bluuebunny/crossref_metadata_2025_split huggingface dataset:
Payments for environmental service’s role in landscape connectivity
Authors: Wood Margot A , Gilbert Jessica A , Lacher Thomas E 
Published: February 2020

SummaryCreating landscapes with connectivity is vital for protecting biodiversity and meeting the environmental targets embedded in the United Nations Sustainable Development Goals, with connectivity specifically mentioned in Target 11 of the Convention on Biological Diversity Aichi Targets. Costa Rica created the National Biological Corridor Program (NBCP) in 2006 to enhance connectivity among protected areas. Targeted investments of payments for environmental services (PES) are the main tools used within the designated biological corridors. We conducted spatially explicit analyses to determine whether Costa Rica’s NBCP, using PES, enhanced landscape connectivity within the Paso de las Nubes Biological Corridor. We conducted landscape modelling in order to determine the connectivity held within PES’s properties by developing connectivity resistance surfaces and electrical current models. The results indicate that PES properties established after the NBCP contributed more to areas with intermediate values of connectivity and less to areas with high connectivity values as compared to properties before the NBCP. Although overall connectivity within the corridor has decreased since NBCP establishment, our results confirm the importance of PES properties for landscape connectivity, but emphasize the need for spatially targeted PES in order to improve viable paths of landscape connectivity among protected areas. Future targeted PES investments could contribute greatly to meeting connectivity goals.
ON A PROBLEM OF TALAGRAND CONCERNING SEPARATELY CONTINUOUS FUNCTIONS
Authors: Mykhaylyuk Volodymyr , Pol Roman 
Published: February 2020

AbstractWe construct a separately continuous function $e:E\times K\rightarrow \{0,1\}$ on the product of a Baire space $E$ and a compact space $K$ such that no restriction of $e$ to any non-meagre Borel set in $E\times K$ is continuous. The function $e$ has no points of joint continuity, and, hence, it provides a negative solution of Talagrand’s problem in Talagrand [Espaces de Baire et espaces de Namioka, Math. Ann.270 (1985), 159–164].
Cocoa and unripe banana flour beverages improve anthropometric and	biochemical markers in overweight women: A randomised double-blind	study
Authors: de Oliveira Lomeu Fernanda Laurides Ribeiro , Vieira Camilla Ribeiro , Lucia Flávia Della , Veiga Sandra Maria Oliveira Moraes , Martino Hércia Stampini Duarte , Silva Roberta Ribeiro 
Published: February 2020

Abstract. Objectives: The objective of this study was to evaluate the effect of a functional cocoa and unripe banana flour (UBF) beverage intake on the anthropometric and biochemical markers of overweight women. Methods: This prospective, double-blinded, randomized clinical trial involved 60 female volunteers aged between 20 and 50 years. One group received a cocoa beverage (n = 30) and one group received a cocoa and UBF beverage (n = 30), for 6 weeks. The cocoa beverage showed 3.07 total g dietary fiber/serving and 29.55 mg gallic acid equivalentes/portion (GAE/portion). Cocoa and UBF beverage contained 8.48% resistant starch by weight, 4.37 g dietary fiber/full portion and 69.24 mg GAE/portion. Weight, waist circumference, hip circumference, glucose, triglycerides, total cholesterol and fractions were evaluated. Results: The UBF and cocoa beverage reduced waist circumference (−2.03 cm, P < 0.001) and the cocoa beverage reduced total cholesterol (−19.3 mg/dL, P < 0.001) and the LDL/HDL ratio (−0.32, P < 0.001); in addition, both beverages promoted the reduction of body fat percentage (−1.98%, P = 0.001 and −1.15%, P < 0.001 Cocoa/UPF group and Cocoa group respectively). Conclusion: The additional dietary fiber did not further improve health status.
Assessing the Kinetics and Pore‐Scale Characteristics of Biological Calcium Carbonate Precipitation in Porous Media using a Microfluidic Chip Experiment
Authors: Kim Daehyun , Mahabadi Nariman , Jang Jaewon , van Paassen Leon A. 
Published: February 2020

