Miracle-dz/UniFAR-FTUs huggingface dataset:
Spatial changes in soil stable isotopic composition in response to carrion decomposition

Abstract. Decomposition provides a critical mechanism for returning nutrients to the surrounding environment. In terrestrial systems, animal carcass, or carrion, decomposition results in a cascade of biogeochemical changes. Soil microbial communities are stimulated, resulting in transformations of carbon (C) and nitrogen (N) sourced from the decaying carrion soft tissues, changes to soil pH, electrical conductivity, and oxygen availability as microbial communities release CO2 and mineralize organic N. While many of the rapid changes to soil biogeochemistry observed during carrion decomposition return to background or starting conditions shortly after soft tissues are degraded, some biogeochemical parameters, particularly bulk soil stable δ15N isotopic composition, have the potential to exhibit prolonged perturbations, extending for several years. The goal of this study was to evaluate the lateral and vertical changes to soil stable isotopic composition 1 year after carrion decomposition in a forest ecosystem. Lateral transects extending 140 cm from three decomposition “hotspots” were sampled at 20 cm intervals, and subsurface cores were collected beneath each hotspot to a depth of 50 cm. Bulk soil stable isotopic composition (δ15N and δ13C) indicated that 1 year after complete soft tissue removal and decay, soils were significantly 15N enriched by 7.5±1.0 ‰ compared to control soils up to 60 cm from the hotspot center, and enrichment extended to a depth of 10 cm. Hotspot soils also contained 10 % more N compared to control soils, indicating that decomposition perturbs N pools. Our results demonstrate that carrion decomposition has the potential to result in long-term changes to soil biogeochemistry, up to at least 1 year after soft tissue degradation, and to contribute to bulk soil stable isotopic composition.
Interference Suppression and Group-Based Power Adjustment via Alternating Optimization for DS-CDMA Networks with Multihop Relaying

This work presents joint interference suppression and power allocation algorithms for DS-CDMA networks with multiple hops and decode-and-forward (DF) protocols. A scheme for joint allocation of power levels across the relays subject to group-based power constraints and the design of linear receivers for interference suppression is proposed. A constrained minimum mean-squared error (MMSE) design for the receive filters and the power allocation vectors is devised along with an MMSE channel estimator. In order to solve the proposed optimization efficiently, a method to form an effective group of users and an alternating optimization strategy are devised with recursive alternating least squares (RALS) algorithms for estimating the parameters of the receiver, the power allocation and the channels. Simulations show that the proposed algorithms obtain significant gains in capacity and performance over existing schemes.
Models of Searching and Browsing: Languages, Studies, and Application

We describe the formulation, construction, and evaluation of predictive models of human information seeking from a large dataset of Web search activities. We first introduce an expressive language for describing searching and browsing behavior, and use this language to characterize several prior studies of search behavior. Then, we focus on the construction of predictive models from the data. We review several analyses, including an exploration of the properties of users, queries, and search sessions that are most predictive of future behavior. We also investigate the influence of temporal delay on user actions, and representational tradeoffs with varying the number of steps of user activity considered. Finally, we discuss applications of the predictive models, and focus on the example of performing principled prefetching of content.
What's in the "pure" prosody?

Detectors for accents and phrase boundaries have been developed which derive prosodic features from the speech signal and its fundamental frequency to support other modules of a speech understanding system in an early analysis stage, or in cases where no word hypotheses are available. The detectors' underlying Gaussian distribution classifiers were trained with 50 minutes and tested with 30 minutes of spontaneous speech, yielding recognition rates of 74% for accents and 86% for phrase boundaries. Since this material was prosodically hand labelled, the question was: which labels for phrase boundaries and accentuation were only guided by syntactic or semantic knowledge, and which ones are really prosodically marked? Therefore a small test subset has been resynthesized in such a way that comprehensibility was lost, but the prosodic characteristics were kept. This subset has been relabelled by 11 listeners with nearly the same accuracy as the detectors.
Assessing children's ultraviolet radiation exposure: the potential usefulness of a colorimeter.

