Miracle-dz/UniFAR-FTUs huggingface dataset:
Expression of Two Related Viral Early Genes in Epstein-Barr Virus-Associated Tumors

ABSTRACT The transcription of two early “leftwardly” expressed genes carrying repetitive sequences, IR2 and IR4, has been studied for Epstein-Barr virus-associated tumors, and for established B-cell lines, using sequence-specific probes generated for this purpose. Whereas the IR4 transcript was identified in every tumor and cell line assessed (except B95-8, with a deletion that removes the gene), expression of the IR2 gene was restricted to B lymphocytes. Though the promoters for both transcripts lie within homologous regions (DL and DR) in the viral genome, the IR2 promoter appears more tightly regulated. Detailed characterization of the IR4 transcript from a nasopharyngeal carcinoma tumor, C15, identifies a sequence variant of this gene that differs from those reported for B cells; in situ hybridization methods show transcription to be restricted to a subset of cells, with the strongest signals seen adjacent to host stroma. As with B cells in culture (Y. Gao, P. R. Smith, L. Karran, Q. L. Lu, and B. E. Griffin, J. Virol. 71:84–94, 1997), chemical induction enhanced transcriptional expression of the IR4 gene in the C15 tumor, although staining for both the IR4 antigen and that of the virus lytic switch, Zta, gave negative results. In a Burkitt's lymphoma biopsy specimen, however, both proteins were found expressed, notably in the same subset of cells. The data here and elsewhere (Gao et al., J. Virol., 1997) are consistent with a block to intracellular transport of the transcript(s) and suggest nuclear roles for it in tumors, possibly in RNA processing and viral lytic replication. Both roles could be fulfilled in the absence of translation.
Identification of Two Tentative Strains of European Subspecies of the Eurasian River Otter Lutra lutra lutra (Linnaeus, 1758) from the Partial Mitochondrial Cytochrome b Gene

The Eurasian river otter Lutra lutra is the most widely distributed otter species. The European subspecies L. lutra lutra (Linnaeus, 1758) kept in European zoos has four strains; two of which (the Aand B-lines) have been introduced into zoos and aquariums in Japan. As the genetic backgrounds of, and differences between, these two strains were unknown, we identified partial nucleotide sequences (307bp) of the mitochondrial cytochrome b gene from an A-line and a B-line individual, A-line cyb and B-line cyb, respectively, kept in an aquarium in Japan. The nucleotide sequence of the A-line cyb and B-line cyb showed 98.7% identity and are distinguishable by the restriction fragment length polymorphism analysis. A-line cyb was 100% identical to the cytochrome b of L. lutra lutra, whereas B-line cyb failed to show 100% identity to the known nucleotide sequences on the database. The phylogenetic analysis of our sequences with those from a previous study revealed that the two strains had already been introduced into Japan by at latest the 1990s. These results suggest that there are slight differences between the Aand B-line individuals used in the present study. However, further investigations, including re-evaluation of the taxonomy of L. lutra subspecies, are needed to clarify the differences between the two strains.
Physical Fitness of South African Primary School Children, 6 to 13 Years of Age: Discovery Vitality Health of the Nation Study

Basic physical fitness was measured using 8 different measures for 10,295 South African children and youths (5,611 boys, 4,684 girls) ages 6 to 13 years. These measurements included height, weight, Body Mass Index, standing long jump, shuttle run, sit-and-reach, sit-up (EUROFIT testing battery), and cricket ball throw scores. Due to the effects of earlier apartheid laws on separating communities, it was hypothesized that scores for different ethnic groups may differ. Therefore, in addition to the calculation of basic norms and sex differences, ethnic differences were also tested. Height and weight, relative to age, were different between the various ethnic groups (Black, White, and Mixed ancestry3) for boys, with Black boys being shorter and lighter than White boys. There were no differences in sit-and-reach flexibility scores between the groups. With the exception of the cricket ball throw for girls, White children had higher scores in most tests. Although not significantly different from the White children, in the majority of cases, the children of mixed ancestral origin had scores that ranged between the other two ethnic groups. These results suggest a need for encouraging fitness in school children, and the reintroduction of formal physical education into the South African school curriculum, especially into schools in which Black children predominate.
Change in anthropometrics and aerobic fitness in Air Force cadets during 3 years of academy studies.

