Miracle-dz/UniFAR-FTUs huggingface dataset:
Improved progressive-edge-growth (PEG) construction of irregular LDPC codes

Progressive-edge-growth (PEG) algorithm is known to construct low-density parity-check codes at finite block lengths with very good performance. In this letter, we propose a very simple modification to PEG construction for irregular codes, which considerably improves the performance at high signal-to-noise (SNR) ratios with no sacrifice in low-SNR performance.
Issuer Quality and the Credit Cycle

We show that the credit quality of corporate debt issuers deteriorates during credit booms, and that this deterioration forecasts low excess returns to corporate bondholders. The key insight is that changes in the pricing of credit risk disproportionately affect the financing costs faced by low quality firms, so the debt issuance of low quality firms is particularly useful for forecasting bond returns. We show that a significant decline in issuer quality is a more reliable signal of credit market overheating than rapid aggregate credit growth. We use these findings to investigate the forces driving time-variation in expected corporate bond returns.
Direct Numerical Simulation of Supersonic Turbulent Boundary Layer with Spanwise Wall Oscillation

Direct numerical simulations (DNS) of Mach = 2.9 supersonic turbulent boundary layers with spanwise wall oscillation (SWO) are conducted to investigate the turbulent heat transport mechanism and its relation with the turbulent momentum transport. The turbulent coherent structures are suppressed by SWO and the drag is reduced. Although the velocity and temperature statistics are disturbed by SWO differently, the turbulence transports of momentum and heat are simultaneously suppressed. The Reynolds analogy and the strong Reynolds analogy are also preserved in all the controlled flows, proving the consistent mechanisms of momentum transport and heat transport in the turbulent boundary layer with SWO. Despite the extra dissipation and heat induced by SWO, a net wall heat flux reduction can be achieved with the proper selected SWO parameters. The consistent mechanism of momentum and heat transports supports the application of turbulent drag reduction technologies to wall heat flux controls in high-speed vehicles.
Imbalanced text classification on host pathogen protein-protein interaction documents

important in understanding the fundamental processes governing cell biology. However, a large number of scientific findings about PPIs are buried in the growing volume of biomedical literature. Document classification systems have been shown to have the potential to accelerate the curation process by retrieving PPI-related documents. However, it is usually a case that a small number of positive documents can be obtained manually or from PPI knowledge bases with literature-based evidence and there are a large number of negative documents. In this paper, we investigate the effects of feature selection and feature weighting as well as kernel function of Support Vector Machines (SVMs) on imbalanced two-class classification based on 1360 host-pathogen protein-protein interactions documents. The results show that the suitable feature weighting approach is the important factor for improving the classification performance. Adjusting cost sensitive parameter of radial basis function (RBF) kernel of SVM can decrease the minority class misclassification ratio and increase the classification accuracy on imbalanced documents classification. An automated classification system to identify MEDLINE abstracts referring to host-pathogen protein-protein interactions can been developed based on the experiment.
A New Broadcast Quality Low Bit Rate Audio Coding Scheme Utilizing Novel Bandwidth Extension Tools

In this paper we describe the components of a novel audio coding algorithm capable of delivering high-fidelity CDlike stereo audio at the bit rates of 40-48 kbps and natural sounding FM grade mono at the bit rates of 18-22 kbps. Bandwidth Extension has emerged as an important tool for the satisfactory performance of low bit rate audio codecs. Recently we proposed two new bandwidth extension algorithms, Fractal Self-Similarity Model (FSSM) and Accurate Spectral Replacement (ASR), which belong to a new class of Bandwidth Extension techniques which are applied directly to the high resolution frequency representation of the signal (e.g., MDCT or ODFT). The proposed coding scheme uses FSSM and ASR in an adaptive and complementary framework. Another important component of the proposed codec is a wideband psychoacoustic model that makes an explicit use of the Comodulation Release of Masking (CMR) phenomenon. It also includes a novel parametric stereo coding technique. The proposed audio coding scheme is geared towards broadcast applications where codec latency and encoder complexity is generally not an overriding concern. In this paper we present algorithmic details of the new codec, audio demonstrations, and, comparison to other audio coding schemes. Further information and audio demonstrations are available at http://www.atc-labs.com/teslapro.
Memory and Communication Efficient Distributed Stochastic Optimization with Minibatch Prox

