Miracle-dz/UniFAR-FTUs huggingface dataset:
An adaptable but threatened big cat: density, diet and prey selection of the Indochinese leopard (Panthera pardus delacouri) in eastern Cambodia

We studied the Indochinese leopard (Panthera pardus delacouri) in eastern Cambodia, in one of the few potentially remaining viable populations in Southeast Asia. The aims were to determine the: (i) current leopard density in Srepok Wildlife Sanctuary (SWS) and (ii) diet, prey selection and predation impact of leopard in SWS. The density, estimated using spatially explicit capture–recapture models, was 1.0 leopard/100 km2, 72% lower than an estimate from 2009 at the same site, and one of the lowest densities ever reported in Asia. Dietary analysis of 73 DNA confirmed scats showed leopard consumed 13 prey species, although ungulates comprised 87% of the biomass consumed (BC). The overall main prey (42% BC) was banteng (Bos javanicus), making this the only known leopard population whose main prey had adult weight greater than 500 kg. Consumption of wild pig (Sus scrofa) was also one of the highest ever reported (22% BC), indicating leopard consistently predated on ungulates with some of the largest adult weights in SWS. There were important differences in diet and prey selection between sexes, as males consumed mostly banteng (62% BC) in proportion to availability, but few muntjac (Muntiacus vaginalis; 7% BC), whereas females selectively consumed muntjac (56% BC) and avoided banteng (less than 1% BC). Predation impact was low (0.5–3.2% of populations) for the three ungulate species consumed. We conclude that the Indochinese leopard is an important apex predator in SWS, but this unique population is declining at an alarming rate and will soon be eradicated unless effective protection is provided.
HYSYS: have you swapped your samples?

Motivation: The application of a genomics assay to samples from a cohort is a frequently applied experimental design in cancer genomics studies. The collection and analysis of cancer sequencing data in the clinical setting is an elaborate process that may involve consenting patients, obtaining possibly‐multiple DNA samples, sequencing and analysis. Many of these steps are manual. At any stage mistakes can occur that cause a DNA sample to be labelled incorrectly. However, there is a paucity of methods in the literature to identify such swaps specifically in cancer studies. Results: Here, we introduce a simple method, HYSYS, to estimate the relatedness of samples and test for sample swaps and contamination. The test uses the concordance of homozygous SNPs between samples. The method is motivated by the observation that homozygous germline population variants rarely change in the disease and are not affected by loss of heterozygosity. Our tools include visualization and a testing framework to flag possible sample swaps. We demonstrate the utility of this approach on a small cohort. Availability and Implementation: http://github.com/PapenfussLab/HaveYouSwappedYourSamples Contact: papenfuss@wehi.edu. au Supplementary information: Supplementary data are available at Bioinformatics online.
PORBS: A parallel observation-based slicer

This paper presents PORBS, a parallelised observation-based slicing tool. The tool itself is written in Java making it platform independent and leverages the build chain of the system being sliced to avoid the need to replicate complex compiler analysis. The target audience of PORBS is software engineers and researchers working with and on tools and techniques for software comprehension, debugging, re-engineering, and maintenance.
Data-Driven Analysis of Virtual 3D Exploration of a Large Sculpture Collection in Real-World Museum Exhibitions

We analyze use of an interactive system for the exploration of highly detailed three-dimensional (3D) models of a collection of protostoric Mediterranean sculptures. In this system, when the object of interest is selected, its detailed 3D model and associated information are presented at high resolution on a large display controlled by a touch-enabled horizontal surface at a suitable distance. The user interface combines an object-aware interactive camera controller with an interactive point-of-interest selector and is implemented within a scalable implementation based on multiresolution structures shared between the rendering and user interaction subsystems. The system was installed in several temporary and permanent exhibitions and was extensively used by tens of thousands of visitors. We provide a data-driven analysis of usage experience based on logs gathered during a 27-month period at four exhibitions in archeological museums for a total of more than 75K exploration sessions. We focus on discerning the main visitor behaviors during 3D exploration by employing tools for deriving interest measures on surfaces and tools for clustering and knowledge discovery from high-dimensional data. The results highlight the main trends in visitor behavior during the interactive sessions. These results provide useful insights for the design of 3D exploration user interfaces in future digital installations.
Regulation of the Hypothalamic-Pituitary-Adrenal Axis Circadian Rhythm by Endocannabinoids Is Sexually Diergic

