Miracle-dz/UniFAR-FTUs huggingface dataset:
Epstein- Barr Virus: Clinical and Epidemiological Revisits and Genetic Basis of Oncogenesis

Epstein-Barr virus (EBV) is classified as a member in the order herpesvirales, family herpesviridae, subfamily gammaherpesvirinae and the genus lymphocytovirus. The virus is an exclusively human pathogen and thus also termed as human herpesvirus 4 (HHV4). It was the first oncogenic virus recognized and has been incriminated in the causation of tumors of both lymphatic and epithelial nature. It was reported in some previous studies that 95% of the population worldwide are serologically positive to the virus. Clinically, EBV primary infection is almost silent, persisting as a life-long asymptomatic latent infection in B cells although it may be responsible for a transient clinical syndrome called infectious mononucleosis. Following reactivation of the virus from latency due to immunocompromised status, EBV was found to be associated with several tumors. EBV linked to oncogenesis as detected in lymphoid tumors such as Burkitt's lymphoma (BL), Hodgkin's disease (HD), post-transplant lymphoproliferative disorders (PTLD) and T-cell lymphomas (e.g. Peripheral T-cell lymphomas; PTCL and Anaplastic large cell lymphomas; ALCL). It is also linked to epithelial tumors such as nasopharyngeal carcinoma (NPC), gastric carcinomas and oral hairy leukoplakia (OHL). In vitro, EBV many studies have demonstrated its ability to transform B cells into lymphoblastoid cell lines (LCLs). Despite these malignancies showing different clinical and epidemiological patterns when studied, genetic studies have suggested that these EBV- associated transformations were characterized generally by low level of virus gene expression with only the latent virus proteins (LVPs) upregulated in both tumors and LCLs. In this review, we summarize some clinical and epidemiological features of EBV- associated tumors. We also discuss how EBV latent genes may lead to oncogenesis in the different clinical malignancies
Together in Bed?: Couples' Mobile Technology Use in Bed

In this paper, we investigate the use of mobile technology in an underexplored context, the bed that couples share. Despite large amounts of research on the impact of pre-bedtime technology use on our sleep and mental state, scant research in the HCI field focuses on the physical bed as a negotiated site of technology use by couples. This paper explores (a) the meaning of the bed accessed by mobile technology and (b) the strategies of both individual and shared technology use in bed, in the context of couple's relationships. We investigate the effects of mobile technology to couples' bed-sharing practices through in-depth interviews (n = 12) and an online survey (n = 117). We report on creative and negotiated bodily practices of mobile technology use by couples in bed, and the perceived effects on couples' verbal and physical interaction and the intimacy of the bed.
A theory of indirection via approximation

Building semantic models that account for various kinds of indirect reference has traditionally been a difficult problem. Indirect reference can appear in many guises, such as heap pointers, higher-order functions, object references, and shared-memory mutexes. We give a general method to construct models containing indirect reference by presenting a "theory of indirection". Our method can be applied in a wide variety of settings and uses only simple, elementary mathematics. In addition to various forms of indirect reference, the resulting models support powerful features such as impredicative quantification and equirecursion; moreover they are compatible with the kind of powerful substructural accounting required to model (higher-order) separation logic. In contrast to previous work, our model is easy to apply to new settings and has a simple axiomatization, which is complete in the sense that all models of it are isomorphic. Our proofs are machine-checked in Coq.
Matrix multiplication beyond auto-tuning: Rewrite-based GPU code generation

