Miracle-dz/UniFAR-FTUs huggingface dataset:
Clinical, Immunological and Molecular Characteristics of 37 Iranian Patients with X-Linked Agammaglobulinemia

Background: X-linked agammaglobulinemia (XLA) is a hereditary immunodeficiency characterized by an early onset of recurrent bacterial infections, a profound deficiency of all immunoglobulin isotypes and a markedly reduced number of peripheral B lymphocytes. Eighty-five percent of the patients with this phenotype have mutations in Bruton’s tyrosine kinase (BTK) gene. Methods: To provide an informative outlook of clinical and immunological manifestations of XLA in Iran, 37 Iranian male patients with an age range of 1–34 years, followed over a period of 25 years, were studied. Twenty-four of the 37 patients were screened for BTK gene mutation using PCR-SSCP followed by direct sequencing. BTK protein expression assay was done by flow cytometry in 9 families. Results: All patients first presented with infectious diseases, the most common of which were respiratory tract infections. Eighteen different mutations were identified, 13 of which were novel: IVS1+5G>C, 1896G>A, 349delA, 1618C>T, 1783T>C, 2084A>G, 1346delT, 1351delGAG, 587A>G, IVS14–1G>A, IVS3+2T>C, 1482G>A, 1975C>A. Conclusion: The fact that we found a great number of novel mutations in a relatively limited number of patients underlines the heterogeneity of BTK mutations in the Iranian population. The large number of new mutations indicates that extended studies in this region would be rewarding.
Colinearity of Reverse Transcriptase Inhibitor Resistance Mutations Detected by Population-Based Sequencing

High-level resistance to multiple drugs is often detected by directly sequencing uncloned polymerase chain reaction products (population-based sequencing). It is not known, however, if this method of identifying mutations gives an accurate picture of individual viral genomes. To determine how often multidrug-resistant isolates consist of clones containing every mutation present in the population-based sequence, a mean of 2.8 molecular clones was sequenced from the plasma of 25 heavily treated persons whose population-based sequence contained multiple reverse transcriptase (RT) inhibitor resistance mutations (71 clones). The 25 population-based sequences contained a mean of 5.7 nucleoside reverse transcriptase inhibitor (NRTI) resistance mutations and 1.2 nonnucleoside reverse transcriptase inhibitor (NNRTI) resistance mutations. The 71 clones contained a mean of 5.3 NRTI resistance mutations and 1.0 NNRTI resistance mutations. Sequences of clones closely resembled the population-based sequence: 36 (51%) clones had each of the RT inhibitor mutations present in the population-based sequence, 25 (35%) had all but 1 RT inhibitor mutation, 4 (6%) had all but 2 RT inhibitor mutations, 3 (4%) had all but 3 RT inhibitor mutations, and 3 (4%) had all but 4 RT inhibitor mutations. Phenotypic testing of 29 clones showed that most clones were resistant to nearly all NRTIs and that those with NNRTI resistance mutations were also resistant to multiple NNRTIs. These data show that in heavily treated persons, most RT inhibitor resistance mutations are present in the same viral genomes (colinear) and that multidrug resistance often occurs within individual clones as well as within virus populations.
Support Vector Machine – Based Prediction System for a Football Match Result

Different techniques have been used to develop result prediction systems. In particular, football match result prediction systems have been developed with techniques such as artificial neural networks, naïve Bayesian system, k-nearest neighbor algorithms (k-nn), and others. The choice of any technique depends on the application domain as well as the feature sets. The priority of a system developer or designer in most cases is to obtain a high prediction accuracy. The objective of this study is to investigate the performance of a Support Vector Machine (SVM) with respect to the prediction of football matches. Gaussian combination kernel type is used to generate 79 support vectors at 100000 iterations. 16 example football match results (data sets) were trained to predict 15 matches. The findings showed 53.3% prediction accuracy, which is relatively low. Until proven otherwise by other studies, an SVM-based system (as devised here) is not good enough in this application domain.
FBI wavelet/scalar quantization standard for gray-scale fingerprint image compression

The FBI has recently adopted a standard for the compression of digitized 8-bit gray-scale fingerprint images. The standard is based on scalar quantization of a 64-subband discrete wavelet transform decomposition of the images, followed by Huffman coding. Novel features of the algorithm include the use of symmetric boundary conditions for transforming finite- length signals and a subband decomposition tailored for fingerprint images scanned at 500 dpi. The standard is intended for use in conjunction with ANSI/NBS-CLS 1-1993, American National Standard Data Format for the Interchange of Fingerprint Information, and the FBI's Integrated Automated Fingerprint Identification System.
Cognitive and Linguistic Processing in the Bilingual Mind

