bluuebunny/crossref_metadata_2025_split huggingface dataset:
Artisanal fish fences pose broad and unexpected threats to the tropical coastal seascape
Authors: Exton Dan A. , Ahmadia Gabby N. , Cullen-Unsworth Leanne C. , Jompa Jamaluddin , May Duncan , Rice Joel , Simonin Paul W. , Unsworth Richard K. F. , Smith David J. 
Published: May 2019

AbstractGear restrictions are an important management tool in small-scale tropical fisheries, improving sustainability and building resilience to climate change. Yet to identify the management challenges and complete footprint of individual gears, a broader systems approach is required that integrates ecological, economic and social sciences. Here we apply this approach to artisanal fish fences, intensively used across three oceans, to identify a previously underrecognized gear requiring urgent management attention. A longitudinal case study shows increased effort matched with large declines in catch success and corresponding reef fish abundance. We find fish fences to disrupt vital ecological connectivity, exploit > 500 species with high juvenile removal, and directly damage seagrass ecosystems with cascading impacts on connected coral reefs and mangroves. As semi-permanent structures in otherwise open-access fisheries, they create social conflict by assuming unofficial and unregulated property rights, while their unique high-investment-low-effort nature removes traditional economic and social barriers to overfishing.
Pheomelanin pigment remnants mapped in fossils of an extinct mammal
Authors: Manning Phillip L. , Edwards Nicholas P. , Bergmann Uwe , Anné Jennifer , Sellers William I. , van Veelen Arjen , Sokaras Dimosthenis , Egerton Victoria M. , Alonso-Mori Roberto , Ignatyev Konstantin , van Dongen Bart E. , Wakamatsu Kazumasa , Ito Shosuke , Knoll Fabien , Wogelius Roy A. 
Published: May 2019

AbstractRecent progress has been made in paleontology with respect to resolving pigmentation in fossil material. Morphological identification of fossilized melanosomes has been one approach, while a second methodology using chemical imaging and spectroscopy has also provided critical information particularly concerning eumelanin (black pigment) residue. In this work we develop the chemical imaging methodology to show that organosulfur-Zn complexes are indicators of pheomelanin (red pigment) in extant and fossil soft tissue and that the mapping of these residual biochemical compounds can be used to restore melanin pigment distribution in a 3 million year old extinct mammal species (Apodemus atavus). Synchotron Rapid Scanning X-ray Fluorescence imaging showed that the distributions of Zn and organic S are correlated within this fossil fur just as in pheomelanin-rich modern integument. Furthermore, Zn coordination chemistry within this fossil fur is closely comparable to that determined from pheomelanin-rich fur and hair standards. The non-destructive methods presented here provide a protocol for detecting residual pheomelanin in precious specimens.
The composition of British bird communities is associated with long-term garden bird feeding
Authors: Plummer Kate E. , Risely Kate , Toms Mike P. , Siriwardena Gavin M. 
Published: May 2019

AbstractThere is a multi-billion dollar global industry dedicated to feeding wild birds in residential gardens. This extraordinary boost to food resources is almost certainly reshaping entire bird communities, yet the large-scale, long-term impacts on community ecology remain unknown. Here we reveal a 40-year transformation of the bird communities using garden bird feeders in Britain, and provide evidence to suggest how this may have contributed to national-scale population changes. We find that increases in bird diversity at feeders are associated with increasing community evenness, as species previously rarely observed in gardens have increasingly exploited the growing variety of foods on offer over time. Urban areas of Britain are consequently nurturing growing populations of feeder-using bird species, while the populations of species that do not use feeders remain unchanged. Our findings illustrate the on-going, gross impact people can have on bird community structure across large spatial scales.
Ubiquitylome study identifies increased histone 2A ubiquitylation as an evolutionarily conserved aging biomarker
Authors: Yang Lu , Ma Zaijun , Wang Han , Niu Kongyan , Cao Ye , Sun Le , Geng Yang , Yang Bo , Gao Feng , Chen Zuolong , Wu Zhen , Li Qingqing , Shen Yong , Zhang Xumin , Jiang Hong , Chen Yelin , Liu Rui , Liu Nan , Zhang Yaoyang 
Published: May 2019

