Miracle-dz/UniFAR-FTUs huggingface dataset:
Recurrent mutations of NOTCH genes in follicular lymphoma identify a distinctive subset of tumours

Follicular lymphoma (FL) is one of the most common malignant lymphomas. The t(14;18)(q32;q21) translocation is found in about 80% of cases and plays an important role in lymphomagenesis. However, the molecular mechanisms involved in the development and transformation of this lymphoma are not fully understood. Gain‐of‐function mutations of NOTCH1 or NOTCH2 have recently been reported in several B cell lymphoid neoplasms but the role of these mutations in FL is not known. In this study we investigated the mutational status of these genes in 112 FLs. NOTCH1 and NOTCH2 mutations were identified in five and two cases, respectively (total 7/112, 6.3%). All mutations predicted for truncated protein in the PEST domain and were identical to those identified in other B cell lymphoid neoplasms. NOTCH‐mutated FL cases were characterized by lower frequency of t(14;18) (14% versus 69%, p = 0.01), higher incidence of splenic involvement (71% versus 25%, p = 0.02) and female predominance (100% versus 55%, p = 0.04). A diffuse large B cell lymphoma (DLBCL) component was more frequently identified in NOTCH‐mutated FL than in wild‐type cases (57% versus 18%, p = 0.03). These results indicate that NOTCH mutations are uncommon in FL but may occur in a subset of cases with distinctive, characteristic, clinicopathological features. Copyright © 2014 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
A simple data transmission scheduling method for Wireless Sensor Networks

Wireless Sensor Network (WSNs) is a network for gathering sensing data in sensing field. When all sensor nodes try to send their data to sink node, the reliability of data transmission decreases because of the congestion in the networks. In this paper we proposed simple data transmission scheduling method to reduce the congestion and verify that our proposed scheme shows g performance through real environment test.
Neutron diffraction studies of Escherichia coli dihydrofolate reductase complexed with methotrexate

Hydrogen atoms play a central role in many biochemical processes yet are difficult to visualize by x-ray crystallography. Spallation neutron sources provide a new arena for protein crystallography with TOF measurements enhancing data collection efficiency and allowing hydrogen atoms to be located in smaller crystals of larger biological macromolecules. Here we report a 2.2-Å resolution neutron structure of Escherichia coli dihydrofolate reductase (DHFR) in complex with methotrexate (MTX). Neutron data were collected on a 0.3-mm3 D2O-soaked crystal at the Los Alamos Neutron Scattering Center. This study provides an example of using spallation neutrons to study protein dynamics, to identify protonation states directly from nuclear density maps, and to analyze solvent structure. Our structure reveals that the occluded loop conformation [monomer (mon.) A] of the DHFR·MTX complex undergoes greater H/D exchange compared with the closed-loop conformer (mon. B), partly because the Met-20 and β(F-G) loops readily exchange in mon. A. The eight-stranded β sheet of both DHFR molecules resists H/D exchange more than the helices and loops. However, the C-terminal strand, βH, in mon. A is almost fully exchanged. Several D2Os form hydrogen bonds with exchanged amides. At the active site, the N1 atom of MTX is protonated and thus charged when bound to DHFR. Several D2Os are observed at hydrophobic surfaces, including two pockets near the MTX-binding site. A previously unidentified D2O hydrogen bonds with the catalytic D27 in mon. B, stabilizing its negative charge.
Processing of hematopoietic stem cells from peripheral blood before cryopreservation: use of a closed automated system

BACKGROUND: Hematopoietic stem cell transplantation is commonly used to treat several oncohematologic diseases. The autologous hematopoietic progenitor cells collected through apheresis (HPC‐A) must be cryopreserved and stored before use in vivo. Cell processing that precedes cryopreservation of HPC‐A includes volume reduction aimed at reducing the amount of dimethyl sulfoxide used, as well as storage space.
Reproducibility of maximal exercise ergometer testing in patients with cystic fibrosis.

