Miracle-dz/UniFAR-FTUs huggingface dataset:
Simian Immunodeficiency Virus Infection in Wild-Caught Chimpanzees from Cameroon

ABSTRACT Simian immunodeficiency viruses (SIVcpz) infecting chimpanzees (Pan troglodytes) in west central Africa are the closest relatives to all major variants of human immunodeficiency virus type 1 ([HIV-1]; groups M, N and O), and have thus been implicated as the source of the human infections; however, information concerning the prevalence, geographic distribution, and subspecies association of SIVcpz still remains limited. In this study, we tested 71 wild-caught chimpanzees from Cameroon for evidence of SIVcpz infection. Thirty-nine of these were of the central subspecies (Pan troglodytes troglodytes), and 32 were of the Nigerian subspecies (Pan troglodytes vellerosus), as determined by mitochondrial DNA analysis. Serological analysis determined that one P. t. troglodytes ape (CAM13) harbored serum antibodies that cross-reacted strongly with HIV-1 antigens; all other apes were seronegative. To characterize the newly identified virus, 14 partially overlapping viral fragments were amplified from fecal virion RNA and concatenated to yield a complete SIVcpz genome (9,284 bp). Phylogenetic analyses revealed that SIVcpzCAM13 fell well within the radiation of the SIVcpzPtt group of viruses, as part of a clade including all other SIVcpzPtt strains as well as HIV-1 groups M and N. However, SIVcpzCAM13 clustered most closely with SIVcpzGAB1 from Gabon rather than with SIVcpzCAM3 and SIVcpzCAM5 from Cameroon, indicating the existence of divergent SIVcpzPtt lineages within the same geographic region. These data, together with evidence of recombination among ancestral SIVcpzPtt lineages, indicate long-standing endemic infection of central chimpanzees and reaffirm a west central African origin of HIV-1. Whether P. t. vellerosus apes are naturally infected with SIVcpz requires further study.
Enhanced Dialogue Markup for Crisis Talk Scenario Resources

We present a method of enhancing dialogue markup by mapping HPSG-based discourse category information into XML. The application scenario is crisis talk, specifically cockpit voice recording (CVR) transcripts of aviation disasters. This approach is new both as a source of richly annotated spoken language corpus resources for a little known scenario, and in grammatical theory and language documentation.
Learning apprentice system for turbine modelling

A learning apprentice system is presented, which learns from examples extracted from user dialogues. The system provides an interface between the user and the turbine modeller. While a dialogue is carried out between the user and the turbine modelling software, the system observes the dialogues and whenever a new example is observed which performs a task completely, the system tries to learn it. The learning methodology used by the system is described and various drawbacks are pointed out. A new learning methodology is proposed which easily overcomes the problems faced by the earlier methodology.
SeSQLite: Security Enhanced SQLite: Mandatory Access Control for Android databases

SQLite is the most widely deployed in-process library that implements a SQL database engine. It offers high storage efficiency, fast query operation and small memory needs. Due to the fact that a complete SQLite database is stored in a single cross-platform disk file and SQLite does not support multiple users, anyone who has direct access to the file can read the whole database content. SELinux was originally developed as a Mandatory Access Control (MAC) mechanism for Linux to demonstrate how to overcome DAC limitations. However, SELinux provides per-file protection, thus the database file is treated as an atomic unit, impeding the definition of a fine-grained mandatory access control (MAC) policy for database objects. We introduce SeSQLite, an SQLite extension that integrates SELinux access controls into SQLite with minimal performance and storage overhead. SeSQLite implements labeling and access control at both schema level (for tables and columns) and row level. This permits the management of a fine-grained access policy for database objects. A prototype has been implemented and it has been used to improve the security of Android Content Providers.
A mosaic of Wheat transmissible to all cereal species in the tribe Sordeae.

