Miracle-dz/UniFAR-FTUs huggingface dataset:
P53 and Cancer-Associated Sialylated Glycans Are Surrogate Markers of Cancerization of the Bladder Associated with Schistosoma haematobium Infection

Background Bladder cancer is a significant health problem in rural areas of Africa and the Middle East where Schistosoma haematobium is prevalent, supporting an association between malignant transformation and infection by this blood fluke. Nevertheless, the molecular mechanisms linking these events are poorly understood. Bladder cancers in infected populations are generally diagnosed at a late stage since there is a lack of non-invasive diagnostic tools, hence enforcing the need for early carcinogenesis markers. Methodology/Principal Findings Forty-three formalin-fixed paraffin-embedded bladder biopsies of S. haematobium-infected patients, consisting of bladder tumours, tumour adjacent mucosa and pre-malignant/malignant urothelial lesions, were screened for bladder cancer biomarkers. These included the oncoprotein p53, the tumour proliferation rate (Ki-67>17%), cell-surface cancer-associated glycan sialyl-Tn (sTn) and sialyl-Lewisa/x (sLea/sLex), involved in immune escape and metastasis. Bladder tumours of non-S. haematobium etiology and normal urothelium were used as controls. S. haematobium-associated benign/pre-malignant lesions present alterations in p53 and sLex that were also found in bladder tumors. Similar results were observed in non-S. haematobium associated tumours, irrespectively of their histological nature, denoting some common molecular pathways. In addition, most benign/pre-malignant lesions also expressed sLea. However, proliferative phenotypes were more prevalent in lesions adjacent to bladder tumors while sLea was characteristic of sole benign/pre-malignant lesions, suggesting it may be a biomarker of early carcionogenesis associated with the parasite. A correlation was observed between the frequency of the biomarkers in the tumor and adjacent mucosa, with the exception of Ki-67. Most S. haematobium eggs embedded in the urothelium were also positive for sLea and sLex. Reinforcing the pathologic nature of the studied biomarkers, none was observed in the healthy urothelium. Conclusion/Significance This preliminary study suggests that p53 and sialylated glycans are surrogate biomarkers of bladder cancerization associated with S. haematobium, highlighting a missing link between infection and cancer development. Eggs of S. haematobium express sLea and sLex antigens in mimicry of human leukocytes glycosylation, which may play a role in the colonization and disease dissemination. These observations may help the early identification of infected patients at a higher risk of developing bladder cancer and guide the future development of non-invasive diagnostic tests.
Accurate Identification of Ortholog Groups among Multiple Genomes

The identification of orthologous genes shared by multiple genomes plays an important role in evolutionary studies and gene functional analyses. Based on a recently developed accurate tool, called MSOAR 2.0, for ortholog assignment between a pair of closely related genomes based on genome rearrangement, we present a new system MultiMSOAR 2.0, to identify ortholog groups among multiple genomes in this paper. In the system, we construct gene families for all the genomes using sequence similarity search and clustering, run MSOAR 2.0 for all pairs of genomes to obtain the pairwise orthology relationship, and partition each gene family into a set of disjoint sets of orthologous genes (called super ortholog groups or SOGs) such that each SOG contains at most one gene from each genome. For each such SOG, we label the leaves of the species tree using 1 or 0 to indicate if the SOG contains a gene from the corresponding species or not. The resulting tree is called a tree of ortholog groups (or TOGs). We then label the internal nodes of each TOG based on the parsimony principle and some biological constraints. Ortholog groups are finally identified from each fully labeled TOG. In comparison with a popular tool MultiParanoid on simulated data, MultiMSOAR 2.0 shows significantly higher prediction accuracy. It also outperforms MultiParanoid and the Roundup multi-ortholog repository in real data experiments using gene symbols as a validation tool. In addition to ortholog group identification, MultiMSOAR 2.0 also provides information about gene births, duplications and losses in evolution, which may be of independent biological interest.
Reengineering the Feature Distillation Process: A case study in detection of Gaming the System