The article reports research investigating the way bilingualism affects cognitive and linguistic performance across the life span. In general, bilingualism appears to have both benefits and costs. Regarding costs, bilinguals typically have lower formal language proficiency than monolinguals do; for example, they have smaller vocabularies and weaker access to lexical items. The benefits, however, are that bilinguals exhibit enhanced executive control in nonverbal tasks requiring conflict resolution, such as the Stroop and Simon tasks. These patterns and their consequences are illustrated and discussed. We also propose some suggestions regarding underlying mechanisms for these effects.
Reliability and Validity of the Japanese Version of the Stanford Presenteeism Scale in Female Employees at 2 Japanese Enterprises

Recent studies have suggested “presenteeism” is a situation often experienced by workers, and it is estimated to be the cause of a large amounts of economic loss for enterprises 1, . We defined presenteeism as “a self-rated measurable loss of work performance due to health problems in the workplace” in a previous investigation . This represents an important concept for health promotion activities in occupational health. Therefore, measurement tools of presenteeism are required in Japan. The 13-item Stanford Presenteeism Scale (SPS) was developed in the United States in 2004 4, 5) and was designed to determine presenteeism due to a specific health condition over a 4-week period. SPS comprises 4 modules: a) selection of all health conditions and a single primary health condition (PHC) of a worker from a health condition list; b) degree of presenteeism due to the PHC (Work Impairment Score [WIS]); c) effect of the PHC on work output (Work Output Score [WOS]), a single visual analog scale, global assessment that asks the respondent what percentage he/she was able to perform effectively, given their PHC; and d) hours of absenteeism due to the PHC. WIS measures decline in work performance due to the PHC—presenteeism—in a variety of situations and comprises ten questions scored with a five-point Likert scale, ranging from “always” to “never”. WIS, including cognitive, emotional, and behavioral aspects, is able to measure presenteeism among not only production-based workers but also knowledge-based workers. The raw WIS is converted to a 100-point scale, with higher scores indicating a higher level of presenteeism and a lower level of work performance. A previous study by Turpin et al. identified two underlying factors of WIS, “completing work” and “avoiding distraction”. Furthermore they found factor loading varied from knowledge-based jobs to production-based jobs. From these applicable and practical features of the SPS, it might be a useful measurement tool of presenteeism for Japanese workers. Therefore, the objective of the present study was to investigate the reliability and validity of the Japanese version of the SPS.
Jaatha: a fast composite‐likelihood approach to estimate demographic parameters

While information about a species’ demography is interesting in its own right, it is an absolute necessity for certain types of population genetic analyses. The most widely used methods to infer a species’ demographic history do not take intralocus recombination or recent divergence into account, and some methods take several weeks to converge. Here, we present Jaatha, a new composite‐likelihood method that does incorporate recent divergence and is also applicable when intralocus recombination rates are high. This new method estimates four demographic parameters. The accuracy of Jaatha is comparable to that of other currently available methods, although it is superior under certain conditions, especially when divergence is very recent. As a proof of concept, we apply this new method to estimate demographic parameters for two closely related wild tomato species, Solanum chilense and S. peruvianum. Our results indicate that these species likely diverged 1.44·N generations ago, where N is the effective population size of S. chilense, and that some introgression between these species continued after the divergence process initiated. Furthermore, S. peruvianum likely experienced a population expansion following speciation.
Feline immunodeficiency virus can be experimentally transmitted via milk during acute maternal infection

Postnatal transmission of feline immunodeficiency virus (FIV) in neonates nursed by acutely infected mothers and infection resulting from oral inoculation of kittens with FIV were evaluated. Ten of 16 kittens nursed by four queens with FIV infection established immediately postpartum developed FIV infection. Five of 11 neonates orally administered cell-free FIV culture supernatant developed FIV infection. Kittens that developed FIV infection had greater proportions of CD4+ and Pan-T+ lymphocytes at birth than negative kittens. Infectious virus was recovered from the milk of acutely infected mothers. We conclude that FIV may be experimentally transmitted via milk from queens with acute infections and that oral administration of FIV to neonatal kittens results in infection.
Resource Characterization of Epithelial Progenitors in Normal Human Palatine Tonsils and Their HPV 16 E 6 / E 7-Induced Perturbation

Sung Yoon Catherine Kang,1,2 Nagarajan Kannan,3,4 Lewei Zhang,5 Victor Martinez,6 Miriam P. Rosin,1,2,8 and Connie J. Eaves3,7,8,* 1Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC V5A 1S6, Canada 2Department of Cancer Control Research, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada 3Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada 4Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 1Z4, Canada 5Faculty of Dentistry, University of British Columbia, Vancouver, BC V6T 1Z4, Canada 6Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada 7Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada 8Co-senior author *Correspondence: ceaves@bccrc.ca http://dx.doi. org/10.1016/j.stemcr. 2015.09. 020 This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
A Transform-Domain Decoding Algorithm for Reed-Solomon Codes

