Miracle-dz/UniFAR-FTUs huggingface dataset:
Simplified decision-feedback-aided multichip binary DPSK receivers

We introduce decision-feedback-based novel realizations of substantially reduced complexity for the recently proposed multichip differential phase-shift keying (MC-DPSK) advanced modulation formats, and interpret the operation of the resulting simplified receivers as synthesizing a lower noise reference for differential phase detection. Full propagation simulations indicate that the resulting binary phase MC-DPSK with three (four) chips display a bit-error-rate advantage of nearly three (four) orders of magnitude relative to conventional DPSK over a nonlinear phase fiber channel
The Bulk Isolation of Oligodendroglia from Whole Rat Forebrain: A New Procedure Using Physiologic Media

Abstract: A method for the isolation of oligodendroglia from undissected rat forebrain is described. The method has been applied to brains from 10‐, 30‐ and 60‐day‐old rats. The procedure uses a balanced salt solution at pH 7.2 throughout. Tissue is briefly exposed to trypsin and DNase and dissociated and the cells are purified on a discontinuous sucrose gradient. The isolates were composed of 90% phase‐bright rounded cells having diameters after fixation of 7‐12 μm. The contamination was primarily by red blood cells and phase‐dark nuclei. Neurons and astroglia were lysed by the procedure. The method is reproducible and should be applicable to other ages of rat or to other species. The cells have been examined by light and electron microscopy and analyzed for protein and nucleic acids. None of the cell parameters measured, including total protein (58 pg/cell), varied significantly with age. With this new method it should be possible to carry out studies on the development and metabolism of oligodendroglia in small laboratory animals.
Laminin-411 Is a Vascular Ligand for MCAM and Facilitates TH17 Cell Entry into the CNS

TH17 cells enter tissues to facilitate pathogenic autoimmune responses, including multiple sclerosis (MS). However, the adhesion molecules involved in the unique migratory capacity of TH17 cells, into both inflamed and uninflamed tissues remain unclear. Herein, we characterize MCAM (CD146) as an adhesion molecule that defines human TH17 cells in the circulation; following in vitro restimulation of human memory T cells, nearly all of the capacity to secrete IL-17 is contained within the population of cells expressing MCAM. Furthermore, we identify the MCAM ligand as laminin 411, an isoform of laminin expressed within the vascular endothelial basement membranes under inflammatory as well as homeotstatic conditions. Purified MCAM-Fc binds to laminin 411 with an affinity of 27 nM, and recognizes vascular basement membranes in mouse and human tissue. MCAM-Fc binding was undetectable in tissue from mice with targeted deletion of laminin 411, indicating that laminin 411 is a major tissue ligand for MCAM. An anti-MCAM monoclonal antibody, selected for inhibition of laminin binding, as well as soluble MCAM-Fc, inhibited T cell adhesion to laminin 411 in vitro. When administered in vivo, the antibody reduced TH17 cell infiltration into the CNS and ameliorated disease in an animal model of MS. Our data suggest that MCAM and laminin 411 interact to facilitate TH17 cell entry into tissues and promote inflammation.
Impact of next-generation sequencing error on analysis of barcoded plasmid libraries of known complexity and sequence

Barcoded vectors are promising tools for investigating clonal diversity and dynamics in hematopoietic gene therapy. Analysis of clones marked with barcoded vectors requires accurate identification of potentially large numbers of individually rare barcodes, when the exact number, sequence identity and abundance are unknown. This is an inherently challenging application, and the feasibility of using contemporary next-generation sequencing technologies is unresolved. To explore this potential application empirically, without prior assumptions, we sequenced barcode libraries of known complexity. Libraries containing 1, 10 and 100 Sanger-sequenced barcodes were sequenced using an Illumina platform, with a 100-barcode library also sequenced using a SOLiD platform. Libraries containing 1 and 10 barcodes were distinguished from false barcodes generated by sequencing error by a several log-fold difference in abundance. In 100-barcode libraries, however, expected and false barcodes overlapped and could not be resolved by bioinformatic filtering and clustering strategies. In independent sequencing runs multiple false-positive barcodes appeared to be represented at higher abundance than known barcodes, despite their confirmed absence from the original library. Such errors, which potentially impact barcoding studies in an application-dependent manner, are consistent with the existence of both stochastic and systematic error, the mechanism of which is yet to be fully resolved.
A Promising Genetic Algorithm Approach to Job-Shop SchedulingRe-Schedulingand Open-Shop Scheduling Problems

