Miracle-dz/UniFAR-FTUs huggingface dataset:
Natural Experiment Demonstrates That Bird Loss Leads to Cessation of Dispersal of Native Seeds from Intact to Degraded Forests

In healthy forests, vertebrate frugivores move seeds from intact to degraded forests, aiding in the passive regeneration of degraded forests. Yet vertebrate frugivores are declining around the world, and little is known about the impact of this loss on regeneration of degraded areas. Here, we use a unique natural experiment to assess how complete vertebrate frugivore loss affects native seed rain in degraded forest. All native vertebrate frugivores (which were primarily avian frugivores) have been functionally extirpated from the island of Guam by the invasive brown tree snake (Boiga irregularis), whereas the nearby island of Saipan has a relatively intact vertebrate frugivore community. We captured seed rain along transects extending from intact into degraded forest and compared the species richness, density and condition of the seed rain from native bird-dispersed tree species between the two islands. Considering seeds from native bird-dispersed species, approximately 1.66 seeds landed per 26 days in each square meter of degraded forest on Saipan, whereas zero seeds landed per 26 days per square meter in degraded forest on Guam. Additionally, on Saipan, 69% of native bird-dispersed seeds in intact forest and 77% of seeds in degraded forest lacked fleshy fruit pulp, suggesting ingestion by birds, compared to 0% of all seeds on Guam. Our results show an absence of seed rain in degraded forests on Guam, correlated with the absence of birds, whereas on Saipan, frugivorous birds regularly disperse seeds into degraded forests, providing a mechanism for re-colonization by native plants. These results suggest that loss of frugivores will slow regeneration of degraded forests on Guam.
Macroscopic morphologic subtypes of laterally spreading colorectal tumors showing distinct molecular alterations

Recent advances in colonoscopic techniques have resulted in more frequent detection of superficial‐type colorectal tumors, that is, laterally spreading tumors (LSTs), although little is known about the characteristic clinical features and genetic alterations of LSTs. To elucidate the molecular characteristics of LSTs, genetic alterations in the KRAS, BRAF and PIK3CA genes and abnormal expression of the p53, β‐catenin and MYC proteins were analyzed using direct DNA sequencing and immunohistochemistry for 50 protruded‐type tumors (Protruded), 35 granular‐type LSTs (LST‐G) and 19 nongranular‐type LSTs (LST‐NG). In addition, loss of heterozygosity (LOH) close to the adenomatous polyposis coli (APC) gene (5q21) was examined in these tumors. In univariate analyses, significant differences were noted in the percentages with KRAS mutations (Protruded, LST‐G, LST‐NG = 30.0%, 54.3%, 21.1%, respectively, p = 0.0156), nuclear accumulation of β‐catenin (Protruded, LST‐G, LST‐NG = 50.0%, 37.1%, 68.4%, respectively, p = 0.0267), expression of MYC (Protruded, LST‐G, LST‐NG = 26.0%, 17.1%, 42.1%, respectively, p = 0.0456) and LOH at the APC gene locus (Protruded, LST‐G, LST‐NG = 22.0%, 20.0%, 47.4%, respectively, p = 0.0302). Multivariate analysis demonstrated that the macroscopic subtype of LST was significantly associated with KRAS mutation (for LST‐NG: odds ratio [OR] 0.23, 95% CI 0.06–0.90) and nuclear accumulation of β‐catenin (for LST‐NG: OR 4.05, 95% CI 1.11–14.8). Our data revealed that the 2 subtypes of LST have different molecular characteristics, suggesting that 2 or more different molecular mechanisms result in colorectal tumors with a similar growth pattern.
Cell Surface Localization of Heparanase on Macrophages Regulates Degradation of Extracellular Matrix Heparan Sulfate1

