Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of ocean acidification on growth and otolith condition of juvenile scup, Stenotomus chrysops

Abstract Increasing amounts of atmospheric carbon dioxide (CO2) from human industrial activities are causing changes in global ocean carbonate chemistry, resulting in a reduction in pH, a process termed “ocean acidification. ” It is important to determine which species are sensitive to elevated levels of CO2 because of potential impacts to ecosystems, marine resources, biodiversity, food webs, populations, and effects on economies. Previous studies with marine fish have documented that exposure to elevated levels of CO2 caused increased growth and larger otoliths in some species. This study was conducted to determine whether the elevated partial pressure of CO2 (pCO2) would have an effect on growth, otolith (ear bone) condition, survival, or the skeleton of juvenile scup, Stenotomus chrysops, a species that supports both important commercial and recreational fisheries. Elevated levels of pCO2 (1200–2600 μatm) had no statistically significant effect on growth, survival, or otolith condition after 8 weeks of rearing. Field data show that in Long Island Sound, where scup spawn, in situ levels of pCO2 are already at levels ranging from 689 to 1828 μatm due to primary productivity, microbial activity, and anthropogenic inputs. These results demonstrate that ocean acidification is not likely to cause adverse effects on the growth and survivability of every species of marine fish. X‐ray analysis of the fish revealed a slightly higher incidence of hyperossification in the vertebrae of a few scup from the highest treatments compared to fish from the control treatments. Our results show that juvenile scup are tolerant to increases in seawater pCO2, possibly due to conditions this species encounters in their naturally variable environment and their well‐developed pH control mechanisms.
A Support Vector Data Description Approach for Background Modeling in Videos with Quasi-Stationary Backgrounds

Video segmentation is one of the most important tasks in high-level video processing applications. Stationary cameras are usually used in applications such as video surveillance and human activity recognition. However, possible changes in the background of the video such as waving flags, fluctuating monitors, water surfaces, etc. make the detection of objects of interest particularly challenging. These types of backgrounds are called quasi-stationary backgrounds. In this paper we propose a novel, non-statistical technique to generate a background model and use this model for background subtraction and foreground region detection in the presence of such challenges. The main advantage of the proposed method over the state of the art is that unlike statistical techniques the accuracy of foreground regions is not limited to the estimate of the probability density. Also, the memory requirements of our method are independent of the number of training samples. This makes the proposed method useful in various scenarios including the presence of slow changes in the background. A comprehensive study is presented on the efficiency of the proposed method. Its performance is compared with various existing techniques quantitatively and qualitatively to show its superiority in various applications.
Exploiting Clustering Techniques for Web User-session Inference

We focus on the definition and identification of “Web user-sessions”, an aggregation of several TCP connections generated by the same source host on the basis of TCP connection opening time. The identification of a user session is non trivial; traditional approaches rely on threshold based mechanisms, which are very sensitive to the value assumed for the threshold, which may be difficult to correctly set. By applying clustering techniques, we define a novel methodology to identify Web user-sessions without requiring an a priori definition of threshold values. We discuss pros and cons of this approach, and we define a methodology to be applied to real traffic traces. The proposed methodology is evaluated on artificially generated traces to show its benefits against traditional threshold based approaches. We then analyze the characteristics of user sessions extracted from real traces, studying the statistical properties of the identified sessions.
Estimating optimal regions for improvement in range acquisition from a single point of view

It is well established that acquiring large amount of data can quickly lead to important data management challenges where processing capabilities become saturated and preempt full usage of the information available for autonomous systems to make educated decisions. While sub-sampling offers a naïve solution for reducing dataset dimension, it does not capitalize on the knowledge available in already acquired data to selectively drive further acquisition over the most significant regions. This paper discusses the development of a probabilistic occupancy grid based algorithm to automatically establish which regions within a single point of view from a range sensor would provide the most improvement if further acquisitions were made. The algorithm, which is independent of the sensor used, is validated with range data acquired from the popular Kinect multi-modal imaging sensor.
Interrater Reliability of Early Childhood Education Professionals Involved in Developmental Surveillance for Autism Spectrum Disorder and Related Conditions