As education technology matures, researches debate whether data mining (EDM) or knowledge engineering (KE) paradigms are best for modeling complex learning constructs. A hybrid paradigm may capture strengths from both approaches. In particular, recent work has argued that successful data mining depends on thoughtful feature engineering. In this paper, we explore the use of cognitive modeling (a form of knowledge engineering) to enhance the feature engineering process for detectors of gaming the system, one of the most studied complex constructs in EDM. Using this construct enables us to measure the extent to which our techniques improve performance over previous models.
Path sharing and predicate evaluation for high-performance XML filtering

XML filtering systems aim to provide fast, on-the-fly matching of XML-encoded data to large numbers of query specifications containing constraints on both structure and content. It is now well accepted that approaches using event-based parsing and Finite State Machines (FSMs) can provide the basis for highly scalable structure-oriented XML filtering systems. The XFilter system [Altinel and Franklin 2000] was the first published FSM-based XML filtering approach. XFilter used a separate FSM per path query and a novel indexing mechanism to allow all of the FSMs to be executed simultaneously during the processing of a document. Building on the insights of the XFilter work, we describe a new method, called "YFilter" that combines all of the path queries into a single Nondeterministic Finite Automaton (NFA). YFilter exploits commonality among queries by merging common prefixes of the query paths such that they are processed at most once. The resulting shared processing provides tremendous improvements in structure matching performance but complicates the handling of value-based predicates.In this article, we first describe the XFilter and YFilter approaches and present results of a detailed performance comparison of structure matching for these algorithms as well as a hybrid approach. The results show that the path sharing employed by YFilter can provide order-of-magnitude performance benefits. We then propose two alternative techniques for extending YFilter's shared structure matching with support for value-based predicates, and compare the performance of these two techniques. The results of this latter study demonstrate some key differences between shared XML filtering and traditional database query processing. Finally, we describe how the YFilter approach is extended to handle more complicated queries containing nested path expressions.
How to attain the ordinary channel capacity securely in wiretap channels

It is known that a message can be transmitted safely against any wiretap per via a noisy channel without a secret key if the coding rate is less than the so-called secrecy capacity Cs, which is usually smaller than the channel capacity C. In order to remove the loss C - Cs, we propose a multiplex coding scheme with plural independent messages. In this paper, it is shown that the proposed multiplex coding scheme can attain the channel capacity as the total rate of the plural messages and the perfect secrecy for each message. The coding theorem is proved by extending Hayashi's proof, in which the coding of the channel resolvability is applied to the wiretap channel
The Role and Reprocessing of Attitudes in Fostering Employee Work Happiness: An Intervention Study

This intervention study examines the iterative reprocessing of explicit and implicit attitudes as the process underlying associations between positive employee attitudes (PsyCap), perception of positive organization culture (organizational virtuousness, OV), and work happiness. Using a quasi-experimental design, a group of school staff (N = 69) completed surveys at three time points. After the first assessment, the treatment group (n = 51) completed a positive psychology training intervention. Results suggest that employee PsyCap, OV, and work happiness are associated with one another through both implicit and explicit attitudes. Further, the Iterative-Reprocessing Model of attitudes (IRM) provides some insights into the processes underlying these associations. By examining the role and processes through which explicit and implicit attitudes relate to wellbeing at work, the study integrates theories on attitudes, positive organizational scholarship, positive organizational behavior and positive education. It is one of the first studies to apply the theory of the IRM to explain associations amongst PsyCap, OV and work happiness, and to test the IRM theory in a field-based setting. In applying attitude theory to wellbeing research, this study provides insights to mechanisms underlying workplace wellbeing that have not been previously examined and in doing so responds to calls for researchers to learn more about the mechanisms underlying wellbeing interventions. Further, it highlights the need to understand subconscious processes in future wellbeing research and to include implicit measures in positive psychology interventions measurement programs. Practically, this research calls attention to the importance of developing both the positive attitudes of employees and the organizational culture in developing employee work happiness.
Non-Physical Forms of Intimate Partner Violence in Lesbian Relationships

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Predicting the accuracy of multiple sequence alignment algorithms by using computational intelligent techniques

