Miracle-dz/UniFAR-FTUs huggingface dataset:
Biosynthesis, Distinct Post-translational Modifications, and Functional Characterization of Lymphoma Proprotein Convertase*

Proprotein convertases are responsible for the endoproteolytic processing of prohormones, neuropeptide precursors, and other proproteins within the constitutive and regulated secretory pathways. Cleavage occurs carboxyl-terminally of basic amino acid motifs, such as RX(K/R)R, RXXR, and (R/K)R. As already available for the other known mammalian members of this enzyme family, we here define structural and functional features of human lymphoma proprotein convertase (LPC). Analysis of expression of recombinant LPC in stably transfected Chinese hamster ovary cells reveals biosynthesis of a 92-kDa nonglycosylated precursor (proLPC) and a 102-kDa endoglycosidase H-sensitive glycosylated form of proLPC. Only the latter is further processed and after propeptide removal converted into a complexlyN-glycosylated mature form of LPC of about 92 kDa. Co-expression experiments of truncated LPC with an active site mutant of LPC (LPCS265A) indicate that prodomain removal of LPC occurs via an autoproteolytic, intramolecular mechanism, as was demonstrated before for some of the other members of this enzyme family. Prodomain removal is shown to be required for LPC to exit the endoplasmic reticulum. As far as subcellular localization is concerned, immunocytochemical, ultrastructural, and biochemical analyses show that LPC is concentrated in the trans-Golgi network, associated with membranes, and not secreted. Carboxyl-terminal domains are critically involved in this cellular retention, because removal of both the hydrophobic region and the cytoplasmic tail of LPC results in secretion. Of interest are the observations that LPC is not phosphorylated like furin but is palmitoylated in its cytoplasmic tail. Finally, substrate specificity of LPC is similar to that of furin but not identical. Whereas for furin a basic substrate residue at position P-2 is dispensable, it is essential for LPC. For optimal LPC substrate processing activity, an arginine at position P-6 is preferred over an arginine at P-4.
Identifying Threat Patterns of Android Applications

Mobile devices have become powerful and popular. Most internet applications or services are ported to mobile platforms. Confidential personal information such as credit card and password usually is stored in mobile devices for ubiquitous computing. Therefore, mobile devices become attack target due to financial gain. Mobile applications are published in various market places without or with little verification; hence malicious mobile applications can be deployed in the marketplaces without any difficulty.In this paper, we present a mobile malware detection approach by identifying the threat patterns. The proposed system analyzes the function invocation and the data flow to identify malicious behaviors in Android mobile devices. The experimental results show that the proposed method can efficiently detect malicious mobile applications including unknown malware.
Sun2 Is a Novel Mammalian Inner Nuclear Membrane Protein*

Sun protein (Sun1 and Sun2) cDNAs were previously cloned based on the homology of their C-terminal regions (SUN (Sad1 and UNC) domain) with the Caenorhabditis elegans protein UNC-84 whose mutation disrupts nuclear migration/positioning. In this study, we raised an anti-Sun2 serum and identified Sun2 in mammalian cells. In HeLa cells, Sun2 displays a nuclear rim-like pattern typical for a nuclear envelope protein. The Sun2 antibody signal co-localizes with nuclear pore and INM markers signals. The rim-like pattern was also observed with the recombinant full-length Sun2 protein fused to either EGFP or V5 epitopes. In addition, we found that a recombinant truncated form of Sun2, extending from amino acids 26 to 339, is sufficient to specify the nuclear envelope localization. Biochemical analyses show that Sun2 is an 85-kDa protein that is partially insoluble in detergent with high salt concentration and in chaotropic agents. Furthermore, Sun2 is enriched in purified HeLa cell nuclei. Electron microscopy analysis shows that Sun2 localizes in the nuclear envelope with a sub-population present in small clusters. Additionally, we show that the SUN domain of Sun2 is localized to the periplasmic space between the inner and the outer nuclear membranes. From our data, we conclude that Sun2 is a new mammalian inner nuclear membrane protein. Because the SUN domain is conserved from fission yeast to mammals, we suggest that Sun2 belongs to a new class of nuclear envelope proteins with potential relevance to nuclear membrane function in the context of the involvement of its components in an increasing spectrum of human diseases.
DNA polymerases α, δ, and ɛ localize and function together at replication forks in Saccharomyces cerevisiae