INTRODUCTION Favorable anthropometrical status and aerobic fitness levels are emphasized in Norwegian Air Force personnel. However, it is unknown how these variables develop in Air Force cadets. Thus, the main aim of the present study was to examine how anthropometrics and maximal oxygen uptake (VO2(max)) change among Norwegian Air Force cadets during 3 yr of Academy studies. METHODS There were 30 male cadets included in the study. Bodyweight, body mass index (BMI), estimated percent body fat, and VO2(max) were measured at entry and at the end of the first year of Academy studies. After the first year, 14 cadets left the Academy, while the remaining cadets were retested at the end of the second and third years. RESULTS63: At entry, mean (95% CI) bodyweight, BMI, percent body fat, and VO2(max) were 78.4 (75.2, 81.6) kg, 24.3 (23.5, 25.1) kg x m(-2), 17.8 (16.3, 19.3)%, and 4.48 (4.25, 4.72) L x min(-1), respectively. Percent body fat decreased significantly by 1.1 (0.2, 2.0) percentage points at the end of the first year, while the other variables did not change during the first year. Between entry and end of third year there was no change in any of the main outcome variables. DISCUSSION Anthropometrical status and VO2(max) did not change in Norwegian Air Force cadets between entry and the end of 3 yr of Air Force Academy studies. From the 1- and 3-yr follow-up analysis, the only significant change was a small reduction in estimated percent body fat from entry to the end of the first year.
Prevention of recurrent urinary tract infection in children

Purpose of review Urinary tract infection (UTI) in children is common (5–10%) and recurs in 10–30%. UTI causes an unpleasant, usually febrile illness in children. This review focuses on studies evaluating interventions to prevent UTI in children and published between January 2007 and June 2008. Recent findings Three relevant updated Cochrane reviews, six randomized trials and an evidence-based guideline were published in the study period. Five of the six trials and one of the three Cochrane updates included data on the effects of relevant interventions in children. Three of the six trials investigated the efficacy of long-term, low-dose antibiotics as prophylaxis, and the other trials and both Cochrane updates evaluated complementary therapies such as vitamin A, probiotics and herbal supplements. Summary The benefit of prophylactic antibiotics for the prevention of recurrent UTI in children remains unclear because of underpowered and suboptimally designed trials, but these studies suggest that any benefit is likely to be small, and clinical significance may be limited. The trials of complementary interventions (vitamin A, probiotics, cranberry, nasturtium and horseradish) generally gave favourable results but were not conclusive. Children and families who use these products should be aware that further infections are possible despite their use.
On Realistically Attacking Tor with Website Fingerprinting

Abstract Website fingerprinting allows a local, passive observer monitoring a web-browsing client’s encrypted channel to determine her web activity. Previous attacks have shown that website fingerprinting could be a threat to anonymity networks such as Tor under laboratory conditions. However, there are significant differences between laboratory conditions and realistic conditions. First, in laboratory tests we collect the training data set together with the testing data set, so the training data set is fresh, but an attacker may not be able to maintain a fresh data set. Second, laboratory packet sequences correspond to a single page each, but for realistic packet sequences the split between pages is not obvious. Third, packet sequences may include background noise from other types of web traffic. These differences adversely affect website fingerprinting under realistic conditions. In this paper, we tackle these three problems to bridge the gap between laboratory and realistic conditions for website fingerprinting. We show that we can maintain a fresh training set with minimal resources. We demonstrate several classification-based techniques that allow us to split full packet sequences effectively into sequences corresponding to a single page each. We describe several new algorithms for tackling background noise. With our techniques, we are able to build the first website fingerprinting system that can operate directly on packet sequences collected in the wild.
Building effective deep neural network architectures one feature at a time