Graphics Processing Units (GPUs) are used as general purpose parallel accelerators in a wide range of applications. They are found in most computing systems, and mobile devices are no exception. The recent availability of programming APIs such as OpenCL for mobile GPUs promises to open up new types of applications on these devices. However, producing high performance GPU code is extremely difficult. Subtle differences in device characteristics can lead to large performance variations when different optimizations are applied. As we will see, this is especially true for a mobile GPU such as the ARM Mali GPU which has a very different architecture than desktop-class GPUs. Code optimized and tuned for one type of GPUs is unlikely to achieve the performance potential on another type of GPUs. Auto-tuners have traditionally been an answer to this performance portability challenge. For instance, they have been successful on CPUs for matrix operations, which are used as building blocks in many high-performance applications. However, they are much harder to design for different classes of GPUs, given the wide variety of hardware characteristics. In this paper, we take a different perspective and show how performance portability for matrix multiplication is achieved using a compiler approach. This approach is based on a recently developed generic technique that combines a high-level programming model with a system of rewrite rules. Programs are automatically rewritten in successive steps, where optimizations decision are made.This approach is truly performance portable, resulting in high-performance code for very different types of architectures such as desktop and mobile GPUs. In particular, we achieve a speedup of 1.7x over a state-of-the-art auto-tuner on the ARM Mali GPU.
The Art and Artifact of GDF9 Activity: Cumulus Expansion and the Cumulus Expansion-Enabling Factor1

Abstract The process of cumulus cell expansion is critical for normal fertility. Oocyte-produced growth and differentiation factor 9 (GDF9) has been thought to play a leading role in this process. Recent studies both support and refute this hypothesis. Central to understanding the physiology of GDF9 is the use of recombinant ligand in in vitro assays. There are several laboratories that currently produce recombinant GDF9 preparations that appear to show variable effects on granulosa cell gene expression and cumulus cell expansion. Several of these studies are reviewed here. Standardization in preparation for recombinant GDF9, as well as a more biochemical analysis of the oocyte-secreted forms of GDF9, may help to resolve the conflicts currently seen in the literature.
Axonal Outgrowth and Dendritic Plasticity in the Cortical Peri-Infarct Area After Experimental Stroke

Background and Purpose— Axonal remodeling is critical to brain repair after stroke. The present study investigated axonal outgrowth after stroke and the signaling pathways mediating axonal outgrowth in cortical neurons. Methods— Using a rodent model of middle cerebral artery occlusion, we examined high-molecular weight neurofilament (NFH) immunoreactive axons and myelin basic protein-positive oligodendrocytes in the peri-infarct area. In vitro, using cultured cortical neurons in a microfluidic chamber challenged by oxygen-glucose deprivation (OGD), we investigated mechanisms selectively regulating axonal outgrowth after OGD. Results— NFH+ axons and MBP+ oligodendrocytes substantially increased in the peri-infarct area during stroke recovery, concomitantly with an increase in dendrites and spines identified by Golgi-Cox staining. In vitro, cortical neurons subjected to OGD exhibited significant increases in axonal outgrowth and in phosphorylated NFH protein levels, concurrently with downregulation of phosphatase tensin homolog deleted on chromosome 10, activation of Akt, and inactivation of glycogen synthase kinase-3&bgr; in regenerated axons. Blockage of phosphoinositide 3-kinase with pharmacological inhibitors suppressed Akt activation and attenuated phosphorylation of glycogen synthase kinase-3&bgr;, which resulted in suppression of phosphorylated NFH and axonal outgrowth after OGD; whereas GSK-3 inhibitors augmented axonal regeneration and elevated phosphorylated NFH levels after OGD. Conclusions— Stroke induces axonal outgrowth and myelination in rodent ischemic brain during stroke recovery, and the phosphoinositide 3-kinase/Akt/glycogen synthase kinase-3&bgr; signaling pathway mediates axonal regeneration of cortical neurons after OGD.
Automatic Mapping tool of local laboratory terminologies to LOINC

Clinical concepts and terminologies usually differ from one software system to another, making the exchange of data between them a very arduous and difficult task. It mainly involves finding the correspondences between the local identifiers of the concepts to be exchanged. In this paper, we describe a software tool called SAM (Automatic Mapping System), a tool for terminological normalization of laboratory tests to LOINC. SAM helps technicians in this task through simplification of the terminological mapping process. It uses approximate string matching techniques along with a thorough mining of previous mappings and LOINC parts.
Report for the Project " CSE 481 E : Capstone Software-- UrbanSim " New Build System Context for the project