The general job-shop scheduling problem is known to be extremely hard. We describe a GA approach which produces reasonably good results very quickly on standard benchmark job-shop scheduling problems, better than previous e(cid:11)orts using genetic algorithms for this task, and comparable to existing conventional search-based methods. The representation used is a variant of one known to work moderately well for the traveling salesman problem. It has the considerable merit that crossover will always produce legal schedules. A novel method for performance enhancement is examined based on dynamic sampling of the convergence rates in di(cid:11)erent parts of the genome. Our approach also promises to e(cid:11)ectively address the open-shop scheduling problem and the job-shop rescheduling problem.
Constraining the star formation histories of spiral bulges

Stellar populations in spiral bulges are investigated using the Lick system of spectral indices. Long-slit spectroscopic observations of line strengths and kinematics made along the minor axes of four spiral bulges are reported. Comparisons are made between central line strengths in spiral bulges and those in other morphological types [elliptical, spheroidal (Sph) and S0]. The bulges investigated are found to have central line strengths comparable to those of single stellar populations of approximately solar abundance or above. Negative radial gradients are observed in line strengths, similar to those exhibited by elliptical galaxies. The bulge data are also consistent with correlations between Mg_2, Mg_2 gradient and central velocity dispersion observed in elliptical galaxies. In contrast to elliptical galaxies, central line strengths lie within the loci defining the range of 〈Fe〉 and Mg_2 achieved by Worthey’s solar abundance ratio, single stellar populations (SSPs). The implication of solar abundance ratios indicates significant differences in the star formation histories of spiral bulges and elliptical galaxies. A ‘single zone with infall’ model of galactic chemical evolution, using Worthey’s SSPs, is used to constrain the possible star formation histories of our sample. We show that the 〈Fe〉, Mg_2 and Hβ line strengths observed in these bulges cannot be reproduced using primordial collapse models of formation but can be reproduced by models with extended infall of gas and star formation (2–17 Gyr) in the region modelled. One galaxy (NGC 5689) shows a central population with a luminosity-weighted average age of ~5 Gyr, supporting the idea of extended star formation. Kinematic substructure, possibly associated with a central spike in metallicity, is observed at the centre of the Sa galaxy NGC 3623.
On uniform nullcontrollability and blow-up estimates

The paper looks at some of the techniques (separation of variables, Fourier series, Carleman estimates) used to obtain observability and nullcontrollability results to determine qualitatively the asymptotic behavior of the estimates obtained with respect to relevant parameters. We are particularly concerned with blow-up as the control time becomes short (T → 0).
Risk Perception and Affect

Humans perceive and act on risk in two fundamental ways. Risk as feelings refers to individuals' instinctive and intuitive reactions to danger. Risk as analysis brings logic, reason, and scientific deliberation to bear on risk management. Reliance on risk as feelings is described as “the affect heuristic. ” This article traces the development of this heuristic and discusses some of the important ways that it impacts how people perceive and evaluate risk.
Occipital nerve stimulation for the treatment of intractable chronic migraine headache: ONSTIM feasibility study

Background: Medically intractable chronic migraine (CM) is a disabling illness characterized by headache ≥15 days per month. Methods: A multicenter, randomized, blinded, controlled feasibility study was conducted to obtain preliminary safety and efficacy data on occipital nerve stimulation (ONS) in CM. Eligible subjects received an occipital nerve block, and responders were randomized to adjustable stimulation (AS), preset stimulation (PS) or medical management (MM) groups. Results: Seventy-five of 110 subjects were assigned to a treatment group; complete diary data were available for 66. A responder was defined as a subject who achieved a 50% or greater reduction in number of headache days per month or a three-point or greater reduction in average overall pain intensity compared with baseline. Three-month responder rates were 39% for AS, 6% for PS and 0% for MM. No unanticipated adverse device events occurred. Lead migration occurred in 12 of 51 (24%) subjects. Conclusion: The results of this feasibility study offer promise and should prompt further controlled studies of ONS in CM.
Novel direct and self-regulating approaches to determine optimum growing multi-experts network structure