OBJECTIVES Exercise testing in patients with cystic fibrosis (CF) has become an important tool in assessing disease severity and predicting overall outcome. The reproducibility of maximal exercise testing was examined in adult subjects with stable CF. METHODS Nine subjects with CF underwent a total of three maximal exercise tests carried out under identical circumstances over a 28-day period. Oxygen uptake (VO2), minute ventilation (VE), respiratory frequency (f), heart rate (HR), and arterial oxygen saturation (SaO2) were measured at rest, at end exercise, and at 40% and 70% of maximum workload. RESULTS There were no significant differences in these measurements among the three tests. Reproducibility of exercise performance was assessed using the coefficient of variation. The mean within-subject coefficient of variation for test variables at end exercise are as follows: VO2, 6.9%; VE, 6.2%; f, 5.8%; IIR, 3.0%; and SaO2, 1.1%. The mean within-subject coefficient of variation for test variables at 40% and 70% of maximal work rates are as follows: VO2, 5.2% and 4.6%; SaO2, 0.3% and 0.9%; HR, 4.0% and 3%; VE, 5.7% and 6.5%; and f, 5.8% and 7.2%, respectively. CONCLUSIONS Variables measured during clinical cycle ergometer exercise testing in adult patients with stable CF are reproducible. No learning effect was found on repeated testing.
Punishment diminishes the benefits of network reciprocity in social dilemma experiments

Significance The evolution of cooperation has a formative role in human societies—civilized life on Earth would be impossible without cooperation. However, it is unclear why cooperation would evolve in the first place because Darwinian selection favors selfish individuals. After struggling with this problem for >150 y, recent scientific breakthroughs have uncovered multiple cooperation-promoting mechanisms. We build on these breakthroughs by examining whether two widely known cooperation-promoting mechanisms—network reciprocity and costly punishment—create synergies in a social dilemma experiment. While network reciprocity fulfilled its expected role, costly punishment proved to be surprisingly ineffective in promoting cooperation. This ineffectiveness suggests that the rational response to punishment assumed in theoretical studies is overly stylized and needs reexamining. Network reciprocity has been widely advertised in theoretical studies as one of the basic cooperation-promoting mechanisms, but experimental evidence favoring this type of reciprocity was published only recently. When organized in an unchanging network of social contacts, human subjects cooperate provided the following strict condition is satisfied: The benefit of cooperation must outweigh the total cost of cooperating with all neighbors. In an attempt to relax this condition, we perform social dilemma experiments wherein network reciprocity is aided with another theoretically hypothesized cooperation-promoting mechanism—costly punishment. The results reveal how networks promote and stabilize cooperation. This stabilizing effect is stronger in a smaller-size neighborhood, as expected from theory and experiments. Contrary to expectations, punishment diminishes the benefits of network reciprocity by lowering assortment, payoff per round, and award for cooperative behavior. This diminishing effect is stronger in a larger-size neighborhood. An immediate implication is that the psychological effects of enduring punishment override the rational response anticipated in quantitative models of cooperation in networks.
Relationship between energy distribution and fold stability: Insights from molecular dynamics simulations of native and mutant proteins

Most proteins must fold to a well‐defined structure with a minimal stability to perform their function. Here we use a simple, molecular dynamics‐based, energy decomposition approach to map the principal energetic interactions in a set of proteins representative of different folds. This work involves the all‐atom simulation and analysis of the native structures and mutants of five different proteins representative of an all‐alpha (yACPB, Protein A), all‐beta (SH3), and a mixed α/β fold (Proteins G and L). Given a certain structure, a native sequence and a set of mutants, we show that our model discriminates the ability of a mutation to yield a more or less stable protein, in agreement with experimental data, catching the principal energetic determinants of protein stabilization. Our approach identifies the interaction determinants responsible to define a fold and shows that mutations can either modulate the strength of pair‐wise coupling between residues important for folding, or modify the profile of the principal interactions. Furthermore, we address the question of how to evaluate the fitness of a sequence to a given structure by comparing the information contained in the energy map, which recapitulates the chemistry of the sequence, to that contained in the contact map, which recapitulates the fold topology. The results show that the better fit between the energetic properties of the sequence and the fold topology corresponds to a higher stabilization of the protein. We discuss the relevance of these observations to the analysis of protein designability and to the rational evolution of new sequences. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Parenting an Adult Child With Bipolar Disorder in Later Life