The Center for Urban Simulation and Policy Analysis (Cuspa) [7] develops the UrbanSim software which provides a platform and models for an urban simulation system [1]. The Software consists of several sub projects, Open Platform for Urban Simulation (Opus) which is the framework to run models, sets of models for different areas or cities, e.g. Urbansim or for the Puget Sound area, and a sub project for documentation. Most of the developers work in the Cuspa lab but contributions are also received from abroad. The development process used by Cuspa applies several agile programming concepts [2]. The most important of which are a test first methodology and short iterations in which tasks determined. In order to always have a runnable system without any failing tests a build system is used. Build systems automatically check source repositories for modifications, run scripts for the source code, and can display the script results in a number of ways. Currently the source code for the projects is stored in a CVS repository and Cuspa is using a home-brewed build system called Fireman. In the case of Fireman, the scripts are used to primarily run unit tests and the results are displayed on a fireman website and traffic lights within the Cuspa lab [3]. Because of the outside contributions to UrbanSim, Cuspa has encountered some difficulties with using CVS. The accounts used by CVS to access the repositories are closely tied to the underlying system, effectively meaning outside contributors must be given UW CSE accounts. Switching to a different version control system, such as Subversion, would eliminate the need to give out UW CSE accounts, as the accounts are independent of the underlying system. However,
Using ontologies to discover fact IDs

Object identification is a crucial step in most information systems. Nowadays, we have many different ways to identify entities such as surrogates, keys and object identifiers. However, not all of them guarantee the entity identity. Many works have been introduced in the literature for discovering meaningful IDs, but all of them work at the logical or data level and they share some constraints inherent to the kind of approach. Addressing it at the logical level, we may miss some important data dependencies, while the cost to identify data dependencies at the data level may not be affordable. In this paper, we propose an approach for discovering fact IDs from domain ontologies. In our approach, we guide the process at the conceptual level and we introduce a set of pruning rules for improving the performance by reducing the number of ID hypotheses generated and to be verified with data. Finally, we also introduce a simulation over a case study to show the feasibility of our method.
On the randomness and seasonality of affective metrics for software development

The role of emotions and human aspects of software development is gaining increasing attention from both academics and developers. Software development is a complex activity, but since software is everywhere and it is necessary to achieve the highest quality possible. High technical skills, knowledge and competence of a software developer are not the only factors which influence the final product. Good attitudes, communication skills and good manners are equally as important. In this paper we focused our attention on understanding how developer sentiment and emotions evolved over time during the development process of 10 systems, considering affectiveness as time series. We studied seasonality, randomness and correlations. Results showed that there was not a significant correlation among joy and love, sadness and anger, sentiment and joy. Regarding seasonality and randomness, results showed that in the majority of the cases, the analysed time series are seasonal and not random.
The Physiological Role of 5-HT2A Receptors in Working Memory

Dorsolateral prefrontal cortex has an essential role in the cognitive process of working memory, dysfunction of which is considered to be a core deficit in schizophrenia. Although this cortical region is densely innervated with 5-HT2A receptors to which atypical antipsychotic drugs bind with high affinity, little is known of the influence of this serotonin receptor subtype on prefrontal function. We addressed this issue by examining the effects of iontophoresis of selective receptor ligands on prefrontal neurons possessing spatially tuned delay activity, or “memory fields,” in monkeys performing a delayed-response task. Memory fields of putative pyramidal cells were attenuated by iontophoresis of 5-HT2A antagonists, which primarily produced a reduction in delay activity for preferred target locations. Conversely, 5-HT2A stimulation by α-methyl-5-HT or 5-HT itself, accentuated the spatial tuning of these neurons by producing a modest increase in activity for preferred target locations and/or a reduction in activity for nonpreferred locations. The agonist effects could be reversed by the selective antagonist MDL100,907, and were dose-dependent, such that high levels attenuated spatial tuning by profoundly reducing delay activity. A role for feedforward inhibitory circuitry in these effects was supported by the finding that 5-HT2A blockade also attenuated the memory fields of putative interneurons. We conclude that prefrontal 5-HT2A receptors have a hitherto unrecognized role in the cognitive function of working memory, which involves actions at both excitatory and inhibitory elements within local circuitry.
Differentially Private Matrix Factorization using Sketching Techniques

