Miracle-dz/UniFAR-FTUs huggingface dataset:
Androgen receptor‐interacting protein HSPBAP1 facilitates growth of prostate cancer cells in androgen‐deficient conditions

Hormonal therapies targeting androgen receptor (AR) are effective in prostate cancer (PCa), but often the cancers progress to fatal castrate‐resistant disease. Improved understanding of the cellular events during androgen deprivation would help to identify survival and stress pathways whose inhibition could synergize with androgen deprivation. Toward this aim, we performed an RNAi screen on 2,068 genes, including kinases, phosphatases, epigenetic enzymes and other druggable gene targets. High‐content cell spot microarray (CSMA) screen was performed in VCaP cells in the presence and absence of androgens with detection of Ki67 and cleaved ADP‐ribose polymerase (cPARP) as assays for cell proliferation and apoptosis. Thirty‐nine candidate genes were identified, whose silencing inhibited proliferation or induced apoptosis of VCaP cells exclusively under androgen‐deprived conditions. One of the candidates, HSPB (heat shock 27 kDa)‐associated protein 1 (HSPBAP1), was confirmed to be highly expressed in tumor samples and its mRNA expression levels increased with the Gleason grade. We found that strong HSPBAP1 immunohistochemical staining (IHC) was associated with shorter disease‐specific survival of PCa patients compared with negative to moderate staining. Furthermore, we demonstrate that HSPBAP1 interacts with AR in the nucleus of PCa cells specifically during androgen‐deprived conditions, occupies chromatin at PSA/klk3 and TMPRSS2/tmprss2 enhancers and regulates their expression. In conclusion, we suggest that HSPBAP1 aids in sustaining cell viability by maintaining AR signaling during androgen‐deprived conditions.
Infection Is Not Dependent on CD40 Listeria monocytogenes Memory after The Development of Functional CD8 T Cell

The immunologic requirements for generating long-lived protective CD8 T cell memory remain unclear. Memory CD8 populations generated in the absence of CD4 Th cells reportedly have functional defects, and at least a subset of CD8 T cells transiently express CD40 after activation, suggesting that direct CD4-CD8 T cell interactions through CD40 may inﬂuence the magnitude and functional quality of memory CD8 populations. To ascertain the role of CD40 in such direct T cell interactions, we investigated CD8 T cell responses in CD40 (cid:1) / (cid:1) mice after infection with Listeria monocytogenes , an intracellular bacterium that induces APC activation and thus priming of CD8 T cells independently of CD4 Th cell help through CD40. In this study we show that memory CD8 T cells generated in CD40-deﬁcient mice show in vivo cytotoxicity and cytokine production equivalent to CD8 memory T cells from wild-type mice. Upon secondary Listeria infection, CD40 (cid:1) / (cid:1) memory CD8 T cells expand to greater numbers than seen in wild-type mice. These results indicate that CD40 ligation on CD8 T cells, although reportedly a part of CD8 T cell memory development in an H-Y-directed response, is not needed for the development of functional memory CD8 T cell populations after Listeria infection. The Journal of Immunology, 2004, 173: 4084–4090.
[Neuropsychiatric Inventory (NPI)].

The NPI is based on responses from an informed caregiver, preferably one living with the patient. If an informed observer is not available, this instrument cannot be used or must be modified. The interview is best conducted with the caregiver in the absence of the patient to facilitate an open discussion of behaviors that may be difficult to describe with the patient present. Several points should be made when you introduce the NPI interview to the caregiver:
Benchmarking and measuring the comparative efficiency of emergency medical services in major US cities

Purpose – The purpose of this paper is to benchmark and measure the comparative efficiency of emergency medical services (EMS) in major US cities (populations greater than 100,000). In so doing, this paper aims to develop a benchmark that can be emulated by cities lagging in EMS efficiency. Also, it seeks to develop a profile of cities that are successful in providing highly efficient EMS as benchmarks.Design/methodology/approach – Data envelopment analysis is used to measure the EMS efficiency of 127 selected large cities in the USA under the premise of a constant‐return to scales method of service delivery. In addition, to identify factors influencing the US cities' EMS efficiency and then to predict their efficiency scores, a Tobit regression analysis is employed, which tended to result in a smaller standard error, a smaller bias, and a smaller mean squared error than ordinary least squares.Findings – This paper examines whether more densely settled and populated areas have greater efficiency in delive.
Application of interruptible contracts to increase wind-power penetration in congested areas