Successful training of convolutional neural networks is often associated with sufficiently deep architectures composed of high amounts of features. These networks typically rely on a variety of regularization and pruning techniques to converge to less redundant states. We introduce a novel bottom-up approach to expand representations in fixed-depth architectures. These architectures start from just a single feature per layer and greedily increase width of individual layers to attain effective representational capacities needed for a specific task. While network growth can rely on a family of metrics, we propose a computationally efficient version based on feature time evolution and demonstrate its potency in determining feature importance and a networks' effective capacity. We demonstrate how automatically expanded architectures converge to similar topologies that benefit from lesser amount of parameters or improved accuracy and exhibit systematic correspondence in representational complexity with the specified task. In contrast to conventional design patterns with a typical monotonic increase in the amount of features with increased depth, we observe that CNNs perform better when there is more learnable parameters in intermediate, with falloffs to earlier and later layers.
INVOLVEMENT OF MULTIPLE SUBPOPULATIONS OF HUMAN BONE MARROW CELLS IN THE REGULATION OF ALLOGENEIC CELLULAR IMMUNE RESPONSES1

Background. The identity of the cells in the human bone marrow that function as effective regulators of in vitro and possibly in vivo cellular immune responses is not well established. Methods. Cell subpopulations were isolated from cadaver donor vertebral-body bone marrow cells (DBMC) by using immuno-magnetic microbeads and were tested as inhibitors ( modulators) in cell-mediated lympholysis (CML) and mixed lymphocyte reaction (MLR) responses of normal peripheral blood lymphocytes stimulated with irradiated cadaver donor spleen cells. Results. Compared with spleen cells as controls, unirradiated T-cell depleted DBMC inhibited both the MLR and CML responses of allogeneic responder cells in a dose dependent manner (as in our previous reports). The inhibition was also mediated by a number of purified subpopulations including pluripotent CD34+ stem cells, and their CD34 negative early progeny of both lymphoid and myeloid lineages. These included DBMC enriched for non-T-cell lymphoid precursors (NT-LP/DBMC; i.e., DBMC depleted of CD3, CD15, and glycophorin-A positive cells) and DBMC positively selected for CD38+, CD2+, CD5+, and CD1+ lymphoid cells (all were depleted of CD3+ cells) as well as CD33+ (but CD15 negative) myeloid precursors. However, positively selected CD19+ B-cells and CD15+ myeloid cells did not inhibit the MLR and CML responses. The NT-LP/DBMC that had been repeatedly stimulated with irradiated allogeneic peripheral blood lymphocytes caused the strongest inhibition of the MLR and CML responses of the same allogeneic cells with 200 times fewer modulator cells needed than uncultured DBMC (P <0.001). Flow cytometric analysis revealed that majority of cells in these cell lines had become CD3+ TcR-&agr;&bgr;+ CD4+ and CD28+ cells. Conclusion. A variety of less differentiated cells of various lineages residing in the human bone marrow are immunoregulatory in vitro. Among them, there is at least one subset that can undergo differentiation in vitro into regulatory T cells that can be maintained in long-term cultures.
Functional characterization of rabbit lymphocytes carrying Fc receptor.

In rabbit spleen, among the 30% of lymphoid cells carrying Fc receptors, 8.7% contain immunoglobulin. Both types of cells, Fc/sup +/Ig/sup +/ and Fc/sup +/Ig, proliferate subsequent to stimulation by a rabbit B-cell mitogen (i.e., Nocardia water-soluble mitogen). In certain cases, this stimulation runs in parallel with an increase in antibody-dependent, cell-mediated cytotoxicity (ADCMC). Anti-a3 and anti-b4 antiallotypic immune sera, as well as anti-rabbit IgG immune serum, enhanced the ADCMC in a system in which rabbit anti-ChRBC antibody (a3/sup +/, b4/sup +/) coated the target cells and rabbit lymphocytes (a3/sup +/, b4/sup +/) were used as effector cells. This enhancement cannot be attributed to lymphocyte proliferation induced by antiallotypic and anti-Ig antibody but is more likely related to the formation of an additional bridge between effector and target cells. This was clearly demonstrated by the fact that a bridge produced by rabbit F(ab')/sub 2/ fragments of anti-b4 antibody between target cells coated with rabbit b4/sup +/ Fab fragments of anti-ChRBC Ig and Ig receptor of effector cells elicited a smaller but significant cytotoxic effect.
Attention-based Vocabulary Selection for NMT Decoding

