Miracle-dz/UniFAR-FTUs huggingface dataset:
Attribute Based Group Signature with Revocation

In real life, one requires signatures to be from people who fulfill certain criteria, implying that they should possess specific attributes. For example, Alice might want a signature from an employee in Bobs company who is a member in the IT staff, a senior manager within the biometrics team or at least a junior manager in the cryptography team. In such a case an Attribute Based Group Signature scheme (ABGS) could be applied. Group signature schemes are those where each member of a group can sign on behalf of the others. An ABGS scheme is a type of group signature scheme, where the signing member has to have certain attributes. In [12], the authors introduced the first ABGS but it lacked the ability to revoke. In this paper, we introduce a new scheme that will enable us to remove a member from a group or remove some of his attributes, when needed.
A comparison of methods for cascade prediction

Information cascades exist in a wide variety of platforms on Internet. A very important real-world problem is to identify which information cascades can “go viral”. A system addressing this problem can be used in a variety of applications including public health, marketing and counter-terrorism. As a cascade can be considered as compound of the social network and the time series. However, in related literature where methods for solving the cascade prediction problem were proposed, the experimental settings were often limited to only a single metric for a specific problem formulation. Moreover, little attention was paid to the run time of those methods. In this paper, we first formulate the cascade prediction problem as both classification and regression. Then we compare three categories of cascade prediction methods: centrality based, feature based and point process based. We carry out the comparison through evaluation of the methods by both accuracy metrics and run time. The results show that feature based methods can outperform others in terms of prediction accuracy but suffer from heavy overhead especially for large datasets. While point process based methods can also run into issue of long run time when the model can not well adapt to the data. This paper seeks to address issues in order to allow developers of systems for social network analysis to select the most appropriate method for predicting viral information cascades.
Relationship Between Carbamoyl-Phosphate Synthetase Genotype and Systemic Vascular Function

Abstract—Endothelial cells can convert l-citrulline to l-arginine, the precursor of nitric oxide. The present study tests the hypothesis that a C-to-A nucleotide transversion (T1405N) in the gene-encoding carbamoyl-phosphate synthetase 1, the enzyme catalyzing the rate-limiting step in l-citrulline formation, influences nitric oxide metabolite concentrations or nitric oxide-mediated vasodilation in humans. Bradykinin (100, 200, and 400 ng/min) was infused via brachial artery in 106 (CC:AC:AA=40:54:12) healthy subjects. Sodium nitroprusside (1.6, 3.2, and 6.4 &mgr;g/min) was also infused in 87 (CC:AC:AA=31:46:10) subjects. Forearm blood flow was measured by plethysmography and blood samples were collected for tissue-type plasminogen activator antigen, nitric oxide metabolites, and cyclic GMP. There was a significant relationship between carbamoyl-phosphate synthetase 1 genotype and nitric oxide metabolites, such that nitric oxide metabolite concentrations were highest in individuals homozygous for the C allele (mean±SD, 14.0±8.5 &mgr;mol/L), lowest in individuals homozygous for the A allele (9.1±3.1 &mgr;mol/L), and intermediate (11.8±6.6 &mgr;mol/L) in heterozygotes (P =0.036). There was a significant effect of carbamoyl-phosphate synthetase 1 genotype on forearm blood flow during bradykinin (P =0.028), such that the vasodilator response was greatest in C allele homozygotes (22.2±9.1 mL/min/100 mL at 400 ng/min), least in A allele homozygotes (13.6±6.2 mL/min/100 mL), and intermediate (19.4±10.7 mL/min/100 mL) in heterozygotes. Similarly, carbamoyl-phosphate synthetase 1 genotype influenced forearm blood flow during nitroprusside (maximal flow 19.2±8.3, 18.1±8.3, and 11.5±4.9 mL/min/100 mL in the CC:AC:AA groups, respectively; P =0.022). In contrast, there was no effect of carbamoyl-phosphate synthetase 1 genotype on the nitric oxide–independent tissue-type plasminogen activator response to bradykinin (P =0.943). These data indicate that a polymorphism in the gene encoding carbamoyl-phosphate synthetase 1 influences nitric oxide production as well as vascular smooth muscle reactivity.
Viscoelasticity of Rabbit Vocal Folds After Injection Augmentation

