LLukas22/scidocs huggingface dataset:
The Y-chromosome point mutation rate in humans

Mutations are the fundamental source of biological variation, and their rate is a crucial parameter for evolutionary and medical studies. Here we used whole-genome sequence data from 753 Icelandic males, grouped into 274 patrilines, to estimate the point mutation rate for 21.3 Mb of male-specific Y chromosome (MSY) sequence, on the basis of 1,365 meioses (47,123 years). The combined mutation rate for 15.2 Mb of X-degenerate (XDG), X-transposed (XTR) and ampliconic excluding palindromes (rAMP) sequence was 8.71 × 10−10 mutations per position per year (PPPY). We observed a lower rate (P = 0.04) of 7.37 × 10−10 PPPY for 6.1 Mb of sequence from palindromes (PAL), which was not statistically different from the rate of 7.2 × 10−10 PPPY for paternally transmitted autosomes. We postulate that the difference between PAL and the other MSY regions may provide an indication of the rate at which nascent autosomal and PAL de novo mutations are repaired as a result of gene conversion.
Lipoblastoma and liposarcoma in children: an analysis of 9 cases and a review of the literature.

OBJECTIVES
To review the experience at a children's hospital of lipoblastoma and liposarcoma and to identify any factors that would differentiate one type of tumour from the other.


DESIGN
A retrospective case series.


SETTING
British Columbia's Children's Hospital a tertiary-care pediatric centre.


PATIENTS
All patients with a pathological diagnosis of lipoblastoma and liposarcoma recorded over 12 years.


MAIN OUTCOME MEASURES
The frequency of lipoblastoma and liposarcoma, identified from biopsy specimens of pediatric adipose tumours. The clinical, pathological and cytogenetic variables between lipoblastoma and liposarcoma.


RESULTS
One hundred and forty-nine adipose tumours were recorded. Seven (4.7%) were lipoblastomas and 2 (1.3%) were liposarcomas. All tumours presented as asymptomatic, slow-growing, soft-tissue masses. The children with lipoblastoma tended to be younger, but 29% were over 3 years of age. The liposarcoma patients were aged 9 and 14 years. One liposarcoma was of myxoid type and the other was a round cell variant. Karyotypes were reported for 1 lipoblastoma and 1 liposarcoma. The myxoid liposarcoma karyotype was 46,XY,t(12;16)(q13;p11), and the lipoblastoma was reported as 46,XY,der(8)?t(8q;?),+mar.


CONCLUSIONS
Lipoblastoma is an unusual childhood neoplasm and liposarcoma is very rare in children. Both tumours may present in a similar fashion, and differentiating them histologically can be difficult. Age cannot be relied upon to accurately predict their behaviour. The tumour karyotype is very helpful in differentiating these neoplasms.
Landmark-driven fundus perimetry using the scanning laser ophthalmoscope.

PURPOSE
To present a new method of performing scanning laser ophthalmoscope perimetry that compensates for eye movements so that the correct retinal location is tested even if fixation changes. This allows for accurate testing of patients with central scotomas and for repeating testing longitudinally at the same retinal locations even if central fixation is lost.


METHODS
The operator views the retina and selects a retinal landmark, such as a vessel bifurcation, that can be identified easily. A testing strategy is preselected, and the computer saves the landmark and stimulus coordinates. To present each stimulus, the operator positions a cursor over the retinal landmark, and the computer adjusts the site of presentation of the stimulus for any change in landmark position caused by an eye movement. At the conclusion of the testing, the results are displayed in the proper retinal location on a fundus image.


RESULTS
Sixty-seven eyes with macular disease were tested with the landmark-driven method, using the same preplanned strategy for each eye for both a bright and a dim stimulus. There was a low rate of inconsistent points (seen with dim but not bright stimuli), and virtually all of these bordered a dense scotoma. Those eyes with more inconsistent points had a significantly greater percentage of dense scotoma points and significantly lower visual acuity. The technique significantly corrected error in retinal localization resulting from large eye movement. There is no significant rotation or magnification change during the procedure, so specifying the change in location of one landmark is sufficient to describe movement of the retina. The technique is rapid and easy to administer to elderly patients and to children.