This study extends prior research on family caregiving in mental illness by investigating late-life parenting of adult children with bipolar disorder using a randomly selected community-based sample. The health and mental health, psychological well-being, marriage, work-life, and social resources of 145 parents of adult children with bipolar disorder were examined when parents were in their mid-60s. Stratified random sampling procedures were used to select a comparison group whose children did not have disabilities. Results indicate that parents of adult children with bipolar disorder had a more compromised profile of health and mental health, and experienced more difficulties in marriage and work-life than comparison parents. Furthermore, parents of adult children with bipolar disorder who were diagnosed with mental illness before the onset of their child's symptoms were more vulnerable on multiple dimensions of mental health, psychological well-being, and work-life than parents without a preexisting mental illness.
Fluorescent proteins for live cell imaging: Opportunities, limitations, and challenges

The green fluorescent protein (GFP) from the jellyfish Aequorea victoria can be used as a genetically encoded fluorescence marker due to its autocatalytic formation of the chromophore. In recent years, numerous GFP‐like proteins with emission colors ranging from cyan to red were discovered in marine organisms. Their diverse molecular properties enabled novel approaches in live cell imaging but also impose certain limitations on their applicability as markers. In this review, we give an overview of key structural and functional properties of fluorescent proteins that should be considered when selecting a marker protein for a particular application and also discuss challenges that lie ahead in the further optimization of the glowing probes. © 2009 IUBMB IUBMB Life, 61(11): 1029–1042, 2009
Assessment of Antioxidant Capacity and Cytotoxicity of Selected Malaysian Plants

Thirteen Malaysian plants; Artocarpus champeden, Azadirachta indica, Fragaria x ananassa, Garcinia mangostana, Lawsonia inermis, Mangifera indica, Nephelium lappaceum, Nephelium mutobile, Peltophorum pterocarpum, Psidium guajava and Syzygium aqueum, selected for their use in traditional medicine, were subjected to a variety of assays. Antioxidant capability, total phenolic content, elemental composition, as well as it cytotoxity to several cell lines of the aqueous and ethanolic extracts from different parts of these selected Malaysian plants were determined. In general, the ethanolic extracts were better free radical scavengers than the aqueous extracts and some of the tested extracts were even more potent than a commercial grape seed preparation. Similar results were seen in the lipid peroxidation inhibition studies. Our findings also showed a strong correlation of antioxidant activity with the total phenolic content. These extracts when tested for its heavy metals content, were found to be below permissible value for nutraceutical application. In addition, most of the extracts were found not cytotoxic to 3T3 and 4T1 cells at concentrations as high as 100 μg/mL. We conclude that although traditionally these plants are used in the aqueous form, its commercial preparation could be achieved using ethanol since a high total phenolic content and antioxidant activity is associated with this method of preparation.
Stress Buffering and Glycemic Control: The Role of Coping Styles

Objective To test the hypotheses that chronic psychosocial stress is associated with worse glycemic control and that coping moderates (buffers) this effect. Research Design and Methods Subjects consisted of 105 insulin-treated adults from the Diabetes Division of Henry Ford Hospital who filled out questionnaires on stress and coping and received an HbA1 test at a clinic appointment. Six coping styles were examined, including both emotion- and problem-focused styles. Two standardized stress inventories were administered. Ineffective coping was defined as scoring below the median for stress-dampening coping styles and above the median for stress-exacerbating styles. Results Stress was significantly (P < 0.05) correlated with higher HbA1 in all but one ineffective coping subgroup. Conversely, none of 12 correlations between stress and glycemic control was significant in the effective coping subgroups. Conclusions Chronic psychosocial stress is associated with worse glycemic control among those who do not cope effectively with stress. Effective coping can protect individuals from the deleterious effects of stress.
In and out of control: brain mechanisms linking fluency of action selection to self-agency in patients with schizophrenia

