Miracle-dz/UniFAR-FTUs huggingface dataset:
In Silico Enhanced Restriction Enzyme Based Methylation Analysis of the Human Glioblastoma Genome Using Agilent 244K CpG Island Microarrays

Genome wide methylation profiling of gliomas is likely to provide important clues to improving treatment outcomes. Restriction enzyme based approaches have been widely utilized for methylation profiling of cancer genomes and will continue to have importance in combination with higher density microarrays. With the availability of the human genome sequence and microarray probe sequences, these approaches can be readily characterized and optimized via in silico modeling. We adapted the previously described HpaII/MspI based Methylation Sensitive Restriction Enzyme (MSRE) assay for use with two-color Agilent 244K CpG island microarrays. In this assay, fragmented genomic DNA is digested in separate reactions with isoschizomeric HpaII (methylation-sensitive) and MspI (methylation-insensitive) restriction enzymes. Using in silico hybridization, we found that genomic fragmentation with BfaI was superior to MseI, providing a maximum effective coverage of 22,362 CpG islands in the human genome. In addition, we confirmed the presence of an internal control group of fragments lacking HpaII/MspI sites which enable separation of methylated and unmethylated fragments. We used this method on genomic DNA isolated from normal brain, U87MG cells, and a glioblastoma patient tumor sample and confirmed selected differentially methylated CpG islands using bisulfite sequencing. Along with additional validation points, we performed a receiver operating characteristics (ROC) analysis to determine the optimal threshold (p ≤ 0.001). Based on this threshold, we identified ∼2,400 CpG islands common to all three samples and 145 CpG islands unique to glioblastoma. These data provide general guidance to individuals seeking to maximize effective coverage using restriction enzyme based methylation profiling approaches.
Cross-cultural experience, strategic motivation and employer hiring preference: An exploratory study in an emerging economy

The relationship between self-complexity, strategic motivation, and organizational processes such as staffing seems lacking in the human resources management and organizational behavior (OB) literatures. In two studies we examined the self-complexity of potential employees with and without cross-cultural experience as determinant of preferences of employers mediated by strategic motivations of organizations. We found in a sample of 40 organizations from an emerging economy, Ghana, that employers seemed to prefer employees with cross-cultural experience who are perceived to facilitate achievement of their strategic motivations. Implications for international human resources management are discussed. Expérience interculturelle, motivation stratégique et préférence d’embauche de l’employeur : une étude exploratoire dans une économie émergeante David B. Zoogah & Augustus Abbey La relation entre l’auto-complexité (ou la complexité de soi), la motivation stratégique et les processus organisationnels, comme le recrutement ne parait pas avoir été prise en compte dans la littérature sur le comportement organisationnel et la gestion des ressources humaines. Nous avons étudié dans deux études l’auto-complexité d’employés potentiels, avec et sans expérience interculturelle, comme déterminant des préférences d’employeurs, déterminant par ailleurs modifié par les motivations stratégiques des organisations. Nous avons découvert, dans le cadre d’un échantillon de quarante organisations d’une économie émergeante, à savoir le Ghana, que les employeurs préfèrent les employés dotés d’expérience interculturelle car ils sont perçus comme pouvant faciliter la réalisation de leurs motivations stratégiques. Les implications en ce qui concerne la gestion des ressources humaines sont aussi étudiées.
Two different mechanisms mediate catabolite repression of the Bacillus subtilis levanase operon

