bluuebunny/crossref_metadata_2025_split huggingface dataset:
Changes in human footprint drive changes in species extinction risk
Authors: Di Marco Moreno , Venter Oscar , Possingham Hugh P. , Watson James E. M. 
Published: October 2018

AbstractPredicting how species respond to human pressure is essential to anticipate their decline and identify appropriate conservation strategies. Both human pressure and extinction risk change over time, but their inter-relationship is rarely considered in extinction risk modelling. Here we measure the relationship between the change in terrestrial human footprint (HFP)—representing cumulative human pressure on the environment—and the change in extinction risk of the world’s terrestrial mammals. We find the values of HFP across space, and its change over time, are significantly correlated to trends in species extinction risk, with higher predictive importance than environmental or life-history variables. The anthropogenic conversion of areas with low pressure values (HFP < 3 out of 50) is the most significant predictor of change in extinction risk, but there are biogeographical variations. Our framework, calibrated on past extinction risk trends, can be used to predict the impact of increasing human pressure on biodiversity.
Role of noise and parametric variation in the dynamics of gene regulatory circuits
Authors: Kohar Vivek , Lu Mingyang 
Published: October 2018

AbstractStochasticity in gene expression impacts the dynamics and functions of gene regulatory circuits. Intrinsic noises, including those that are caused by low copy number of molecules and transcriptional bursting, are usually studied by stochastic simulations. However, the role of extrinsic factors, such as cell-to-cell variability and heterogeneity in the microenvironment, is still elusive. To evaluate the effects of both the intrinsic and extrinsic noises, we develop a method, named sRACIPE, by integrating stochastic analysis with random circuit perturbation (RACIPE) method. RACIPE uniquely generates and analyzes an ensemble of models with random kinetic parameters. Previously, we have shown that the gene expression from random models form robust and functionally related clusters. In sRACIPE we further develop two stochastic simulation schemes, aiming to reduce the computational cost without sacrificing the convergence of statistics. One scheme uses constant noise to capture the basins of attraction, and the other one uses simulated annealing to detect the stability of states. By testing the methods on several synthetic gene regulatory circuits and an epithelial–mesenchymal transition network in squamous cell carcinoma, we demonstrate that sRACIPE can interpret the experimental observations from single-cell gene expression data. We observe that parametric variation (the spread of parameters around a median value) increases the spread of the gene expression clusters, whereas high noise merges the states. Our approach quantifies the robustness of a gene circuit in the presence of noise and sheds light on a new mechanism of noise-induced hybrid states. We have implemented sRACIPE as an R package.
Coevolution of Environmental Perception and Cooperative Behavior in Evacuation Crowd
Authors: Dong Zehua , Chen Maoyin , Cheng Yuan , Zheng Xiaoping 
Published: October 2018

AbstractFor the evacuation crowd of social agents, environment plays a big effect on the behavior and decision of the agents. When facing the uncertain environment, the behavior and decision of agents depend heavily on the perception of environment. Therefore, the cooperation between agents and their perception of environment may coexist during evacuation. Here we establish a mechanism to analyze the coevolution between the cooperation of agents and the perception of environment. In detail, we use a regular square lattice with periodic boundaries, where two payoff matrices are used to describe two kinds of games between neighbors in the safe and dangerous environments. For individual agent, its perception can be adjusted by interacting with neighboring agents. When the environment is generally considered dangerous, the fraction of cooperative agents keeps at a high level, even if the value of b is very large. When all the agents think that the environment is safe, the fraction of cooperation will decrease as the value of b increases.
Proteomic landscape of seminal plasma associated with dairy bull fertility
Authors: Viana A. G. A. , Martins A. M. A. , Pontes A. H. , Fontes W. , Castro M. S. , Ricart C. A. O. , Sousa M. V. , Kaya A. , Topper E. , Memili E. , Moura A. A. 
Published: October 2018

