bluuebunny/crossref_metadata_2025_split huggingface dataset:
Landscape dynamics revealed by luminescence signals of feldspars from fluvial terraces
Authors: Bonnet Stéphane , Reimann Tony , Wallinga Jakob , Lague Dimitri , Davy Philippe , Lacoste Aurélien 
Published: June 2019

AbstractLuminescence signals of quartz and feldspar minerals are widely used to determine the burial age of Quaternary sediments. Although luminescence signals bleach rapidly with sunlight exposure, incomplete bleaching may affect luminescence ages, in particular in fluvial settings where an unbleached remnant signal is commonly encountered in modern alluvium. Here, we use feldspar single-grain post-infrared IR stimulation (pIRIR) dating to show that recent (<11 ka) fluvial terraces of the Rangitikei River (New Zealand) were formed in a context of non-linear incision rate. We relate this pattern to the rapid reinstatement of steady-state incision following the formation of a major, climate-driven, aggradation terrace, causing a phase of accelerated incision. In addition, we show systematic variations in the proportion of unbleached grains in the fluvial sediments over time, mirroring incision rate at the time of deposition. Deposits formed during rapid incision contain fewer bleached grains, which we attribute to large input of unbleached material and limited bleaching opportunities during fluvial transport. This finding demonstrates that the luminescence signals recorded in fluvial terraces not only yield age information, but also inform us on past fluvial transport and ultimately, landscape dynamics.
Quantitative Imaging features Improve Discrimination of Malignancy in Pulmonary nodules
Authors: Balagurunathan Yoganand , Schabath Matthew B. , Wang Hua , Liu Ying , Gillies Robert J. 
Published: June 2019

AbstractPulmonary nodules are frequently detected radiological abnormalities in lung cancer screening. Nodules of the highest- and lowest-risk for cancer are often easily diagnosed by a trained radiologist there is still a high rate of indeterminate pulmonary nodules (IPN) of unknown risk. Here, we test the hypothesis that computer extracted quantitative features (“radiomics”) can provide improved risk-assessment in the diagnostic setting. Nodules were segmented in 3D and 219 quantitative features are extracted from these volumes. Using these features novel malignancy risk predictors are formed with various stratifications based on size, shape and texture feature categories. We used images and data from the National Lung Screening Trial (NLST), curated a subset of 479 participants (244 for training and 235 for testing) that included incident lung cancers and nodule-positive controls. After removing redundant and non-reproducible features, optimal linear classifiers with area under the receiver operator characteristics (AUROC) curves were used with an exhaustive search approach to find a discriminant set of image features, which were validated in an independent test dataset. We identified several strong predictive models, using size and shape features the highest AUROC was 0.80. Using non-size based features the highest AUROC was 0.85. Combining features from all the categories, the highest AUROC were 0.83.
Climate change will decrease the range size of snake species under negligible protection in the Brazilian Atlantic Forest hotspot
Authors: Lourenço-de-Moraes Ricardo , Lansac-Toha Fernando Miranda , Schwind Leilane Talita Fatoreto , Arrieira Rodrigo Leite , Rosa Rafael Rogério , Terribile Levi Carina , Lemes Priscila , Fernando Rangel Thiago , Diniz-Filho José Alexandre Felizola , Bastos Rogério Pereira , Bailly Dayani 
Published: June 2019

AbstractReptiles are highly susceptible to climate change, responding negatively to thermal and rainfall alterations mainly in relation to their reproductive processes. Based on that, we evaluated the effects of climate change on climatically suitable areas for the occurrence of snakes in the Atlantic Forest hotspot, considering the responses of distinct reproductive groups (oviparous and viviparous). We assessed the species richness and turnover patterns affected by climate change and projected the threat status of each snake species at the end of the century. We also evaluated the effectiveness of the protected areas in safeguarding the species by estimating the mean percentage overlap between snake species distribution and protected areas (PAs) network and by assessing whether such areas will gain or lose species under climate change. Our results showed greater species richness in the eastern-central portion of the Atlantic Forest at present. In general, we evidenced a drastic range contraction of the snake species under climate change. Temporal turnover tends to be high in the western and north-eastern edges of the biome, particularly for oviparous species. Our predictions indicate that 73.6% of oviparous species and 67.6% of viviparous species could lose at least half of their original range by 2080. We also found that existing protected areas of the Atlantic Forest Hotspot have a very limited capacity to safeguard snakes at the current time, maintaining the precarious protection in the future, with the majority of them predicted to lose species at the end of this century. Although oviparous and viviparous snakes have been designated to be dramatically impacted, our study suggests a greater fragility of the former in the face of climate change. We advocated that the creation of new protected areas and/or the redesign of the existing network to harbour regions that maximize the snake species occupancy in the face of future warming scenarios are crucial measures for the conservation of this group.
Secondhand Smoke Exposure During Pregnancy and Mothers’ Subsequent Breastfeeding Outcomes: A Systematic Review and Meta-Analysis
Authors: Suzuki Daichi , Wariki Windy M. V. , Suto Maiko , Yamaji Noyuri , Takemoto Yo , Rahman Mosfequr , Ota Erika 
Published: June 2019