OBJECTIVES This study evaluated the colorimeter as an objective measure of children's ultraviolet (UV) radiation exposure. METHODS Fifty-eight children, ages 6 to 9 years, attended two summer measurement sessions, with 46 attending a subsequent winter session. RESULTS Comparisons between summer sessions for the L* scale showed that only the upper arm significantly changed in the tanner direction, while b* scale values indicated significant tanning for all body sites. All exposed body sites changed significantly in the less tan direction between summer and winter measurements. CONCLUSIONS Using colorimeters to objectively measure children's UV exposure has potential applications for skin cancer prevention programs.
A Deep Fusion Model for Domain Adaptation in Phrase-based MT

We present a novel fusion model for domain adaptation in Statistical Machine Translation. Our model is based on the joint source-target neural network Devlin et al., 2014, and is learned by fusing in- and out-domain models. The adaptation is performed by backpropagating errors from the output layer to the word embedding layer of each model, subsequently adjusting parameters of the composite model towards the in-domain data. On the standard tasks of translating English-to-German and Arabic-to-English TED talks, we observed average improvements of +0.9 and +0.7 BLEU points, respectively over a competition grade phrase-based system. We also demonstrate improvements over existing adaptation methods.
The Symmetry of a Simple Optimization Problem in Lasso Screening

Recently dictionary screening has been proposed as an effective way to improve the computational efficiency of solving the lasso problem, which is one of the most commonly used method for learning sparse representations. To address today's ever increasing large dataset, effective screening relies on a tight region bound on the solution to the dual lasso. Typical region bounds are in the form of an intersection of a sphere and multiple half spaces. One way to tighten the region bound is using more half spaces, which however, adds to the overhead of solving the high dimensional optimization problem in lasso screening. This paper reveals the interesting property that the optimization problem only depends on the projection of features onto the subspace spanned by the normals of the half spaces. This property converts an optimization problem in high dimension to much lower dimension, and thus sheds light on reducing the computation overhead of lasso screening based on tighter region bounds.
Perceptions of Domestic Violence: Leaving vs. Staying in Abusive Relationships

This study examined whether participants’ attributions of blame and responsibility toward a victim of domestic violence were influenced by whether or not the victim left her abuser. It also looked at whether or not educational information regarding the difficulties of leaving a violent partner would affect these attributions. Participants, all adults from the United States, either read a vignette in which a woman victim of domestic violence stayed with her abusive husband, or left him. Prior to reading the vignette, some participants were given information about the problems associated with leaving a violent partner, and some were not. All participants completed a scale measuring victim blame. No main effects of whether the victim left or whether the participant received information were found on attributions of blame, and there was not a statistically significant interaction between the victim leaving and presence of information. An interaction between whether or not the participant was a victim of domestic violence and the presence of information was found on victim blame, but further research should examine this more closely with a study specifically designed to investigate victims and their perceptions. Keywords: domestic violence, attribution theory, victim blame PERCEPTIONS OF DOMESTIC VIOLENCE 5
Whale Detection & Identification from Aerial Photography

The North Atlantic Right Whale is a critically endangered species of baleen whale, with an estimated fewer than 500 individuals living in our oceans [1, 2]. In the interests of science and conservation, it is necessary to track and monitor these animals. Currently, only a few experienced researchers are able to identify and tag individual whales through the use of custom software and this process is extremely time consuming [1, 3]. This project focuses on detecting and identifying whales from aerial imagery using techniques from machine learning and image processing.
Heteroepitaxial Growth Dynamics of Inp Nanowires on Silicon

Highly lattice-mismatched InP/Si nanowire heterostructures were synthesized using the metal-organic chemical vapor deposition (MOCVD) process at 450 ºC. The InP nanowire diameter as high as 500 nm is much thicker than the critical diameter (~24 nm for InP/Si) predicted by a recent theoretical work on the coherent growth of nanowire heterostructures. We investigated possible factors that lead to the unusually large diameters in a highly lattice-mismatched material system. Dislocations formed at the interfacial plane of the heterostructure due to high lattice mismatch were found to contribute to the growth of nanowires with very large diameters. An extra pair of dislocation lines at the interfacial plane was found to support an increase in nanowire diameter by ~12 nm.
Design of wireless mesh networks for aggregating traffic of fast moving users