There are two levels of control of the expression of the levanase operon in Bacillus subtilis: induction by fructose, which involves a positive regulator, LevR, and the fructose phosphotransferase system encoded by this operon (lev-PTS), and a global regulation, catabolite repression. The LevR activator interacts with its target, the upstream activating sequence (UAS), to stimulate the transcription of the E sigma L complex bound at the "-12, -24" promoter. Levanase operon expression in the presence of glucose was tested in strains carrying a ccpA gene disruption or a ptsH1 mutation in which Ser-46 of HPr is replaced by Ala. In a levR+ inducible genetic background, the expression of the levanase operon was partially resistant to catabolite repression in both mutants, indicating that the CcpA repressor and the HPr-SerP protein are involved in the glucose control of this operon. In addition, a cis-acting catabolite-responsive element (CRE) of the levanase operon was identified and investigated by site-directed mutagenesis. The CRE sequence TGAAAACGCTT(a)ACA is located between positions -50 and -36 from the transcriptional start site, between the UAS and the -12, -24 promoter. However, in a background constitutive for levanase, neither HPr, CcpA, nor CRE is involved in glucose repression, suggesting the existence of a different pathway of glucose regulation. Using truncated LevR proteins, we showed that this CcpA-independent pathway required the presence of the domain of LevR (amino acids 411 to 689) homologous to the BglG family of bacterial antiterminators.
Draft Genome Sequence of Phaeobacter leonis Type Strain 306, an Alphaproteobacterium Isolated from Mediterranean Sea Sediments

ABSTRACT Phaeobacter leonis strain 306T is an alphaproteobacterium isolated from Mediterranean Sea sediments. It belongs to the genus Phaeobacter, which was recently proposed and is still poorly characterized. In an effort to better understand the fundamental aspects of the microbiology of this genus, we present here the 4.82-Mb draft genome sequence of Phaeobacter leonis strain 306T.
Isolation and Characterization of an Ovoinhibitor, a Multidomain Kazal-Like Inhibitor from Turkey (Meleagris gallopavo) Seminal Plasma1

ABSTRACT Turkey seminal plasma contains three serine proteinase inhibitors. Two of them, with low molecular masses (6 kDa), were identified as single-domain Kazal-type inhibitors responsible for regulating acrosin activity. Our experimental objective was to isolate and characterize the inhibitor with the high molecular weight from turkey seminal plasma. The inhibitor was purified using hydrophobic interaction and affinity chromatography. Pure preparations of the inhibitor were used for identification by mass spectrometry, for determination of physicochemical properties (molecular weight, pI, and content and composition of the carbohydrate component), for kinetic studies, and for antibacterial tests. Gene expression and immunohistochemical detection of the inhibitor were analyzed in the testis, epididymis, and ductus deferens. The inhibitor with a high molecular weight from turkey seminal plasma was identified as an ovoinhibitor, which was found in avian semen for the first time. The turkey seminal plasma ovoinhibitor was a six-tandem homologous Kazal-type domain serine proteinase inhibitor that targeted multiple proteases, including subtilisin, trypsin, and elastase, but not acrosin. Our results suggested that hepatocyte growth factor activator was a potential target proteinase for the ovoinhibitor in turkey seminal plasma. The presence of the ovoinhibitor within the turkey reproductive tract suggested that its role was to maintain a microenvironment for sperm in the epididymis and ductus deferens. The turkey seminal plasma ovoinhibitor appeared to play a significant role in an antibacterial semen defense against Bacillus subtilis and Staphylococcus aureus.
Covariance of cross-correlations: towards efficient measures for large-scale structure

