Miracle-dz/UniFAR-FTUs huggingface dataset:
Draft Genome Sequences of Dermacoccus nishinomiyaensis Strains UCD-KPL2534 and UCD-KPL2528 Isolated from an Indoor Track Facility

ABSTRACT We present here the draft genome sequences of Dermacoccus nishinomiyaensis strains UCD-KPL2534 and UCD-KPL2528, which were isolated at an indoor track facility in Medford, MA, USA (42.409716, -71.115169) from an exit door handle and settle dust, respectively. The genome assemblies contain 3,088,111 bp in 58 contigs and 3,162,381 bp in 100 contigs, respectively.
The Penn Lambda Calculator

AbstractThis paper describes a novel pedagogical software program that can beseen as an online companion to one of the standard textbooks of formal nat-ural language semantics, Heim and Kratzer (1998). The Penn Lambda Cal-culator isamultifunctionalapplicationdesignedforuseinstandardgraduateand undergraduate introductions to formal semantics: Teachers can use theapplication to demonstrate complex semantic derivations in the classroomand modify them interactively, and students can use it to work on problemsets provided by the teacher. The program supports demonstrations and ex-ercises in two main areas: (1) performing beta reduction in the simply typedlambda calculus; (2) application of the bottom-up algorithm for computingthe compositional semantics of natural language syntax trees. The programis able to represent the full range of phenomena covered in the Heim andKratzertextbookbyfunctionapplication,predicatemodiﬁcation,andlambdaabstraction. This includes phenomena such as intersective adjectives, rela-tiveclausesandquantiﬁerraising. Inthestudentusecase, emphasishasbeenplaced on providing “live” feedback for incorrect answers. Heuristics areused to detect the most frequent student errors and to return speciﬁc, interac-tive suggestions.
A Radar Reflectivity Operator with Ice-Phase Hydrometeors for Variational Data Assimilation (RadZIceVarv1.0) and Its Evaluation with Real Radar Data

Abstract. A reflectivity forward operator and its associated tangent linear and adjoint operators (together named RadZIceVar) were developed for variational data assimilation (DA). RadZIceVar can analyze both rainwater and ice-phase species (snow and graupel) by directly assimilating radar reflectivity observations. The results of three-dimensional variational (3DVAR) DA experiments with a 3 km grid mesh setting of the Weather Research and Forecasting (WRF) model showed that RadZIceVar was effective at producing an analysis of reflectivity pattern and intensity similar to the observed data. Two to three outer loops with 50–100 iterations in each loop were needed to obtain a converged 3D analysis of rainwater, snow, and graupel, including the melting layers with mixed-phase hydrometeors. The deficiencies in the analysis using this operator could be caused by the poor quality of the background fields and the use of the static background error covariance, and these issues can be partially resolved by using radar-retrieved hydrometeors in a preprocessing step and tuning the spatial correlation length scales of the background errors. The direct radar reflectivity assimilation using RadZIceVar also improved the short-term (2 h–5 h) precipitation forecasts compared to those of the experiment without DA.
Searchable Public Key Encryption Based on RSA Assumption and Extended to Multi-user Setting

In this paper, we study the problem of keyword searches over asymmetrically encrypted data. Our scheme is based on strong RSA assumption, which provides the high efficient search technique and is proven secure in the standard model. In comparison with previous schemes, our scheme requires only simpler computation without pairing operation, and lower storage overheads on servers and clients. Moreover, most servers are not only about to serve for single user, but to support query and search operations for multiple users. As a result, we extend our scheme to multiuser environment, which provides an efficient search scheme of remote storage for a number of users. Furthermore, we define the secure model for mPEKS scheme and prove the security and availability of our scheme.
Influence of Induced Reactive Oxygen Species in p53-Mediated Cell Fate Decisions