AbstractThe long-lived proteome constitutes a pool of exceptionally stable proteins with limited turnover. Previous studies on ubiquitin-mediated protein degradation primarily focused on relatively short-lived proteins; how ubiquitylation modifies the long-lived proteome and its regulatory effect on adult lifespan is unclear. Here we profile the age-dependent dynamics of long-lived proteomes in Drosophila by mass spectrometry using stable isotope switching coupled with antibody-enriched ubiquitylome analysis. Our data describe landscapes of long-lived proteins in somatic and reproductive tissues of Drosophila during adult lifespan, and reveal a preferential ubiquitylation of older long-lived proteins. We identify an age-modulated increase of ubiquitylation on long-lived histone 2A protein in Drosophila, which is evolutionarily conserved in mouse, monkey, and human. A reduction of ubiquitylated histone 2A in mutant flies is associated with longevity and healthy lifespan. Together, our data reveal an evolutionarily conserved biomarker of aging that links epigenetic modulation of the long-lived histone protein to lifespan.
Relict subduction initiation along a passive margin in the northwest Indian Ocean
Authors: Pandey Dhananjai K. , Pandey Anju , Whattam Scott A. 
Published: May 2019

AbstractThe tectonic evolution of Laxmi basin, presently located along western Indian passive margin, remains debated. Prevailing geodynamic models of Laxmi basin include two mutually competing hypotheses, culminating in either a hyper-stretched continental crust or an oceanic crust overlying an extinct spreading centre. The longstanding conundrum surrounding its precise crustal affinity precludes a complete understanding of the early opening of the Indian Ocean. Here, we present distinct geochemical and geophysical imprints from the igneous crust in Laxmi basin obtained through International Ocean Discovery Program Expedition 355. The geochemical and isotopic signatures of the Laxmi basin crust exhibit uncanny similarities with forearc tectonic settings. Our observations imply a relict subduction initiation event occurred in the Laxmi basin in the Late Cretaceous-Early Cenozoic that marks a significant Cenozoic plate reorganisation record in the northwest Indian Ocean. New findings therefore warrant re-evaluation of the Gondwana breakup to account for the nascent subduction in the northwest Indian Ocean.
Publisher Correction: Scaling of domain cascades in stripe and skyrmion phases
Authors: Singh A. , Lee J. C. T. , Avila K. E. , Chen Y. , Montoya S. A. , Fullerton E. E. , Fischer P. , Dahmen K. A. , Kevan S. D. , Sanyal M. K. , Roy S. 
Published: May 2019

The original version of this Article contained an error in Fig. 4d, in which the label of the region to the left of the white dashed lines incorrectly read ‘Order stripes’. The correct version states ‘Disorder stripes’. This has been corrected in both the PDF and HTML versions of the Article.
Implantable hyaluronic acid-deferoxamine conjugate prevents nonunions through stimulation of neovascularization
Authors: Donneys Alexis , Yang Qiuhong , Forrest Marcus Laird , Nelson Noah S. , Zhang Ti , Ettinger Russell , Ranganathan Kavitha , Snider Alicia , Deshpande Sagar S. , Cohen Mark S. , Buchman Steven R. 
Published: May 2019

AbstractApproximately 6.3 million fractures occur in the U.S. annually, with 5–10% resulting in debilitating nonunions. A major limitation to achieving successful bony union is impaired neovascularization. To augment fracture healing, we designed an implantable drug delivery technology containing the angiogenic stimulant, deferoxamine (DFO). DFO activates new blood vessel formation through iron chelation and upregulation of the HIF-1α pathway. However, due to its short half-life and rapid clearance, maintaining DFO at the callus site during peak fracture angiogenesis has remained challenging. To overcome these limitations, we composed an implantable formulation of DFO conjugated to hyaluronic acid (HA). This compound immobilizes DFO within the fracture callus throughout the angiogenic window, making it a high-capacity iron sponge that amplifies blood vessel formation and prevents nonunions. We investigated implanted HA-DFO’s capacity to facilitate fracture healing in the irradiated rat mandible, a model whereby nonunions routinely develop secondary to obliteration of vascularity. HA-DFO implantation significantly improved radiomorphometrics and metrics of biomechanical strength. In addition, HA-DFO treated mandibles exhibited a remarkable 91% bone union rate, representing a 3.5-fold improvement over non-treated/irradiated controls (20% bone union rate). Collectively, our work proposes a unique methodology for the targeted delivery of DFO to fracture sites in order to facilitate neovascularization. If these findings are successfully translated into clinical practice, millions of patients will benefit from the prevention of nonunions.
Characterization of different bubble formulations for blood-brain barrier opening using a focused ultrasound system with acoustic feedback control
Authors: Bing Chenchen , Hong Yu , Hernandez Christopher , Rich Megan , Cheng Bingbing , Munaweera Imalka , Szczepanski Debra , Xi Yin , Bolding Mark , Exner Agata , Chopra Rajiv 
Published: May 2019

