Miracle-dz/UniFAR-FTUs huggingface dataset:
Morphological integration and developmental progress during fish ontogeny in two contrasting habitats

SUMMARY Morphological integration can respond to environmental conditions, a response that may be dynamic through ontogeny. Among fishes, brook charrs (Salvelinus fontinalis) display a trophic polymorphism that makes it a good species for analyzing the ontogeny of morphological integration. To better understand the processes regulating variation and integration, we assess the ontogenetic dynamics of covariances and developmental progress for populations of S. fontinalis from two habitats that differ in water velocity; lake and stream. Geometric morphometrics and developmental progress were evaluated on 751 and 198 specimens, respectively. In both habitats, most ossification events occur before the transition from alevin to juvenile. This threshold defines two distinct periods. During the first period representing free‐embryos and alevins, there are important shape changes and rapid ossification, integration tends to be relatively low and decreasing and the variance of shape drastically decreases. During the juvenile period, the rate of shape change decreases and the onset of ossification is nearly complete, plus integration increases and shape variance stabilizes. While we find two distinct developmental periods, we nonetheless find a notable stability underlying the ontogenetic dynamics of variability as well as gradual change in the structure of covariation within each habitat. Our results imply that the variability of juvenile body shape does not seem to retain signals of variability determined early in ontogeny and warrants caution in using juvenile as guides to the earlier causes of variability. Overall, this study highlights the difficulty of inferring causes of integration from studies of static covariance.
CBCT of skeletal changes following rapid maxillary expansion to increase arch-length with a development-dependent bonded or banded appliance.

OBJECTIVE To assess the three-dimensional (3D) skeletal response to a standardized 5 mm of rapid maxillary expansion (RME) in growing children (6-15 years) with maxillary width deficiency and crowding. MATERIALS AND METHODS A bonded appliance was used prior to the eruption of the maxillary first premolars (Mx4s), and a banded appliance was used thereafter. A consecutive sample of 89 patients (29 boys and 60 girls) from a large pediatric dentistry and orthodontics practice was divided into four groups: 1) 6-8 years old (n = 26), 2) 9-11 years old with unerupted Mx4s (n = 21), 3) 9-11 years with erupted Mx4s (n = 23), and 4) 12-15 years (n = 19). For all patients, the 3D evaluation of dental and skeletal effects was performed with cone-beam computed tomography (CBCT). RESULTS For both appliances in all patients, CBCT confirmed a triangular pattern of expansion in both the frontal and sagittal planes. Overall, both appliances produced significant maxillary expansion (>80% of the 5-mm activation), but older children showed a progressively more dental (less skeletal) response. Comparison of the two types of expanders in the crossover sample, children aged 9-11 years, showed that the bonded RME produced the most efficient skeletal expansion in the preadolescent sample. Increased maxillary width at the level of the zygomaticomaxillary suture was the best indicator for development of maxillary arch circumference. CONCLUSION Development-dependent appliances (bonded RPE before Mx4s erupt, and a banded device thereafter) provided optimal RME treatment for all children from age 6-15 years.
Hepatitis B virus with antigenically altered hepatitis B surface antigen is selected by high‐dose hepatitis B immune globulin after liver transplantation

