Miracle-dz/UniFAR-FTUs huggingface dataset:
Elevation accuracy of laser scanning-derived digital terrain and target models in forest environment

This paper evaluates and discusses the accuracy of laser scanner in DTM (digital terrain model) generation and digital 3-D height model generation in forested areas. High-pulse-rate laser scanners are capable of detecting single trees in a boreal forest zone, since a significant amount of the laser pulses reflect directly from the ground without any interaction with the canopy. This allows for a detailed investigation of forest areas and the creation of a 3-dimensional tree height model. Special emphasis is laid on the optimisation of the selection of ground hits used for the creation of the DTM of future high-pulse-rate laser scanners. A novel DTM algorithm is depicted in detail. In order to develop the algorithm, five phases were created: 1) Calculation of the original reference surface, 2) removal of the vegetation from the reference surface, 3) classificatio n of the original cloud of points, 4) calculation of the DTM based on the classified ground hits, and 5) interpolation of the missing points. A standard error of 15 cm was obtained for flat forest areas and the error increased with increasing terrain slope to the value of approximately 40 cm at the slope of 40 %. The average standard error for forest area was about 22 cm. The laser-derived DTM of the forest road deviated from the true height by 8.5 cm only. An optimum performance for the DTM generation was obtained by averaging the ground hits which were located, at the maximum, 60 cm above the minimum terrain values. It was also shown that tree heights of individual trees in the dominating storey can be obtained with less than 1 m standard error.
Disrupted Intestinal Microbiota and Intestinal Inflammation in Children with Cystic Fibrosis and Its Restoration with Lactobacillus GG: A Randomised Clinical Trial

Background & Aims Intestinal inflammation is a hallmark of cystic fibrosis (CF). Administration of probiotics can reduce intestinal inflammation and the incidence of pulmonary exacerbations. We investigated the composition of intestinal microbiota in children with CF and analyzed its relationship with intestinal inflammation. We also investigated the microflora structure before and after Lactobacillus GG (LGG) administration in children with CF with and without antibiotic treatment. Methods The intestinal microbiota were analyzed by denaturing gradient gel electrophoresis (DGGE), real-time polymerase chain reaction (RT-PCR), and fluorescence in situ hybridization (FISH). Intestinal inflammation was assessed by measuring fecal calprotectin (CLP) and rectal nitric oxide (rNO) production in children with CF as compared with healthy controls. We then carried out a small double-blind randomized clinical trial with LGG. Results Twenty-two children with CF children were enrolled in the study (median age, 7 years; range, 2–9 years). Fecal CLP and rNO levels were higher in children with CF than in healthy controls (184±146 µg/g vs. 52±46 µg/g; 18±15 vs. 2.6±1.2 µmol/L NO2 −, respectively; P<0.01). Compared with healthy controls, children with CF had significantly different intestinal microbial core structures. The levels of Eubacterium rectale, Bacteroides uniformis, Bacteroides vulgatus, Bifidobacterium adolescentis, Bifidobacterium catenulatum, and Faecalibacterium prausnitzii were reduced in children with CF. A similar but more extreme pattern was observed in children with CF who were taking antibiotics. LGG administration reduced fecal CLP and partially restored intestinal microbiota. There was a significant correlation between reduced microbial richness and intestinal inflammation. Conclusions CF causes qualitative and quantitative changes in intestinal microbiota, which may represent a novel therapeutic target in the treatment of CF. Administration of probiotics restored gut microbiota, supporting the efficacy of probiotics in reducing intestinal inflammation and pulmonary exacerbations. Trial Registration ClinicalTrials.gov NCT 01961661
Effect of ECRG2 in combination with cisplatin on the proliferation and apoptosis of EC9706 cells