We have examined the effects of acute administration of the cannabinoid receptor type 1 (CB1) antagonist AM251 on the rat hypothalamic-pituitary-adrenal (HPA) axis with respect to both gender and time of day. Blood samples were collected from conscious male and female rats every 5 min using an automated blood sampling system, and corticosterone concentrations were determined. In male rats, there was a distinct diurnal effect of AM251 with a greater activation of the HPA axis in the morning (diurnal trough) compared with the evening (diurnal peak). At both times of the day, circulating corticosterone concentrations were elevated for approximately 4 h after AM251 administration. In female rats, there was also diurnal variation in the activation of the HPA axis; however, these effects were not as profound as those in males. Corticosterone concentrations were only slightly elevated at the diurnal trough and for a shorter time period than in males (2 compared with 4 h). Moreover, there was no effect of AM251 on corticosterone concentrations when administered at the diurnal peak. Subsequent studies, only in males, in which both ACTH and corticosterone were measured, confirmed that the effects of AM251 on corticosterone were mediated by ACTH. Moreover, the elevation of both ACTH and corticosterone could be replicated using another CB1 antagonist, AM281. These data demonstrate that the extent and duration of HPA axis activation after CB1 blockade are clearly dependent on both gender and time of day.
Asynchronous Stochastic Gradient Descent with Delay Compensation

With the fast development of deep learning, it has become common to learn big neural networks using massive training data. Asynchronous Stochastic Gradient Descent (ASGD) is widely adopted to fulfill this task for its efficiency, which is, however, known to suffer from the problem of delayed gradients. That is, when a local worker adds its gradient to the global model, the global model may have been updated by other workers and this gradient becomes "delayed". We propose a novel technology to compensate this delay, so as to make the optimization behavior of ASGD closer to that of sequential SGD. This is achieved by leveraging Taylor expansion of the gradient function and efficient approximation to the Hessian matrix of the loss function. We call the new algorithm Delay Compensated ASGD (DC-ASGD). We evaluated the proposed algorithm on CIFAR-10 and ImageNet datasets, and the experimental results demonstrate that DC-ASGD outperforms both synchronous SGD and asynchronous SGD, and nearly approaches the performance of sequential SGD.
Uncertainty in multispectral lidar signals caused by incidence angle effects

Multispectral terrestrial laser scanning (TLS) is an emerging technology. Several manufacturers already offer commercial dual or three wavelength airborne laser scanners, while multispectral TLS is still carried out mainly with research instruments. Many of these research efforts have focused on the study of vegetation. The aim of this paper is to study the uncertainty of the measurement of spectral indices of vegetation with multispectral lidar. Using two spectral indices as examples, we find that the uncertainty is due to systematic errors caused by the wavelength dependency of laser incidence angle effects. This finding is empirical, and the error cannot be removed by modelling or instrument modification. The discovery and study of these effects has been enabled by hyperspectral and multispectral TLS, and it has become a subject of active research within the past few years. We summarize the most recent studies on multi-wavelength incidence angle effects and present new results on the effect of specular reflection from the leaf surface, and the surface structure, which have been suggested to play a key role. We also discuss the consequences to the measurement of spectral indices with multispectral TLS, and a possible correction scheme using a synthetic laser footprint.
Pomosynthesis and biological activity of silver nanoparticles using Passiflora tripartita fruit extracts