“Escape” variants of hepatitis B virus (HBV) can cause infection despite previous immunization. These viruses show alterations of the immunogenic major hydrophilic loop of the HBV small surface protein (s‐protein). We studied whether HBV “escape” variants were selected in patients with graft infection after liver transplantation for HBV‐related diseases who received passive immunoprophylaxis with high‐dose polyclonal hepatitis B hyperimmune globulin (HBIG). For that, pre‐ and posttransplantation sera of 34 patients were analyzed for the occurence of HBV S‐gene variants. In addition, binding of in vitro–translated variant s‐proteins to HBIG was studied. Variants with exchanges of amino acid (aa) 144 (s144) in HBV genotype A and 145 in genotype D (s145) were found to emerge, persist, and predominate during HBIG, and thus fulfilled criteria of “escape” variants selected. In addition to already‐known variants sG145R/K/E, we could demonstrate that newly described variants sX144G and sG145A were antigenically altered and showed impaired recognition by polyclonal HBIG in vitro. Diminished recognition of variant s‐proteins correlated with the failure of HBIG to prevent infection of the liver graft with antigenically altered variant HBV. Patients infected with “escape” variants s144 or s145 showed a worse clinical outcome compared with the other patients on high‐dose, long‐term HBIG prophylaxis (44% vs. 23% graft failure caused by HBV infection). Our results suggest that antigenically altered HBV variants s144 and s145 can be selected by HBIG and can influence clinical outcome after liver transplantation.
Integration of electric vehicles within microgrid

This paper presents an analytical approach to integrate electric vehicles (EVs) into the microgrid in order to enhance its voltage stability. Analytical characterization equations linking the microgrid and the EVs are first developed. Then, based on a practical distribution network and realistic load conditions, case studies are undertaken to show the positive impacts of EV integration. Matpower program is used to formulate and perform the power flow analysis. Eigenvalue, eigenvector and participation factor analysis are used to monitor voltage stability and identify the weakest bus on the system. The results show quantitatively the extent to which the addition of electric vehicles can enhance voltage level and voltage stability of the system under study.
Vaccines and Autoimmunity

Vaccines have eradicated or controlled many infectious diseases, saving each year millions of lives and quality of life of many other millions of people. In spite of the success of vaccines over the last two centuries, parents (and also some health care workers) gloss over the devastating consequences of diseases, which are now avoided thanks to vaccines, and direct their attention to possible negative effects of immunization. Three immunological objections are raised: vaccines cause antigenic overload, natural immunity is safer and better than vaccine-induced immunity, and vaccines induce autoimmunity. The last point is examined in this review. Theoretically, vaccines could trigger autoimmunity by means of cytokine production, anti-idiotypic network, expression of human histocompatibility leukocyte antigens, modification of surface antigens and induction of novel antigens, molecular mimicry, bystander activation, epitope spreading, and polyclonal activation of B cells. There is strong evidence that none of these mechanisms is really effective in causing autoimmune diseases. Vaccines are not a source of autoimmune diseases. By contrast, absolute evidence exists that infectious agents can trigger autoimmune mechanisms and that they do cause autoimmune diseases.
My head is your tail: applying link analysis on long-tailed music listening behavior for music recommendation

Collaborative filtering, being a popular method for generating recommendations, produces satisfying results for users by providing extremely relevant items. Despite being popular, however, this method is prone to many problems. One of these problems is popularity bias, in which the system becomes skewed towards items that are popular amongst the general user population. These 'obvious' items are, technically, extremely relevant items but fail to be novel. In this paper, we maintain using collaborative filtering methods while still managing to produce novel yet relevant items. This is achieved by utilizing the long-tailed distribution of listening behavior of users, in which their playlists are biased towards a few songs while the rest of the songs, those in the long tail, have relatively low play counts. In addition, we also apply a link analysis method to users and define links between them to create an increasingly fine-grained approach in calculating weights for the recommended items. The proposed recommendation method was available online as a user study in order to measure the relevancy and novelty of the recommended items. Results show that the algorithm manages to include novel recommendations that are still relevant, and shows the potential for a new way of generating novel recommendations.
Flexible multimode polymer waveguides for versatile high-speed optical interconnects

In this work, the loss and bandwidth performance of flexible multimode polymer waveguides are investigated under different launch conditions. It is shown that bending excess loss below 2 dB is achieved for radii larger than 3 mm for a 50 µm MMF input, and twisting excess loss below 0.6 dB for up to 1 full 360-degree turn even for a relatively overfilled launch. The bandwidth studies reveal that bending the waveguides does not significantly impact their bandwidth performance, with bandwidth-length product values in excess of 150 GHz×m recorded for the launch conditions studied.
Budesonide/Formoterol for bronchiolitis obliterans after hematopoietic stem cell transplantation.

