Miracle-dz/UniFAR-FTUs huggingface dataset:
Highly active anti‐retroviral therapy (HAART) is associated with a lower level of CD4+ T cell apoptosis in HIV‐infected patients

HAART may increase CD4+ T cell counts despite a persistently detectable HIV load. The impact of HAART on apoptosis, which may play a role in the disease process in HIV‐infected patients, has not been extensively studied. We performed a study to compare the level of spontaneous T cell apoptosis and anti‐retroviral treatments in a cohort of HIV‐1‐infected patients. Data were obtained from a computerized medical record. Quantification of apoptotic cells was by cytofluorometric technique. From November 1995 to December 1997 we studied T cell apoptosis in 112 HIV‐infected patients. Forty patients were classified A, 36 B and 36 C. Thirty patients were naive and 82 received an anti‐retroviral treatment, 49 including a protease inhibitor (PI). The median plasma viraemia determined in 63 patients was 3.6 (range 1.3–5.6) log10. The median apoptotic cell count was 22% (range 2–73%) and 12% (range 2–60%) for CD4+ and CD8+ T cells, respectively. We did not observe any correlation between the HIV viraemia and the level of apoptosis of T cell subsets. Patients with HAART showed a lower percentage of apoptotic CD4+ T cells only: 16% (range 2–61%) versus 25% (range 5–73%) for patients receiving two nucleoside analogues (P = 0.02). This effect was significant in stage A patients and remained observable during the whole course of HIV disease. In conclusion, HAART, without any relation to plasma viraemia, is able to reduce apoptosis of CD4+ T cells.
Tumor-Infiltrating Dendritic Cells Are Potent Antigen-Presenting Cells Able to Activate T Cells and Mediate Tumor Rejection1

Dendritic cells (DC) are potent inducers of immune responses. DC have been shown to infiltrate tumors, but very little is known about the functional status of these naturally occurring tumor-infiltrating DC (TIDC). In this study, the status and function of TIDC from several types of mouse melanoma were investigated in detail. CD11c+/MHC II+ cells, consistent with a DC phenotype, were found in all of transplantable or spontaneous melanomas studied. These TIDC were predominantly myeloid (CD11c+/CD8α−/B220−) in nature with small numbers of plasmacytoid (CD11c+/B220+). TIDC had an intermediate maturation phenotype with some expression of costimulatory molecules and the capacity to take up particles. Upon culture overnight ex vivo, the TIDC markedly up-regulated the expression of costimulatory molecules and also increased IL-12 production. Importantly, such ex vivo-matured TIDC pulsed with OVA were able to migrate to lymph nodes, to activate naive OVA-specific CD4+ and CD8+ T cells, and to confer protection against a challenge with OVA-expressing tumor cells. In conclusion, melanomas are infiltrated by functional DC that can act as fully competent APC. These APC have the potential to be manipulated and may therefore represent a promising target for cancer immunotherapy.
CD44s is useful in the differentiation of benign and malignant papillary lesions of the breast

Background/Aims: CD44s, the standard form of CD44, has been shown to be downregulated during malignant transformation of breast cancers. It has also been reported recently to be a useful marker in differentiating between benign and malignant papillary lesions of the breast, with high expression in the former. CD44s expression in benign and malignant papillary lesions was evaluated. Methods: CD44s expression was assessed by immunohistochemistry in 101 benign papillomas and 59 papillary carcinomas (seven invasive papillary carcinomas, 41 papillary ductal carcinomas in situ, and 11 ductal carcinomas involving papillomas). Results: Patients’ age and tumour size were significantly different between the papilloma and papillary carcinoma groups (p < 0.0001). CD44s showed positive staining in 45 papillomas (45%) and five papillary carcinomas (8%), and the difference was significant (p < 0.0001). The myoepithelial cells, when present, were also positive for CD44s in both groups, with no observable differences. Using CD44s positive staining to differentiate between benign and malignant papillary lesions gives a sensitivity, specificity, and accuracy of 45%, 92%, and 62%, respectively. Conclusions: CD44s may be useful as an adjunct in the evaluation of morphologically problematic cases of papillary lesion of the breast.
Neighbor Discovery Latency in BLE-Like Protocols

