Miracle-dz/UniFAR-FTUs huggingface dataset:
Late Replicating Domains Are Highly Recombining in Females but Have Low Male Recombination Rates: Implications for Isochore Evolution

In mammals sequences that are either late replicating or highly recombining have high rates of evolution at putatively neutral sites. As early replicating domains and highly recombining domains both tend to be GC rich we a priori expect these two variables to covary. If so, the relative contribution of either of these variables to the local neutral substitution rate might have been wrongly estimated owing to covariance with the other. Against our expectations, we find that sex-averaged recombination rates show little or no correlation with replication timing, suggesting that they are independent determinants of substitution rates. However, this result masks significant sex-specific complexity: late replicating domains tend to have high recombination rates in females but low recombination rates in males. That these trends are antagonistic explains why sex-averaged recombination is not correlated with replication timing. This unexpected result has several important implications. First, although both male and female recombination rates covary significantly with intronic substitution rates, the magnitude of this correlation is moderately underestimated for male recombination and slightly overestimated for female recombination, owing to covariance with replicating timing. Second, the result could explain why male recombination is strongly correlated with GC content but female recombination is not. If to explain the correlation between GC content and replication timing we suppose that late replication forces reduced GC content, then GC promotion by biased gene conversion during female recombination is partly countered by the antagonistic effect of later replicating sequence tending increase AT content. Indeed, the strength of the correlation between female recombination rate and local GC content is more than doubled by control for replication timing. Our results underpin the need to consider sex-specific recombination rates and potential covariates in analysis of GC content and rates of evolution.
Comparison of Biodistribution of 79 IT / 36 Monoclonal Antibody and Its Fab / c Fragment in BALB / c Mice and Nude Mice Bearing Human Tumor Xenografts 1

Fab/c fragments, purified from pepsin digest of mouse IgG2b mono clonal antibody (MoAb) 791T/36, consist of one Fab arm and the intact Fc portion. Pharmacokinetic and biodistribution studies in BALB/c mice of radioiodine-labeled 791T/36 MoAb and its Fab/c fragments showed that, due to the presence of the Fc portion, the Fab/c fragment has the same catabolic rate as whole antibody ( I. = 64 h). Due to its lower molecular weight (105,000), the Fab/c fragment extravasated more quickly and to a greater extent than whole MoAb in organs in which the vascular endothelium was fenestrated or continuous. In organs in which the vascular endothelium is sinusoidal, such as in liver and spleen, their diffusion capacities were identical. Therefore, Fab/c fragments reconcile advantages of the intact antibody molecule (slow catabolic rate) and Fab or F(ab)2 fragments (increased extravascular diffusion), features required to improve targeting to solid tumors. Data from biodistribution studies in nude mice bearing subcutaneous 79IT tumor (antigen positive) and Colo205 tumor (antigen negative) contralaterally showed important dif ferences in the behavior of whole MoAb and Fab/c fragment: (a) Whole MoAb was cleared more rapidly from the body and from the blood than Fab/c fragment; (b) The MoAb was taken up by the spleen (tissue to blood ratio >1 from 12 h after injection over the 3 days of the experiment) and the liver (0.6), whereas Fab/c fragment tissue to blood ratios were only slightly increased (0.34 and 0.35) compared to control nude mice (0.25 and 0.28) for the spleen and liver, respectively, 3 days after injection. Since both MoAb and Fab/c fragment bear the Fc portion, these data suggest that the reputed "nonspecific uptake" of antibodies due to the Fc portion could be an Fc-mediated specific uptake, e.g., uptake of immune complexes; (c) The tumor to blood ratios were 1.7 and 1.2 for MoAb and Fab/c fragment, respectively, from 24 h throughout the experiment, whereas the percentage of injected dose (% of ID) present/g of 791T tumor was at any time greater for Fab/c fragment (8% maximum of ID) than for MoAb (5% of ID). These results were not expected in view of the low immunoreactivity in vitro of F"ab/cfragments compared to whole antibody. It is suggested that the distribution and the catabolic rate of whole antibody and its Fab/c fragment at the tumor level are modulated by their respective valency and Â¡mmunoreactivityfor the target cell.
Detailed characterization of the lipid composition of detergent-resistant membranes from photoreceptor rod outer segment membranes.

