Miracle-dz/UniFAR-FTUs huggingface dataset:
Lax science can have negative impacts on conservation: A rebuttal to Lau and Jacobs (2017)

A recent paper by Lau and Jacobs (2017, PeerJ) negatively contributes to a critical conservation problem in the Gulf of California. Since ~2000, a small group of people have argued that decreased Colorado River flow has led to decreased productivity and health of the Upper Gulf, and even “ecosystem collapse” in the region. This group has clung to this idea despite the fact that there is little or no empirical evidence to support it, and despite the consistent flow of research from oceanographers and other researchers showing this not to be the case, and instead, showing that that the Upper Gulf’s ecosystem, aside from poor fishing practices, is as healthy as ever (see recent summaries in Mercado-Santana et al. 2017 and Brusca et al. 2017, the latter reviewing the situation in considerable detail). Importantly, this unproven “flow-ecosystem collapse” argument has been the key leverage used for years, by fishermen and CONAPESCA (the government fisheries agency), to argue against the need for stronger fisheries regulations for the Upper Gulf (Villa-Ramírez 1993; Fleischer 1996; Fleischer et al. 1996; Bobadilla et al. 2011; Ramírez-León, et al. 2015). As a direct result of delaying better fisheries management in the region, gill-netting and bottom trawling has driven vaquita porpoise numbers so low that this rare marine mammal is now on the verge of extinction. Papers such as Lau and Jacobs (2017) only add fuel for those who argue that changes in the Upper Gulf’s ecosystem due to reduced Colorado River flow, not illegal and unsustainable fishing, is the primary culprit in the demise of the vaquita.
Time Reproduction Performance Is Associated With Age and Working Memory in High‐Functioning Youth With Autism Spectrum Disorder

Impaired temporal processing has historically been viewed as a hallmark feature of attention deficit hyperactivity disorder. Recent evidence suggests temporal processing deficits may also be characteristic of autism spectrum disorder (ASD). However, little is known about the factors that impact temporal processing in children with ASD. The purpose of this study was to assess the effects of co‐morbid attention problems, working memory (WM), age, and their interactions, on time reproduction in youth with and without ASD.
Stabilization of Frozen Lactobacillus delbrueckii subsp. bulgaricus in Glycerol Suspensions: Freezing Kinetics and Storage Temperature Effects

ABSTRACT The interactions between freezing kinetics and subsequent storage temperatures and their effects on the biological activity of lactic acid bacteria have not been examined in studies to date. This paper investigates the effects of three freezing protocols and two storage temperatures on the viability and acidification activity of Lactobacillus delbrueckii subsp. bulgaricus CFL1 in the presence of glycerol. Samples were examined at −196°C and −20°C by freeze fracture and freeze substitution electron microscopy. Differential scanning calorimetry was used to measure proportions of ice and glass transition temperatures for each freezing condition tested. Following storage at low temperatures (−196°C and −80°C), the viability and acidification activity of L. delbrueckii subsp. bulgaricus decreased after freezing and were strongly dependent on freezing kinetics. High cooling rates obtained by direct immersion in liquid nitrogen resulted in the minimum loss of acidification activity and viability. The amount of ice formed in the freeze-concentrated matrix was determined by the freezing protocol, but no intracellular ice was observed in cells suspended in glycerol at any cooling rate. For samples stored at −20°C, the maximum loss of viability and acidification activity was observed with rapidly cooled cells. By scanning electron microscopy, these cells were not observed to contain intracellular ice, and they were observed to be plasmolyzed. It is suggested that the cell damage which occurs in rapidly cooled cells during storage at high subzero temperatures is caused by an osmotic imbalance during warming, not the formation of intracellular ice.
Drought regulates the burned forest areas in Mexico: the case of 2011, a record year

