Miracle-dz/UniFAR-FTUs huggingface dataset:
Arginine methylation and citrullination of splicing factor proline- and glutamine-rich (SFPQ/PSF) regulates its association with mRNA

Splicing factor proline- and glutamine-rich (SFPQ) also commonly known as polypyrimidine tract-binding protein-associated-splicing factor (PSF) and its binding partner non-POU domain-containing octamer-binding protein (NONO/p54nrb), are highly abundant, multifunctional nuclear proteins. However, the exact role of this complex is yet to be determined. Following purification of the endogeneous SFPQ/NONO complex, mass spectrometry analysis identified a wide range of interacting proteins, including those involved in RNA processing, RNA splicing, and transcriptional regulation, consistent with a multifunctional role for SFPQ/NONO. In addition, we have identified several sites of arginine methylation in SFPQ/PSF using mass spectrometry and found that several arginines in the N-terminal domain of SFPQ/PSF are asymmetrically dimethylated. Furthermore, we find that the protein arginine N-methyltransferase, PRMT1, catalyzes this methylation in vitro and that this is antagonized by citrullination of SFPQ. Arginine methylation and citrullination of SFPQ/PSF does not affect complex formation with NONO. However, arginine methylation was shown to increase the association with mRNA in mRNP complexes in mammalian cells. Finally we show that the biochemical properties of the endogenous complex from cell lysates are significantly influenced by the ionic strength during purification. At low ionic strength, the SFPQ/NONO complex forms large heterogeneous protein assemblies or aggregates, preventing the purification of the SFPQ/NONO complex. The ability of the SFPQ/NONO complex to form varying protein assemblies, in conjunction with the effect of post-translational modifications of SFPQ modulating mRNA binding, suggests key roles affecting mRNP dynamics within the cell.
Japan's Orient: Rendering Pasts into History.

This study examines how Japanese historians during the late 19th and early 20th centuries created the equivalent of an "Orient" for their new nation state. After the Meiji Restoration, Japan faced the necessity of becoming modern while both shedding the Western characterization of "Oriental" and maintaining its own identity. The concept of "toyoshi" (Oriental studies) made it possible to fit the changes of the previous century - the arrival of the West with its technical and cultural baggage and the decline of China - into a comprehensive ideological system. Unlike other scholars, who depict the encounter between Japan and the West as a struggle between modernity and tradition, Tanaka argues that the Japanese were, in fact, attempting to use a variety of pasts - Chinese, Indian, and proto-historic Japanese - to construct an identity that was both modern and Asian.
Improving the Detection of Malware Behaviour Using Simplified Data Dependent API Call Graph

Malware stands for malicious software. It is software that is designed with a harmful intent. A malware detector is a system that attempts to identify malware using Application Programming Interface (API) call graph technique and/or other techniques. Matching the API call graph using graph matching algorithm have NP-complete problem and is slow because of computational complexity . In this study, a malware detection system based on API call graph is proposed. Each malware sample is represented as data dependent API call graph. After transforming the input sample into a simplified data dependent graph, graph matching algorithm is used to calculate similarity between the input sample and malware API call graph samples stored in a database. The graph matching algorithm is based on Longest Common Subsequence (LCS) algorithm which is used on the simplified graphs. Such strategy reduces the computation complexity by selecting paths with the same edge label in the API call graph. Experimental results on 85 samples demonstrate 98% detection rate and 0% false positive rate for the proposed malware detection system.
Two-Stage Offshoring: An Investigation of the Irish Bridge

