Miracle-dz/UniFAR-FTUs huggingface dataset:
An improved ant routing algorithm for HAP networks

This paper explains the potential role of HAP network for providing air traffic control(ATC) and air passenger communication services(APC) in aeronautical communication. An improved ant routing algorithm based on delay of node is presented, which is used to find the shortest path from source to destination and satisfy the QoS metrics. Simulations have been performed to evaluate the performance of the proposed algorithm. The results show that the proposed algorithm could significantly reduce call blocking probability in aeronautical communication.
Paradoxical reflection in quantum mechanics

We discuss a phenomenon of elementary quantum mechanics that is counterintuitive, non-classical, and apparently not widely known: the reflection of a particle at a downward potential step. In contrast, classically, particles are reflected only at upward steps. The conditions for this effect are that the wavelength is much greater than the width of the potential step and the kinetic energy of the particle is much smaller than the depth of the potential step. The phenomenon is suggested by non-normalizable solutions to the time-independent Schrodinger equation. We present numerical and mathematical evidence that it is also predicted by the time-dependent Schrodinger equation. The paradoxical reflection effect suggests and we confirm mathematically that a particle can be trapped for a long time (though not indefinitely) in a region surrounded by downward potential steps, that is, on a plateau.
Intraductal papillomas on core biopsy can be upgraded to malignancy on subsequent excisional biopsy regardless of the presence of atypical features

Intraductal papillary lesions of the breast constitute a heterogeneous entity, including benign intraductal papilloma (IDP) with or without atypia and malignant papillary carcinoma. Differentiating between these diagnoses can be challenging. We re‐evaluated core biopsy specimens that were diagnosed as IDP and the corresponding surgical excision specimens, and assessed the potential risk for the diagnosis to be modified to malignancy based on excision. By sorting the pathology database of the National Cancer Center Hospital, Tokyo, we identified 146 core biopsy cases that were histologically diagnosed as IDP between 1997 and 2013. The re‐evaluated diagnosis was IDP without atypia in 79 (54%) patients, IDP with atypia in 66 (45%), and ductal carcinoma in situ (DCIS) in 1 (1%). Among the 34 patients (23%) who underwent surgical excision subsequent to core biopsy, histological diagnosis was upgraded to carcinoma, excluding lobular carcinoma in situ (LCIS), in 14 (41%) cases, including 4 (33%) of 12 IDPs without atypia and 10 (45%) of 22 IDPs with atypia. Complete surgical excision should be kept in mind for all IDPs diagnosed on core biopsy, not only IDPs with atypia but IDPs without atypia, especially when clinical or imaging diagnosis findings cannot rule out the possibility of malignancy, because papillary lesions comprise a variety of morphological appearances.
Analyzing the Impact of System Architecture on the Scalability of OLTP Engines for High-Contention Workloads

Main-memory OLTP engines are being increasingly deployed on multicore servers that provide abundant thread-level parallelism. However, recent research has shown that even the state-of-the-art OLTP engines are unable to exploit available parallelism for high contention workloads. While previous studies have shown the lack of scalability of all popular concurrency control protocols, they consider only one system architecture---a non-partitioned, shared everything one where transactions can be scheduled to run on any core and can access any data or metadata stored in shared memory.In this paper, we perform a thorough analysis of the impact of other architectural alternatives (Data-oriented transaction execution, Partitioned Serial Execution, and Delegation) on scalability under high contention scenarios. In doing so, we present Trireme, a main-memory OLTP engine testbed that implements four system architectures and several popular concurrency control protocols in a single code base. Using Trireme, we present an extensive experimental study to understand i) the impact of each system architecture on overall scalability, ii) the interaction between system architecture and concurrency control protocols, and iii) the pros and cons of new architectures that have been proposed recently to explicitly deal with high-contention workloads.
Optimization of thermoplastic composites resistance welding parameters based on transient heat transfer finite element modeling