In this paper, we examine wireless mesh networks and present a theoretical model for evaluating the expected throughput for fast moving users. We propose intelligent techniques for improving the throughput: distribution of neighbour nodes over the available wireless interfaces and distributed channel assignment for minimising the interference. Evaluations show that the neighbour nodes should be equally distributed over the wireless interfaces based on the relative difference in hop count to the closest gateway. We also present load-aware techniques which dynamically adapt the nodes according to the current traffic conditions. Load-aware techniques are able to achieve larger throughput but in many cases gain margins are smaller than expected. It is also shown that a poor choice in neighbour interface binding or channel assignment technique leads to a decreased performance in such away that adding interfaces or channels would not further improve the throughput.
Crystal structure of the [2Fe-2S] oxidative-stress sensor SoxR bound to DNA

The [2Fe-2S] transcription factor SoxR, a member of the MerR family, functions as a bacterial sensor of oxidative stress such as superoxide and nitric oxide. SoxR is activated by reversible one-electron oxidation of the [2Fe-2S] cluster and then enhances the production of various antioxidant proteins through the soxRS regulon. In the active state, SoxR and other MerR family proteins activate transcription from unique promoters, which have a long 19- or 20-bp spacer between the −35 and −10 operator elements, by untwisting the promoter DNA. Here, we show the crystal structures of SoxR and its complex with the target promoter in the oxidized (active) state. The structures reveal that the [2Fe-2S] cluster of SoxR is completely solvent-exposed and surrounded by an asymmetric environment stabilized by interaction with the other subunit. The asymmetrically charged environment of the [2Fe-2S] cluster probably causes redox-dependent conformational changes of SoxR and the target promoter. Compared with the promoter structures with the 19-bp spacer previously studied, the DNA structure is more sharply bent, by ≈1 bp, with the two central base pairs holding Watson–Crick base pairs. Comparison of the target promoter sequences of the MerR family indicates that the present DNA structure represents the activated conformation of the target promoter with a 20-bp spacer in the MerR family.
Automatic volumetric localization of the liver in abdominal CT scans using low level processing and shape priors

In this paper we present an automatic volumetric liver localization method as an approach for liver segmentation. In the proposed method the aim is to localise a mean shape model of the liver in the target CT scan. The framework consists of three main steps: shape model construction, low level processing and shape model registration. We evaluated our method on the MICCAI 2007 liver segmentation challenge dataset. The Leave-one-out validation results demonstrate the effectiveness of the proposed method. The average volume overlap between our method and the ground truth, using the Jaccard index, is 0.64±0.11 which is acceptable for an initial localisation of the liver prior to further refinement.
An OFDM Impulse Canceller with Impulse Detection

Generally, OFDM has immunity to the impulse noise. However, the performance of OFDM system will degrade seriously if the power of the impulse noise is above a certain threshold. In this paper, an impulse noise canceller based on the Reed-Solomon decoding with impulse detection will be proposed. As the uniform spaced pilots in frequency domain are employed as the syndromes, and the space between the pilots is coprime with the number of the subcarriers, such an assignment of the pilots will possess an innate interleaving property. The recursive extension is proposed to reconstruct the impulsive noise in frequency domain. And it can reduce the implementation complexity. The effectiveness of the algorithms is verified by simulations
Long-term Outcomes and Risk Factors for Reoperation After Surgical Treatment for Gastrointestinal Crohn Disease According to Anti-tumor Necrosis Factor-α Antibody Use: 35 Years of Experience at a Single Institute in Korea

