Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification and Characterization of a 25 kDa Protein That Is Indispensable for the Efficient Saccharification of Eisenia bicyclis in the Digestive Fluid of Aplysia kurodai

The digestive fluid of the sea hare Aplysia kurodai can liberate approximately 2.5 mg of glucose from 10 mg of dried Eisenia bicyclis powder. Although laminaran, a major storage polysaccharide in E. bicyclis, is easily digested to glucose by the synergistic action of the 110 and 210 kDa A. kurodai β-glucosidases (BGLs), glucose is not liberated from E. bicyclis by direct incubation with these BGLs. To clarify this discrepancy, we searched for an Eisenia hydrolysis enhancing protein (EHEP) in the digestive fluid of A. kurodai. A novel 25 kDa protein that enhances E. bicyclis saccharification by β-glucosidases was purified to a homogeneous state from the digestive fluid of A. kurodai, and its cDNA was cloned from total cDNAs reverse-transcribed from hepatopancreas total RNA. The E. bicyclis extract strongly inhibited BGLs, suggesting some compound within this brown alga functioned as a feeding deterrent. However, when E. bicyclis was incubated with BGLs in the presence of EHEP, glucose production was markedly increased. As E. bicyclis is rich in phlorotannin, which are only found in brown algae, our study suggested that these compounds are the main BGL inhibitors in E. bicyclis extract. EHEP protects BGLs from phlorotannin inhibition by binding to phlorotannins and forming an insoluble complex with phloroglucinol and phlorotannins. These findings indicated that EHEP plays a key role in the saccharification of brown seaweeds containing phlorotannins in the digestive fluid of A. kurodai. This is the first report of EHEP as a phlorotannin-binding protein that protects BGLs from inhibition.
Forces generated during actin-based propulsion: a direct measurement by micromanipulation.

Dynamic actin networks generate forces for numerous types of movements such as lamellipodia protrusion or the motion of endocytic vesicles. The actin-based propulsive movement of Listeria monocytogenes or of functionalized microspheres have been extensively used as model systems to identify the biochemical components that are necessary for actin-based motility. However, quantitative force measurements are required to elucidate the mechanism of force generation, which is still under debate. To directly probe the forces generated in the process of actin-based propulsion, we developed a micromanipulation experiment. A comet growing from a coated polystyrene bead is held by a micropipette while the bead is attached to a force probe, by using a specially designed "flexible handle. " This system allows us to apply both pulling and pushing external forces up to a few nanonewtons. By pulling the actin tail away from the bead at high speed, we estimate the elastic modulus of the gel and measure the force necessary to detach the tail from the bead. By applying a constant force in the range of -1.7 to 4.3 nN, the force-velocity relation is established. We find that the relation is linear for pulling forces and decays more weakly for pushing forces. This behavior is explained by using a dimensional elastic analysis.
Long-Term Outcome of 4,040 Children Diagnosed With Pediatric Low-Grade Gliomas: An Analysis of the Surveillance Epidemiology and End Results (SEER) Database

Children with pediatric low‐grade gliomas (PLGG) are known to have excellent 10‐year survival rates; however the outcomes of adult survivors of PLGG are unknown. We identified patients diagnosed with PLGG diagnosed between 1973 and 2008 through the Surveillance Epidemiology and End Results (SEER) database to examine outcomes of adult survivors of PLGG.
Antagonistic Cross-talk between Rac and Cdc42 GTPases Regulates Generation of Reactive Oxygen Species*

Cross-talk between Rho GTPase family members (Rho, Rac, and Cdc42) plays important roles in modulating and coordinating downstream cellular responses resulting from Rho GTPase signaling. The NADPH oxidase of phagocytes and nonphagocytic cells is a Rac GTPase-regulated system that generates reactive oxygen species (ROS) for the purposes of innate immunity and intracellular signaling. We recently demonstrated that NADPH oxidase activation involves sequential interactions between Rac and the flavocytochrome b558 and p67phox oxidase components to regulate electron transfer from NADPH to molecular oxygen. Here we identify an antagonistic interaction between Rac and the closely related GTPase Cdc42 at the level of flavocytochrome b558 that regulates the formation of ROS. Cdc42 is unable to stimulate ROS formation by NADPH oxidase, but Cdc42, like Rac1 and Rac2, was able to specifically bind to flavocytochrome b558 in vitro. Cdc42 acted as a competitive inhibitor of Rac1- and Rac2-mediated ROS formation in a recombinant cell-free oxidase system. Inhibition was dependent on the Cdc42 insert domain but not the Switch I region. Transient expression of Cdc42Q61L inhibited ROS formation induced by constitutively active Rac1 in an NADPH oxidase-expressing Cos7 cell line. Inhibition of Cdc42 activity by transduction of the Cdc42-binding domain of Wiscott-Aldrich syndrome protein into human neutrophils resulted in an enhanced fMetLeuPhe-induced oxidative response, consistent with inhibitory cross-talk between Rac and Cdc42 in activated neutrophils. We propose here a novel antagonism between Rac and Cdc42 GTPases at the level of the Nox proteins that modulates the generation of ROS used for host defense, cell signaling, and transformation.
IL-21: An Executor of B Cell Fate1