The aim of the present study was to explore the effect of esophageal cancer-related gene 2 (ECRG2) protein in combination with cisplatin (DDP) on the proliferation and apoptosis of esophageal cancer cells. A 3-(4, 5-dimethylthiazol-2-yl) 2,5-diphenyltetrazolium bromide (MTT) assay was used to examine the effects of ECRG2 alone and ECRG2 in combination with DDP on the proliferation of EC9706 esophageal cancer cells. Hoechst 33258 staining was performed to analyze the effects of ECRG2 alone and ECRG2 in combination with DDP on apoptosis in the EC9706 cells. The expression levels of Bcl-2-associated X protein (Bax) mRNA and protein were determined by reverse transcription polymerase chain reaction (RT-PCR) and western blot analysis, respectively. The results from the MTT assay revealed that ECRG2 inhibited the proliferation of EC9706 cells and that ECRG2 in combination with DDP had a greater inhibitory effect on cell proliferation. The antiproliferative effects were time- and concentration-dependent, within a certain range of concentrations. The Hoechst 33258 staining results demonstrated that the number of apoptotic cells following treatment with ECRG2 in combination with DDP for 24 h was higher than that following treatment with ECRG2 alone for the same duration. Western blot analysis and RT-PCR results revealed that the expression levels of Bax mRNA and protein were upregulated in cells treated with ECRG2 in combination with DDP compared with those in cells treated with ECRG2 alone. Thus, ECRG2 in combination with DDP had an enhanced inhibitory effect on EC9706 cell proliferation compared with that of ECRG2 alone, and an increased inductive effect on EC9706 cell apoptosis, possibly due to the upregulation of the expression of Bax.
RocA Truncation Underpins Hyper-Encapsulation, Carriage Longevity and Transmissibility of Serotype M18 Group A Streptococci

Group A streptococcal isolates of serotype M18 are historically associated with epidemic waves of pharyngitis and the non-suppurative immune sequela rheumatic fever. The serotype is defined by a unique, highly encapsulated phenotype, yet the molecular basis for this unusual colony morphology is unknown. Here we identify a truncation in the regulatory protein RocA, unique to and conserved within our serotype M18 GAS collection, and demonstrate that it underlies the characteristic M18 capsule phenotype. Reciprocal allelic exchange mutagenesis of rocA between M18 GAS and M89 GAS demonstrated that truncation of RocA was both necessary and sufficient for hyper-encapsulation via up-regulation of both precursors required for hyaluronic acid synthesis. Although RocA was shown to positively enhance covR transcription, quantitative proteomics revealed RocA to be a metabolic regulator with activity beyond the CovR/S regulon. M18 GAS demonstrated a uniquely protuberant chain formation following culture on agar that was dependent on excess capsule and the RocA mutation. Correction of the M18 rocA mutation reduced GAS survival in human blood, and in vivo naso-pharyngeal carriage longevity in a murine model, with an associated drop in bacterial airborne transmission during infection. In summary, a naturally occurring truncation in a regulator explains the encapsulation phenotype, carriage longevity and transmissibility of M18 GAS, highlighting the close interrelation of metabolism, capsule and virulence.
Analyzing Implicit Social Networks in Multiplayer Online Games

Understanding the social structures that people implicitly form when playing networked games helps developers create innovative gaming services to benefit both players and operators. But how can we extract and analyze this implicit social structure? The authors' proposed formalism suggests various ways to map interactions to social structure. Applying this formalism to real-world data collected from three game genres reveals the implications of the mappings on in-game and gaming-related services, ranging from network and socially aware player matchmaking to an investigation of social network robustness against player departure.
Attention to visual speech gestures enhances hemodynamic activity in the left planum temporale

Observing a speaker's articulatory gestures can contribute considerably to auditory speech perception. At the level of neural events, seen articulatory gestures can modify auditory cortex responses to speech sounds and modulate auditory cortex activity also in the absence of heard speech. However, possible effects of attention on this modulation have remained unclear. To investigate the effect of attention on visual speech‐induced auditory cortex activity, we scanned 10 healthy volunteers with functional magnetic resonance imaging (fMRI) at 3 T during simultaneous presentation of visual speech gestures and moving geometrical forms, with the instruction to either focus on or ignore the seen articulations. Secondary auditory cortex areas in the bilateral posterior superior temporal gyrus and planum temporale were active both when the articulatory gestures were ignored and when they were attended to. However, attention to visual speech gestures enhanced activity in the left planum temporale compared to the situation when the subjects saw identical stimuli but engaged in a nonspeech motion discrimination task. These findings suggest that attention to visually perceived speech gestures modulates auditory cortex function and that this modulation takes place at a hierarchically relatively early processing level. Hum Brain Mapp, 2005. © 2005 Wiley‐Liss, Inc.
Realistic and Scalable Benchmarking Cloud File Systems: Practices and Lessons from AliCloud