Abstract During 2011, Mexico experienced record figures in terms of forest fires, with an affected area of 956,405 ha, and an association between this activity and the meteorological conditions is suspected. We addressed the question: Are the burned areas in Mexico associated with the duration and accumulation of drought? Using the G statistic, the cluster zones of burned areas in Mexico in 2011 were analyzed, and the value of accumulated drought that was most related to these cluster zones was determined. Global and local regression models were used to evaluate the drought-burned areas association. Two cluster zones were found (zones A and B). Accumulated drought of 24 and 12 months significantly explained the burned areas of zones A and B, respectively. The burned areas of Mexico in 2011 were non-randomly distributed, and accumulated drought significantly explained the magnitude of the areas affected by fire.
Concurrent Guiding Template Assignment and Redundant via Insertion for DSA-MP Hybrid Lithography

Directed Self-Assembly (DSA) is a very promising emerging lithography for 7nm and beyond, where a coarse guiding template produced by conventional optical lithography can "magically" generate fine-pitch vias/contacts through self-assembly process. A key challenge for DSA-friendly layout is the guiding template assignment to cover all vias under consideration. Meanwhile, redundant via insertion has been widely adopted to improve yield and reliability of the circuit. In this paper, we propose a comprehensive framework for concurrent DSA guiding template assignment and redundant via insertion with consideration of multiple patterning (MP) in guiding template generation. We first formulate the problem as an integer linear programming (ILP), and then propose a novel approximation algorithm to achieve good performance and runtime trade-off. The experimental results demonstrate the effectiveness of the proposed algorithms. To our best knowledge, this is the first work in concurrent guiding template assignment and redundant via insertion for DSA-MP hybrid lithography.
Wearable social camera: Egocentric video summarization for social interaction

Wearable social camera is an egocentric camera that summarizes the video of the user's social activities. This paper proposes a core technology of the wearable social camera: egocentric video summarization for social interaction. Different from other works of third-person action/interaction recognition in egocentric videos, which focus on distinguishing different actions, this work finds the common features among all the interactions, which is called interaction features (IF). IF of the third-person is proposed to be composed of three parts: physical information of head, body languages, and emotional expression. Furthermore, hidden Markov model (HMM) is employed to model the interaction sequences, and a summarized video is generated with hidden Markov support vector machine (HM-SVM). Experimental results with a life-log dataset show that the proposed system performs well for summarizing life-log videos.
Humans and Ferrets with Prior H1N1 Influenza Virus Infections Do Not Exhibit Evidence of Original Antigenic Sin after Infection or Vaccination with the 2009 Pandemic H1N1 Influenza Virus

ABSTRACT The hypothesis of original antigenic sin (OAS) states that the imprint established by an individual's first influenza virus infection governs the antibody response thereafter. Subsequent influenza virus infection results in an antibody response against the original infecting virus and an impaired immune response against the newer influenza virus. The purpose of our study was to seek evidence of OAS after infection or vaccination with the 2009 pandemic H1N1 (2009 pH1N1) virus in ferrets and humans previously infected with H1N1 viruses with various antigenic distances from the 2009 pH1N1 virus, including viruses from 1935 through 1999. In ferrets, seasonal H1N1 priming did not diminish the antibody response to infection or vaccination with the 2009 pH1N1 virus, nor did it diminish the T-cell response, indicating the absence of OAS in seasonal H1N1 virus-primed ferrets. Analysis of paired samples of human serum taken before and after vaccination with a monovalent inactivated 2009 pH1N1 vaccine showed a significantly greater-fold rise in the titer of antibody against the 2009 pH1N1 virus than against H1N1 viruses that circulated during the childhood of each subject. Thus, prior experience with H1N1 viruses did not result in an impairment of the antibody response against the 2009 pH1N1 vaccine. Our data from ferrets and humans suggest that prior exposure to H1N1 viruses did not impair the immune response against the 2009 pH1N1 virus.
Generalized Sphere Packing Bound