Extravasation of peripheral blood monocytes through vascular basement membranes requires degradation of extracellular matrix components including heparan sulfate proteoglycans (HSPGs). Heparanase, the heparan sulfate-specific endo-β-glucuronidase, has previously been shown to be a key enzyme in melanoma invasion, yet its involvement in monocyte extravasation has not been elucidated. We examined a potential regulatory mechanism of heparanase in HSPG degradation and transmigration through basement membranes in leukocyte trafficking using human promonocytic leukemia U937 and THP-1 cells. PMA-treated cells were shown to degrade 35S-sulfated HSPG in endothelial extracellular matrix into fragments of an approximate molecular mass of 5 kDa. This was not found with untreated cells. The gene expression levels of heparanase or the enzyme activity of the amount of cell lysates were no different between untreated and treated cells. Immunocytochemical staining with anti-heparanase mAb revealed pericellular distribution of heparanase in PMA-treated cells but not in untreated cells. Cell surface heparanase capped into a restricted area on PMA-treated cells when they were allowed to adhere. Addition of a chemoattractant fMLP induced polarization of the PMA-treated cells and heparanase redistribution at the leading edge of migration. Therefore a major regulatory process of heparanase activity in the cells seems to be surface expression and capping of the enzyme. Addition of the anti-heparanase Ab significantly inhibited enzymatic activity and transmigration of the PMA-treated cells, suggesting that the cell surface redistribution of heparanase is involved in monocyte extravasation through basement membranes.
Secure Tracking in Sensor Networks

Target tracking is a canonical issue in sensor networks research. However, tracking security has gained little or no attention. Once a sensor node is compromised, it will be able to inject false location information into the network, and those nodes receiving such information will suffer greatly in terms of tracking precision. This paper, to the best of our knowledge, is the first to explore the topic of security in the context of Bayesian tracking for sensor networks. We propose to activate more than one nodes at each time step, and use a relaxation labeling algorithm to detect malicious nodes whose reports are then removed. Simulations based on both linear and nonlinear motion models demonstrate that out algorithm works better than simply averaging over the results based on the redundant sets of nodes.
Small network completion using frequent subnetworks

Prediction of missing or potential links and edges is currently the central theme in network analysis. Most of the work is focused on large unlabelled networks, with techniques based on global network models and, on a local level, on using patterns of temporal evolution. We define a problem of small network completion, which deals with sets of small networks, possibly with no recorded temporal dynamics. This problem requires a different set of methods and evaluation procedures. We present a method named Hyspan that extracts frequent patterns from small networks and uses them to predict missing vertices and edges in new networks. It ranks the predicted vertices and edges according to their likelihood estimated from the number and support of the patterns that suggest a particular missing part. Empirical evaluation on real and synthetic data sets shows that the method performs reasonably well. The quality of results depends upon the number and size of the used patterns; a larger number of patterns yields better results but requires longer – although still acceptable – running times.
Design of an ultra-low power SAR ADC for biomedical applications

In this paper, an ultra-low power 12-bit 2kS/s successive approximation register (SAR) analog-to-digital converter (ADC) is presented. For power optimization, the voltage supply of the digital part is lowered, and the offset voltage of the latch is self-calibrated. Targeted for lower noise, a low kick-back noise latch is proposed. The chip was fabricated using 0. 18µm 1P6M CMOS technology. The ADC achieves SNDR of 61.8dB and dissipates only 455nW, resulting in a figure of merit (FOM) of 220fJ/conversion-step. The ADC core occupies an active area of 674×639µm2.
Effect of Vitamin K2 on Cortical and Cancellous Bones in Orchidectomized and/or Sciatic Neurectomized Rats