IL-21 is a type I cytokine that shares the common receptor γ-chain with IL-2, IL-4, IL-7, IL-9, and IL-15. B cells are one of the lymphoid cell types whose development and function are regulated by IL-21. Depending on the interplay with costimulatory signals and on the developmental stage of a B cell, IL-21 can induce proliferation, differentiation into Ig-producing plasma cells, or apoptosis in both mice and humans. Alone and in combination with Th cell-derived cytokines IL-21 can regulate class switch recombination to IgG, IgA, or IgE isotypes, indicating its important role in shaping the effector function of B cells. This review highlights the role of IL-21 in B cell development, function, and disease and provides some perspectives on the future studies in this area.
Presymptomatic testing for BRCA1 andBRCA2: how distressing are the pre-test weeks?

Presymptomatic DNA testing for autosomal dominant hereditary breast/ovarian cancer (HBOC) became an option after the identification of the BRCA1 andBRCA2 genes in 1994-1995. Healthy female mutation carriers have a high lifetime risk for breast cancer (56-87%) or ovarian cancer (10-60%) and may opt for intensive breast and ovary surveillance or prophylactic surgery (mastectomy/oophorectomy). We studied general and cancer related distress in 85 healthy women with a 25% or 50% risk of being carrier of aBRCA1/BRCA2 gene mutation and 66 partners in the six to eight week period between genetic counselling/blood sampling and disclosure of the test result. Questionnaire and interview data are analysed. Associations are explored between levels of distress and (1) expected consequences of being identified as a mutation carrier, (2) personality traits, (3) sociodemographic variables, and (4) experiences related to HBOC. Mean pre-test anxiety and depression levels in women at risk of being a carrier and partners were similar to those of a normal Dutch population. In about 25% of those at risk of being a carrier and 10% of the partners, increased to high levels of general and cancer related distress were found. Increased levels of distress were reported by women who (1) anticipated an increase in problems after an unfavourable test outcome, (2) considered prophylactic mastectomy if found to be mutation carrier, (3) had an unoptimistic personality, (4) tended to suppress their emotions, (5) were younger than 40 years, and (6) were more familiar with the serious consequences of HBOC. Recently obtained awareness of the genetic nature of cancer in the family was not predictive of distress. The majority of the women and their partners experienced a relatively calm period before the disclosure of the test result and seemed to postpone distressing thoughts until the week of disclosure of the result. The low distress levels may partly be explained by the use of strategies to minimise the emotional impact of a possibly unfavourable test outcome. However, a minority reported feeling very distressed. Several factors were found to be predictive for increased distress levels.
Temperature Effects on Neuromuscular Transmission (Opener Muscle of Crayfish, Astacus Leptodactylus)

In experiments on the opener muscle of the third walking legs of crayfish ( Astacus leptodactylus ) it was found that the mechanical tension developed in response to repetitive stimulation of the single motor axon increases over the entire temperature range from 30 down to 0°C. In contrast to this, the tension elicited by depolarizing single muscle fibres decreases with decreasing temperature; the threshold for excitation-contraction coupling is not significantly altered. With decreasing temperature the resting potential decreases (up to 2 mV/°C) but the amplitude and decay time of the e.p.s.p.'s increase. The time constant, λ, of e.p.s.p. decay has a Q 10 of less than −2 in the range above 15 °C but reaches a value of −7 between 10 and 0°C. This pattern of temperature dependence is fully accounted for by a parallel change of membrane resistance and its reciprocal, the membrane conductance. The corresponding activation energies computed from λ-values approximate 3 kcal/mol at high temperature and 46 kcal/mol in the low temperature range. The combined effects of a lowered resting potential, an increased amplitude, and especially an increased decay time of e.p.s.p.s result in a drastic enhancement of the depolarization reached during summation of e.p.s.p.s as the temperature is decreased. These effects overcompensate the declining effectiveness of excitation-contraction coupling so that the entire process of neuromuscular transmission becomes more and more effective as the temperature declines. In order to reach the same tension lower frequencies of nerve stimulation are needed at lower temperatures.
A Randomized Trial of Three Renal Transplant Induction Antibodies: Early Comparison of Tacrolimus, Mycophenolate Mofetil, and Steroid Dosing, and Newer Immune-Monitoring1