This work presents two novel approaches to determine optimum growing multi-experts network (GMN) structure. The first method called direct method deals with expertise domain and levels in connection with local experts. The growing neural gas (GNG) algorithm is used to cluster the local experts. The concept of error distribution is used to apportion error among the local experts. After reaching the specified size of the network, redundant experts removal algorithm is invoked to prune the size of the network based on the ranking of the experts. However, GMN is not ergonomic due to too many network control parameters. Therefore, a self-regulating GMN (SGMN) algorithm is proposed. SGMN adopts self-adaptive learning rates for gradient-descent learning rules. In addition, SGMN adopts a more rigorous clustering method called fully self-organized simplified adaptive resonance theory in a modified form. Experimental results show SGMN obtains comparative or even better performance than GMN in four benchmark examples, with reduced sensitivity to learning parameters setting. Moreover, both GMN and SGMN outperform the other neural networks and statistical models. The efficacy of SGMN is further justified in three industrial applications and a control problem. It provides consistent results besides holding out a profound potential and promise for building a novel type of nonlinear model consisting of several local linear models.
The relationship between alexithymia, shame, trauma, and body image disorders: investigation over a large clinical sample

Background The connections between eating disorders (EDs) and alexithymia have not been fully clarified. This study aims to define alexithymia’s connections with shame, trauma, dissociation, and body image disorders. Methods We administered the Dissociative Experience Scale-II, Trauma Symptom Inventory, Experience of Shame Scale, Toronto Alexithymia Scale-20, and Body Uneasiness Test questionnaires to 143 ED subjects. Extensive statistical analyses were performed. Results The subjects showed higher scores on alexithymia, shame, dissociation, and traumatic feelings scales than the nonclinical population. These aspects are linked with each other in a statistically significant way. Partial correlations highlighted that feelings of shame are correlated to body dissatisfaction, irrespective of trauma or depressed mood. Multiple regression analysis demonstrates that shame (anorexic patients) and perceived traumatic conditions (bulimic and ED not otherwise specified) are associated with adverse image disorders. Conclusion Shame seems to hold a central role in the perception of an adverse self-image. Alexithymia may be interpreted as being a consequence of previous unelaborated traumatic experiences and feelings of shame, and it could therefore be conceptualized as a maladaptive–reactive construct.
High Prevalence and Clinical Relevance of Genes Affected by Chromosomal Breaks in Colorectal Cancer

Background Cancer is caused by somatic DNA alterations such as gene point mutations, DNA copy number aberrations (CNA) and structural variants (SVs). Genome-wide analyses of SVs in large sample series with well-documented clinical information are still scarce. Consequently, the impact of SVs on carcinogenesis and patient outcome remains poorly understood. This study aimed to perform a systematic analysis of genes that are affected by CNA-associated chromosomal breaks in colorectal cancer (CRC) and to determine the clinical relevance of recurrent breakpoint genes. Methods Primary CRC samples of patients with metastatic disease from CAIRO and CAIRO2 clinical trials were previously characterized by array-comparative genomic hybridization. These data were now used to determine the prevalence of CNA-associated chromosomal breaks within genes across 352 CRC samples. In addition, mutation status of the commonly affected APC, TP53, KRAS, PIK3CA, FBXW7, SMAD4, BRAF and NRAS genes was determined for 204 CRC samples by targeted massive parallel sequencing. Clinical relevance was assessed upon stratification of patients based on gene mutations and gene breakpoints that were observed in >3% of CRC cases. Results In total, 748 genes were identified that were recurrently affected by chromosomal breaks (FDR <0.1). MACROD2 was affected in 41% of CRC samples and another 169 genes showed breakpoints in >3% of cases, indicating that prevalence of gene breakpoints is comparable to the prevalence of well-known gene point mutations. Patient stratification based on gene breakpoints and point mutations revealed one CRC subtype with very poor prognosis. Conclusions We conclude that CNA-associated chromosomal breaks within genes represent a highly prevalent and clinically relevant subset of SVs in CRC.
Characterization of cellular immune response to chemically defined glycoconjugates from Leishmania mexicana subsp. amazonensis