Wind-power penetration in many cases faces significant barriers due to limited transmission capability. In Greece (and in most countries in Europe), the guaranteed access to the grid offered to wind parks, in conjunction with the existing planning practices, has led to severe limitations in wind power installed in certain congested areas. This paper presents some simple ideas that are currently being applied to the Hellenic Interconnected System, in order to increase the wind-power penetration. The main concept is the introduction of interruptible generator contracts and the control of the power flow through congested corridors by issuing power reduction commands, whenever security limits are violated. The proposed control is implemented using common PLCs of low cost and the existing SCADA system, and is both simple and transparent. The paper presents also a methodology to assess the impact of the proposed techniques on the wind penetration achieved.
Screening of the 1 Mb SOX9 5′ control region by array CGH identifies a large deletion in a case of campomelic dysplasia with XY sex reversal

Campomelic dysplasia (CD; OMIM #114290) is a semi-lethal, autosomal dominant osteochondrodysplasia, characterised by congenital shortening and bowing of the long bones (campomelia) in combination with other skeletal anomalies such as hypoplasia of the scapular and pelvic bones, lack of mineralisation of thoracic pedicles, a missing pair of ribs, and clubbed feet. Severe respiratory distress resulting from Robin sequence, hypoplastic lungs with narrow airways, and a bell shaped narrow thorax are the major cause of death, which mostly occurs during the neonatal period. About two thirds of karyotypic male CD patients show XY sex reversal. As is the case for any of the symptoms, campomelia is not an obligatory feature and is absent in about 10% of the cases, referred to as the acampomelic form of CD (ACD). 1,2 Most CD cases have heterozygous de novo mutations in the coding region of the transcription factor gene SOX9 on 17q.3,4 The mutations cause loss of DNA binding or of the transactivation function of SOX9, implying that CD results from haploinsufficiency for SOX9. In accordance with the human phenotype caused by SOX9 mutations, studies in the mouse have shown that Sox9 functions as an essential developmental regulator at various steps of chondrogenesis5,6 and during the initial phase of testis determination and differentiation.7–9 Furthermore, heterozygous Sox9 knockout mice recapitulate essentially all the symptoms seen in CD patients but for the sex reversal.5,10 Some CD cases have two intact copies of the SOX9 structural gene but a chromosomal rearrangement in the vicinity of one SOX9 allele. These rearrangements, which include translocations and inversions, occur de novo, and their breakpoints are always 5′ to SOX9 . In 11 of these cases, the breakpoints have been mapped from 50 kb up to 950 kb upstream of SOX9 . …
Arousals and sleep stages in patients with obstructive sleep apnoea syndrome: changes under nCPAP treatment

Nocturnal arousals are the essential cause of disturbed sleep structure in patients with obstructive sleep apnoea syndrome (OSAS). The aim of this study was to analyse the relationship between sleep stages, respiratory (type‐R) and movement (type‐M) related EEG arousals. Furthermore, the value of these arousals as a criterion for the efficiency of nCPAP treatment was estimated. We examined 38 male patients aged between 30 and 71 (49.1±20.9 SD) y. All patients suffered from OSAS. The mean respiratory disturbance index (RDI) was 47.3±27.8 per h. Polysomnographic monitoring was carried out on 4 subsequent nights: baseline night, 2 nights of nCPAP titration and nCPAP control night. Sleep was visually scored and EEG arousals were classified into type R and M, depending on whether changes of respiration or movement caused the arousal. The RDI, the R index (type‐R/h), the M index (type‐M/h) and the R and M indices in different sleep stages were calculated. During the baseline night a deficit of slow wave sleep (SWS) and REM sleep was found. Furthermore there were more type‐R than type‐M arousals registered (17.4 h−1[3.6–43.6] vs. 5.9 h−1[1.6–11.8]) (P<0.01). They occurred during stages NREM 1, NREM 2 and REM (P<0.01). An SWS sleep rebound and a reduction of the SWS and REM latencies were already found during the first CPAP night. The R index was reduced during the first CPAP night in all sleep stages (P<0.01) and remained approximately the same in the following 2 nights (3. CPAP night: 1.1 h−1[0.3–5.0]). Type M arousals occurred more in stages 1 and 2 (P<0.01), and remained unchanged under nCPAP. We concluded that differentiation of nocturnal arousals may provide more detailed information regarding the influence of breathing disturbances on sleep. Respiratory related, not movement related, arousals may be a useful additional tool in judging the efficiency of OSAS.
Quality model for the world wide web