This paper presents a Reed-Solomon decoding algorithm based on the Euclidean algorithm. The algorithm is conceptually simple and operates only in transform domain. The spectrum of the codeword is directly computed without the explicit knowledge of error-locator and error-evaluator polynomials; the Chien search and the Forney algorithm are not necessary
Genome-wide RNAi screening implicates the E3 ubiquitin ligase Sherpa in mediating innate immune signaling by Toll in Drosophila adults

Ubiquitylation and SUMOylation of the adaptor protein dMyd88 are required for Toll-dependent immune responses in Drosophila. Sherpa guides Toll signaling Mammalian Toll-like receptors (TLRs) recognize pathogen-derived molecular patterns and stimulate the innate immune response. These proteins are named for their counterparts in the fruit fly Drosophila in which the first of these, Toll, was identified. Kanoh et al. showed that the fly Toll innate immune signaling pathway required an E3 ubiquitin ligase called Sherpa. Flies expressing a ligase-defective mutant Sherpa had compromised immune responses to bacterial infection. The adaptor protein dMyd88, which interacts with Toll, relied on both Sherpa and the Drosophila SUMO homolog for proper subcellular localization. Thus, this study reveals additional similarities between the fly and mammalian innate immune systems. The Drosophila Toll pathway plays important roles in innate immune responses against Gram-positive bacteria and fungi. To identify previously uncharacterized components of this pathway, we performed comparative, ex vivo, genome-wide RNA interference screening. In four screens, we overexpressed the Toll adaptor protein dMyd88, the downstream kinase Pelle, or the nuclear factor κB (NF-κB) homolog Dif, or we knocked down Cactus, the Drosophila homolog of mammalian inhibitor of NF-κB. On the basis of these screens, we identified the E3 ubiquitin ligase Sherpa as being necessary for the activation of Toll signaling. A loss-of-function sherpa mutant fly exhibited compromised production of antimicrobial peptides and enhanced susceptibility to infection by Gram-positive bacteria. In cultured cells, Sherpa mediated ubiquitylation of dMyd88 and Sherpa itself, and Sherpa and Drosophila SUMO (small ubiquitin-like modifier) were required for the proper membrane localization of an adaptor complex containing dMyd88. These findings highlight a role for Sherpa in Drosophila host defense and suggest the SUMOylation-mediated regulation of dMyd88 functions in Toll innate immune signaling.
XY-Theta Positioning Table with Parallel Kinematics and Unlimited Theta Rotation

Parallel robots are increasingly being used in industry for positioning and alignment. They have the advantage of being rigid, quick, and accurate. However, most parallel robots have very limited rotational capabilities and in cases where unlimited rotation is necessary, the only option used to be adding a rotary table. There however exists one overlooked XY-theta parallel robot design that can reach any point within a circular workspace at any orientation. This unique design consists of three pivots moving independently along a common circular path. These pivots are connected individually to three linear guides attached to a mobile platform in a symmetric "Y" shape. By studying the kinematics of this parallel robot, this paper shows that not only is the dextrous workspace large but the kinematic accuracy is high and uniform
Stromal cell‐derived factor‐1/CXCL12 directly enhances survival/antiapoptosis of myeloid progenitor cells through CXCR4 and Gαi proteins and enhances engraftment of competitive, repopulating stem cells

Stromal cell‐derived factor‐1 (SDF‐1/CXCL12) enhances survival of myeloid progenitor cells. The two main questions addressed by us were whether these effects on the progenitors were direct‐acting and if SDF‐1/CXCL12 enhanced engrafting capability of competitive, repopulating mouse stem cells subjected to short‐term ex vivo culture with other growth factors. SDF‐1/CXCL12 had survival‐enhancing/antiapoptosis effects on human bone marrow (BM) and cord blood (CB) and mouse BM colony‐forming units (CFU)‐granulocyte macrophage, burst‐forming units‐erythroid, and CFU‐granulocyte‐erythroid‐macrophage‐megakaryocyte with similar dose responses. The survival effects were direct‐acting, as assessed on colony formation by single isolated human BM and CB CD34+++ cells. Effects were mediated through CXCR4 and Gαi proteins. Moreover, SDF‐1/CXCL12 greatly enhanced the engrafting capability of mouse long‐term, marrow‐competitive, repopulating stem cells cultured ex vivo with interleukin‐6 and steel factor for 48 h. These results extend information on the survival effects mediated through the SDF‐1/CXCL12–CXCR4 axis and may be of relevance for ex vivo expansion and gene‐transduction procedures.
Mechanical Heart—Lung for Use in Man