RATIONALE Systemic steroids are the standard treatment for bronchiolitis obliterans syndrome (BOS) after allogeneic hematopoietic stem cell transplantation (HSCT) despite their poor efficacy and disabling side effects. OBJECTIVES To evaluate the effectiveness and tolerance of budesonide/formoterol as an alternative treatment for BOS after HSCT. METHODS In this randomized, double-blind, placebo-controlled study, we randomly assigned 32 HSCT recipients with mild/severe BOS to receive budesonide/formoterol or placebo for 6 months. The primary outcome was the change in the FEV1 after 1 month of treatment (M1) compared with the baseline value. Patients were unblinded at M1 if there was no improvement in the FEV1. Those who had initially received placebo were switched to budesonide/formoterol. Intention-to-treat analysis was performed to assess the primary outcome. Additional analyses took scheduled treatment contamination into account. MEASUREMENTS AND MAIN RESULTS At M1, the median FEV1 increased by 260 ml in the budesonide/formoterol arm compared with 5 ml in the placebo arm (P = 0.012). The median increases in the FEV1 at M1 relative to the baseline value for the treated and placebo groups were 13 and 0%, respectively (P = 0.019). Twenty-five patients received budesonide/formoterol during the study. The median difference in the FEV1 between the baseline and after 1 month of treatment for these patients was +240 ml (P = 0.0001). The effect of budesonide/formoterol on the FEV1 was maintained in the 13 patients who completed 6 months of treatment. CONCLUSIONS Budesonide/formoterol administration led to a significant improvement in the FEV1 in patients with mild/severe BOS after allogeneic HSCT. Clinical trial registered with www.clinicaltrials. gov (NCT00624754).
Towards a standard for annotating abstract anaphora

This paper presents a survey on the annotation of abstract (= discourse-deictic) anaphora, i.e. anaphora that involves reference to abstract entities such as events and propositions. The survey identifies features that are common to the majority of relevant annotation efforts. Based on these, we propose a small set of recommendations, which can be viewed as a first, small step towards a standard for the annotation of abstract anaphora. As the overview shows, English is the language that most of the resources have been created for. However, many of them contain only few instances of abstract anaphora. Hence, the currently available evidence only supports preliminary conclusions.
The incidence of colorectal cancer following a negative screening sigmoidoscopy: implications for screening interval.

BACKGROUND & AIMS Current guidelines recommend a 5-year interval for colorectal cancer (CRC) screening by sigmoidoscopy. However, the optimal screening interval is uncertain. We estimated the annual incidence of distal and proximal CRC in the first 5 years following a negative sigmoidoscopy examination to gauge the potential benefit of rescreening in <5 years. METHODS A cohort of 72,483 participants in the Colon Cancer Prevention program of Kaiser Permanente of Northern California (KP) was defined using computerized databases. Men and women aged 50 years and older who had a negative screening flexible sigmoidoscopy examination between 1994 and 1996 and were considered not to be at high risk for developing CRC were included. Subjects were censored at the time of diagnosis (for cases), death, termination of KP membership, or subsequent colon examination. RESULTS Thirty cases of distal and 80 cases of proximal CRC occurred. Age-adjusted incidence rates of distal CRC ranged from a low of 2.8 per 100,000 person-years in the first year of follow-up to a high of 13.0 per 100,000 in the fourth year (rate difference, 10.2; 95% confidence interval, 1.1-19.3). However, for the entire follow-up period, incidence of distal CRC remained much lower than age-adjusted rates of 70.6 in the general population (Surveillance, Epidemiology, and End Results registry). The incidence of proximal CRC was also decreased modestly over population rates of disease. CONCLUSIONS Screening by sigmoidoscopy more frequently than every 5 years would likely lead, at best, to only modest improvements as compared with a 5-year screening interval.
Microstructural Feature-based Processing and Analysis of Diffusion Tensor MRI