AbstractFocused ultrasound combined with bubble-based agents serves as a non-invasive way to open the blood-brain barrier (BBB). Passive acoustic detection was well studied recently to monitor the acoustic emissions induced by the bubbles under ultrasound energy, but the ability to perform reliable BBB opening with a real-time feedback control algorithm has not been fully evaluated. This study focuses on characterizing the acoustic emissions of different types of bubbles: Optison, Definity, and a custom-made nanobubble. Their performance on reliable BBB opening under real-time feedback control based on acoustic detection was evaluated bothin-vitroandin-vivo. The experiments were conducted using a 0.5 MHz focused ultrasound transducer within-vivofocal pressure ranges from 0.1–0.7 MPa. Successful feedback control was achieved with all three agents when combining with infusion injection. Localized opening was confirmed with Evans blue dye leakage. Microscopic images were acquired to review the opening effects. Under similar total gas volume, nanobubble showed a more reliable opening effect compared to Optison and Definity (p < 0.05). The conclusions obtained from this study confirm the possibilities of performing stable opening using a feedback control algorithm combined with infusion injection. It also opens another potential research area of BBB opening using sub-micron bubbles.
Analytical Validation of Multiplex Biomarker Assay to Stratify Colorectal Cancer into Molecular Subtypes
Authors: Ragulan Chanthirika , Eason Katherine , Fontana Elisa , Nyamundanda Gift , Tarazona Noelia , Patil Yatish , Poudel Pawan , Lawlor Rita T. , Del Rio Maguy , Koo Si-Lin , Tan Wah-Siew , Sclafani Francesco , Begum Ruwaida , Teixeira Mendes Larissa S. , Martineau Pierre , Scarpa Aldo , Cervantes Andrés , Tan Iain Beehuat , Cunningham David , Sadanandam Anguraj 
Published: May 2019

AbstractPreviously, we classified colorectal cancers (CRCs) into five CRCAssigner (CRCA) subtypes with different prognoses and potential treatment responses, later consolidated into four consensus molecular subtypes (CMS). Here we demonstrate the analytical development and validation of a custom NanoString nCounter platform-based biomarker assay (NanoCRCA) to stratify CRCs into subtypes. To reduce costs, we switched from the standard nCounter protocol to a custom modified protocol. The assay included a reduced 38-gene panel that was selected using an in-house machine-learning pipeline. We applied NanoCRCA to 413 samples from 355 CRC patients. From the fresh frozen samples (n = 237), a subset had matched microarray/RNAseq profiles (n = 47) or formalin-fixed paraffin-embedded (FFPE) samples (n = 58). We also analyzed a further 118 FFPE samples. We compared the assay results with the CMS classifier, different platforms (microarrays/RNAseq) and gene-set classifiers (38 and the original 786 genes). The standard and modified protocols showed high correlation (> 0.88) for gene expression. Technical replicates were highly correlated (> 0.96). NanoCRCA classified fresh frozen and FFPE samples into all five CRCA subtypes with consistent classification of selected matched fresh frozen/FFPE samples. We demonstrate high and significant subtype concordance across protocols (100%), gene sets (95%), platforms (87%) and with CMS subtypes (75%) when evaluated across multiple datasets. Overall, our NanoCRCA assay with further validation may facilitate prospective validation of CRC subtypes in clinical trials and beyond.
Methyl-β-cyclodextrin, an actin depolymerizer augments the antiproliferative potential of microtubule-targeting agents
Authors: Mundhara Nikita , Majumder Abhijit , Panda Dulal 
Published: May 2019

