Miracle-dz/UniFAR-FTUs huggingface dataset:
The Human RNA Polymerase II-Associated Factor 1 (hPaf1): A New Regulator of Cell-Cycle Progression

Background The human PAF (hPAF) complex is part of the RNA polymerase II transcription apparatus and regulates multiple steps in gene expression. Further, the yeast homolog of hPaf1 has a role in regulating the expression of a subset of genes involved in the cell-cycle. We therefore investigated the role of hPaf1 during progression of the cell-cycle. Methodology/Findings Herein, we report that the expression of hPaf1, a subunit of the hPAF complex, increases with cell-cycle progression and is regulated in a cell-cycle dependant manner. hPaf1 specifically regulates a subclass of genes directly implicated in cell-cycle progression during G1/S, S/G2, and G2/M. In prophase, hPaf1 aligns in filament-like structures, whereas in metaphase it is present within the pole forming a crown-like structure, surrounding the centrosomes. Moreover, hPaf1 is degraded during the metaphase to anaphase transition. In the nucleus, hPaf1 regulates the expression of cyclins A1, A2, D1, E1, B1, and Cdk1. In addition, expression of hPaf1 delays DNA replication but favors the G2/M transition, in part through microtubule assembly and mitotic spindle formation. Conclusion/Significance Our results identify hPaf1 and the hPAF complex as key regulators of cell-cycle progression. Mutation or loss of stoichiometry of at least one of the members may potentially lead to cancer development.
Human MR 1-Restricted ProcessingTools To Study Microbial Antigen System : MR 1 with a CRISPR / Cas 9 Lentiviral Engineering of Isogenic Cells Deficient for Lewinsohn and

The nonclassical HLA molecule MHC-related protein 1 (MR1) presents metabolites of the vitamin B synthesis pathways to mucosal-associated invariant T (MAIT) cells and other MR1-restricted T cells. This new class of Ags represents a variation on the classical paradigm of self/non-self discrimination because these T cells are activated through their TCR by small organic compounds generated during microbial vitamin B 2 synthesis. Beyond the fundamental significance, the invariant nature of MR1 across the human population is a tantalizing feature for the potential development of universal immune therapeutic and diagnostic tools. However, many aspects of MR1 Ag presentation and MR1-restricted T cell biology remain unknown, and the ubiquitous expression of MR1 across tissues and cell lines can be a confounding factor for experimental purposes. In this study, we report the development of a novel CRISPR/Cas9 genome editing lentiviral system and its use to efficiently disrupt MR1 expression in A459, THP-1, and K562 cell lines. We generated isogenic MR1 2/2 clonal derivatives of the A549 lung carcinoma and THP-1 monocytic cell lines and used these to study T cell responses to intracellular pathogens. We confirmed that MAIT cell clones were unable to respond to MR1 2/2 clones infected with bacteria whereas Ag presentation by classical and other nonclassical HLAs was unaffected. This system represents a robust and efficient method to disrupt the expression of MR1 and should facilitate investigations into the processing and presentation of MR1 Ags as well as into the biology of MAIT cells. M ucosal-associated invariant T (MAIT) cells are the most abundant nonconventional T cell subset, accounting for up to 5% of all T cells in humans, and are thought to be important for the control of a number of bacterial, fungal, and yeast infections (1–5). These so-called innate-like T cells, which are mostly found in the blood, the liver, and at mucosal surfaces, express a semi-invariant TCR consisting of an a-chain using the canonical TRAV1-2–TRAJ33/12/20 (Va7.2-Ja33/12/20) rearrangements (6). MAIT cells acquire effector functions during thymic selection and readily respond to Ags derived from many (but not all) bacteria such as Escherichia coli, Klebsiella pneu-moniae, Mycobacterium tuberculosis, or Staphylococcus epider-mis as well as several yeast species in the periphery without prior priming (3, 7). MAIT cell activation is mediated by the interaction between the TCR and microbe-derived Ags presented by the nonclassical MHC-related protein 1 (MR1) and results in the secretion of cytokines as well as in granzyme-and …
Increased sex chromosome expression and epigenetic abnormalities in spermatids from male mice with Y chromosome deletions

