Miracle-dz/UniFAR-FTUs huggingface dataset:
Systematic identification of pseudogenes through whole genome expression evidence profiling

The identification of pseudogenes is an integral and significant part of the genome annotation because of their abundance and their impact on the experimental analysis of functional genes. Most of the computational annotation systems are not optimized for systematic pseudogene recognition, often annotating pseudogenes as functional genes, and users then propagate these errors to subsequent analyses and interpretations. In order to validate gene annotations and to identify pseudogenes that are potentially mis-annotated, we developed a novel approach based on whole genome profiling of existing transcript and protein sequences. This method has two important features: (i) equally detects both processed and non-processed pseudogenes and (ii) can identify transcribed pseudogenes. Applying this method to the human Ensembl gene predictions, we discovered that 2011 (9% of total) Ensembl genes in the categories of known and novel might be pseudogenes based on expression evidence. Of these, 1200 genes are found to have no existing evidence of transcription, and 811 genes are found with transcription evidence but contain significant translation disruption. Approximately 40% of the 2011 identified pseudogenes presented a multi-exon structure, representing non-processed pseudogenes. We have demonstrated the power of whole genome profiling of expression sequences to improve the accuracy of gene annotations.
Evaluation of the Diagnostic Accuracy of CareStart G6PD Deficiency Rapid Diagnostic Test (RDT) in a Malaria Endemic Area in Ghana, Africa

Background Glucose-6-phosphate dehydrogenase (G6PD) deficiency is the most widespread enzyme defect that can result in red cell breakdown under oxidative stress when exposed to certain medicines including antimalarials. We evaluated the diagnostic accuracy of CareStart G6PD deficiency Rapid Diagnostic Test (RDT) as a point-of-care tool for screening G6PD deficiency. Methods A cross-sectional study was conducted among 206 randomly selected and consented participants from a group with known G6PD deficiency status between February 2013 and June 2013. A maximum of 1.6ml of capillary blood samples were used for G6PD deficiency screening using CareStart G6PD RDT and Trinity qualitative with Trinity quantitative methods as the “gold standard”. Samples were also screened for the presence of malaria parasites. Data entry and analysis were done using Microsoft Access 2010 and Stata Software version 12. Kintampo Health Research Centre Institutional Ethics Committee granted ethical approval. Results The sensitivity (SE) and specificity (SP) of CareStart G6PD deficiency RDT was 100% and 72.1% compared to Trinity quantitative method respectively and was 98.9% and 96.2% compared to Trinity qualitative method. Malaria infection status had no significant (P=0.199) change on the performance of the G6PD RDT test kit compared to the “gold standard”. Conclusions The outcome of this study suggests that the diagnostic performance of the CareStart G6PD deficiency RDT kit was high and it is acceptable at determining the G6PD deficiency status in a high malaria endemic area in Ghana. The RDT kit presents as an attractive tool for point-of-care G6PD deficiency for rapid testing in areas with high temperatures and less expertise. The CareStart G6PD deficiency RDT kit could be used to screen malaria patients before administration of the fixed dose primaquine with artemisinin-based combination therapy.
The Role of Organizational Perception, Perceived Consumer Effectiveness and Self-efficacy in Recycling Advocacy Advertising Effectiveness

ABSTRACT Previous academic research into how consumers evaluate advocacy advertising identified many possible paths involving potentially reflexive effects on how people perceive an advocacy advertising sponsor, the advocated issue and themselves. This paper has examined one possible scenario within this complicated phenomenon: that of advertising advocating a specific environmental consumer action, recycling. In the specific context of this study, structural equation modelling demonstrated clear causal relationships among consumer perceptions of the recycling advertisements’ sponsoring organization, consumer self-efficacy and perceived consumer effectiveness of complying with the advocated issue (recycling behaviour). These factors were shown to impact specific advocacy advertising goals (termed message effectiveness in this study) such as behavioural intention toward the advocated recycling issue and perceived changes in how consumers evaluate the sponsoring organization.
Learning Adversary-Resistant Deep Neural Networks