Two defined glycoconjugates (GP-10/20 and FR II Phe) purified from Leishmania mexicana subsp. amazonensis were analyzed with respect to their ability to induce cellular responses in immunized and infected mice. Each glycoconjugate was recognized by specific immune cells, as assessed by the proliferative response of lymph node cells of immunized mice. The response to GP-10/20 depended on helper T cells and antigen-presenting cells and was restricted by a major histocompatibility complex class II gene product. A specific anti-GP-10/20 T-cell line was established, and it was able to transfer a delayed-type hypersensitivity (DTH) response to normal mice. Both antigens were also recognized during an ongoing disease, as assessed by DTH response of infected mice. By this response, it was possible to distinguish susceptible from resistant strains of mice. In the course of the disease in resistant mice a correlation between the size of the primary lesion and the DTH response to GP-10/20 was observed. The presence of the glycoproteins on both promastigote and amastigote forms of the parasite, the antigenic similarities between both fractions, and the distribution of the GP-10/20 antigen in other trypanosomatids were studied. The results showed that both antigens were present on promastigotes and amastigotes. GP-10/20 shared no epitopes with FR II Phe, was included as part of the crude preparation leishmanin, and had some cross-reactive determinants with Leishmania donovani and Crithidia deanei.
Questioning the Rise of Gelatinous Zooplankton in the World's Oceans

During the past several decades, high numbers of gelatinous Zooplankton species have been reported in many estuarine and coastal ecosystems. Coupled with media-driven public perception, a paradigm has evolved in which the global ocean ecosystems are thought to he heading toward being dominated by “nuisance” jellyfish. We question this current paradigm by presenting a broad overview of gelatinous Zooplankton in a historical context to develop the hypothesis that population changes reflect the human-mediated alteration of global ocean ecosystems. To this end, we synthesize information related to the evolutionary context of contemporary gelatinous Zooplankton blooms, the human frame of reference for changes in gelatinous Zooplankton populations, and whether sufficient data are available to have established the paradigm. We conclude that the current paradigm in which it is believed that there has been a global increase in gelatinous Zooplankton is unsubstantiated, and we develop a strategy for addressing the critical questions about long-term, human-related changes in the sea as they relate to gelatinous Zooplankton blooms.
Historical Legacies in World Amphibian Diversity Revealed by the Turnover and Nestedness Components of Beta Diversity

Historic processes are expected to influence present diversity patterns in combination with contemporary environmental factors. We hypothesise that the joint use of beta diversity partitioning methods and a threshold-based approach may help reveal the effect of large-scale historic processes on present biodiversity. We partitioned intra-regional beta diversity into its turnover (differences in composition caused by species replacements) and nestedness-resultant (differences in species composition caused by species losses) components. We used piecewise regressions to show that, for amphibian beta diversity, two different world regions can be distinguished. Below parallel 37, beta diversity is dominated by turnover, while above parallel 37, beta diversity is dominated by nestedness. Notably, these regions are revealed when the piecewise regression method is applied to the relationship between latitude and the difference between the Last Glacial Maximum (LGM) and the present temperature but not when present energy-water factors are analysed. When this threshold effect of historic climatic change is partialled out, current energy-water variables become more relevant to the nestedness-resultant dissimilarity patterns, while mountainous areas are associated with higher spatial turnover. This result suggests that nested patterns are caused by species losses that are determined by physiological constraints, whereas turnover is associated with speciation and/or Pleistocene refugia. Thus, the new threshold-based view may help reveal the role of historic factors in shaping present amphibian beta diversity patterns.
Pathogenicity of avian leukosis viruses related to fowl glioma-inducing virus