Early in eukaryotic cell cycle, a pre‐RC is assembled at each replication origin with ORC, Cdc6, Cdt1 and Mcm2‐7 proteins to license the origin for use in the subsequent S phase. Licensed origin must then be activated by S‐Cdk and Ddk. At the onset of S phase, RPA is loaded on to the ARS in a reaction stimulated by S‐Cdk and Ddk, followed by Cdc45‐dependent loading of pol α, ‐δ, and ‐ɛ. This study examines cell cycle‐dependent localization of pol α, ‐δ and ‐ɛ in Saccharomyces cerevisiae using immuno‐histochemical and chromatin immuno‐precipitation methods. The results show that pol α, ‐δ, or ‐ɛ localizes on chromatin as punctate foci at all stages of the cell cycle. However, some foci overlap with or are adjacent to foci pulse‐labeled with bromodeoxyuridine during S phase, indicating these are replicating foci. DNA microarray analysis localized pol α, ‐δ, and ‐ɛ to early firing ARSs on yeast chromosome III and VI at the beginning of S phase. These data collectively suggest that bidirectional replication occurs at specific foci in yeast chromosomes and that pol α, ‐δ, and ‐ɛ localize and function together at multiple replication forks during S phase.
Feedforward Inhibitory Control of Sensory Information in Higher-Order Thalamic Nuclei

Sensory stimuli evoke strong responses in thalamic relay cells, which ensure a faithful relay of information to the neocortex. However, relay cells of the posterior thalamic nuclear group in rodents, despite receiving significant trigeminal input, respond poorly to vibrissa deflection. Here we show that sensory transmission in this nucleus is impeded by fast feedforward inhibition mediated by GABAergic neurons of the zona incerta. Intracellular recordings of posterior group neurons revealed that the first synaptic event after whisker deflection is a prominent inhibition. Whisker-evoked EPSPs with fast rise time and longer onset latency are unveiled only after lesioning the zona incerta. Excitation survives barrel cortex lesion, demonstrating its peripheral origin. Electron microscopic data confirm that trigeminal axons make large synaptic terminals on the proximal dendrites of posterior group cells and on the somata of incertal neurons. Thus, the connectivity of the system allows an unusual situation in which inhibition precedes ascending excitation resulting in efficient shunting of the responses. The dominance of inhibition over excitation strongly suggests that the paralemniscal pathway is not designed to relay inputs triggered by passive whisker deflection. Instead, we propose that this pathway operates through disinhibition, and that the posterior group forwards to the cerebral cortex sensory information that is contingent on motor instructions.
Health-Related Quality-of-Life in Low-Income, Uninsured Men with Prostate Cancer

The objective was to describe health-related quality-of-life (HRQOL) in low-income men with prostate cancer. Subjects were drawn from a statewide public assistance prostate cancer program. Telephone and mail surveys included the RAND 12-item Health Survey and UCLA Prostate Cancer Index Short Form and were compared with normative age-matched men without cancer from the general population reported on in the literature. Of 286 eligible men, 233 (81%) agreed to participate and completed the necessary items. The sample consisted of 51% Hispanics, 23% non-Hispanic whites, and 17% African Americans. The low-income men had worse scores in every domain of prostate-specific and general HRQOL than had the age-matched general population controls. The degree of disparity indicated substantial clinical differences in almost every domain of physical and emotional functioning between the sample group and the control group. Linear regression modeling determined that among the low-income men, Hispanic race, and income level were predictive of worse physical functioning, whereas only comorbidities predicted mental health. Low-income patients with prostate cancer appear to have quality-of-life profiles that are meaningfully worse than age-matched men from the general population without cancer reported on in the literature.
Identification of a Novel Variant of Staphylococcal Cassette Chromosome mec, Type II.5, and Its Truncated Form by Insertion of Putative Conjugative Transposon Tn6012

