Miracle-dz/UniFAR-FTUs huggingface dataset:
Beyond Junk-Variable Tandem Repeats as Facilitators of Rapid Evolution of Regulatory and Coding Sequences

Copy Number Variations (CNVs) and Single Nucleotide Polymorphisms (SNPs) have been the major focus of most large-scale comparative genomics studies to date. Here, we discuss a third, largely ignored, type of genetic variation, namely changes in tandem repeat number. Historically, tandem repeats have been designated as non functional “junk” DNA, mostly as a result of their highly unstable nature. With the exception of tandem repeats involved in human neurodegenerative diseases, repeat variation was often believed to be neutral with no phenotypic consequences. Recent studies, however, have shown that as many as 10% to 20% of coding and regulatory sequences in eukaryotes contain an unstable repeat tract. Contrary to initial suggestions, tandem repeat variation can have useful phenotypic consequences. Examples include rapid variation in microbial cell surface, tuning of internal molecular clocks in flies and the dynamic morphological plasticity in mammals. As such, tandem repeats can be useful functional elements that facilitate evolvability and rapid adaptation.
Evaluation of different grafting methods to citrus cultivars

Citrus is one of the most important fruit crops of the world and are propagated by sexual and asexual methods. Citrus rootstocks are produced by seed (zygotic seedling) while scion cultivars are propagated by asexual methods such as budding, cutting, layering and grafting. In Punjab-Pakistan, mostly T-budding and T-grafting as well as side grafting are used to propagate new plants with low success rate. In the current study, we investigated the effects of different methods of grafting such as ‘side grafting’, ‘wedge (or cleft) grafting’ and ‘tongue grafting’ to propagate mandarin cv. Kinnow and sweet orange [Citrus sinensis (L.) Osbeck] cvs. Succri and Jaffa on rough lemon (C. jambhiri Lush.) rootstock. The experiment was designed as a split-plot in a randomized complete block designed, with three replications, where a single plant was considered as an experimental unit. Thirty plants were grafted in each method of grafting. The results showed that wedge and side grafting had the highest graft take with Kinnow mandarin (90.00% and 86.67%, respectively); tongue grafting had the highest graft take with the Jaffa sweet orange (76.67%); and, the side grafting alone had the highest graft take with the Succri sweet orange. The shoot length was significantly higher in mandarins cv. Kinnow (16.00 cm) followed by sweet orange cv. Succri (11.67 cm) as compared to Jaffa (11.00 cm). In general, the results showed that side grafting was the most effective method of propagation for all evaluated cultivars in the province of Punjab-Pakistan.
Interlaboratory Comparison of Three Multiplexed Bead-Based Immunoassays for Measuring Serum Antibodies to Pneumococcal Polysaccharides

ABSTRACT Serotype-specific IgG, as quantified by a standardized WHO enzyme-linked immunosorbent assay (ELISA), is a serologic end point used to evaluate pneumococcal polysaccharide-based vaccine immunogenicity. Antibodies to each vaccine polysaccharide in licensed multivalent vaccines are quantified separately; this is laborious and consumes serum. We compared three bead-based immunoassays: a commercial assay (xMAP Pneumo14; Luminex) and two in-house assays (of the Health Protection Agency [HPA] and Centers for Disease Control and Prevention [CDC]), using the WHO-recommended standard reference and reference sera (n = 11) from vaccinated adults. Multiple comparisons of the IgG concentrations for seven conjugate vaccine serotypes were performed by sample (percent error), serotype (equivalency testing), and laboratory (concordance correlation coefficient [CCC]). When comparing concentrations by sample, bead-based immunoassays generally yielded higher antibody concentrations than the ELISA and had higher variability for serotypes 6B, 18C, and 23F. None of the three assays met the current WHO recommendation of 75% of sera falling within 40% of the assigned antibody concentrations for all seven serotypes. When compared by serotype, the CDC and HPA tests were equivalent for five of seven serotypes, whereas the Luminex assay was equivalent for four of seven serotypes. When overall mean IgG concentrations were compared by laboratory, a higher level of agreement (CCC close to 1) was found among bead-based immunoassays than between the assays and WHO assignments. When compared to WHO assignments, the HPA assay outperformed the other assays (r = 0.920; CCC = 0.894; coefficient of accuracy = 0.972). Additional testing with sera from immunogenicity studies should demonstrate the applicability of this methodology for vaccine evaluation.
Evaluating the travel, physical activity and carbon impacts of a ‘natural experiment’ in the provision of new walking and cycling infrastructure: methods for the core module of the iConnect study