ABSTRACT The p53 tumor suppressor gene can induce either apoptosis or a permanent growth arrest (also termed senescence) phenotype in response to cellular stresses. We show that the increase in intracellular reactive oxygen species (ROS) associated with the magnitude of p53 protein expression correlated with the induction of either senescence or apoptosis in both normal and cancer cells. ROS inhibitors ameliorated both p53-dependent cell fates, implicating ROS accumulation as an effector in each case. The absence of Bax or PUMA strongly inhibited both p53-induced apoptosis and ROS increase, indicating an important role these p53 targets affecting mitochondrial function genes in p53-mediated ROS accumulation. Moreover, physiological p53 levels in combination with an exogenous ROS source were able to convert a p53 senescence response into apoptosis. All of these findings establish a critical role of ROS accumulation and mitochondrial function in p53-dependent cell fates and show that other ROS inducers can collaborate with p53 to influence these fate decisions. Thus, our studies imply that therapeutic agents that generate ROS are more likely to be toxic for normal cells than p53-negative tumor cells and provide a rationale for identifying therapeutic agents that do not complement p53 in ROS generation to ameliorate the cytotoxic side effects in normal cells.
A Feedfordward Adaptive Controller to Reduce the Imaging Time of Large-Sized Biological Samples with a SPM-Based Multiprobe Station

The time required to image large samples is an important limiting factor in SPM-based systems. In multiprobe setups, especially when working with biological samples, this drawback can make impossible to conduct certain experiments. In this work, we present a feedfordward controller based on bang-bang and adaptive controls. The controls are based in the difference between the maximum speeds that can be used for imaging depending on the flatness of the sample zone. Topographic images of Escherichia coli bacteria samples were acquired using the implemented controllers. Results show that to go faster in the flat zones, rather than using a constant scanning speed for the whole image, speeds up the imaging process of large samples by up to a 4× factor.
MuLES: An Open Source EEG Acquisition and Streaming Server for Quick and Simple Prototyping and Recording

The past few years have seen the availability of consumer electroencephalography (EEG) devices increase significantly. These devices, usually with a compact form factor and affordable price, now allow researchers and enthusiasts to use EEG in various new contexts and environments. However, the many consumer headsets often require extensive programming experience to interface with their respective drivers; moreover, standardization of the access and recording of EEG data across the devices still remains to be done. Consequently, a tool is needed to facilitate the recording and streaming of EEG data from consumer headsets that can easily be interfaced with different programming languages and software, and that allows interchangeability between devices. This paper describes the open source MuSAE Lab EEG Server (MuLES), an EEG acquisition and streaming server that aims at creating a standard interface for portable EEG headsets, in order to accelerate the development of brain-computer interfaces (BCIs) and of general EEG use in novel contexts. In addition to the EEG server interface which currently supports five different consumer devices and session playback, clients are developed for use on different platforms and in various programming languages, making prototyping and recording a quick and simple task. To validate the functionality and usability of the EEG server, a use case highlighting its main features is presented. The developed tool simplifies the acquisition and recording of EEG data from portable consumer devices by providing a single efficient interface, with applications in areas such as basic and behavioural research, prototyping, neurogaming, live performance and arts.
External Debt , Defaults and Exchange Rate Dynamics

Emerging countries experience exchange rate depreciations around defaults. This paper explores this observed evidence within a dynamic stochastic general equilibrium model in which bond issuances in local and foreign currencies are explicitly embedded and exchange rate and default risk are determined endogenously. Our quantitative analysis replicates the link between exchange rate depreciation and default probability around defaults. In pre-default periods, interactions of exchange rate depreciation originated by lower traded goods income with its large share of foreign currency denominated debt trigger default. In post-default periods, exchange rate in turn, depreciates further due to output costs and loss in market access. JEL Classi cation Codes: E43; F32; F34; G12
Register file reliability enhancement through adjacent narrow-width exploitation