The past decade has witnessed the rapid boom of cloud computing. Many public cloud infrastructures have been implemented and serve millions of tenants. Cloud file systems, which take charge of petabyte-scale data storage, play a crucial role in the performance of cloud infrastructures. Typical cloud file systems, including GFS, HDFS and Ceph, have attracted notable research efforts for performance evaluation and optimization. However, due to the heterogeneity and complexity of I/O workload characteristics in cloud environments, it is still challenging to conduct an accurate and efficient performance evaluation. To address this problem, we collected a two-week I/O workload trace from a 2,500-node production cluster in AliCloud, which is one of the largest cloud providers in Asia. Using the AliCloud trace, we characterized the I/O workload and data distribution, and compared two cloud services in multiple perspectives, including the request arrival pattern, request size, data population and so on. A list of observations and implications were derived and applied to help design a cloud file system benchmarking suite, called Porcupine. Porcupine aims to deploy a scalable and efficient performance evaluation on cloud file systems using realistic I/O workloads. We conducted a group of validation experiments, which demonstrated that Porcupine can achieve high accuracy and scalability. This paper provides our experiences and lessons in generating I/O workloads and deploying performance tests on cloud file systems, which we believe will be insightful to the cloud computing community in general.
Complete Genome Sequence of Nitrosospira multiformis, an Ammonia-Oxidizing Bacterium from the Soil Environment

ABSTRACT The complete genome of the ammonia-oxidizing bacterium Nitrosospira multiformis (ATCC 25196T) consists of a circular chromosome and three small plasmids totaling 3,234,309 bp and encoding 2,827 putative proteins. Of the 2,827 putative proteins, 2,026 proteins have predicted functions and 801 are without conserved functional domains, yet 747 of these have similarity to other predicted proteins in databases. Gene homologs from Nitrosomonas europaea and Nitrosomonas eutropha were the best match for 42% of the predicted genes in N. multiformis. The N. multiformis genome contains three nearly identical copies of amo and hao gene clusters as large repeats. The features of N. multiformis that distinguish it from N. europaea include the presence of gene clusters encoding urease and hydrogenase, a ribulose-bisphosphate carboxylase/oxygenase-encoding operon of distinctive structure and phylogeny, and a relatively small complement of genes related to Fe acquisition. Systems for synthesis of a pyoverdine-like siderophore and for acyl-homoserine lactone were unique to N. multiformis among the sequenced genomes of ammonia-oxidizing bacteria. Gene clusters encoding proteins associated with outer membrane and cell envelope functions, including transporters, porins, exopolysaccharide synthesis, capsule formation, and protein sorting/export, were abundant. Numerous sensory transduction and response regulator gene systems directed toward sensing of the extracellular environment are described. Gene clusters for glycogen, polyphosphate, and cyanophycin storage and utilization were identified, providing mechanisms for meeting energy requirements under substrate-limited conditions. The genome of N. multiformis encodes the core pathways for chemolithoautotrophy along with adaptations for surface growth and survival in soil environments.
Impaired familiarity with preserved recollection after anterior temporal-lobe resection that spares the hippocampus

