Miracle-dz/UniFAR-FTUs huggingface dataset:
Basic Concepts of Microarrays and Potential Applications in Clinical Microbiology

SUMMARY The introduction of in vitro nucleic acid amplification techniques, led by real-time PCR, into the clinical microbiology laboratory has transformed the laboratory detection of viruses and select bacterial pathogens. However, the progression of the molecular diagnostic revolution currently relies on the ability to efficiently and accurately offer multiplex detection and characterization for a variety of infectious disease pathogens. Microarray analysis has the capability to offer robust multiplex detection but has just started to enter the diagnostic microbiology laboratory. Multiple microarray platforms exist, including printed double-stranded DNA and oligonucleotide arrays, in situ-synthesized arrays, high-density bead arrays, electronic microarrays, and suspension bead arrays. One aim of this paper is to review microarray technology, highlighting technical differences between them and each platform's advantages and disadvantages. Although the use of microarrays to generate gene expression data has become routine, applications pertinent to clinical microbiology continue to rapidly expand. This review highlights uses of microarray technology that impact diagnostic microbiology, including the detection and identification of pathogens, determination of antimicrobial resistance, epidemiological strain typing, and analysis of microbial infections using host genomic expression and polymorphism profiles.
Reduction of Ventricular Sodium Current in a Mouse Model of HIV

Effect of HIV on Cardiac Sodium Current. Introduction: Cardiac arrhythmias have been reported in AIDS patients. Arrhythmias can arise from alterations in ventricular Na+ channel function. However, it is unknown whether HIV affects cardiac Na+ channel function. Therefore, the purpose of this study was to characterize the effect of HIV on ventricular Na+ current (INa) in a transgenic model of HIV (CD4C/HIV mice), which exhibit a severe AIDS‐like disease.
Differentially Private Datasets via Stable Microaggregation

In recent years, differential privacy has emerged as one formal notion of privacy. Data release based on differential privacy can help researchers to perform statistical analysis on sensitive data of individuals. To publish differentially private datasets, there is a need for preserving data utility, along with data privacy. However, the utility of differentially private datasets is often limited, due to the amount of noise being added to the results of queries. In this paper, we address this issue by proposing a microaggregation-based framework that incorporates microaggregation and differential privacy into the data publishing process. We formulate a new notion of stable microaggregation to characterize a desired property of microaggregation and further develop a simple yet effective stable microaggregation algorithm. We experimentally verify the utility reduction of our proposed framework on real-world datasets. The experiments show that the proposed framework outperforms the state-of-the-art methods by providing better with-in cluster homogeneity and also reducing noise added into differentially private datasets significantly.
Stimulus Selectivity in Dorsal and Ventral Prefrontal Cortex after Training in Working Memory Tasks

The prefrontal cortex is known to represent different types of information in working memory. Contrasting theories propose that the dorsal and ventral regions of the lateral prefrontal cortex are innately specialized for the representation of spatial and nonspatial information, respectively (Goldman-Rakic, 1996), or that the two regions are shaped by the demands of cognitive tasks imposed on them (Miller, 2000). To resolve this issue, we recorded from neurons in the two regions, before and at multiple stages of training monkeys on visual working memory tasks. Before training, substantial functional differences were present between the two regions. Dorsal prefrontal cortex exhibited higher overall responsiveness to visual stimuli and higher selectivity for spatial information. After training, stimulus selectivity generally decreased, although dorsal prefrontal cortex retained higher spatial selectivity regardless of task performed. Ventral prefrontal cortex appeared to be affected to a greater extent by the nature of the task. Our results indicate that regional specialization for stimulus selectivity is present in the primate prefrontal cortex regardless of training. Dorsal areas of the prefrontal cortex are inherently organized to represent spatial information, and training has little influence on this spatial bias. Ventral areas are biased toward nonspatial information, although they are more influenced by training both in terms of activation and changes in stimulus selectivity.
A Genetic Method for Selective and Quickly Reversible Silencing of Mammalian Neurons