VALID AND RELIABLE TOOLS have recently been developed to accurately detect early signs of Autism Spectrum Disorder (ASD) and other developmental challenges in children as young as 12 months of age. Translation of research findings to practice and policy through routine implementation of evidence-based tools in the community, particularly early childhood education and childcare settings, is limited. This study establishes that the interrater reliability (IRR) of early childhood educators in administering the Social Attention and Communication Surveillance System (SACS-R) is very high (k = 0.909). This paper reports the results of the first step in the Right Kids, Right Time, Right Services project—a prospective cohort study that aims to implement and evaluate routine developmental surveillance for early signs of social and communication challenges in young children in childcare settings.
Cellular Automata Models for Diffusion of Innovations

We propose a probabilistic cellular automata model for the spread of innovations, rumors, news, etc. in a social system. The local rule used in the model is outertotalistic, and the range of interaction can vary. When the range R of the rule increases, the takeover time for innovation increases and converges toward its mean-field value, which is almost inversely proportional to R when R is large. Exact solutions for R=1 and $R=\infty$ (mean-field) are presented, as well as simulation results for other values of R. The average local density is found to converge to a certain stationary value, which allows us to obtain a semi-phenomenological solution valid in the vicinity of the fixed point n=1 (for large t).
Ex vivo culture of human colorectal tissue for the evaluation of candidate microbicides

Objectives:Establishment of an in vitro model to evaluate rectal safety and the efficacy of microbicide candidates. Design:An investigation and characterization of human colorectal explant culture for screening candidate microbicides to prevent rectal transmission of HIV-1 infection. Methods:Human colorectal explants were cultured at the liquid–air interface on gelfoam rafts. Phenotypic characterization of HIV-1 target cells was performed by fluorescence-activated cell sorter analysis. HIV-1 infection was determined by the measurement of p24 antigen release, viral RNA, and proviral DNA accumulation. Results:Colorectal explant CD4 T cells expressed higher CCR5 and CXCR4 levels compared with blood. Minor differences between the rectal and sigmoid colon were observed with a trend for slightly higher CCR5 and HLA-DR expression in cells from the sigmoid colon. Favourable culture conditions were established for colorectal tissue. Although tissue structure degenerated with time, CD4: CD8 cell ratios remained constant, and tissue supported productive HIV-1 infection. The ability of candidate microbicides to inhibit R5 HIV-1 infection was evaluated. Polyanion candidates, PRO2000 and dextrin sulphate, provided 99% protection at 1 μg/ml and 1 mg/ml, respectively, equivalent to 1/5000 and 1/40 of the vaginal formulations. The nucleotide reverse transcriptase inhibitor (NRTI) 9-[2-(phosphonomethoxy)propyl]adenine (PMPA) provided protection at concentrations 1000-fold lower (10 μg/ml) than the proposed vaginal formulation (1%). Furthermore, non-NRTI UC-781 and TMC-120 provided greater than 99% inhibition at 3.3 or 0.33 μg/ml, respectively. No products demonstrated toxicity to rectal mucosa at inhibitory concentrations. Conclusion:Colorectal explant culture was shown to be a useful tool for the preclinical evaluation of potential microbicides. The data suggest that rectally applied microbicides might provide protection from HIV-1 transmission.
Towards a Vertex and Edge Label Aware Force Directed Layout Algorithm

