated with these syndromes. Not surprisingly, the Education Committee Writing Group of the American Geriatric Society recommended that undergraduate medical training should include at least five psychiatric or psychiatrically related symptoms and problems out of the 13 most common geriatric syndromes, including depression, delirium, dementia, failure to thrive and sleep disorders [6]. This stresses the importance of both psychological skills and the role of liaison psychiatry services in the treatment of physical illness. Indeed, pharmacological and behavioural treatments of depression improve activities of daily living function post-stroke, protect against myocardial infarction, improve glycaemic control and give relief from physical symptoms in somatoform disorders. Furthermore, psych-oeducational interventions and …
Psychological distress and help seeking amongst higher education students: findings from a mixed method study of undergraduate nursing/midwifery and teacher education students in Ireland

Psychological distress as experienced by higher education students is of major concern because of its potential to adversely impact academic performance, retention, mental health and lifestyle. This paper reports a mixed method investigation of student self-reported psychological distress and help-seeking behaviour. The sample comprised all students (n = 1557) registered on undergraduate nursing/midwifery and teacher education programmes at an Irish university. Participants (n = 1112) completed the General Health Questionnaire (GHQ) to determine their self-reported psychological distress and the Lifestyle Behaviour Questionnaire to examine sources of distress, lifestyle and demographic variables. Individual interviews (n = 59) explored student experiences of psychological distress and their help-seeking behaviours. Forty two percent of respondents exceeded the GHQ threshold ≥5, which signifies risk of mental or physical health problems. Sources of distress included academic, financial and psychosocial stressors. Regression analysis identified that demographic, programmatic and lifestyle variables predicted GHQ scores. Despite the distress experienced, students were reluctant users of support services. Many actively avoided seeking help. These findings raise serious concerns about the extent of psychological distress among this population. They also alert education providers to be vigilant for student psychological distress and to provide effective interventions, cognisant of the impact of stigma on help seeking.
Hearing in noisy environments: noise invariance and contrast gain control

Contrast gain control has recently been identified as a fundamental property of the auditory system. Electrophysiological recordings in ferrets have shown that neurons continuously adjust their gain (their sensitivity to change in sound level) in response to the contrast of sounds that are heard. At the level of the auditory cortex, these gain changes partly compensate for changes in sound contrast. This means that sounds which are structurally similar, but have different contrasts, have similar neuronal representations in the auditory cortex. As a result, the cortical representation is relatively invariant to stimulus contrast and robust to the presence of noise in the stimulus. In the inferior colliculus (an important subcortical auditory structure), gain changes are less reliably compensatory, suggesting that contrast‐ and noise‐invariant representations are constructed gradually as one ascends the auditory pathway. In addition to noise invariance, contrast gain control provides a variety of computational advantages over static neuronal representations; it makes efficient use of neuronal dynamic range, may contribute to redundancy‐reducing, sparse codes for sound and allows for simpler decoding of population responses. The circuits underlying auditory contrast gain control are still under investigation. As in the visual system, these circuits may be modulated by factors other than stimulus contrast, forming a potential neural substrate for mediating the effects of attention as well as interactions between the senses.
State Capacity and Military Conflict

In 1500, Europe was composed of hundreds of statelets and principalities, with weak central authority, no monopoly over the legitimate use of violence, and multiple, overlapping levels of jurisdiction. By 1800, Europe had consolidated into a handful of powerful, centralized nation states. We build a model that simultaneously explains both the emergence of capable states and growing divergence between European powers. In our model, the impact of war on the European state system depends on: i) the importance of money for determining the war outcome (which stands for the cost of war), and ii) a country's initial level of domestic political fragmentation. We emphasize the role of the 'Military Revolution', which raised the cost of war. Initially, this caused more internally cohesive states to invest more in state capacity, while other (more divided) states rationally dropped out of the competition. This mechanism leads to both increasing divergence between European states, and greater average investments in state building on the continent overall.
Scale-invariant groups

