bluuebunny/crossref_metadata_2025_split huggingface dataset:
Preliminary Study of Digital Laminography Parameters on Carbon Steel Plate
Authors: Hamidi Shahfuan Hanif A. , Salleh Khairul Anuar M. , Hamzah Ab Razak , Wahab Mahamad Noor , Azaman Noorhazleena , Ahmad Anis Salwa 
Published: June 2019

Abstract
Laminography is a technique used to determine the depth of a defect in Radiographic Testing (RT). It enables RT operators to accurately locate the defect from the object’s surface especially for welded components. The technique will ensure the quality of weld components meets the standard requirement for reliability and safety purposes. This paper intends to study the exposure parameters of laminography technique on carbon steel plate by using Radiographic Testing – Digital. (RT-D). The important exposure parameters that are considered in this preliminary study are voltage, current, and frame time. The radiography images with achievable level of contrast sensitivity and image quality are analyzed according to the ISO 17636-2. Discussion on correlation between the normalized Signal to Noise ratio (SNRN) and the exposure parameters are done based on the plotting graphs. The results show the exposure parameters has significantly influenced the value of SNRN. Further experimental works are performed using triangulation technique on welded sample. The deviation between the calculated depth of defects and actual results is less than 1.0mm.
Shearography Technique on Inspection of Advanced Aircraft Composite Material
Authors: Yusof Mohd Yusnisyam , Loganathan Tamil Moli , Burhan Ibrahim , Abdullah Wan Saffiey Wan , Mohamed Mohd Noorul Ikhsan , Abidin Ilham Mukriz Zainal , Zakaria Norhayati 
Published: June 2019

Abstract
The A320 aft fixed fairing is an advanced composite structure fabricated from laminate carbon woven and combines with honeycomb core which is externally mounted on the flap track fairing as a wing part of Airbus aircraft. These flaps are movable control surfaces to widen up the surface of the wing in order to increase the lifting. This paper discussed on the inspection of A320 aft fixed fairing by using shearography NDT technique. Shearography technique reveals the stress-affected zone due to additional loading that can be realized by the laser speckle correlation on the inspected composite panel. This A320 aft fixed fairing is identified as a scrap composite panel which having different sizes and orientations of defect. The results showed that the changes of shearing direction in laser shearography technique are an effective means to reveal the defects propagation in the composite component. The shearing at Y-axes direction is able to detect the cracks at horizontal orientation while shearing at X-axis has successfully detects the cracks at vertical orientation. Therefore, shearography could be utilized as an alternative inspection for other NDT method for inspection of composite material.
Ultrasonic Evaluation at the Interface of Aluminum/Steel Obtained by TIG Welding
Authors: Ahsan Qumrul , Kato Hiroshi 
Published: June 2019

Abstract
Aluminum filler (Al-5%Si) is bonded on steel substrate by gas tungsten arc welding process under different current setting conditions. After welding a thorough metallographic analyses using optical and scanning electron microscopy were carried out to observe Al-Steel interface. Ultrasonic measurements by immersion and scanning acoustic microscopy were made to characterise the bond at Al-Steel interface. The ultrasonic wave reflected from the Al-Steel interface clearly indicated the more debonded area when the welding current is changed from direct current straight polarity (DCSP) mode to alternate current high frequency (ACHF) or the welding current in case of current for DCSP mode is reduced. This may be attributed either adequate amount of oxides along with intermediate phase make the bond interface rough and uneven due to introduction of ACHF mode or debonded areas are higher due to lower heat input when the current reduced to 125 amps from 150 amps in DCSP mode. Whereas smooth and even bond interface due to uniform heat input resulted stable Al-Steel interface and the mapping of bonded area by ultrasonic measurement showed spectrum of minimum peak for using current of 150 amps in DC mode. Thus the non-destructive assessments of interface between dissimilar materials through ultrasonic measurements could be important tools for evaluating the state of the bond.
Food deprivation affects egg laying and maternal care but not offspring performance in a beetle
Authors: Richardson Jon , Ross Jennifer , Smiseth Per T 
Published: June 2019