Many automatic graph layout algorithms can cause shaped vertices and edge labels (which have a size when drawn on the screen) to overlap in the resulting visualisation. Overlaps can hide information that users expect to see in cases where the graph is small. We perform two experiments on a large real-world set of small (10-110 vertex) graphs to compare how different combinations of forces in Eades' force directed layout algorithm affect the final graph layout. We identify an optimal combination of forces from those we tested. In particular, we found that adding charged walls, variable node charge and edge label charges, minimises overlaps. We also found that using Hooke's Law over Eades' logarithmic attractive force tends to reduce edge crossings.
The Genomic Distribution of Sex-Biased Genes in Drosophila serrata: X Chromosome Demasculinization, Feminization, and Hyperexpression in Both Sexes

The chromosomal distribution of genes with sex-biased expression is often nonrandom, and in species with XY sex chromosome systems, it is common to observe a deficit of X-linked male-biased genes and an excess of X-linked female-biased genes. One explanation for this pattern is that sex-specific selection has shaped the gene content of the X. Alternatively, the deficit of male-biased and excess of female-biased genes could be an artifact of differences between the sexes in the global expression level of their X chromosome(s), perhaps brought about by a lack of dosage compensation in males and hyperexpression in females. In the montium fruit fly, Drosophila serrata, both these explanations can account for a deficit of male-biased and excess of female-biased X-linked genes. Using genome-wide expression data from multiple male and female tissues (n = 176 hybridizations), we found that testis- and accessory gland-specific genes are underrepresented whereas female ovary-specific genes are overrepresented on the X chromosome, suggesting that X-linkage is disfavored for male function genes but favored for female function genes. However, genes with such sex-specific functions did not fully account for the deficit of male-biased and excess of female-biased X-linked genes. We did, however, observe sex differences in the global expression level of the X chromosome and autosomes. Surprisingly, and in contrast to other species where a lack of dosage compensation in males is responsible, we found that hyperexpression of X-linked genes in both sexes leads to this imbalance in D. serrata. Our results highlight how common genomic distributions of sex-biased genes, even among closely related species, may arise via quite different evolutionary processes.
Systematic Review of Methods and Results of Studies of the Genetic Epidemiology of Ischemic Stroke

Background and Purpose— To design appropriate molecular genetic studies, we first need to understand the genetic epidemiology of stroke. We therefore performed a systematic review of the literature to assess the heritability of stroke according to methodological quality of studies and to determine any heterogeneity in findings between studies and possible publication bias. Methods— We searched for twin studies and studies of family history of stroke using bibliographic databases and by hand-searching reference lists and journals. Odds ratios (ORs) for family history as a risk factor for stroke were calculated within studies and combined by meta-analysis. Heterogeneity between studies, methodological quality of studies, and the influence of the age at which stroke occurred in both probands and relatives were assessed. Results— We identified 53 independent studies (3 twin, 33 case-control, and 17 cohort). Monozygotic twins were more likely to be concordant than dizygotic twins (OR, 1.65; 95% CI, 1.2 to 2.3; P =0.003). A positive family history was a risk factor for stroke in both case-control (OR, 1.76; 95% CI, 1.7 to 1.9; P <0.00001) and cohort (OR, 1.30; 95% CI, 1.2 to 1.5; P <0.00001) studies. However, there was major heterogeneity between studies (cohort P =0.0001; case-control P <0.00001), with much stronger associations in small studies and methodologically less rigorous studies. Moreover, studies that reported insufficient data to allow meta-analysis tended to have found weaker associations. Family history of stroke was more frequent in studies that were confined to probands or relatives aged <70 years. However, few studies considered the number of affected and unaffected relatives, only 2 studies considered stroke phenotypes in detail, and only 19 studies (38%) adjusted associations for intermediate phenotypes. No twin study, only 5 cohort studies (26%), and 20 case-control studies (61%) differentiated between ischemic and hemorrhagic stroke in the proband. Family history of stroke was more frequent in large- and small-vessel stroke than in cardioembolic stroke. There were very few data on the influence of family history on stroke severity and no data on stroke recovery. Conclusions— Twin studies suggest a small genetic contribution to stroke, but reliable interpretation of published family history studies is undermined by major heterogeneity, insufficient detail, and potential publication and reporting bias. More detailed large-scale genetic epidemiology is required.
Solution structure of the first RNA recognition motif domain of human spliceosomal protein SF3b49 and its mode of interaction with a SF3b145 fragment