PURPOSE In recent years, detergent-resistant membranes (DRMs) have been isolated in in vitro models of lipid rafts, from photoreceptor outer segments (ROS), and the localization of a specific complement of photoreceptor proteins has been demonstrated. However, surprisingly little is known about the lipid composition of these important membrane domains. The present study provides the first characterization of phospholipids and fatty acids from ROS-derived DRMs. METHODS Bovine ROS membranes were incubated with 1% Triton X-100 at 4 degrees C and subjected to density gradient centrifugation to isolate DRMs from the parent membranes. Lipids of ROS and DRMs were separated by two-dimensional, thin-layer chromatography and converted to methyl esters, and fatty acids were analyzed by gas chromatography. Proteins of ROS and DRMs were analyzed by SDS-PAGE and Western blot analysis. RESULTS The DRMs represented 8% and 3%, respectively, of total ROS lipid and protein. In general, DRMs were enriched in saturated fatty acids when compared with ROS membranes. Relative to ROS, DRMs were enriched in free fatty acids (FFAs) and a specific phosphatidylcholine (PC) fraction that was almost devoid of polyunsaturated fatty acids (PUFAs). DRMs contained less phosphatidylethanolamine (PE) and phosphatidylserine (PS). Ceramide (CM) from ROS contained PUFAs but no saturated fatty acids; the converse was true of CM from DRMs. Docosahexaenoic acid was diminished in DRM PS and was not detected in the FFAs, but was equally abundant in ROS and DRM PE. ROS-derived DRMs were dramatically enriched in caveolin-1, contained significant amounts of transducin-alpha and c-Src, and were relatively devoid of arrestin. CONCLUSIONS The relatively saturated lipid environment observed in DRMs is likely to promote the localization of signaling proteins modified with saturated fatty acyl chains. Based on the lipid composition of DRMs, the authors conclude that they would not efficiently support phototransduction.
Ideal Japanese Class for Taiwanese High School Students: A Gender Comparison

Learning Japanese has become very common amongst Taiwanese high school and university students, ranking thesecond most sought for language. A concise study of the likeable activities in a typical language class for theTaiwanese students seems to be quite useful. Therefore, the present study has concentrated on the senior high schoolstudents’ opinion about the ideal Japanese class. Subjects in this research were 478 students (181 boys, and 297 girls)in nine private schools in three counties. The instrument was a 10-item multiple-choice Chinese questionnaire basedon Littlewood (2010). The findings illustrated that females and males had similar opinions concerning thecommunicative language activities in an ideal Japanese class. They revealed much more differences related tonon-communicative activities, though. Moreover, both boys and girls displayed the highest interest in a relaxed classatmosphere, and the lowest interest in the usage of smartphones in the activities in the class.
A system to restore walking in the vicinity of a wheelchair for people with paraplegia resulting from spinal cord injury is under development

cord injury is under development. The approach combines single channel surface electrical stimulation with an orthosis. The orthosis is spring loaded and contains a pneumatic system that stores energy during knee extension caused by quadriceps stimulation and transfers it to hip joint for hip extension. A laboratory version of the prototype of the gait system has been fabricated and engineering bench tests were performed. The paper presents the design of the wearable prototype and results of bench testing.
DNA sequence templates adjacent nucleosome and ORC sites at gene amplification origins in Drosophila