Deep neural networks (DNNs) have proven to be quite effective in a vast array of machine learning tasks, with recent examples in cyber security and autonomous vehicles. Despite the superior performance of DNNs in these applications, it has been recently shown that these models are susceptible to a particular type of attack that exploits a fundamental flaw in their design. This attack consists of generating particular synthetic examples referred to as adversarial samples. These samples are constructed by slightly manipulating real data-points in order to"fool"the original DNN model, forcing it to mis-classify previously correctly classified samples with high confidence. Addressing this flaw in the model is essential if DNNs are to be used in critical applications such as those in cyber security. Previous work has provided various learning algorithms to enhance the robustness of DNN models, and they all fall into the tactic of"security through obscurity". This means security can be guaranteed only if one can obscure the learning algorithms from adversaries. Once the learning technique is disclosed, DNNs protected by these defense mechanisms are still susceptible to adversarial samples. In this work, we investigate this issue shared across previous research work and propose a generic approach to escalate a DNN's resistance to adversarial samples. More specifically, our approach integrates a data transformation module with a DNN, making it robust even if we reveal the underlying learning algorithm. To demonstrate the generality of our proposed approach and its potential for handling cyber security applications, we evaluate our method and several other existing solutions on datasets publicly available. Our results indicate that our approach typically provides superior classification performance and resistance in comparison with state-of-art solutions.
Antiphospholipid antibodies during 6-month treatment with infliximab: A preliminary report

Background The introduction of tumor necrosis factor (TNF) antagonists (adalimumab, infliximab, and etanercept) was a major advance and was highly important and beneficial in most rheumatoid arthritis (RA) patients. The adverse effects of this treatment are infrequent, but include opportunistic intracellular infection (especially the reactivation of latent Mycobacterium tuberculosis); exacerbation of demyelinating disorders; and the production of various types of antibodies such as antinuclear antibodies (ANA) or double-stranded DNA autoantibodies (dsDNA) and antiphospholipid antibodies (aPL) such as anti-cardiolipin antibodies (aCL) and anti-B2GP-I antibodies (B2GP-I). The aim of the study was to determine the prevalence of aCL and B2GP-I in IgM and IgG classes, using ELISA tests, during 6 months of follow-up in patients with refractory RA successfully treated with infliximab. Material/Methods We determined the prevalence of aCL and B2GP-I in IgM and IgG classes, using ELISA tests, during 6 months of follow-up in patients with refractory RA successfully treated with infliximab. Results We observed a statistically important increase only in the group of B2GP-I IgM (p<0.05). There are contradictory results concerning the ability of infliximab to induce aPL, but most authors confirm this phenomenon. Conclusions Further investigations are needed to determine if the new aPL appears in patients with β2-GPI gene polymorphisms such as leucine-to-valine substitution at position 247, which can lead to a conformational changes in β2-GPI protein, leading to aPL synthesis. The role of aPL in pathogenesis of APS is still unclear, but we should remember the immunogenic aspect of TNF antagonist treatment. Therefore, we recommend early detection of aPL and observation of the patient, paying special attention to signs and symptoms of thromboembolism.
Cardiomyocytes from AKAP7 knockout mice respond normally to adrenergic stimulation