We present and analyze an approach for distributed stochastic optimization which is statistically optimal and achieves near-linear speedups (up to logarithmic factors). Our approach allows a communication-memory tradeoff, with either logarithmic communication but linear memory, or polynomial communication and a corresponding polynomial reduction in required memory. This communication-memory tradeoff is achieved through minibatch-prox iterations (minibatch passive-aggressive updates), where a subproblem on a minibatch is solved at each iteration. We provide a novel analysis for such a minibatch-prox procedure which achieves the statistical optimal rate regardless of minibatch size and smoothness, thus significantly improving on prior work.
Tumor Suppressor p53 Binds with High Affinity to CTG·CAG Trinucleotide Repeats and Induces Topological Alterations in Mismatched Duplexes*

DNA binding is central to the ability of p53 to function as a tumor suppressor. In line with the remarkable functional versatility of p53, which can act on DNA as a transcription, repair, recombination, replication, and chromatin accessibility factor, the modes of p53 interaction with DNA are also versatile. One feature common to all modes of p53-DNA interaction is the extraordinary sensitivity of p53 to the topology of its target DNA. Whereas the strong impact of DNA topology has been demonstrated for p53 binding to sequence-specific sites or to DNA lesions, the possibility that DNA structure-dependent recognition may underlie p53 interaction with other types of DNA has not been addressed until now. We demonstrate for the first time that conformationally flexible CTG·CAG trinucleotide repeats comprise a novel class of p53-binding sites targeted by p53 in a DNA structure-dependent mode in vitro and in vivo. Our major finding is that p53 binds to CTG·CAG tracts by different modes depending on the conformation of DNA. Although p53 binds preferentially to hairpins formed by either CTG or CAG strands, it can also bind to linear forms of CTG·CAG tracts such as canonic B DNA or mismatched duplex. Intriguingly, by binding to a mismatched duplex p53 can induce further topological alterations in DNA, indicating that p53 may act as a DNA topology-modulating factor.
A Thresholder for all-optical Digitising Radio-over-Fibre transceivers

This paper describes an optical Thresholder (o-Thresholder) intended to be part of a transmitter module for future all-optical Digitising Radio-over-Fibre (o-DRoF) transceivers. The proposed device is based on an Attenuation-Imbalanced Semiconductor Laser Amplifier Loop Mirror (AI-SLALOM) in self-switching regime, using the nonlinearities of a semiconductor optical amplifier. Simulations of the proposed AI-SLALOM based o-Thresholder have shown promising results in comparison with the use of standard optical fibre and highly nonlinear fibre only. The newly proposed device is rather compact, optically integrable and requires much less input optical power than conventional devices (by several orders of magnitude). It provides enhanced optical RZ bits at 1550 nm wavelength window, 1.25 GHz repetition rate and 80 ps time-width.
oes postfire management affect the recovery of Mediterranean communities ? he case study of terrestrial gastropods icenç

In fire-prone regions, understanding the response of species to fire is a major goal in order to predict the effects on biodiversity. Furthermore, postfire management can also model this response through the manipulation of environmental characteristics of the burnt habitat. We have examined the taxonomic and functional response to fire and postfire management of a Mediterranean snail community affected by a summer fire in 2003. After the fire, the area was logged, leaving wood debris on the ground, and three alternative practices were implemented in several plots within the burnt area: subsoiling, removal of trunks having branches, total removal of trunks and branches, as well as one area not logged. Our results indicated that fire exerted a major impact on the snail community, strongly reducing diversity errestrial snails ostfire management ildfires iodiversity editerranean and species richness, particularly for forest species living in the humus and having European distribution ranges. By contrast, we found slight differences within the postfire practices, presumably because of the strong initial impact of fire and subsequent xerophilous postfire conditions. However, the area with only trunk removal showed a positive response of generalist snail species, probably due to moist microhabitats provided by the accumulation of wood debris on the ground. The effects of postfire management should be further explored due to the expected increase of fire risk associated with climate change and land-use histories.
Effects of Dietary Garlic Powder on Growth, Feed Utilization and Whole Body Composition Changes in Fingerling Sterlet Sturgeon, Acipenser ruthenus