Objectives/Hypothesis Vocal fold function is related to the viscoelasticity of the vocal fold tissue. Augmentation substances used for injection treatment of voice insufficiency may alter the viscoelastic properties of vocal folds and their vibratory capacity. The objective was to compare the mechanical properties (viscoelasticity) of various injectable substances and the viscoelasticity of rabbit vocal folds, 6 months after injection with one of these substances.
Awareness in the Wild: Why Communication Breakdowns Occur

Global software teams face challenges when collaborating over long distances, such as communicating changes in the project. During a four-month case study at IBM Ottawa Software Lab we observed the collaboration patterns of a multi-site development project team. In this period, we inspected project documentation, interviewed team leaders, attended project meetings, and spoke with developers to identify problems originated by the lack of awareness of changes related to the implementation of work items. Our observations show (1) that organizational culture has an effect on how developers are made aware; (2) that communication-based social networks revolving around particular work items are dynamic throughout development, and therefore awareness needs to be maintained in infrastructures of work; and (3) that information overload and communication breakdowns contributed to the generation of a broken integration build. We discuss these breakdowns in communication and implications for the design of collaboration tools that could mitigate these problems.
diCal-IBD: demography-aware inference of identity-by-descent tracts in unrelated individuals

Summary: We present a tool, diCal-IBD, for detecting identity-by-descent (IBD) tracts between pairs of genomic sequences. Our method builds on a recent demographic inference method based on the coalescent with recombination, and is able to incorporate demographic information as a prior. Simulation study shows that diCal-IBD has significantly higher recall and precision than that of existing IBD detection methods, while retaining reasonable accuracy for IBD tracts as small as 0.1 cM. Availability: http://sourceforge.net/p/dical-ibd Contact: yss@eecs.berkeley. edu
Estimating Conditional Probability Densities for Periodic Variables

Most of the common techniques for estimating conditional probability densities are inappropriate for applications involving periodic variables. In this paper we introduce three novel techniques for tackling such problems, and investigate their performance using synthetic data. We then apply these techniques to the problem of extracting the distribution of wind vector directions from radar scatterometer data gathered by a remote-sensing satellite.
Hepatitis C virus triggers Golgi fragmentation and autophagy through the immunity-related GTPase M

Significance Without a vaccine or cost-effective antivirals against hepatitis C virus (HCV) there is a need to understand better the molecular mechanisms underlying the establishment of productive HCV infection and chronic liver disease. Recently, the Crohn's disease and tuberculosis risk factor immunity-related GTPase M (IRGM) was found to promote HCV replication, but the mechanisms involved are unknown. Here we provide mechanistic insight into how IRGM stimulates the two membrane-remodeling pathways, Golgi fragmentation and autophagy, to facilitate HCV replication. Our findings offer insights into the replication strategies used by HCV that should be useful for antiviral approaches. Also, these findings might aid understanding how IRGM functions in infection and inflammation in the setting of other diseases, e.g., in Crohn’s disease. Positive-stranded RNA viruses, such as hepatitis C virus (HCV), assemble their viral replication complexes by remodeling host intracellular membranes to a membranous web. The precise composition of these replication complexes and the detailed mechanisms by which they are formed are incompletely understood. Here we show that the human immunity-related GTPase M (IRGM), known to contribute to autophagy, plays a previously unrecognized role in this process. We show that IRGM is localized at the Golgi apparatus and regulates the fragmentation of Golgi membranes in response to HCV infection, leading to colocalization of Golgi vesicles with replicating HCV. Our results show that IRGM controls phosphorylation of GBF1, a guanine nucleotide exchange factor for Arf-GTPases, which normally operates in Golgi membrane dynamics and vesicle coating in resting cells. We also find that HCV triggers IRGM-mediated phosphorylation of the early autophagy initiator ULK1, thereby providing mechanistic insight into the role of IRGM in HCV-mediated autophagy. Collectively, our results identify IRGM as a key Golgi-situated regulator that links intracellular membrane remodeling by autophagy and Golgi fragmentation with viral replication.
Identification of palladin isoforms and characterization of an isoform-specific interaction between Lasp-1 and palladin