Tensors increasingly arise in a variety of medical imaging and image processing contexts. Diffusion tensor magnetic resonance imaging (DT-MRI) measures the self-diffusion rate of water molecules within small volumes of biological tissues to characterize their microstructural features. The diffusion tensor can be decomposed into shape and orientation components, and the shape components are intuitively and saliently characterized by tensor invariants. Hence the invariant and orientation information implies the microstructural features of tissues. The mathematical framework that freely builds tensors from tensor invariants has been recently established, and allowed for developing novel approaches for processing and analysis of diffusion tensor fields. New tensor interpolation methods are devised that linearly interpolate each of tensor invariants and orientations to preserve cardiac microstructural features. The uniform tensor invariant set is proposed that linearly characterizes tensor shape, and provides more accurate tensor field interpolation and analysis of cardiac diffusion tensor fields. A microstructural feature-based tensor distance is also defined by a linear combination of tensor invariant and orientation distances, and applied to graph-based segmentation of cardiac diffusion tensor fields. Finally, the effects of noise in DT-MRI are evaluated on tensor invariants characterizing tensor shape over the complete space of tensor shape. In addition, a new framework is developed for determining the distribution of the likely true values of tensor invariants given their noisy measures.
A Sub-2 W Low Power IA Processor for Mobile Internet Devices in 45 nm High-k Metal Gate CMOS

This paper describes a low power Intel Architecture (IA) processor specifically designed for Mobile Internet Devices (MID) with performance similar to mainstream Ultra-Mobile PCs. The design relies on high residency in a new low-power state in order to keep average power and idle power below 220 and 80 mW, respectively. The design consists of an in-order pipeline capable of issuing 2 instructions per cycle supporting 2 threads, 32 KB instruction and 24 KB data L1 caches, independent integer and floating point execution units, times86 front end execution unit, a 512 KB L2 cache and a 533 MT/s dual-mode (GTL and CMOS) front-side-bus (FSB). The design contains 47 million transistors in a die size under 25 mm2 manufactured in a 9-metal 45 nm CMOS process with optimized transistors for low leakage. Maximum thermal design power (TDP) consumption is measured at 2 W at 1.0 V, 90degC using a synthetic power-virus test at a frequency of 1.86 GHz.
Inter-cluster Topology Control: An Evolutionary Game Perspective

Topology control (TC) is one of the most important techniques used in wireless ad hoc and sensor networks, the goal of which is to assign appropriate transmission power to each node such that the resulting topology is energy efficient and satisfies some global graph properties such as connectivity. In practical networks, with nodes distributed in clusters generally, setting up links between clusters and maintaining inter-cluster connectivity is important. In this paper, we focus on inter-cluster topology control and examine the following question: if nodes behave in a selfish and bounded rational manner, how does it impact the inter-cluster connectivity and energy consumption in the resulting topologies? To model the complicated interactions among intra-cluster and inter-cluster nodes, we formulate the inter-cluster topology control problem as an evolutionary game and derive the evolutionarily stable strategy (ESS) that no one will deviate from. Moreover, we propose a distributed learning algorithm for the nodes to converge to the ESS. With the proposed algorithm, each node chooses its transmission power with the probabilities learned purely from its own past utility history. Simulation results show that our system can quickly converges to the ESS, which is robust to sudden unfavorable deviations of the selfish nodes.
Transat—A Method for Detecting the Conserved Helices of Functional RNA Structures, Including Transient, Pseudo-Knotted and Alternative Structures