Foreword Some years ago the department of surgery in the Postgraduate Medical School of London was concerned with research in the perfusion of isolated human organs. The perfusion of isolated organs by blood artificially oxygenated and propelled by a mechanical pump cannot be continued for more than a few hours. After some hours the perfused organ swells visibly and the outflow of blood from it progressively and rapidly diminishes. After a short and not very successful examination of the problem of prolongation of the survival time of isolated organs in these conditions attention was turned to the extracorporeal heart-lung circulation for the maintenance of the circulation of the experimental animal by a total replacement of its own heart and lungs, comparable to that which would be required in the application of an apparatus of this kind to intracardiac surgery. It seemed to us, after some experience in this field, that a machine to undertake the whole function of heart and lungs in a patient subjected to intracardiac surgery was not yet an immediately attainable aim. Animals maintained entirely on an extracorporeal heartlung circulation sometimes survive for indefinite periods, but a high proportion fail to survive, perhaps for reasons not dissimilar to those which make prolonged perfusion of the isolated organ impossible. The natural lung may have other functions than oxygenation. In any case, there are immediate practical difficulties in employing a heart-lung machine to replace the heart and lungs of a patient subjected to cardiac surgery. Heparinization must be complete, and the difficulty of obtaining a bloodless field even in a heart to which blood is not returned ,by the venae cavae has already been demonstrated at least once in man. Our attention accordingly passed to the use of a heart-lung machine as a form of " assisted circulation. " Our aim in this field became the ultimate use of an artificial heart-lung machine for the treatment of certain acute forms of cardiac or pulmonary failure. The value of artificial oxygenation of the blood for even a short period in acute pulmonary oedema or status asthmaticus seemed obvious enough, for, provided the patient can be kept oxygenated for a time, these pathological circumstances are often self-limiting. In coronary thrombosis there are patients in whom it might be expected that the
Multicriteria shape design of a sheet contour in stamping

One of the hottest challenges in automotive industry is related to weight reduction in sheet metal forming processes, in order to produce a high quality metal part with minimal material cost. Stamping is the most widely used sheet metal forming process; but its implementation comes with several fabrication flaws such as springback and failure. A global and simple approach to circumvent these unwanted process drawbacks consists in optimizing the initial blank shape with innovative methods. The aim of this paper is to introduce an efficient methodology to deal with complex, computationally expensive multicriteria optimization problems. Our approach is based on the combination of methods to capture the Pareto Front, approximate criteria (to save computational costs) and global optimizers. To illustrate the efficiency, we consider the stamping of an industrial workpiece as test-case. Our approach is applied to the springback and failure criteria. To optimize these two criteria, a global optimization algorithm was chosen. It is the Simulated Annealing algorithm hybridized with the Simultaneous Perturbation Stochastic Approximation in order to gain in time and in precision. The multicriteria problems amounts to the capture of the Pareto Front associated to the two criteria. Normal Boundary Intersection and Normalized Normal Constraint Method are considered for generating a set of Pareto-optimal solutions with the characteristic of uniform distribution of front points. The computational results are compared to those obtained with the well-known Non-dominated Sorting Genetic Algorithm II. The results show that our proposed approach is efficient to deal with the multicriteria shape optimization of highly non-linear mechanical systems.
Calcium dependent formation of tubular assemblies by recombinant S-layer proteins in vivo and in vitro

Surface layer proteins have the appealing property to self-assemble in nanosized arrays in solution and on solid substrates. In this work, we characterize the formation of assembly structures of the recombinant surface layer protein SbsC of Geobacillus stearothermophilus ATTC 12980, which was tagged with enhanced green fluorescent protein and expressed in the yeast Saccharomyces cerevisiae. The tubular structures formed by the protein in vivo are retained upon bursting the cells by osmotic shock; however, their average length is decreased. During dialysis, monomers obtained by treatment with chaotropic chemicals recrystallize again to form tube-like structures. This process is strictly dependent on calcium (Ca2 + ) ions, with an optimal concentration of 10 mM. Further increase of the Ca2 + concentration results in multiple non-productive nucleation points. We further show that the lengths of the S-layer assemblies increase with time and can be controlled by pH. After 48 h, the average length at pH 9.0 is 4.13 µm compared to 2.69 µm at pH 5.5. Successful chemical deposition of platinum indicates the potential of recrystallized mSbsC-eGFP structures for nanobiotechnological applications.