The spliceosomal protein SF3b49, a component of the splicing factor 3b (SF3b) protein complex in the U2 small nuclear ribonucleoprotein, contains two RNA recognition motif (RRM) domains. In yeast, the first RRM domain (RRM1) of Hsh49 protein (yeast orthologue of human SF3b49) reportedly interacts with another component, Cus1 protein (orthologue of human SF3b145). Here, we solved the solution structure of the RRM1 of human SF3b49 and examined its mode of interaction with a fragment of human SF3b145 using NMR methods. Chemical shift mapping showed that the SF3b145 fragment spanning residues 598–631 interacts with SF3b49 RRM1, which adopts a canonical RRM fold with a topology of β1‐α1‐β2‐β3‐α2‐β4. Furthermore, a docking model based on NOESY measurements suggests that residues 607–616 of the SF3b145 fragment adopt a helical structure that binds to RRM1 predominantly via α1, consequently exhibiting a helix–helix interaction in almost antiparallel. This mode of interaction was confirmed by a mutational analysis using GST pull‐down assays. Comparison with structures of all RRM domains when complexed with a peptide found that this helix–helix interaction is unique to SF3b49 RRM1. Additionally, all amino acid residues involved in the interaction are well conserved among eukaryotes, suggesting evolutionary conservation of this interaction mode between SF3b49 RRM1 and SF3b145.
GMTI on short sequences of pulses with compressed sensing

Due to the sparse distribution of ground moving targets, compressed sensing (CS) is a natural approach for their detection. Especially the detection from short CPIs of around 100 pulses is of high interest, since it allows to monitor large areas. In this paper we compare two approaches for handling of the non-sparse clutter - i. e. weighting and filtering - and put special emphasis on radar parameters fulfilling CS requirements.
PLAAC: a web and command-line application to identify proteins with prion-like amino acid composition

UNLABELLED Prions are self-templating protein aggregates that stably perpetuate distinct biological states and are of keen interest to researchers in both evolutionary and biomedical science. The best understood prions are from yeast and have a prion-forming domain with strongly biased amino acid composition, most notably enriched for Q or N. PLAAC is a web application that scans protein sequences for domains with P: rion- L: ike A: mino A: cid C: omposition. Users can upload sequence files, or paste sequences directly into a textbox. PLAAC ranks the input sequences by several summary scores and allows scores along sequences to be visualized. Text output files can be downloaded for further analyses, and visualizations saved in PDF and PNG formats. AVAILABILITY AND IMPLEMENTATION http://plaac.wi. mit.edu/. The Ruby-based web framework and the command-line software (implemented in Java, with visualization routines in R) are available at http://github.com/whitehead/plaac under the MIT license. All software can be run under OS X, Windows and Unix.
Cooperative coevolution of artificial neural network ensembles for pattern classification

This paper presents a cooperative coevolutive approach for designing neural network ensembles. Cooperative coevolution is a recent paradigm in evolutionary computation that allows the effective modeling of cooperative environments. Although theoretically, a single neural network with a sufficient number of neurons in the hidden layer would suffice to solve any problem, in practice many real-world problems are too hard to construct the appropriate network that solve them. In such problems, neural network ensembles are a successful alternative. Nevertheless, the design of neural network ensembles is a complex task. In this paper, we propose a general framework for designing neural network ensembles by means of cooperative coevolution. The proposed model has two main objectives: first, the improvement of the combination of the trained individual networks; second, the cooperative evolution of such networks, encouraging collaboration among them, instead of a separate training of each network. In order to favor the cooperation of the networks, each network is evaluated throughout the evolutionary process using a multiobjective method. For each network, different objectives are defined, considering not only its performance in the given problem, but also its cooperation with the rest of the networks. In addition, a population of ensembles is evolved, improving the combination of networks and obtaining subsets of networks to form ensembles that perform better than the combination of all the evolved networks. The proposed model is applied to ten real-world classification problems of a very different nature from the UCI machine learning repository and proben1 benchmark set. In all of them the performance of the model is better than the performance of standard ensembles in terms of generalization error. Moreover, the size of the obtained ensembles is also smaller.
Performance Analysis of Next Generation Mobility Protocols for IMS/MMD Networks