Kulkarni and Kiyavash recently introduced a new method to establish upper bounds on the size of deletion-correcting codes. This method is based upon tools from hypergraph theory. The deletion channel is represented by a hypergraph whose edges are the deletion balls (or spheres), so that a deletion-correcting code becomes a matching in this hypergraph. Consequently, a bound on the size of such a code can be obtained from bounds on the matching number of a hypergraph. Classical results in hypergraph theory are then invoked to compute an upper bound on the matching number as a solution to a linear-programming problem: the problem of finding fractional transversal. The method by Kulkarni and Kiyavash can be applied not only for the deletion channel but also for other error channels. This paper studies this method in its most general setup. First, it is shown that if the error channel is regular and symmetric then the upper bound by this method coincides with the well-known sphere packing bound and thus is called here the generalized sphere packing bound. Even though this bound is explicitly given by a linear programming problem, finding its exact value may still be a challenging task. The art of finding the exact upper bound (or slightly weaker ones) is the assignment of weights to the hypergraph's vertices in a way that they satisfy the constraints in the linear programming problem. In order to simplify the complexity of the linear programming, we present a technique based upon graph automorphisms that in many cases significantly reduces the number of variables and constraints in the problem. We then apply this method on specific examples of error channels. We start with the Z channel and show how to exactly find the generalized sphere packing bound for this setup. Next studied is the nonbinary limited magnitude channel both for symmetric and asymmetric errors, where we focus on the single-error case. We follow up on the deletion channel, which was the original motivation of the work by Kulkarni and Kiyavash, and show how to improve upon their upper bounds for single-deletion-correcting codes. Since the deletion and grain-error channels have a similar structure for a single error, we also improve upon the existing upper bounds on single-grain error-correcting codes. Finally, we apply this method for projective spaces and find its generalized sphere packing bound for the single-error case.
Evidence-based trust metrics in web services

In a service ecosystem of complementary and competing web services, clients have many options but, at the same time, determining which one to trust can be a challenge. While there have been several proposals in literature about web services trust measurement, none has been actually adopted. Even the notion of trust itself is not clearly established in the context of the web-services' stack of standards. In this paper, we propose a service that collects different types of service-quality measurements from clients, as well as evidence in the form of relevant request/response headers, in order to produce aggregate trust metrics of service providers. Our experimental analysis using simulations shows that the proposed trust-aggregator service framework is feasible and effective in measuring trust metrics.
Correlation of some water quality parameters and Pb in sediment to gastropod diversity in Ambon Island Waters

The coastal waters of Ambon Island have quite diverse ecosystems that allow for the presence of various organisms, one of which is gastropods. This study aims to analyze the correlation of some water parameters and Pb in sediment to the diversity of gastropods. The research method was carried out by observing the density, water quality parameters, and Pb metal in sediments. Water parameters were measured in situ and analyzed in the laboratory. The distribution of gastropods was analyzed through Principal Component Analysis (PCA). At the same time, the correlation analysis was carried out using the Pearson correlation approach using SPSS v.16. The results showed that the types of gastropods with the highest density in the waters of Ambon Island were Terebralia sulcata, Hebra corticata, and Nerita patula. While the species with the lowest density value were Nassarius olivaceus, Polinices didyma, Lunella cinerea, Conus eburneus, Cypraea isabella, Vexillum plicarium, and Columbella scripta. The Shannon-Wienner Diversity Index ranges from 1.253–2.622, and the diversity index ranges from 0.083-0.207. It was included in the low category caused by the disturbance of water pollution and Pb metal in sediments. Meanwhile, the dominance index ranged from 0.098 to 0.511 indicating species dominance at several observation stations. The waters' physical-chemical parameters strongly correlating with gastropod diversity are DO and Pb, with respective correlation values ​​of r = 0.656 and r = -0.785.
NL q theory: checking and imposing stability of recurrent neural networks for nonlinear modelling (cid:3)