The use of resistance welding technology to join thermoplastic composite aerospace structures is still contingent upon a better understanding of the heat transfer mechanisms occurring during welding, which govern the joint quality and mechanical performance. In this study, two-dimensional (2D) and three-dimensional (3D) transient heat transfer finite element models were developed to simulate resistance welding of thermoplastic composites. The 2D model was used to investigate the effect of the length of the exposed areas of the heating element to air (clamping distance) on the local overheating at the edges and the effects of the input power level on the thermal behavior of the welds. It is shown that controlling the clamping distance improves the thermal uniformity of the weld. The 3D model shows that heat conduction along the length of the laminates influences the thermal uniformity of the weld interface. An optimization chart is developed in order to minimize the undesirable edge effect and to define the conditions required to obtain a complete weld. The results of the 3D model are compared with experimental data.
Risk Factors for Gestational Diabetes Mellitus in a Large Population of Women Living in Spain: Implications for Preventative Strategies

The aim of this study is to establish a risk appraisal model for GDM by identifying modifiable factors that can help predict the risk of GDM in a large population of 2194 women living in Spain. They were recruited between 2009-2010 when screening for GDM was performed. Participants completed a questionnaire on socio-demographic, anthropomorphic and behavioral characteristics, and reproductive and medical history. A total of 213 (9.7%) women were diagnosed as having GDM. Age, pregestational body weight (BW) and body mass index (BMI), and number of events of medical, obstetric and family history were significantly associated with GDM. After logistic regression model, biscuits and pastries intake <4 times/week, red and processed meats intake <6 servings/week, sugared drinks <4 servings/week, light walking >30 minutes/day, and 30 minutes/day of sports at least 2 days/week, compared with opposite consumption, was associated with less GDM risk. Our study identified several pregestational modifiable lifestyle risk factors associated with an increase in the risk of developing GDM. This may represent a promising approach for the prevention of GDM and subsequent complications. Further intervention studies are needed to evaluate if this appraisal model of risk calculation can be useful for prevention and treatment of GDM.
Result Analysis of the NIPS 2003 Feature Selection Challenge

The NIPS 2003 workshops included a feature selection competition organized by the authors. We provided participants with five datasets from different application domains and called for classification results using a minimal number of features. The competition took place over a period of 13 weeks and attracted 78 research groups. Participants were asked to make on-line submissions on the validation and test sets, with performance on the validation set being presented immediately to the participant and performance on the test set presented to the participants at the workshop. In total 1863 entries were made on the validation sets during the development period and 135 entries on all test sets for the final competition. The winners used a combination of Bayesian neural networks with ARD priors and Dirichlet diffusion trees. Other top entries used a variety of methods for feature selection, which combined filters and/or wrapper or embedded methods using Random Forests, kernel methods, or neural networks as a classification engine. The results of the benchmark (including the predictions made by the participants and the features they selected) and the scoring software are publicly available. The benchmark is available at www.nipsfsc. ecs.soton. ac.uk for post-challenge submissions to stimulate further research.
Low-complexity iterative joint source-channel decoding for variable-length encoded Markov sources

In this paper, we present a novel packetized bit-level decoding algorithm for variable-length encoded Markov sources, which calculates reliability information for the decoded bits in the form of a posteriori probabilities (APPs). An interesting feature of the proposed approach is that symbol-based source statistics in the form of the transition probabilities of the Markov source are exploited as a priori information on a bit-level trellis. This method is especially well-suited for long input blocks, since in contrast to other symbol-based APP decoding approaches, the number of trellis states does not depend on the packet length. When additionally the variable-length encoded source data is protected by channel codes, an iterative source-channel decoding scheme can be obtained in the same way as for serially concatenated codes. Furthermore, based on an analysis of the iterative decoder via extrinsic information transfer charts, it can be shown that by using reversible variable-length codes with a free distance of two, in combination with rate-1 channel codes and residual source redundancy, a reliable transmission is possible even for highly corrupted channels. This justifies a new source-channel encoding technique where explicit redundancy for error protection is only added in the source encoder.
GENETIC STUDY: BclI glucocorticoid receptor polymorphism and smoking in the general population