CONCLUSIONS
This technique allows for accurate and repeatable measures of retinal sensitivity in specific locations. It is useful in following change over time. It can be developed further to allow for fully automated, retinally correct testing.
Maternal weight and excessive weight gain during pregnancy modify the immunomodulatory potential of breast milk

Introduction:Breast milk is an optimal source of nutrition for infants. It contains bioactive components including bacteria that support the microbial colonization and immune system development of the infant. The determinants of human milk composition remain poorly understood, although maternal nutritional and immunological status as well as lifestyle and dietary habits seem to have an impact.Methods:The subjects selected were women from a prospective follow-up study categorized by BMI. Milk samples were taken after delivery and at 1 and 6 mo later for analysis of composition in regard to transforming growth factor (TGF)-β2, soluble CD14 (sCD14), cytokines, and microbiota.Results:TGF-β2 and sCD14 levels in the breast milk of overweight mothers tended to be lower than the levels in that of normal-weight mothers. Also, higher levels of Staphylococcus group bacteria and lower levels of Bifidobacterium group bacteria were detected in overweight mothers as compared with normal-weight ones. The prevalence of Akkermansia muciniphila–type bacteria was also higher in overweight mothers, and the numbers of these bacteria were related to the interleukin (IL)-6 concentration in the colostrum, which was in turn related to lower counts of Bifidobacterium group bacteria in the breast milk of overweight women.Discussion:Complex interactions of cytokines and microbiota in breast milk guide the microbiological, immunological, and metabolic programming of infant health. Our data may indicate the presence of an additional mechanism that may explain the heightened risk of obesity for infants of overweight and excessive weight gain mothers.
What is the solar influence on climate? Overview of activities during CAWSES-II

This paper presents an overview of the main advances in the Key Questions identified by the Task Group ‘What is the Solar Influence on Climate’ by the SCOSTEP CAWSES-II science program. We go through different aspects of solar forcing from solar irradiance, including total solar irradiance (TSI) and solar spectral irradiance (SSI), to energetic particle forcing, including energetic particle precipitation (EPP) and cosmic rays (CR). Besides discussing the main advances in the timeframe 2009 to 2013, we also illustrate the proposed mechanism for climate variability for the different solar variability sources listed above. The key questions are as follows: What is the importance of spectral variations to solar influences on climate? What is the effect of energetic particle forcing on the whole atmosphere and what are the implications for climate? How well do models reproduce and predict solar irradiance and energetic particle influences on the atmosphere and climate?
Bayesian Locality Sensitive Hashing for Fast Similarity Search

Given a collection of objects and an associated similarity measure, the all-pairs similarity search problem asks us to find all pairs of objects with similarity greater than a certain user-specified threshold. Locality-sensitive hashing (LSH) based methods have become a very popular approach for this problem. However, most such methods only use LSH for the first phase of similarity search i.e. efficient indexing for candidate generation. In this paper, we presentBayesLSH, a principled Bayesian algorithm for the subsequent phase of similarity search performing candidate pruning and similarity estimation using LSH. A simpler variant, BayesLSHLite, which calculates similarities exactly, is also presented. BayesLSH is able to quickly prune away a large majority of the false positive candidate pairs, leading to significant speedups over baseline approaches. For BayesLSH, we also provide probabilistic guarantees on the quality of the output, both in terms of accuracy and recall. Finally, the quality of BayesLSH’s output can be easily tuned and does not require any manual setting of the number of hashes to use for similarity estimation, unlike standard approaches. For two state-of-the-art candidate generation algorithms, AllPairs [3] and LSH, BayesLSH enables significant speedups, typically in the range 2x-20x for a wide variety of datasets.
Persistent systems techniques in forensic acquisition of memory

In this paper we discuss how operating system design and implementation influence the methodology for computer forensics investigations, with the focus on forensic acquisition of memory. In theory the operating system could support such investigations both in terms of tools for analysis of data and by making the system data readily accessible for analysis. Conventional operating systems such as Windows and UNIX derivatives offer some memory-related tools that are geared towards the analysis of system crashes, rather than forensic investigations. In this paper we demonstrate how techniques developed for persistent operating systems, where lifetime of data is independent of the method of its creation and storage, could support computer forensics investigations delivering higher efficiency and accuracy. It is proposed that some of the features offered by persistent systems could be built into conventional operating systems to make illicit activities easier to identify and analyse. We further propose a new technique for forensically sound acquisition of memory based on the persistence paradigm. a 2008 Elsevier Ltd. All rights reserved.
Programs Leadership in the Absence of Formal Succession Management Tapping the Principal Pipeline : Identifying Talent for Future School

Purpose: In light of the difficulty many districts face finding quality principal candidates, this article explores an informal recruitment mechanism of teachers to become principals, which the authors call tapping. The authors assess the extent to which current teachers are being approached by school leaders to consider leadership and whether this tapping prompts these teachers to consider pursuing leadership positions. Research Design: This study uses survey and administrative data on teachers and principals from the Miami-Dade County Public Schools from the 2007–2008 school year. The authors describe the extent to which principals tap teachers to become school leaders. They use multiple regression with and without school fixed effects to model which teachers are most likely to be tapped and which principals are most likely to tap teachers. They also estimate the extent to which Article at Stanford University Libraries on January 29, 2012 eaq.sagepub.com Downloaded from 696 Educational Administration Quarterly 47(5) tapping is effective at motivating teachers to become school leaders. Findings: A vast majority of principals report having been tapped by their own principal when they were teachers. The authors find that principals tend to tap teachers who feel better equipped to take on the principalship and who have more school-level leadership experience, but they also disproportionately tap teachers who are male and share their ethnicity. Conclusions: The findings provide evidence that principals are capable of effectively identifying and encouraging teachers with strong leadership potential to enter the principal pipeline, although additional training and a succession management plan may help ensure that teachers are selected based on clear leadership competencies.
Strainer: software for analysis of population variation in community genomic datasets