AbstractMale fertility is the ability of sperm to fertilize the egg and sustain embryo development. Several factors determine the fertilizing capacity of mammalian sperm, including those intrinsic to sperm and components of the seminal plasma. The present study analyzed the seminal fluid proteome ofBos taurusand potential associations between proteins and fertility scores. Mass spectrometry coupled with nano HPLC allowed the identification of 1,159 proteins in the dairy bull seminal plasma. There were 50 and 29 seminal proteins more abundant in high (HF) low fertility (LF) bulls, respectively. Based on multivariate analysis, C-type natriuretic peptide, TIMP-2, BSP5 and sulfhydryl oxidase indicated relationship with HF bulls. Clusterin, tissue factor pathway inhibitor 2, galectin-3-binding protein and 5′-nucleotidase were associated with LF bulls. Abundance of NAD(P)(+)-arginine ADP-ribosyltransferase, prosaposin and transmembrane protein 2 proteins had the highest positive correlations with fertility ranking. Quantities of vitamin D-binding protein, nucleotide exchange factor SIL1 and galectin-3-binding protein showed the highest negative correlations with fertility ranking. A fertility ranking score was calculated and the relationship with these proteins was significant (Spearman’s rho = 0.94). The present findings represent a major and novel contribution to the study of bovine seminal proteins. Indicators of fertility can be used to improve reproductive biotechnologies.
Angstrom Thick ZnO Passivation Layer to Improve the Photoelectrochemical Water Splitting Performance of a TiO2 Nanowire Photoanode: The Role of Deposition Temperature
Authors: Ghobadi Amir , Ghobadi Turkan Gamze Ulusoy , Karadas Ferdi , Ozbay Ekmel 
Published: October 2018

AbstractIn this paper, we demonstrate that angstrom thick single atomic layer deposited (ALD) ZnO passivation can significantly improve the photoelectrochemical (PEC) activity of hydrothermally grown TiO2 NWs. It is found that this ultrathin ZnO coating can passivate the TiO2 surface defect states without hampering the carrier’s transfer dynamics. Moreover, a substantial improvement can be acquired by changing the deposition temperature of the ZnO layer (80 °C, and 250 °C) and named as 80 °C TiO2-ZnO, and 250 °C TiO2-ZnO. It was found that the deposition of this single layer in lower temperatures can lead to higher PEC activity compared to that deposited in higher ones. As a result of our PEC characterizations, it is proved that photoconversion efficiency of bare TiO2 NWs can be improved by a factor of 1.5 upon coating it with a single ZnO layer at 80 °C. Moreover, considering the fact that this layer is a passivating coating rather than a continuous layer, it also keeps the PEC stability of the design while this feature cannot be obtained in a thick shell layer case. This paper proposes a bottom up approach to control the electron transfer dynamics in a heterojunction design and it can be applied to other metal oxide combinations.
UV light assisted antibiotics for eradication of in vitro biofilms
Authors: Argyraki Aikaterini , Markvart Merete , Stavnsbjerg Camilla , Kragh Kasper Nørskov , Ou Yiyu , Bjørndal Lars , Bjarnsholt Thomas , Petersen Paul Michael 
Published: October 2018

AbstractThe overuse of antibiotics is accelerating the bacterial resistance, and therefore there is a need to reduce the amount of antibiotics used for treatment. Here, we demonstrate in vitro that specific wavelengths in a narrow range around 296 nm are able to eradicate bacteria in the biofilm state (grown for 24 hours) more effectively, than antibiotics and the combination of irradiation and antibiotics is even better, introducing a novel concept light assisted antibiotics. The investigated wavelength range was 249 nm to 338 nm with an approximate step of 5 nm. The novel concept that consists of a UV irradiation treatment followed by a tobramycin treatment can significantly reduce the amount of antibiotics needed for eradicating mature bacterial biofilms. The efficiency of the proposed light assisted antibiotics method was compared to combinatory antibiotic treatment and highly concentrated antibiotic monotherapy. The eradication efficacies, on mature biofilms, achieved by light assisted antibiotic and by the antibiotic monotherapy at approximately 10-fold higher concentration, were equivalent. The present achievement could motivate the development of light assisted antibiotic treatments for treating infections.
Genetic analysis of endangered hog deer (Axis porcinus) reveals two distinct lineages from the Indian subcontinent
Authors: Gupta Sandeep Kumar , Kumar Ajit , Angom Sangeeta , Singh Bhim , Ghazi Mirza Ghazanfar Ullah , Tuboi Chongpi , Hussain Syed Ainul 
Published: October 2018