Due to the increasing vulnerability of CMOS circuits, new generations of microprocessors require an inevitable focus on reliability issues. As the Register File (RF) constitutes a critical element within the processor pipeline, it is mandatory to enhance the RF reliability to develop fault tolerant architectures. This paper proposes Adjacent Register Hardened RF (ARH), a new RF architecture that exploits the adjacent byte-level narrow-width values for hardening registers at runtime. Registers are paired together by some special switches referred to as joiners. Dummy sign bits of each register are used to keep redundant data of its counterpart register. We use 7T/14T SRAM cell [6] to combine redundant bits together to make a single bit cell which is, by far, more resilient against faults. Our simulations show that with 3% to 12% power overhead and 10% to 20% increase in area, in comparison to baseline RF, we can obtain up to 80% reduction in soft error rate (SER).
Rab27a-mediated protease release regulates neutrophil recruitment by allowing uropod detachment

Neutrophil migration is vital for immunity and precedes effector functions such as pathogen killing. Here, we report that this process is regulated by the Rab27a GTPase, a protein known to control granule exocytosis. Rab27a-deficient (Rab27a KO) neutrophils exhibit migration defects in vitro and in vivo, and live-cell microscopy suggests that delayed uropod detachment causes the migratory defect. Surface expression of CD11b, a key adhesion molecule, is increased in chemokine-stimulated Rab27a KO neutrophils compared with the control, suggesting a turnover delay caused by a defect in elastase secretion from azurophilic granules at the rear of bone marrow polymorphonuclear leukocytes (BM-PMNs). We suggest that Rab27a-dependent protease secretion regulates neutrophil migration through proteolysis-dependent de-adhesion of uropods, a mechanism that could be conserved in cell migration and invasion.
Feature selection and Ensemble Hierarchical Cluster-based Under-sampling approach for extremely imbalanced datasets: Application to gene classification

Class distribution in many informative datasets is highly imbalance. In high imbalance dataset there are large amount of negative samples and a small part of positives. It is difficult to classify imbalanced datasets. In this paper we propose an Ensemble Hierarchical Cluster-based Undersampling approach for classification of huge and extremely imbalance datasets. Hierarchical Clustering is used to remove negative samples which are dissimilar to positive samples. Ensemble technique collects results from multiple classifiers to predict class labels. Our experimental results show that our approach is very effective for the classification of extremely imbalanced datasets. Keywords-Extremely imbalanced dataset, Feature selection, ensemble method, hierarchical clustering, under-sampling, gene classification.
Exploiting Module Locality to Improve Software Fault Prediction

Receiving bug reports, developers usually need to spend significant amount of time resolving where to fix the faults. Although previous studies have shown that the revision frequency of a file location is an important measure to reflect the possibility of containing bugs, the frequency-based approaches achieve limited prediction accuracy for file locations having low revision frequencies. Our empirical observations show that the files of low revision frequencies in the same file directory or package of the files of high revision frequencies may be potential bug-fixing candidates for future bug reports. In this paper, we present a novel enhancement by exploiting module locality to improve the frequency-based approaches. Our experiments on three open source projects reveal that module locality can be employed to consistently improve the hit rate of a frequency-based approach and achieve the highest improvement of about 14%.
Sleep and Aggressive Behavior Among Toddlers: Investigating Directionality of Associations

Abstract:This study examined the reciprocal associations between sleep (duration and quality) and aggressive behavior in toddlers. The sample consisted of 82 children (43 boys and 39 girls) and their parents who completed two assessments, when children were 2 and 3 years old. At both time points, children wore an actigraph for 3 consecutive days to assess their sleep patterns, and both their parents reported on their child’s aggressive behavior. The results indicated negative associations between sleep quality at age 2 and both parents’ evaluations of aggressive behavior at age 3; in contrast, the relations between aggression at age 2 and sleep (duration or quality) at age 3 were small and nonsignificant. In line with studies of older children and adolescents, these results suggest that sleep difficulties are more likely to favor the emergence of aggressive behavior among young children than the converse.
Application Considerations in Specifying High Frequency Ultrasonic Transducers