Eukaryotic origins of DNA replication are bound by the origin recognition complex (ORC), which scaffolds assembly of a pre-replicative complex (pre-RC) that is then activated to initiate replication. Both pre-RC assembly and activation are strongly influenced by developmental changes to the epigenome, but molecular mechanisms remain incompletely defined. We have been examining the activation of origins responsible for developmental gene amplification in Drosophila. At a specific time in oogenesis, somatic follicle cells transition from genomic replication to a locus-specific replication from six amplicon origins. Previous evidence indicated that these amplicon origins are activated by nucleosome acetylation, but how this affects origin chromatin is unknown. Here, we examine nucleosome position in follicle cells using micrococcal nuclease digestion with Ilumina sequencing. The results indicate that ORC binding sites and other essential origin sequences are nucleosome-depleted regions (NDRs). Nucleosome position at the amplicons was highly similar among developmental stages during which ORC is or is not bound, indicating that being an NDR is not sufficient to specify ORC binding. Importantly, the data suggest that nucleosomes and ORC have opposite preferences for DNA sequence and structure. We propose that nucleosome hyperacetylation promotes pre-RC assembly onto adjacent DNA sequences that are disfavored by nucleosomes but favored by ORC.
LBSNRank: personalized pagerank on location-based social networks

Different from traditional social networks, the location-based social networks allow people to share their locations according to location-tagged user-generated contents, such as checkins, trajectories, text, photos, etc. In location-based social networks, which are based on users' checkins, people could share his or her location according to checkin while visiting around. However, people's locations change frequently and the rankings of people change dynamically too, which makes ranking on graphs a challenging work. To address this challenge, we propose the LBSNRank algorithm on graphs with nodes whose contents change dynamically. To validate our algorithm on real datasets, we have crawled and analyzed a dataset from the Dianping website. Experiments on this real dataset show that our LBSNRank algorithm performs better than traditional personalized PageRank in efficiency.
Hiding in Plain Sight: The Anatomy of Malicious Facebook Pages

Facebook is the world's largest Online Social Network, having more than 1 billion users. Like most other social networks, Facebook is home to various categories of hostile entities who abuse the platform by posting malicious content. In this paper, we identify and characterize Facebook pages that engage in spreading URLs pointing to malicious domains. We used the Web of Trust API to determine domain reputations of URLs published by pages, and identified 627 pages publishing untrustworthy information, misleading content, adult and child unsafe content, scams, etc. which are deemed as "Page Spam" by Facebook, and do not comply with Facebook's community standards. Our findings revealed dominant presence of politically polarized entities engaging in spreading content from untrustworthy web domains. Anger and religion were the most prominent topics in the textual content published by these pages. We found that at least 8% of all malicious pages were dedicated to promote a single malicious domain. Studying the temporal posting activity of pages revealed that malicious pages were more active than benign pages. We further identified collusive behavior within a set of malicious pages spreading adult and pornographic content. We believe our findings will enable technologists to devise efficient automated solutions to identify and curb the spread of malicious content through such pages. To the best of our knowledge, this is the first attempt in literature, focused exclusively on characterizing malicious Facebook pages.
Contribution of primary carbonaceous aerosol to cloud condensation nuclei: processes and uncertainties evaluated with a global aerosol microphysics model