Protein kinase A (PKA) is activated during sympathetic stimulation of the heart and phosphorylates key proteins involved in cardiac Ca2+ handling, including the L-type Ca2+ channel (CaV1.2) and phospholamban (PLN). This results in acceleration and amplification of the beat-to-beat changes in cytosolic Ca2+ in cardiomyocytes and, in turn, an increased rate and force of contraction. PKA is held in proximity to its substrates by protein scaffolds called A kinase anchoring proteins (AKAPs). It has been suggested that the short and long isoforms of AKAP7 (also called AKAP15/18) localize PKA in complexes with CaV1.2 and PLN, respectively. We generated an AKAP7 KO mouse in which all isoforms were deleted and tested whether Ca2+ current, intracellular Ca2+ concentration, or Ca2+ reuptake were impaired in isolated adult ventricular cardiomyocytes following stimulation with the β-adrenergic agonist isoproterenol. KO cardiomyocytes responded normally to adrenergic stimulation, as measured by whole-cell patch clamp or a fluorescent intracellular Ca2+ indicator. Phosphorylation of CaV1.2 and PLN were also unaffected by genetic deletion of AKAP7. Immunoblot and RT-PCR revealed that only the long isoforms of AKAP7 were detectable in ventricular cardiomyocytes. The results indicate that AKAP7 is not required for regulation of Ca2+ handling in mouse cardiomyocytes.
The visual processing of human faces and bodies as visual stimuli in natural scenes

How faces are recognized and detected has been the focus of an extensive corpus of research. As such, it is now well established that human faces can be detected rapidly in a visual scene and that they automatically capture a viewer’s attention over other objects. However, under natural viewing conditions the human face is attached to a substantial cue, the human body. The evidence to-date of a similar attentional processing advantage for human bodies is less clear. This is remarkable given the social significance and evidence of neural specificity for these stimuli. Additionally, most previous investigations of preferential attention towards faces and bodies have presented these stimuli in simple displays, namely uniform colour backgrounds (Bindemann, Scheepers, Ferguson & Burton, 2010). Therefore, this thesis aimed to address the relationship between attention and face and body processing in natural scenes directly by assessing the consequences of numerous experimental manipulations in both a visual search paradigm and additional singleton paradigm. The first line of enquiry examined participants’ ability to detect face and body stimuli in comparison to other objects in natural scenes. Subsequent experiments examined whether faces and bodies captured attention when they were task-irrelevant. In line with previous research, the main findings indicate that human faces do have attentional advantages and capture attention in both natural and grey scenes. They also indicate that human bodies (without the head) do not have detection advantages over other objects, nor do they capture attention in a bottom-up manner. Any biases or detection advantages observed for body targets are because they larger in size than other objects or because they are odd stimuli in that scene. Human full-body targets (including the face), which are perceived on a day-to-day basis, capture attention partly because they include face and partly because they are large objects in the scene. These findings modify claims of person perception suggesting that the detection of a full-body in natural scenes is facilitated by attention capture by faces, any advantages from bodies are the result of attention capture by their large size, rather than some attentional advantage. Future investigating into face and body processing should use natural backgrounds to gain a more realistic insight in to face and body processing in the real world.
Private returns to investment in education: an empirical study of urban China

This article draws on a survey of urban Chinese workers in 2005 to estimate the private returns to education and the income elasticity of education. Differences in the rates of return to schooling are examined between gender and between age groups. The estimated returns to schooling are found to be higher than those documented in existing studies for the mid-1980s to late 1990s. In particular, considerably higher returns to education are observed among people aged 35 or under, representing those who received standardised education and entered the labour market during the urban economic reform era. The study finds that the income elasticity of education expenditure is relatively low and that expenditure on education is less sensitive to changes in income than expenditure on either food or clothing.
Analysing emerging memory technologies for big data and signal processing applications

In this paper, we investigate and compare different emerging memory technologies as on-chip cache for big data and signal processing applications. Static Random Access Memory (SRAM) has been widely used as level 1 and last level caches for multicore processors. Server chips integrate Dynamic Random Access Memory (DRAM) as an additional cache for better server-level applications that process more data. Both SRAM and DRAM have advantages and disadvantages. Therefore new types of RAMs are proposed and prototyped. For big data and signal processing applications nowadays, enormous amount of data are processed, usually with time limitations. We analyse novel RAMs, including Phase-change RAM (PRAM), Magnetoresistive RAM (MRAM), Ferroelectric RAM (FRAM) and Resistive RAM (RRAM). The conventional and new memories are analysed in terms of size, area, access latency and power consumption. We present benchmark results using a full system simulator. Workloads are selected from several big data, server, signal processing and video processing applications. Experiments show that, in consideration of these applications, it is crucial to replace SRAM and DRAM caches with MRAM and RRAM.
Quantitative studies of pinocytosis. II. Kinetics of protein uptake and digestion by rat yolk sac cultured in vitro