Genetic methods for neuronal silencing have great promise for allowing selective inactivation of specific cell types within complex neural systems. Present methods, however, are limited in their reversibility by the slow time scale (days) of transcriptional regulation. We report the rapid and reversible inactivation of mammalian cortical neurons expressing the insect G-protein-coupled receptor AlstR (none Drosophilanone allatostatin receptor) after application of its peptide ligand allatostatin (AL). The onset and reversal of inactivation could be achieved rapidly, within minutes. Moreover, the effects of AL were selective for AlstR-transfected neurons. The AlstR/AL system is therefore a promising genetic method for selective and quickly reversible silencing of neuronal activity.
Inactivation of the tumour suppressor, PTEN, in smooth muscle promotes a pro-inflammatory phenotype and enhances neointima formation.

AIMS Phosphatase and tensin homolog (PTEN) is implicated as a negative regulator of vascular smooth muscle cell (SMC) proliferation and injury-induced vascular remodelling. We tested if selective depletion of PTEN only in SMC is sufficient to promote SMC phenotypic modulation, cytokine production, and enhanced neointima formation. METHODS AND RESULTS Smooth muscle marker expression and induction of pro-inflammatory cytokines were compared in cultured SMC expressing control or PTEN-specific shRNA. Compared with controls, PTEN-deficient SMC exhibited increased phosphoinositide 3-kinase (PI3K)/protein kinase B (Akt)/mammalian target of rapamycin (mTOR) signalling and nuclear factor kappa-light-chain-enhancer of activated B cells (NF-kappaB) activity, reduced expression of SM markers (SM-alpha-actin and calponin), and increased production of stromal cell-derived factor-1alpha (SDF-1alpha), monocyte chemotactic protein-1 (MCP-1), interleukin-6 (IL-6), and chemokine (C-X-C motif) ligand 1 (KC/CXCL1) under basal conditions. PI3K/Akt or mTOR inhibition reversed repression of SM marker expression, whereas PI3K/Akt or NF-kappaB inhibition blocked cytokine induction mediated by PTEN depletion. Carotid ligation in mice with genetic reduction of PTEN specifically in SMC (SMC-specific PTEN heterozygotes) resulted in enhanced neointima formation, increased SMC hyperplasia, reduced SM-alpha-actin and calponin expression, and increased NF-kappaB and cytokine expression compared with wild-types. Lesion formation in SMC-specific heterozygotes was similar to lesion formation in global PTEN heterozygotes, indicating that inactivation of PTEN exclusively in SMC is sufficient to induce considerable increases in neointima formation. CONCLUSION PTEN activation specifically in SMC is a common upstream regulator of multiple downstream events involved in pathological vascular remodelling, including proliferation, de-differentiation, and production of multiple cytokines.
The importin β/importin 7 heterodimer is a functional nuclear import receptor for histone H1

Import of proteins into the nucleus proceeds through nuclear pore complexes and is largely mediated by nuclear transport receptors of the importin β family that use direct RanGTP‐binding to regulate the interaction with their cargoes. We investigated nuclear import of the linker histone H1 and found that two receptors, importin β (Impβ) and importin 7 (Imp7, RanBP7), play a critical role in this process. Individually, the two import receptors bind H1 weakly, but binding is strong for the Impβ/Imp7 heterodimer. Consistent with this, import of H1 into nuclei of permeabilized mammalian cells requires exogenous Impβ together with Imp7. Import by the Imp7/Impβ heterodimer is strictly Ran dependent, the Ran‐requiring step most likely being the disassembly of the cargo–receptor complex following translocation into the nucleus. Disassembly is brought about by direct binding of RanGTP to Impβ and Imp7, whereby the two Ran‐binding sites act synergistically. However, whereas an Impβ/RanGTP interaction appears essential for H1 import, Ran‐binding to Imp7 is dispensable. Thus, Imp7 can function in two modes. Its Ran‐binding site is essential when operating as an autonomous import receptor, i.e. independently of Impβ. Within the Impβ/Imp7 heterodimer, however, Imp7 plays a more passive role than Impβ and resembles an import adapter.
W-Coolstreaming a Protocol for Collaborative Data Streaming for Wireless Networks

