Miracle-dz/UniFAR-FTUs huggingface dataset:
BipC, a Predicted Burkholderia pseudomallei Type 3 Secretion System Translocator Protein with Actin Binding Activity

Burkholderia pseudomallei is an intracellular bacterial pathogen and the causative agent of melioidosis, a severe disease of humans and animals. Like other clinically important Gram-negative bacteria, fundamental to B. pseudomallei pathogenesis is the Bsa Type III Secretion System. The Bsa system injects bacterial effector proteins into the cytoplasm of target host cells subverting cellular pathways for the benefit of the bacteria. It is required for invasion of non-phagocytic host cells, escape from the endocytic compartment into the host cell cytoplasm, and for virulence in murine models of melioidosis. We have recently described the repertoire of effector proteins secreted by the B. pseudomallei Bsa system, however the functions of many of these effector proteins remain an enigma. One such protein is BipC, a homolog of the translocator/effector proteins SipC and IpaC from Salmonella spp. and Shigella flexneri respectively. SipC and IpaC each have separate and distinct roles acting both as translocators, involved in creating a pore in the eukaryotic cell membrane through which effector proteins can transit, and as effectors by interacting with and polymerizing host cell actin. In this study, pull-down assays demonstrate an interaction between BipC and actin. Furthermore, we show that BipC directly interacts with actin, preferentially with actin polymers (F-actin) and has the ability to polymerize actin in a similar manner as that described for SipC. Yet unlike SipC, BipC does not stabilize F-actin filaments, indicating a functionally distinct interaction with actin. Expression of Myc-tagged BipC in HeLa cells induces the formation of pseudopodia similar to that seen for IpaC. This study explores the effector function of BipC and reveals that actin interaction is conserved within the BipC/SipC/IpaC family of translocator/effector proteins.
The Droplet Digital PCR: A New Valid Molecular Approach for the Assessment of B-RAF V600E Mutation in Hairy Cell Leukemia

Hairy cell leukemia (HCL) is a chronic lymphoproliferative B-cell disorder where the B-RAF V600E mutation has been recently detected, as reported for solid neoplasias but not for other B-cell lymphomas. The digital droplet PCR (dd-PCR) is a molecular technique that, without standard references, is able to accurately quantitate DNA mutations. ddPCR could be an useful instrument for the detection of the B-RAF V600E mutation in HCL, where the minimal residual disease monitoring is fundamental for planning a patients-targeted treatment in the era of new anti-CD20 and anti-RAF compounds. This retrospective study enrolled 47 patients observed at the Hematology Unit of the University of Pisa, Italy, from January 2005 to January 2014: 27 patients were affected by “classic” HCL, two by the variant HCL (vHCL), and 18 by splenic marginal zone lymphoma (SMZL). The aim of the study was to compare dd-PCR to “classic” quantitative PCR (QT-PCR) in terms of sensitivity and specificity and to demonstrate its possible use in HCL. Results showed that: (1) the sensitivity of dd-PCR is about half a logarithm superior to QT-PCR (5 × 10-5 vs. 2.5 × 10-4), (2) the specificity of the dd-PCR is comparable to QT-PCR (no patient with marginal splenic lymphoma or HCL variant resulted mutated), (3) its high sensitivity would allow to use dd-PCR in the monitoring of MRD. At the end of treatment, among patients in complete remission, 33% were still MRD-positive by dd-PCR versus 28% by QT-PCR versus 11% by the evaluation of the B-cell clonality, after 12 months, dd-PCR was comparable to QT-PCR and both detected the B-RAF mutation in 15% of cases defined as MRD-negative by IgH rearrangement. Moreover, (4) the feasibility and the costs of dd-PCR are comparable to those of QT-PCR. In conclusion, our study supports the introduction of dd-PCR in the scenario of HCL, also during the follow-up.
Is Synaesthesia an X-Linked Dominant Trait with Lethality in Males?