Motivated by the renormalization method in statistical physics, Itai Benjamini defined a finitely generated infinite group G to be scale-invariant if there is a nested sequence of finite index subgroups G_n that are all isomorphic to G and whose intersection is a finite group. He conjectured that every scale-invariant group has polynomial growth, hence is virtually nilpotent. We disprove his conjecture by showing that the following groups (mostly finite-state self-similar groups) are scale-invariant: the lamplighter groups F\wr\Z, where F is any finite Abelian group; the solvable Baumslag-Solitar groups BS(1,m); the affine groups A\ltimes\Z^d, for any A\leq GL(\Z,d). However, the conjecture remains open with some natural stronger notions of scale-invariance for groups and transitive graphs. We construct scale-invariant tilings of certain Cayley graphs of the discrete Heisenberg group, whose existence is not immediate just from the scale-invariance of the group. We also note that torsion-free non-elementary hyperbolic groups are not scale-invariant.
VLSI implementation of a hardware-optimized lattice reduction algorithm for WiMAX/LTE MIMO detection

This paper presents the first ASIC implementation of an LR algorithm which achieves ML diversity. The VLSI implementation is based on a novel hardware-optimized LLL algorithm that has 70% lower complexity than the traditional complex LLL algorithm. This reduction is achieved by replacing all the computationally intensive CLLL operations (multiplication, division and square root) with low-complexity additions and comparisons. The VLSI implementation uses a pipelined architecture that produces an LR-reduced matrix every 40 cycles, which is a 60% reduction compared to current implementations. The proposed design was synthesized in both 130µm and 65nm CMOS resulting in clock speeds of 332MHz and 833MHz, respectively. The 65nm result is a 4X improvement over the fastest LR implementation to date. The proposed LR implementation is able to sustain a throughput of 2Gbps, thus achieving the high data rates required by future standards such as IEEE 802.16m (WiMAX) and LTE-Advanced.
On the Potential of NoC Virtualization for Multicore Chips

As the end of Moores-law is on the horizon, power becomes a limiting factor to continuous increases in performance gains for single-core processors. Processor engineers have shifted to the multicore paradigm and many-core processors are a reality. Within the context of these multi-core chips, three key metrics point themselves out as being of major importance, performance, fault-tolerance (including yield), and power consumption. A solution that optimizes all three of these metrics is challenging. As the number of cores increases the importance of the interconnection network-on-chip (NoC) grows as well, and chip designers should aim to optimize these three key metrics in the NoC context as well. In this paper we identify and discuss the main properties that a NoC must exhibit in order to enable such optimizations. In particular, we propose the use of virtualization techniques at the NoC level. AS a major finding, we identify the implementation of routing algorithms to become a key design parameter in order to achieve an effective virtualization of the chip should also supporting broadcast within the virtualized context. The intention behind this paper is for it to serve as a position paper on the topic of virtualization for NoC and the challenges that should be met at the routing layer in order to maximize performance, fault-tolerance and power consumption in multicore chips.
Nivel de integración de las empresas de economía social andaluzas en la sociedad de la información: un modelo contingente

La finalidad de este articulo es aportar utilidad directa a dos agentes sociales de la comunidad andaluza: cooperativas y sociedades laborales. Para ello se ofrece conocimiento sobre el nivel de implantacion de las TIC en las empresas de Economia Social referidas y sobre la relacion de esta variable con los siguientes factores de contingencia: propension a innovar, tipo de asociacion, facturacion anual, numero de empleados, sector de actividad y autonomia financiera. Los datos primarios finalmente obtenidos se corresponden con una muestra de 515 empresas y son objeto de analisis factorial y de diversos analisis de contingencia
Trusted Tree-Based Trust Management Scheme for Secure Routing in Wireless Sensor Networks