Neighbor discovery is the procedure in which two wireless devices initiate a first contact. In low power ad-hoc networks, radios are duty-cycled and the latency until a packet meets a reception phase of another device is determined by a random process. Most research considers slotted protocols, in which the points in time for reception are temporally coupled to beacon transmissions. In contrast, many recent protocols, such as ANT/ANT+ and Bluetooth Low Energy (BLE) use a slotless, periodic-interval based scheme for neighbor discovery. Here, one device periodically broadcasts packets, whereas the other device periodically listens to the channel. Both periods are independent from each other and drawn over continuous time. Such protocols provide 3 degrees of freedom (viz., the intervals for advertising and scanning and the duration of each scan phase). Though billions of existing BLE devices rely on these protocols, neither their expected latencies nor beneficial configurations with good latency-duty-cycle relations are known. Parametrizations for the participating devices are usually determined based on a “good guess”. In this paper, we, for the first time, present a mathematical theory which can compute the neighbor discovery latencies for all possible parametrizations. Further, our theory shows that upper bounds on the latency can be guaranteed for all parametrizations, except for a finite number of singularities. Therefore, slotless, periodic interval-based protocols can be used in applications with deterministic latency demands, which have been reserved for slotted protocols until now. Our proposed theory can be used for analyzing the neighbor discovery latencies, for tweaking protocol parameters and for developing new protocols.
Apical sensory neurones mediate developmental retardation induced by conspecific environmental stimuli in freshwater pulmonate snails

Freshwater pond snails Helisoma trivolvis and Lymnaea stagnalis undergo larval development and metamorphosis inside egg capsules. We report that their development is permanently under slight tonic inhibitory influence of the anterior sensory monoaminergic neurones, which are the remnants of the apical sensory organ. Conspecific juvenile snails, when reared under conditions of starvation and crowding, release chemical signals that are detected by these neurones in encapsulated larvae and reversibly suppress larval development, thus providing a link between environmental signals and developmental regulation. Induced retardation starts from the trochophore stage and results in up to twofold prolongation of the larval lifespan. Upon stimulation with the signal, the neurones increase synthesis and release of monoamines [serotonin (5-HT) in Helisoma and dopamine in Lymnaea] that inhibit larval development acting via ergometrine-sensitive internal receptors. Thus, the novel regulatory mechanism in larval development of molluscs is suggested and compared with the phenomenon of dauer larvae formation in the nematode Caenorhabditis elegans.
Assessing yourself as an emotional eater: Mission impossible?

OBJECTIVE The extent to which individuals are emotional eaters has typically been assessed by people's self-reported desire to eat when they experience negative emotions. Elevated scores on these emotional eater scales have been associated with eating pathology and obesity. However, evidence that individuals scoring high on these scales truly increase their food intake during emotional encounters is inconclusive. The current studies tested whether emotional eater scales capture the proposed tendency to eat when feeling emotional. DESIGN In four experiments with different emotion induction procedures, female participants were randomly assigned to negative emotion or control conditions. In the control conditions positive or no emotions were induced. Next, food consumption was assessed by bogus taste tests. MAIN OUTCOME MEASURES Emotional eater status, emotional experience, and actual consumption of different food types. RESULTS Individuals describing themselves as emotional eaters did not increase food intake during emotional encounters as compared to control conditions or individuals not judging themselves as emotional eaters. CONCLUSION The results suggest that self-reported emotional eaters do not increase food intake during emotional encounters in the laboratory. Implications of these findings are discussed, including the idea that it may be complex to adequately assess one's own emotional eating behavior.
Pre-shaping for various objects by the robot hand equipped with resistor network structure proximity sensors