Purpose Crohn disease is characterized by high rates of recurrence and reoperations. However, few studies have investigated long-term surgical outcomes in Asian populations. We investigated risk factors for reoperation, particularly those associated with anti-tumor necrosis factor-α (anti-TNF-α) antibody use, and long-term follow-up results. Methods We reviewed the records of 148 patients (100 males and 48 females) who underwent surgery for gastrointestinal Crohn disease and retrospectively analyzed long-term outcomes and risk factors. Results The mean age at diagnosis was 28.8 years. Thirty-eight patients (25.7%) received monoclonal antibody treatment before reoperation. A small bowel and colon resection was most commonly performed (83 patients, 56.1%). The median follow-up was 149 months, during which 47 patients underwent reoperation. The median interval between the primary and the secondary surgeries was 65 months, with accumulated reoperation rates of 16.5%, 31.8%, and 57.2% after 5, 10, and 15 years, respectively. Obstruction was the most common indication for reoperation (37 patients, 25.0%). In a multivariable analysis, age <17 years at diagnosis (A1) (odds ratio [OR], 2.20; P = 0.023), penetrating behavior (B3) (OR, 4.39; P < 0.001), and no azathioprine use (OR, 2.87; P = 0.003) were associated with reoperation. Anti-TNF-α antibody use did not affect the reoperation rate (P = 0.767). Conclusion We showed a high reoperation rate regardless of treatment with anti-TNF-α antibody, which indicates that recurrent surgery is still needed to cure patients with gastrointestinal Crohn diseases. Younger age at primary operation, penetrating behavior, and no azathioprine use were significant factors associated with reoperation for gastrointestinal Crohn disease.
On-demand node-disjoint multipath routing in wireless ad hoc networks

An on-demand node-disjoint multipath routing protocol is proposed to overcome the shortcomings of on-demand unipath routing protocols like AODV and DSR. The protocol has two novel aspects compared to the other on-demand multipath protocols: it reduces routing overhead dramatically and achieves multiple node-disjoint routing paths. Simulation results show that the proposed protocol achieves lower data delay and control overhead as well as higher packet delivery ratio.
NeuroLines: A Subway Map Metaphor for Visualizing Nanoscale Neuronal Connectivity

We present NeuroLines, a novel visualization technique designed for scalable detailed analysis of neuronal connectivity at the nanoscale level. The topology of 3D brain tissue data is abstracted into a multi-scale, relative distance-preserving subway map visualization that allows domain scientists to conduct an interactive analysis of neurons and their connectivity. Nanoscale connectomics aims at reverse-engineering the wiring of the brain. Reconstructing and analyzing the detailed connectivity of neurons and neurites (axons, dendrites) will be crucial for understanding the brain and its development and diseases. However, the enormous scale and complexity of nanoscale neuronal connectivity pose big challenges to existing visualization techniques in terms of scalability. NeuroLines offers a scalable visualization framework that can interactively render thousands of neurites, and that supports the detailed analysis of neuronal structures and their connectivity. We describe and analyze the design of NeuroLines based on two real-world use-cases of our collaborators in developmental neuroscience, and investigate its scalability to large-scale neuronal connectivity data.
A new time domain convolutive BSS of heart and lung sounds

In this paper the objective is to separate nonstationary heart and lung sounds from their convolutive mixtures in time domain. In order to separate the sources an orthogonal source model and a gradient based optimization have been used to best model the mixing system and best estimate the parameters respectively. Having diagonal or quasi diagonal covariance matrices for different source segments and also having independent profiles/envelops for different sources (which implies nonstationarity of the sources) are the requirements for our convolutive method. We applied the method to synthetically mixed real heart and lung sound signals. Compared to the other methods, the results show the high capability of the method for separating nonstationary heart and lung sound signals.
Analysis of the xplAB-Containing Gene Cluster Involved in the Bacterial Degradation of the Explosive Hexahydro-1,3,5-Trinitro-1,3,5-Triazine