During male meiosis, the X and Y chromosomes are transcriptionally silenced, a process termed meiotic sex chromosome inactivation (MSCI). Recent studies have shown that the sex chromosomes remain substantially transcriptionally repressed after meiosis in round spermatids, but the mechanisms involved in this later repression are poorly understood. Mice with deletions of the Y chromosome long arm (MSYq–) have increased spermatid expression of multicopy X and Y genes, and so represent a model for studying post-meiotic sex chromosome repression. Here, we show that the increase in sex chromosome transcription in spermatids from MSYq– mice affects not only multicopy but also single-copy XY genes, as well as an X-linked reporter gene. This increase in transcription is accompanied by specific changes in the sex chromosome histone code, including almost complete loss of H4K8Ac and reduction of H3K9me3 and CBX1. Together, these data show that an MSYq gene regulates sex chromosome gene expression as well as chromatin remodelling in spermatids.
Structural, functional, and idiotypic characteristics of a phosphorylcholine-binding IgA myeloma protein of C57BL/ka allotype

An IgA phosphorylcholine (PC)-binding myeloma protein with IgCH allotypic determinants different from those of BALB/c mice is characterized. The myeloma, CBPC 2, was induced in the CB-20 strain of mice which is congenic to BALB/c but differs from it by carrying the A15 allotypic determinant of C57BL/ka mice. Sequence analysis of the CBPC 2 light chain through the first hypervariable region, as well as isoelectric point analysis, show that this chain is indistinguishable from that of T15, a PC-binding myeloma protein of BALB/c origin. The heavy chains of CBPC 2 and T15 differ by only two amino acids (positions 14 and 16) through the first hypervariable region. As measured by inhibition of precipitation, both CBPC 2 and T15 have the same specificity for PC, glycerophosphorylcholine, acetylcholine, and choline. In addition, CBPC 2 possesses the binding site-associated idiotypic determinant which is present on T15. However, like normal or induced C57BL/6 anti-PC antibody, it does not possess the nonbinding site idiotypic determinant.
A robust hashing of ID photos

The paper proposes an image hashing method that is highly robust to a series of currently encountered attacks on digital images. It is dedicated to images representing ID photos. The extraction of hash value is based on a global method for face recognition. Such approaches need a registration stage which is often obtained by means of face characteristic points. The detection of the characteristic points easily fails in the case of attacks like filtering, noise addition, random line deletion or jpg compression, mainly when they overcome certain limits. Our solution is to attach the characteristic points to the final hash, in order to obtain increased robustness to such attacks. The final hash is obtained by stabilizing an intermediary hash extracted by using Independent Component Analysis. The stabilization is done by clustering. The final hash is given by the cluster label having attached the coordinates of three characteristic points. We show that intermediate hashes of the attacked image approximate a hyper-sphere centered on the original image hash. Due to this fact, the minimization of a cost function representing the proximity to original hashes is sufficient to stabilize the intermediate hashes. We also evaluate the system capacity by estimating the number of freedom degrees for the intermediate hashes of the non-attacked ID photos.
ZeroTrace : Oblivious Memory Primitives from Intel SGX

—We are witnessing a conﬂuence between applied cryptography and secure hardware systems in enabling secure cloud computing. On one hand, work in applied cryptography has enabled efﬁcient, oblivious data-structures and memory primitives. On the other, secure hardware and the emergence of Intel SGX has enabled a low-overhead and mass market mechanism for isolated execution. By themselves these technologies have their disadvantages. Oblivious memory primitives carry high performance overheads, especially when run non-interactively. Intel SGX, while more efﬁcient, suffers from numerous software-based side-channel attacks, high context switching costs, and bounded memory size. In this work we build a new library of oblivious memory primitives, which we call ZeroTrace . ZeroTrace is designed to carefully combine state-of-the-art oblivious RAM techniques and SGX, while mitigating individual disadvantages of these technologies. To the best of our knowledge, ZeroTrace represents the ﬁrst oblivious memory primitives running on a real secure hardware platform. ZeroTrace simultaneously enables a dramatic speed-up over pure cryptography and protection from software-based side-channel attacks. The core of our design is an efﬁcient and ﬂexible block-level memory controller that provides oblivious execution against any active software adversary, and across asynchronous SGX enclave terminations. Performance-wise, the memory controller can service requests for 4 B blocks in 1.2 ms and 1 KB blocks in 3.4 ms (given a 10 GB dataset). On top of our memory controller, we evaluate Set/Dictionary/List interfaces which can all perform basic operations (e.g., get/put/insert).
AKI complications in critically ill patients: association with mortality rates and RRT.