Introduction Improving infrastructure to support walking and cycling is often regarded as fundamental to encouraging their widespread uptake. However, there is little evidence that specific provision of this kind has led to a significant increase in walking or cycling in practice, let alone wider impacts such as changes in overall physical activity or carbon emissions. Connect2 is a major new project that aims to promote walking and cycling in the UK by improving local pedestrian and cycle routes. It therefore provides a useful opportunity to contribute new evidence in this field by means of a natural experimental study. Methods and analysis iConnect is an independent study that aims to integrate the perspectives of public health and transport research on the measurement and evaluation of the travel, physical activity and carbon impacts of the Connect2 programme. In this paper, the authors report the study design and methods for the iConnect core module. This comprised a cohort study of residents living within 5 km of three case study Connect2 projects in Cardiff, Kenilworth and Southampton, supported by a programme of qualitative interviews with key informants about the projects. Participants were asked to complete postal questionnaires, repeated before and after the opening of the new infrastructure, which collected data on demographic and socioeconomic characteristics, travel, car fuel purchasing and physical activity, and potential psychosocial and environmental correlates and mediators of those behaviours. In the absence of suitable no-intervention control groups, the study design drew on heterogeneity in exposure both within and between case study samples to provide for a counterfactual. Ethics and dissemination The study was approved by the University of Southampton Research Ethics Committee. The findings will be disseminated through academic presentations, peer-reviewed publications and the study website (http://www.iconnect.ac.uk) and by means of a national seminar at the end of the study.
Orthodontic Space Closure versus Prosthetic Replacement of Missing Upper Lateral Incisors in Patients with Bilateral Cleft Lip and Palate

Objective To compare dental aesthetics and function of orthodontic space closure versus prosthetic replacement of upper lateral incisors in patients with bilateral cleft lip and palate. The predominant mode of prosthetic replacement was resin-bonded bridges. Patients and Methods The retrospective study group consisted of 17 patients treated with orthodontic space closure (13 men, four women; median age, 27.1 years; interquartile range, 20.6 to 33.3 years) and 10 patients treated with prosthetic replacement (five men, five women; median age, 27.7 years; interquartile range, 20.9 to 39.7 years). Dental aesthetics were evaluated by the patients and by a professional panel. Mandibular function was evaluated by means of the mandibular function impairment questionnaire. The level of mandibular impairment was calculated using the Function Impairment Rating Scale. Results With respect to dental aesthetics, no significant differences between patients treated with orthodontic space closure and prosthetic replacement were found. With respect to function, the level of mandibular impairment was significantly higher in patients treated with prosthetic replacement compared with patients treated with orthodontic space closure, as indicated by high scores on specific masticatory functions. Conclusion Orthodontic space closure and prosthetic replacement in bilateral cleft lip and palate patients produce similar results in terms of aesthetics. In terms of function, prosthetic replacement results in significantly more impairment of specific masticatory functions.
Proportional Hazards Mixed Models: A Review with Applications to Twin Models

We describe our recent work on mixed effects models for right-censored data. Vaida and Xu (2000) provided a general framework for handling random effects in proportional hazards (PH) regression, in a way similar to the linear, non-linear and generalized linear mixed effects models that allow random effects of arbitrary covariates. This general framework includes the frailty models as a special case. Maximum likelihood estimates of the regression parameters, the variance components and the baseline hazard, and empirical Bayes estimates of the random effects can be obtained via an MCEM algoritm. Variances of the parameter estimates are approximated using Louis’ formula. We show interesting applications of the PH mixed effects model (PHMM) to a US Vietnam Era Twin Registry study on alcohol abuse, with the primary goal of identifying genetic contributions to such events. The twin pairs in the registry consist of monozygotic and dizygotic twins. After model fitting and for interpretation purposes, the proportional hazards formulation is converted to a linear transformation model before the results on genetic contributions are reported. The model also allows examination of gene and covariate interactions, as well as the modelling of multivariate outcomes (comorbidities).
Monitoring endangered freshwater biodiversity using environmental DNA.