In this paper, we demonstrate a preliminary motion before grasping by a robot hand, for adjusting the object-fingertip distance and 2-axis postures simultaneously, using a Resistor Network Structure Proximity sensor (RNSP sensor). Through this motion (called “pre-shaping”) and the grasping of an object, the surface of each fingertip is brought into contact with the object surface so that in the next stage grasping can be undertaken. In the next stage, a force can be applied from the fingertips onto the object surface directly. The pre-shaping enhances the reliability of the feedback control for the after-contact tactile sensors. To realize the pre-shaping, we use fingertips equipped with RNSP sensors, which can detect the distance between the fingertip and the object, to determine the relative position between fingertips and an object. The RNSP sensor has a fast response (<;1 [ms]) and simple connectivity (only 6 wires), and can be mounted easily. Additionally, a characteristics of the RNSP sensor output can be designed by the arrangement of the sensor elements. To perform the pre-shaping by simple sensor feedback control based on the configuration between the fingertip and object, we designed the RNSP sensor so that it had the appropriate characteristics for the pre-shaping.
LightNet: A Versatile, Standalone Matlab-based Environment for Deep Learning

LightNet is a lightweight, versatile, purely Matlab-based deep learning framework. The idea underlying its design is to provide an easy-to-understand, easy-to-use and efficient computational platform for deep learning research. The implemented framework supports major deep learning architectures such as Multilayer Perceptron Networks (MLP), Convolutional Neural Networks (CNN) and Recurrent Neural Networks (RNN). The framework also supports both CPU and GPU computation, and the switch between them is straightforward. Different applications in computer vision, natural language processing and robotics are demonstrated as experiments.
An Efficient Design of Doubly Selective Channel Estimation for OFDM Systems

We find that placing each pilot tone in an equally spaced manner according to the conventional placement scheme is not suitable for doubly selective channel estimation. In this paper, we propose an efficient pilot tone placement scheme enabling accurate channel estimation in OFDM systems regardless of time variations of a channel. Since the number of channel impulse response taps to be estimated is typically much greater than the number of pilot tones, linear minimum mean square error (LMMSE) estimation schemes for time-invariant channels cannot be straightforwardly extended to doubly selective channel estimation. To overcome this problem, we propose an accurate LMMSE channel estimator that exploits a small number of pilot tones located according to the derived pilot placement. To achieve performance close to the LMMSE estimator but with lower complexity, an approximate LMMSE (ALMMSE) channel estimator is also proposed. Finally, we propose a novel iterative ALMMSE channel estimator that achieves better performance than the LMMSE and ALMMSE estimators, while having complexity in between the two.
SAVVYSEARCH: A Metasearch Engine That Learns Which Search Engines to Query

Search engines are among the most successful applications on the web today. So many search engines have been created that it is difficult for users to know where they are, how to use them, and what topics they best address. Metasearch engines reduce the user burden by dispatching queries to multiple search engines in parallel. The SAVVYSEARCH metasearch engine is designed to efficiently query other search engines by carefully selecting those search engines likely to return useful results and responding to fluctuating load demands on the web. SAVVYSEARCH learns to identify which search engines are most appropriate for particular queries, reasons about resource demands, and represents an iterative parallel search strategy as a simple plan.
Candidate microRNAs as biomarkers of thyroid carcinoma: a systematic review, meta‐analysis, and experimental validation

Thyroid cancer is one of the most common carcinomas of the endocrine system with an increasing incidence. A growing number of studies have focused on the diagnostic and prognostic values of dysregulated microRNAs (miRNAs) in thyroid carcinoma. However, differences in the measurement platforms, variations in lab protocols, and small sample sizes can make gene profiling data incomparable. A meta‐review of the published studies that compared miRNA expression data of thyroid carcinoma and paired normal tissues was performed to identify potential miRNA biomarkers of thyroid carcinoma with the vote‐counting strategy. Two hundred and thirty‐six aberrantly expressed miRNAs were reported in 19 microRNA expression profiling studies. Among them, 138 miRNAs were reported in at least two studies. We also provided a meta‐signature of differentially expressed miRNAs between individual histological types of thyroid carcinoma and normal tissues. The experimental validation with qRT‐PCR analysis verified that the profiles identified with the meta‐review approach could effectively discriminate papillary thyroid carcinoma tissues from paired noncancer tissues. The meta‐review of miRNA expression profiling studies of thyroid carcinoma would provide information on candidate miRNAs that could potentially be used as biomarkers in thyroid carcinoma.
Comparative proteome analysis of Milnesium tardigradum in early embryonic state versus adults in active and anhydrobiotic state