It is known that many discrete time recurrent neural networks, such as e.g. neural state space models, multilayer Hop(cid:12)eld networks and locally recurrent globally feedforward neural networks, can be represented as NLq systems. Su(cid:14)cient conditions for global asymptotic stability and input/output stability of NLq systems are available, including three types of criteria: diagonal scaling and criteria depending on diagonal dominance and condition number factors of certain matrices. In this paper, it is discussed how Narendra's dynamic backpropagation procedure, used for identifying recurrent neural network from I/O measurements, can be modi(cid:12)ed with an NLq stability constraint in order to ensure globally asymptotically stable identi(cid:12)ed models. An example illustrates how system identi(cid:12)cation of an internally stable model, corrupted by process noise, may lead to unwanted limit cycle behaviour and how this problem can be avoided by adding the stability constraint.
Estimate of within population incremental selection through branch imbalance in lineage trees

Incremental selection within a population, defined as a limited fitness change following a mutation, is an important aspect of many evolutionary processes and can significantly affect a large number of mutations through the genome. Strongly advantageous or deleterious mutations are detected through the fixation of mutations in the population, using the synonymous to non-synonymous mutations ratio in sequences. There are currently to precise methods to estimate incremental selection occurring over limited periods. We here provide for the first time such a detailed method and show its precision and its applicability to the genomic analysis of selection. A special case of evolution is rapid, short term micro-evolution, where organism are under constant adaptation, occurring for example in viruses infecting a new host, B cells mutating during a germinal center reactions or mitochondria evolving within a given host. The proposed method is a novel mixed lineage tree/sequence based method to detect within population selection as defined by the effect of mutations on the average number of offspring. Specifically, we propose to measure the log of the ratio between the number of leaves in lineage trees branches following synonymous and non-synonymous mutations. This method does not suffer from the need of a baseline model and is practically not affected by sampling biases. In order to show the wide applicability of this method, we apply it to multiple cases of micro-evolution, and show that it can detect genes and intergenic regions using the selection rate and detect selection pressures in viral proteins and in the immune response to pathogens.
Generalized video deblurring for dynamic scenes

Several state-of-the-art video deblurring methods are based on a strong assumption that the captured scenes are static. These methods fail to deblur blurry videos in dynamic scenes. We propose a video deblurring method to deal with general blurs inherent in dynamic scenes, contrary to other methods. To handle locally varying and general blurs caused by various sources, such as camera shake, moving objects, and depth variation in a scene, we approximate pixel-wise kernel with bidirectional optical flows. Therefore, we propose a single energy model that simultaneously estimates optical flows and latent frames to solve our deblurring problem. We also provide a framework and efficient solvers to optimize the energy model. By minimizing the proposed energy function, we achieve significant improvements in removing blurs and estimating accurate optical flows in blurry frames. Extensive experimental results demonstrate the superiority of the proposed method in real and challenging videos that state-of-the-art methods fail in either deblurring or optical flow estimation.
A comparative study of far-field tsunami amplitudes and ocean-wide propagation properties: insight from major trans-Pacific tsunamis of 2010–2015

Mohammad Heidarzadeh,1 Kenji Satake,2 Tomohiro Takagawa,3 Alexander Rabinovich4,5 and Satoshi Kusumoto2 1Department of Civil & Environmental Engineering, Brunel University London, Uxbridge UB8 3PH, UK. E-mail: mohammad.heidarzadeh@brunel.ac. uk 2Earthquake Research Institute, The University of Tokyo, Tokyo 113-0032, Japan 3Port and Airport Research Institute, Yokosuka 239–0826, Japan 4Institute of Ocean Sciences, Sidney, British Columbia, V8L 4B2, Canada 5Shirshov Institute of Oceanology, Russian Academy of Sciences, Moscow 117997, Russia
Within-Host Evolution of Simian Arteriviruses in Crab-Eating Macaques