This paper investigates two-stage offshoring as experienced by the Irish sites of two large global companies, headquartered in the United States, with significant software development operations. As part of these companies, the Irish sites act as a bridge in their offshoring arrangements: While the U.S. sites offshore work to Ireland, the Irish sites offshore work further to India and, hence, have experience of being both customer and vendor in two-stage offshore sourcing relationships. Using a framework derived from relational exchange theory (RET), we conducted multiple case study research to investigate and develop an initial theoretical model of the implementation of this two-stage offshoring bridge model. Our study shows that while both companies act as bridges in two-stage offshoring arrangements, their approaches differ in relation to (1) team integration, (2) organizational level implementation, and (3) site hierarchy. Although, there are opportunities afforded by the bridge model at present, the extent to which these opportunities will be viable into the future is open to question. As revealed in our study, temporal location seems to favor a bridge location such as Ireland, certainly with United States-Asian partners. However, location alone will not be enough to maintain position in future two-stage offshoring arrangements. Furthermore, our research supports the view that offshoring tends to progress through a staged sequence of progressively lower cost destinations. Such a development suggests that two-stage offshoring, as described in this paper, will eventually become what we would term multistage offshoring.
Blind source separation based on the array-averaged Fractional Fourier Transform

In this paper, a novel blind source separation method based on the array-averaged Fractional Fourier Transform is proposed. This method can decrease the noise levels, and suppress the interactions of the source signals, which lead to better separation performance. Compared with the previous blind source separation techniques based on the time-frequency distributions, this proposed method produces little crossterms, and it does not require whitening, joint-diagonalization, and bilinear signal synthesis. The improved efficiency of the method is verified by the simulation.
OpenVDB: an open-source data structure and toolkit for high-resolution volumes

OpenVDB has already been integrated into the next major release of the high-end 3D animation package Houdini, and there is anecdotal evidence that many of the major VFX and production houses are in the process of either evaluating or adopting VDB. This course presents a comprehensive overview of OpenVDB, an open-source C++ library comprising a novel hierarchical data structure and a suite of tools for efficient storage and manipulation of sparse volumetric data discretized on three-dimensional grids.
Calcineurin Inhibitor Minimization With Ixazomib, an Investigational Proteasome Inhibitor, for the Prevention of Antibody Mediated Rejection in a Preclinical Model

Background There is a need for new immunosuppression strategies to minimize calcineurin inhibitor (CNI) toxicity while effectively preventing antibody-mediated rejection (AMR). Methods We tested the efficacy of an investigational proteasome inhibitor, ixazomib, alone and in a CNI minimization strategy in a rat kidney transplant model of transfusion-elicited acute AMR. Nonsensitized (naïve) and sensitized allograft recipients were randomized into 4 treatment groups (8 groups total, n = 3 to 6 in each group) and treated for 1 week. Groups included: no treatment, full dose cyclosporine (CsA, 10 mg/kg per day), ixazomib (0.25 mg/kg on days −5, −2 and +2) alone, and half dose CsA (5 mg/kg per day) + ixazomib. Results Compared to untreated animals, ixazomib alone or in combination with ½ dose CsA reduced donor-specific antibody, intragraft transcripts for chemokines CCL-21 and CXCL-13, and CD19 expression in both sensitized and naïve transplants. Compared to full dose CsA, the CNI minimization strategy with ixazomib inhibited AMR and allograft injury as evidenced by reduced C4d staining in peritubular capillaries, microcirculation inflammation, splenic plasma cells, circulating B cell activating factor, and intragraft transcripts for major histocompatibility complex class II, Toll-like receptors (TLR-1, TLR-10, and TLR-12) and CCL-21 and CXCL-13 in sensitized animals, indicating downregulation of B cell activation, antigen presentation and T-cell and B-cell signaling. Conclusions These studies suggest that CNI minimization strategies including ixazomib are effective to prevent AMR including in sensitized kidney allograft recipients. Clinical studies are needed to determine the role of novel proteasome inhibitors for the prevention and treatment of AMR.
Terrain Aided Navigation for Long Range AUV operations at arctic latitudes