BACKGROUND AND OBJECTIVES AKI is associated with short- and long-term mortality. However, the exact contribution of AKI complications to the burden of mortality and whether RRT has any beneficial effect on reducing mortality rates in critically ill AKI patients are unknown. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS This was a retrospective analysis using data from the Multiparameter Intelligent Monitoring in Intensive Care II project. A total of 18,410 adult patients were enrolled from four intensive care units from a university hospital from 2001 to 2008. RESULTS Overall, 10,245 patients developed AKI. After adjustments, the odds ratios (ORs) for hospital mortality were 1.73 (95% confidence interval [95% CI], 1.52 to 1.98) for AKI stage 1, 1.88 (95% CI, 1.57 to 2.25) for stage 2, and 2.89 (95% CI, 2.41 to 3.46) for stage 3. Totals of 33%, 59%, and 70% of the excess mortality rates associated with AKI stages 1, 2, and 3, respectively, were attenuated by the inclusion of each AKI-related complication in the model. The main burden of excess hospital mortality associated with AKI was attenuated by metabolic acidosis and cumulative fluid balance. Long-term mortality was not attenuated by any of the associated complications. Next, we used two different approaches to explore the associations between RRT, AKI complications, and hospital mortality: multivariate analysis and propensity score matching. In both approaches, the sensitivity analysis for RRT was associated with a better hospital survival in only the following AKI-related subgroups: hyperkalemia (OR, 0.55; 95% CI, 0.35 to 0.85), metabolic acidosis (OR, 0.70; 95% CI, 0.53 to 0.92), cumulative fluid balance >5% of body weight (OR, 0.60; 95% CI, 0.40 to 0.88), and azotemia (OR, 0.57; 95% CI, 0.40 to 0.81). CONCLUSIONS A majority of the excess risk of mortality associated with AKI was attenuated by its fluid volume and metabolic complications, particularly in severe AKI. In addition, this study demonstrated that RRT is associated with a better outcome in patients with AKI-related complications.
Axillary Lymph Node Status and Prognosis in Multifocal and Multicentric Breast Carcinoma

According to tumor‐node‐metastasis classification, tumor size should be based only on the largest tumor for multifocal and multicentric (MFMC) carcinomas. We estimated tumor size of MFMC carcinoma using either largest dimension of the largest tumor (dominant tumor size) or sum of the largest dimension of all tumors (aggregate tumor size), and compared the risk of axillary lymph node metastasis and prognosis between MFMC and unifocal carcinoma. We retrospectively reviewed the file records of 3,616 patients with MFMC (258 patients, 7.1%) and unifocal (3,358 patients) carcinoma. In T1 and T2 tumor subgroups, using dominant (p = 0.001 and p < 0.001) and aggregate (p = 0.017 and p = 0.004) tumor size axilla‐positivity ratio was significantly higher in MFMC carcinoma compared with unifocal carcinoma. In stage I and II disease classified according to either dominant or aggregate tumor size, there was no significant survival difference between MFMC and unifocal carcinoma patients. In patients with stage III disease by dominant and aggregate tumor size disease‐free survival was significantly worse in MFMC carcinoma compared with unifocal carcinoma (p = 0.036 and p = 0.041); multifocality and multicentricity had no independent prognostic significance (p = 0.074 and p = 0.079). The risk of axillary metastasis in MFMC carcinoma was higher than unifocal carcinoma, regardless of the method employed for tumor size estimation. MFMC carcinoma staged according to either dominant or aggregate tumor size had similar survival with unifocal carcinoma. We recommend using the largest dimension of the largest tumor in estimation of tumor size for MFMC carcinoma.
Mid-term haemodynamic and clinical results after aortic valve replacement using the Freedom Solo stentless bioprosthesis versus the Carpentier Edwards Perimount stented bioprosthesis.