Sense of agency refers to the feeling of control over one's actions, and their consequences. It involves both predictive processes linked to action control, and retrospective 'sense-making' causal inferences. Schizophrenia has been associated with impaired predictive processing, but the underlying mechanisms that impair patients' sense of agency remain unclear. We introduce a new 'prospective' aspect of agency and show that subliminally priming an action not only influences response times, but also influences reported sense of agency over subsequent action outcomes. This effect of priming was associated with altered connectivity between frontal areas and the angular gyrus. The effects on response times and on frontal action selection mechanisms were similar in patients with schizophrenia and in healthy volunteers. However, patients showed no effects of priming on sense of agency, no priming-related activation of angular gyrus, and no priming-related changes in fronto-parietal connectivity. We suggest angular gyrus activation reflects the experiences of agency, or non-agency, in part by processing action selection signals generated in the frontal lobes. The altered action awareness that characterizes schizophrenia may be due to impaired communication between these areas.
An Interprofessional Simulation Using the SBAR Communication Tool

Objective. To determine the impact of an interprofessional simulation using the SBAR (situation-background-assessment-recommendation/request) communication tool on pharmacy students’ self-perception of interprofessional competence and reactions towards interprofessional collaboration. Design. Ninety-six pharmacy students participated in an interprofessional simulation within a required applications-based capstone course. Pharmacy students collaborated with nursing students on multiple patient cases in various settings using the SBAR communication tool over the telephone. Assessment. Pharmacy students’ responses to all 20 items on the Interprofessional Collaborative Competency Attainment Survey (ICCAS) completed after participating in the simulation indicated significant positive changes. The themes identified in students’ reflection papers indicated the simulation was beneficial and student responses on satisfaction surveys were positive with a mean score of 4.2 on a 5-point Likert scale. Conclusion. Implementation of an interprofessional simulation using the SBAR communication tool improved pharmacy students’ self-perception of interprofessional competence and attitudes toward interprofessional collaboration.
Molecular Evolution of the dotA Gene in Legionella pneumophila

ABSTRACT The molecular evolution of dotA, which is related to the virulence of Legionella pneumophila, was investigated by comparing the sequences of 15 reference strains (serogroups 1 to 15). It was found that dotA has a complex mosaic structure. The whole dotA gene of Legionella pneumophila subsp. pneumophila serogroups 2, 6, and 12 has been transferred from Legionella pneumophila subsp. fraseri. A discrepancy was found between the trees inferred from the nucleotide and deduced amino acid sequences of dotA, which suggests that multiple hits, resulting in synonymous substitutions, have occurred. Gene phylogenies inferred from three different segments (the 5′-end region, the central, large periplasmic domain, and the 3′-end region) showed impressively dissimilar topologies. This was concordant with the sequence polymorphisms, indicating that each region has experienced an independent evolutionary history, and was evident even within the same domain of each strain. For example, the PP2 domain was found to have a heterogeneous structure, which led us hypothesize that the dotA gene of L. pneumophila may have originated from two or more different sources. Comparisons of synonymous and nonsynonymous substitutions demonstrated that the PP2 domain has been under strong selective pressure with respect to amino acid change. Split decomposition analysis also supported the intragenic recombination of dotA. Multiple recombinational exchange within the dotA gene, encoding an integral cytoplasmic membrane protein that is secreted, probably provided increased fitness in certain environmental niches, such as within a particular biofilm community or species of amoebae.
Genotoxic effects of chlorophenoxy herbicide diclofop-methyl in mice in vivo and in human lymphocytes in vitro