AbstractThe hog deer (Axis porcinus) is threatened by habitat alteration, fragmentation, and poaching, which have led to a drastic decline of its wild population. Two subspecies of A. porcinus have been described from its distribution range. A. p. porcinus is reported to occur from Pakistan along the Himalayan foothills through Nepal, India and Myanmar, and A. p. annamiticus is found in Thailand, Indo-China, Laos, Cambodia, and Vietnam. However, the current distribution range of A. p. annamiticus is still unclear. We used the partial control region (CR) of mitochondrial DNA (mtDNA) and seven microsatellite loci to investigate the intra-species structure, differentiation, and demographic history of hog deer populations from three landscapes, the Terai Arc, Northeast, and Indo-Burma (Keibul Lamjao National Park (KLNP), Manipur, India) landscapes. We also carried out divergence time estimation using the complete mitogenome. The level of variation was ~4%, and the time of divergence of the KLNP population and the other Indian populations was about 0.22 Mya, i.e., during the last glaciation periods of the Late Pleistocene/Early Holocene. The KLNP haplotypes of the control region were shared with the Southeast Asian subspecies, A. p. annamiticus. The results of the investigations of the microsatellite loci supported the mtDNA results unambiguously. Two genetically distinct lineages are found in India: one is found from the Terai Arc to Assam (A. p. porcinus) and the other in Manipur (A. p. annamiticus). The genetic diversity in KLNP was low and exhibited a higher degree of genetic differentiation compared with major Indian populations. The Bayesian skyline plots indicated that after a long phase of historic demographic stability, the populations of both the lineages of hog deer suffered pronounced declines during the period from ~800 years BP to 5000 years BP. In summary, our finding provided evidence that the KLNP population is probably a prime, isolated and sustaining stock of A. p. annamiticus and should be managed as evolutionarily significant units (ESUs).
Discovery of Novaculina myanmarensis sp. nov. (Bivalvia: Pharidae: Pharellinae) closes the freshwater razor clams range disjunction in Southeast Asia
Authors: Bolotov Ivan N. , Vikhrev Ilya V. , Lopes-Lima Manuel , Lunn Zau , Chan Nyein , Win Than , Aksenova Olga V. , Gofarov Mikhail Yu. , Kondakov Alexander V. , Konopleva Ekaterina S. , Tumpeesuwan Sakboworn 
Published: October 2018

AbstractThe razor clam genus Novaculina represents an example of a marine-derived, secondary freshwater group. It was thought to comprise three species: N. gangetica (Ganges and smaller basins in Bangladesh and northwestern Myanmar), N. siamensis (Bang Pakong and Pasak rivers in Thailand and Mekong River in Vietnam), and N. chinensis (lower Yangtze River, China). Here we describe Novaculina myanmarensis sp. nov., an additional species from the Ayeyarwady and Salween basins representing a divergent lineage that appears to be sister to N. gangetica. This new record closes a Novaculina range disjunction between northwestern Myanmar and Thailand. The populations of this novel species share a shallow molecular divergence from each other indicating potential dispersal events between the two distant freshwater basins during the Late Pleistocene. Our ancestral area modeling suggests that the MRCA of Novaculina crown group was a salt-tolerant freshwater species. The recent Novaculina species most likely originated via allopatric speciation. Our findings highlight that generalist estuarine species could have played the role as a source for bivalve expansions into freshwater and that western Indochina is a separate biogeographic subregion, which is clearly distinct from India. A new synonymy is proposed as follows: Pharellinae Stoliczka, 1870 = Novaculininae Ghosh, 1920 syn. nov.
Genetic variation determines VEGF-A plasma levels in cancer patients
Authors: Innocenti Federico , Jiang Chen , Sibley Alexander B. , Etheridge Amy S. , Hatch Ace J. , Denning Stefanie , Niedzwiecki Donna , Shterev Ivo D. , Lin Jiaxing , Furukawa Yoichi , Kubo Michiaki , Kindler Hedy L. , Auman J. Todd , Venook Alan P. , Hurwitz Herbert I. , McLeod Howard L. , Ratain Mark J. , Gordan Raluca , Nixon Andrew B. , Owzar Kouros 
Published: October 2018