A 12 week growth study was carried out to investigate the supplemental effects of dietary garlic powder (GP) on growth, feed utilization and whole body composition changes of fingerling sterlet sturgeon Acipenser ruthenus (averaging weight, 5.5 g). Following a 24-h fasting, 540 fish were randomly distributed to each of 18 tanks (30 fish/tank) under a semi-recirculation freshwater system. The GP of 0.5% (GP0.5), 1% (GP1), 1.5% (GP1.5), 2% (GP2) and 3% (GP3) was added to the control diet (GP0) containing 43% protein and 16% lipid. After the feeding trial, weight gain (WG) of fish fed GP1.5, GP2 and GP3 were significantly higher (p<0.05) than those of fish fed GP0, GP0.5 and GP1. Feed efficiency and specific growth rate (SGR) showed a similar trend to WG. Protein efficiency ratio of fish fed GP1.5, GP2, and GP3 were significantly higher (p<0.05) than those of fish groups fed the other diets. A significant difference (p<0.05) was found in whole body composition (moisture, crude protein, crude lipid, ash, and fiber) of fish at the end of the experiment. Significantly higher (p<0.05) protein and lipid retention efficiencies (PRE and LRE) were also found in GP1.5, GP2, and GP3 groups. Broken-line regression model analysis and second order polynomial regression model analysis relation on the basis of SGR and WG indicated that the dietary optimal GP level could be greater than 1.77% and 1.79%, but less than 2.95% and 3.18% in fingerling sterlet sturgeon. The present study suggested that dietary GP for fingerling sterlet sturgeon could positively affect growth performance and protein retention.
A Robust Scheme for Feature-Preserving Mesh Denoising

In recent years researchers have made noticeable progresses in mesh denoising, that is, recovering high-quality 3D models from meshes corrupted with noise (raw or synthetic). Nevertheless, these state of the art approaches still fall short for robustly handling various noisy 3D models. The main technical challenge of robust mesh denoising is to remove noise while maximally preserving geometric features. In particular, this issue becomes more difficult for models with considerable amount of noise. In this paperwe present a novel scheme for robust feature-preserving mesh denoising. Given a noisy mesh input, our method first estimates an initial mesh, then performs feature detection, identification and connection, and finally, iteratively updates vertex positions based on the constructed feature edges. Through many experiments, we show that our approach can robustly and effectively denoise various input mesh models with synthetic noise or raw scanned noise. The qualitative and quantitative comparisons between our method and the selected state of the art methods also show that our approach can noticeably outperform them in terms of both quality and robustness.
Examining the blue line in the rainbow: the interactions and perceptions of law enforcement among lesbian, gay, bisexual, transgender and queer communities

ABSTRACT Despite the fact that LGBTQ individuals are at greater risk of victimization than the average citizen, the LGBTQ community’s relationship with law enforcement has been a turbulent one. Using a mixed-methods approach, including surveys, semi-structured interviews and observations of town hall meetings, and following the participatory action research framework, this study examines the interactions between the LGBTQ community and law enforcement, and the perceptions of police within the LGBTQ community. The current study demonstrates how members of the LGBTQ community continue to have negative experiences with police that adversely impact their perceptions of law enforcement. Moreover, the findings underline the importance of examining how multiple identities impact an individual’s experiences with and their perceptions of law enforcement. Expanding past research on this topic, this study offers an analysis based upon suggestions of the study’s participants of what steps must be taken in order to improve relations between these two groups.
Improving the Robustness and Accuracy of the Marching Cubes Algorithm for Isosurfacing