It is well established that the medial-temporal lobe (MTL) is critical for recognition memory. The MTL is known to be composed of distinct structures that are organized in a hierarchical manner. At present, it remains controversial whether lower structures in this hierarchy, such as perirhinal cortex, support memory functions that are distinct from those of higher structures, in particular the hippocampus. Perirhinal cortex has been proposed to play a specific role in the assessment of familiarity during recognition, which can be distinguished from the selective contributions of the hippocampus to the recollection of episodic detail. Some researchers have argued, however, that the distinction between familiarity and recollection cannot capture functional specialization within the MTL and have proposed single-process accounts. Evidence supporting the dual-process view comes from demonstrations that selective hippocampal damage can produce isolated recollection impairments. It is unclear, however, whether temporal-lobe lesions that spare the hippocampus can produce selective familiarity impairments. Without this demonstration, single-process accounts cannot be ruled out. We examined recognition memory in NB, an individual who underwent surgical resection of left anterior temporal-lobe structures for treatment of intractable epilepsy. Her resection included a large portion of perirhinal cortex but spared the hippocampus. The results of four experiments based on three different experimental procedures (remember-know paradigm, receiver operating characteristics, and response-deadline procedure) indicate that NB exhibits impaired familiarity with preserved recollection. The present findings thus provide a crucial missing piece of support for functional specialization in the MTL.
Double-blind study of the safety of clopidogrel with and without a loading dose in combination with aspirin compared with ticlopidine in combination with aspirin after coronary stenting : the clopidogrel aspirin stent international cooperative study (CLASSICS).

BACKGROUND Combination therapy with the ADP receptor antagonist ticlopidine plus aspirin has emerged as standard care after coronary stenting. Clopidogrel, a new ADP receptor antagonist, has greater molar potency than ticlopidine and better safety/tolerability. METHODS AND RESULTS Patients (n=1020) were randomized after successful stent placement and initiated on a 28-day regimen of either (1) 300-mg clopidogrel loading dose and 325 mg/d aspirin on day 1, followed by 75 mg/d clopidogrel and 325 mg/d aspirin; (2) 75 mg/d clopidogrel and 325 mg/d aspirin; or (3) 250 mg BID ticlopidine and 325 mg/d aspirin. The primary end point consisted of major peripheral or bleeding complications, neutropenia, thrombocytopenia, or early discontinuation of study drug as the result of a noncardiac adverse event during the study-drug treatment period. The primary end point occurred in 9.1% of patients (n=31) in the ticlopidine group and 4.6% of patients (n=31) in the combined clopidogrel group (relative risk 0.50; 95% CI 0.31 to 0.81; P=0.005). Overall rates of major adverse cardiac events (cardiac death, myocardial infarction, target lesion revascularization) were low and comparable between treatment groups (0.9% with ticlopidine, 1.5% with 75 mg/d clopidogrel, 1.2% with the clopidogrel loading dose; P=NS for all comparisons). CONCLUSIONS The safety/tolerability of clopidogrel (plus aspirin) is superior to that of ticlopidine (plus aspirin) (P=0.005). The 300-mg loading dose was well tolerated, notably with no increased risk of bleeding. Secondary end point data are consistent with the hypothesis that clopidogrel and ticlopidine have comparable efficacy with regard to cardiac events after successful stenting.
Exploiting Dynamic Timing Slack for Energy Efficiency in Ultra-Low-Power Embedded Systems

Many emerging applications such as the internet of things, wearables, and sensor networks have ultra-low-power requirements. At the same time, cost and programmability considerations dictate that many of these applications will be powered by general purpose embedded microprocessors and microcontrollers, not ASICs. In this paper, we exploit a new opportunity for improving energy efficiency in ultralow-power processors expected to drive these applications -- dynamic timing slack. Dynamic timing slack exists when an embedded software application executed on a processor does not exercise the processor's static critical paths. In such scenarios, the longest path exercised by the application has additional timing slack which can be exploited for power savings at no performance cost by scaling down the processor's voltage at the same frequency until the longest exercised paths just meet timing constraints. Paths that cannot be exercised by an application can safely be allowed to violate timing constraints. We show that dynamic timing slack exists for many ultra-low-power applications and that exploiting dynamic timing slack can result in significant power savings for any ultra-low-power processors. We also present an automated methodology for identifying dynamic timing slack and selecting a safe operating point for a processor and a particular embedded software. Our approach for identifying and exploiting dynamic timing slack is non-speculative, requires no programmer intervention and little or no hardware support, and demonstrates potential power savings of up to 32%, 25% on average, over a range of embedded applications running on a common ultra-low-power processor, at no performance cost.
Using spatial embeddedness and physical embodiment for computation in multi-robot systems