This paper investigates the potential of use of Terrain Aided Navigation (TAN) methods to exploit the extended endurance capabilities of an enhanced 1500m depth rated variant of the Autosub Long Range (ALR), the ALR1500 Autonomous Underwater Vehicle (AUV), for operations under the Arctic ice. A simulator for the TAN system using a low resolution Arctic bathymetric map is developed to study the capability to reduce/bound the positioning error growth due to the Dead Reckoning (DR) drift over time. Bathymetric measurements are obtained using a low sample rated single beam echo sounder and a Jittered Bootsrap Particle Filter (JBPF) is used for the multi-sensor data fusion problem. Sensitivity analysis of JBPF has been performed for a range of values of number of particles, jittering variances and measurement frequencies and a discussion over the results is given. Results from the simulation demonstrate that JBPF is capable of providing a robust and accurate solution to the localization problem provided that the AUV follows a trajectory with a sufficiently variant terrain. Finally, a brief discussion regarding the future extension of this work is also provided.
Sequence Diversity and Molecular Evolution of the Heat-Modifiable Outer Membrane Protein Gene (ompA) of Mannheimia(Pasteurella) haemolytica, Mannheimia glucosida, and Pasteurella trehalosi

ABSTRACT The OmpA (or heat-modifiable) protein is a major structural component of the outer membranes of gram-negative bacteria. The protein contains eight membrane-traversing β-strands and four surface-exposed loops. The genetic diversity and molecular evolution of OmpA were investigated in 31 Mannheimia (Pasteurella) haemolytica, 6 Mannheimia glucosida, and 4 Pasteurella trehalosi strains by comparative nucleotide sequence analysis. The OmpA proteins of M. haemolytica and M. glucosida contain four hypervariable domains located at the distal ends of the surface-exposed loops. The hypervariable domains of OmpA proteins from bovine and ovine M. haemolytica isolates are very different but are highly conserved among strains from each of these two host species. Fourteen different alleles representing four distinct phylogenetic classes, classes I to IV, were identified in M. haemolytica and M. glucosida. Class I, II, and IV alleles were associated with bovine M. haemolytica, ovine M. haemolytica, and M. glucosida strains, respectively, whereas class III alleles were present in certain M. haemolytica and M. glucosida isolates. Class I and II alleles were associated with divergent lineages of bovine and ovine M. haemolytica strains, respectively, indicating a history of horizontal DNA transfer and assortative (entire gene) recombination. Class III alleles have mosaic structures and were derived by horizontal DNA transfer and intragenic recombination. Our findings suggest that OmpA is under strong selective pressure from the host species and that it plays an important role in host adaptation. It is proposed that the OmpA protein of M. haemolytica acts as a ligand and is involved in binding to specific host cell receptor molecules in cattle and sheep. P. trehalosi expresses two OmpA homologs that are encoded by different tandemly arranged ompA genes. The P. trehalosi ompA genes are highly diverged from those of M. haemolytica and M. glucosida, and evidence is presented to suggest that at least one of these genes was acquired by horizontal DNA transfer.
Parallels in lignin biosynthesis

A hallmark of vascular plants is the development of a complex water-conducting system, which is physically reinforced by the heterogeneous aromatic polymer lignin. Syringyl lignin, a major building block of lignin, is often thought to be uniquely characteristic of angiosperms; however, it was demonstrated over fifty years ago that that syringyl lignin is found in another group of plants, known as the lycophytes, the ancestors of which diverged from all the other vascular plant lineages 400 million years ago.1 To determine the biochemical basis for this common biosynthetic ability, we isolated and characterized cytochrome P450-dependent monooxygenases (P450s) from the lycophyte Selaginella moellendorffii and compared them to the enzyme that is required for syringyl lignin synthesis in angiosperms. Our results showed that one of these P450s encodes an enzyme that is functionally analogous to but phylogenetically independent from its angiosperm counterpart. Here, we discuss the evolution of lignin biosynthesis in vascular plants and the role of Selaginella moellendorffii in plant comparative biology and genomics.
Ensembles based combined learning for improved software fault prediction: A comparative study

Software Fault Prediction (SFP) research has made enormous endeavor to accurately predict fault proneness of software modules to maximize precious software test resources, reduce maintenance cost, help to deliver software products on time and satisfy customer, which ultimately contribute to produce quality software products. In this regard, Machine Learning (ML) has been successfully applied to solve classification problems for SFP. Moreover, from ML, it has been observed that Ensemble Learning Algorithms (ELA) are known to improve the performance of single learning algorithms. However, neither of ELA alone handles the challenges created by redundant and irrelevant features and class imbalance problem in software defect datasets. Therefore, the objective of this paper is to independently examine and compare prominent ELA and improves their performance combined with Feature Selection (FS) and Data Balancing (DB) techniques to identify more efficient ELA that better predict the fault proneness of software modules. Accordingly, a new framework that efficiently handles those challenges in a combined form is proposed. The experimental results confirm that the proposed framework has exhibited the robustness of combined techniques. Particularly the framework has high performance when using combined bagging ELA with DB on selected features. Therefore, as shown in this study, ensemble techniques used for SFP must be carefully examined and combined with both FS and DB in order to obtain robust performance.
Subjective judgements in scientiﬁc practice and art