AbstractSecondhand smoke exposure of non-smoking women during pregnancy is associated with a higher risk of adverse birth outcomes. However, the available evidence regarding the association between expectant mothers’ secondhand smoke exposure and breastfeeding outcomes remains limited. This systematic review aimed to examine associations between secondhand smoke exposure of nonsmoking women during pregnancy with the initiation, prevalence, and duration or breastfeeding compared to women who were breastfeeding and had not been exposed to secondhand smoke. Women who smoked during pregnancy were excluded. We included case-control, cross-sectional, and cohort studies with a comparison control group. Medline CINAHL, and EMBASE were searched in January 2017. After screening 2777 records we included eight prospective cohort studies. The risk of bias assessment tool for non-randomized studies indicated a high risk of outcome assessment blinding. Meta-analysis of two studies established that the odds of discontinuation of any brestfeeding before six months were significantly increased in the secondhand smoke exposed women (pooled odds = 1.07 [95%CI = 1.01, 1.14], two studies, 1382 women). Therefore, secondhand smoke might be associated with discontinuing any breastfeeding before six months. More research is necessary to understand the association between secondhand smoke and the initiation, prevalence and duration of breastfeeding.
Towards a reliable assessment of Asian elephant population parameters: the application of photographic spatial capture–recapture sampling in a priority floodplain ecosystem
Authors: Goswami Varun R. , Yadava Mahendra K. , Vasudev Divya , Prasad Parvathi K. , Sharma Pragyan , Jathanna Devcharan 
Published: June 2019

AbstractThe hitherto difficult task of reliably estimating populations of wide-ranging megafauna has been enabled by advances in capture–recapture methodology. Here we combine photographic sampling with a Bayesian spatially-explicit capture–recapture (SCR) model to estimate population parameters for the endangered Asian elephantElephas maximusin the productive floodplain ecosystem of Kaziranga National Park, India. Posterior density estimates of herd-living adult females and sub-adult males and females (herd-adults) was 0.68 elephants/km2(95% Credible Intervals, CrI = 0.56−0.81) while that of adult males was 0.24 elephants/km2(95% CrI = 0.18−0.30), with posterior density estimates highlighting spatial heterogeneity in elephant distribution. Estimates of the space-usage parameter suggested that herd-adults ($${\hat{\sigma }}_{HA}$$σˆHA = 5.91 km, 95% CrI = 5.18–6.81) moved around considerably more than adult males ($${\hat{\sigma }}_{AM}$$σˆAM = 3.64 km, 95% CrI = 3.09–4.34). Based on elephant movement and age–sex composition, we derived the population that contributed individuals sampled in Kaziranga to be 908 herd-adults, 228 adult males and 610 young (density = 0.46 young/km2, SD = 0.06). Our study demonstrates how SCR is suited to estimating geographically open populations, characterising spatial heterogeneity in fine-scale density, and facilitating reliable monitoring to assess population status and dynamics for science and conservation.
The domain swapping of human cystatin C induced by synchrotron radiation
Authors: Taube Michal , Pietralik Zuzanna , Szymanska Aneta , Szutkowski Kosma , Clemens Daniel , Grubb Anders , Kozak Maciej 
Published: June 2019