Silver nanoparticles (AgNPs) have been synthesized via the green pomosynthetic procedure, using Passiflora tripartita var. mollissima fruit pigments as both the reducing and stabilizing agents. UV-Vis Spectroscopy, Dynamic Light Scattering, Transmission Electron Microscopy with Selected Area Electron Diffraction and Powder X-Ray Diffraction are used to completely characterize the AgNPs. The prepared AgNPs are found to be mostly spherical shapes with an average diameter of 49.7 ± 24.6 nm at room temperature. XRD analysis revealed the face-centered cubic geometry of AgNPs whereas Infrared spectrum and cyclic voltammetry measurements hypothesize the possible biomolecules (flavonoid C & O-glycosides) responsible for stabilization of the AgNPs. Synthesized AgNPs shows significant antioxidant efficacy (67%, 0.15 mM) against 1, 1-diphenyl-2- picrylhydrazyl. The AgNPs (0.01 - 20 μM) did not affect cell proliferation of the human cancer cell lines A - 549 and HeLa, from lung and cervix, respectively. The use of environmentally benign, cost-effective and renewable materials like P. tripartita extract offers numerous benefits of eco-friendliness and compatibility for potential future pharmaceutical and biomedical applications. Copyright © 2015 VBRI press.
Automated cardiac event change detection for continuous remote patient monitoring devices

Recently, wireless body area network (WBAN) plays an important role in remote cardiac patient monitoring, and mobile healthcare applications. Generally, the use of WBAN technology is restricted by size, power consumption, transmission capacity (bandwidth), and computational loads. In this paper, we therefore propose an automated cardiac event change detection for continuous remote patient monitoring devices. The proposed event change detection algorithm consists of two stages: i) ECG beat extraction; and ii) ECG beat similarity measure. In the first stage, the onset of each QRS complex is identified using the Gaussian derivative based QRS detector and the two heuristics rules. In the second stage, we employ the weighted wavelet distance (WWD) metric for finding the similarity between two ECG beats in wavelet domain. The WWD is the weighted normalized Euclidean wavelet distance between the wavelet subband coefficients vectors of the current and past ECG beats, where weights are equal to the relative wavelet subband energies of the corresponding subbands. The experimental results show that the weighted wavelet distance measure works substantially better than the conventional PRD and the wavelet based weighted PRD (WWPRD) measures under noisy environments. The proposed approach has been tested and yielded an accuracy of 99.76% on MIT-BIH Arrhythmia Database.
Time lapse in vivo microscopy reveals distinct dynamics of microglia‐tumor environment interactions—a new role for the tumor perivascular space as highway for trafficking microglia

Microglial cells are critical for glioma growth and progression. However, only little is known about intratumoral microglial behavior and the dynamic interaction with the tumor. Currently the scarce understanding of microglial appearance in malignant gliomas merely originates from histological studies and in vitro investigations. In order to understand the pattern of microglia activity, motility and migration we designed an intravital study in an orthotopic murine glioma model using CX3CR1‐eGFPGFP/wt mice. We analysed the dynamics of intratumoral microglia accumulation and activity, as well as microglia/tumor blood vessel interaction by epi‐illumination and 2‐photon laser scanning microscopy. We further investigated cellular and tissue function, including the enzyme activity of intratumoral and microglial NADPH oxidase measured by in vivo fluorescence lifetime imaging. We identified three morphological phenotypes of tumor‐associated microglia cells with entirely different motility patterns. We found that NADPH oxidase activation is highly divergent in these microglia subtypes leading to different production levels of reactive oxygen species (ROS). We observed that microglia motility is highest within the perivascular niche, suggesting relevance of microglia/tumor blood vessel interactions. In line, reduction of tumor blood vessels by antivascular therapy confirmed the relevance of the tumor vessel compartment on microglia biology in brain tumors. In summary, we provide new insights into in vivo microglial behavior, regarding both morphology and function, in malignant gliomas. GLIA 2016;64:1210–1226
Frequency‐dependent resemblance of male‐colored females to males in a damselfly