AbstractBiomineralization through microbially or enzymatically induced calcium carbonate precipitation (MICP/EICP) by urea hydrolysis has been widely investigated for various engineering applications. Empirical correlations relating the amount of mineral precipitation to engineering properties like strength, stiffness, or permeability show large variations, which can be partly attributed to the pore‐scale characteristics of the precipitated minerals. This study aimed to gain insight into the precipitation kinetics and pore‐scale characteristics of calcium carbonate minerals through time lapse imaging of a transparent microfluidic chip, which was flushed 10 times with a reactive solution to stimulate EICP. An image processing algorithm was developed to detect the individual precipitated minerals and separate them from the grains and trapped air. Statistical analysis was performed to quantify the number and size distribution of precipitated minerals during each treatment cycle and the cumulative volume, surface area, bulk precipitation rate, nucleation rate, and supersaturation were calculated and compared with a simple numerical model and more complex theory on precipitation kinetics. The analysis showed that results were significantly affected by the assumed particle shape. The supersaturation, which controls the crystal nucleation and growth rates, was shown to be a function of the hydrolysis rate, the kinetic order and growth rate constant, and available surface area for mineral growth. Possible explanations for observed discrepancies between observations and theory, including diffusion limitations, the presence of inhibiting compounds, local pore clogging or observation bias, and limitations of the methodology, are discussed.
Synergistic lethality between PARP-trapping and alantolactone-induced oxidative DNA damage in homologous recombination-proficient cancer cells
Authors: Wang Hongge , Zhang Shan , Song Liyan , Qu Meng , Zou Zhihua 
Published: February 2020

AbstractPARP1 and PARP2 play critical roles in regulating DNA repair and PARP inhibitors have been approved for the treatment of BRCA1/2-mutated ovarian and breast cancers. It has long been known that PARP inhibition sensitizes cancer cells to DNA-damaging cytotoxic agents independent of BRCA status, however, clinical use of PARP inhibitors in combination with DNA-damaging chemotherapy is limited by the more-than-additive cytotoxicity. The natural compound alantolactone (ATL) inhibits the thioredoxin reductase to induce ROS accumulation and oxidative DNA damage selectively in cancer cells. Here, we showed that nontoxic doses of ATL markedly synergized with the PARP inhibitor olaparib to result in synthetic lethality irrespective of homologous recombination status. Synergistic cytotoxicity was seen in cancer but not noncancerous cells and was reduced by the ROS inhibitor NAC or knockdown of OGG1, demonstrating that the cytotoxicity resulted from the repair of ATL-induced oxidative DNA damage. PARP1 knockdown suppressed the synergistic lethality and olaparib was much more toxic than veliparib when combined with ATL, suggesting PARP-trapping as the primary inducer of cytotoxicity. Consistently, combined use of ATL and olaparib caused intense signs of replication stress and formation of double strand DNA breaks, leading to S and G2 arrest followed by apoptosis. In vivo, the combination effectively induced regression of tumor xenografts, while either agent alone had no effect. Hence, PARP trapping combined with specific pro-oxidative agents may provide safe and effective ways to broaden the therapeutic potential of PARP inhibitors.
Identification of a parasitic symbiosis between respiratory metabolisms in the biogeochemical chlorine cycle
Authors: Barnum Tyler P , Cheng Yiwei , Hill Kaisle A , Lucas Lauren N , Carlson Hans K , Coates John D 
Published: February 2020

Abstract
A key step in the chlorine cycle is the reduction of perchlorate (ClO4−) and chlorate (ClO3−) to chloride by microbial respiratory pathways. Perchlorate-reducing bacteria and chlorate-reducing bacteria differ in that the latter cannot use perchlorate, the most oxidized chlorine compound. However, a recent study identified a bacterium with the chlorate reduction pathway dominating a community provided only perchlorate. Here we confirm a metabolic interaction between perchlorate- and chlorate-reducing bacteria and define its mechanism. Perchlorate-reducing bacteria supported the growth of chlorate-reducing bacteria to up to 90% of total cells in communities and co-cultures. Chlorate-reducing bacteria required the gene for chlorate reductase to grow in co-culture with perchlorate-reducing bacteria, demonstrating that chlorate is responsible for the interaction, not the subsequent intermediates chlorite and oxygen. Modeling of the interaction suggested that cells specialized for chlorate reduction have a competitive advantage for consuming chlorate produced from perchlorate, especially at high concentrations of perchlorate, because perchlorate and chlorate compete for a single enzyme in perchlorate-reducing cells. We conclude that perchlorate-reducing bacteria inadvertently support large populations of chlorate-reducing bacteria in a parasitic relationship through the release of the intermediate chlorate. An implication of these findings is that undetected chlorate-reducing bacteria have likely negatively impacted efforts to bioremediate perchlorate pollution for decades.
Molecular profiling of immunoglobulin heavy-chain gene rearrangements unveils new potential prognostic markers for multiple myeloma patients
Authors: Medina Alejandro , Jiménez Cristina , Sarasquete M. Eugenia , González Marcos , Chillón M. Carmen , Balanzategui Ana , Prieto-Conde Isabel , García-Álvarez María , Puig Noemí , González-Calle Verónica , Alcoceba Miguel , Cuenca Isabel , Barrio Santiago , Escalante Fernando , Gutiérrez Norma C. , Gironella Mercedes , Hernández Miguel T. , Sureda Anna , Oriol Albert , Bladé Joan , Lahuerta Juan-José , San Miguel Jesús F. , Mateos María-Victoria , Martínez-López Joaquín , Calasanz María-José , García-Sanz Ramón 
Published: February 2020