Freshwater ecosystems are among the most endangered habitats on Earth, with thousands of animal species known to be threatened or already extinct. Reliable monitoring of threatened organisms is crucial for data-driven conservation actions but remains a challenge owing to nonstandardized methods that depend on practical and taxonomic expertise, which is rapidly declining. Here, we show that a diversity of rare and threatened freshwater animals--representing amphibians, fish, mammals, insects and crustaceans--can be detected and quantified based on DNA obtained directly from small water samples of lakes, ponds and streams. We successfully validate our findings in a controlled mesocosm experiment and show that DNA becomes undetectable within 2 weeks after removal of animals, indicating that DNA traces are near contemporary with presence of the species. We further demonstrate that entire faunas of amphibians and fish can be detected by high-throughput sequencing of DNA extracted from pond water. Our findings underpin the ubiquitous nature of DNA traces in the environment and establish environmental DNA as a tool for monitoring rare and threatened species across a wide range of taxonomic groups.
Sense Tagging and Language Engineering

Language engineering is a new, practical, branch of NLP and Computational Linguistics. We describe two language engineering systems: GATE (General Architecture for Text Engineering), an architecture to aid in the production and delivery of language engineering systems which signiic-antly reduces development time and ease of reuse. We also describe a sense tagger which we implemented within the GATE architecture, and which achieves high accuracy (93% of all words in text to a broad semantic level). The implementation of the sense tagger was used as a practical task on which to evaluate the usefulness of the GATE architecture and identify its strengths and weaknesses.
Differential postsynaptic compartments in the laterocapsular division of the central nucleus of amygdala for afferents from the parabrachial nucleus and the basolateral nucleus in the rat

Neurons in the laterocapsular division of the central nucleus of the amygdala (CeC), which is known as the “nociceptive amygdala,” receive glutamatergic inputs from the parabrachial nucleus (PB) and the basolateral nucleus of amygdala (BLA), which convey nociceptive information from the dorsal horn of the spinal cord and polymodal information from the thalamus and cortex, respectively. Here, we examined the ultrastructural properties of PB– and BLA–CeC synapses identified with EGFP‐expressing lentivirus in rats. In addition, the density of synaptic AMPA receptors (AMPARs) on CeC neurons was studied by using highly sensitive SDS‐digested freeze‐fracture replica labeling (SDS‐FRL). Afferents from the PB made asymmetrical synapses mainly on dendritic shafts (88%), whereas those from the BLA were on dendritic spines (81%). PB–CeC synapses in dendritic shafts were significantly larger (median 0.072 μm2) than BLA–CeC synapses in spines (median 0.058 μm2; P = 0.02). The dendritic shafts that made synapses with PB fibers were also significantly larger than those that made synapses with BLA fibers, indicating that the PB fibers make synapses on more proximal parts of dendrites than the BLA fibers. SDS‐FRL revealed that almost all excitatory postsynaptic sites have AMPARs in the CeC. The density of AMPAR‐specific gold particles in individual synapses was significantly higher in spine synapses (median 510 particles/μm2) than in shaft synapses (median 427 particles/μm2; P = 0.01). These results suggest that distinct synaptic impacts from PB– and BLA–CeC pathways contribute to the integration of nociceptive and polymodal information in the CeC. J. Comp. Neurol. 518:4771–4791, 2010. © 2010 Wiley‐Liss, Inc.
Prediction of unsteady heat transfer from a cylinder in crossflow By

The accuracy of a tensorial eddy diffusivity subgrid scale model for large-eddy simulation (LES) of passive scalar transport is investigated for a heated cylinder in crossflow at Re = 3000 and 8900. LES at the higher Reynolds number relies on local mesh refinement in the near wake of the cylinder using an estimate of subgrid scale (SGS) fluctuations of the passive scalar field. Predictions of mean and fluctuating heat transfer at both Reynolds numbers agree reasonably well with the experimental measurements of Nakamura & Igarashi (2004).
Continuous Flow Polymer Synthesis toward Reproducible Large-Scale Production for Efficient Bulk Heterojunction Organic Solar Cells.