Coolstreaming is one of the first and currently most popular collaborative content distribution system working over the Internet. Such a system has demonstrated how live video streaming can be delivered by exploiting the peer-to-peer (p2p) paradigm. In this paper we propose W-Coolstreaming, a porting of Coolstreaming tailored to work over a mobile wireless network. We show how porting the whole architecture as-is provides very poor performance, whereas the performance of our implementation, which takes the main peculiarities of the wireless environment into account, are very encouraging in terms of scalability and adaptability to topological changes.
Vascular endothelial growth factor protects post‐ganglionic sympathetic neurones from the detrimental effects of hydrogen peroxide by increasing catalase

Aim: Vascular production of hydrogen peroxide (H2O2) is implicated in the development and progression of vascular disease. Hydrogen peroxide also promotes neuronal degeneration, which suggests that vascular H2O2 would promote degeneration of perivascular sympathetic nerves. Vascular cells also produce vascular endothelial growth factor (VEGF), which could protect perivascular nerves from the detrimental effects of H2O2. The aim of this study was to test these hypotheses.
Dengue in Java, Indonesia: Relevance of Mosquito Indices as Risk Predictors

Background No vaccine is currently available for dengue virus (DENV), therefore control programmes usually focus on managing mosquito vector populations. Entomological surveys provide the most common means of characterising vector populations and predicting the risk of local dengue virus transmission. Despite Indonesia being a country strongly affected by DENV, only limited information is available on the local factors affecting DENV transmission and the suitability of available survey methods for assessing risk. Methodology/principal findings We conducted entomological surveys in the Banyumas Regency (Central Java) where dengue cases occur on an annual basis. Four villages were sampled during the dry and rainy seasons: two villages where dengue was endemic, one where dengue cases occurred sporadically and one which was dengue-free. In addition to data for conventional larvae indices, we collected data on pupae indices, and collected adult mosquitoes for species identification in order to determine mosquito species composition and population density. Traditionally used larval indices (House indices, Container indices and Breteau indices) were found to be inadequate as indicators for DENV transmission risk. In contrast, species composition of adult mosquitoes revealed that competent vector species were dominant in dengue endemic and sporadic villages. Conclusions/significance Our data suggested that the utility of traditional larvae indices, which continue to be used in many dengue endemic countries, should be re-evaluated locally. The results highlight the need for validation of risk indicators and control strategies across DENV affected areas here and perhaps elsewhere in SE Asia.
Expression of Arabidopsis FCS-Like Zinc finger genes is differentially regulated by sugars, cellular energy level, and abiotic stress

Cellular energy status is an important regulator of plant growth, development, and stress mitigation. Environmental stresses ultimately lead to energy deficit in the cell which activates the SNF1-RELATED KINASE 1 (SnRK1) signaling cascade which eventually triggering a massive reprogramming of transcription to enable the plant to survive under low-energy conditions. The role of Arabidopsis thaliana FCS-Like Zinc finger (FLZ) gene family in energy and stress signaling is recently come to highlight after their interaction with kinase subunits of SnRK1 were identified. In a detailed expression analysis in different sugars, energy starvation, and replenishment series, we identified that the expression of most of the FLZ genes is differentially modulated by cellular energy level. It was found that FLZ gene family contains genes which are both positively and negatively regulated by energy deficit as well as energy-rich conditions. Genetic and pharmacological studies identified the role of HEXOKINASE 1- dependent and energy signaling pathways in the sugar-induced expression of FLZ genes. Further, these genes were also found to be highly responsive to different stresses as well as abscisic acid. In over-expression of kinase subunit of SnRK1, FLZ genes were found to be differentially regulated in accordance with their response toward energy fluctuation suggesting that these genes may work downstream to the established SnRK1 signaling under low-energy stress. Taken together, the present study provides a conceptual framework for further studies related to SnRK1-FLZ interaction in relation to sugar and energy signaling and stress response.
Vaccine-induced Immunity Circumvented by Typical Mycobacterium tuberculosis Beijing Strains