The unique characteristics of wireless sensor networks make them susceptible to the attacks. The secure scheme is considered in designing the routing protocol and algorithm. The cryptography and authentication secure technology can defend the external attacks but have no way to protect the network when the internal attacks occur. However, the trust management scheme with attack-resistance and robustness can efficiently detect the internal attack. On the condition of defending the attacks, it is also an issue that the trust management scheme aids routing algorithm to improve the security and performance. In this paper, we proposed a Trusted Tree-based trust management for secure routing in wireless sensor networks. The common attacks are firstly analyzed. And then the dynamic time window is designed in the distributed trust model with the detection of direct trust and indirect trust. Based on the trusted nodes, Trusted Tree is constructed. And the path quality of nodes in Trusted Tree is used as the gradient for routing. Finally, we add Trusted Tree-based trust management into the QoS based routing protocol and algorithm. Experimental results show that the QoS based routing algorithm with Trusted Tree has better performance and security.
Diverse Dengue Type 2 Virus Populations Contain Recombinant and Both Parental Viruses in a Single Mosquito Host

ABSTRACT Envelope (E) protein genes sampled from populations of dengue 2 (DEN-2) virus in individual Aedes aegypti mosquitoes and in serum from dengue patients were copied to cDNA, cloned, and sequenced. The nucleotide sequences of the E genes in more than 70% of the clones differed from the consensus sequence for the corresponding virus population at up to 11 sites, and 24 of the 94 clones contained at least one stop codon. Virus populations recovered up to 2 years apart yielded clones with similar polymorphisms in the E gene. For one mosquito, the clones obtained fell into two genotypes. One group of sequences was closely related to those of viruses recovered from dengue patients in the same locality (Yangon, Myanmar) since 1995 and were classified as Asian 1 genotype. The second group were Cosmopolitan genotype viruses which were also circulating in Yangon in 2000 and which were related to DEN-2 viruses sampled from southern China in 1999. Finally, one clone was identified as a recombinant genome composed of portions of these two “parental” genotypes. This is the first report of recombinant and parental dengue viruses in a single host.
Interpretation of the Detection of Antibodies to Sarcocystis neurona in the serum and CSF of young horses

ii DEDICATION.iv ACKNOWLEDGEMENTS.v TABLE OF CONTENTS.vi LIST OF FIGURES.viii LIST OF TABLES.ix LIST OF ABBREVIATIONS.x INTRODUCTION.1 CHAPTER 1: Equine Protozoal Myeloencephalitis.3 1.1 History and life cycle.3 1.2 Clinical signs.7 1.3 Differential diagnoses.7 1.4 Diagnosis.8 1.5 Pathology.14 1.6 Treatment.15 1.7 Epidemiology.18 1.8 Prevention.20 CHAPTER 2: Passive Transfer of Maternal Antibodies to Sarcocystis neurona . 21 2.1 Passive transfer and immunologic considerations in the neonatal foal.21 2.1.1 General. 21 2.1.2 Colostrum.22 2.1.3 Other colostral components.27 2.1.4 Failure of passive transfer.29 2.1.5 Metabolism of maternal antibodies.32 2.1.6 Foal immunity.35 2.1.7 Summary.38
Disrupted light-dark cycle induces obesity with hyperglycemia in genetically intact animals.

BACKGROUND The environmental light-dark (LD) cycle entrains the circadian clock located in the suprachiasmatic nucleus (SCN) of mammals. Recent studies of genetically impaired animals with clock gene mutations have revealed associations between metabolic disorders and the circadian clock. However, whether such disordered phenotypes are due to a loss of circadian clock function within specific metabolically relevant tissues, or the result of disrupted circadian behavioral activities governed by the SCN remains unknown. OBJECTIVES The present study examines the effect of disrupted LD cycles that might perturb the circadian clock in the SCN and peripheral organs on a high-fat/high-sucrose diet-induced obesity in genetically intact mice. METHODS The behavioral patterns of the mice were disturbed under an ultradian 3 h light-3 h dark cycle (LD 3:3) due to light-induced direct suppression of the behavior (masking effect). RESULTS Obesity with hyperglycemia was significantly enhanced and levels of hemoglobin A1c were significantly higher under LD 3:3 compared with LD 12:12. CONCLUSIONS These findings provide a link between metabolic disorders and the "environmental mutation" in genetically intact animals.
The human homologue of yeast CRM1 is in a dynamic subcomplex with CAN/Nup214 and a novel nuclear pore component Nup88