We study the covariance of the cross-power spectrum of different tracers for the large-scale structure. We develop the counts-in-cells framework for the multitracer approach, and use this to derive expressions for the full non-Gaussian covariance matrix. We show that for the usual autopower statistic, besides the off-diagonal covariance generated through gravitational mode-coupling, the discreteness of the tracers and their associated sampling distribution can generate strong off-diagonal covariance, and that this becomes the dominant source of covariance as spatial frequencies become larger than the fundamental mode of the survey volume. On comparison with the derived expressions for the cross-power covariance, we show that the off-diagonal terms can be suppressed, if one cross-correlates a high tracer-density sample with a low one. Taking the effective estimator efficiency to be proportional to the signal-to-noise ratio (S/N), we show that, to probe clustering as a function of physical properties of the sample, i.e. cluster mass or galaxy luminosity, the cross-power approach can outperform the autopower one by factors of a few. We confront the theory with measurements of the mass-mass, halo-mass and halo-halo power spectra from a large ensemble of N-body simulations. We show that there is a significant S/N advantage to be gained from using the cross-power approach when studying the bias of rare haloes. The analysis is repeated in configuration space and again S/N improvement is found. We estimate the covariance matrix for these samples, and find strong off-diagonal contributions. The covariance depends on halo mass, with higher mass samples having stronger covariance. In agreement with theory, we show that the covariance is suppressed for the cross-power. This work points the way towards improved estimators for studying the clustering of tracers as a function of their physical properties.
Plasma Urate and Risk of a Hospital Stay with AKI: The Atherosclerosis Risk in Communities Study.

BACKGROUND AND OBJECTIVES Higher urate levels are associated with higher risk of CKD, but the association between urate and AKI is less established. This study evaluated the risk of hospitalized AKI associated with urate concentrations in a large population-based cohort. To explore whether urate itself causes kidney injury, the study also evaluated the relationship between a genetic urate score and AKI. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS A total of 11,011 participants from the Atherosclerosis Risk in Communities study were followed from 1996-1998 (baseline) to 2010. The association between baseline plasma urate and risk of hospitalized AKI, adjusted for known AKI risk factors, was determined using Cox regression. Interactions of urate with gout and CKD were tested. Mendelian randomization was performed using a published genetic urate score among the participants with genetic data (n=7553). RESULTS During 12 years of follow-up, 823 participants were hospitalized with AKI. Overall, mean participant age was 63.3 years, mean eGFR was 86.3 ml/min per 1.73 m(2), and mean plasma urate was 5.6 mg/dl. In patients with plasma urate >5.0 mg/dl, there was a 16% higher risk of hospitalized AKI for each 1-mg/dl higher urate (adjusted hazard ratio, 1.16; 95% confidence interval, 1.10 to 1.23; P<0.001). When stratified by history of gout, the association between higher urate and AKI was significant only in participants without a history of gout (P for interaction=0.02). There was no interaction of CKD and urate with AKI, nor was there an association between genetic urate score and AKI. CONCLUSIONS Plasma urate >5.0 mg/dl was independently associated with risk of hospitalized AKI; however, Mendelian randomization did not provide evidence for a causal role of urate in AKI. Further research is needed to determine whether lowering plasma urate might reduce AKI risk.
Searching to Translate and Translating to Search: When Information Retrieval Meets Machine Translation

Title of dissertation: SEARCHING TO TRANSLATE AND TRANSLATING TO SEARCH: WHEN INFORMATION RETRIEVAL MEETS MACHINE TRANSLATION Ferhan Ture, Doctor of Philosophy, 2013 Dissertation directed by: Professor Jimmy Lin Department of Computer Science and College of Information Studies With the adoption of web services in daily life, people have access to tremendous amounts of information, beyond any human’s reading and comprehension capabilities. As a result, search technologies have become a fundamental tool for accessing information. Furthermore, the web contains information in multiple languages, introducing another barrier between people and information. Therefore, search technologies need to handle content written in multiple languages, which requires techniques to account for the linguistic differences. Information Retrieval (IR) is the study of search techniques, in which the task is to find material relevant to a given information need. Cross-Language Information Retrieval (CLIR) is a special case of IR when the search takes place in a multi-lingual collection. Of course, it is not helpful to retrieve content in languages the user cannot understand. Machine Translation (MT) studies the translation of text from one language into another efficiently (within a reasonable amount of time) and effectively (fluent and retaining the original meaning), which helps people understand what is being written, regardless of the source language. Putting these together, we observe that search and translation technologies are part of an important user application, calling for a better integration of search (IR) and translation (MT), since these two technologies need to work together to produce high-quality output. In this dissertation, the main goal is to build better connections between IR and MT, for which we present solutions to two problems: Searching to translate explores approximate search techniques for extracting bilingual data from multilingual Wikipedia collections to train better translation models. Translating to search explores the integration of a modern statistical MT system into the cross-language search processes. In both cases, our best-performing approach yielded improvements over strong baselines for a variety of language pairs. Finally, we propose a general architecture, in which various components of IR and MT systems can be connected together into a feedback loop, with potential improvements to both search and translation tasks. We hope that the ideas presented in this dissertation will spur more interest in the integration of search and translation technologies. SEARCHING TO TRANSLATE AND TRANSLATING TO SEARCH: WHEN INFORMATION RETRIEVAL MEETS MACHINE TRANSLATION
The Subjective Experience of Poverty