Since art and science went their separate ways in the 18th century, the purpose of science has been to generate true knowledge based on reason and objectivity. However, during the second half of the 20th century, opinions emerged within science that showed the impossibility of eliminating subjectivity in scientiﬁc practice. This paper describes the similarity of the subjective judgements that form part of the peer-review system d the method devised by the scientiﬁc community to guarantee truth and objectivity d and the subjective judgements involved in artistic evaluation.
Synchroneity of Tropical and High-Latitude Atlantic Temperatures over the Last Glacial Termination

A high-resolution western tropical Atlantic sea surface temperature (SST) record from the Cariaco Basin on the northern Venezuelan shelf, based on Mg/Ca values in surface-dwelling planktonic foraminifera, reveals that changes in SST over the last glacial termination are synchronous, within ±30 to ±90 years, with the Greenland Ice Sheet Project 2 air temperature proxy record and atmospheric methane record. The most prominent deglacial event in the Cariaco record occurred during the Younger Dryas time interval, when SSTs dropped by 3° to 4°C. A rapid southward shift in the atmospheric intertropical convergence zone could account for the synchroneity of tropical temperature, atmospheric methane, and high-latitude changes during the Younger Dryas.
Predictive Channel Quantization and Beamformer Design for MIMO-BC with Limited Feedback

For a cellular system based on frequency division duplexing where the base station (BS) is equipped with multiple antennas and the mobile terminals (MTs) have one antenna each, we propose joint techniques to a) feed back channel state information from MTs to the BS, b) design the beamformer and c) schedule downlink transmissions. We propose that both BS and MT predict channel variations, and the feedback (FB) information from MT to BS is given by the prediction error. For the beamformer design we both consider a zero forcing approach and investigate a new solution based on the minimum mean square error criterion, which takes into account the quantization error. By exploiting the FB information, we derive approximated expressions of the signal to noise ratio relative to each MT, used at BS to perform scheduling with an efficient greedy algorithm. Performance assessment on realistic 3GPP channel models show that the proposed techniques provide a significant improvement of the network throughput at a lower FB rate than existing solutions.
Expression and Enzymatic Characterization of Recombinant Human Kallikrein 14

Abstract Human kallikrein 14 (KLK14) is a member of the human kallikrein gene family of serine proteases, and its protein, hK14, has recently been suggested to serve as a new ovarian and breast cancer marker. To gain insights into hK14's physiological functions, the active recombinant enzyme was obtained in an enzymatically pure state for biochemical and enzymatic characterizations. We studied its substrate specificity and behavior to various protease inhibitors, and identified candidate physiological substrates. hK14 had trypsin-like activity with a strong preference for Arg over Lys in the P1 position, and its activity was inhibited by typical serine protease inhibitors. The protease degraded casein, fibronectin, gelatin, collagen type I, collagen type IV, fibrinogen, and high-molecular-weight kininogen. Furthermore, it rapidly hydrolyzed insulin-like growth factor binding protein-3 (IGFBP-3). These findings suggest that hK14 may be implicated in tumor progression in ovarian carcinoma.
Pathophysiology of type 1 and type 2 diabetes mellitus: a 90-year perspective