OBJECTIVES The aim of this study was to investigate the mid-term haemodynamic and clinical results after aortic valve replacement (AVR) using the Sorin Freedom Solo (SFS) stentless bioprosthesis, compared with the standard Carpentier Edwards Perimount (CEP) stented bioprosthesis. METHODS In this retrospective cohort study of prospectively collected data, 116 patients were included in the SFS group (53 males; median age 74 years, range 56-85 years), and 122 patients in the CEP group (85 males; median age 73 years, range 43-88 years) between July 2007 and January 2013. Echocardiography was performed at 6 weeks after surgery in our centre, and the most recent echocardiography (in our centre or in referring cardiology departments) was requested. Between September 2013 and April 2014, all patients were called by the same researcher to gain clinical follow-up data. RESULTS Mid-term mortality was 16.4% in the SFS group (19 patients) and 21.3% in the CEP group (26 patients); (P = 0.3). The mean transvalvular gradient was 7.4 ± 3.1 mmHg in the SFS group, and 11.6 ± 3.2 mmHg in the CEP group at 6 weeks postoperatively (P < 0.001). When stratified by labelled valve size, mean gradients were significantly lower in the SFS group for every size (P ≤ 0.03). After 3.3 ± 1.4 years of follow-up, the mean gradient was still significantly lower in the SFS group than that in the CEP group (P < 0.001). Clinical follow-up showed relatively low complication rates. CONCLUSION These data suggest that the Sorin Freedom Solo stentless bioprosthesis is as safe as the Carpentier Edwards bioprosthesis, and provides better short- and mid-term haemodynamic performance than the Carpentier Edwards bioprosthesis.
Demographics for Segmentation in Online Travel

—The relationship between various demographics and online leisure travel booking intention was investigated yielding some interesting results. Consequently, this study recommends these demographic variables be considered in segmenting travelers to find those more likely to book online. Spearman correlation analysis and the Kruskal-Wallis test revealed insights on the demographic data that are valuable for targeting leisure travelers in the online marketplace.
On the (Non-)Equivalence of IRR and NPV

The internal rate of return (IRR) is generally considered inferior to the net present value (NPV) as a tool for evaluating and ranking projects, despite its inherently useful comparability to the cost of capital and the return of other investment opportunities. We introduce the “selective IRR”, a return criterion which, as a selection of an extended set of possible IRRs, is NPV-consistent. The selective IRR always exists, is unique, easy to compute, and does not suffer from drawbacks that befall the project investment rate, the only other known NPV-consistent return criterion.
Feature selection for clustering categorical data with an embedded modelling approach

Research on the problem of feature selection for clustering continues to develop. This is a challenging task, mainly due to the absence of class labels to guide the search for relevant features. Categorical feature selection for clustering has rarely been addressed in the literature, with most of the proposed approaches having focused on numerical data. In this work, we propose an approach to simultaneously cluster categorical data and select a subset of relevant features. Our approach is based on a modification of a finite mixture model (of multinomial distributions), where a set of latent variables indicate the relevance of each feature. To estimate the model parameters, we implement a variant of the expectation‐maximization algorithm that simultaneously selects the subset of relevant features, using a minimum message length criterion. The proposed approach compares favourably with two baseline methods: a filter based on an entropy measure and a wrapper based on mutual information. The results obtained on synthetic data illustrate the ability of the proposed expectation‐maximization method to recover ground truth. An application to real data, referred to official statistics, shows its usefulness.
The Trouble with Machine Translation Coherence

This paper introduces the problem of measuring coherence in Machine Translation. Previously, local coherence has been assessed in a monolingual context using essentially coherent texts. These are then artiﬁcially shufﬂed to create an incoherent one. We investigate existing models for the task of measuring the coherence of machine translation output. This is a much more challenging case where coherent source documents are machine translated into a target language and the task is to distinguish them from their human translated counterparts. We benchmark state-of-the-art coherence models, and propose a new model which explores syntax following a more principled method to learn the syntactic patterns. This extension outperforms existing ones in the monolingual shufﬂing task on news data, and performs well in our new, more challenging task. Additionally, we show that breaches in coherence in the translation task are much more difﬁcult to capture by any model.
Immunopathology and Infectious Diseases Osteopontin Mediates Citrobacter rodentium-Induced Colonic Epithelial Cell Hyperplasia and Attaching-Effacing Lesions