Abstract What significance should the subjective experiences of poor people have in a normative philosophical critique of poverty? In this paper, we take up this question and answer it by looking at two different normative theories: the capability approach of Amartya Sen and Martha Nussbaum and the recognition approach of Axel Honneth. While Sen and Nussbaum are largely quite reluctant toward the role of subjective experiences of poor people, the recognition approach views them as central for its social critique of poverty. We will defend the thesis that a more inclusive view on the role of the subjects of suffering and injustice is needed, that such subjective experiences and the unique first-hand knowledge it produces cannot be substituted by objective criteria, while such criteria are needed to bolster – and in some cases also criticize – the poverty knowledge of poor people.
Markov Models to Classify M. tuberculosis Spoligotypes

In this paper we use Markov Models to classify automatically spoligotypes. A spoligotype is a sequence of 43 binary values provided by a DNA analysis technique. These methods, robust and well adapted to sequential data, allow us to generate a model on the basis of probabilities, calculated directly on the observations. We use these techniques to create one classifier for each searched class.
Air-ground channel characterization for unmanned aircraft systems: The near-urban environment

Use of unmanned aircraft systems (UAS) (or, drones) is expected to grow dramatically in the coming decades. For civil UAS that must share airspace with piloted aircraft, safety is paramount. Hence, requirements for a highly-reliable control and non-payload communication (CNPC) link are under development. Since designing a reliable link requires accurate knowledge of the channel characteristics, validated models for the air-ground (AG) channel are essential. In this paper we report results of SIMO AG measurements made for a NASA project in a near-urban environment (Cleveland, OH), for the two bands recently allocated for civil UAS CNPC: L-band (~970 MHz) and C-band (~5.06 GHz). Example channel characteristics are provided for a single flight track. For this flight track, path loss exponents were found to be 1.6 in L-band and 1.9 in C-band. Small scale fading Ricean K factors were 13 dB in L-band and 27 dB in C-band. The C-band root mean square delay spread was approximately 10 ns for most of the time, but reached 180 ns when reflections from buildings in the urban area were present. Spatial and inter-band correlation statistics are also reported. Tapped delay line models for near-urban AG channels will be presented in the near future.
INTERVIEWING A NATIONAL SAMPLE BY LONG-DISTANCE TELEPHONE

Changing emphases in programs of social welfare, including public health, make it increasingly necessary to plan and conduct programs responsive to the subjective needs and values of the consumer groups for whom they are intended. Obtaining information about such needs in turn requires the development of inexpensive but valid tools for collecting data. In recent years the telephone has seen increasing use as a means of collecting data quickly and inexpensively. Despite some limitations, a small number of published studies generally support the usefulness of the telephone as a means of obtaining personal information. Unfortunately, most of these studies have focused on a relatively small geographic area, where the cost of telephoning is minimal and where it is feasible to undertake intensive efforts to reduce nonresponse rates. The present report is one of the very few which attempted to obtain personal information via the telephone from a probability sample of the U. S. adult population. It also provides detailed data on the costs of this method, and on nonresponse rates, and estimates possible sample bias stemming from differences in personal characteristics of telephone owners and nonowners. The results of an effort to reduce bias are also described. Finally, since the sample interviewed by telephone had earlier given personal interviews, data are provided on the consistency of information obtained by the two methods.
Mutations in the ExbB Cytoplasmic Carboxy Terminus Prevent Energy-Dependent Interaction between the TonB and ExbD Periplasmic Domains