Diabetes mellitus is a complex metabolic disorder associated with an increased risk of microvascular and macrovascular disease; its main clinical characteristic is hyperglycaemia. The last century has been characterised by remarkable advances in our understanding of the mechanisms leading to hyperglycaemia. The central role of insulin in glucose metabolism regulation was clearly demonstrated during the early 1920s, when Banting, Best, Collip and Macleod successfully reduced blood glucose levels and glycosuria in a patient treated with a substance purified from bovine pancreata. Later, during the mid-1930s, clinical observations suggested a possible distinction between ‘insulin-sensitive’ and ‘insulin-insensitive’ diabetes. Only during the 1950s, when a reliable measure of circulating insulin was available, was it possible to translate these clinical observations into pathophysiological and biochemical differences, and the terms ‘insulin-dependent’ (indicating undetectable insulin levels) and ‘non-insulin-dependent’ (normal or high insulin levels) started to emerge. The next 30 years were characterised by pivotal progress in the field of immunology that were instrumental in demonstrating an immune-mediated loss of insulin-secreting β-cells in subjects with ‘insulin-dependent’ diabetes. At the same time, new experimental techniques allowing measurement of insulin ‘impedance’ showed a reduced peripheral effect of insulin in subjects with ‘non-insulin-dependent’ diabetes (insulin resistance). The difference between the two types of diabetes emerging from decades of observations and experiments was further formally recognised in 1979, when the definitions ‘type I’ and ‘type II’ diabetes were introduced to replace the former ‘insulin-dependent’ and ‘non-insulin-dependent’ terms. In the following years, many studies elucidated the natural history and temporal contribution of insulin resistance and β-cell insulin secretion in ‘type II’ diabetes. Furthermore, a central role for insulin resistance in the development of a cluster of cardiometabolic alterations (dyslipidaemia, inflammation, high blood pressure) was suggested. Possibly as a consequence of the secular changes in diabetes risk factors, in the last 10 years the limitation of a simple distinction between ‘type I’ and ‘type II’ diabetes has been increasingly recognised, with subjects showing the coexistence of insulin resistance and immune activation against β-cells. With the advancement of our cellular and molecular understanding of diabetes, a more pathophysiological classification that overcomes the historical and simple ‘glucocentric’ view could result in a better patient phenotyping and therapeutic approach.
Optimized large size signed multipliers and applications in FPGAs

Arithmetic computation decomposition is a powerful strategy used to solve large and complicated computing problems. In this paper, efficient design methodologies and systematic approaches for realizing large size signed multipliers are presented based on the use of small-size embedded blocks in FPGAs. To demonstrate the effectiveness of our approach, two large size operand computations are realized using our optimized large size multipliers. These functions are complex multiplication and matrix multiplication. The implementations targeted Xilinx' and Altera's FPGAs. Significant improvements of performance and area usage have been achieved for both applications compared to traditional techniques.
Twice‐a‐day radiotherapy for squamous cell carcinoma of the head and neck: The University of Florida experience

Between March 1978 and March 1989, 419 patients with 439 moderately advanced or advanced primary squamous cell carcinomas of the head and neck received treatment with curative intent with twice‐a‐day radiotherapy (120 cGy per fraction with a 4‐ to 6‐hour interfraction interval). Seventy‐nine percent of the patients had AJCC stage III or stage IV cancers. The primary site in most patients was the oropharynx, hypopharynx, or larynx. All patients received radiotherapy alone to the primary site, with or without planned neck dissection after radiotherapy. Surgery at the primary site was reserved for salvage of radiotherapy failures. No patient received chemotherapy as part of the initial treatment plan. Total doses were 7440 cGy to 7920 cGy in the majority of patients. In 54 patients with oropharyngeal lesions, an interstitial implant was used to add a 1,000‐ to 1,500‐cGy boost after the basic dose. Local control results were compared on a site‐by‐site and stage‐by‐stage basis with the results of continuous‐course, once‐a‐day radiotherapy at the University of Florida; the control results were the same as or better than after once‐a‐day radiotherapy for each site and stage (T2 to T4). Severe complications of radiotherapy occurred in 4% of patients and correlated with tumor dose, T stage, and disease site (oropharynx or larynx/hypopharynx). The addition of a neck dissection 4 to 6 weeks after radiotherapy of patients with advanced‐stage neck disease was accomplished with an acceptable rate of morbidity and significantly improved the rate of control of neck metastases compared with radiotherapy alone.