Palladin is a recently described phosphoprotein with an important role in cytoskeletal organization. The major palladin isoform (90-92 kDa) binds to three actin-associated proteins (ezrin, VASP and α-actinin), suggesting that palladin functions as a cytoskeletal scaffold. Here, we describe the organization of the palladin gene, which encodes multiple isoforms, including one (140 kDa) with a similar localization pattern to 90 kDa palladin. Overexpression of the 90 kDa or 140 kDa isoforms in COS-7 cells results in rearrangements of the actin cytoskeleton into super-robust bundles and star-like arrays, respectively. Sequence analysis of 140 kDa palladin revealed a conserved binding site for SH3 domains, suggesting that it binds directly to the SH3-domain protein Lasp-1. Binding of 140 kDa palladin, but not 90 kDa palladin, to Lasp-1 was confirmed by yeast two-hybrid and GST-pull-down assays. Isoform-specific siRNA experiments suggested that 140 kDa palladin plays a role in recruiting Lasp-1 to stress fibers. These results add Lasp-1, an actin-binding protein with a crucial role in cell motility, to the growing list of palladin's binding partners, and suggest that 140 kDa palladin has a specialized function in organizing the actin arrays that participate in cell migration and/or cellular contractility.
Spatial Distribution of Osteocyte Lacunae in Equine Radii and Third Metacarpals: Considerations for Cellular Communication, Microdamage Detection and Metabolism

Osteocytes, which are embedded in bone matrix, are the most abundant cells in bone. Despite the ideal location of osteocytes to sense the local environment and influence bone remodeling, their functions, and the relative importance of these functions, remain controversial. In this study, we tested several hypotheses that address the possibilities that population densities of osteocyte lacunae (Ot.Lc.N/B.Ar) correlate with strain-, remodeling- or metabolism-related aspects of the local biomechanical environments of mid-third diaphyseal equine radii and third metacarpals from skeletally mature animals. Ot.Lc. N/B.Ar data, quantified in multiple cortical locations, were analyzed for possible correlations with (1) structural and material characteristics (e.g., cortical thickness, percent ash, secondary osteon population density, mean osteon cross-sectional area, and predominant collagen fiber orientation), (2) strain characteristics, including prevalent/predominant strain magnitude and mode (tension, compression, shear), (3) hypothesized strain-mode-related microdamage characteristics, which might be perceived by osteocyte ‘operational’ networks, and (4) variations in remodeling dynamics and/or metabolism (i.e. presumably higher in endocortical regions than in other transcortical locations). Results showed relatively uniform Ot.Lc. N/B.Ar between regions with highly non-uniform strain and strain-related environments and markedly heterogeneous structural and material organization. These results suggest that population densities of these cells are poorly correlated with mechanobiological characteristics, including local variations in metabolic rate and strain magnitude/mode. Although osteocytes hypothetically evolved both as strain sensors and fatigue damage sensors able to direct the removal of damage as needed, the mechanisms that govern the distribution of these cells remain unclear. The results of this study provide little or no evidence that the number of osteocyte lacunae has a functional role in mechanotransduction pathways that are typically considered in bone adaptation.
Conserved queen pheromones in bumblebees: a reply to Amsalem et al.

In a recent study, Amsalem, Orlova & Grozinger (2015) performed experiments with Bombus impatiens bumblebees to test the hypothesis that saturated cuticular hydrocarbons are evolutionarily conserved signals used to regulate reproductive division of labor in many Hymenopteran social insects. They concluded that the cuticular hydrocarbon pentacosane (C25), previously identified as a queen pheromone in a congeneric bumblebee, does not affect worker reproduction in B. impatiens. Here we discuss some shortcomings of Amsalem et al.’s study that make its conclusions unreliable. In particular, several confounding effects may have affected the results of both experimental manipulations in the study. Additionally, the study’s low sample sizes (mean n per treatment = 13.6, range: 4–23) give it low power, not 96–99% power as claimed, such that its conclusions may be false negatives. Inappropriate statistical tests were also used, and our reanalysis found that C25 substantially reduced and delayed worker egg laying in B. impatiens. We review the evidence that cuticular hydrocarbons act as queen pheromones, and offer some recommendations for future queen pheromone experiments.
Elastic, piezoelectric, and dielectric properties of multidomain 0.67Pb(Mg1/3Nb2/3)O3–0.33PbTiO3 single crystals