AbstractMultiple myeloma is a heterogeneous disease whose pathogenesis has not been completely elucidated. Although B-cell receptors play a crucial role in myeloma pathogenesis, the impact of clonal immunoglobulin heavy-chain features in the outcome has not been extensively explored. Here we present the characterization of complete heavy-chain gene rearrangements in 413 myeloma patients treated in Spanish trials, including 113 patients characterized by next-generation sequencing. Compared to the normal B-cell repertoire, gene selection was biased in myeloma, with significant overrepresentation ofIGHV3,IGHD2andIGHD3, as well asIGHJ4gene groups. Hypermutation was high in our patients (median: 8.8%). Interestingly, regarding patients who are not candidates for transplantation, a high hypermutation rate (≥7%) and the use ofIGHD2andIGHD3groups were associated with improved prognostic features and longer survival rates in the univariate analyses. Multivariate analysis revealed prolonged progression-free survival rates for patients usingIGHD2/IGHD3groups (HR: 0.552, 95% CI: 0.361−0.845,p = 0.006), as well as prolonged overall survival rates for patients with hypermutation ≥7% (HR: 0.291, 95% CI: 0.137−0.618,p = 0.001). Our results provide new insights into the molecular characterization of multiple myeloma, highlighting the need to evaluate some of these clonal rearrangement characteristics as new potential prognostic markers.
miR-210-5p promotes epithelial–mesenchymal transition by inhibiting PIK3R5 thereby activating oncogenic autophagy in osteosarcoma cells
Authors: Liu Wei , Jiang Dongdong , Gong Fangyi , Huang Yumin , Luo Yongjun , Rong Yuluo , Wang Jiaxing , Ge Xuhui , Ji Chengyue , Fan Jin , Cai Weihua 
Published: February 2020

AbstractOsteosarcoma (OS) is a malignant bone tumor which occurs mainly in adolescents with frequent pulmonary metastasis and a high mortality rate. Accumulating evidence has indicated that microRNAs (miRNAs) play a vital role in various tumors by modulating target genes as well as signal pathways, and aberrant expression of miRNAs may contribute to OS progression. This study aimed to determine the association between miR-210-5p expression and OS progression and to investigate its potential underlying mechanism. Using reverse transcription-polymerase chain reaction (RT-PCR), miR-210-5p was found to be upregulated in clinical OS specimens and cell lines. Further functional analysis demonstrated that miR-210-5p promoted epithelial–mesenchymal transition (EMT) and induced oncogenic autophagy. Luciferase reporter assay, RNA-ChIP, and western blot analysis confirmed that PIK3R5, an essential regulator in the AKT/mTOR signaling pathway, is a target downstream gene of miR-210-5p. Overexpression or knockdown of PIK3R5 reversed the functional role of overexpression or knockdown of miR-210-5p, respectively. Silencing autophagy-related gene 5 (ATG5) abolished the functional effects of miR-210-5p upregulation or PIK3R5 knockdown in OS cells. In vivo, miR-210-5p overexpression promoted OS tumor growth and pulmonary metastasis. Taken together, our results demonstrated that miR-210-5p promoted EMT and oncogenic autophagy by suppressing the expression of PIK3R5 and regulating the AKT/mTOR signaling pathway. Therefore, inhibition of miR-210-5p may represent a promising treatment for OS.
A cathelicidin-related antimicrobial peptide suppresses cardiac hypertrophy induced by pressure overload by regulating IGFR1/PI3K/AKT and TLR9/AMPKα
Authors: Wang Xiaofang , Chen Linlin , Zhao Xiaoyan , Xiao Lili , Yi Shanting , Kong Yawei , Jiang Yan , Zhang Jinying 
Published: February 2020