Multiple sequence alignments (MSAs) have become one of the most studied approaches in bioinformatics to perform other outstanding tasks such as structure prediction, biological function analysis or next-generation sequencing. However, current MSA algorithms do not always provide consistent solutions, since alignments become increasingly difficult when dealing with low similarity sequences. As widely known, these algorithms directly depend on specific features of the sequences, causing relevant influence on the alignment accuracy. Many MSA tools have been recently designed but it is not possible to know in advance which one is the most suitable for a particular set of sequences. In this work, we analyze some of the most used algorithms presented in the bibliography and their dependences on several features. A novel intelligent algorithm based on least square support vector machine is then developed to predict how accurate each alignment could be, depending on its analyzed features. This algorithm is performed with a dataset of 2180 MSAs. The proposed system first estimates the accuracy of possible alignments. The most promising methodologies are then selected in order to align each set of sequences. Since only one selected algorithm is run, the computational time is not excessively increased.
Vector Space Models for Phrase-based Machine Translation

This paper investigates the application of vector space models (VSMs) to the standard phrase-based machine translation pipeline. VSMs are models based on continuous word representations embedded in a vector space. We exploit word vectors to augment the phrase table with new inferred phrase pairs. This helps reduce out-of-vocabulary (OOV) words. In addition, we present a simple way to learn bilingually-constrained phrase vectors. The phrase vectors are then used to provide additional scoring of phrase pairs, which fits into the standard log-linear framework of phrase-based statistical machine translation. Both methods result in significant improvements over a competitive in-domain baseline applied to the Arabic-to-English task of IWSLT 2013.
A Low Noise Sub-Sampling PLL in Which Divider Noise is Eliminated and PD/CP Noise is Not Multiplied by  $N ^{2}$

This paper presents a 2.2-GHz low jitter sub-sampling based PLL. It uses a phase-detector/charge-pump (PD/CP) that sub-samples the VCO output with the reference clock. In contrast to what happens in a classical PLL, the PD/CP noise is not multiplied by N 2 in this sub-sampling PLL, resulting in a low noise contribution from the PD/CP. Moreover, no frequency divider is needed in the locked state and hence divider noise and power can be eliminated. An added frequency locked loop guarantees correct frequency locking without degenerating jitter performance when in lock. The PLL is implemented in a standard 0.18- ¿m CMOS process. It consumes 4.2 mA from a 1.8 V supply and occupies an active area of 0.4 × 0.45 mm2. With a frequency division ratio of 40, the in-band phase noise at 200 kHz offset is measured to be -126 dBc/Hz. The rms PLL output jitter integrated from 10 kHz to 40 MHz is 0.15 ps.
Effects of dietary 1,4-phenylenebis(methylene)selenocyanate on 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone-induced DNA adduct formation in lung and liver of A/J mice and F344 rats.