AbstractMethyl-β-cyclodextrin (MCD), an established pharmacological excipient, depolymerizes the actin cytoskeleton. In this work, we investigated the effect of MCD-mediated actin depolymerization on various cellular phenotypes including traction force, cell stiffness, focal adhesions, and intracellular drug accumulation. In addition to a reduction in the contractile cellular traction, MCD acutely inhibits the maturation of focal adhesions. Alteration of contractile forces and focal adhesions affects the trypsin-mediated detachment kinetics of cells. Moreover, MCD-mediated actin depolymerization increases the intracellular accumulation of microtubule-targeting agents (MTAs) by ~50% with respect to the untreated cells. As MCD treatment enhances the intracellular concentration of drugs, we hypothesized that the MCD-sensitized cancer cells could be effectively killed by low doses of MTAs. Our results in cervical, breast, hepatocellular, prostate cancer and multidrug-resistant breast cancer cells confirmed the above hypothesis. Further, the combined use of MCD and MTAs synergistically inhibits the proliferation of tumor cells. These results indicate the potential use of MCD in combination with MTAs for cancer chemotherapy and suggest that targeting both actin and microtubules simultaneously may be useful for cancer therapy. Importantly, the results provide significant insight into the crosstalk between actin and microtubules in regulating the traction force and dynamics of cell deadhesion.
Restoration of correct βIVS2-654-globin mRNA splicing and HbA production by engineered U7 snRNA in β-thalassaemia/HbE erythroid cells
Authors: Nualkaew Tiwaporn , Jearawiriyapaisarn Natee , Hongeng Suradej , Fucharoen Suthat , Kole Ryszard , Svasti Saovaros 
Published: May 2019

AbstractA cytosine to thymine mutation at nucleotide 654 of human β-globin intron 2 (βIVS2-654) is one of the most common mutations causing β-thalassaemia in Chinese and Southeast Asians. This mutation results in aberrant β-globin pre-mRNA splicing and prevents synthesis of β-globin protein. Splicing correction using synthetic splice-switching oligonucleotides (SSOs) has been shown to restore expression of the β-globin protein, but to maintain therapeutically relevant levels of β-globin it would require lifelong administration. Here, we demonstrate long-term splicing correction using U7 snRNA lentiviral vectors engineered to target several pre-mRNA splicing elements on the βIVS2-654-globin pre-mRNA such as cryptic 3′ splice site, aberrant 5′ splice site, cryptic branch point and an exonic splicing enhancer. A double-target engineered U7 snRNAs targeted to the cryptic branch point and an exonic splicing enhancer, U7.BP + 623, was the most effective in a model cell line, HeLa IVS2-654. Moreover, the therapeutic potential of the vector was demonstrated in erythroid progenitor cells derived from βIVS2-654-thalassaemia/HbE patients, which showed restoration of correctly spliced β-globin mRNA and led to haemoglobin A synthesis, and consequently improved thalassaemic erythroid cell pathology. These results demonstrate proof of concept of using the engineered U7 snRNA lentiviral vector for treatment of β-thalassaemia.
Gender and Child Behavior Problems in Rural Nepal: Differential Expectations and Responses
Authors: Langer Julia A. , Ramos Julia V. , Ghimire Lajina , Rai Sauharda , Kohrt Brandon A. , Burkey Matthew D. 
Published: May 2019

AbstractWhereas epidemiologic studies consistently identify different rates and types of problematic behavior in boys and girls, there has been little research examining the ecocultural context in which these gender differences in child behavior problems develop, especially in non-Western settings. This qualitative study in rural Nepal explored how behavioral expectations differed based on gender role, gender discrimination, inequity, and treatment of children based on their gender identity. We conducted semi-structured interviews with a total of 14 parents, school workers, and community leaders from a village in rural Nepal. Interview transcripts were coded by two authors using predetermined and emergent codes to identify expectations, behavior problems, and responses to behavior problems, stratified by gender. Authors then arranged codes into categories based on emergent themes. Four major themes in the interviews were identified: (1) self-reported gender non-bias; (2) differentiated role expectations; (3) gender, “goodness”, and differential thresholds for problem behaviors; and (4) boys and girls require different responses for misbehavior. Results from our study in Nepal reflect nearly universal models of gender differences in behavior. Of particular importance in South Asia, patrilocal marital practices were used to frame gender differences in expectations. To protect girls’ future potential to marry, local cultural practices provide girls with lesser opportunities and less cultural space to conduct themselves in a disruptive manner than boys. Greater understanding of differential expectations and responses to disruptive behaviors by gender will be important for culturally-appropriate equitable programming in child development.
Long-term drift of Si-MOS quantum dots with intentional donor implants
Authors: Rudolph M. , Sarabi B. , Murray R. , Carroll M. S. , Zimmerman Neil M. 
Published: May 2019