Organic photovoltaics (OPV) have attracted great interest as a solar cell technology with appealing mechanical, aesthetical, and economies-of-scale features. To drive OPV toward economic viability, low-cost, large-scale module production has to be realized in combination with increased top-quality material availability and minimal batch-to-batch variation. To this extent, continuous flow chemistry can serve as a powerful tool. In this contribution, a flow protocol is optimized for the high performance benzodithiophene-thienopyrroledione copolymer PBDTTPD and the material quality is probed through systematic solar-cell evaluation. A stepwise approach is adopted to turn the batch process into a reproducible and scalable continuous flow procedure. Solar cell devices fabricated using the obtained polymer batches deliver an average power conversion efficiency of 7.2 %. Upon incorporation of an ionic polythiophene-based cathodic interlayer, the photovoltaic performance could be enhanced to a maximum efficiency of 9.1 %.
The relationship between breastfeeding self‐efficacy and LATCH scores and affecting factors

AIMS AND OBJECTIVES This study investigates the relationship between breastfeeding self-efficacy and LATCH scores and affecting factors in Turkish mothers. BACKGROUND The benefits of breastfeeding for newborns and mothers are well documented. Type of birth, maternal and neonatal complications; lack of support from healthcare professionals during breastfeeding, hospital routines, time and duration of mother-newborn attachment; and insufficiency of husband and family support are the most significant factors affecting breastfeeding initiation and mothers' breastfeeding self-efficacy in early postpartum period. Therefore, it is important to determine how all these factors affect breastfeeding. DESIGN This was a cross-sectional, descriptive study. METHODS The sample of the study consisted of 303 postpartum women who were recruited at the obstetrics clinic of maternity hospital in one of the three largest city of Turkey. The data were obtained using Personal Identification Form, Breastfeeding Self-Efficacy Scale-Short Form and LATCH Breastfeeding Assessment Tool to determine breastfeeding success. The mean, standard deviation, frequency, percentages, correlation analysis and Kruskal-Wallis variance analysis were used in data collection. RESULTS The main finding of the study was a weak positive correlation between average LATCH scores and average Breastfeeding Self-Efficacy Scale-Short Form scores of women in the postpartum period. The women becoming pregnant four times or more got significantly higher average Breastfeeding Self-Efficacy Scale-Short Form and average LATCH scores, and the women married for 11 years or longer and the mothers starting to breastfeed their babies within 30 minutes of their birth got significantly higher average LATCH scores. CONCLUSIONS The results of the present research affirm the beneficial role of high self-efficacy in successful breastfeeding. RELEVANCE TO CLINICAL PRACTICE It is of great importance that midwives and obstetric nurses routinely evaluate breastfeeding self-efficacy and the capability of breastfeeding for early detection of problems related to breastfeeding.
Genealogical Relatedness: Geographies of Shared Descent and Difference

This paper explores genealogy through a focus on what I describe as the idea of genealogical relatedness. This is a model of human relations which emphasizes relationships between people defined through the reckoning of connections based on birth and parentage. I offer a geographical analytical framework for exploring both popular genealogy and ideas of genealogical relatedness, shared descent and difference. It is one that both attends to the variety of ways that collective identity is defined or explored through genealogy and is alert to the troubling nature of genealogical categorizations and differentiations especially those which are figured in terms of concepts that seem to be most progressive, including ideas hybridity, diversity, and universal humanity.
Model selection criterion for causal parameters in structural mean models based on a quasi‐likelihood