We examined the effect of vitamin K2 on cortical and cancellous bones in orchidectomized and/or sciatic neurectomized rats. Ninety male Sprague‐Dawley rats, 3 months of age, were randomized by stratified weight method into nine groups with 10 rats in each group: baseline control (BLC), age‐matched intact control (IN), IN+vitamin K2 administration (K), orchidectomy (ORX), ORX+K, unilateral sciatic neurectomy (NX), NX+K, ORX+NX (ONX), and ONX+K. Vitamin K2 (menatetrenone) was administered orally twice a week at a dose of 30 mg/kg each. After 10 weeks of feeding, the tibial shaft and proximal tibia were processed for cortical and cancellous bone histomorphometric analyses, respectively. An ORX‐induced reduction in maturation‐related cortical bone gain and ORX‐induced cancellous bone loss were attributable to increased endocortical and trabecular bone turnover, respectively. NX‐ and ONX‐induced reductions in maturation‐related cortical bone gain were attributable to decreased periosteal bone formation and increased endocortical bone turnover, while NX‐ and ONX‐induced cancellous bone loss was attributable to increased bone resorption and decreased bone formation. ORX‐induced cancellous bone loss was more pronounced when combined with immobilization. Vitamin K2 administration did not significantly alter any parameters in IN rats. Vitamin K2 administration in ORX rats suppressed endocortical bone resorption and trabecular bone turnover, retarding a reduction in maturation‐related cortical bone gain and cancellous bone loss. This effect on cancellous bone loss was primarily because of prevention of a reduction of trabecular thickness. Vitamin K2 administration in NX and ONX rats suppressed bone resorption and stimulated bone formation (mineralization), with retardation of a reduction of trabecular thickness without any significant effect on cancellous bone mass, and suppressed endocortical bone resorption, retarding a reduction in maturation‐related cortical bone gain. The present study provides evidence indicating that vitamin K2 has the potential to suppress bone resorption or bone turnover and/or stimulate bone formation in vivo in ORX and/or NX rats.
Tuning the Photocatalytic Activity of Anatase TiO2 Thin Films by Modifying the Preferred Grain Orientation with Reactive DC Magnetron Sputtering

Anatase TiO2 thin films were deposited by DC reactive magnetron sputtering on glass substrates at 20 mTorr pressure in a flow of an Ar and O2 gas mixture. The O2 partial pressure (PO2) was varied from 0.65 mTorr to 1.3 mTorr to obtain two sets of films with different stoichiometry. The structure and morphology of the films were characterized by secondary electron microscopy, atomic force microscopy, and grazing-angle X-ray diffraction complemented by Rietveld refinement. The as-deposited films were amorphous. Post-annealing in air for 1 h at 500 °C resulted in polycrystalline anatase film structures with mean grain size of 24.2 nm (PO2 = 0.65 mTorr) and 22.1 nm (PO2 = 1.3 mTorr), respectively. The films sputtered at higher O2 pressure showed a preferential orientation in the direction, which was associated with particle surfaces exposing highly reactive {001} facets. Films sputtered at lower O2 pressure exhibited no, or very little, preferential grain orientation, and were associated with random distribution of particles exposing mainly the thermodynamically favorable {101} surfaces. Photocatalytic degradation measurements using methylene blue dye showed that oriented films exhibited approximately 30% higher reactivity. The measured intensity dependence of the degradation rate revealed that the UV-independent rate constant was 64% higher for the oriented film compared to randomly oriented films. The reaction order was also found to be higher for films compared to randomly oriented films, suggesting that the oriented film exposes more reactive surface sites.
Private similarity searchable encryption for Euclidean distance

In this paper, we propose a similarity searchable encryption in the symmetric key setting for Euclidean distance, by extending the functional encryption scheme for inner product proposed by Bishop et al. [2]. Our scheme performs predeter­mined encoding independently of vectors x and y, and it obtains the Euclidean distance between the two vectors while they remain encrypted.
Legged Elastic Multibody Systems: Adjusting Limit Cycles to Close-to-Optimal Energy Efficiency

Compliant elements in robotic systems can strongly increase the energy efficiency of highly dynamic periodic motions with large energy consumption such as jumping. Their control is a challenging task for multijoint systems. Typical control algorithms are model-based and thus fail to adjust to unexpected mechanical environments or make limited use of mechanical resonance properties. Here, we apply numerical optimal control theory to demonstrate that close-to-optimal energy-efficient movements can be induced from a one-dimensional (1-D) submanifold in jumping systems that show nonlinear hybrid dynamics. Linear weights transform sensory information into this 1-D controller space and reverse transform 1-D motor signals back into the multidimensional joint space. In Monte-Carlo-based simulations and experiments, we show that an algorithm that we derived previously can extract these weights online from sensory information about joint positions of a moving system. The algorithm is computationally cheap, modular, and adjusts to varying mechanical conditions. Our results demonstrate that it reduces the problem of energy-efficient control of multiple compliant joints that move with high synchronicity to a low-dimensional task.
Connected Edge Ends for Object Recognition