AbstractCharge noise can be detrimental to the operation of quantum dot (QD) based semiconductor qubits. We study the low-frequency charge noise by charge offset drift measurements for Si-MOS devices with intentionally implanted donors near the QDs. We show that the MOS system exhibits non-equilibrium drift characteristics, in the form of transients and discrete jumps, that are not dependent on the properties of the donor implants. The equilibrium charge noise indicates a 1/f noise dependence, and a noise strength as low as $$1\,\mu {\rm{eV}}/\sqrt{{\rm{Hz}}}$$
1

μ
eV
/

Hz

, comparable to that reported in more model GaAs and Si/SiGe systems (which have also not been implanted). We demonstrate that implanted qubits, therefore, can be fabricated without detrimental effects on long-term drift or 1/f noise for devices with less than 50 implanted donors near the qubit.
Ring roads and urban biodiversity: distribution of butterflies in urban parks in Beijing city and correlations with other indicator species
Authors: Sing Kong-Wah , Luo Jiashan , Wang Wenzhi , Jaturas Narong , Soga Masashi , Yang Xianzhe , Dong Hui , Wilson John-James 
Published: May 2019

AbstractThe capital of China, Beijing, has a history of more than 800 years of urbanization, representing a unique site for studies of urban ecology. Urbanization can severely impact butterfly communities, yet there have been no reports of the species richness and distribution of butterflies in urban parks in Beijing. Here, we conducted the first butterfly survey in ten urban parks in Beijing and estimated butterfly species richness. Subsequently, we examined the distribution pattern of butterfly species and analyzed correlations between butterfly species richness with park variables (age, area and distance to city center), and richness of other bioindicator groups (birds and plants). We collected 587 individual butterflies belonging to 31 species from five families; 74% of the species were considered cosmopolitan. The highest butterfly species richness and abundance was recorded at parks located at the edge of city and species richness was significantly positively correlated with distance from city center (p < 0.05). No significant correlations were detected between the species richness and park age, park area and other bioindicator groups (p > 0.05). Our study provides the first data of butterfly species in urban Beijing, and serves as a baseline for further surveys and conservation efforts.
Characterization of Mechanical Stability and Immunological Compatibility for Functionalized Modification Interfaces
Authors: Hsu Yao-Tsung , Wu Chih-Yu , Guan Zhen-Yu , Sun Ho-Yi , Mei Chieh , Chen Wen-Chien , Cheng Nai-Chen , Yu Jiashing , Chen Hsien-Yeh 
Published: May 2019

AbstractSurface modification layers are performed on the surfaces of biomaterials and have exhibited promise for decoupling original surface properties from bulk materials and enabling customized and advanced functional properties. The physical stability and the biological compatibility of these modified layers are equally important to ensure minimized delamination, debris, leaching of molecules, and other problems that are related to the failure of the modification layers and thus can provide a long-term success for the uses of these modified layers. A proven surface modification tool of the functionalized poly-para-xylylene (PPX) system was used as an example, and in addition to the demonstration of their chemical conjugation capabilities and the functional properties that have been well-documented, in the present report, we additionally devised the characterization protocols to examine stability properties, including thermostability and adhesive strength, as well as the biocompatibility, including cell viability and the immunological responses, for the modified PPX layers. The results suggested a durable coating stability for PPXs and firmly attached biomolecules under these stability and compatibility tests. The durable and stable modification layers accompanied by the native properties of the PPXs showed high cell viability against fibroblast cells and macrophages (MΦs), and the resulting immunological activities created by the MΦs exhibited excellent compatibility with non-activated immunological responses and no indication of inflammation.