AbstractDomain swapping is observed for many proteins with flexible conformations. This phenomenon is often associated with the development of conformational diseases. Importantly, domain swapping has been observed for human cystatin C (HCC), a protein capable of forming amyloid deposits in brain arteries. In this study, the ability of short exposure to high-intensity X-ray radiation to induce domain swapping in solutions of several HCC variants (wild-type HCC and V57G, V57D, V57N, V57P, and L68V mutants) was determined. The study was conducted using time-resolved small-angle X-ray scattering (TR-SAXS) synchrotron radiation. The protein samples were also analysed using small-angle neutron scattering and NMR diffusometry. Exposing HCC to synchrotron radiation (over 50 ms) led to a gradual increase in the dimeric fraction, and for exposures longer than 150 ms, the oligomer fraction was dominant. In contrast, the non-irradiated protein solutions, apart from the V57P variant, were predominantly monomeric (e.g., V57G) or in monomer/dimer equilibrium. This work might represent the first observation of domain swapping induced by high-intensity X-rays.
Acid specific dark quencher QC1 pHLIP for multi-spectral optoacoustic diagnoses of breast cancer
Authors: Roberts Sheryl , Strome Arianna , Choi Crystal , Andreou Chrysafis , Kossatz Susanne , Brand Christian , Williams Travis , Bradbury Michelle , Kircher Moritz F. , Reshetnyak Yana K. , Grimm Jan , Lewis Jason S. , Reiner Thomas 
Published: June 2019

AbstractBreast cancer is the most common type of malignant growth in women. Early detection of breast cancer, as well as the identification of possible metastatic spread poses a significant challenge because of the structural and genetic heterogeneity that occurs during the progression of the disease. Currently, mammographies, biopsies and MRI scans are the standard of care techniques used for breast cancer diagnosis, all of which have their individual shortfalls, especially when it comes to discriminating tumors and benign growths. With this in mind, we have developed a non-invasive optoacoustic imaging strategy that targets the acidic environment of breast cancer. A pH low insertion peptide (pHLIP) was conjugated to the dark quencher QC1, yielding a non-fluorescent sonophore with high extinction coefficient in the near infrared that increases signal as a function of increasing amounts of membrane insertion. In an orthotopic murine breast cancer model, pHLIP-targeted optoacoustic imaging allowed us to differentiate between healthy and breast cancer tissues with high signal/noise ratios. In vivo, the sonophore QC1-pHLIP could detect malignancies at higher contrast than its fluorescent analog ICG-pHLIP, which was developed for fluorescence-guided surgical applications. PHLIP-type optoacoustic imaging agents in clinical settings are attractive due to their ability to target breast cancer and a wide variety of other malignant growths for diagnostic purposes. Intuitively, these agents could also be used for visualization during surgery.
Randomized Evaluation of Anagliptin vs Sitagliptin On low-density lipoproteiN cholesterol in diabetes (REASON) Trial: A 52-week, open-label, randomized clinical trial
Authors: Morimoto Takeshi , Sakuma Ichiro , Sakuma Mio , Tokushige Akihiro , Natsuaki Masahiro , Asahi Tomohiro , Shimabukuro Michio , Nomiyama Takashi , Arasaki Osamu , Node Koichi , Ueda Shinichiro 
Published: June 2019

AbstractAdditional reductions in low-density lipoprotein-cholesterol (LDL-C) via antidiabetic therapies should be considered in statin-using patients with sub-optimal LDL-C levels. We compared the efficacy of anagliptin and sitagliptin, two antidiabetic therapies, in reducing LDL-C in type 2 diabetic patients. A randomized, open-label, parallel-group trial was conducted at 17 centres in Japan between April 2015 and January 2018. Adults (age ≥20 years) with type 2 diabetes, any atherosclerotic vascular lesions, and statin prescriptions were included. Anagliptin or sitagliptin were administered for 52 weeks. Primary and secondary endpoints were changes in LDL-C and haemoglobin A1C (HbA1c) levels, respectively. We assessed the superiority (primary endpoint) and non-inferiority (secondary endpoint) of anagliptin over sitagliptin. This study was registered at Clinicaltrials.gov (NCT02330406). Of 380 participants, 353 were eligible and randomized. Mean participant age was 68 years, and 61% were males. Baseline median LDL-C and HbA1c were 108 mg/dL and 6.9%, respectively. Changes in LDL-C were −3.7 mg/dL with anagliptin and +2.1 mg/dL with sitagliptin at 52 weeks, and the estimated treatment difference was a significant −4.5 mg/dL (P = 0.01 for superiority). Changes in HbA1c were +0.02% with anagliptin and +0.12% with sitagliptin (P < 0.0001 for non-inferiority). Overall, anagliptin was superior to sitagliptin in lowering LDL-C without deteriorating HbA1c.
Element-centric clustering comparison unifies overlaps and hierarchy
Authors: Gates Alexander J. , Wood Ian B. , Hetrick William P. , Ahn Yong-Yeol 
Published: June 2019