Ultrasonic NDT applications involving frequencies of 50 MHz and higher require consideration of a number of special factors when selecting transducers. This paper discusses issues relating to material attenuation, transducer design and performance, and instrumentation design for ultrasonic imaging, thickness gaging, and flaw detection at 50 MHz and up. Advances in transducer manufacturing technology and associated instrument electronics have led to the introduction of commercial products that provide the capability for ultrasonic imaging, thickness gaging, flaw detection, and material analysis at test frequencies greater than 50 MHz. In many materials like fine grain metals, ceramics, and thin polymers, these higher test frequencies permit measurement of significantly lower thickness limits and detection of significantly smaller flaws and other internal structures as compared to conventional test frequencies of 20 MHz and below. However, when working in this very high frequency range, it is especially important to consider a number of fundamental factors when selecting transducers. These include echo recovery time as determined by center frequency and bandwidth, relative sensitivity, beam diameter, focal zone, and attenuation effects in water paths and test materials. Pulser/receiver design and setup also has a major effect on performance, as does cable length. Knowledge of how these factors interact and how they affect echo response from typical test targets is important for optimizing resolution and sensitivity in very high frequency work. This paper also includes examples of specific test applications utilizing the frequency range from 50 MHz to 225 MHz. 1. Test Material Properties In any ultrasonic test, it is necessary to consider how physical properties of the test material will affect sound transmission, and this becomes increasingly important as frequency increases. Attenuation and scattering in the test material are frequently limiting factors in very high frequency testing, typically restricting its use to applications involving relatively thin materials with good sound transmission properties, and making use of very high frequencies impractical in situations involving thick test pieces or materials that exhibit high levels of ultrasonic attenuation or scattering, such as soft polymers and coarse grain cast metals. The theory of attenuation and scattering is complex and has been described elsewhere in detail. The loss of amplitude due across a given sound path will be the sum of absorption effects, which increase linearly with frequency, and scattering effects, which vary through three zones depending on the ratio of the size of grain boundaries or other scatterers to wavelength. In all cases scattering effects increase with frequency. For a given material at a given temperature, tested at a given frequency, there will be a specific ECNDT 2006 We.4. 6.1
Highly Efficient Image Stitching Based on Energy Map

We present a simple and efficient method to seamlessly stitch the images according to a stitching line based on an energy map. The power of this method lies in the integration of many superior features and at the same time, it is still efficient. One striking feature of our approach is that it is based on the philosophy that human eyes mostly notice only the salient features of an image and the stitching line skirts round the important objects like human faces to avoid distorting the content of image in the seam area. Robustness is another salient characteristic of our method in de-ghosting when moving objects are left in which will appear blurry and "ghosted. " Unlike previous approaches to the same problem, the method also has least distortion of the original images. We finally present several useful applications of this method such as Quick Texture Stitching.
The IRCAL Polarimeter: Design, Calibration, and Data Reduction for an Adaptive Optics Imaging Polarimeter

We have upgraded IRCAL, the near-infrared science camera of the Lick Observatory adaptive optics system, to add a dual-channel imaging polarimetry mode. This mode uses an optically contacted YLF (LiYF4) Wollaston prism to provide simultaneous images in perpendicular linear polarizations, providing high-resolution high–dynamic-range polarimetry in the near-infrared. We describe the design and construction of the polarimeter, discuss in detail the data reduction algorithms adopted, and evaluate the instrument’s on-the-sky performance. The IRCAL polarimeter is capable of reducing the stellar PSF halo by about 2 orders of magnitude, thereby increasing contrast for studies of faint circumstellar dust-scattered light. We discuss the various factors that limit the achieved contrast, and present lessons applicable to future high-contrast imaging polarimeters.
White Matter of the CNS Supports or Inhibits Neurite Outgrowth In Vitro Depending on Geometry