ABSTRACT Repeated use of the explosive compound hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) on military land has resulted in significant soil and groundwater pollution. Rates of degradation of RDX in the environment are low, and accumulated RDX, which the U.S. Environmental Protection Agency has determined is a possible human carcinogen, is now threatening drinking water supplies. RDX-degrading microorganisms have been isolated from RDX-contaminated land; however, despite the presence of these species in contaminated soils, RDX pollution persists. To further understand this problem, we studied RDX-degrading species belonging to four different genera (Rhodococcus, Microbacterium, Gordonia, and Williamsia) isolated from geographically distinct locations and established that the xplA and xplB (xplAB) genes, which encode a cytochrome P450 and a flavodoxin redox partner, respectively, are nearly identical in all these species. Together, the xplAB system catalyzes the reductive denitration of RDX and subsequent ring cleavage under aerobic and anaerobic conditions. In addition to xplAB, the Rhodococcus species studied here share a 14-kb region flanking xplAB; thus, it appears likely that the RDX-metabolizing ability was transferred as a genomic island within a transposable element. The conservation and transfer of xplAB-flanking genes suggest a role in RDX metabolism. We therefore independently knocked out genes within this cluster in the RDX-degrading species Rhodococcus rhodochrous 11Y. Analysis of the resulting mutants revealed that XplA is essential for RDX degradation and that XplB is not the sole contributor of reducing equivalents to XplA. While XplA expression is induced under nitrogen-limiting conditions and further enhanced by the presence of RDX, MarR is not regulated by RDX.
Dilated cardiomyopathy associated with simian AIDS in nonhuman primates.

BACKGROUND Cardiomyopathy is being recognized with increasing frequency in patients with AIDS, yet the relationship between HIV infection and cardiac contractile dysfunction remains obscure. The purpose of the present study was to determine if infection with simian immunodeficiency virus (SIV) in nonhuman primates is associated with cardiac dysfunction and myocardial injury. METHODS AND RESULTS Left ventricular size and function were determined by 2D echocardiography in 16 rhesus macaques before and at weekly intervals following infection with cloned pathogenic SIV(mac) 239 or the highly attenuated SIV(mac) 239 nef deletion mutant. A second group of 15 rhesus macaques chronically infected with pathogenic (n=6) or nonpathogenic (n=9) virus were studied at >2 years following infection. Cardiac tissues from 24 rhesus macaques chronically infected (>2 years) with pathogenic SIV were reviewed for evidence of cardiac pathology. Acute infection (<6 weeks) with either pathogenic or nonpathogenic SIV caused neither contractile dysfunction nor cardiac pathology. However, LV ejection fraction was significantly (P<0.05) depressed (43+/-7%) in rhesus macaques chronically infected with pathogenic SIV compared with rhesus macaques chronically infected with nonpathogenic SIV (61+/-3%). Furthermore, two thirds of rhesus macaques that succumbed to simian AIDS had myocardial pathology including lymphocytic myocarditis (n=9) and coronary arteriopathy (n=6), with complete vessel occlusion (n=4) and associated myocardial infarction and necrosis. CONCLUSIONS This unique model is valuable in understanding the pathogenesis of cardiac injury associated with retroviral infection in a relevant nonhuman primate model of AIDS.
A non-invasive method for gastrointestinal parameter monitoring.

AIM To propose a new, non-invasive method for monitoring 24-h pressure, temperature and pH value in gastrointestinal tract. METHODS The authors developed a miniature, multi-functional gastrointestinal monitoring system, which comprises a set of indigestible biotelemetry capsules and a data recorder. The capsule, after ingested by patients, could measure pressure, temperature and pH value in the gastrointestinal tract and transmit the data to the data recorder outside the body through a 434 MHz radio frequency data link. After the capsule passed out from the body, the data saved in the recorder were downloaded to a workstation via a special software for further analysis and comparison. RESULTS Clinical experiments showed that the biotelemetry capsules could be swallowed by volunteers without any difficulties. The data recorder could receive the radio frequency signals transmitted by the biotelemetry in the body. The biotelemetry capsule could pass out from the body without difficulties. No discomfort was reported by any volunteer during the experiment. In vivo pressure and temperature data were acquired. CONCLUSION A non-invasive method for monitoring 24-h gastrointestinal parameters was proposed and tested by the authors. The feasibility and functionality of this method are verified by laboratory tests and clinical experiments.