In this paper we exploit edges in images to build features for object category recognition. We build a line based image approximation to identify the dominant edge structures and use SIFT descriptors to capture the object shape. Combinations of co-occurring features improve the recognition performance but suffer from complexity due to combinatorial problems. To represent more complex structures we combine descriptors connected by lines fitted to dominant edges. In this way we incorporate weak topological constraints into the representation which improve its discriminative
Cooperative caching with keep-me and evict-me

Cooperative caching seeks to improve memory system performance by using compiler locality hints to assist hardware cache decisions. In this paper, the compiler suggests cache lines to keep or evict in set-associative caches. A compiler analysis predicts data that will be and will not be reused, and annotates the corresponding memory operations with a keep-me or evict-me hint. The architecture maintains these hints on a cache line and only acts on them on a cache miss. Evict-me caching prefers to evict lines marked evict-me. Keep-me caching retains keep-me lines if possible. Otherwise, the default replacement algorithm evicts the least-recently-used (LRU) line in the set. This paper introduces the keep-me hint, the associated compiler analysis, and architectural support. The keep-me architecture includes very modest ISA support, replacement algorithms, and decay mechanisms that avoid retaining keep-me lines indefinitely. Our results are mixed for our implementation of keep-me, but show it has potential. We combine keep-me and evict-me from previous work, but find few additive benefits due to limitations in our compiler algorithm, which only applies each independently rather than performing a combined analysis.
An unsupervised head-dependency language model

Language models are an important component of speech recognition. They aim to predict the probability of any word sequence. Traditional n-gram language models consider only adjacent lexical dependencies and so ignore longer-spanning dependencies. One might capture these long-spanning dependencies by augmenting traditional models with head-dependency information. A head word is the critical element in a phrase. Dependents modify the head. Prior research has shown that head-dependency relationships acquired from an annotated corpus can improve n-gram models. We propose a probabilistic parser and language model which incorporate head-dependency relationships obtained from the unsupervised algorithm in [10]. Preliminary information theoretic measures suggest that a model which combines n-grams and unsupervised head-dependencies will outperform traditional n-gram models. We describe a probabilistic model. We discuss the algorithms and data structures necessary to implement the model efficiently in a chart parser. We also outline strategies for pruning and reestimation. Our results reveal that the automatically acquired head-dependency information yields a small improvement, through interpolation, over traditional models. A shift-reduce parser outperforms our new chart parser, but further research on pruning strategies for the chart parser needs to be done.
Microsatellite Instability and Expression of hMLH-1 and hMSH-2 in Sebaceous Gland Carcinomas as Markers for Muir-Torre Syndrome 1

Sebaceous gland carcinomas (SGCs) are rare malignant skin tumors occurring sporadically or as a phenotypic feature of the Muir-Torre syndrome (MTS). A subset of patients with MTS have a variant of the hereditary nonpolyposis colorectal cancer syndrome caused by mutations in mismatch repair (MMR) genes, which lead to microsatellite instability (MSI). We evaluated the value of MSI and loss of expression of the MMR genes, hMLH-1 and hMSH-2, as a marker to identify and distinguish MTS from sporadic SGC. Using a nationwide pathology report database system, we identified patients with the MTS phenotype. SGCs from 10 MTS patients and the colorectal carcinomas from 3 additional MTS patients were collected. In addition, SGCs from eight patients without a history of visceral neoplasm were collected. MSI was detected in 9 of 13 MTS-associated tumors (69%) versus 0 of 8 sporadic SGCs (P5 0.002). Except for the age of onset of colorectal carcinoma [58 years in the MSI-positive group versus 69.8 years in the MSInegative group (P5 0.17)], no differences were seen between the MSI-negative and the MSI-positive MTS patients. Loss of expression of hMLH-1 (n 5 4) or hMSH-2 (n 5 4) was found in MSI-positive patients only. MSI and loss of expression of MMR genes can be used as markers for MTS in patients with SGC. Consequently, MSI and loss of MMR gene expression in a patient presenting with SGC as the initial malignancy have important consequences for the patient and family. There are at least two variants of MTS with different molecular genetic mechanisms because 31% of the patients with the MTS phenotype had no MSI.
A multistep approach for micro tomography obtained medical image segmentation