Metagenomic analyses of microbial communities that are comprehensive enough to provide multiple samples of most loci in the genomes of the dominant organism types will also reveal patterns of genetic variation within natural populations. New bioinformatic tools will enable visualization and comprehensive analysis of this sequence variation and inference of recent evolutionary and ecological processes. We have developed a software package for analysis and visualization of genetic variation in populations and reconstruction of strain variants from otherwise co-assembled sequences. Sequencing reads can be clustered by matching patterns of single nucleotide polymorphisms to generate predicted gene and protein variant sequences, identify conserved intergenic regulatory sequences, and determine the quantity and distribution of recombination events. The Strainer software, a first generation metagenomic bioinformatics tool, facilitates comprehension and analysis of heterogeneity intrinsic in natural communities. The program reveals the degree of clustering among closely related sequence variants and provides a rapid means to generate gene and protein sequences for functional, ecological, and evolutionary analyses.
Design of solid wood panels with cross layers

The objective of this paper is to present a method for the design of solid wood panels with cross layers. The stress distribution in and the deformation behaviour of solid wood panels were analysed using the composite theory. The shear influence in solid wood panels was determined using the shear analogy method. A strength class system is proposed for the design of solid wood panels with cross layers depending on the type of stress and the panel build-up.
Assessing Diabetes Self-Management with the Diabetes Self-Management Questionnaire (DSMQ) Can Help Analyse Behavioural Problems Related to Reduced Glycaemic Control.

AIM
To appraise the Diabetes Self-Management Questionnaire (DSMQ)'s measurement of diabetes self-management as a statistical predictor of glycaemic control relative to the widely used SDSCA.


METHODS
248 patients with type 1 diabetes and 182 patients with type 2 diabetes were cross-sectionally assessed using the two self-report measures of diabetes self-management DSMQ and SDSCA; the scales were used as competing predictors of HbA1c. We developed a structural equation model of self-management as measured by the DSMQ and analysed the amount of variation explained in HbA1c; an analogue model was developed for the SDSCA.


RESULTS
The structural equation models of self-management and glycaemic control showed very good fit to the data. The DSMQ's measurement of self-management showed associations with HbA1c of -0.53 for type 1 and -0.46 for type 2 diabetes (both P < 0.001), explaining 21% and 28% of variation in glycaemic control, respectively. The SDSCA's measurement showed associations with HbA1c of -0.14 (P = 0.030) for type 1 and -0.31 (P = 0.003) for type 2 diabetes, explaining 2% and 10% of glycaemic variation. Predictive power for glycaemic control was significantly higher for the DSMQ (P < 0.001).


CONCLUSIONS
This study supports the DSMQ as the preferred tool when analysing self-reported behavioural problems related to reduced glycaemic control. The scale may be useful for clinical assessments of patients with suboptimal diabetes outcomes or research on factors affecting associations between self-management behaviours and glycaemic control.
Production and comparison of fuel properties, engine performance, and emission characteristics of biodiesel from various non-edible vegetable oils: a review.

Energy demand is increasing dramatically because of the fast industrial development, rising population, expanding urbanization, and economic growth in the world. To fulfill this energy demand, a large amount of fuel is widely used from different fossil resources. Burning of fossil fuels has caused serious detrimental environmental consequences. The application of biodiesel has shown a positive impact in resolving these issues. Edible vegetable oils are one of the potential feedstocks for biodiesel production. However, as the use of edible oils will jeopardize food supplies and biodiversity, non-edible vegetable oils, also known as second-generation feedstocks, are considered potential substitutes of edible food crops for biodiesel production. This paper introduces some species of non-edible vegetables whose oils are potential sources of biodiesel. These species are Pongamia pinnata (karanja), Calophyllum inophyllum (Polanga), Maduca indica (mahua), Hevea brasiliensis (rubber seed), Cotton seed, Simmondsia chinesnsis (Jojoba), Nicotianna tabacum (tobacco), Azadirachta indica (Neem), Linum usitatissimum (Linseed) and Jatropha curcas (Jatropha). Various aspects of non-edible feedstocks, such as biology, distribution, and chemistry, the biodiesel’s physicochemical properties, and its effect on engine performance and emission, are reviewed based on published articles. From the review, fuel properties are found to considerably vary depending on feedstocks. Analysis of the performance results revealed that most of the biodiesel generally give higher brake thermal efficiency and lower brake-specific fuel consumption. Emission results showed that in most cases, NOx emission is increased, and HC, CO, and PM emissions are decreases. It was reported that a diesel engine could be successfully run and could give excellent performance and the study revealed the most effective regulated emissions on the application of karanja, mahua, rubber seed, and tobacco biodiesel and their blends as fuel in a CI engine. 2014 Elsevier Ltd. All rights reserved.
Sustained economic benefits of resistance training in community-dwelling senior women.