AbstractIndividuals vary with respect to their nutritional state and such variation is an important determinant of the amount of resources individuals allocate toward reproductive functions. Currently, we have a relatively poor understanding of the downstream consequences of food deprivation on different traits associated with reproduction. Here, we address this gap by investigating how food deprivation affected different traits across the breeding cycle in the burying beetle, Nicrophorus vespilloides; a species that breeds on carcasses of small vertebrates serving as food for both parents and offspring. We found that food-deprived females took longer to start egg laying than control females, which may allow them more time to feed from the carcass. There was no difference between food-deprived and control females in the number, size, laying pattern, or hatching success of eggs, suggesting that this delay allowed females to compensate for their poor initial state. However, food-deprived females spent less time providing care, suggesting that this compensation was incomplete. Finally, we found no evidence for negative effects of food deprivation on the offspring’s growth or survival, which is surprising given that food-deprived females took longer to initiate egg laying and provided less care to their offspring. Our results highlight that food deprivation can have complex effects on parental and offspring traits, and suggest that females face a trade-off between the benefits of mitigating downstream consequences of nutritional stress and the costs associated with delaying the start of reproduction.
Testing clonal relatedness of two tumors from the same patient based on their mutational profiles: update of the Clonality R package
Authors: Mauguen Audrey , Seshan Venkatraman E , Begg Colin B , Ostrovnaya Irina 
Published: June 2019

Abstract

Summary
The Clonality R package is a practical tool to assess the clonal relatedness of two tumors from the same patient. We have previously presented its functionality for testing tumors using loss of heterozygosity data or copy number arrays. Since then somatic mutation data have been more widely available through next generation sequencing and we have developed new methodology for comparing the tumors’ mutational profiles. We thus extended the package to include these two new methods for comparing tumors as well as the mutational frequency estimation from external data required for their implementation. The first method is a likelihood ratio test that is readily available on a patient by patient basis. The second method employs a random-effects model to estimate both the population and individual probabilities of clonal relatedness from a group of patients with pairs of tumors. The package is available on Bioconductor.

Availability and implementation
Bioconductor (http://bioconductor.org/packages/release/bioc/html/Clonality.html).

Supplementary information
Supplementary data are available at Bioinformatics online.
Gestation alters the gut microbiota of an oviparous lizard
Authors: Trevelline Brian K , MacLeod Kirsty J , Langkilde Tracy , Kohl Kevin D 
Published: June 2019

ABSTRACTMammalian pregnancy can alter the diversity, membership and structure of the maternal gut microbiota, but it is unclear whether this phenomenon occurs in vertebrates with different reproductive strategies. We conducted 16S rRNA bacterial inventories to investigate whether oviparous lizards exhibit shifts in gut microbiota similar to those observed in mammals. Using wild-caught eastern fence lizards from Alabama, USA, we collected and extracted fecal DNA from gravid and non-gravid individuals over 54 days in captivity. We predicted that, like mammals, the alpha diversity of lizard gut microbiota would decrease over gestation, and that inter-individual variation in community composition would increase. Indeed, we found that individuals in late-gestation harbored lower gut bacterial richness compared to non-gravid females. Lizard gut microbial communities of late-gestational females exhibited higher pairwise distances for both community membership and community structure compared to earlier gestation stages, indicating a higher degree of inter-individual variation as gestation progressed. Additionally, we found that the relative abundance and prevalence of the candidate phylum Melainabacteria tended to decrease over the course of gestation. While the consequences of these specific alterations are unknown, our results suggest that a general restructuring of gut microbial communities over gestation may be widespread across vertebrate reproductive strategies.
A multidimensional perspective on microbial interactions
Authors: Pacheco Alan R , Segrè Daniel 
Published: June 2019