Collaborative filtering is a popular technique for recommendation system due to its domain independence and reliance on user behavior data alone. But the possibility of identification of users based on these personal data raise privacy concerns. Differential privacy aims to minimize these identification risks by adding controlled noise with known characteristics. The addition of noise impacts the utility of the system and does not add any other value to the system other than enhanced privacy. We propose using sketching techniques to implicitly provide the differential privacy guarantees by taking advantage of the inherent randomness of the data structure. In particular, we use count sketch as a storage model for matrix factorization, one of the successful collaborative filtering techniques. Our model is also compact and scales well with data, making it well suitable for large scale applications.
corona Is Required for Higher-Order Assembly of Transverse Filaments into Full-Length Synaptonemal Complex in Drosophila Oocytes

The synaptonemal complex (SC) is an intricate structure that forms between homologous chromosomes early during the meiotic prophase, where it mediates homolog pairing interactions and promotes the formation of genetic exchanges. In Drosophila melanogaster, C(3)G protein forms the transverse filaments (TFs) of the SC. The N termini of C(3)G homodimers localize to the Central Element (CE) of the SC, while the C-termini of C(3)G connect the TFs to the chromosomes via associations with the axial elements/lateral elements (AEs/LEs) of the SC. Here, we show that the Drosophila protein Corona (CONA) co-localizes with C(3)G in a mutually dependent fashion and is required for the polymerization of C(3)G into mature thread-like structures, in the context both of paired homologous chromosomes and of C(3)G polycomplexes that lack AEs/LEs. Although AEs assemble in cona oocytes, they exhibit defects that are characteristic of c(3)G mutant oocytes, including failure of AE alignment and synapsis. These results demonstrate that CONA, which does not contain a coiled coil domain, is required for the stable ‘zippering’ of TFs to form the central region of the Drosophila SC. We speculate that CONA's role in SC formation may be similar to that of the mammalian CE proteins SYCE2 and TEX12. However, the observation that AE alignment and pairing occurs in Tex12 and Syce2 mutant meiocytes but not in cona oocytes suggests that the SC plays a more critical role in the stable association of homologs in Drosophila than it does in mammalian cells.
Is There Evidence for Continued Learning Over Multiple Years in Perimetry?

Purpose. The existence of learning effects in perimetry, whereby a subject's first test is more variable and has lower mean sensitivity (MS) than subsequent tests, is well established. However, studies have typically examined this issue by testing subjects at a frequency that would be unusual in a clinical setting. This study seeks to determine the validity of these conclusions for less frequent, yet more clinically realistic, testing rates. Methods. One hundred sixty eyes of 80 subjects with suspected or early glaucoma were included. Subjects were tested annually for 8 years using white-on-white standard automated perimetry (SAP) and short wavelength automated perimetry (SWAP). All subjects had undergone at least one test with both paradigms before entering the study. Results. For SAP, MS increased by 0.5 dB over the first year, and then showed no significant change until after year 5 (despite expected effects of aging and disease progression), after which it started to decline. For SWAP, MS of the average eye continued to improve until year 6 of the study. Conclusions. Our findings seem to indicate a prolonged learning effect for SWAP, with MS increasing for several years. A smaller prolonged learning effect may also be present for SAP, counteracting the effects of aging and disease progression. Deterioration of the subject's visual field may be underestimated within this period.
Global Mutational Analysis of NtrC-Like Activators in Myxococcus xanthus: Identifying Activator Mutants Defective for Motility and Fruiting Body Development