This paper proposes a modification of the Marching Cubes algorithm for isosurfacing, with the intent of improving the representation of the surface in the interior of each grid cell. Our objective is to create a representation which correctly models the topology of the trilinear interpolant within the cell and which is robust under perturbations of the data and threshold value. To achieve this, we identify a small number of key points in the cell interior that are critical to the surface definition. This allows us to efficiently represent the different topologies that can occur, including the possibility of "tunnels. " The representation is robust in the sense that the surface is visually continuous as the data and threshold change in value. Each interior point lies on the isosurface. Finally, a major feature of our new approach is the systematic method of triangulating the polygon in the cell interior.
Downregulation of ATOH8 induced by EBV-encoded LMP1 contributes to the malignant phenotype of nasopharyngeal carcinoma

Mechanism for the malignant phenotype of nasopharyngeal carcinoma (NPC) remains poorly understood. Epstein-Barr virus (EBV) consistently appears in nearly all malignant NPC patient samples, suggesting the strong etiological link between the malignant phenotype and EBV infection. Here we found that the EBV-encoded latent membrane protein (LMP1) enhanced cell growth, motility, invasion and xenograft tumor growth of NPC. RNA-seq profiling analysis of LMP1-positive NPC patient tissues indicated that widespread gene repression contributed to malignant phenotype of NPC. The transcription factor binding site (TFBS) enrichment analysis indicated a subset of transcription factors including ATOH8, a novel transcript factor which belongs to the basic helix-loop-helix (bHLH) gene family inversely enriched in promoters of up-regulated genes and down-regulated genes. Importantly, the expression of ATOH8 was suppressed in both immortalized normal nasopharyngeal epithelial cells (NPEC) and NPC cells with LMP1 overexpression. The Real-Time PCR and Western Blot assays indicated that ATOH8 decreased expression in NPC cell lines and patient samples. Moreover, by gain- or loss-of-function assays, we demonstrated that ATOH8 inhibition promoted malignant phenotype, whereas ATOH8 restoration reversed malignant phenotype of NPC. Finally, we demonstrated that LMP1 inhibited ATOH8 expression by epigenetically impairing the occupancy of activating H3K4me3 and enhancing the occupancy of repressive H3K27me3 on ATOH8 promoter. Collectively, our study uncovered the occurrence of malignant phenotype of NPC induced by EBV infection and characterized a novel bHLH transcription factor ATOH8 as a new downstream target of LMP1.
Direct ex vivo evaluation of long-lived protective antiviral memory B cell responses against hepatitis B virus.

BACKGROUND The frequency of protective antiviral memory B cells after hepatitis B virus (HBV) vaccination is unknown. METHODS A novel 2-step immunomagnetic protocol to assess the ex vivo frequency of protective HBV surface antigen (HBsAg)-specific memory B cells was used. RESULTS HBsAg-specific memory B cells were detected in vaccinated individuals, although at very low frequency (median, 0.2% of CD19(+) cells [range, 0%-4% of CD19(+) cells]). No correlation existed between the frequency of HBsAg-specific memory B cells and the corresponding serum antibody titer or B cell enzyme-linked immunosorbent spot findings. CONCLUSION Our results indicate sustained B cell-mediated protection against HBV despite waning antibody titers, which is consistent with clinical observations.
Subglacial Lake Whillans microbial biogeochemistry: a synthesis of current knowledge

Liquid water occurs below glaciers and ice sheets globally, enabling the existence of an array of aquatic microbial ecosystems. In Antarctica, large subglacial lakes are present beneath hundreds to thousands of metres of ice, and scientific interest in exploring these environments has escalated over the past decade. After years of planning, the first team of scientists and engineers cleanly accessed and retrieved pristine samples from a West Antarctic subglacial lake ecosystem in January 2013. This paper reviews the findings to date on Subglacial Lake Whillans and presents new supporting data on the carbon and energy metabolism of resident microbes. The analysis of water and sediments from the lake revealed a diverse microbial community composed of bacteria and archaea that are close relatives of species known to use reduced N, S or Fe and CH4 as energy sources. The water chemistry of Subglacial Lake Whillans was dominated by weathering products from silicate minerals with a minor influence from seawater. Contributions to water chemistry from microbial sulfide oxidation and carbonation reactions were supported by genomic data. Collectively, these results provide unequivocal evidence that subglacial environments in this region of West Antarctica host active microbial ecosystems that participate in subglacial biogeochemical cycling.
Components of field potentials evoked by white matter stimulation in isolated slices of primary visual cortex: spatial distributions and synaptic order.