ABSTRACT We identified two novel staphylococcal cassette chromosome mec (SCCmec) elements in sequence type 8 methicillin-resistant Staphylococcus aureus strains isolated in Japan: type II.5 SCCmec, whose J1 region was highly homologous to that of type I.2 SCCmec of strain PL72 (previously isolated in Poland), and its J1 region variant caused by the deletion/insertion of putative conjugative transposon Tn6012, identified in four S. aureus genomes.
Physical vs. surrogate models of passive RF devices

The accuracy of high-frequency models of passive RF devices, e.g., inductors or transformers, presents one of the most challenging problems for RF integrated circuits. Accuracy limitations lead RF designers to time-consuming iterations with electromagnetic simulators. This paper will explore and compare two advanced modeling techniques. The first one is based on the segmented model approach, in which each device segment is characterized with a lumped element model. The second technique is based on the generation of surrogate models from the electromagnetic simulation of a set of device samples. Different modeling strategies (frequency separation, filtering according to self-resonance frequency, etc.) will be considered. Efficiency and accuracy of both, physical and surrogate, modeling techniques will be compared using a Si process technology.
A Digital Ultrasonic System for Small Animal Imaging

In this paper, a 50 MHz digital ultrasonic imaging system designed for small animals and its applications to mouse embryos and tumors are presented. Utilizing the programmability of a fully digital system, several advanced imaging techniques are developed and implemented. A synthetic aperture focusing technique is implemented to increase the penetration and extend the depth of focus of a mechanical scan system using a high frequency single crystal transducer. An adaptive weighting technique is introduced to further reduce the sidelobes and enhance image contrast. Experimental results demonstrate efficacy of the proposed two-step adaptive focusing technique. For flow imaging, several flow estimation algorithms are evaluated. Simulations and flow phantom experiments show that the butterfly search technique offers superior flow imaging performance particularly when the SNR is low and the pulse bandwidth is high. The system is tested by imaging mouse embryos and microcirculation of a mouse tumor in vivo. It is demonstrated that the system is capable of simultaneously acquiring B-mode, color Doppler mode and power Doppler mode small animal images. The system set-up, adaptive focusing technique, flow estimation algorithms and imaging results are shown.
Intertemporal Rules with Variable Speed of Adjustment: An Application to U.K. Manufacturing Employment

This paper presents a procedure to estimate intertemporal dynamic decision rules where adjustment costs are assumed to be variable. The estimation is based on the Euler equation. For purposes of illustration, the authors concentrate on an employment function for the U.K. manufacturing sector where they find very significant effects of some variables that influence adjustment costs. Finally, they point out an empirical result that has interesting implications when evaluating tests of "efficient bargain" models. Copyright 1989 by Royal Economic Society.
Genetic consultations in primary care: GPs’ responses to three scenarios

Objective This study investigated general practitioners’ responses to three scenarios in which patients consulted regarding genetic conditions. Design. Self-completed postal study. Setting. Primary care in Northern Ireland. Subjects Questionnaire were distributed to all the GPs in Northern Ireland (n=1079). A total of 541 GPs participated (50%). Main outcome measures Responses to three scenarios in which patients consulted regarding their family history and risk of bowel cancer, breast cancer, and cystic fibrosis. Results. Most GPs correctly identified the patients’ risk of bowel cancer, recommended regular colonoscopy, advised lifestyle changes, and did not refer to the genetic clinic. GPs who were qualified for longer were more likely to recommend colonoscopy and less likely to advise lifestyle changes. With the breast cancer patient GPs adopted a cautious approach; most would refer to the genetic and mammography clinics. With the cystic fibrosis example, most correctly identified the patient's risk of carrying the gene, would refer to the genetic clinic, and would encourage the patient to discuss the risk with his partner. In general, doctors were unsure, but would pass on genetic information to insurance companies if requested. Conclusion The study suggests that, in most cases, general practitioners correctly identify at-risk individuals but there may still be some uncertainty regarding referrals. The results suggest that ways of educating GPs should be explored. Educational interventions should be linked to a greater understanding of factors involved in referral (including the influence of gender and experience). The guidelines provided to GPs in relation to the provision of genetic information to insurance companies may need to be reviewed in some countries.
Beyond factual to formulated silhouettes