ABSTRACT
Beyond being simply positive or negative, beneficial or inhibitory, microbial interactions can involve a diverse set of mechanisms, dependencies and dynamical properties. These more nuanced features have been described in great detail for some specific types of interactions, (e.g. pairwise metabolic cross-feeding, quorum sensing or antibiotic killing), often with the use of quantitative measurements and insight derived from modeling. With a growing understanding of the composition and dynamics of complex microbial communities for human health and other applications, we face the challenge of integrating information about these different interactions into comprehensive quantitative frameworks. Here, we review the literature on a wide set of microbial interactions, and explore the potential value of a formal categorization based on multidimensional vectors of attributes. We propose that such an encoding can facilitate systematic, direct comparisons of interaction mechanisms and dependencies, and we discuss the relevance of an atlas of interactions for future modeling and rational design efforts.
Effects of even-aged and uneven-aged management on carbon dynamics and timber yield in boreal Norway spruce stands: a forest ecosystem model approach
Authors: Kellomäki S , Strandman H , Peltola H 
Published: June 2019

Abstract
We used a gap-type forest ecosystem model to study how even- and uneven-aged management affected the carbon dynamics and timber production in boreal Norway spruce stands. In business-as-usual management, the intensity of thinnings (from below) and single-tree selective cuttings followed those recommended for even-aged (BT) and uneven-aged management (BSC) in practical forestry in Finland. Moreover, higher or lower basal area thresholds, and shorter or longer production cycles, were used in simulations. We found that, the mean annual carbon uptake, volume growth, and carbon stock in trees and harvested timber, were nearly the same under even-aged (BT) and uneven-aged (BSC) management, when assuming full seed crop in latter one. However, the carbon stock in the soil and ecosystem and the mean annual net ecosystem exchange were slightly smaller under BT. The carbon retention time was longer under BSC. The net present value (NPV with interest rate of 3 per cent) of timber production was clearly lower under BT, when the calculation was initiated at planting on clear-cutting area, in opposite to when initiating calculation a few years before the second thinning. Higher basal area thresholds and longer production cycles increased carbon stocks, carbon retention and timber yield, regardless of management system. On the other hand, the results of uneven-aged management (BSC) were very sensitive to the success of natural regeneration and ingrowth of seedlings, as a reduction of the seed crop by 25–75 per cent from the full seed crop decreases the volume growth by 44–74 per cent and timber yield up to 46 per cent.
Estimating Biological Age in the Singapore Longitudinal Aging Study
Authors: Zhong Xin , Lu Yanxia , Gao Qi , Nyunt Ma Shwe Zin , Fulop Tamas , Monterola Christopher Pineda , Tong Joo Chuan , Larbi Anis , Ng Tze Pin 
Published: June 2019

Abstract

Background
Biological age (BA) is a more accurate measure of the rate of human aging than chronological age (CA). However, there is limited consensus regarding measures of BA in life span and healthspan.

Methods
This study investigated measurement sets of 68 physiological biomarkers using data from 2,844 Chinese Singaporeans in two age subgroups (55–70 and 71–94 years) in the Singapore Longitudinal Aging Study (SLAS-2) with 8-year follow-up frailty and mortality data. We computed BA estimate using three commonly used algorithms: Principal Component Analysis (PCA), Multiple Linear Regression (MLR), and Klemera and Doubal (KD) method, and additionally, explored the use of machine learning methods for prediction of mortality and frailty. The most optimal algorithmic estimate of BA compared to CA was evaluated for their associations with risk factors and health outcome.

Results
Stepwise selection procedures resulted in the final selection of 8 biomarkers in males and 10 biomarkers in females. The highest-ranking biomarkers were estimated glomerular filtration rate for both genders, and the forced expiratory volume in 1 second in males and females. The BA estimates robustly predicted frailty and mortality and outperformed CA. The best performing KD measure of BA was notably predictive in the younger group (aged 55–70 years). BA estimates obtained using a machine learning train-test method were not more accurate than conventional BA estimates in predicting mortality and frailty in most situations. Biologically older people with the same CA as biologically younger individuals had higher prevalence of frailty and 8-year mortality, and worse health, behavioral, and functional characteristics.