In previous research the inheritance patterns of synaesthesia (eg experiencing colours from graphemes) has been studied and it was concluded that synaesthesia is most likely to be the outcome of a single gene passed on the X chromosome in a dominant fashion. In addition, it has been reported that the female – male ratio of synaesthetes is as high as 6: 1 and the families of synaesthetes contain more female than male members. This raises the possibility that the gene may be associated with lethality in males. In this study we replicate and extend previous research by investigating the female – male ratio and inheritance patterns in a large sample of synaesthetic families (N = 85). We were able to verify the authenticity of grapheme – colour associates in at least one proband from each family using internal consistency. As before, our results show a female – male bias and are broadly consistent with an X-linked dominant mode of inheritance. However, there was no evidence of male lethality (eg synaesthetes are just as likely to give birth to sons as to daughters). Moreover, our female – male ratio of synaesthetes within families was 2: 1 —considerably lower than previous estimates. We speculate that men may be more reluctant to disclose synaesthesia than women (indeed, our female – male ratio based on self-referral was 3.7: 1). Finally, we discuss how the genotype may give rise to the phenotype in terms of changes in synaptogenesis or plasticity extending into childhood, to be subsequently shaped by the environment.
Prevalence of HIV Infection among U.S. Hodgkin Lymphoma Cases

Background: Hodgkin lymphoma is uncommon in the U.S. general population; however, Hodgkin lymphoma risk is elevated in people with human immunodeficiency virus (HIV) infection. Thus, despite the low HIV prevalence in the United States, the HIV epidemic may have contributed substantially to the general population burden of Hodgkin lymphoma. Methods: We used data from 14 U.S. cancer registries in the Surveillance, Epidemiology, and End Results Program that recorded HIV status of Hodgkin lymphoma cases at diagnosis during 2000 to 2010. We computed the HIV prevalence in Hodgkin lymphoma cases by demographic and tumor characteristics, the proportion of deaths among Hodgkin lymphoma cases because of HIV, and 5-year mortality by HIV status. Results: Of 22,355 Hodgkin lymphoma cases, 848 (3.79%) were HIV infected at diagnosis. HIV prevalence in Hodgkin lymphoma cases was greater among males than females (6.0% vs. 1.2%). Among males, HIV prevalence was greatest among 40- to 59-year-olds (14.2%), non-Hispanic blacks (16.9%), Hispanics (9.9%), and among cases of lymphocyte-depleted (15.1%), and mixed cellularity Hodgkin lymphoma (10.5%). Eight percent of male and 1.5% of female Hodgkin lymphoma cases died from HIV. Five-year mortality was two-fold higher in HIV-infected Hodgkin lymphoma cases (36.9% vs. 17.5%). Conclusion: In the United States, a substantial proportion of lymphocyte-depleted and mixed cellularity Hodgkin lymphoma cases and Hodgkin lymphoma cases among non-Hispanic black, Hispanic, and middle-aged men are HIV infected. In addition, HIV is an important cause of death among Hodgkin lymphoma cases. Impact: Clinicians should be aware of the high prevalence of HIV in certain subgroups of patients with Hodgkin lymphoma and routine HIV testing should be recommended for all patients presenting with Hodgkin lymphoma. Cancer Epidemiol Biomarkers Prev; 23(2); 274–81. ©2013 AACR.
Recognition: An Information Content Perspective

This essay offers a synthesis of the varied accounting literature on recognition. First, in a review of the historical evolution of accounting thoughts, two debates on accounting measurements stand out: historical cost as the basis for asset valuation and realization as the basic test for income determination. These debates have specific implications for the recognition issue. Second, I examine the shift from the traditional measurement perspective to an information content perspective in both rhetorical policy debates and academic accounting thoughts. Under the information content perspective, the (strategic) decision‐making context becomes particularly important. Last, I advocate information content as a combining perspective, not as a replacement of the measurement perspective. In particular, I draw attention to the recent academic studies with an explicit or implicit theme of recognition. These studies combine modern information economics with the accounting measurement structure. This line of researc.
Glucagon‐like peptide‐1 acutely affects renal blood flow and urinary flow rate in spontaneously hypertensive rats despite significantly reduced renal expression of GLP‐1 receptors