This thesis contributes to the understanding of computational capabilities of multi-robot systems by viewing them as devices in which mechanical and electronic components jointly perform computation. We show that a multi-robot system can use physical embodiment and spatial embeddedness as computational resources for two types of problems: (i) a continuous optimization problem of achieving optimal joint robot team configuration, and (ii) a combinatorial problem of sorting robots. In the continuous problem domain we describe a general approach for developing decentralized distributed gradient descent optimization algorithms for teams of embodied agents that need to rearrange their configuration over space and time to approach some optimal and initially unknown configuration. We provide examples of the application of this general method by solving two non-trivial problems of multi-robot coordination: energy-efficient single point and multiple point rendezvous. In the combinatorial problem domain we demonstrate a multi-robot system controller that sorts a team of robots by means of its continuous movement dynamics. Between-robot rank comparisons suggested by traditional discrete state sorting algorithms are avoided by coupling neighbors in the order in a Brockett double bracket flow system.
Microbiological Profile of Organisms Causing Bloodstream Infection in Critically Ill Patients

Background Bloodstream infection (BSI) is the most frequent infection in critically ill patients. As BSI’s among patients in intensive care units (ICU’s) are usually secondary to intravascular catheters, they can be caused by both Gram-positive and Gram-negative microorganisms as well as fungi. Infection with multidrug-resistant (MDR) organisms is becoming more common, making the choice of empirical antimicrobial therapy challenging. The objective of this study is to evaluate the spectrum of microorganisms causing BSI’s in a Medical-Surgical Intensive Care Unit (MSICU) and their antimicrobial resistance patterns. Methods A prospective observational study among all adult patients with clinical signs of sepsis was conducted in a MSICU of an inner-city hospital in New York City between May 1, 2010 and May 30, 2011. Results A total of 722 adult patients with clinical signs of systemic inflammatory response syndrome (SIRS) and/or sepsis were admitted to the MSICU between May 1, 2010 and May 30, 2011. From those patients, 91 (12.6%) had one or more positive blood culture. A 122 isolates were identified: 72 (59%) were Gram-positive bacteria, 38 (31.1%) were Gram-negative organisms, and 12 (9.8%) were fungi. Thirteen (34.2%) Gram-negative organisms and 14 (19.4%) Gram-positive bacteria were classified as MDR. Conclusions Antimicrobial resistance, particularly among Gram-negative organisms, continues to increase at a rapid rate, especially in the ICU’s. Coordinated infection control interventions and antimicrobial stewardship policies are warranted in order to slow the emergence of resistance.
Influence of Atmospheric Path Delay on the Absolute Geolocation Accuracy of TerraSAR-X High-Resolution Products

Two coupled investigations of TerraSAR-X (TSX) high-resolution data are described in this paper: geometric validation, and estimation of the tropospheric path delay using measurements of corner reflectors (CRs) placed at different altitudes but nearly identical ranges. The CRs were placed within Alpine and valley sites in Switzerland, where terrain diversity provides ideal territory for geometric validation studies. Geometric validation was conducted using slant-range complex products from the spotlight and stripmap (SM) modes in ascending and descending configurations. Based on the delivered product annotations, the CR image positions were predicted, and these predictions were compared to their measured image positions. To isolate path delays caused by the atmosphere, six TSX SM scenes ( ~ 35 x 50 km) were examined containing four identical CRs with the same ranges and an altitude difference of ~ 3000 m. The CR arrangement made it possible to verify the annotated TSX atmospheric path delay by comparing the predicted slant range with the slant range obtained by measuring the reflector image coordinates. Range differences between the high- and low-altitude reflectors helped to quantify small variations in the path delay. Both SM and spotlight TSX products were verified to meet the specified accuracy requirements, even for scenes with extreme terrain variations, in spite of the simplicity of the atmospheric model currently integrated into the processor. Small potential improvements of the geolocation accuracy through the implementation of more comprehensive atmospheric modeling were demonstrated.