Conclusions
BA is better than CA for measuring life span (mortality) and healthspan (frailty). This measurement set of physiological markers of biological aging among Chinese robustly differentiate biologically old from younger individuals with the same CA.
Variability in synthetic earthquake ground motions caused by source variability and errors in wave propagation models
Authors: Spudich Paul , Cirella Antonella , Scognamiglio Laura , Tinti Elisa 
Published: June 2019

SUMMARYNumerical simulations of earthquake ground motions are used both to anticipate the effects of hypothetical earthquakes by forward simulation and to infer the behaviour of the real earthquake source ruptures by the inversion of recorded ground motions. In either application it is necessary to assume some Earth structure that is necessarily inaccurate and to use a computational method that is also inaccurate for simulating the wavefield Green's functions. We refer to these two sources of error as ‘propagation inaccuracies’, which might be considered to be epistemic. We show that the variance of the Fourier spectrum of the synthetic earthquake seismograms caused by propagation inaccuracies is related to the spatial covariance on the rupture surface of errors in the computed Green's functions, which we estimate for the case of the 2009 L'Aquila, Italy, earthquake by comparing erroneous computed Green's functions with observed L'Aquila aftershock seismograms (empirical Green's functions). We further show that the variance of the synthetic seismograms caused by the rupture variability (aleatory uncertainty) is related to the spatial covariance on the rupture surface of aleatory variations in the rupture model, and we investigate the effect of correlated variations in Green's function errors and variations in rupture models. Thus, we completely characterize the variability of synthetic earthquake seismograms induced by errors in propagation and variability in the rupture behaviour. We calculate the spectra of the variance of the ground motions of the L'Aquila main shock caused by propagation inaccuracies for two specific broad-band stations, the AQU and the FIAM stations. These variances are distressingly large, being comparable or in some cases exceeding the data amplitudes, suggesting that the best-fitting L'Aquila rupture model significantly overfits the data and might be seriously in error. If these computed variances are typical, the accuracy of many other rupture models for past earthquakes may need to be reconsidered. The results of this work might be useful in seismic hazard estimation because the variability of the computed ground motion, caused both by propagation inaccuracies and variations in the rupture model, can be computed directly, not requiring laborious consideration of multiple Earth structures.
Integration and the Developmental Genetics of Allometry
Authors: Hallgrímsson Benedikt , Katz David C , Aponte Jose D , Larson Jacinda R , Devine Jay , Gonzalez Paula N , Young Nathan M , Roseman Charles C , Marcucio Ralph S 
Published: June 2019

AbstractAllometry refers to the ways in which organismal shape is associated with size. It is a special case of integration, or the tendency for traits to covary, in that variation in size is ubiquitous and evolutionarily important. Allometric variation is so commonly observed that it is routinely removed from morphometric analyses or invoked as an explanation for evolutionary change. In this case, familiarity is mistaken for understanding because rarely do we know the mechanisms by which shape correlates with size or understand their significance. As with other forms of integration, allometric variation is generated by variation in developmental processes that affect multiple traits, resulting in patterns of covariation. Given this perspective, we can dissect the genetic and developmental determinants of allometric variation. Our work on the developmental and genetic basis for allometric variation in craniofacial shape in mice and humans has revealed that allometric variation is highly polygenic. Different measures of size are associated with distinct but overlapping patterns of allometric variation. These patterns converge in part on a common genetic basis. Finally, environmental modulation of size often generates variation along allometric trajectories, but the timing of genetic and environmental perturbations can produce deviations from allometric patterns when traits are differentially sensitive over developmental time. These results question the validity of viewing allometry as a singular phenomenon distinct from morphological integration more generally.
Andrographolide Exerts Significant Antidepressant-Like Effects Involving the Hippocampal BDNF System in Mice
Authors: Zhang Jing-Jing , Gao Ting-Ting , Wang Yuan , Wang Jin-Liang , Guan Wei , Wang Ying-Jie , Wang Cheng-Niu , Liu Jian-Feng , Jiang Bo 
Published: June 2019

Abstract

Background
Major depressive disorder is a worldwide neuropsychiatric disorder associated with various symptoms, but current antidepressants used in clinical practice have various side effects and high failure rates. Andrographolide is the main bioactive ingredient of Andrographis paniculata and exhibits numerous pharmacological actions. This study aimed to evaluate the antidepressant-like effects of andrographolide in male C57BL/6J mice.