AbstractClustering is one of the most universal approaches for understanding complex data. A pivotal aspect of clustering analysis is quantitatively comparing clusterings; clustering comparison is the basis for many tasks such as clustering evaluation, consensus clustering, and tracking the temporal evolution of clusters. In particular, the extrinsic evaluation of clustering methods requires comparing the uncovered clusterings to planted clusterings or known metadata. Yet, as we demonstrate, existing clustering comparison measures have critical biases which undermine their usefulness, and no measure accommodates both overlapping and hierarchical clusterings. Here we unify the comparison of disjoint, overlapping, and hierarchically structured clusterings by proposing a new element-centric framework: elements are compared based on the relationships induced by the cluster structure, as opposed to the traditional cluster-centric philosophy. We demonstrate that, in contrast to standard clustering similarity measures, our framework does not suffer from critical biases and naturally provides unique insights into how the clusterings differ. We illustrate the strengths of our framework by revealing new insights into the organization of clusters in two applications: the improved classification of schizophrenia based on the overlapping and hierarchical community structure of fMRI brain networks, and the disentanglement of various social homophily factors in Facebook social networks. The universality of clustering suggests far-reaching impact of our framework throughout all areas of science.
Cancer cell killing by target antigen engagement with engineered complementary intracellular antibody single domains fused to pro-caspase3
Authors: Chambers Jennifer S. , Brend Tim , Rabbitts Terence H. 
Published: June 2019

AbstractMany tumour causing proteins, such as those expressed after chromosomal translocations or from point mutations, are intracellular and are not enzymes per se amenable to conventional drug targeting. We previously demonstrated an approach (Antibody-antigen Interaction Dependent Apoptosis (AIDA)) whereby a single anti-β-galactosidase intracellular single chain Fv antibody fragment, fused to inactive procaspase-3, induced auto-activation of caspase-3 after binding to the tetrameric β-galactosidase protein. We now demonstrate that co-expressing an anti-RAS heavy chain single VH domain, that binds to mutant RAS several thousand times more strongly than to wild type RAS, with a complementary light chain VL domain, caused programmed cell death (PCD) in mutant RAS expressing cells when each variable region is fused to procaspase-3. The effect requires binding of both anti-RAS variable region fragments and is RAS-specific, producing a tri-molecular complex that auto-activates the caspase pathway leading to cell death. AIDA can be generally applicable for any target protein inside cells by involving appropriate pairs of antigen-specific intracellular antibodies.
Spectroscopic and Biophysical Interaction Studies of Water-soluble Dye modified poly(o-phenylenediamine) for its Potential Application in BSA Detection and Bioimaging
Authors: Riaz Ufana , Ashraf S. M. , Jadoun Sapana , Budhiraja Vaibhav , Kumar Prabhat 
Published: June 2019