1,4-Phenylenebis(methylene)selenocyanate (p-XSC) was tested for its ability to inhibit DNA adduct formation induced by the tobacco-specific N-nitrosamine 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) in the liver and lung of A/J mice and F344 rats. Dietary p-XSC, providing a dose of 5 p.p.m. selenium, significantly inhibited the formation of 7-methylguanine (7-mGua) induced by a single i.p. injection of 10 mumol of NNK(12.8% inhibition at 4 h and 19.9% at 96 h) and O6-methylguanine (O6-mGua) (16.5% at 4 h and 34.8% at 96 h) in the liver of A/J mice. Dietary supplements of p-XSC providing 15 p.p.m. of selenium reduced the levels of 7-mGua by 17.3% (4 h) and 33.6% (96 h). The formation of O6-mGua was inhibited by 69.5% (4th) and 73.8 (96h). In A/J mouse lung DNA the most significant reduction was observed in levels of O6-mGua. Dietary p-XSC at 5 p.p.m. as selenium inhibited the formation of this adduct by 73.1% (4 h). Ninety-six hours after NNK injection, and at both time points with p-XSC providing 15 p.p.m. selenium, O6-mGua was not detected. Although levels of 7- mGua in mouse lung DNA were also reduced, this was significant only 4 h after carcinogen administration. In general, selenite at a5 p.p.m. as selenium had no significant effect on the levels of these lesions; however, it inhibited O6-mGua in the liver only 4 h after NNK administration. These effects may explain why there is chemopreventive activity for p-XSC, but not for selenite, in NNK-induced lung carcinogenesis in A/J mice. Moreover, these findings raised our interest in determining the potential chemopreventive activity of p-XSC against NNK-induced lung adenocarcinomas in male F344 rats by first determining its effects on NNK-induced DNA methylation in the lungs of rats. Diet supplemented with 10 p.p.m. selenium as p-XSC did indeed inhibit the formation of adducts in pulmonary DNA of F344 rats treated with four consecutive injections of 81 mg/kg of NNK. Statistically significant inhibition of O6-mGua formation was observed 4 h after carcinogen treatment in both pulmonary (49.1% inhibition) and hepatic (39.8%) DNA. Statistically significant inhibition of 7-mGua formation was also measured in lung DNA isolated 24 h after the last NNK injection (45.0%) and in liver DNA 4 h after carcinogen treatment (31.8%). These results suggest that p-XSC would also inhibit induction of lung adenocarcinoma in male F344 rats by NNK.
Monoclonal Leukocyte Antibody Does Not Decrease the Injury of Transient Focal Cerebral Ischemia in Cats

We tested the hypothesis that inhibition of leukocyte function by administration of monoclonal antibody 60.3 (MoAb 60.3) improves electrophysiological recovery and decreases injury volume following transient focal cerebral ischemia in cats. Methods Halothane-anesthetized cats underwent 90 minutes of left middle cerebral artery and bilateral common carotid artery occlusion followed by 180 minutes of reperfusion. Cats were assigned to receive either 2 mg/kg MoAb 60.3 (n=8) directed at the CDw18 leukocyte antigen complex or an equal volume of diluent (sterile saline; n=10) at 45 minutes of ischemia in a blinded fashion. Results Blood flow to the left temporoparietal cortex decreased to <5 ml/min/100 g with ischemia, but was minimally affected on the right side. Postischemic hyperemia occurred in the left caudate nucleus, whereas blood flow in other brain regions returned to control. No region demonstrated delayed hypoperfusion, and there were no differences between groups. Somatosensory evoked potential recorded over the left cortex was ablated during ischemia and recovered to <10% of baseline amplitude at 180 minutes of reperfusion in both groups. Left hemispheric injury volume, as assessed by 2,3,5 -triphenyltetrazolium chloride staining, was not affected by drug treatment (mean±SE values: MoAb 60.3, 37±5%; placebo, 38±7% of hemisphere). Conclusions Inhibition of leukocyte function with MoAb 60.3 does not afford protection from severe focal ischemia and reperfusion in cats.
Generalised Sphere Decoding for Spatial Modulation

In this paper, Sphere Decoding (SD) algorithms for Spatial Modulation (SM) are developed to reduce the computational complexity of Maximum-Likelihood (ML) detectors. Two SDs specifically designed for SM are proposed and analysed in terms of Bit Error Ratio (BER) and computational complexity. Using Monte Carlo simulations and mathematical analysis, it is shown that by carefully choosing the initial radius the proposed sphere decoder algorithms offer the same BER as ML detection, with a significant reduction in the computational complexity. A tight closed form expression for the BER performance of SM-SD is derived in the paper, along with an algorithm for choosing the initial radius which provides near to optimum performance. Also, it is shown that none of the proposed SDs are always superior to the others, but the best SD to use depends on the target spectral efficiency. The computational complexity trade-off offered by the proposed solutions is studied via analysis and simulation, and is shown to validate our findings. Finally, the performance of SM-SDs are compared to Spatial Multiplexing (SMX) applying ML decoder and applying SD. It is shown that for the same spectral efficiency, SM-SD offers up to 84% reduction in complexity compared to SMX-SD, with up to 1 dB better BER performance than SMX-ML decoder.
Effect of Angiotensin II on the Left Ventricular Function in a Near-Term Fetal Sheep with Metabolic Acidemia