Glucagon‐like peptide‐1 (GLP‐1) is an incretin hormone increasing postprandial insulin release. GLP‐1 also induces diuresis and natriuresis in humans and rodents. The GLP‐1 receptor is extensively expressed in the renal vascular tree in normotensive rats where acute GLP‐1 treatment leads to increased mean arterial pressure (MAP) and increased renal blood flow (RBF). In hypertensive animal models, GLP‐1 has been reported both to increase and decrease MAP. The aim of this study was to examine expression of renal GLP‐1 receptors in spontaneously hypertensive rats (SHR) and to assess the effect of acute intrarenal infusion of GLP‐1. We hypothesized that GLP‐1 would increase diuresis and natriuresis and reduce MAP in SHR. Immunohistochemical staining and in situ hybridization for the GLP‐1 receptor were used to localize GLP‐1 receptors in the kidney. Sevoflurane‐anesthetized normotensive Sprague–Dawley rats and SHR received a 20 min intrarenal infusion of GLP‐1 and changes in MAP, RBF, heart rate, dieresis, and natriuresis were measured. The vasodilatory effect of GLP‐1 was assessed in isolated interlobar arteries from normo‐ and hypertensive rats. We found no expression of GLP‐1 receptors in the kidney from SHR. However, acute intrarenal infusion of GLP‐1 increased MAP, RBF, dieresis, and natriuresis without affecting heart rate in both rat strains. These results suggest that the acute renal effects of GLP‐1 in SHR are caused either by extrarenal GLP‐1 receptors activating other mechanisms (e.g., insulin) to induce the renal changes observed or possibly by an alternative renal GLP‐1 receptor.
Abnormalities in Metabolic Network Activity Precede the Onset of Motor Symptoms in Parkinson's Disease

Imaging studies show that Parkinson's disease (PD) alters the activity of motor- and cognition-related metabolic brain networks. However, it is not known whether the network changes appear at or before symptom onset. In this study, we examined 15 hemiparkinsonian patients who underwent serial metabolic imaging with [18F]-fluorodeoxyglucose (FDG) PET at baseline and again 2.1 ± 0.6 (mean ± SD) and 3.9 ± 0.7 years later. We assessed longitudinal changes in network activity in each cerebral hemisphere, focusing specifically on the “presymptomatic” hemisphere—ipsilateral to the initially involved body side. At the network level, the activity of the PD motor-related pattern (PDRP) increased symmetrically in both hemispheres over time (p < 0.001), with significant bilateral elevations at each of the three time points. Hemispheric expression of the PD cognition-related pattern likewise increased symmetrically (p < 0.001), although significant elevations were not evident on either side until 4 years. At the regional level, putamen metabolism contralateral to the initially affected body side was elevated at all three time points, without longitudinal change. In contrast, in the initially presymptomatic hemisphere, putamen metabolic activity increased steadily over time, reaching abnormal levels only at 4 years. Metabolic activity in the contralateral precuneus fell to subnormal levels by the final time point. These findings suggest that abnormal PDRP activity antecedes the appearance of motor signs by ∼2 years. The timing and laterality of symptom onset relates to focal asymmetric metabolic changes at the putamenal node of this network.
A comparison of active set method and genetic algorithm approaches for learning weighting vectors in some aggregation operators

In this article we compare two contrasting methods, active set method (ASM) and genetic algorithms, for learning the weights in aggregation operators, such as weighted mean (WM), ordered weighted average (OWA), and weighted ordered weighted average (WOWA). We give the formal definitions for each of the aggregation operators, explain the two learning methods, give results of processing for each of the methods and operators with simple test datasets, and contrast the approaches and results. © 2001 John Wiley & Sons, Inc.
Manual therapy program induced alterations in autonomic nervous system modulation of students preparing to apply for the universities: One-group, pre- and post-test study