The green and the yellow types of mosaic discussed in this paper occur on winter wheat and winter rye in several counties in Illinois and Indiana {3j 4) ^ and on winter wheat in Davidson County, N. C. An extreme dwarfing or rosette condition is associated with the green mosaic on several varieties of winter wheat, and on this account the malady has previously been designated by the name rosette disease. Although this name characterizes the rosette condition, it appears that the more inclusive name mosaic is more appropriate. The green and the yellow types of mottling associated with this malady may be caused by one virus or by distinct viruses. This point will be discussed later. Throughout this paper they are treated as a single disease on account of their close association in the infested soils that have been studied. This mosaic shows certain characteristics which differ from those manifested by the tropical mosaic occurring on sugarcane, Indian corn, and other species belonging largely to the higher tribes of the grasses as classified by Hitchcock (1). The most notable difference is in the matter of soil transmission. This mosaic of the small grains is perpetuated from year to year by means of virus present in the soil stratum (5, 4,10j 11). As yet experiments have not supplied the evidence that might lead to the determination of the exact relationship between the soil and the virus. It is possible that subterranean vectors such as nematodes, soilborne insects, other animal forms, or even fungi, may carry the virus. It is possible also that the virus is held by the finely divided particles of soil and organic matter. The occurrence of this mosaic depends largely on the fall and winter conditions that influence growth and dormancy. The disease does not develop when susceptible varieties are sown in infested soil during the summer, and it is difficult to obtain infection experimentally from expressed juice when the inoculated plants are propagated in warm locations. This mosaic has not been transmitted experimentally by Aphis maidis or by aphids which commonly feed on wheat. Its host range as determined thus far is within the tribe Hordeae, which is one of the lower tribes of grasses.
Statistical methods of background correction for Illumina BeadArray data

MOTIVATION Advances in technology have made different microarray platforms available. Among the many, Illumina BeadArrays are relatively new and have captured significant market share. With BeadArray technology, high data quality is generated from low sample input at reduced cost. However, the analysis methods for Illumina BeadArrays are far behind those for Affymetrix oligonucleotide arrays, and so need to be improved. RESULTS In this article, we consider the problem of background correction for BeadArray data. One distinct feature of BeadArrays is that for each array, the noise is controlled by over 1000 bead types conjugated with non-specific oligonucleotide sequences. We extend the robust multi-array analysis (RMA) background correction model to incorporate the information from negative control beads, and consider three commonly used approaches for parameter estimation, namely, non-parametric, maximum likelihood estimation (MLE) and Bayesian estimation. The proposed approaches, as well as the existing background correction methods, are compared through simulation studies and a data example. We find that the maximum likelihood and Bayes methods seem to be the most promising. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
STRATIFICATION : A PROBLEM IN RANGELAND MONITORING

Resource stratification for ground-based and remotely-sensed methods of rangeland assessment is essential for locating appropriate sampling sites. This is particularly the case when site comparisons are required, as in the case of grazing gradient analysis, wherein the objective is to limit the number of environmental variables. This study compared stratified units derived from supervised, unsupervised and object-based classification with pre-defined sites from visual interpretation of satellite imagery and discusses the advantages and disadvantages of these technologies for stratification as pre-consideration in ground-based and remotely-sensed studies. Landsat Thematic Mapper (TM) images have been used for this study. Derived strata were controlled by the collected data prior to image interpretation from 30 systematic sampling sites (5 paddocks and 6 distances from water points) at Middleback Field Center in South Australia. Allocated time for pixeland object-based stratification is very low compared with the manual interpretation. Overall accuracy and Kappa statistics for pixel-based classification was very low (<33%). Overall, the object-oriented method provided results with more accuracy (50%) in comparison with pixel-based classification, indicating that object-oriented image analysis has more potential for stratification of arid rangelands. However, results from an ecological perspective need further investigation using high spatial resolution imagery and with more samples for ground-truthing. This may create more reliable and robust results.
3DUI design inspired by assistive technology