The prediction of functional RNA structures has attracted increased interest, as it allows us to study the potential functional roles of many genes. RNA structure prediction methods, however, assume that there is a unique functional RNA structure and also do not predict functional features required for in vivo folding. In order to understand how functional RNA structures form in vivo, we require sophisticated experiments or reliable prediction methods. So far, there exist only a few, experimentally validated transient RNA structures. On the computational side, there exist several computer programs which aim to predict the co-transcriptional folding pathway in vivo, but these make a range of simplifying assumptions and do not capture all features known to influence RNA folding in vivo. We want to investigate if evolutionarily related RNA genes fold in a similar way in vivo. To this end, we have developed a new computational method, Transat, which detects conserved helices of high statistical significance. We introduce the method, present a comprehensive performance evaluation and show that Transat is able to predict the structural features of known reference structures including pseudo-knotted ones as well as those of known alternative structural configurations. Transat can also identify unstructured sub-sequences bound by other molecules and provides evidence for new helices which may define folding pathways, supporting the notion that homologous RNA sequence not only assume a similar reference RNA structure, but also fold similarly. Finally, we show that the structural features predicted by Transat differ from those assuming thermodynamic equilibrium. Unlike the existing methods for predicting folding pathways, our method works in a comparative way. This has the disadvantage of not being able to predict features as function of time, but has the considerable advantage of highlighting conserved features and of not requiring a detailed knowledge of the cellular environment.
Entropically driven self–assembly and interaction in suspension

In this paper we present fundamental studies elucidating the role of entropy in particle suspensions. We focus on systems composed of large colloidal particles along with a second, usually smaller species such as a particle or polymer. We describe direct measurements of these interactions in suspension, and we systematically show how these forces can be used to control the self–assembly of colloidal particles. The paper provides a unified review of the experiments from our laboratory, and in a few cases touches on very recent results.
Non-Clear Typhoon Eye Tracking by Artificial Ant Colony

Generally, large volumes of complicate and precise computation are required during the tracking process of typhoon eye, especially non-clear ones, which is one of the most important aspects in the forecast and analysis of typhoon. Satellite digital photograph and corresponding interpretation technology make it possible to carry out such task by aid of modern digital and computer means of image processing. By means of constructing solution space and heuristic information, artificial ant colony (AAC) can be used to search for the best path in a constrained region, which provides an approach to obtain precise contour, and is proved to reach the best feasible boundary with minimum energy function value. Therefore, the contour of non-clear typhoon eye can be tracked intelligently, based on the satellite photograph. As an example, the computing methodology produced in this paper was applied in experimental cyclone forecasting by the Shanghai Meteorology Center. The proposed solutions was confirmed to have the potential for successful application to the problem of non-clear typhoon eye tracking, and the system is effective and the performance errors are acceptable for practical applications
Theoretical Analyses of Photoinduced Electron Transfer from Aromatic Amino Acids to the Excited Flavins in Some Flavoproteins

Kiattisak Lugsanangarm1, Nadtanet Nunthaboot2, Somsak Pianwanit1,3,*, Sirirat Kokpol1,3 and Fumio Tanaka1,4,* 1Department of Chemistry, Faculty of Science, Chulalongkorn University, 2Department of Chemistry, Faculty of Science, Mahasarakham University, Mahasarakham, 3Center of Excellence for Petroleum, Petrochemicals, and Advanced Materials, Chulalongkorn University, Bangkok, 4Laser Biochemistry Division, Institute for Laser Technology, Osaka, 1,2,3Thailand 4Japan
Online multitasking and user engagement

Users often access and re-access more than one site during an online session, effectively engaging in multitasking. In this paper, we study the effect of online multitasking on two widely used engagement metrics designed to capture users browsing behavior with a site. Our study is based on browsing data of 2.5M users across 760 sites encompassing diverse types of services such as social media, news and mail. To account for multitasking we need to redefine how user sessions are represented and we need to adapt the metrics under study. We introduce a new representation of user sessions: tree-streams -- as opposed to the commonly used click-streams -- present a more accurate picture of the browsing behavior of a user that includes how users switch between sites (e.g., hyperlinking, teleporting, backpaging). We then discuss a number of insights on multitasking patterns, and show how these help to better understand how users engage with sites. Finally, we define metrics that characterize multitasking during online sessions and show how they provide additional insights to standard engagement metrics.