Neural Machine Translation (NMT) models usually use large target vocabulary sizes to capture most of the words in the target language. The vocabulary size is a big factor when decoding new sentences as the final softmax layer normalizes over all possible target words. To address this problem, it is widely common to restrict the target vocabulary with candidate lists based on the source sentence. Usually, the candidate lists are a combination of external word-to-word aligner, phrase table entries or most frequent words. In this work, we propose a simple and yet novel approach to learn candidate lists directly from the attention layer during NMT training. The candidate lists are highly optimized for the current NMT model and do not need any external computation of the candidate pool. We show significant decoding speedup compared with using the entire vocabulary, without losing any translation quality for two language pairs.
Developing sustainable trading strategies using directional changes with high frequency data

Market prices are traditionally recorded in fixed time intervals. Directional Change is an alternative approach to summarize price movements in financial markets that is consistent with across all time scales. Unlike time series, directional change summarizes the big data in finance by focusing on the intrinsic time of the data. This captures deeper intrinsic data qualities and thus trading strategies based on directional change are more sustainable and less disruptive. In this paper, we propose four trading strategies using the concept of directional change and explore the combination with technical analysis. The trading strategies are tested using EUR/USD and GBP/USD high frequency FX market data. Empirical results show good performance of our trading strategies based on thresholds, and that combining with technical analysis brings further improvement.
Homotopic and heterotopic callosal afferents of caudal inferior parietal lobule in Macaca mulatta

We have examined callosal‐axon neurons giving rise to homotopic and heterotopic callosal projections to caudal inferior parietal lobule (area PG) in Macaca mulatta, identifying these neurons by means of retrograde axonal transport of horseradish peroxidase. The labeled neurons in the homotopic region occur predominantly in layers IIIB and V. A moderate number are seen also in layer VI, a smaller number in layer IV, and rare cells occur in layer II. These neurons occupy a region very similar in outline to the injection area, and though variable in density in the horizontal plane are continuously distributed in this plane.
Suxamethonium (Succinylcholine) Chloride and Muscle Pains

In normal human subjects both decamethonium and suxamethonium salts act by depolarization, the onset of paralysis being preceded by a momentary period of stimulation which is often visible as muscle fasciculations throughout the body. Conscious volunteers have often noted the characteristic tight feeling in the jaw and calf muscles that may persist for 12 to 24 hours after an injection of decamethonium (Organe et al., 1949; Churchill-Davidson and Richardson, 1952). An investigation has been carried out to determine whether similar muscle pains follow the injection of suxamethonium.
Nonviral In Vivo Gene Therapy for Tissue Engineering of Articular Cartilage and Tendon Repair

Heretofore, nonviral methods have been used primarily for in vitro transfection of cultured cell lines. These methods were substantially less efficient when compared with the use of viruses, particularly when used in vivo. Herein a three-step, highly efficient method of nonviral gene delivery is presented. Using this method, genes have been delivered successfully into tissues of orthopaedic importance with high-efficiency by nonviral means. Transforming growth factor-beta 1, parathyroid hormone related protein, and a marker gene were transfected into primary perichondrium and cartilage cells with efficiencies in excess of 70%. They overexpressed their cognate gene products showing efficacy of expression in a rabbit model of osteochondral defect repair. Using the same method, a marker gene was delivered into a canine model for intrasynovial flexor tendon injury and repair. This was achieved by direct gene delivery during surgery. An estimated 5 additional minutes were required during surgery to complete the transfection steps. High efficiency gene delivery was achieved in the flexor tendons, tendon sheaths, tendon pulleys, surrounding tissues, and skin. The efficiency of transfection approached 100% in the exposed superficial tissue layers and transfected cells were found several layers below the exposed tissue surfaces. The data show the potential of direct nonviral gene therapy in orthopaedics for ex vivo and in vivo applications.
DNA metabarcoding and the cytochrome c oxidase subunit I marker: not a perfect match