Within this article, we offer a new design perspective for the analysis, creation, and validation of 3D user interfaces using assistive technology as source of inspiration. While 3DUI design has matured over the last decade, many open issues remain to be solved. An assistive technology design perspective can aid: it can offer a stringent test environment to uncover issues and provides a different view on design by looking at human potential. Subsequently, we will look at major fields of interest, identifying pitfalls in 3DUI design and how assistive technology can be used to overcome these issues, outlining particular fields of research, or research directions, that deserve further attention.
The Internship: Bridge Between Marketplace and Liberal Arts Education in the Catholic Tradition

Internships can be distinctive pedagogical opportunities within a Catholic liberal arts education. The applied marketplace experience provided by an internship, properly understood, is consistent with the Catholic understanding of education. The value of internships for Catholic higher education can be illustrated by focusing on communication and rhetorical studies. This essay consists of a selected review of literature situating internships within liberal arts education, followed by the articulation of a Thomistic framework for rhetorical education.
A Parameterizable FPGA Prototype of a Vector-Thread Processor

The SCALE prototype board has been fabricated and consists of a single Xilinx XC2V4000 FPGA connected to a number of Micron DDR2 DRAMs that form the SCALE memory system. To support power measurements, the board is divided into multiple separate power islands. The board is attached to a test baseboard that provides sixteen independently measurable power supply connections and a byte-serial connection to a Linux PC that acts as the system host. The current version of the board has a variety of additional DRAM parts with independent power supplies to support experiments in DRAM power control. The final version of the SCALE board will replace these additional DRAMs with a socket for the SCALE chip.
Detyrosination of alpha tubulin does not stabilize microtubules in vivo [published erratum appears in J Cell Biol 1990 Sep;111(3):1325-6]

The relationship between alpha tubulin detyrosination and microtubule (MT) stability was examined directly in cultured fibroblasts by experimentally converting the predominantly tyrosinated MT array to a detyrosinated (Glu) array and then assaying MT stability. MTs in mouse Swiss 3T3 cells displayed an increase in Glu immunostaining fluorescence approximately 1 h after microinjecting antibodies to the tyrosinating enzyme, tubulin tyrosine ligase. Detyrosination progressed to virtual completion after 12 h and persisted for 30-35 h before tyrosinated subunits within MTs were again detected. The stability of these experimentally detyrosinated MTs was tested by first injecting either biotinylated or Xrhodamine-labeled tubulin and then measuring bulk turnover by hapten-mediated immunocytochemistry or fluorescence recovery after photobleaching, respectively. By both methods, turnover was found to be similarly rapid, possessing a half time of approximately 3 min. As a final test of MT stability, the level of acetylated tubulin staining in antibody-injected cells was compared with that observed in adjacent, uninjected cells and also with the staining observed in cells whose MTs had been stabilized with taxol. Although intense Glu staining was observed in both injected and taxol- treated cells, increased acetylated tubulin staining was observed only in the taxol-stabilized MTs, indicating that the MTs were not stabilized by detyrosination. Together, these results demonstrated clearly that detyrosination does not directly confer stability on MTs. Therefore, the stable MTs observed in these and other cell lines must have arisen by another mechanism, and may have become posttranslationally modified after their stabilization.
Differences of immune disorders between Alzheimer’s disease and breast cancer based on transcriptional regulation