AbstractUltrasound-assisted synthesis of water soluble poly(o-phenylenediamine) (POPD) and its doping with Acid Orange (AO), Fluorescein (Fluo) and Rhodamine-6G (R6G) dyes was carried out with a view to enhance the photophysical properties of POPD. XPS studies confirmed that doping of POPD occured through hydrogen bonding between NH group of POPD and C=O/SO−, S=O groups of the dyes. The presence of strong hydrogen bonding was also confirmed via UV-vis studies by the addition of urea and sodium chloride to the dye modified POPD adducts. Molar extinction coefficient of these adducts was found to bear a close relationship with the molecular structure. Fluorescence life time, (τf,) was found to be lowest (1.8 ns) for AO-POPD and highest (3.2 ns) for Fluo-POPD. The structure of AO-POPD was more strained, while that of Fluo-POPD was least strained. Intrinsic fluorescence decay constant, (k0f) showed increasing values for POPD, AO-POPD, Fluo-POPD, R6G-POPD as 0.071, 0.072, 0.153, and 0.172 (108s−1), which could be correlated to the increasing strain-free molecular structure of the adducts. Circular dichroism spectra (CD) of BSA in presence of POPD and R6G- POPD revealed that it partially broke its helical structure, while Fluo-POPD and AO-POPD showed enhancement in the helical content. The 3-D fluorescence studies confirmed enhancement in hydrophobicity of POPD and R6G- POPD and increase in hydrophylicity of AO-POP and Fluo-POPD in the microenvironment of tryptophan residue-213 of BSA. Fluo-POPD and R6G-POPD adducts were chosen to find out the lowest detection limit (LOD) of BSA by differential pulse voltammetry (DPV) which was found to be 1.35 nM, and 1.65 nM using Fluo-POPD and R6G -POPD respectively. The binding constant of BSA with Fluo-POPD- and R6G-POPD was obtained as 3.98 × 106Lmol−1and 5.27 × 102Lmol−1. These polymers could therefore, be used for the detection of BSA. Live cell imaging revealed that POPD nanoparticles were bound to the outer membrane ofE.coli, while R6G-POPD, showed penetration into the cytoplasm and excellent labeling ofE.coli. This facile technique could be used to design tunable biomarkers by tailoring the conjugated polymer with a desired dye molecule.
Evolution of the avian digital pattern
Authors: Kawahata Kenta , Cordeiro Ingrid Rosenburg , Ueda Shogo , Sheng Guojun , Moriyama Yuuta , Nishimori Chika , Yu Reiko , Koizumi Makoto , Okabe Masataka , Tanaka Mikiko 
Published: June 2019

AbstractVariation in digit number has occurred multiple times in the history of archosaur evolution. The five digits of dinosaur limbs were reduced to three in bird forelimbs, and were further reduced in the vestigial forelimbs of the emu. Regulation of digit number has been investigated previously by examining genes involved in anterior-posterior patterning in forelimb buds among emu (Dromaius novaehollandiae), chicken (Gallus gallus) and zebra finch (Taeniopygia guttata). It was described that the expression of posterior genes are conserved among these three birds, whereas expression of anterior genesGli3andAlx4varied significantly. Here we re-examined the expression pattern ofGli3andAlx4in the forelimb of emu, chicken and zebra finch. We found thatGli3is expressed in the anterior region, although its range varied among species, and that the expression pattern ofAlx4in forelimb buds is broadly conserved in a stage-specific manner. We also found that the dynamic expression pattern of the BMP antagonistGremlin1(Grem1) in limb buds, which is critical for autopodial expansion, was consistent with the digital pattern of emu, chicken and zebra finch. Furthermore, in emu, variation among individuals was observed in the width ofGrem1expression in forelimb buds, as well as in the adult skeletal pattern. Our results support the view that the signalling system that regulates the dynamic expression ofGrem1in the limb bud contributes substantially to variations in avian digital patterns.
Segmentation, Tracing, and Quantification of Microglial Cells from 3D Image Stacks
Authors: Abdolhoseini Mahmoud , Kluge Murielle G. , Walker Frederick R. , Johnson Sarah J. 
Published: June 2019

AbstractMicroglia play a central role in modulating synaptic structure and physiology, learning and memory processes. They exhibit morphological changes to perform these roles, therefore the morphological study of microglia can help to understand their functionality. Many promising methods are proposed to automatically segment the blood vessels or reconstruct the neuronal morphology. However, they often fail to accurately capture microglia organizations due to the striking structural differences. This requires a more sophisticated approach of reconstruction taking into account the varying nature of branch structures and soma sizes. To this end, we propose an automated method to reconstruct microglia, and quantify their features from 2D/3D image datasets. We first employ multilevel thresholding to segment soma volumes(3D)/areas(2D) and recognize foreground voxels/pixels. Seed points sampled from the foreground, are connected to form the skeleton of the branches via the tracing process. The reconstructed data is quantified and written in SWC standard file format. We have applied our method to 3D image datasets of microglia, then evaluated the results using ground truth data, and compared them to those achieved via the state-of-the-art methods. Our method outperforms the others both in accuracy and computational time.