Methods
The antidepressant-like effects of andrographolide in mice were explored in a forced swim test, tail suspension test, and chronic unpredictable mild stress model of depression. Western blotting and immunofluorescence were further performed to assess the effects of chronic unpredictable mild stress and andrographolide on the brain-derived neurotrophic factor signalling cascade and hippocampal neurogenesis. Moreover, a pharmacological inhibitor (K252a) and a lentiviral-short hairpin RNA (LV-TrkB-shRNA) were used to clarify the antidepressant-like mechanism of andrographolide.

Results
Andrographolide exhibited antidepressant-like potential in the forced swim test and tail suspension test without influencing the locomotor activity of mice. Repeated andrographolide treatment not only produced significant antidepressant-like effects in the chronic unpredictable mild stress model but also prevented the decreasing effects of chronic unpredictable mild stress on hippocampal brain-derived neurotrophic factor signalling and neurogenesis in mice. Importantly, blockade of the hippocampal brain-derived neurotrophic factor system by K252a and TrkB-shRNA fully abolished the antidepressant-like effects of andrographolide in mice.

Conclusions
Andrographolide exerts antidepressant-like effects in mice via promoting the hippocampal brain-derived neurotrophic factor signalling cascade.
Guidance for Studies Evaluating the Accuracy of Tuberculosis Triage Tests
Authors: Nathavitharana Ruvandhi R , Yoon Christina , Macpherson Peter , Dowdy David W , Cattamanchi Adithya , Somoskovi Akos , Broger Tobias , Ottenhoff Tom H M , Arinaminpathy Nimalan , Lonnroth Knut , Reither Klaus , Cobelens Frank , Gilpin Christopher , Denkinger Claudia M , Schumacher Samuel G 
Published: June 2019

Abstract
Approximately 3.6 million cases of active tuberculosis (TB) go potentially undiagnosed annually, partly due to limited access to confirmatory diagnostic tests, such as molecular assays or mycobacterial culture, in community and primary healthcare settings. This article provides guidance for TB triage test evaluations. A TB triage test is designed for use in people with TB symptoms and/or significant risk factors for TB. Triage tests are simple and low-cost tests aiming to improve ease of access and implementation (compared with confirmatory tests) and decrease the proportion of patients requiring more expensive confirmatory testing. Evaluation of triage tests should occur in settings of intended use, such as community and primary healthcare centers. Important considerations for triage test evaluation include study design, population, sample type, test throughput, use of thresholds, reference standard (ideally culture), and specimen flow. The impact of a triage test will depend heavily on issues beyond accuracy, primarily centered on implementation.
Invasive Meningococcal Disease in Africa’s Meningitis Belt: More Than Just Meningitis?
Authors: Reese Heather E , Ronveaux Olivier , Mwenda Jason M , Bita Andre , Cohen Adam L , Novak Ryan T , Fox LeAnne M , Soeters Heidi M 
Published: June 2019

Abstract
Since the progressive introduction of the meningococcal serogroup A conjugate vaccine within Africa’s meningitis belt beginning in 2010, the burden of meningitis due to Neisseria meningitidis serogroup A (NmA) has substantially decreased. Non-A serogroups C/W/X are now the most prevalent. Surveillance within the belt has historically focused on the clinical syndrome of meningitis, the classic presentation for NmA, and may not adequately capture other presentations of invasive meningococcal disease (IMD). The clinical presentation of infection due to serogroups C/W/X includes nonmeningeal IMD, and there is a higher case-fatality ratio associated with these non-A serogroups; however, data on the nonmeningeal IMD burden within the belt are scarce. Expanding surveillance to capture all cases of IMD, in accordance with the World Health Organization’s updated vaccine-preventable disease surveillance standards and in preparation for the anticipated introduction of a multivalent meningococcal conjugate vaccine within Africa’s meningitis belt, will enhance meningococcal disease prevention across the belt.