In an effort to provide seamless mobility support in IMS/MMD networks, operators need to choose a specific IP- based mobility protocol. However, there are several micro- and macro-mobility protocols available that the operators can choose from. Operators often face the challenges of selecting the appropriate mobility protocol that can provide the most cost efficient solution under a specific operating environment. Thus, it is important to analyze the effectiveness of these protocols before they are actually deployed in the IMS/MMD networks. In this paper, we analyze a number of candidate mobility protocols and conduct a performance analysis of some of these using a prototype implementation in an IPv6-based IMS/MMD testbed. These analyses provide us with some guidelines in terms of the applicability of these protocols when operators plan to deploy their IMS/MMD networks.
Efficient operating system support for group unicast

A common requirement of many Internet services is to send exactly the same data to a number of hosts at the same time. Without IP-level multicast, this form of group communication is realized by unicasting the data to each desired host. Although this approach is portable and easy to implement, it is extremely inefficient for the sending host. In this paper, we propose a kernel-based technique to efficiently facilitate unicast send operations for group communication with only minimal additions to the sending operating system interface and implementation. We present the design and prototype implementation of our approach and experimentally demonstrate the significant performance improvements it provides. Additionally, we conduct experiments to decompose the processing costs in the network stack and show that the biggest cost reductions are not necessarily due to reduced memory copying.
Financial Development , Consumption Smoothing , and the Reduced Volatility of Real Growth

Over the past quarter century, much of the developed and developing world has experienced a great moderation. Economic growth is more stable than it once was. Using data from 13 OECD countries, we analyze the role of financial development in relieving household liquidity constraints, thereby allowing for smoother consumption and less volatile growth. In the paper we begin by documenting the combined reduction in the volatility of both consumption and real growth, together with the increases in credit extended to the private sector. Our data allows us estimate the time variation in the proportion of the population that is limited to consuming, at most, its current income (thus violating the life-cycle permanent income hypothesis). We then proceed to make the case for a causal relationship: Financial development increases access to credit markets, enabling households to smooth their consumption, which reduces the volatility of consumption and real growth. JEL classification: E21, E32, E44
Confocal Endomicroscopy of Colorectal Polyps

Confocal laser endomicroscopy (CLE) is one of several novel methods that provide real-time, high-resolution imaging at a micron scale via endoscopes. CLE has the potential to be a disruptive technology in that it can change the current algorithms that depend on biopsy to perform surveillance of high-risk conditions. Furthermore, it allows on-table decision making that has the potential to guide therapy in real time and reduce the need for repeated procedures. CLE and related technologies are often termed “virtual biopsy” as they simulate the images seen in traditional histology. However, the imaging of living tissue allows more than just pragmatic convenience; it also allows imaging of living tissue such as active capillary circulation, cellular death, and vascular and endothelial translocation, thus extending beyond what is capable in traditional biopsy. Immediate potential applications of CLE are to guide biopsy sampling in Barrett's esophagus and inflammatory bowel disease surveillance, evaluation of colorectal polyps, and intraductal imaging of the pancreas and bile duct. Data on these applications is rapidly emerging, and more is needed to clearly demonstrate the optimal applications of CLE. In this paper, we will focus on the role of CLE as applied to colorectal polyps detected during colonoscopy.