When sketching terrain, a view-dependent framework of silhouette-related cues is required. This framework is prominent in manual sketches and is especially important in small-scale depictions viewed obliquely from above. Occluding contours, namely the lines delineating depth discontinuities in the projected surface, are insufficient for forming this framework. The role which the occluding contour, or Factual Silhouette, plays in structuring the sketch becomes increasingly minimal as more of the terrain becomes visible, as the viewpoint is raised. The aim of this research is to extend the set of occluding contours to encompass situations that are perceived as causing an occlusion and would therefore be sketched in a similar manner. These locations, termed Formulated Silhouettes supplement the set of occluding contours and provide a successful structuring framework. The proposed method processes visible areas of terrain, which are turning away from view, to extract a classified, vector-based description for a given view of a Digital Elevation Model. Background approaches to silhouette rendering are reviewed and the specific contributions of this thesis are discussed. The method is tested using case studies composed of terrain of varying scale and character and two application studies demonstrate how silhouettes can be used to enhance existing terrain visualization techniques, both abstract and realistic. In addition, consultation with cartographic designers provides external verification of the research. The thesis concludes by noting how silhouette contours relate to perceived entities rather than actual occlusions.
Examining Acculturative Stressors of the International Student: Following Study Abroad Students in South Korea and Morocco

International students, particularly students studying abroad for a limited period of time, face certain challenges in entering and adjusting to a new cultural environment. This research focuses on different acculturative stressors including language, differences in nonverbal communication, discrimination, and academic pressure. By comparing and contrasting the perspectives of various students with the researcher’s experience, this qualitative study provides insight into the lived experience of international students and the research through on-site fieldwork conducted over a year on university campuses in South Korea and Morocco. It discusses the results of the undertaken research and offers suggestions for resolving or minimizing these acculturative challenges. Disclaimer The findings and suggestions expressed in this thesis are those of the student and do not necessarily express the views of the University of Dayton. Dedication To my father, who taught me never to give up, and to my mother, whose undying spirit and love will always be a part of me. Acknowledgements This thesis would not have been possible without my thesis advisor Dr. Karen Korn, whose valuable advice and encouragement assisted in the planning and development of this study. I would also like to acknowledge the people in the International Studies department – my academic advisor Dr. Marybeth Carlson for her invaluable guidance and support, and Paula Braley for her help through these four years. I am also thankful to the University of Dayton Honors Program for making this study possible. My sincere thanks to Dr. Carissa Krane, who saw the potential in this research, and Ramona Speranza, who assisted in guiding this thesis process along. Thank you to the staff of the Center for International Programs and the Education Abroad Office, especially Tina Newton, for ensuring that my travel abroad was as smooth as possible. Special thanks to the participants who contributed their opinions and voices to the richness of the content in this thesis. My thanks to the many funding sources that made this research possible, including the Cordell W. Hull International Fellows Fund, Daniel J. Curran and Claire M. Renzetti International Studies Fund, Global KU Scholarship, Honors Thesis Research Award, Palermo Founders Fund, and the University of Dayton Trustees’ Scholarship. Finally, I would like to express my heartfelt gratitude to my family for their love and support, and to my best friend, whose good advice and encouragement sustained me throughout this thesis process.
A decomposition algorithm for surface electrode-array electromyogram