DNA metabarcoding enables efficient characterization of species composition in environmental DNA or bulk biodiversity samples, and this approach is making significant and unique contributions in the field of ecology. In metabarcoding of animals, the cytochrome c oxidase subunit I (COI) gene is frequently used as the marker of choice because no other genetic region can be found in taxonomically verified databases with sequences covering so many taxa. However, the accuracy of metabarcoding datasets is dependent on recovery of the targeted taxa using conserved amplification primers. We argue that COI does not contain suitably conserved regions for most amplicon-based metabarcoding applications. Marker selection deserves increased scrutiny and available marker choices should be broadened in order to maximize potential in this exciting field of research.
The use of the practice walk test in pulmonary rehabilitation program: National COPD Audit Pulmonary Rehabilitation Workstream

Our aim was to evaluate the use and impact of the practice walk test on enrolment, completion, and clinical functional response to pulmonary rehabilitation (PR) using the 2015 UK National Chronic Obstructive Pulmonary Disease (COPD) Pulmonary Rehabilitation audit data. Patients were assessed according to whether a baseline practice walk test was performed or not. Study outcomes included use of the practice walk test, baseline and change in incremental shuttle walk test distance (ISWD) or 6-minute walk test distance (6MWD), and enrolment to and completion of PR program. Of 7,355 patients, only 1,666 (22.6%) had a baseline practice test. At baseline, the practice walk test group walked further as compared to the no practice walk test group: ISWD, 17.9 m [95% confidence interval (CI) 8.2–27.5 m] and 6MWD, 34.8 m (95% CI 24.7–44.9 m). The practice walk test group were 2.2 times (95% CI 1.8–2.6) more likely to enroll and 17% (95% CI 1.03–1.34) more likely to complete PR. Although the change in ISWD and 6MWD with PR was lower in the practice walk test group, they walked further at discharge assessment. Only 22.6% of the patients in the 2015 National PR audit had a practice walk test at assessment. Those who did had better enrolment, completion, and better baseline walking distance, from which the prescription is set.
Comparisons of CD8+ T Cells Specific for Human Immunodeficiency Virus, Hepatitis C Virus, and Cytomegalovirus Reveal Differences in Frequency, Immunodominance, Phenotype, and Interleukin-2 Responsiveness

ABSTRACT To better understand the components of an effective immune response to human immunodeficiency virus (HIV), the CD8+ T-cell responses to HIV, hepatitis C virus (HCV), and cytomegalovirus (CMV) were compared with regard to frequency, immunodominance, phenotype, and interleukin-2 (IL-2) responsiveness. Responses were examined in rare patients exhibiting durable immune-mediated control over HIV, termed long-term nonprogressors (LTNP) or elite controllers, and patients with progressive HIV infection (progressors). The magnitude of the virus-specific CD8+ T-cell response targeting HIV, CMV, and HCV was not significantly different between LTNP and progressors, even though their capacity to proliferate to HIV antigens was preserved only in LTNP. In contrast to HIV-specific CD8+ T-cell responses of LTNP, HLA B5701-restricted responses within CMV pp65 were rare and did not dominate the total CMV-specific response. Virus-specific CD8+ T cells were predominantly CD27+45RO+ for HIV and CD27−45RA+ for CMV; however, these phenotypes were highly variable and heavily influenced by the degree of viremia. Although IL-2 induced significant expansions of CMV-specific CD8+ T cells in LTNP and progressors by increasing both the numbers of cells entering the proliferating pool and the number of divisions, the proliferative capacity of a significant proportion of HIV-specific CD8+ T cells was not restored with exogenous IL-2. These results suggest that immunodominance by HLA B5701-restricted cells is specific to HIV infection in LTNP and is not a feature of responses to other chronic viral infections. They also suggest that poor responsiveness to IL-2 is a property of HIV-specific CD8+ T cells of progressors that is not shared with responses to other viruses over which immunologic control is maintained.