Fowl glioma-inducing virus (FGV), which belongs to avian leukosis virus subgroup A, causes the so-called fowl glioma and cerebellar hypoplasia in chickens. In the present study, the complete nucleotide sequences of four isolates (Tym-43, U-1, Sp-40 and Sp-53) related to the FGV prototype were determined and their pathogenicity was investigated. Phylogenetic analysis showed that the 3′-long terminal repeat of all isolates grouped together in a cluster, while sequences of the surface (SU) proteins encoded by the env gene of these viruses had 85 to 96% identity with the corresponding region of FGV. The SU regions of Tym-43, U-1 and FGV grouped together in a cluster, but those of Sp-40 and Sp-53 formed a completely separate cluster. Next, C/O specific-pathogen-free chickens were inoculated in ovo with these isolates as well as the chimeric virus RCAS(A)-(FGVenvSU), constructed by substituting the SU region of FGV into the retroviral vector RCAS(A). The four variants induced fowl glioma and cerebellar hypoplasia and the birds inoculated with Sp-53 had the most severe lesions. In contrast, RCAS(A)-(FGVenvSU) provoked only mild non-suppurative inflammation. These results suggest that the ability to induce brain lesions similar to those of the FGV prototype is still preserved in these FGV variants.
Human beta defensin-1 and -2 expression in the gingiva of patients with specific periodontal diseases.

BACKGROUND AND OBJECTIVE beta defensin antimicrobial peptides are important in epithelial innate immunity, and their differential expression is associated with periodontal diseases. The aims of this study were to determine the mRNA expression of human beta defensin-1 and -2 in the gingival tissue of patients with gingivitis, aggressive periodontitis and chronic periodontitis, and to evaluate the relationship between defensin expression and type and/or severity of periodontal destruction. MATERIAL AND METHODS Fifteen patients in each group with gingivitis, aggressive periodontitis and chronic periodontitis, and 10 healthy subjects, were included in the study (n=55). The periodontal status of the subjects was determined by periodontal clinical measurements and radiographical evaluations. Transcriptional levels of human beta defensin-1 and -2 genes in gingival samples were assessed by using the quantitative real-time polymerase chain reaction technique, and the data were evaluated statistically by the relative expression Software Tool 2 for groupwise comparisons. RESULTS Expression of the human beta defensin-1 gene was lower in gingivitis and aggressive periodontitis groups, and significantly higher in the chronic periodontitis group, than in the control group (p<0.001). Human beta defensin-2 mRNA expression in the gingivitis group was lower than in the control group; however, the difference was statistically significant only in half of the gingivitis patients (p<0.001). Human beta defensin-2 mRNA levels were higher in some chronic periodontitis patients, but lower in the others when compared with the control group (p<0.001). Expression of the human beta defensin-2 gene increased in the aggressive periodontitis group relative to the control group. CONCLUSION This study suggests that human beta defensin-1 and -2 genes in the gingival epithelium show differential expression in patients with specific periodontal diseases, and aggressive and chronic periodontitis types demonstrate different gingival beta defensin-1 and -2 expression patterns.
Between Data Cleaning and Inference: Pre-Averaging and Robust Estimators of the Efficient Price

Pre-averaging is a popular strategy for mitigating microstructure in high frequency financial data. As the term suggests, transaction or quote data are averaged over short time periods ranging from 30 seconds to five minutes, and the resulting averages approximate the efficient price process much better than the raw data. Apart from reducing the size of the microstructure, the methodology also helps synchronise data from different securities. The procedure is robust to short term dependence in the noise.Since averages can be subject to outliers, and since they can pulverise jumps, we have developed a broader theory which also applies to cases where M-estimation is used to pin down the efficient price in local neighbourhoods. M-estimation serves the same function as averaging, but we shall see that it is safer. Good choices of M-estimating function greatly enhance the identification of jumps. The methodology applies off-the-shelf to any high frequency econometric problem.In this paper, we develop a general theory for pre-averaging and M-estimation based inference. We show that, up to a contiguity adjustment, the pre-averaged process behaves as if one sampled from a semimartingale (with unchanged volatility) plus an independent error. Estimating the efficient price is a form of pre-processing of the data, and hence the methods in this paper also serve the purpose of data cleaning.