The elastic, piezoelectric, and dielectric constants of 0.67Pb(Mg1/3Nb2/3)O3–0.33PbTiO3 domain engineered single crystal were determined experimentally by using ultrasonic and resonance methods. It was confirmed that the single crystal system has large electromechanical coupling coefficient k33 (∼94%) and piezoelectric constant d33 (∼2800 pC/N) if the poling is done along the [001] of pseudocubic directions. A soft shear mode with a velocity of 880 m/s was observed in the [110] direction with displacement in [110]. Using the measured data, the orientation dependence of phase velocities and electromechanical coupling coefficients were calculated. The origin of experimental errors and their influence on measured results are also examined.
Genome-Wide Identification and Characterization of Long Intergenic Non-Coding RNAs in Ganoderma lucidum

Ganoderma lucidum is a white-rot fungus best-known for its medicinal activities. We have previously sequenced its genome and annotated the protein coding genes. However, long non-coding RNAs in G. lucidum genome have not been analyzed. In this study, we have identified and characterized long intergenic non-coding RNAs (lincRNA) in G. lucidum systematically. We developed a computational pipeline, which was used to analyze RNA-Seq data derived from G. lucidum samples collected from three developmental stages. A total of 402 lincRNA candidates were identified, with an average length of 609 bp. Analysis of their adjacent protein-coding genes (apcGenes) revealed that 46 apcGenes belong to the pathways of triterpenoid biosynthesis and lignin degradation, or families of cytochrome P450, mating type B genes, and carbohydrate-active enzymes. To determine if lincRNAs and these apcGenes have any interactions, the corresponding pairs of lincRNAs and apcGenes were analyzed in detail. We developed a modified 3′ RACE method to analyze the transcriptional direction of a transcript. Among the 46 lincRNAs, 37 were found unidirectionally transcribed, and 9 were found bidirectionally transcribed. The expression profiles of 16 of these 37 lincRNAs were found to be highly correlated with those of the apcGenes across the three developmental stages. Among them, 11 are positively correlated (r>0.8) and 5 are negatively correlated (r<−0.8). The co-localization and co-expression of lincRNAs and those apcGenes playing important functions is consistent with the notion that lincRNAs might be important regulators for cellular processes. In summary, this represents the very first study to identify and characterize lincRNAs in the genomes of basidiomycetes. The results obtained here have laid the foundation for study of potential lincRNA-mediated expression regulation of genes in G. lucidum.
Intracranial Aneurysms: Review of Current Treatment Options and Outcomes

Intracranial aneurysms are present in roughly 5% of the population, yet most are often asymptomatic and never detected. Development of an aneurysm typically occurs during adulthood, while formation and growth are associated with risk factors such as age, hypertension, pre-existing familial conditions, and smoking. Subarachnoid hemorrhage, the most common presentation due to aneurysm rupture, represents a serious medical condition often leading to severe neurological deficit or death. Recent technological advances in imaging modalities, along with increased understanding of natural history and prevalence of aneurysms, have increased detection of asymptomatic unruptured intracranial aneurysms (UIA). Studies reporting on the risk of rupture and outcomes have provided much insight, but the debate remains of how and when unruptured aneurysms should be managed. Treatment methods include two major intervention options: clipping of the aneurysm and endovascular methods such as coiling, stent-assisted coiling, and flow diversion stents. The studies reviewed here support the generalized notion that endovascular treatment of UIA provides a safe and effective alternative to surgical treatment. The risks associated with endovascular repair are lower and incur shorter hospital stays for appropriately selected patients. The endovascular treatment option should be considered based on factors such as aneurysm size, location, patient medical history, and operator experience.
Differential neonatal and postneonatal infant mortality rates across US counties: the role of socioeconomic conditions and rurality.