Although chronic inflammation and immune disorders are of great importance to the pathogenesis of both dementia and cancer, the pathophysiological mechanisms are not clearly understood. In recent years, growing epidemiological evidence and meta-analysis data suggest an inverse association between Alzheimer’s disease (AD), which is the most common form of dementia, and cancer. It has been revealed that some common genes and biological processes play opposite roles in AD and cancer; however, the biological immune mechanism for the inverse association is not clearly defined. An unsupervised matrix decomposition two-stage bioinformatics procedure was adopted to investigate the opposite behaviors of the immune response in AD and breast cancer (BC) and to discover the underlying transcriptional regulatory mechanisms. Fast independent component analysis (FastICA) was applied to extract significant genes from AD and BC microarray gene expression data. Based on the extracted data, the shared transcription factors (TFs) from AD and BC were captured. Second, the network component analysis (NCA) algorithm in this study was presented to quantitatively deduce the TF activities and regulatory influences because quantitative dynamic regulatory information for TFs is not available via microarray techniques. Based on the NCA results and reconstructed transcriptional regulatory networks, inverse regulatory processes and some known innate immune responses were described in detail. Many of the shared TFs and their regulatory processes were found to be closely related to the adaptive immune response from dramatically different directions and to play crucial roles in both AD and BC pathogenesis. From the above findings, the opposing cellular behaviors demonstrate an invaluable opportunity to gain insights into the pathogenesis of these two types of diseases and to aid in developing new treatments.
Word- and Partition-Level Write Variation Reduction for Improving Non-Volatile Cache Lifetime

Non-volatile memory technologies are among the most promising technologies for implementing the main memories and caches in future microprocessors and replacing the traditional DRAM and SRAM technologies. However, one of the most challenging design issues of the non-volatile memory technologies is the limited write. In this article, we first propose to exploit the narrow-width values to improve the lifetime of non-volatile last-level caches with word-level write variation reduction. Leading zeros masking scheme is proposed to reduce the write stress to the upper half of the narrow-width data. To balance the write variations between the upper half and the lower half of the narrow-width data, two swapping schemes, the swap on write (SW) and swap on replacement (SRepl), are proposed. Two existing optimization schemes, the multiple dirty bit (MDB) and read before write (RBW), are adopted with our word-level swapping design. To further reduce the write variation on the partition level, we propose to exploit the cache partitioning design to improve the lifetime. Based on the observation that different applications demonstrate different cache access (write) behaviors, we propose to partition the last-level cache for different applications and balance the write variations by partition swapping. Both software-based and hardware-based partitioning and swapping schemes are proposed and evaluated for different situations. Our experimental results show that both our word- and partition-level designs can improve the lifetime of the non-volatile caches effectively with low performance and energy overheads.
NRIP, a Novel Calmodulin Binding Protein, Activates Calcineurin To Dephosphorylate Human Papillomavirus E2 Protein

ABSTRACT Previously, we found a gene named nuclear receptor interaction protein (NRIP) (or DCAF6 or IQWD1). We demonstrate that NRIP is a novel binding protein for human papillomavirus 16 (HPV-16) E2 protein. HPV-16 E2 and NRIP can directly associate into a complex in vivo and in vitro, and the N-terminal domain of NRIP interacts with the transactivation domain of HPV-16 E2. Only full-length NRIP can stabilize E2 protein and induce HPV gene expression, and NRIP silenced by two designed small interfering RNAs (siRNAs) decreases E2 protein levels and E2-driven gene expression. We found that NRIP can directly bind with calmodulin in the presence of calcium through its IQ domain, resulting in decreased E2 ubiquitination and increased E2 protein stability. Complex formation between NRIP and calcium/calmodulin activates the phosphatase calcineurin to dephosphorylate E2 and increase E2 protein stability. We present evidences for E2 phosphorylation in vivo and show that NRIP acts as a scaffold to recruit E2 and calcium/calmodulin to prevent polyubiquitination and degradation of E2, enhancing E2 stability and E2-driven gene expression.
The dopaminergic network and genetic susceptibility to schizophrenia