We tested the hypothesis that, in acute metabolic acidemia, the fetal left ventricle (LV) has the capacity to increase its contractility in response to angiotensin II infusion. Eleven ewes and their fetuses were instrumented at 127–138/145 days of gestation. The effect of angiotensin II on fetal LV function was assessed using intraventricular pressure catheter and tissue Doppler imaging (TDI). Angiotensin II increased fetal arterial blood pressure, whereas pH and pO2 decreased. The heart rate and systemic venous pressure were not affected significantly. The LV end-diastolic and end-systolic pressures, as well as dP/dtmax, increased. The TDI-derived LV longitudinal myocardial isovolumic contraction velocity and its acceleration and velocity during early filling were higher than those at baseline. The incidence of absent isovolumic relaxation velocity was greater during angiotensin II infusion. In summary, during acute metabolic acidemia, the fetal left ventricle could increase its contractility in response to inotropic stimulus even in the presence of increased afterload. The diastolic LV function parameters were altered by angiotensin II.
Cecal microbiota of Tibetan Chickens from five geographic regions were determined by 16S rRNA sequencing

Tibetan Chickens should have unique gastrointestinal microbiota because of their particular habitats. Thus, the aim of this study was to investigate the cecal microbiota of Tibetan Chickens from five typical high‐altitude regions of China. Lohmann egg‐laying hens (LMs) and Daheng broiler chickens (DHs) were chosen as controls. The cecal bacterial populations of Tibetan Chickens were surveyed by high‐throughput sequencing (HTS) of the bacterial 16S rRNA hypervariable region V3‐V4 (16S rRNAV3‐V4) combined with community‐fingerprinting analysis of the 16S rRNA gene based on polymerase chain reaction‐denaturing gradient gel electrophoresis (PCR‐DGGE). The results revealed that the majority of cecal microbiota differed between the Tibetan Chicken and LM/DH. The microbial communities in the cecum were composed of 16 phyla, 28 classes, 36 orders, 57 families, 101 genera, and 189 species. Represented phyla were Bacteroidetes (>47%), Firmicutes (>18.8%), Spirochaetae (>0.3%), and Proteobacteria (>0.4%). Bacteroides and the RC9 gut group were the two most abundant genera. There were relatively more Christensenellaceae, Subdoligranulum, Spirochaeta, and Treponema in Tibetan Chickens, whereas there were more Phascolarctobacterium, Faecalibacterium, Megamonas, and Desulfovibrio in LMs and DHs. The cecal microbiota of Tibetan Chicken have slightly diverged due to exposure to different geographic environments. Differences in the intestinal bacterial communities of Tibetan Chicken and LM/DH were noted.
Association of Childhood Autism Spectrum Disorders and Loss of Family Income

BACKGROUND. Parents of children with autism have significant out-of-pocket expenditures related to their child's care. The impact of having a child with autism on household income is not known. OBJECTIVE. The purpose of this work was to estimate the loss of household income associated with childhood autism using a nationally representative sample. METHODS. Parents of 11684 children enrolled in kindergarten to eighth grade were surveyed by the National Household Education Survey-After School Programs and Activities in 2005. An autism spectrum disorder was defined as an affirmative response to the questions, “has a health professional told you that [child] has any of the following disabilities? 1) autism? 2) pervasive developmental disorder or PDD? ” There were 131 children with autism spectrum disorder in the sample and 2775 children with other disabilities. We used ordinal logistic regression analyses to estimate the expected income of families of children with autism given their education level and demographic characteristics and compared the expected income with their reported income. RESULTS. Both having a child with autism spectrum disorder and having a child with other disabilities were associated with decreased odds of living in a higher income household after controlling for parental education, type of family, parental age, location of the household, and minority ethnicity. The average loss of annual income associated with having a child with autism spectrum disorder was $6200 or 14% of their reported income. CONCLUSION. Childhood autism is associated with a substantial loss of annual household income. This likely places a significant burden on families in the face of additional out-of-pocket expenditures.