1. We have recorded profiles of the spatial distributions of extracellular field potentials in transverse slices of rat primary visual cortex. Responses were evoked by electrical stimulation near the white matter/layer VI border and sampled from layers I to V along the radial axis orthogonal to the laminae and intersecting the stimulation site ("on-beam" recording). To assess the activity of "horizontal" connections, we also recorded profiles along axes parallel to the cortical lamination ("off-beam" recording), usually in layer III. Overall, our goal was to extend understanding of the physiology and organization of neocortical circuitry and to provide a basis for comparisons of data from different experiments and experimenters when neocortical field potentials are used in studies of plasticity and pharmacology. 2. Responses were highly specific with respect to the cortical layers. We distinguish four major components: two kinds of population spike ("S1" and "S2") and two slower waveforms ("W1" and "W2"). The latter appear to represent flow of current in apical dendrites of the supragranular layers. Component W1, the earliest slow component, is a synaptically driven field potential dipole that is positive in layer I and negative in layer II. Based on estimates of current source densities (CSDs), we attribute this to entry of depolarizing current into dendrites and/or cell somata in layer II, ascending intradendritic current, and passive depolarization of inactive dendritic membrane in layer I. Component W1 rises during the 20 ms after stimulation and falls during the 50-100 ms thereafter. Component W2 is also positive in layer I but maximally negative in layer III. It rises for approximately 100 ms after stimulation and decays during the following 400-800 ms. 3. Component S1 does not depend on synaptic transmission because it persists during the application of glutamate receptor antagonists or medium that is low in Ca2+. This component is largest in layer III, radial to the site of stimulation. There, it is a negative deflection, typically 1-2 mV in amplitude and lasting roughly 2 ms, with a latency to peak between 2 and 4.5 ms. Component S1 is most likely a population spike due to synchronized firing of cell somata activated antidromically via unmyelinated efferent axons. 4. Component S2 is a short (less than 20 ms) burst of population spikes specifically in layer III. Individual S2 spikes closely resemble S1 spikes, and we propose that the same neuronal population generates both. However, S2 spikes require glutamatergic synaptic transmission. (ABSTRACT TRUNCATED AT 400 WORDS)
Cost-analysis of treatment of childhood acute lymphoblastic leukemia with asparaginase preparations: the impact of expensive chemotherapy

Asparaginase is an expensive drug, but important in childhood acute lymphoblastic leukemia. In order to compare costs of PEGasparaginase, Erwinia asparaginase and native E. coli asparaginase, we performed a cost-analysis in the Dutch Childhood Oncology Group ALL-10 medium-risk group intensification protocol. Treatment costs were calculated based on patient level data of 84 subjects, and were related to the occurrence of allergy to PEGasparaginase. Simultaneously, decision tree and sensitivity analyses were conducted. The total costs of the intensification course of 30 weeks were $57,893 in patients without PEGasparaginase allergy (n=64). The costs were significantly higher ($113,558) in case of allergy (n=20) necessitating a switch to Erwinia asparaginase. Simulated scenarios (decision tree analysis) using native E. coli asparaginase in intensification showed that the costs of PEGasparaginase were equal to those of native E. coli asparaginase. Also after sensitivity analyses, the costs for PEGasparaginase were equal to those of native E. coli asparaginase. Intensification treatment with native E. coli asparaginase, followed by a switch to PEGasparaginase, and subsequently to Erwinia asparaginase in case of allergy had similar overall costs compared to the treatment with PEGasparaginase as the first-line drug (followed by Erwinia asparaginase in the case of allergy). PEGasparaginase is preferred over native E. coli asparaginase, because it is administered less frequently, with less day care visits. PEGasparaginase is less immunogenic than native E. coli asparaginase and is not more expensive. Asparaginase costs are mainly determined by the percentage of patients who are allergic and require a switch to Erwinia asparaginase.