Background: Schizophrenia is a disabling illness with unknown pathogenesis. Estimates of heritability suggest a substantial genetic contribution; however genetic studies to date have been equivocal. Uncovering liability loci may therefore require analyses of functionally related genes. Rooted in this assumption, this dissertation describes a series of studies investigating a genetic epidemiological foundation for the commonly cited hypothesis suggesting dopaminergic dysfunction in schizophrenia pathogenesis, i.e. the 'dopamine hypothesis'. Studies: The initial study investigated DRD3 and identified novel associations across the gene. The second study considered a larger network of dopaminergic genes in two independent Caucasian samples, detecting replicated associations and epistatic interactions. This study proposed a risk model for schizophrenia centered on the dopamine transporter. Study #3 investigated a dopamine precursor, phenylalanine hydroxylase, in four independent samples, identifying a single SNP (rs1522305) that was significantly replicated in two samples. Study #4 was motivated by the hypothesis of a shared genetic etiology for schizophrenia and bipolar disorder. This study comprehensively evaluated the dopaminergic network, selecting 431 'tag' SNPs from 40 genes among large schizophrenia and bipolar cohorts contrasted with adult controls. Across all genes 60% of nominally significant schizophrenia risk factors were also associated with bipolar disorder. The results supported DRD3 variations as risk factors for both disorders, confirmed several previously reported associations, and proposed new targets for future research. Conclusion: These results suggest dopaminergic gene variations could play an etiological role in the pathogenesis of schizophrenia and possibly bipolar 1 disorder. Additional replicate studies are warranted. Public Health Significance: Schizophrenia (SZ) is devastating. When the Global Burden of Disease study calculated disability adjusted life years, weighted for the severity of disability, they determined active psychosis seen in schizophrenia produces disability equal to quadriplegia. Schizophrenia has been estimated to be among the top ten causes of disability worldwide. As schizophrenia is common (roughly 1% point prevalence worldwide), the economic burden to society is substantial. Pathogenesis is unknown and treatment is palliative. Therefore understanding the genetic etiology could facilitate development of promising therapeutics.
An Adaptive Source-Channel Coding with Feedback for Progressive Transmission of Medical Images

A novel adaptive source-channel coding with feedback for progressive transmission of medical images is proposed here. In the source coding part, the transmission starts from the region of interest (RoI). The parity length in the channel code varies with respect to both the proximity of the image subblock to the RoI and the channel noise, which is iteratively estimated in the receiver. The overall transmitted data can be controlled by the user (clinician). In the case of medical data transmission, it is vital to keep the distortion level under control as in most of the cases certain clinically important regions have to be transmitted without any visible error. The proposed system significantly reduces the transmission time and error. Moreover, the system is very user friendly since the selection of the RoI, its size, overall code rate, and a number of test features such as noise level can be set by the users in both ends. A MATLAB-based TCP/IP connection has been established to demonstrate the proposed interactive and adaptive progressive transmission system. The proposed system is simulated for both binary symmetric channel (BSC) and Rayleigh channel. The experimental results verify the effectiveness of the design.
TCR/CD3 coupling to Fas-based cytotoxicity

We studied the coupling of the TCR/CD3 complex to a T cell effector function, namely Fas-based T-cell-mediated cytotoxicity. Encounter or re-encounter with antigen was mimicked by treating 5 d mixed lymphocyte culture cells or T cell hybridomas with anti-CD3 antibody. This TCR/CD3 engagement induced swift expression of Fas-based cytotoxicity in these cells. Induction of Fas-based cytotoxicity was Ca(2+)-dependent, while its execution was not; induction was sensitive to macromolecular synthesis inhibitors, in line with a demonstrable increase of the Fas ligand (Fas-L) message. We also used T cell hybridomas transfected with various constructs to dissect the involvement of distinct components of the TCR/CD3 complex. The cytoplasmic domain of the CD3 zeta chain was able to transduce by itself a signal leading to Fas-L expression, unless there were mutations in its activation receptor homology sequence 1 (ARH-1) motifs. On the one hand, these findings are relevant to signal transduction pathways coupled to the TCR/CD3, and on the other hand, to the involvement of Fas-based T cell-mediated cytotoxicity in various physiological and possibly pathophysiological situations.
Smartphone cases and human friendliness in information technologies

This position paper introduces a new paradigm in human friendly computing and systems such that the shape, material and touch of a device case significantly matter. While casing has been considered as an auxiliary, that for mobile devices such as smart-phones becomes quite critical for their use. Since casing is an important part of user experiences of mobile devices, we believe that its integrity within information technologies plays an important role, thus needs to be well established.