The frequency of typical and atypical Beijing strains of Mycobacterium tuberculosis was determined in the Netherlands; Vietnam; and Hong Kong Special Administrative Region, People’s Republic of China. The strains’ associations with drug resistance, M. bovis BCG vaccination, and patient characteristics were assessed. BCG vaccination may have positively selected the prevalent typical Beijing strains.
Personal Information Organization using Web Annotations

As more information is made available online, users collect information in personal information spaces like bookmarks and emails. While most users feel that organizing these collections is crucial to improve access, studies have shown that this activity is time consuming and highly cognitive. Automatic classification has been used but by relying on the full text of the documents, they do not generate personalized classifications. Our approach is to give users the ability to annotate their documents as they first access them. This annotation tool is unobtrusive and welcome by most users who generally miss this facility when dealing with digital documents. Our experiments show that these annotations can be used to generate personalized classifications of annotated Web pages.
Female-biased dispersal and patrilocal kin groups in a mammal with resource-defence polygyny

In most mammals, dispersal rates are higher in males than in females. Using behavioural and genetic data of individually marked bats, we show that this general pattern is reversed in the greater sac-winged bat (Saccopteryx bilineata). Dispersal is significantly female biased and male philopatry in combination with rare male immigration causes a patrilineal colony structure. Female dispersal helps avoid father–daughter inbreeding, as male tenure exceeds female age at first breeding in this bat species. Furthermore, our data suggest that females may engage in extra-harem copulations to mate with genetically dissimilar males, and thus avoid their male descendants as mating partners. Acquaintance with the natal colony might facilitate territory takeover since male sac-winged bats queue for harem access. Given the virtual absence of male immigration and the possible lower reproductive success of dispersing males, we argue that enhancing the likelihood of settlement of male descendants could be adaptive despite local mate competition. We conclude that resource defence by males is important in promoting male philopatry, and argue that the potential overlap of male tenure and female first conception is the driving force for females to disperse.
Bud morphology and shoot growth dynamics in two species of Mediterranean sub-shrubs co-existing in gypsum outcrops.

BACKGROUND AND AIMS Understanding the effects of the environment on the morphology and shoot growth activities of plants is crucial to identifying plant ecological strategies. This study analysed the bud morphology, bud activity, shoot growth dynamics and shoot water content at full hydration (WC(h)) of two species of Mediterranean sub-shrubs, Lepidium subulatum and Linum suffruticosum, co-existing in gypsum outcrops in north-east Spain. METHODS Sampling was conducted monthly over 2 years in one population per species. Buds were dissected under a stereo-microscope. Shoot growth was measured as the mean increase in shoot length of 15 marked individuals between two consecutive samplings. Bud activity was studied following the variations in the number of leaf primordia shorter than 1 mm and longer than 0.025 mm in the buds. KEY RESULTS Both species bore naked buds and displayed discontinuous seasonal patterns of shoot growth, leaf primordia formation and WC(h). The number of leaf primordia in the bud peaked before the beginning of shoot expansion. In both species, organogenesis and expansion were uncoupled throughout the year. The time lapse between these two processes varied throughout the year, and was greatest for those elements differentiated in autumn. WC(h) was more closely related to shoot expansion than to organogenesis. CONCLUSIONS Both species displayed similar bud morphology and similar seasonal patterns of bud and shoot growth, and WC(h) as a result of the strong seasonality of the Mediterranean climate in gypsum outcrops. The beginning of the spring period of expansion of long branches coincided with maximum values of WC(h), while the rest period of summer matched minimum values. These results support the hypothesis that the growth of long branches is strongly related to WC(h).
Effect of Thymine Starvation on Deoxyribonucleic Acid Repair Systems of Escherichia coli K-12