This paper explores the impacts of primary carbonaceous aerosol on cloud condensation nuclei (CCN) concentrations in a global climate model with size-resolved aerosol microphysics. Organic matter (OM) and elemental carbon (EC) from two emissions inventories were incorporated into a preexisting model with sulfate and sea-salt aerosol. The addition of primary carbonaceous aerosol increased CCN(0.2%) concentrations by 65–90% in the globally averaged surface layer depending on the carbonaceous emissions inventory used. Sensitivity studies were performed to determine the relative importance of organic solubility/hygroscopicity in predicting CCN. In a sensitivity study where carbonaceous aerosol was assumed to be completely insoluble, concentrations of CCN(0.2%) still increased by 40–50% globally over the no carbonaceous simulation because primary carbonaceous emissions were able to become CCN via condensation of sulfuric acid. This shows that approximately half of the contribution of primary carbonaceous particles to CCN in our model comes from the addition of new particles (seeding effect) and half from the contribution of organic solute (solute effect). The solute effect tends to dominate more in areas where there is less inorganic aerosol than organic aerosol and the seeding effect tends to dominate in areas where there is more inorganic aerosol than organic aerosol. It was found that an accurate simulation of the number size distribution is necessary to predict the CCN concentration but assuming an average chemical composition will generally give a CCN concentration within a factor of 2. If a "typical" size distribution is assumed for each species when calculating CCN, such as is done in bulk aerosol models, the mean error relative to a simulation with size resolved microphysics is on the order of 35%. Predicted values of carbonaceous aerosol mass and aerosol number were compared to observations and the model showed average errors of a factor of 3 for carbonaceous mass and a factor of 4 for total aerosol number; however, errors in the accumulation mode concentrations were found to be lower in comparisons with European and marine observations. The errors in CN and carbonaceous mass may be reduced by improving the emission size distributions of both primary sulfate and primary carbonaceous aerosol.
Influence of large woody debris and a bankfull flood on movement of adult resident coastal cutthroat trout (Oncorhynchus clarki) during fall and winter

To improve understanding of the significance of large woody debris to stream fishes, we examined the influence of woody debris on fall and winter movement by adult coastal cutthroat trout (Oncorhynchus clarki) using radiotelemetry. Fish captured in stream pools containing large woody debris moved less than fish captured in pools lacking large woody debris or other cover. Fish from pools lacking cover commonly moved to habitats with large boulders or brush, particularly during the day. Movements by fish over 1-day periods were strongly influenced by large woody debris or other elements providing cover. Fish initially found in habitats lacking large woody debris, large boulders, or brush cover moved the most extensively, while fish initially found in pools with large woody debris moved the least. Fish did not move extensively in response to a bankfull flood, although some moved to habitat downstream of large woody debris in tributaries or secondary channels. Habitat downstream of woody debris in the main ch.
How valid are culture-level mean personality scores?

How does culture impact personality traits? To answer that question, the three volumes in this set address current theory and research on culture and personality in an effort to determine how people differ—and how they are alike. Detailed chapters by scholars from around the world unveil a fascinating picture of the relationship between culture and important aspects of personality. They also address the accuracy or meaningfulness of trait comparisons across cultures and the methods and limitations of research on the subject. As most psychological research is conducted on participants from Western industrialized countries, a work that includes a wide range of cultures not only fosters a more complete understanding of human personality, but also broadens perspectives on value systems and ways to live.
Why Nitpicking Works: Evidence for Occam’s Razor in Error Correctors

Empirical experience and observations have shown us when powerful and highly tunable classifiers such as maximum entropy classifiers, boosting and SVMs are applied to language processing tasks, it is possible to achieve high accuracies, but eventually their performances all tend to plateau out at around the same point. To further improve performance, various error correction mechanisms have been developed, but in practice, most of them cannot be relied on to predictably improve performance on unseen data; indeed, depending upon the test set, they are as likely to degrade accuracy as to improve it. This problem is especially severe if the base classifier has already been finely tuned.In recent work, we introduced N-fold Templated Piped Correction, or NTPC ("nitpick"), an intriguing error corrector that is designed to work in these extreme operating conditions. Despite its simplicity, it consistently and robustly improves the accuracy of existing highly accurate base models. This paper investigates some of the more surprising claims made by NTPC, and presents experiments supporting an Occam's Razor argument that more complex models are damaging or unnecessary in practice.
Arterial Stiffness Is Inversely Related to Plasma Adiponectin Levels in Young Normotensive Patients With Type 1 Diabetes