AbstractCathelicidin-related antimicrobial peptide (CRAMP), an antimicrobial peptide, was reported to protect against myocardial ischemia/reperfusion injury. However, the effect of CRAMP on pressure overload-induced cardiac hypertrophy was unknown. This study explored the role of CRAMP on cardiac hypertrophy. A cardiac hypertrophy mouse model was induced by aortic banding surgery. Seven days after surgery, mice were given mCRAMP by intraperitoneal injection (8 mg/kg/d) for 7 weeks. Cardiac hypertrophy was evaluated by the hypertrophic response and fibrosis level as well as cardiac function. Mice were also injected with AAV9-shCRAMP to knockdown CRAMP in the mouse heart. CRAMP levels first increased and then reduced in the remodeling heart, as well as in angiotensin II-stimulated endothelial cells but not in cardiomyocytes and fibroblasts. mCRAMP protected against the pressure overload-induced cardiac remodeling process, while CRAMP knockdown accelerated this process. mCRAMP reduced the inflammatory response and oxidative stress in the hypertrophic heart, while mCRAMP deficiency deteriorated the pressure overload-induced inflammatory response and oxidative stress. mCRAMP inhibited the angiotensin II-stimulated hypertrophic response and oxidative stress in neonatal rat cardiomyocytes, but mCRAMP did not help the angiotensin II-induced inflammatory response and oxidative stress in endothelial cells. Mechanistically, we found that mCRAMP suppressed the cardiac hypertrophic response by activating the IGFR1/PI3K/AKT pathway via directly binding to IGFR1. AKT knockout mice completely reversed the anti-hypertrophic effect of mCRAMP but not its anti-oxidative effect. We also found that mCRAMP ameliorated cardiac oxidative stress by activating the TLR9/AMPKa pathway. This was confirmed by a TLR9 knockout mouse experiment, in which a TLR9 knockout partly reversed the anti-hypertrophic effect of mCRAMP and completely counteracted the anti-oxidative effect of mCRAMP. In summary, mCRAMP protected against pressure overload-induced cardiac hypertrophy by activating both the IGFR1/PI3K/AKT and TLR9/AMPKa pathways in cardiomyocytes.
Lipid droplets: platforms with multiple functions in cancer hallmarks
Authors: Cruz André L. S. , Barreto Ester de A. , Fazolini Narayana P. B. , Viola João P. B. , Bozza Patricia T. 
Published: February 2020

AbstractLipid droplets (also known as lipid bodies) are lipid-rich, cytoplasmic organelles that play important roles in cell signaling, lipid metabolism, membrane trafficking, and the production of inflammatory mediators. Lipid droplet biogenesis is a regulated process, and accumulation of these organelles within leukocytes, epithelial cells, hepatocytes, and other nonadipocyte cells is a frequently observed phenotype in several physiologic or pathogenic situations and is thoroughly described during inflammatory conditions. Moreover, in recent years, several studies have described an increase in intracellular lipid accumulation in different neoplastic processes, although it is not clear whether lipid droplet accumulation is directly involved in the establishment of these different types of malignancies. This review discusses current evidence related to the biogenesis, composition and functions of lipid droplets related to the hallmarks of cancer: inflammation, cell metabolism, increased proliferation, escape from cell death, and hypoxia. Moreover, the potential of lipid droplets as markers of disease and targets for novel anti-inflammatory and antineoplastic therapies will be discussed.
Recommendations for designing genetic test reports to be understood by patients and non-specialists
Authors: Farmer George D. , Gray Harry , Chandratillake Gemma , Raymond F Lucy , Freeman Alexandra L. J. 
Published: February 2020

AbstractPatients and non-specialist healthcare professionals are increasingly expected to understand and interpret the results of genetic or genomic testing. These results are currently reported using a variety of templates, containing different amounts, levels, and layouts of information. We set out to establish a set of recommendations for communicating genetic test results to non-expert readers. We employed a qualitative-descriptive study design with user-centred design principles, including a mixture of in-person semi-structured interviews and online questionnaires with patients, healthcare professionals and the general public. The resulting recommendations and example template include providing at-a-glance comprehension of what the test results mean for the patient; suggested next steps; and details of further information and support. Separation and inclusion of technical methodological details enhances non-specialists’ understanding, while retaining important information for specialists and the patients’ records. The recommendations address the high-level needs of patients and their non-specialist clinicians when receiving genetic test results. These recommendations provide a solid foundation for the major content and structure of reports, and we recommend further engagement with patients and clinicians to tailor reports to specific types of test and results.
Modelling floppy iris syndrome and the impact of pupil size and ring devices on iris displacement
Authors: Lockington David , Wang Zhaokun , Qi Nan , Malyugin Boris , Cai Li , Wang Chenglei , Tang Hui , Ramaesh Kanna , Luo Xiaoyu 
Published: February 2020

Abstract
Introduction
The aim of this paper was to further develop a previously described finite element model which equates clinical iris billowing movements with mechanical buckling behaviour, simulating floppy iris syndrome. We wished to evaluate the impact of pupil dilation and mechanical devices on normal iris and floppy iris models.