Tardigrades have fascinated researchers for more than 300 years because of their extraordinary capability to undergo cryptobiosis and survive extreme environmental conditions. However, the survival mechanisms of tardigrades are still poorly understood mainly due to the absence of detailed knowledge about the proteome and genome of these organisms. Our study was intended to provide a basis for the functional characterization of expressed proteins in different states of tardigrades. High-throughput, high-accuracy proteomics in combination with a newly developed tardigrade specific protein database resulted in the identification of more than 3000 proteins in three different states: early embryonic state and adult animals in active and anhydrobiotic state. This comprehensive proteome resource includes protein families such as chaperones, antioxidants, ribosomal proteins, cytoskeletal proteins, transporters, protein channels, nutrient reservoirs, and developmental proteins. A comparative analysis of protein families in the different states was performed by calculating the exponentially modified protein abundance index which classifies proteins in major and minor components. This is the first step to analyzing the proteins involved in early embryonic development, and furthermore proteins which might play an important role in the transition into the anhydrobiotic state.
Recombinant Mycobacterium bovis Bacillus Calmette-Guérin Secreting Merozoite Surface Protein 1 (MSP1) Induces Protection against Rodent Malaria Parasite Infection Depending on MSP1-stimulated Interferon γ and Parasite-specific Antibodies

The merozoite surface protein 1 (MSP1) has emerged as a leading malaria vaccine candidate at the erythrocytic stage. Recombinant bacillus Calmette-Guérin (rBCG), which expressed a COOH-terminal 15-kD fragment of MSP1 of Plasmodium yoelii (MSP1-15) as a fusion protein with a secretory protein of Mycobacterium kansasii, was constructed. Immunization of mice with this rBCG induced a higher degree of protection against blood-stage parasite infection than with recombinant MSP1-15 in the RIBI adjuvant (RIBI ImmunoChem Research, Inc., Hamilton, MT) or incomplete Freund's adjuvant systems. We studied the mechanism of protection induced by MSP1-15, and found that interferon (IFN)-γ had a major role in protection in all adjuvant systems we examined. Mice that produced low amounts of MSP1-15 stimulated IFN-γ and could not control parasite infection. The antibody against MSP1-15 did not play a major role in protection in this system. After parasite infection, immunoglobulin G2a antibodies, which had been produced by IFN-γ stimulation, were induced and subsequently played an important role in eradicating parasites. Thus, both cellular and humoral immune responses were essential for protection from malaria disease. These data revealed that BCG is a powerful adjuvant to induce such a protective immune response against malaria parasites.
Metagenomic Profiling Reveals Lignocellulose Degrading System in a Microbial Community Associated with a Wood-Feeding Beetle

The Asian longhorned beetle ( Anoplophoraglabripennis ) is an invasive, wood-boring pest that thrives in the heartwood of deciduous tree species. A large impediment faced by A . glabripennis as it feeds on woody tissue is lignin, a highly recalcitrant biopolymer that reduces access to sugars and other nutrients locked in cellulose and hemicellulose. We previously demonstrated that lignin, cellulose, and hemicellulose are actively deconstructed in the beetle gut and that the gut harbors an assemblage of microbes hypothesized to make significant contributions to these processes. While lignin degrading mechanisms have been well characterized in pure cultures of white rot basidiomycetes, little is known about such processes in microbial communities associated with wood-feeding insects. The goals of this study were to develop a taxonomic and functional profile of a gut community derived from an invasive population of larval A . glabripennis collected from infested host trees and to identify genes that could be relevant for the digestion of woody tissue and nutrient acquisition. To accomplish this goal, we taxonomically and functionally characterized the A . glabripennis midgut microbiota through amplicon and shotgun metagenome sequencing and conducted a large-scale comparison with the metagenomes from a variety of other herbivore-associated communities. This analysis distinguished the A. glabripennis larval gut metagenome from the gut communities of other herbivores, including previously sequenced termite hindgut metagenomes. Genes encoding enzymes were identified in the A . glabripennis gut metagenome that could have key roles in woody tissue digestion including candidate lignin degrading genes (laccases, dye-decolorizing peroxidases, novel peroxidases and β-etherases), 36 families of glycoside hydrolases (such as cellulases and xylanases), and genes that could facilitate nutrient recovery, essential nutrient synthesis, and detoxification. This community could serve as a reservoir of novel enzymes to enhance industrial cellulosic biofuels production or targets for novel control methods for this invasive and highly destructive insect.
Guidelines for scheduling in primary care under different patient types and stochastic nurse and provider service times