This paper proposes the quality model and methodology that guides the Web site quality evaluation. The model can be viewed as a hierarchical tree with three levels. The first level is composed of six quality characteristics defined by ISO standards: functionality, usability, reliability, efficiency, maintainability and portability. The second level decomposes characteristics into subcharacteristics, which are further decomposed into third-level measurable indicators. The four stages of evaluation process are defined. The paper proposes the application of Goal-Question-Metrics model to evaluate indicators, subcharacteristics and characteristics, as well as the overall quality of the site. The proposed model and metrics are verified on the selected set of Web sites at the Faculty of Electrical Engineering and Computing. In spite of tremendeous growth of the World Wide Web in the last several years, the number of Web sites that offer useful and reliable information is still negligable. The quality of the information delivered through the Web is not merely the result of good design and visual appereance of the site, but is a part of a much broader process in which the information and its presentation are tailored according to users' needs and expectations. Therefore, a high-quality Web site is the one that meets the users'
Assessing putative interlocus sexual conflict in Drosophila melanogaster using experimental evolution

The theoretical foundation of sexually antagonistic coevolution is that females suffer a net fitness cost through their interactions with males. The empirical prediction is that direct costs to female lifetime fecundity will exceed indirect benefits despite a possible increase in the genetic quality of offspring. Although direct costs of males have been repeatedly shown, to date no study has comprehensively tested whether females are compensated for this direct harm through indirect benefits. Here we use experimental evolution to show that a mutation giving Drosophila melanogaster females nearly complete resistance to the direct costs of male courtship and remating, but which also excluded almost all indirect benefits, is strongly favoured by selection. We estimated the selection coefficient favouring the resistance allele to be +20%. These results demonstrate that any indirect benefits that females accrued were not sufficient to counter-balance the direct costs of males, and reinforce a large body of past studies by verifying interlocus sexual conflict in this model system.
Biomarker selection and sample prediction for multi-category disease on MALDI-TOF data

MOTIVATION Diseases normally progress through several stages. Therefore, biomarkers corresponding to each stage may exist. To deal with such a multi-category problem, including sample stage prediction and biomarker selection, we propose methods for classification and feature selection. The proposed classification method is based on two schemes: error-correcting output coding (ECOC) and pairwise coupling (PWC). The final decision for a test sample prediction is an integration of these two schemes. The biomarker pattern for distinguishing each disease category from another one is achieved by the development of an extended Markov blanket (EMB) feature selection method. RESULTS In this study, a liver cancer matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) dataset was used, which comprises hepatocellular carcinoma (HCC), cirrhosis, and healthy spectra. Peak patterns were discovered for distinguishing pairwise categories among the three classes. Importance and reliability of individual peaks were presented by the measurements of certain weight values and frequencies. The classification capability of the proposed approach was compared with classical ECOC, random forest, Naive Bayes, and J48 methods. AVAILABILITY Supplementary materials are available at http://visionlab.uta. edu/biomarker/bioinfo.htm.
Tour Planning for Mobile Data-Gathering Mechanisms in Wireless Sensor Networks