The purpose of the present study was to fully and reliably decompose surface electromyograms (s-EMGs) into their constitutive motor action unit potential trains (MUAPTs) at higher levels of contraction than that possible by using established methods. An algorithm for s-EMG signals decomposition based on preprocessing filters, independent component analysis (ICA), and on a template-matching technique was developed. In this study, it was demonstrated how ICA can be used successfully for solving overlaps of MUAPs. In each iteration of the algorithm, the action potentials of one motor unit (MU) could generally be separated from the others. Subsequently, using a template-matching technique, we were able to identify the action potential train of the selected MU. Results show that the algorithm satisfactorily decomposed the s-EMGs into their constitutive MUAPTs up to 30, 50, and even 60% maximum voluntary contraction (MVC). The results are in agreement with the generally accepted behavior of MUs firing rates.
Ceramide Kinase Mediates Cytokine- and Calcium Ionophore-induced Arachidonic Acid Release*

Despite the importance of prostaglandins, little is known about the regulation of prostanoid synthesis proximal to the activation of cytosolic phospholipase A2, the initial rate-limiting step. In this study, ceramide-1-phosphate (C-1-P) was shown to be a specific and potent inducer of arachidonic acid (AA) and prostanoid synthesis in cells. This study also demonstrates that two well established activators of AA release and prostanoid synthesis, the cytokine, interleukin-1β (IL-1β), and the calcium ionophore, A23187, induce an increase in C-1-P levels within the relevant time-frame of AA release. Furthermore, the enzyme responsible for the production of C-1-P in mammalian cells, ceramide kinase, was activated in response to IL-1β and A23187. RNA interference targeted to ceramide kinase specifically down-regulated ceramide kinase mRNA and activity with a concomitant decrease of AA release in response to IL-1β and A23187. Down-regulation of ceramide kinase had no effect on AA release induced by exogenous C-1-P. Collectively, these results indicate that ceramide kinase, via the formation of C-1-P, is an upstream modulator of phospholipase A2 activation. This study identifies previously unknown roles for ceramide kinase and its product, C-1-P, in AA release and production of eicosanoids and provides clues for potential new targets to block inflammatory responses.
The Prevalence of food hypersensitivity in young adults

A rising prevalence of food hypersensitivity (FHS) and severe allergic reactions to foods have been reported in the last decade. However, little is known on the prevalence in young adults. This study estimated the prevalence of FHS to the most common allergenic foods in an unselected population of young adults. We investigated a cohort of 1272 young adults 22 years of age by questionnaire, skin prick test (SPT) and histamin release (HR) followed by oral challenge to the most common allergenic foods. FHS was divided into primary and secondary FHS. Primary FHS was defined as being independent of pollen sensitization, whereas secondary FHS was defined as reactions to pollen related fruits and vegetables in pollen allergic patients. The questionnaire was returned by 77.1%. Primary FHS was reported by 19.6% and secondary FHS by 16.7% of the participants. Confirmed primary FHS by oral challenge was 1.7% [1.1% ‐ 2.95%]. In primary FHS, the most common allergenic food was peanut (0.6%) followed by additives (0.5%), shrimp (0.2%), codfish (0.1%), cow’s milk (0.1%), octopus (0.1%) and soy (0.1%). In secondary FHS, kiwi allergy was reported by 7.8% of the participants followed by hazelnut (6.6%), pineapple (4.4%), apple (4.3%), orange (4.2%), tomato (3.8%), peach (3.0%) and brazil nut (2.7%). This study found a 1.7% [1.1% ‐ 2.95%] prevalence of primary FHS confirmed by oral challenge to the most common allergenic foods in an unselected population of young adults.
dlmmc: Dynamical linear model regression for atmospheric time-series analysis

Regression analysis of atmospheric time-series observations is a key endeavour for identifying long-term trends and studying underlying drivers of variability in the data. Multiple linear regression (MLR) has been a standard tool for climate and atmospheric time-series data analysis. However, MLR has a number of well-known shortcomings that can, in the worst case, lead to biased scientific inferences being drawn from the data. Dynamical linear modeling (DLM) provides a more flexible regression framework that addresses a number of the key issues faced by MLR (reviewed below), providing an attractive and more robust alternative.