Pinocytic uptake of 125I-labeled bovine serum albumin by 17.5-day rat visceral yolk sac cultured in vitro has been examined. Uptake was followed by intracellular digestion and, after an initial period, the content of radioactivity in the tissue itself remained constant during the incubation. Radiolabel was returned to the culture medium predominantly as (125I)iodotyrosine; exocytosis of undigested protein did not occur. The rate of uptake of labeled protein, which was constant within an experiment and reproducible between experiments, was much higher than that of a nondigestible macromolecule, 125I-labeled polyvinylpyrrolidone. The higher rate of uptake was a consequence of the protein entering the cells chiefly by adsorption to the plasma membrane being internalized; 125I-labeled albumin did not stimualte, nor did 125I-labeled polyvinylpyrrolidone inhibit pinocytosis. Different preparations of 125I-labeled albumin had characteristically different rates of uptake, probably reflecting differences in affinity for plasma membrane receptors. The physiological significance of the findings is discussed.
Effect of Investment in Malaria Control on Child Mortality in Sub-Saharan Africa in 2002–2008

Background Around 8.8 million children under-five die each year, mostly due to infectious diseases, including malaria that accounts for 16% of deaths in Africa, but the impact of international financing of malaria control on under-five mortality in sub-Saharan Africa has not been examined. Methods and Findings We combined multiple data sources and used panel data regression analysis to study the relationship among investment, service delivery/intervention coverage, and impact on child health by observing changes in 34 sub-Saharan African countries over 2002–2008. We used Lives Saved Tool to estimate the number of lives saved from coverage increase of insecticide-treated nets (ITNs)/indoor residual spraying (IRS). As an indicator of outcome, we also used under-five mortality rate. Global Fund investments comprised more than 70% of the Official Development Assistance (ODA) for malaria control in 34 countries. Each $1 million ODA for malaria enabled distribution of 50,478 ITNs [95%CI: 37,774–63,182] in the disbursement year. 1,000 additional ITNs distributed saved 0.625 lives [95%CI: 0.369–0.881]. Cumulatively Global Fund investments that increased ITN/IRS coverage in 2002–2008 prevented an estimated 240,000 deaths. Countries with higher malaria burden received less ODA disbursement per person-at-risk compared to lower-burden countries ($3.90 vs. $7.05). Increased ITN/IRS coverage in high-burden countries led to 3,575 lives saved per 1 million children, as compared with 914 lives in lower-burden countries. Impact of ITN/IRS coverage on under-five mortality was significant among major child health interventions such as immunisation showing that 10% increase in households with ITN/IRS would reduce 1.5 [95%CI: 0.3–2.8] child deaths per 1000 live births. Conclusions Along with other key child survival interventions, increased ITNs/IRS coverage has significantly contributed to child mortality reduction since 2002. ITN/IRS scale-up can be more efficiently prioritized to countries where malaria is a major cause of child deaths to save greater number of lives with available resources.
Children's Attentional Biases and 5-HTTLPR Genotype: Potential Mechanisms Linking Mother and Child Depression