Background. New trends in immunosuppression in clinical transplantation include the use of antibody induction agents in protocols that emphasize reduction or avoidance of steroids and calcineurin inhibitors. Methods. In a randomized trial using three different antibody induction agents in 90 first renal transplant recipients from cadaver donors, group A received Thymoglobulin, group B received Alemtuzumab, and group C received Daclizumab. Maintenance immunosuppression included tacrolimus and mycophenolate in all three arms, and methylprednisolone in groups A and C only (standard clinical institutional practice). The targeted trough level of tacrolimus was between 8 and 10 ng/mL for groups A and C, respectively, with a targeted mycophenolate dose of 1 g twice daily. However, in group B, the target tacrolimus trough level was 4 to 7 ng/mL to reduce long-term nephrotoxicity, with 500 mg twice-daily doses of mycophenolate, without steroid maintenance. Results. In this 15-month median postoperative interval report, there were no notable differences in demographics and patient and graft survivals. Acute rejection rates at 1 year were equivalent, that is, 5 of 30 in all three groups (16.6%). In group B, there was slightly lower renal function at 1 month, but no difference at 1 year. There was also significantly more leukopenia, but a greater percentage of T-regulatory cells and number of Fox-P3 mRNA copies by flow cytometry and semiquantitative polymerase chain reaction analysis, respectively, in group B. Conclusions. This preliminary analysis indicates that 80% of the patients in group B remained steroid-free 1 year postoperatively, with lower tacrolimus trough levels and no difference in other adverse events.
Confirmation Bias in Software Development and Testing: An Analysis of the Effects of Company Size, Experience and Reasoning Skills

During all levels of software testing, the goal should be to fail the code to discover software defects and hence to increase software quality. However, software developers and testers are more likely to choose positive tests rather than negative ones. This is due to the phenomenon called confirmation bias which is defined as the tendency to verify one’s own hypotheses rather than trying to refute them. In this work, we aimed at identifying the factors that may affect confirmation bias levels of software developers and testers. We have investigated the effects of company size, experience and reasoning skills on bias levels. We prepared pen-and-paper and interactive tests based on two tasks from cognitive psychology literature. During pen-and-paper test, subjects had to test given hypotheses, whereas interactive test required both hypotheses generation and testing. These tests were conducted on employees of one large scale telecommunications company, three small and medium scale software companies and graduate computer engineering students resulting in a total of eighty-eight subjects. Results showed regardless of experience and company size, abilities such as logical reasoning and strategic hypotheses testing are differentiating factors in low confirmation bias levels. Therefore, education and/or training programs that emphasize mathematical reasoning techniques are useful towards production of high quality software. Moreover, in order to investigate the relationship between code defect density and confirmation bias of software developers, we performed an analysis among developers who are involved with a software project in a large scale telecommunications company. We also analyzed the effect of confirmation bias during software testing phase. Our results showed that there is a direct correlation between confirmation bias and defect proneness of the code.
The influence of environment and life‐history traits on the distribution of genes and individuals: a comparative study of 11 rainforest trees

This study investigates patterns of genetic connectivity among 11 co‐distributed tropical rainforest tree species from the genus Elaeocarpus across a biogeographic barrier, the Black Mountain Corridor (BMC) in the Australian Wet Tropics (AWT). We analysed a combination of allelic and flanking region sequence data from microsatellite markers, and evaluated the relative influence of environmental preferences and functional traits on genetic diversity and gene flow. The results indicate that only in three species geographic structuring of haplotype distribution reflects a north vs. south of the BMC pattern. Environmental factors linked with altitude were recognized as affecting genetic trends, but the selective processes operating on upland species appear to be associated with competitiveness and regeneration opportunities on poor soil types rather than climate variables alone. In contrast to previous observations within southeastern Australian rainforests, genetic differentiation in the AWT appears to be associated with small‐fruited rather than large‐fruited species, highlighting how external factors can influence the dispersal dimension. Overall, this study emphasizes the importance of considering functional and environmental factors when attempting generalizations on landscape‐level patterns of genetic variation. Understanding how plant functional groups respond to environmental and climatic heterogeneity can help us predict responses to future change.
Interferon Administered Orally: Protection of Neonatal Mice from Lethal Virus Challenge