PURPOSE To examine differences in correlates of neonatal and postneonatal infant mortality rates, across counties, by degree of rurality. METHODS Neonatal and postneonatal mortality rates were calculated from the 1998 to 2002 Compressed Mortality Files from the National Center for Health Statistics. Bivariate analyses assessed the relationship between neonatal and postneonatal mortality by Urban Influence (UI) codes. Multivariable, weighted least-squares regression models included measures of county socioeconomic conditions, health services and environmental risks. FINDINGS The bivariate analysis indicated neonatal and postneonatal mortality was significantly higher in the most nonmetropolitan counties compared to the most metropolitan counties. However the relationship was not linear across the Urban Influence codes. In the multivariable models, a nonmetropolitan advantage was observed for counties not adjacent to metropolitan areas for neonatal mortality. However, postneonatal mortality rates were higher in the most rural nonmetropolitan counties. CONCLUSIONS Certain characteristics of nonmetropolitan counties not adjacent to metropolitan counties and with an urban area of 2,500 population or more are protective against neonatal mortality (UI = 7, UI = 8). This may indicate that just having access to health services is more important to creating a protective effect for these nonmetropolitan counties than having a high concentration of medical facilities. The nonmetropolitan, not adjacent (UI = 9) disadvantage observed for postneonatal mortality supports the idea that the isolation of these areas combined with the combination of risk factors across the most nonmetropolitan counties leads to poorer postneonatal health outcomes in these areas.
DiarTk : An Open Source Toolkit for Research in Multistream Speaker Diarization and its Application to Meetings Recordings

The speaker diarization task consists of inferring “who spoke when” in an audio stream without any prior knowledge and has been object of several NIST international evaluation campaigns is last years. A common trend for improving performances has been the use of several different feature streams as diverse as speaker location features, visual features or noise robust acoustic features. This paper describes an open source toolkit released under GPL license aiming at facilitating research in multistream speaker diarization and reproducing state-of-the-art results. In contrary to other related diarization toolkits, it is explicitly designed to handle an arbitrary number of features with very different statistics while limiting the computational complexity. The release includes a set of scripts to replicate benchmark results on previous NIST evaluations and is intended to provide an easy to use software to study and include novel features into diarization systems.
Early exercise in critically ill patients enhances short-term functional recovery*

Objectives:To investigate whether a daily exercise session, using a bedside cycle ergometer, is a safe and effective intervention in preventing or attenuating the decrease in functional exercise capacity, functional status, and quadriceps force that is associated with prolonged intensive care unit stay. A prolonged stay in the intensive care unit is associated with muscle dysfunction, which may contribute to an impaired functional status up to 1 yr after hospital discharge. No evidence is available concerning the effectiveness of an early exercise training intervention to prevent these detrimental complications. Design:Randomized controlled trial. Setting:Medical and surgical intensive care unit at University Hospital Gasthuisberg. Patients:Ninety critically ill patients were included as soon as their cardiorespiratory condition allowed bedside cycling exercise (starting from day 5), given they still had an expected prolonged intensive care unit stay of at least 7 more days. Interventions:Both groups received respiratory physiotherapy and a daily standardized passive or active motion session of upper and lower limbs. In addition, the treatment group performed a passive or active exercise training session for 20 mins/day, using a bedside ergometer. Measurements and Main Results:All outcome data are reflective for survivors. Quadriceps force and functional status were assessed at intensive care unit discharge and hospital discharge. Six-minute walking distance was measured at hospital discharge. No adverse events were identified during and immediately after the exercise training. At intensive care unit discharge, quadriceps force and functional status were not different between groups. At hospital discharge, 6-min walking distance, isometric quadriceps force, and the subjective feeling of functional well-being (as measured with “Physical Functioning” item of the Short Form 36 Health Survey questionnaire) were significantly higher in the treatment group (p < .05). Conclusions:Early exercise training in critically ill intensive care unit survivors enhanced recovery of functional exercise capacity, self-perceived functional status, and muscle force at hospital discharge.