Structural mean models (SMMs) have been proposed for estimating causal parameters in the presence of non‐ignorable non‐compliance in clinical trials. To obtain a valid causal estimate, we must impose several assumptions. One of these is the correct specification of the structural model. Building on Pan's work (2001, Biometrics 57, 120–125) on developing a model selection criterion for generalized estimating equations, we propose a new approach for model selection of SMMs based on a quasi‐likelihood. We provide a formal model selection criterion that is an extension of Akaike's information criterion. Using subset selection of baseline covariates, our method allows us to understand whether the treatment effect varies across the available baseline covariate levels, and/or to quantify the treatment effect on a specific covariates level to target specific individuals to maximize treatment benefit. We present simulation results in which our method performs reasonably well compared to other testing methods in terms of both the probability of selecting the correct model and the predictive performances of the individual treatment effects. We use a large randomized clinical trial of pravastatin as a motivation.
Vinculin Motion Modes Analysis with Elastic Network Model

Vinculin is an important protein for the linkage between adhesion molecules and the actin cytoskeleton. The activation mechanism of vinculin is still controversial. In order to provide useful information for a better understanding of its activation, we analyze the motion mode of vinculin with elastic network model in this work. The results show that, to some extent, the five domains will present structural rigidity in the motion process. The differences between the structure fluctuations of these domains are significant. When vinculin interacted with other partners, the central long alpha-helix of the first domain becomes bent. This bending deformation can weaken the interaction between the first domain and the tail domain. This motion mode of the first domain is in good agreement with the information extracted from some realistic complex structures. With the aid of the anisotropy elastic network mode, we analyze the motion directions of these domains. The fourth domain has a rotational motion. This rotation is favorable for the releasing of the tail domain from the pincer-like clamp, which is formed by the first and the third domain. All these motion modes are an inherent feature of the structure, and these modes mainly depend on the topology character of the structure.
Development of polystyrene-geopolymer composite for thermal insulating material and its properties with special regards to flame resistance

As a first part of the research, systematic experimental series were conducted in order to develop an appropriate fly ash-based geopolymer binder focusing on the workability of the paste. In these series, the NaOH molar ratio and water glass/NaOH ratio were investigated and the fineness of the fly ash was optimized presented in a recent paper. Based on these results the effect of metakaolin on the mechanical properties was studied. After developing the appropriate binder, experimental series were carried out using ground polystyrene as light aggregate in various concentration (from 30 V/V% up to 98 V/V%) and geopolymer as a binder in order to develop a heat insulating material. Compressive and flexural strength, specimen density, flammability, freeze-thaw resistance were determined in order to characterize the composite product. As a result of the experimental investigation, it was found that the flexural strength of the composite was found to be ~400 kPa which is as high as the original polystyrene heat insulating panel. Additionally, the flammability was much better than the original pure PS product, the sample was not ignited even at higher PS content (90%). Furthermore, the freeze-thaw resistance of the composite improved compared with the neat geopolymer.
Study of interpolation filters for motion estimation with application in H.264/AVC encoders

The current paper studies low-complexity image super-resolution techniques for improving the motion estimation process of video encoding. Aiming at speeding up the generation of candidate blocks during the computationally intensive search algorithm, we present interpolation techniques with reduced cost compared to standard 6-tap filtering procedures. Furthermore, we compare their performance to that of commonly used half-pixel interpolation techniques with respect to the resulting image quality and the processing time. The research has been based on using a typical fractional motion estimation algorithm preceding the processing of the H.264/AVC standard motion compensation, and thus, the research benefits the design of H.264/AVC encoders.
Joint Decoding for Chinese Word Segmentation and POS Tagging Using Character-Based and Word-Based Discriminative Models

For Chinese word segmentation and POS tagging problem, both character-based and word-based discriminative approaches can be used. Experiments show that these two approaches bring different errors and can complement each other. In this paper, we propose a joint decoding model based on both character-based and word-based models using multi-beam search algorithm. Experimental results show that the joint decoding model outperforms character-based and word-based baseline models.