Interferon was identified in the milk of mice injected with an interferon inducer. The kinetics of interferon appearance in serum and in milk were similar, but maximum concentrations in milk were 10 to 20 percent of those in serum. Interferon administered orally to neonatal mice was detected in their serums. Significantly more newborns survived an oral challenge with vesicular stomatitis virus when interferon had been induced in the lactating mothers.
Two constructive embedding‐extension theorems with applications to continuity principles and to Banach‐Mazur computability

We prove two embedding and extension theorems in the context of the constructive theory of metric spaces. The first states that Cantor space embeds in any inhabited complete separable metric space (CSM) without isolated points, X, in such a way that every sequentially continuous function from Cantor space to ℤ extends to a sequentially continuous function from X to ℝ. The second asserts an analogous property for Baire space relative to any inhabited locally non‐compact CSM. Both results rely on having careful constructive formulations of the concepts involved.
Design of LDPC Codes Based on Progressive Edge Growth Techniques for Block Fading Channels

A novel algorithm to design Root-Check LDPC codes based on Progressive Edge Growth (PEG) techniques for block-fading channels is proposed. The performance of the new codes is investigated in terms of the Frame Error Rate (FER) and the Bit Error Rate (BER). Numerical results show that the codes constructed by the proposed algorithm outperform codes constructed by the existing methods by 0.5dB.
Grand challenge competition to predict in vivo knee loads

Impairment of the human neuromusculoskeletal system can lead to significant mobility limitations and decreased quality of life. Computational models that accurately represent the musculoskeletal systems of individual patients could be used to explore different treatment options and optimize clinical outcome. The most significant barrier to model‐based treatment design is validation of model‐based estimates of in vivo contact and muscle forces. This paper introduces an annual “Grand Challenge Competition to Predict In Vivo Knee Loads” based on a series of comprehensive publicly available in vivo data sets for evaluating musculoskeletal model predictions of contact and muscle forces in the knee. The data sets come from patients implanted with force‐measuring tibial prostheses. Following a historical review of musculoskeletal modeling methods used for estimating knee muscle and contact forces, we describe the first two data sets used for the first two competitions and summarize four subsequent data sets to be used for future competitions. These data sets include tibial contact force, video motion, ground reaction, muscle EMG, muscle strength, static and dynamic imaging, and implant geometry data. Competition participants create musculoskeletal models to predict tibial contact forces without having access to the corresponding in vivo measurements. These blinded predictions provide an unbiased evaluation of the capabilities and limitations of musculoskeletal modeling methods. The paper concludes with a discussion of how these unique data sets can be used by the musculoskeletal modeling research community to improve the estimation of in vivo muscle and contact forces and ultimately to help make musculoskeletal models clinically useful. © 2011 Orthopaedic Research Society. © 2011 Orthopaedic Research Society Published by Wiley Periodicals, Inc. J Orthop Res 30:503–513, 2012
Neural basis of global resting-state fMRI activity

Functional MRI (fMRI) has uncovered widespread hemodynamic fluctuations in the brain during rest. Recent electroencephalographic work in humans and microelectrode recordings in anesthetized monkeys have shown this activity to be correlated with slow changes in neural activity. Here we report that the spontaneous fluctuations in the local field potential (LFP) measured from a single cortical site in monkeys at rest exhibit widespread, positive correlations with fMRI signals over nearly the entire cerebral cortex. This correlation was especially consistent in a band of upper gamma-range frequencies (40–80 Hz), for which the hemodynamic signal lagged the neural signal by 6–8 s. A strong, positive correlation was also observed in a band of lower frequencies (2–15 Hz), albeit with a lag closer to zero. The global pattern of correlation with spontaneous fMRI fluctuations was similar whether the LFP signal was measured in occipital, parietal, or frontal electrodes. This coupling was, however, dependent on the monkey's behavioral state, being stronger and anticipatory when the animals’ eyes were closed. These results indicate that the often discarded global component of fMRI fluctuations measured during the resting state is tightly coupled with underlying neural activity.
Family caregivers articulating the social network of a child with special health care needs.

UNLABELLED In Brazil, studies rarely address the social network of a child with special health care needs (CSHCN). OBJECTIVE the study sought to characterize the social network of the child and analyze the role of the family in its creation. METHOD a qualitative approach was developed through five dynamics (Speaking Map) based on the creative sensitive method, with five groups of families (12 participants) in their homes. RESULTS the critical discourse analysis of the caregivers (grandparents, siblings and neighbors) showed that the mother plays the main role in articulating the social network, with its points being linked by the hospital, primary and rehabilitation care, household, school, etc. Familial care becomes more visible at home and within the community. CONCLUSION with the insufficient public policy that articulating healthcare facilities for CSHCN in the community, family members shape a social network characterized by a dense and fluid mesh.