UNLABELLED
To determine whether the health and cost benefits of resistance training were sustained 12 months after formal cessation of the intervention.


DESIGN
Cost-utility analysis conducted alongside a randomized controlled trial.


SETTING
Community-dwelling women aged 65 to 75 living in Vancouver, British Columbia.


PARTICIPANTS
One hundred twenty-three of the 155 community-dwelling women aged 65 to 75 years who originally were randomly allocated to once-weekly resistance training (n=54), twice-weekly resistance training (n=52), or twice-weekly balance and tone exercises (control group; n=49) participated in the 12-month follow-up study. Of these, 98 took part in the economic evaluation (twice-weekly balance and tone exercises, n=28; once-weekly resistance training, n=35; twice-weekly resistance training, n=35).


MEASUREMENTS
The primary outcome measure was incremental cost per quality-adjusted life year (QALY) gained. Healthcare resource utilization was assessed over 21 months (2009 prices); health status was assessed using the EuroQol-5D to calculate QALYs using a 21-month time horizon.


RESULTS
Once- and twice-weekly resistance training were less costly than balance and tone classes, with incremental mean healthcare costs of Canadian dollars (CAD$)1,857 and CAD$1,077, respectively. The incremental QALYs for once- and twice-weekly resistance training were -0.051 and -0.081, respectively, compared with balance and tone exercises.


CONCLUSION
The cost benefits of participating in a 12-month resistance training intervention were sustained for the once- and twice-weekly resistance training group, whereas the health benefits were not.
Speeding Up Permutation Based Indexing with Indexing

A recent probabilistic approach for searching in high dimensional metric spaces is based on predicting the distances between database elements according to how they order their distances towards some set of distinguished elements, called permutants. In the preprocessing phase a set of permutants is chosen, and are sorted (permuted) by their distances against every database element. The permutations form the index. When a query is given, its corresponding permutation is computed, and --- as similar elements will (probably) have a similar permutation --- the database is compared in the order induced by the similarity between permutations. This works well but has relatively high CPU time due to computing the distances between permutations and (partially) sorting the database by the similarity. We improve this by identifying and solving this as another metric space problem. This avoids many distance computations between the permutants. The experimental results show that this works extremely well in practice.
Nonlinear optical spectroscopy of photonic metamaterials

We probe the nonlinear optical properties of a fishnet metamaterial via second harmonic generation (SHG) and third harmonic generation (THG) spectroscopy. We show that the resonance enhancement of nonlinear response in metamaterials is distinct from molecular case.
Estimation of soil parameters over bare agriculture areas from C-band polarimetric SAR data using neural networks

The purpose of this study was to develop an approach to estimate soil surface parameters from C-band polarimetric SAR data in the case of bare agricultural soils. An inversion technique based on multi-layer perceptron (MLP) neural networks was introduced. The neural networks were trained and validated on a noisy simulated dataset generated from the Integral Equation Model (IEM) on a wide range of surface roughness and soil moisture, as it is encountered in agricultural contexts for bare soils. The performances of neural networks in retrieving soil moisture and surface roughness were tested for several inversion cases using or not using a-priori knowledge on soil parameters. The inversion approach was then validated using RADARSAT-2 images in polarimetric mode. The introduction of expert knowledge on the soil moisture (dry to wet soils or very wet soils) improves the soil moisture estimates, whereas the precision on the surface roughness estimation remains unchanged. Moreover, the use of polarimetric parameters α1 and anisotropy were used to improve the soil parameters estimates. These parameters provide to neural networks the probable ranges of soil moisture (lower or higher than 0.30 cm 3 cm−3) and surface roughness (root mean square surface height lower or higher than 1.0 cm). Soil moisture can be retrieved correctly from C-band SAR data by using the neural networks technique. Soil moisture errors were estimated at about 0.098 cm 3 −3 without a-priori information on soil parameters and 0.065 cm 3 −3 (RMSE) applying a-priori information on the soil moisture. The retrieval of surface roughness is possible only for low and medium values (lower than 2 cm). Results show that the precision on the soil roughness estimates was about 0.7 cm. For surface roughness lower than 2 cm, the precision on the soil roughness is better with an RMSE about 0.5 cm. The use of polarimetric parameters improves only slightly the soil parameters estimates.