ABSTRACT The TonB system of Gram-negative bacteria provides passage across the outer membrane (OM) diffusion barrier that otherwise limits access to large, scarce, or important nutrients. In Escherichia coli, the integral cytoplasmic membrane (CM) proteins TonB, ExbB, and ExbD couple the CM proton motive force (PMF) to active transport of iron-siderophore complexes and vitamin B12 across the OM through high-affinity transporters. ExbB is an integral CM protein with three transmembrane domains. The majority of ExbB occupies the cytoplasm. Here, the importance of the cytoplasmic ExbB carboxy terminus (residues 195 to 244) was evaluated by cysteine scanning mutagenesis. D211C and some of the substitutions nearest the carboxy terminus spontaneously formed disulfide cross-links, even though the cytoplasm is a reducing environment. ExbB N196C and D211C substitutions were converted to Ala substitutions to stabilize them. Only N196A, D211A, A228C, and G244C substitutions significantly decreased ExbB activity. With the exception of ExbB(G244C), all of the substituted forms were dominant. Like wild-type ExbB, they all formed a formaldehyde cross-linked tetramer, as well as a tetramer cross-linked to an unidentified protein(s). In addition, they could be formaldehyde cross-linked to ExbD and TonB. Taken together, the data suggested that they assembled normally. Three of four ExbB mutants were defective in supporting both the PMF-dependent formaldehyde cross-link between the periplasmic domains of TonB and ExbD and the proteinase K-resistant conformation of TonB. Thus, mutations in a cytoplasmic region of ExbB prevented a periplasmic event and constituted evidence for signal transduction from cytoplasm to periplasm in the TonB system.
Supporting Parents to Facilitate Communication and Joint Attention in Their Young Children With Autism Spectrum Disorders: Two Pilot Studies

THIS ARTICLE describes 2 pilot studies partnering early interventionists and families in targeting social communication and joint attention abilities for young children with autism spectrum disorders. Both parent-intervention trainings involved opportunities for interventionists to partner with families. One pilot utilized More than Words (MTW; Sussman, 1999), a parent-training program designed to facilitate communication and vocabulary development. Outcomes of the MTW study were measured as changes in children's vocabulary development and social communication skills and parents' perceptions of changes in their responsiveness to their child. The second pilot-trained interventionists to collaborate with parents in selecting 1 of 2 approaches to teach joint attention: a discrete trial plus pivotal response training based in behaviorist theory or developmental-mediated learning, based in social–interactionist theory. This collaboration involved interviewing families about their current interaction styles, the structure of their day, and their typical routines to help determine if a more behavioral or naturalistic approach was best matched to the family's preferences. It also involved the collaborative selection of motivating toys and activities to be used during intervention. Outcomes of the Joint Attention Training (JAT) study were measured primarily as impressions on the part of interventionists about the process of negotiating and implementing intervention approaches with parents. Findings for the MTW pilot-confirmed previous research identifying positive change for children in their social interaction and vocabulary development when their parents are engaged and trained as language interventionists. Interventionists' impressions after JAT also were positive for collaborating with families to select intervention approaches that best fit their needs and priorities.
“Says Who?!” how the Source of Price Information and Affect Influence Perceived Price (Un)fairness

Three experiments show that the source of price change information—whether human or nonhuman—moderates the effect of price change on perceptions of price fairness. Both inferences of the marketer's motive and stimulus-induced affect mediate the effects of the source and price change. Opportunity and motivation to process also affect the relative influence of inferred motive and affect. This research demonstrates antecedent roles of both price source and affect.