In this study, we examined the roles of specific cognitive (attentional bias) and genetic (5-HTTLPR) risk factors in the intergenerational transmission of depression. Focusing first on the link between maternal history of major depressive disorder (MDD) and children's attentional biases, we found that children of mothers with a history of MDD during their children's lives, compared to children of mothers with no depression history, exhibited greater attentional avoidance of sad faces. This attention bias was specific to sad, rather than happy or angry, faces. There was also preliminary evidence that this relation is stronger among children carrying the 5-HTTLPR S or LG allele than among those homozygous for the LA allele. Next, conceptualizing mothers' levels of depressive symptoms during the multi-wave prospective follow-up within a vulnerability-stress framework, we found evidence for a three-way child 5-HTTLPR × attentional bias × mother depressive symptom interaction predicting children's depressive symptoms. Specifically, the relation between mother and child depressive symptom levels over time was strongest among children carrying the 5-HTTLR S or LG allele who also exhibited attentional avoidance of sad faces. These findings provide initial support for role of children's 5-HTTLPR genotype and attentional biases for sad faces in the intergenerational transmission of depression.
Apprehensive QoS monitoring of Service choreographies

Service choreographies specify the intended interaction protocol among a set of cooperating services at the business application level. For end-users the non-functional properties exposed by a choreographed service composition can be as important as its functional behaviour, if not even more. Therefore, in any choreography development process, the capability of specifying and assessing the established Service Level Agreements (SLAs) becomes a crucial requisite. However, by their very nature, choreography requirements can be quite abstract and may on purpose avoid formalizing non-functional properties for every step of each individual service, nonetheless the overall QoS choreography will be affected by them. In this paper, we propose a monitor enhanced with the capability to detect potential deviations from a choreography-prescribed QoS level, based on the observed non-functional behaviour of the contributing services. Such an apprehensive monitor, as we call it, can thus contribute to predict SLA violations in due time for taking useful counter-measures, and not only detect them after they have occurred. We illustrate the feasibility of the approach on a use-case from the European Project CHOReOS.
Pancreatic extragastrointestinal stromal tumors, interstitial Cajal like cells, and telocytes.

CONTEXT The discovery and subsequent ultrastructural characterization of the interstitial Cajal like cells (now called telocytes) in virtually every anatomic sites of the human body, by Laurentiu M Popescu and co-workers, have dramatically improved the understanding the function of these cells and pathogenesis of extragastrointestinal stromal tumors (EGIST). Pancreatic extragastrointestinal stromal tumors (pEGIST), phenotypically similar to pancreatic interstitial Cajal like cells, are extremely rare with an unpredictable biological behavior. OBJECTIVE To review the clinicopathological, radiological, immunohistochemical, and therapeutic outcome data of all reported cases of pEGIST, and highlight the developments in the field of pancreatic interstitial Cajal like cells/telocytes. METHODS A systematic review of English literature (January 2000 to July 2012) was done by using the search engine of PubMed, PubMed Central, Google Scholar, and the Directory of Open Access Journals. RESULTS There have been 19 reported cases of pEGIST during the last decade, over an age range of 31 to 84 years (mean: 56 years) with equal gender predilection ((male:female ratio: 9:10). Preoperative radiological characteristics have been mostly nondiagnostic though these were used, in some, for tissue diagnosis. Majority of pEGIST were localized to pancreatic head (8/19, 42.1%), and 15 of 19 patients (78.9%) were symptomatic at first presentation. The mean size ranged from 2.5 to 35cm (mean: 14 cm). Histomorphological features were that of predominantly spindle cell tumor which consistently expressed c-KIT/CD117 and CD34 by immunohistochemistry, making these two as the most sensitive markers at this site. RESULTS from studies involving discovery on gastrointestinal stromal tumor 1 (DOG-1), the most specific biomarker of GIST/EGIST, has been inconclusive and this was found to be positive in one case only. Neoadjuvant chemotherapy with imatinib mesylate and sunitinib were used in few cases, and genetic analysis of c-KIT proto-oncogene was done in two. By univariate analysis, none of the clinicopathological parameters, except surgical resection with microscopic free margin (R0 resection) (P<0.05), were found to be an important indicators of outcome. CONCLUSION The biological behavior of pEGIST, at present, seems unpredictable which requires indefinite period of follow-up. Large number of such cases with genetic analysis supplemented with immunohistochemistry studies will hopefully throw more light in these tumors.