The oncogenic nucleoporin CAN/Nup214 is essential in vertebrate cells. Its depletion results in defective nuclear protein import, inhibition of messenger RNA export and cell cycle arrest. We recently found that CAN associates with proteins of 88 and 112 kDa, which we have now cloned and characterized. The 88 kDa protein is a novel nuclear pore complex (NPC) component, which we have named Nup88. Depletion of CAN from the NPC results in concomitant loss of Nup88, indicating that the localization of Nup88 to the NPC is dependent on CAN binding. The 112 kDa protein is the human homologue of yeast CRM1, a protein known to be required for maintenance of correct chromosome structure. This human CRM1 (hCRM1) localized to the NPC as well as to the nucleoplasm. Nuclear overexpression of the FG‐repeat region of CAN, containing its hCRM1‐interaction domain, resulted in depletion of hCRM1 from the NPC. In CAN−/− mouse embryos lacking CAN, hCRM1 remained in the nuclear envelope, suggesting that this protein can also bind to other repeat‐containing nucleoporins. Lastly, hCRM1 shares a domain of significant homology with importin‐β, a cytoplasmic transport factor that interacts with nucleoporin repeat regions. We propose that hCRM1 is a soluble nuclear transport factor that interacts with the NPC.
Underwater Photogrammetry and Object Modeling: A Case Study of Xlendi Wreck in Malta

In this paper we present a photogrammetry-based approach for deep-sea underwater surveys conducted from a submarine and guided by knowledge-representation combined with a logical approach (ontology). Two major issues are discussed in this paper. The first concerns deep-sea surveys using photogrammetry from a submarine. Here the goal was to obtain a set of images that completely covered the selected site. Subsequently and based on these images, a low-resolution 3D model is obtained in real-time, followed by a very high-resolution model produced back in the laboratory. The second issue involves the extraction of known artefacts present on the site. This aspect of the research is based on an a priori representation of the knowledge involved using systematic reasoning. Two parallel processes were developed to represent the photogrammetric process used for surveying as well as for identifying archaeological artefacts visible on the sea floor. Mapping involved the use of the CIDOC-CRM system (International Committee for Documentation (CIDOC)—Conceptual Reference Model)—This is a system that has been previously utilised to in the heritage sector and is largely available to the established scientific community. The proposed theoretical representation is based on procedural attachment; moreover, a strong link is maintained between the ontological description of the modelled concepts and the Java programming language which permitted 3D structure estimation and modelling based on a set of oriented images. A very recently discovered shipwreck acted as a testing ground for this project; the Xelendi Phoenician shipwreck, found off the Maltese coast, is probably the oldest known shipwreck in the western Mediterranean. The approach presented in this paper was developed in the scope of the GROPLAN project (Généralisation du Relevé, avec Ontologies et Photogrammétrie, pour l'Archéologie Navale et Sous-marine). Financed by the French National Research Agency (ANR) for four years, this project associates two French research laboratories, an industrial partner, the University of Malta, and Texas A & M University.
Lower Bounds for Quantum Algorithms on Independent Set and Subgraph Isomorphism

This project is a basic explanation of the paper Quantum Algorithms and Lower Bounds for Independent Set and Subgraph Isomorphism Problem by S. Dörn in my own words, elaborating on and explaining points that were glossed over in the original paper. The algorithms have been kept intact, the proof of lower bounds have also not been fundamentally changed. The purpose of this paper is to give the lower bounds for computing graph problems, mainly independent set and subgraph isomorphism.