ABSTRACT The multicellular developmental cycle of Myxococcus xanthus requires large-scale changes in gene transcription, and recent findings indicate that NtrC-like activators play a prominent role in regulating these changes. In this study, we made insertions in 28 uncharacterized ntrC-like activator (nla) genes and found that eight of these insertions cause developmental defects. Hence, these results are consistent with the idea that M. xanthus uses a series of different NtrC-like activators during fruiting body development. Four of the eight developmental mutants we identified have motility defects. The nla1, nla19, and nla23 mutants show S-motility defects, while the nla24 mutant shows defects in both S-motility and A-motility. During development, aggregation of the nla1, nla19, and nla23 mutants is delayed slightly and the nla24 mutant shows no signs of aggregation or sporulation. The nla4, nla6, nla18, and nla28 mutants have no appreciable loss in motility, but they fail to aggregate and to sporulate normally. The nla18 mutant belongs to a special class of developmental mutants whose defects can be rescued when they are codeveloped with wild-type cells, suggesting that nla18 fails to produce a cell-cell signal required for development. The three remaining activator mutants, nla4, nla6, and nla28, appear to have complex developmental phenotypes that include deficiencies in cell-cell developmental signals.
Boredom-computer interaction: boredom proneness and the use of smartphone

Mobile technology is becoming a loyal companion in our lives. It is used for increasing amounts of time during the day and night, enabling the development of intelligent user interfaces that characterize their users' traits and adapt to them. In this paper, we show how an individual's tendency to experience boredom, i.e. the personal trait called boredom proneness, affects the use of technology -- specifically a smartphone. We develop machine learning models to automatically classify individuals into high/low boredom proneness from their typical daily patterns of smartphone use. We thus propose boredom proneness as a trait with high potential to enable the design of personalized mobile services that are more meaningful to their users.
Mesoporous Silica Nanoparticles for Protein Protection and Delivery

Therapeutic proteins are widely used in clinic for numerous therapies such as cancer therapy, immune therapy, diabetes management and infectious diseases control. The low stability and large size of proteins generally compromise their therapeutic effects. Thus, it is a big challenge to deliver active forms of proteins into targeted place in a controlled manner. Nanoparticle based delivery systems offer a promising method to address the challenges. In particular, mesoporous silica nanoparticles (MSNs) are of special interest for protein delivery due to their excellent biocompatibility, high stability, rigid framework, well-defined pore structure, easily controllable morphology and tuneable surface chemistry. Therefore, enhanced stability, improved activity, responsive release, and intracellular delivery of proteins have been achieved using MSNs as delivery vehicles. Here, we systematically review the effects of various structural parameters of MSNs on protein loading, protection, and delivery performance. We also highlight the status of the most recent progress using MSNs for intracellular delivery, extracellular delivery, antibacterial proteins delivery, enzyme mobilization, and catalysis.
Immunohistochemical Localization of the Aquaporins AQP1, AQP3, AQP4, and AQP5 in the Mouse Respiratory System

Aquaporins are membrane water channel proteins that function mainly in water transfer across cellular membranes. In our present study, we investigated the immunohistochemical distribution of aquaporin 1 (AQP1), AQP3, AQP4, and AQP5 in the mouse respiratory system by immunofluorescence, immunoperoxidase, and immunoelectron microscopy. AQP3, AQP4, and AQP5 are expressed in epithelial cells, whereas AQP1 is expressed in subepithelial connective tissues and capillaries. In the airway surface epithelia from the nasal cavity to the intrapulmonary bronchioles, AQP5 was found to be mainly localized to the luminal side and both AQP3 and AQP4 to the abluminal side. In the alveolar epithelium, AQP5 is localized to the apical membranes of both type I and type II alveolar cells. Compared with the previous studies on the rat respiratory system, in which AQP5 is restricted to the alveolar type I cells and absent from the airway surface epithelia, we found that AQP5 in the mouse is much more widely distributed throughout the surface epithelia. These results suggest that AQP5 has a critical role in water-handling, such as the maintenance of airway surface liquid and clearance of alveolar fluid in the mouse respiratory system.