Dear editor, Mimetic protection is most effective when mimics are relatively rare (Pfennig et al., 2001). In polymorphic damselfly species, male-colored female morphs may avoid costly male mating attempts because they are not immediately recognized as a suitable mating partner (van Gossum et al., 2008). We investigated morphological resemblance of male-colored females to males across six populations of the polymorphic blue-tailed damselfly Ischnura elegans (Vander Linden). We found that male-colored females resembled males more closely with an increasing ratio of male-colored females to other female morphs. Our results suggest that the degree of mimetic fidelity is frequencydependent. Genetically determined color polymorphisms have evolved throughout the tree of life and studying them helps in understanding the selective forces that affect the maintenance of genetic diversity (Gray & McKinnon, 2007). In some species, color polymorphism is limited to one sex. Such sex-limited color polymorphisms has probably evolved in response to sex-specific predation, sexual competition, or sexual conflict (Stamps & Gon III, 1983; Gross, 1996; Svensson et al., 2009). In I. elegans, mature males occur in one color (blue) and mature females occur in three genetically controlled color morphs (Sánchez-Guillén et al., 2005): infuscans (olive green), rufescens-obsoleta (brown-red) and androchrome (“male-colored”: blue or green-blue). In this species, females suffer from excessive male mating harassment, which is costly in terms of female fitness (Gosden & Svensson, 2009). Female morph frequencies differ greatly between populations (Cordero-Rivera & Sánchez-Guillén, 2007) and frequency-dependent male
NovaCube: A low latency Torus-based network architecture for data centers

This paper presents the design, analysis, and implementation of a novel data center network architecture, named NovaCube. Based on regular Torus topology, NovaCube is constructed by adding a number of most beneficial jump-over links, which offers many distinct advantages and practical benefits. Moreover, in order to enable NovaCube to achieve its maximum theoretical performance, a probabilistic oblivious routing algorithm PORA is carefully designed. PORA is a both deadlock and livelock free routing algorithm, which achieves near-optimal performance in terms of average routing path length with better load balancing thus leading to higher throughput. Theoretical derivation and mathematical analysis further prove the good performance of NovaCube and PORA.
Unraveling an old cloak: k-anonymity for location privacy

There is a rich collection of literature that aims at protecting the privacy of users querying location-based services. One of the most popular location privacy techniques consists in cloaking users' locations such that k users appear as potential senders of a query, thus achieving k-anonymity. This paper analyzes the effectiveness of k-anonymity approaches for protecting location privacy in the presence of various types of adversaries. The unraveling of the scheme unfolds the inconsistency between its components, mainly the cloaking mechanism and the k-anonymity metric. We show that constructing cloaking regions based on the users' locations does not reliably relate to location privacy, and argue that this technique may even be detrimental to users' location privacy. The uncovered flaws imply that existing k-anonymity scheme is a tattered cloak for protecting location privacy.
Decentralized Robust Dynamic State Estimation in Power Systems Using Instrument Transformers

This paper proposes a decentralized method for estimation of dynamic states of a power system. The method remains robust to time-synchronization errors and high noise levels in measurements. Robustness of the method has been achieved by incorporating internal angle in the dynamic model used for estimation and by decoupling the estimation process into two stages with continuous updation of measurement-noise variances. Additionally, the proposed estimation method does not need measurements obtained from phasor measurement units; instead, it just requires analog measurements of voltages and currents directly acquired from instrument transformers. This is achieved through statistical signal processing of analog voltages and currents to obtain their magnitudes and frequencies, followed by application of unscented Kalman filtering for nonlinear estimation. The robustness and feasibility of the method have been demonstrated on a benchmark power system model.
The Future for Solid Propellant Rockets

Ten years ago it seemed that the solid propellant rocket engine could make only a limited contribution to rocketry. Although it was simpler and more compact than its liquid propellant rival it suffered from three serious drawbacks. The nozzle was uncooled and so the burning time had to be short, the entire propellant container was subjected to the full combustion pressure and temperature and therefore the inert weight of the engine was high and, since the specific impulse of solid propellants is in general lower than that of liquid propellants (because solids are partially reacted systems) the engine performance was consequently poor, and finally, no means were available for controlling the magnitude and duration of the rocket thrust. These facts were the foundation of the opinion, still held by some people, that solid propellant engines were only suitable as boosters or short burning time sustainers for small missiles.
Epithelial cells supply Sonic Hedgehog to the perinatal dentate gyrus via transport by platelets