Methods
Theoretical mathematical modelling and computer simulations were used to assess billowing/buckling patterns of the iris under loading pressures for the undilated and dilated normal iris, the undilated and dilated floppy iris, and additionally with a mechanical ring device.

Results
For the normal iris, billowing/buckling occurred at a critical pressure of 19.92 mmHg for 5 mm pupil size, which increased to 28.00 mmHg (40.56%) with a 7 mm pupil. The Malyugin ring device significantly increased critical initiating buckling pressures in the normal iris scenario, to 34.58 mmHg (73.59%) for 7 mm ring with boundary conditions I (BC I) and 34.51 mmHg (73.24%) with BC II. For the most floppy iris modelling (40% degradation), initiating buckling value was 18.04 mmHg (−9.44%), which increased to 28.39 mmHg (42.52%) with the 7 mm ring. These results were much greater than for normal undilated iris without restrictive mechanical expansion (19.92 mmHg).

Conclusion
This simulation demonstrates that pupil expansion devices inhibit iris billowing even in the setting of floppy iris syndrome. Our work also provides a model to further investigate the impact of pupil size or pharmacological interventions on anterior segment conditions affected by iris position.
Characterizing chromatin landscape from aggregate and single-cell genomic assays using flexible duration modeling
Authors: Gabitto Mariano I. , Rasmussen Anders , Wapinski Orly , Allaway Kathryn , Carriero Nicholas , Fishell Gordon J. , Bonneau Richard 
Published: February 2020

AbstractATAC-seq has become a leading technology for probing the chromatin landscape of single and aggregated cells. Distilling functional regions from ATAC-seq presents diverse analysis challenges. Methods commonly used to analyze chromatin accessibility datasets are adapted from algorithms designed to process different experimental technologies, disregarding the statistical and biological differences intrinsic to the ATAC-seq technology. Here, we present a Bayesian statistical approach that uses latent space models to better model accessible regions, termed ChromA. ChromA annotates chromatin landscape by integrating information from replicates, producing a consensus de-noised annotation of chromatin accessibility. ChromA can analyze single cell ATAC-seq data, correcting many biases generated by the sparse sampling inherent in single cell technologies. We validate ChromA on multiple technologies and biological systems, including mouse and human immune cells, establishing ChromA as a top performing general platform for mapping the chromatin landscape in different cellular populations from diverse experimental designs.
Bacillus cereus non-haemolytic enterotoxin activates the NLRP3 inflammasome
Authors: Fox Daniel , Mathur Anukriti , Xue Yansong , Liu Yunqi , Tan Wei Hong , Feng Shouya , Pandey Abhimanu , Ngo Chinh , Hayward Jenni A. , Atmosukarto Ines I. , Price Jason D. , Johnson Matthew D. , Jessberger Nadja , Robertson Avril A. B. , Burgio Gaetan , Tscharke David C. , Fox Edward M. , Leyton Denisse L. , Kaakoush Nadeem O. , Märtlbauer Erwin , Leppla Stephen H. , Man Si Ming 
Published: February 2020

AbstractInflammasomes are important for host defence against pathogens and homeostasis with commensal microbes. Here, we show non-haemolytic enterotoxin (NHE) from the neglected human foodborne pathogenBacillus cereusis an activator of the NLRP3 inflammasome and pyroptosis. NHE is a non-redundant toxin to haemolysin BL (HBL) despite having a similar mechanism of action. Via a putative transmembrane region, subunit C of NHE initiates binding to the plasma membrane, leading to the recruitment of subunit B and subunit A, thus forming a tripartite lytic pore that is permissive to efflux of potassium. NHE mediates killing of cells from multiple lineages and hosts, highlighting a versatile functional repertoire in different host species. These data indicate that NHE and HBL operate synergistically to induce inflammation and show that multiple virulence factors from the same pathogen with conserved function and mechanism of action can be exploited for sensing by a single inflammasome.