In this paper, we propose a new data-gathering mechanism for large-scale wireless sensor networks by introducing mobility into the network. A mobile data collector, for convenience called an M-collector in this paper, could be a mobile robot or a vehicle equipped with a powerful transceiver and battery, working like a mobile base station and gathering data while moving through the field. An M-collector starts the data-gathering tour periodically from the static data sink, polls each sensor while traversing its transmission range, then directly collects data from the sensor in single-hop communications, and finally transports the data to the static sink. Since data packets are directly gathered without relays and collisions, the lifetime of sensors is expected to be prolonged. In this paper, we mainly focus on the problem of minimizing the length of each data-gathering tour and refer to this as the single-hop data-gathering problem (SHDGP). We first formalize the SHDGP into a mixed-integer program and then present a heuristic tour-planning algorithm for the case where a single M-collector is employed. For the applications with strict distance/time constraints, we consider utilizing multiple M-collectors and propose a data-gathering algorithm where multiple M-collectors traverse through several shorter subtours concurrently to satisfy the distance/time constraints. Our single-hop mobile data-gathering scheme can improve the scalability and balance the energy consumption among sensors. It can be used in both connected and disconnected networks. Simulation results demonstrate that the proposed data-gathering algorithm can greatly shorten the moving distance of the collectors compared with the covering line approximation algorithm and is close to the optimal algorithm for small networks. In addition, the proposed data-gathering scheme can significantly prolong the network lifetime compared with a network with static data sink or a network in which the mobile collector can only move along straight lines.
KDPI score is a strong predictor of future graft function: Moderate KDPI (35 - 85) and high KDPI (> 85) grafts yield similar graft function and survival .

BACKGROUND Efforts have been made to maximize the utility of each organ transplanted. Policy changes to capture unrealized graft years have been implemented utilizing the kidney donor profile index (KDPI). Understanding the impact of KDPI on long-term graft function is critical to an informed organ acceptance decision. METHODS We reviewed the records of 309 consecutive deceased adult donor kidney recipients who underwent kidney transplantation at our center. We obtained KDPI of the allografts directly from United Network for Organ Sharing (UNOS) and patients were divided into four categories: KDPI ≤ 20, KDPI 21 - 35, KDPI 36 - 85, and KDPI > 85. RESULTS Of the 309 recipients, 48 (15.5%) received kidneys from donors with KDPI ≤ 20, 57 (18.4%) from donors with KDPI 21 - 35, 161 (52.1%) from donors with KDPI 36 - 85, and 43 (13.9%) from donors with KDPI > 85. Older recipients were more likely to receive high KDPI kidneys (p = 0.025). Kaplan-Meier analysis demonstrated the KDPI > 35 group had worse survival than the KDPI ≤ 20 group, but KDPI 36 - 85 was not different from KDPI > 85. The rate of poor graft function differed at 1 year: 14.6% of KDPI ≤ 20 recipients, 14.3% of KDPI 21 - 35 recipients, 30.6% of KDPI 35 - 85 recipients, and 40.5% of KDPI > 85 recipients had serum creatinine greater than 2.0 mg/dL at 1 year. KDPI > 35 had statistically significantly greater incidence of poor graft function than KDPI ≤ 35 (p < 0.05). CONCLUSIONS Our study demonstrates that high KDPI grafts behave more like moderate KDPI grafts (KDPI 35 - 85). Creatinine (Cr) greater than 2.0 mg/dL portends poorer long-term graft survival, and this outcome is similar amongst all recipients of KDPI > 35 allografts.
Interactive detection of incrementally learned concepts in images with ranking and semantic query interpretation

The number of networked cameras is growing exponentially. Multiple applications in different domains result in an increasing need to search semantically over video sensor data. In this paper, we present the GOOSE demonstrator, which is a real-time general-purpose search engine that allows users to pose natural language queries to retrieve corresponding images. Top-down, this demonstrator interprets queries, which are presented as an intuitive graph to collect user feedback. Bottom-up, the system automatically recognizes and localizes concepts in images and it can incrementally learn novel concepts. A smart ranking combines both and allows effective retrieval of relevant images.
Insight provenance for spatiotemporal visual analytics: Theory, review, and guidelines