From Pediatric Gastroenterology,* University of Alberta, Edmonton, Alberta, Canada; the Research Institute, Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada; the Canadian Institutes of Health Research Group in Skeletal Development and Remodeling, School of Dentistry, University of Western Ontario, London, Ontario, Canada; and the Department of Molecular Biology, University of Aarhus, Denmark
Dual band dual polarized frequency reconfigurable antenna using meta-surface

A frequency re-configurable dual band dual polarized antenna is proposed. This consists of a rectangular feed patch layer and two MS layers of same thickness. MS layers are made of rectangular loop based unit cells periodically placed in both X and Y direction. The total profile of the antenna is 0.07 λ0 only. Simulation result shows that the operating frequency of the antenna can be changed by physically rotating both the MS layers with respect to the centre of the patch antenna. As the MS is rotated the excitation and the polarization with the electric field of the patch to the MS layers change which changes the effective permittivity of the whole substrate and hence the frequency of the operation also changes. Measured results are well matched with the simulation results. At all the frequencies antenna has peak gain of more than 5.5 dB and the minimum efficiency is more than 89%.
Protocol testing: review of methods and relevance for software testing

Communication protocols are the rules that govern the communication between the different components within a distributed computer system. Since protocols are implemented in software and/or hardware, the question arises whether the existing hardware and software testing methods would be adequate for the testing of communication protocols. The purpose of this paper is to explain in which way the problem of testing protocol implementations is different from the usual problem of software testing. We review the major results in the area of protocol testing and discuss in which way these methods may also be relevant in the more general context of software testing.
The face detection algorithm based on local elastic potential energy feature

Face detection is an important step in face recognition. Ineffective algorithm used for face detection will have a negative impact on the performance of face recognition. Face detection technology is not only a key step in face recognition technology, but also is an independent widely-used technology. It is important to design a suitable feature for face detection technology. This paper proposes a new face feature, which can be used in face detection. The face feature has the property of rotation and scaling invariant under some certain conditions. The algorithm regards an image as an elastic surface and regards the grey level as deformation. The algorithm calculates local elastic potential vectors and uses them as the input to the adaboost classifier. The output of the classifier is the final result. Theoretical analysis and experiments demonstrate that the feature proposed in the paper can improve accuracy to some certain extent and is robust to rotation and scaling transformation.
Inverse correspondence between hippocampal perfusion and verbal memory performance in older adults

Understanding physiological changes that precede irreversible tissue damage in age‐related pathology is central to optimizing treatments that may prevent, or delay, cognitive decline. Cerebral perfusion is a tightly regulated physiological property, coupled to tissue metabolism and function, and abnormal (both elevated and reduced) hippocampal perfusion has been reported in a range of cognitive disorders. However, the size and location of the hippocampus complicates perfusion quantification, as many perfusion techniques acquire data with spatial resolution on the order of or beyond the size of the hippocampus, and are thus suboptimal in this region (especially in the presence of hippocampal atrophy and reduced flow scenarios). Here, the relationship between hippocampal perfusion and atrophy as a function of memory performance was examined in cognitively normal healthy older adults (n = 20; age=67 ± 7 yr) with varying genetic risk for dementia using a custom arterial spin labeling acquisition and analysis procedure. When controlling for hippocampal volume, it was found that hippocampal perfusion correlated inversely (P = 0.04) with memory performance despite absent hippocampal tissue atrophy or white matter disease. The hippocampal flow asymmetry (left hippocampus perfusion–right hippocampus perfusion) was significantly (P = 0.04) increased in APOE‐ϵ4 carriers relative to noncarriers. These findings demonstrate that perfusion correlates more strongly than tissue volume with memory performance in cognitively normal older adults, and furthermore that an inverse trend between these two parameters suggests that elevation of neuronal activity, possibly mediated by neuroinflammation and/or excitation/inhibition imbalance, may be closely associated with minor changes in memory performance. © 2012 Wiley Periodicals, Inc.