We studied the hypothesis that the BclI polymorphism of the glucocorticoid receptor gene is associated with an increased probability of being a (heavy) smoker and a decreased ability to quit smoking. The study cohort consisted of all subjects in the Rotterdam Study, a Dutch population‐based cohort of people aged 55 years and older, for whom BclI genotyping and smoking status at baseline were available. In prospective analyses, the smoking status was reassessed during three additional examination rounds. Logistic regression analysis was used to study the association between BclI polymorphism and being a smoker or a heavy smoker at baseline. Furthermore, the relationship between BclI polymorphism and incident smoking cessation was tested with Cox proportional hazards analysis within those who smoked at baseline. In total, 6358 subjects were included in the study. The presence of a G‐allele was not associated with current smoking at baseline [odds ratio (OR) = 0.96, 95%confidence interval (CI): 0.85–1.09] or with the incidence of smoking cessation during follow‐up [hazard ratio (HR) = 0.98, 95%CI: 0.80–1.19]. Within current smokers, having a G‐allele was not significantly associated with the risk of being a heavy smoker when measured by pack‐years smoked (OR = 1.07, 95%CI: 0.85–1.35) or daily consumption of tobacco (OR = 1.10, 95%CI: 0.88–1.37). We were not able to replicate the earlier findings indicating that the proportion of current smokers is lower among carriers of the CC‐genotype of the BclI glucocorticoid receptor. Furthermore, the BclI glucocorticoid receptor polymorphism did not predict the incidence of smoking cessation in the general elderly population.
Inflexible Minds: Impaired Attention Switching in Recent-Onset Schizophrenia

Impairment of sustained attention is assumed to be a core cognitive abnormality in schizophrenia. However, this seems inconsistent with a recent hypothesis that in schizophrenia the implementation of selection (i.e., sustained attention) is intact but the control of selection (i.e., switching the focus of attention) is impaired. Mounting evidence supports this hypothesis, indicating that switching of attention is a bigger problem in schizophrenia than maintaining the focus of attention. To shed more light on this hypothesis, we tested whether schizophrenia patients are impaired relative to controls in sustaining attention, switching attention, or both. Fifteen patients with recent-onset schizophrenia and fifteen healthy volunteers, matched on age and intelligence, performed sustained attention and attention switching tasks, while performance and brain potential measures of selective attention were recorded. In the sustained attention task, patients did not differ from the controls on these measures. In the attention switching task, however, patients showed worse performance than the controls, and early selective attention related brain potentials were absent in the patients while clearly present in the controls. These findings support the hypothesis that schizophrenia is associated with an impairment of the mechanisms that control the direction of attention (attention switching), while the mechanisms that implement a direction of attention (sustained attention) are intact.
ChimeRScope: a novel alignment-free algorithm for fusion transcript prediction using paired-end RNA-Seq data

Abstract The RNA-Seq technology has revolutionized transcriptome characterization not only by accurately quantifying gene expression, but also by the identification of novel transcripts like chimeric fusion transcripts. The ‘fusion’ or ‘chimeric’ transcripts have improved the diagnosis and prognosis of several tumors, and have led to the development of novel therapeutic regimen. The fusion transcript detection is currently accomplished by several software packages, primarily relying on sequence alignment algorithms. The alignment of sequencing reads from fusion transcript loci in cancer genomes can be highly challenging due to the incorrect mapping induced by genomic alterations, thereby limiting the performance of alignment-based fusion transcript detection methods. Here, we developed a novel alignment-free method, ChimeRScope that accurately predicts fusion transcripts based on the gene fingerprint (as k-mers) profiles of the RNA-Seq paired-end reads. Results on published datasets and in-house cancer cell line datasets followed by experimental validations demonstrate that ChimeRScope consistently outperforms other popular methods irrespective of the read lengths and sequencing depth. More importantly, results on our in-house datasets show that ChimeRScope is a better tool that is capable of identifying novel fusion transcripts with potential oncogenic functions. ChimeRScope is accessible as a standalone software at (https://github.com/ChimeRScope/ChimeRScope/wiki) or via the Galaxy web-interface at (https://galaxy.unmc.edu/).
Identification of Putative Cytoskeletal Protein Homologues in the Protozoan Host Hartmannella vermiformis as Substrates for Induced Tyrosine Phosphatase Activity upon Attachment to the Legionnaires' Disease Bacterium, Legionella pneumophila