Images were acquired using micro tomography technique (μCT ). That technique allows to study nondestructive internal structures imaging of any object. X-ray tube generates x-ray electromagnetic radiation which penetrates through the studied sample. Attenuation of x-rays intensity is registered at the opposite side of the sample by two-dimensional detector. Value of x-ray intensity registered in each pixel of the detector depend on materials property across beam path. Captured image is called “projection”. After acquiring one projection sample is rotated by small angle and another projection is captured. Few hundreds or few thousands of projections are acquired. Software reconstruct 3D object from set of projections using one of existing methods. For example filtered back projection method based on Radon transform theorem [8]. The reconstructed object is represented by 3D matrix of voxels. To separate material phases every 2D slice of that matrix should be segmented. That allows to create 3D model of studied sample and calculate volumes of each individual phases. The X-ray measurements presented in this paper were obtained using ”nanotom 180N” device produced by GE Sensing & Inspection Technologies phoenix X-ray Gmbh equipped with nanofocus X-ray tube with maximum 180kV voltage. The tomograms were registered on Hamamatsu 2300x2300 pixel detector and reconstruction of measured objects was done using of proprietary GE software datosX ver. 2.1. 0 with Feldkamp algorithm for cone beam X-ray CT [4].
Novel snubberless bidirectional ZCS/ZVS current-fed half-bridge isolated Dc/Dc converter for fuel cell vehicles

This paper presents a novel snubberless bidirectional current-fed half-bridge isolated dc/dc converter for fuel cell vehicles. The proposed converter achieves zero-current switching (ZCS) for the primary-side switches and zero-voltage switching (ZVS) for the secondary-side switches. It is a potential topology for fuel cell vehicles, front-end dc/dc power conversion for fuel cell inverters etc. This proposed converter is unique, not reported in literature and provides a simple solution to switch turn-off problem with ZCS without increase in components count. Therefore, it eliminates the need of active-clamp and passive snubbers to absorb the turn-off voltage spike. This will lead to reduced size, lower cost and higher efficiency. Steady-state analysis, design, simulation and experimental results of the proposed converter are reported in this paper.
Communally Nesting Migratory Birds Create Ecological Hot-Spots in Tropical Australia

Large numbers of metallic starlings (Aplonis metallica) migrate annually from New Guinea to the rainforests of tropical Australia, where they nest communally in single emergent trees (up to 1,000 birds). These aggregations create dense and species-rich faunal “hot-spots”, attracting a diverse assemblage of local consumers that utilise this seasonal resource. The starlings nested primarily in poison-dart trees (Antiaris toxicaria) near the rainforest-woodland boundary. Surveys underneath these colonies revealed that bird-derived nutrients massively increased densities of soil invertebrates and mammals (primarily wild pigs) beneath trees, year-round. Flying invertebrates, nocturnal birds, reptiles, and amphibians congregated beneath the trees when starlings were nesting (the wet-season). Diurnal birds (primarily cockatoos and bush turkeys) aggregated beneath the trees during the dry-season to utilise residual nutrients when the starlings were not nesting. The abundance of several taxa was considerably higher (to > 1000-fold) under colony trees than under nearby trees. The system strikingly resembles utilisation of bird nesting colonies by predators in other parts of the world but this spectacular system has never been described, emphasizing the continuing need for detailed natural-history studies in tropical Australia.
Re-Identifying the Rebound – What About Asymmetry ? # 276

Rebound eff ects measure the behaviorally induced off set in the reduction of energy consumption following effi ciency improvements. Using panel estimation methods and household travel diary data collected in Germany between 1997 and 2009, this study identifi es the rebound eff ect in private transport by allowing for the possibility that fuel price elasticities – from which rebound eff ects can be derived – are asymmetric. This approach rests on evidence that has emerged from the empirical literature suggesting that the response in individual travel demand to price increases is stronger than to decreases. Such an asymmetric response would necessitate reference to the fuel price elasticity derived from price decreases in order to identify the rebound eff ect, as the rebound occurs in response to a decrease in unit cost for car travel due to improved fuel effi ciency. While we fail to reject the hypothesis that the magnitude of the response to a price increase is equal to that of a price decrease, our rebound eff ect estimate for single-vehicle households of 58% is in line with a recent German study by Frondel, Peters, and Vance (2008). JEL Classifi cation: D13, Q41