OBJECTIVES: We aimed to appraise the effects of a manual therapy program (MTP) on stress by modulation of autonomic nervous system evaluated by rate heart variability before and after the treatment. METHODS: The study design used was quasi-experimental, pre-post-test of MTP. The sessions were applied during 45 min, twice a week, for 9 weeks. Psychological stress was evaluated using adolescents stress questionnaire (ASQ). Beat-to-beat rate heart frequency (HR, bpm) were recorded in 16 young healthy volunteers (19-20 years old; 8 women) 15 min before and after the first and the last session with S810i - Polar® -Finland in supine position. Descriptors of the Poincare plot and time domain of HR variability (HRV) were analyzed in 5 min (Kubios HRV Analysis Software). STATISTICAL ANALYSIS: ANOVA followed Tukey or Bonferroni and t Student tests paired and unpaired tests, considering p<0.05 as significant. RESULTS: MTP reduced ASQ values from 143 ± 8 to 114 ± 6 and HR from 81+4 to 71+2 bpm. Significantly effects were also found post-MTP in HRV time domain, analyzed at linear and geometric way, sowing an overall increased on parasympathetic tonus and on global activity of heart. CONCLUSION: The students enrolled in the MTP showed improved psychological and physiological health status from pre to post-treatment and the increased on parasympathetic tonus and in the global activity of heart contributed to this effect.
Integrative Modeling of eQTLs and Cis-Regulatory Elements Suggests Mechanisms Underlying Cell Type Specificity of eQTLs

Genetic variants in cis-regulatory elements or trans-acting regulators frequently influence the quantity and spatiotemporal distribution of gene transcription. Recent interest in expression quantitative trait locus (eQTL) mapping has paralleled the adoption of genome-wide association studies (GWAS) for the analysis of complex traits and disease in humans. Under the hypothesis that many GWAS associations tag non-coding SNPs with small effects, and that these SNPs exert phenotypic control by modifying gene expression, it has become common to interpret GWAS associations using eQTL data. To fully exploit the mechanistic interpretability of eQTL-GWAS comparisons, an improved understanding of the genetic architecture and causal mechanisms of cell type specificity of eQTLs is required. We address this need by performing an eQTL analysis in three parts: first we identified eQTLs from eleven studies on seven cell types; then we integrated eQTL data with cis-regulatory element (CRE) data from the ENCODE project; finally we built a set of classifiers to predict the cell type specificity of eQTLs. The cell type specificity of eQTLs is associated with eQTL SNP overlap with hundreds of cell type specific CRE classes, including enhancer, promoter, and repressive chromatin marks, regions of open chromatin, and many classes of DNA binding proteins. These associations provide insight into the molecular mechanisms generating the cell type specificity of eQTLs and the mode of regulation of corresponding eQTLs. Using a random forest classifier with cell specific CRE-SNP overlap as features, we demonstrate the feasibility of predicting the cell type specificity of eQTLs. We then demonstrate that CREs from a trait-associated cell type can be used to annotate GWAS associations in the absence of eQTL data for that cell type. We anticipate that such integrative, predictive modeling of cell specificity will improve our ability to understand the mechanistic basis of human complex phenotypic variation.
Antenna selection for NR-STAR-MQAM spatial modulation

A new multiple-ring star- M -ary quadrature amplitude modulation-aided spatial modulation ( N R-STAR- M QAM-SM) scheme is proposed. The aim is to minimise the average bit error probability (ABEP) of the system. Then in the interest of further minimising the ABEP, the authors formulate a low-complexity algorithm to achieve the optimum radii of N R-STAR- M QAM-SM. This algorithm is based on a specific multiple-input multiple-output configuration and the pairwise error probability function. To validate the results of the proposed scheme, a closed-form union-bound theoretical ABEP expression is derived. Finally, to improve the error performance of N R-STAR- M QAM-SM, the authors propose a low-complexity Euclidean distance-based antenna selection (EDAS) algorithm for N R-STAR- M QAM-SM (EDAS- N R-STAR- M QAM-SM). Since all amplitude/phase modulation schemes are considered to have rotational symmetry and symmetric constellation points have the same EDAS solution, the authors achieve EDAS- N R-STAR- M QAM-SM by searching only one constellation point per symmetric constellation set. The EDAS- N R-STAR- M QAM-SM solution exhibits a significant reduction in the computational complexity compared with the conventional EDAS solution.
Genome Sequence of Lactococcus lactis subsp. lactis NCDO 2118, a GABA-Producing Strain

ABSTRACT Lactococcus lactis subsp. lactis NCDO 2118 is a nondairy lactic acid bacterium, a xylose fermenter, and a gamma-aminobutyric acid (GABA) producer isolated from frozen peas. Here, we report the complete genome sequence of L. lactis NCDO 2118, a strain with probiotic potential activity.
Validity of a low-cost wearable device for body sway parameter evaluation