Scheduling in primary care is challenging because of the diversity of patient cases (acute versus chronic), mix of appointments (pre-scheduled versus same-day), and uncertain time spent with providers and non-provider staff (nurses/medical assistants). In this paper, we present an empirically driven stochastic integer programming model that schedules and sequences patient appointments during a work day session. The objective is to minimize a weighted measure of provider idle time and patient wait time. Key model features include: an empirically based classification scheme to accommodate different chronic and acute conditions seen in a primary care practice; adequate coordination of patient time with a nurse and a provider; and strategies for introducing slack in the schedule to counter the effects of variability in service time with providers and nurses. In our computational experiments we characterize, for each patient type in our classification, where empty slots should be positioned in the schedule to reduce waiting time. Our results also demonstrate that the optimal start times for a variety of patient-centered heuristic sequences consistently follow a pattern that results in easy to implement guidelines. Moreover, these heuristic sequences and appointment times perform significantly better than the practice's schedule. Finally, we also compare schedules suggested by our two-service-stage model (nurse and provider) with those that only consider the provider stage and find that the performance of the provider-only model is 21% worse than that of the two-service-stage model.
The Incidence of Cancer in a Population‐Based Cohort of Canadian Heart Transplant Recipients

To assess the long‐term risk of developing cancer among heart transplant recipients compared to the Canadian general population, we carried out a retrospective cohort study of 1703 patients who received a heart transplant between 1981 and 1998, identified from the Canadian Organ Replacement Register database. Vital status and cancer incidence were determined through record linkage to the Canadian Mortality Database and Canadian Cancer Registry. Cancer incidence rates among heart transplant patients were compared to those of the general population. The observed number of incident cancers was 160 with 58.9 expected in the general population (SIR = 2.7, 95% CI = 2.3, 3.2). The highest ratios were for non‐Hodgkin's lymphoma (NHL) (SIR = 22.7, 95% CI = 17.3, 29.3), oral cancer (SIR = 4.3, 95% CI = 2.1, 8.0) and lung cancer (SIR = 2.0, 95% CI = 1.2, 3.0). Compared to the general population, SIRs for NHL were particularly elevated in the first year posttransplant during more recent calendar periods, and among younger patients. Within the heart transplant cohort, overall cancer risks increased with age, and the 15‐year cumulative incidence of all cancers was estimated to be 17%. There is an excess of incident cases of cancer among heart transplant recipients. The relative excesses are most marked for NHL, oral and lung cancer.
miR-34a induces cellular senescence via modulation of telomerase activity in human hepatocellular carcinoma by targeting FoxM1/c-Myc pathway

Increasing evidence suggests that miRNAs can act as either tumor suppressors or oncogenes in carcinogenesis. In the present study, we identified the role of miR-34a in regulating telomerase activity, with subsequent effect on cellular senescence and viability. We found the higher expression of miR-34a was significantly correlated with the advanced clinicopathologic parameters in hepatocellular carcinoma. Furthermore, tumor tissues of 75 HCC patients demonstrated an inverse correlation between the miR-34a level and telomere indices (telomere length and telomerase activity). Transient introduction of miR-34a into HCC cell lines inhibited the telomerase activity and telomere length, which induced senescence-like phenotypes and affected cellular viability. We discovered that miR-34a potently targeted c-Myc and FoxM1, both of which were involved in the activation of telomerase reverse transcriptase (hTERT) transcription, essential for the sustaining activity of telomerase to avoid senescence. Taken together, our results demonstrate that miR-34a functions as a potent tumor suppressor through the modulation of telomere pathway in cellular senescence.