Thymine starvation of Escherichia coli K-12 results in greatly increased sensitivity to ultraviolet light (UV). Our studies, using isogenic strains carrying rec and uvr mutations, have shown the following. (i) Common to all strains tested is a change from multihit to single-hit kinetics of survival to UV after 60 min of thymine starvation. However, the limiting slope of UV survival curves decreases in the rec+uvr+ strain and changes very little in several rec mutant strains and one uvrB mutant strain. Thus, when either the rec or uvr system is functioning alone, the limiting slopes of the UV survival curves are relatively unaffected by thymine starvation. (ii) Thymine starvation does not significantly inhibit repair processes carried out by either repair system alone; i.e., host cell reactivation of irradiated phage (carried out by the uvr system), excision of thymine dimers (uvr), or X-ray repair (rec). (iii) In a rec+uvr+ strain, repair appears to be a synergistic rather than additive function of the two systems. However, after thymine starvation, repair capacity is reduced to about the sum of the repair capacities of the independent systems. (iv) The kinetics of thymineless death are not changed by rec and uvr mutations. This indicates that the lesions responsible for thymineless death are not repaired by rec or uvr systems. (v) Withholding thymine from thy rec+uvr+ bacteria not undergoing thymineless death has no effect on UV sensitivity. Under these conditions one sees higher than normal UV resistance in the presence or absence of thymine. This is due to increased repair carried out by the uvr system. To explain these results we postulate that thymine starvation does not inhibit either the rec or uvr repair pathway directly. Rather it appears that thymine starvation results in increased UV sensitivity in part by inhibiting a function which normally carries out efficient coordination of rec and uvr pathways.
False alarms in radar detection within sparse-signal processing

Radar-detection metrics are assessed in outcomes of sparse-signal processing (SSP) with test statistics based on the subgradient and the dual feasibility in the SSP optimization via an approach separating false alarms (FAs) from targets. In radar, SSP is aimed for estimating a sparse solution whose FAs are fixed and whose detection of targets is optimal as in traditional detection. Existing detection schemes employing thresholds are based on the theory for a single target and ideal sensing coherence. SSP facilitates development of generic radar-detection metrics by including sensing coherence and multiple targets. We focus on assessing FAs in detection within SSP at different values of sensing coherence, signal-to-noise ratio and a number of targets, and also as compared with the existing detection. The theoretical analysis of detection within SSP is validated with numerical results from range processing.
Functional and neuroanatomic correlations in poststroke depression: the Sunnybrook Stroke Study.

BACKGROUND AND PURPOSE The purpose of our study was to determine the functional and neuroanatomic correlates of poststroke depressive symptoms. METHODS Patients with consecutive admissions to a regional stroke center for new-onset unilateral hemispheric stroke who met World Health Organization and National Institute of Neurological and Communicative Disorders and Stroke criteria were eligible for inclusion in a longitudinal study. Acutely, patients underwent CT scanning, and at 3 months and 1 year after stroke, depressive symptoms were assessed by using both the Montgomery-Asberg Depression Rating Scale and the Zung Self-Rating Depression Scale. The Functional Independence Measure (FIM) served as an indication of functional outcome and was obtained at 1 month, 3 months, and 1 year after stroke, along with other demographic information. The Talairach and Tournoux stereotactic atlas was used for the primary determination of CT lesion localization. Lesion proximity to the anterior frontal pole was also measured. RESULTS Eighty-one patients participated in the longitudinal study. Stepwise linear regression analyses generated a highly significant model (F(3,76)=9.8, R(2)=28%, P<0.0005), with lower 1-month total FIM scores, living at home, and damage to the inferior frontal region predicting higher depression scores at 3 months. Similarly, lower 3-month total FIM scores correlated with higher 3-month depression scores, and lower 1-year total FIM scores correlated with higher 1-year depression scores. CONCLUSIONS Functional measures correlated with poststroke depression across time and, together with neuroanatomic measures, predicted depressive symptoms longitudinally. Although inferior frontal lesion location, irrespective of side, appeared to play a role as a risk factor in this study, the degree of functional dependence after stroke imparted the greatest risk.