OBJECTIVE This study investigated the association between arterial stiffness and plasma adiponectin in patients with type 1 diabetes. RESEARCH DESIGN AND METHODS Participants were normotensive patients with type 1 diabetes who were up to age 40 years. Subjects on statins with macrovascular disease or overt nephropathy were excluded. Large artery stiffness was assessed by measurement of carotid-femoral pulse wave velocity (PWV), whereas plasma adiponectin was measured by radioimmunoassay. RESULTS Data from 80 patients (age 27.1 ± 6.1 years, BMI 24.2 ± 3.1 kg/m2, HbA1c 7.5 ± 1.6%, 39 men, adiponectin 13.9 ± 6.7 μg/mL, and PWV 5.6 ± 0.9 m/s) were analyzed. Log adiponectin inversely correlated with age-adjusted PWV (r = −0.291, P = 0.009) and waist circumference (r = −0.427, P < 0.001). In a fully adjusted model, age, expiration/inspiration index, and log adiponectin were independently associated with PWV, explaining 39.6% of its variance. CONCLUSIONS Arterial stiffness is inversely related to adiponectin concentration in young patients with type 1 diabetes without major complications.
Exponential Approximations for Tail Probabilities in Queues II: Sojourn Time and Workload

We continue to focus on simple exponential approximations for steady-state tail probabilities in queues based on asymptotics. For the G/GI/1 model with i.i. d. service times that are independent of an arbitrary stationary arrival process, we relate the asymptotics for the steady-state waiting time, sojourn time, and workload. We show that the three asymptotic decay rates coincide and that the three asymptotic constants are simply related. We evaluate the exponential approximations based on the exact asymptotic parameters and their approximations by making comparisons with exact numerical results for BMAP/G/1 queues, which have batch Markovian arrival processes. Numerical examples show that the exponential approximations for the tail probabilities are remarkably accurate at the 90th percentile and beyond. Thus, these exponential approximations appear very promising for applications.
Shape But Not Color Facilitates Two-Year-Olds’ Search Performance in a Spatial Rotation Task

Children younger than three years of age often fail to track hidden objects that are rotated together with identical hiding containers, which might be due to relatively complex paradigms. We examined whether 2-year-olds ( N = 28) are already able to track spatial rotations (i.e., by 90° and 180°) if the task is facilitated by increasing the visual discriminability of the hiding containers by means of different shapes and different colors. Children performed above chance level in all conditions except for the condition in which containers had the same color and shape and were rotated by 180°. Moreover, children found the hidden object more often when the containers had different – as compared to identical – shapes, whereas performance was similar when the containers had the same or different colors. Furthermore, their performance was better after 90° rotations than after 180° rotations and children in all conditions showed an inhibition bias. Our findings suggest that 2-year-olds are already able to track spatial rotations if the task is kept simple and focuses solely on the ability of interest. In addition, young children use shape – rather than color – as a salient dimension in spatial rotation tasks.
Energy Balance in the Solar Transition Region. IV. Hydrogen and Helium Mass Flows with Diffusion

In this paper we extend our previous modeling of energy balance in the chromosphere-corona transition region to cases with particle and mass flows. The cases considered here are quasi-steady and satisfy the momentum and energy balance equations in the transition region. We assume one-dimensional geometry and include the flow velocity terms in all equations, but we neglect the partial derivatives with respect to time. We present a complete and physically consistent formulation and method for solving the non-LTE and energy balance equations in these situations, including both particle diffusion and flows of H and He. Our calculations include partial frequency redistribution in the Lyα and Lyβ lines. Our results show quantitatively how mass flows affect the ionization and radiative losses of H and He, thereby affecting the structure and extent of the transition region. Furthermore, our computations show that the H and He line profiles are greatly affected by flows. We find that line shifts are much less important than the changes in line intensity and central reversal as a result of the influence of flows on the excitation and ionization. In this paper we use fixed conditions at the base of the transition region and in the underlying chromosphere. Our intent is to show the physical effects of flows on the transition region, not to match any particular observations. However, our computed Lyα profiles can account for the range of observed high spectral and spatial resolution from the quiet Sun. We suggest that dedicated modeling of specific sequences of observations based on physically consistent methods like those presented here will substantially improve our understanding of the energy balance in the chromosphere and corona.