: Research on provenance, which focuses on different ways to describe and record the history of changes and advances made throughout an analysis process, is an integral part of visual analytics. This paper focuses on providing the provenance of insight and rationale through visualizations while emphasizing, ﬁrst, that this entails a profound understanding of human cognition and reasoning and that, second, the special nature of spatiotemporal data needs to be acknowledged in this process. A recently proposed human reasoning framework for spatiotemporal analysis, and four guidelines for the creation of visualizations that provide the provenance of insight and rationale published in relation to that framework, work as a starting point for this paper. While these guidelines are quite abstract, this paper set out to create a set of more concrete guidelines. On the basis of a review of available provenance solutions, this paper identiﬁes a set of key features that are of relevance when providing the provenance of insight and rationale and, on the basis of these features, produces a new set of complementary guidelines that are more practically oriented than the original ones. Together, these two sets of guidelines provide both a theoretical and practical approach to the problem of providing the provenance of insight and rationale. Providing these kinds of guidelines represents a new approach in provenance research.
Investors' Behavioural Biases and the Security Market: An Empirical Study of the Nigerian Security Market

Behavioural biases describe a replicable pattern in perceptual distortion, inaccurate judgment, illogical interpretation, or what is broadly called irrationality. This paper adopts a primary data approach to investigate the effects of behavioural biases on security market performance in Nigeria. The objectives are in twofold: one, to examine the extent of behavioural biases among security market investors in Nigeria and, to examine the effects of behavioural biases on stock market performance in Nigeria. The paper employed questionnaire as instrument and the technique of correlation with Pearson Product Moment Coefficient to analyze a survey of 300 randomly selected investors in Nigeria security market. We find strong evidence that behavioural biases exists but not so dominant in the Nigeria security market because a weak negative relationship exists between behavioural biases and stock market performance in Nigeria. The paper recommends that individual investors in the market should engage the services of investment advisors which will reduce personal biases in the management of their portfolios.
Pseudomonas aeruginosa Virulence Analyzed in a Dictyostelium discoideum Host System

ABSTRACT Pseudomonas aeruginosa is an important opportunistic pathogen that produces a variety of cell-associated and secreted virulence factors. P. aeruginosa infections are difficult to treat effectively because of the rapid emergence of antibiotic-resistant strains. In this study, we analyzed whether the amoeba Dictyostelium discoideum can be used as a simple model system to analyze the virulence of P. aeruginosa strains. The virulent wild-type strain PAO1 was shown to inhibit growth of D. discoideum. Isogenic mutants deficient in the las quorum-sensing system were almost as inhibitory as the wild type, while rhl quorum-sensing mutants permitted growth of Dictyostelium cells. Therefore, in this model system, factors controlled by the rhl quorum-sensing system were found to play a central role. Among these, rhamnolipids secreted by the wild-type strain PAO1 could induce fast lysis of D. discoideum cells. By using this simple model system, we predicted that certain antibiotic-resistant mutants of P. aeruginosa should show reduced virulence. This result was confirmed in a rat model of acute pneumonia. Thus, D. discoideum could be used as a simple nonmammalian host system to assess pathogenicity of P. aeruginosa.
Morphological and molecular identification of Fusarium head blight isolates from wheat in north of Iran

Fusarium head blight (FHB) is one of the most economically important and destructive fungal diseases of wheat (Triticum aestivum L.). Golestan province, one of the most important zones of wheat cultivation in Iran, is also known for its high rate of digestive tract cancer, which has been attributed to many biotic factors such as fungal toxins. In order to investigate the distribution of toxicogenic Fusarium spp. in wheat in this region, 344 Fusarium isolates were collected from 7 sub-regions in Golestan province during 2010- 2011. Single-spore cultures were established using routine plant pathology methods and the isolates were identified using chemotyping analysis based on morphological criteria and species-specific PCR assays. The following Fusarium isolates were identified: F. graminearum, F. culmorum, F. equiseti, F. croockwellens, F. acuminatum, F. poae, F. lateritium, F. proliferatum and F. subglutinans. F. graminearum was the most dominant species, representing 48.2% of the isolates. PCR analysis using the speciesspecific primers Fg161 1/2 and OPT 1/2 confirmed 96.3% isolates as F. graminearum and 86.4% as F. culmorum. Isolates morphologically identified as F. subglutinans or F. proliferatum did not show any positive reaction in species-specific PCR. The present study revealed a high occurrence of FHB in Golestan province, especially in Gonbad-Kavoos sub-regions.