ABSTRACT Simian arteriviruses are a diverse clade of viruses infecting captive and wild nonhuman primates. We recently reported that Kibale red colobus virus 1 (KRCV-1) causes a mild and self-limiting disease in experimentally infected crab-eating macaques, while simian hemorrhagic fever virus (SHFV) causes lethal viral hemorrhagic fever. Here we characterize how these viruses evolved during replication in cell culture and in experimentally infected macaques. During passage in cell culture, 68 substitutions that were localized in open reading frames (ORFs) likely associated with host cell entry and exit became fixed in the KRCV-1 genome. However, we did not detect any strong signatures of selection during replication in macaques. We uncovered patterns of evolution that were distinct from those observed in surveys of wild red colobus monkeys, suggesting that these species may exert different adaptive challenges for KRCV-1. During SHFV infection, we detected signatures of selection on ORF 5a and on a small subset of sites in the genome. Overall, our data suggest that patterns of evolution differ markedly among simian arteriviruses and among host species. IMPORTANCE Certain RNA viruses can cross species barriers and cause disease in new hosts. Simian arteriviruses are a diverse group of related viruses that infect captive and wild nonhuman primates, with associated disease severity ranging from apparently asymptomatic infections to severe, viral hemorrhagic fevers. We infected nonhuman primate cell cultures and then crab-eating macaques with either simian hemorrhagic fever virus (SHFV) or Kibale red colobus virus 1 (KRCV-1) and assessed within-host viral evolution. We found that KRCV-1 quickly acquired a large number of substitutions in its genome during replication in cell culture but that evolution in macaques was limited. In contrast, we detected selection focused on SHFV ORFs 5a and 5, which encode putative membrane proteins. These patterns suggest that in addition to diverse pathogenic phenotypes, these viruses may also exhibit distinct patterns of within-host evolution both in vitro and in vivo.
Field-Programmable LNAs With Interferer-Reflecting Loop for Input Linearity Enhancement

A field-programmable (FP) low-noise amplifier (LNA) with interferer-reflecting (IR) loop is introduced. The user can program its gain, noise figure, linearity and power consumption during operation. The IR loop uses a frequency-selective shunt-shunt feedback around the noise-canceling LNA to reduce the input impedance out of band and to suppress the input voltage swing created by blockers. A notch filter at the desired operation frequency in the feedback path results in selectivity at the RF input so that all out-of-band blockers are suppressed without the need to know blocker locations and the LNA input linearity is improved. 65 nm CMOS chip prototypes have been implemented with on-chip LC, bondwire LC or N-path notch filters. The FP N-path IR-LNA operates from 0.2 to 1.6 GHz; with the IR disabled, the NF is 2.4 dB, B1 dB is -15 dBm, and the OOB-IIP3 is +2.5 dBm with a 13 mW power consumption; with the IR on, the NF is 3.6 dB, the RF channel input bandwidth is 20 MHz, the B1 dB is -4 dBm and the OOB-IIP3 is +14.5 dBm. The LNA has an analog VDD of 1.6 V and an LO VDD of 1 V and dissipates 15.8 to 20.2 mW across operating frequencies.
Discovery of General Knowledge in Large Spatial Databases

Extraction of interesting and general knowledge from large spatial databases is an important task in the development of spatial dataand knowledge-base systems. In this paper, we investigate knowledge discovery in spatial databases and develop a generalization-based knowledge discovery mechanism which integrates attribute-oriented induction on nonspatial data and spatial merge and generalization on spatial data. The study shows that knowledge discovery has wide applications in spatial databases, and relatively efficient algorithms can be developed for discovery of general knowledge in large spatial databases.
Joint image coding and image authentication based on absolute moment block truncation coding

Abstract. A joint image coding and image authentication scheme based on absolute moment block truncation coding (AMBTC) is proposed. In the proposed scheme, the authentication data is generated by using the pseudo random sequence. Then, the authentication codes are embedded into the bit maps of AMBTC-compressed image blocks. The embedded bit maps and these quantization levels are further losslessly compressed to cut down the required storage cost. Experimental results demonstrate that the proposed scheme achieves good image quality of the embedded image while keeping good detecting accuracy.