Dentate neural stem cells produce neurons throughout life in mammals. Sonic hedgehog (Shh) is critical for maintenance of these cells; however, the perinatal source of Shh is enigmatic. In the present study, we examined the role of Shh expressed by hair follicles (HFs) that expand perinatally in temporal concordance with the proliferation of Shh-responding dentate stem cells. Specific inhibition of Shh from HFs or from epithelial sources in general hindered development of Shh-responding dentate stem cells. We also found that the blood–brain barrier (BBB) of the perinatal dentate gyrus (DG) is leaky with stem cells in the dentate exposed to blood-born factors. In attempting to identify how Shh might be transported in blood, we found that platelets contain epithelial Shh, provide Shh to the perinatal DG and that inhibition of platelet generation reduced hedgehog-responsive dentate stem cells. DOI: http://dx.doi. org/10.7554/eLife.07834. 001
ASAP: Accelerated Short-Read Alignment on Programmable Hardware

The proliferation of high-throughput sequencing machines ensures rapid generation of up to billions of short nucleotide fragments in a short period of time. This massive amount of sequence data can quickly overwhelm today's storage and compute infrastructure. This paper explores the use of hardware acceleration to significantly improve the runtime of short-read alignment, a crucial step in preprocessing sequenced genomes. We focus on the Levenshtein distance (edit-distance) computation kernel and propose the ASAP accelerator, which utilizes the intrinsic delay of circuits for edit-distance computation elements as a proxy for computation. Our design is implemented on an Xilinx Virtex 7 FPGA in an IBM POWER8 system that uses the CAPI interface for cache coherence across the CPU and FPGA. Our design is $200\times$ faster than an equivalent Smith-Waterman-C implementation of the kernel running on the host processor, $40-60\times$ faster than an equivalent Landau-Vishkin-C++ implementation of the kernel running on the IBM Power8 host processor, and $2\times$ faster for an end-to-end alignment tool for 120–150 base-pair short-read sequences. Further the design represents a $3760\times$ improvement over the CPU in performance/Watt terms.
Biomarkers are used to predict quantitative metabolite concentration profiles in human red blood cells

Deep-coverage metabolomic profiling has revealed a well-defined development of metabolic decay in human red blood cells (RBCs) under cold storage conditions. A set of extracellular biomarkers has been recently identified that reliably defines the qualitative state of the metabolic network throughout this metabolic decay process. Here, we extend the utility of these biomarkers by using them to quantitatively predict the concentrations of other metabolites in the red blood cell. We are able to accurately predict the concentration profile of 84 of the 91 (92%) measured metabolites (p < 0.05) in RBC metabolism using only measurements of these five biomarkers. The median of prediction errors (symmetric mean absolute percent error) across all metabolites was 13%. The ability to predict numerous metabolite concentrations from a simple set of biomarkers offers the potential for the development of a powerful workflow that could be used to evaluate the metabolic state of a biological system using a minimal set of measurements.
Linked color imaging identified ulcerative colitis‐associated colorectal cancer: A case report

Ulcerative colitis (UC)-associated colorectal cancer (CRC) is an important problem in long-term management of patients with UC. Lesions with background chronic inflammatory mucosa may often be difficult to identify even by endoscopic observation. Traditionally, a random biopsy strategy was recommended, but problems with patient compliance, increased burden on endoscopic staff and pathologists remained. The effectiveness of target biopsy has been reported in recent years. Currently, the most recommended method is chromoendoscopy by indigocarmine spraying. Although it has not been established, effectiveness of observation by narrow band imaging and magnified endoscopy has also been investigated. For target biopsy regimen, how to elevate the lesion is the most important task. Linked color imaging (LCI) has recently been developed using a laser endoscopic system (Fujifilm Co., Tokyo, Japan) to provide an expanded color range, resulting in more emphasized color difference between red and white. Here we report a case with successfully identified UC-associated CRC using LCI (EC-L600ZP; Fujifilm Co.) for the first time. A 53-year-old man with a 6-year history of UC developed UC-associated CRC in the rectum. LCI could