The Legionnaires' disease bacterium, Legionella pneumophila, is a facultative intracellular pathogen that invades and replicates within two evolutionarily distant hosts, free living protozoa and mammalian cells. Invasion and intracellular replication within protozoa are thought to be major factors in the transmission of Legionnaires' disease. We have recently reported the identification of a galactose/N-acetyl-d-galactosamine (Gal/GalNAc) lectin in the protozoan host Hartmannella vermiformis as a receptor for attachment and invasion by L. pneumophila (Venkataraman, C., B.J. Haack, S. Bondada, and Y.A. Kwaik. 1997. J. Exp. Med. 186:537–547). In this report, we extended our studies to the effects of bacterial attachment and invasion on the cytoskeletal proteins of H. vermiformis. We first identified the presence of many protozoan cytoskeletal proteins that were putative homologues to their mammalian counterparts, including actin, pp125FAK, paxillin, and vinculin, all of which were basally tyrosine phosphorylated in resting H. vermiformis. In addition to L. pneumophila–induced tyrosine dephosphorylation of the lectin, bacterial attachment and invasion was associated with tyrosine dephosphorylation of paxillin, pp125FAK, and vinculin, whereas actin was minimally affected. Inhibition of bacterial attachment to H. vermiformis by Gal or GalNAc monomers blocked bacteria-induced tyrosine dephosphorylation of detergent-insoluble proteins. In contrast, inhibition of bacterial invasion but not attachment failed to block bacteria-induced tyrosine dephosphorylation of H. vermiformis proteins. This was further supported by the observation that 10 mutants of L. pneumophila that were defective in invasion of H. vermiformis were capable of inducing tyrosine dephosphorylation of H. vermiformis proteins. Entry of L. pneumophila into H. vermiformis was predominantly mediated by noncoated receptor-mediated endocytosis (93%) but coiling phagocytosis was infrequently observed (7%). We conclude that attachment but not invasion by L. pneumophila into H. vermiformis was sufficient and essential to induce protein tyrosine dephosphorylation in H. vermiformis. These manipulations of host cell processes were associated with, or followed by, entry of the bacteria by a noncoated receptor-mediated endocytosis. A model for attachment and entry of L. pneumophila into H. vermiformis is proposed.
Efficacy of anti-sclerostin monoclonal antibody BPS804 in adult patients with hypophosphatasia

BACKGROUND. Hypophosphatasia (HPP) is a rare genetic disorder resulting in variable alterations of bone formation and mineralization that are caused by mutations in the ALPL gene, encoding the tissue-nonspecific alkaline phosphatase (ALP) enzyme. METHODS. In this phase IIA open-label, single-center, intra-patient, dose-escalating study, adult patients with HPP received 3 ascending intravenous doses of 5, 10, and 20 mg/kg BPS804, a fully human anti-sclerostin monoclonal antibody, on days 1, 15, and 29, respectively. Patients were followed for 16 weeks after the last dose. We assessed the pharmacodynamics, pharmacokinetics, preliminary efficacy, and safety of BPS804 administrations at specified intervals during treatment and follow-up. RESULTS. Eight patients (mean age 47.8 years) were enrolled in the study (6 females, 2 males). BPS804 treatment increased mean ALP and bone-specific ALP enzymatic activity between days 2 and 29. Transient increases in the bone formation markers procollagen type-I N-terminal propeptide (PINP), osteocalcin, and parathyroid hormone as well as a transient decrease in the bone resorption marker C-telopeptide of type I collagen (CTX-1) were observed. Lumbar spine bone mineral density showed a mean increase by day 85 and at end of study. Treatment-associated adverse events were mild and transient. CONCLUSION. BPS804 treatment was well tolerated and resulted in increases in bone formation biomarkers and bone mineral density, suggesting that sclerostin inhibition could be applied to enhance bone mineral density, stability, and regeneration in non-life-threatening clinical situations in adults with HPP. TRIAL REGISTRATION. Clinicaltrials.gov NCT01406977. FUNDING. Novartis Institutes for BioMedical Research, Basel, Switzerland.
Phenotypic effects of overexpression of the MMAC1 gene in prostate epithelial cells