Axonal regeneration is normally limited within myelinated fiber tracts in the CNS of higher vertebrates. Numerous studies suggest that CNS myelin contains inhibitors that may contribute to abortive axonal growth. In contrast to the evidence of myelin-associated neurite inhibitors, embryonic neurons transplanted into the CNS can regenerate extensively within myelinated tracts in vivo. It has been speculated that embryonic neurons do not yet express the appropriate receptors for myelin-associated inhibitors. Recently, however, extensive regeneration from transplanted adult neurons has also been reported within myelinated tracts of the CNS, casting doubt on the role myelin-associated inhibitors play in abortive regeneration. The present study reexamined the potential of white matter to support neurite growth in vitro. By the use of Neurobasal medium, neurons were cultured onto unfixed cryostat sections of mature rat CNS tissue. As documented previously, robust neuronal attachment and neurite outgrowth occurred on gray matter but these neurites were sharply inhibited by white matter. In addition, however, increased rates of neuronal attachment directly to white matter occurred with neurite outgrowth comparable in length with that on gray matter but limited to directions parallel to the fiber tract. Frequently, the same section of white matter was found to inhibit neurite outgrowth from neurons on gray matter while supporting parallel neurite outgrowth from neurons on white matter. These results suggest that whether white matter supports or inhibits axonal growth depends on the geometric relationship between the axon and the fiber tract; more specifically, white matter supports parallel growth but inhibits nonparallel growth.
To Construct Implicit Link Structure by Using Frequent Sequence Miner (FS-Miner)

Generally, link analysis is based re-ranking web-page retrieval in current web search engine. The primary reason lies in the difference of link structures and data scale between global web and website. In this paper, we propose a framework to construct implicit link structure by using Frequent Sequence Miner (FS-Miner) in the User Web Log. And then, the Page Rank algorithm is applied to re-ranked Web Pages. The popular web paths are used to extract in user’s navigation web log and predict current user’s next step. Our system can solve the sparsity of Web links and the diversity problem of user’s access behavior. Moreover, our approach discovers users’ relevant documents to improve the performance of search results.
Museum epigenomics: characterizing cytosine methylation in historic museum specimens

Museum genomics has transformed the field of collections-based research, opening up a range of new research directions for paleontological specimens as well as natural history specimens collected over the past few centuries. Recent work demonstrates that it is possible to characterize epigenetic markers such as DNA methylation in well-preserved ancient tissues. This approach has not yet been tested in traditionally-prepared natural history specimens such as dried bones and skins, the most common specimen types in vertebrate collections. In this study, we develop and test methods to characterize cytosine methylation in dried skulls up to 76 years old. Using a combination of ddRAD and bisulfite treatment, we characterized patterns of cytosine methylation in two species of deer mouse (Peromyscus spp.) collected in the same region in Michigan in 1940, 2003, and 2013-2016. We successfully estimated methylation in specimens of all age groups, though older specimens yielded less data and showed greater interindividual variation in data yield than newer specimens. Global methylation estimates were reduced in the oldest specimens (76 years old) relative to the newest specimens (1-3 years old), which may reflect post mortem hydrolytic deamination. Methylation was reduced in promoter regions relative to gene bodies and showed greater bimodality in autosomes relative to female X chromosomes, consistent with expectations for methylation in mammalian somatic cells. Our work demonstrates the utility of historic specimens for methylation analyses, as with genomic analyses; however, such studies will need to accommodate the large variance in the quantity of data produced by older specimens.
Journal of Graph Algorithms and Applications towards an Optimal Algorithm for Recognizing Laman Graphs

A graph G with n vertices and m edges is a generically minimally rigid graph (Laman graph), if m = 2n−3 and every induced subset of k vertices spans at most 2k − 3 edges. Laman graphs play a fundamental role in rigidity theory. We discuss the Verification problem: Given a graph G with n ver-tices, decide if it is Laman. We present an algorithm that recognizes Laman graphs in O(Tst(n) + n log n) time, where Tst(n) is the best time to extract two edge disjoint spanning trees from a graph with n vertices and 2n − 2 edges, or decide no such trees exist. So far, it is known that Tst(n) is O(n 3/2 √ log n).