Diclofop-methyl (DM) is a chlorophenoxy derivative used in large quantities for the control of annual grasses in grain and vegetable crops. In this study, the genotoxic effects of DM were investigated by measuring chromosomal aberrations (CAs) in mouse bone-marrow cells and CA and the comet assay in human peripheral lymphocytes. Mice were treated with 15.63, 31.25, 62.5, and 125 mg/kg body weight of DM intraperitoneally for 24 hours, and 15.63-, 31.25-, 62.5-, 125-, and 250-µg/mL concentrations were applied to human lymphocytes for both 24 and 48 hours. In in vivo treatments, DM significantly, but not dose dependently, increased the total chromosome aberrations, compared to both negative and solvent controls. Cell proliferation was significantly, but not dose dependently, affected by all doses. In in vitro treatments, DM (except 15.63 µg/mL) significantly and dose dependently increased the frequency of chromosome aberrations. Also, 250 µg/mL of 48-hour treatment was found to be toxic. Cell proliferation was significantly and dose dependently affected by DM applications, when compared to negative control. In in vitro treatments, DM significantly decreased the mitotic index only at the highest concentration for 24 hours, and 62.5- and 125-µg/mL concentrations for 48 hours. In the comet assay, a significant and dose-dependent increase in comet-tail intensity was observed at 62.5-, 125-, and 250-µg/mL concentrations. The mean comet-tail length was significantly increased in all concentrations. Our results demonstrate that DM is genotoxic in mammalian cells in vivo and in vitro.
Developmental coordination disorder and aerobic fitness: is it all in their heads or is measurement still the problem?

Developmental coordination disorder (DCD) is characterized by motor inproficiency, resulting in significant impairments in social and/or academic functioning. About 5–9% of all school‐age children are affected. Previous research has shown that children with DCD have lower aerobic fitness levels than children without the disorder, although the reasons for this have not been tested in the literature. A potential explanation may lie in perceived adequacy regarding performance in physical activity. Although negative perceptions of adequacy in children with DCD likely reflect an accurate appraisal of actual physical abilities, aerobic fitness tests typically require minimal coordination skills. Children who perceive themselves to be less adequate are unlikely to persist at a task and may give up sooner on these tests of endurance. Using a large community based sample of children ages 9 through 14 (n = 586), we examine whether differences in aerobic fitness (assessed by performance on a 20‐m shuttle run test) between children who meet the criteria for DCD (n = 44) and those who do not (n = 542) is due to differences in perceived adequacy toward physical activity. Our results show that one‐third of the effect of DCD on VO2 can be attributed to differences in perceived adequacy. These results suggest that at least part of the reason children perform less well on tests of aerobic endurance is because they do not believe themselves to be as adequate as other children at physically active pursuits. The implications of this for further research are discussed. Am. J. Hum. Biol. 18:66–70, 2006. © 2005 Wiley‐Liss, Inc.
Sub-5 nm gap formation for low power NEM switches

To utilize nanoelectromechanical (NEM) switches for ultra-low power applications, sub-1 V actuation is one of the most important challenges to overcome [1-4]. We develop a CMOS-compatible technique that introduces ultra-small air gaps (<;5 nm) for lateral NEM switches to achieve zero-leakage and zero-crowbar-current circuits operating at sub-1 V. Ultra-small gap formation is achieved using growth/transfer of thin film/2D materials as sacrificial material before beam release. The gap size can be well controlled by the thickness of the thin film/2D materials. The lateral NEM switch has a single-pole double-throw configuration consisting of a freely suspended cantilever and two pairs of gate/drain electrodes placed symmetrically on both sides (Fig. 1a). The NEM operation was simulated using the Coventor MEMS+ software with Brick element model [6]. The length, width, and thickness of the poly-Si beam are 50, 1 and 1 μm, respectively. The initial gap between the beam and the gate (gbg) is 0.25 μm, and the gap between the beam and the drain (gbd) ranges from 1 to 40 nm. Fig. 1b shows that for gbd<; (1/3)gbg, the pull-in voltage of the NEM switch decreases efficiently by shrinking gbd. In order to obtain sub-1 V switching, the contact gap gbd has to be minimized to sub-5 nm, which is difficult to achieve in the lateral NEM structure using a “top-down” pattern-and-etch approach.