The evaluation of body sway during quiet standing is an established mean to assess the capacity of the neuromuscular system of one individual to maintain the standing posture (Winter 1995). Parameters obtained from the centre of pressure (COP) path are indirect measures of postural sway as they are related to the displacement of the body centre of mass (Winter 1995). Classically, these parameters are obtained through a force platform (Prieto et al. 1996). They are known to be sensitive to age (Martinez-Mendez et al. 2012), pathology (Mancini et al. 2012) and training (Lamoth et al. 2009), therefore, providing important information on the subject motricity. Alternative systems based on accelerometers have proven to be effective for body sway evaluation. To date, these systems are still expensive and mostly available in research laboratories or at hospitals. The fast development of wireless sensors and MEMS opens a large field of applications in which body sway parameters can be assessed with low-cost solutions. They allow selfevaluation outside research laboratories or clinical structures in everyday life condition at home or during sport activities. Such evaluation linked to specific balance improvement exercises can be a source of motivation for physical training and therefore prevention of sedentary lifestyle troubles. Nevertheless these devices need to be validated. In this framework, the aim of this work was to compare body sway parameters, during quite standing, obtained by a low-cost ultralow power wearable device (BodyTrack; Esphi, Marseille, France) to those estimated from the COP data collected by a force platform.
Increasing the reliability of data analysis of functional magnetic resonance imaging by applying a new blockwise permutation method

A recent paper by Eklund et al. (2012) showed that up to 70% false positive results may occur when analyzing functional magnetic resonance imaging (fMRI) data using the statistical parametric mapping (SPM) software, which may mainly be caused by insufficient compensation for the temporal correlation between successive scans. Here, we show that a blockwise permutation method can be an effective alternative to the standard correction method for the correlated residuals in the general linear model, assuming an AR(1)-model as used in SPM for analyzing fMRI data. The blockwise permutation approach including a random shift developed by our group (Adolf et al., 2011) accounts for the temporal correlation structure of the data without having to provide a specific definition of the underlying autocorrelation model. 1465 publicly accessible resting-state data sets were re-analyzed, and the results were compared with those of Eklund et al. (2012). It was found that with the new permutation method the nominal familywise error rate for the detection of activated voxels could be maintained approximately under even the most critical conditions in which Eklund et al. found the largest deviations from the nominal error level. Thus, the method presented here can serve as a tool to ameliorate the quality and reliability of fMRI data analyses.
Distinct pinned triangle areas on algebraic curves

Any p, q ∈ R2 together with the origin determine a pinned triangle. We prove that any finite set S contained in an irreducible algebraic curve C of degree d in R2 determines Ωd(|S| 4/3) distinct pinned triangle areas, unless C is a line, or an ellipse or hyperbola centered at the origin. This improves the bound Ω(|S|5/4) obtained by Charalambides [1]. The proof is based on that of Pach and De Zeeuw [6], who proved a similar statement for Euclidean distances. The main motivation for this paper is that for pinned triangle areas, this approach becomes more natural, and should better lend itself to generalization.
Adolescent friendship quality and emotional adjustment: Examining the role of mothers' own friendships

The present study examines associations between youths’ friendships and the friendships their mothers have with other adults. It was hypothesized that youth whose mothers have friendships high in positive qualities would have more positive friendships themselves and report decreased internalizing symptoms. Similarly, children of mothers whose friendships were high in negative qualities were expected to report increased negative qualities in their own friendships as well as increased internalizing symptoms. A sample of 172 fifth, eighth, and eleventh grade youth and their mothers were recruited to test these hypotheses, however, only the latter hypothesis was supported. Although mothers who reported high levels of conflict in their own friendships had children whose friendships were characterized by increased conflict, similar associations did not emerge for positive qualities. Further, youth whose mothers reported higher levels of negative qualities in their friendships were more likely to report increased internalizing symptoms themselves, even after reports of the mother-child relationship, youths’ friendship quality, and mothers’ own internalizing symptoms were controlled.