The prostate cancer cell lines PC3 and LNCaP have been shown to lack expression of the tumour suppressor gene MMAC1/PTEN, in contrast to the immortalized non-tumorigenic epithelial lines PNT1a and PNT2. We have measured the effects of reintroduction of wild type (wt) and mutant MMAC1 genes on to these genetic backgrounds, using gene constructs expressing either wt MMAC1 or various mutants deficient in the dual specificity phosphatase domain of the protein. Over-expression of wild type PTEN protein induced cell shrinkage and rounding, but did not result in increased levels of classical apoptosis. Permanently transfected lines containing the MMAC1 gene could only be obtained from the PNT cells, as PTEN expression resulted in rapid loss of both tumour lines. In contrast, mutation of the phosphatase domain resulted in partial attenuation of the phenotypic effects of MMAC1 after transient transfection, and also allowed the derivation of permanent tumour cell lines containing the mutated MMAC1 gene. The results suggest that re-expression of wt PTEN is incompatible with survival of human prostate cancer cells in vitro, and that the full biological activity of this common tumour suppressor requires functions additional to the established protein and lipid phosphatase activities in epithelial systems. © 2000 Cancer Research Campaign
A Novel Model-Free Data Analysis Technique Based on Clustering in a Mutual Information Space: Application to Resting-State fMRI

Non-parametric data-driven analysis techniques can be used to study datasets with few assumptions about the data and underlying experiment. Variations of independent component analysis (ICA) have been the methods mostly used on fMRI data, e.g., in finding resting-state networks thought to reflect the connectivity of the brain. Here we present a novel data analysis technique and demonstrate it on resting-state fMRI data. It is a generic method with few underlying assumptions about the data. The results are built from the statistical relations between all input voxels, resulting in a whole-brain analysis on a voxel level. It has good scalability properties and the parallel implementation is capable of handling large datasets and databases. From the mutual information between the activities of the voxels over time, a distance matrix is created for all voxels in the input space. Multidimensional scaling is used to put the voxels in a lower-dimensional space reflecting the dependency relations based on the distance matrix. By performing clustering in this space we can find the strong statistical regularities in the data, which for the resting-state data turns out to be the resting-state networks. The decomposition is performed in the last step of the algorithm and is computationally simple. This opens up for rapid analysis and visualization of the data on different spatial levels, as well as automatically finding a suitable number of decomposition components.
Implicit Motor Sequence Learning in Individuals with Parkinson Disease: A Meta-Analysis.

BACKGROUND Deficits in implicit motor sequence learning (IMSL) in individuals with Parkinson disease (PD) compared to age matched healthy controls (HC) are unclear. OBJECTIVE The purpose of this paper is to present results of a systematic review with a meta-analysis examining the hypothesis that IMSL is impaired in individuals with PD when compared to HC. METHODS Fifteen articles met our final criteria and assessed 299 individuals with PD and 244 HC. Raw mean and standard deviation data for the final block of repeated and final block of random practice trials were obtained to calculate sequence-specific learning (SSL) for individuals with PD and HC. Forest plots were used to depict the comparison of the groups by assessing standardized mean difference with random effect size. RESULTS A significant and moderate effect size, 0.83 was found suggesting that individuals with PD demonstrated impaired SSL of motor sequences compared to HC. CONCLUSIONS Individuals with PD demonstrate a deficit compared with HC in their ability to implicitly learn motor tasks. Existing research lacks detail on the factors which may alter IMSL, either negatively or positively, such as the design features of current IMSL paradigms utilized and disease-specific characteristics. Successful motor rehabilitation of functional tasks in persons with PD is highly dependent on IMSL; therefore, an improved knowledge of the influence of these additional variables is critical.