AbstractAngiogenesis is essential in tumor biology and is regulated by vascular endothelial growth factor (VEGF) ligands and receptors. Here we aimed to discover genetic variants associated with levels of circulating angiogenic proteins in cancer patients. Plasma was collected at baseline in 216 pancreatic and 114 colorectal cancer patients. Thirty-one angiogenic proteins were measured by ELISA. 484,523 Single Nucleotide Polymorphisms (SNP) were tested for association with plasma levels for each protein in pancreatic cancer patients. Three top-ranked hits were then genotyped in colorectal cancer patients, where associations with the same proteins were measured. The results demonstrated rs2284284 and MCP1 (P-value = 6.7e–08), rs7504372 and VEGF-C (P-value = 9.8e–09), and rs7767396 and VEGF-A (P-value = 5.8e–09) were SNP-protein pairs identified in pancreatic cancer patients. In colorectal cancer patients, only rs7767396 (A > G) and VEGF-A was validated (P-value = 5.18e–05). The AA genotype of rs7767396 exhibited 2.04–2.3 and 2.7–3.4-fold higher VEGF-A levels than those with AG and GG genotypes. The G allele of rs7767396 reduces binding of the NF-AT1 transcription factor. In conclusion, a common genetic variant predicts the plasma levels of VEGF-A in cancer patients through altered binding of NF-AT1.
Timing variability of sensorimotor integration during vocalization in individuals who stutter
Authors: Sares Anastasia G. , Deroche Mickael L. D. , Shiller Douglas M. , Gracco Vincent L. 
Published: October 2018

AbstractPersistent developmental stuttering affects close to 1% of adults and is thought to be a problem of sensorimotor integration. Previous research has demonstrated that individuals who stutter respond differently to changes in their auditory feedback while speaking. Here we explore a number of changes that accompany alterations in the feedback of pitch during vocal production. Participants sustained the vowel /a/ while hearing on-line feedback of their own voice through headphones. In some trials, feedback was briefly shifted up or down by 100 cents to simulate a vocal production error. As previously shown, participants compensated for the auditory pitch change by altering their vocal production in the opposite direction of the shift. The average compensatory response was smaller for adults who stuttered than for adult controls. Detailed analyses revealed that adults who stuttered had fewer trials with a robust corrective response, and that within the trials showing compensation, the timing of their responses was more variable. These results support the idea that dysfunctional sensorimotor integration in stuttering is characterized by timing variability, reflecting reduced coupling of the auditory and speech motor systems.
How wind drives the correlation between leaf shape and mechanical properties
Authors: Louf Jean-François , Nelson Logan , Kang Hosung , Song Pierre Ntoh , Zehnbauer Tim , Jung Sunghwan 
Published: October 2018

AbstractFrom a geometrical point of view, a non-sessile leaf is composed of two parts: a large flat plate called the lamina, and a long beam called the petiole which connects the lamina to the branch/stem. While wind is exerting force (e.g. drag) on the lamina, the petiole undergoes twisting and bending motions. To survive in harsh abiotic conditions, leaves may have evolved to form in different shapes, resulting from a coupling between the lamina geometry and the petiole mechanical properties. In this study, we measure the shape of laminae from 120 simple leaf species (no leaflets). Leaves of the same species are found to be geometrically similar regardless of their size. From tensile/torsional tests, we characterize the bending rigidity (EI) and the twisting rigidity (GJ) of 15 petioles of 4 species in the Spring/Summer: Red Oak (Quercus Rubra), American Sycamore (Platanus occidentalis), Yellow Poplar (Liriodendron tulipifera), and Sugar Maple (Acer saccharum). A twist-to-bend ratio EI/GJ is found to be around 4.3, within the range in previous studies conducted on similar species (EI/GJ = 2.7~8.0 reported in S. Vogel, 1992). In addition, we develop a simple energetic model to find a relation between geometrical shapes and mechanical properties (EI/GJ = 2LL/WC where LL is the laminar length and WC is the laminar width), verified with experimental data. Lastly, we discuss leaf’s ability to reduce stress at the stem-petiole junction by choosing certain geometry, and also present exploratory results on the effect that seasons have on the Young’s and twisting moduli.
Potential of Oryza officinalis to augment the cold tolerance genetic mechanisms of Oryza sativa by network complementation
Authors: Kitazumi Ai , Pabuayon Isaiah C. M. , Ohyanagi Hajime , Fujita Masahiro , Osti Bipush , Shenton Matthew R. , Kakei Yusuke , Nakamura Yasukazu , Brar Darshan S. , Kurata Nori , de los Reyes Benildo G. 
Published: October 2018

AbstractOryza officinalis is an accessible alien donor for genetic improvement of rice. Comparison across a representative panel of Oryza species showed that the wild O. officinalis and cultivated O. sativa ssp. japonica have similar cold tolerance potentials. The possibility that either distinct or similar genetic mechanisms are involved in the low temperature responses of each species was addressed by comparing their transcriptional networks. General similarities were supported by shared transcriptomic signatures indicative of equivalent metabolic, hormonal, and defense status. However, O. officinalis has maintained an elaborate cold-responsive brassinosteroid-regulated BES1-network that appeared to have been fragmented in O. sativa. BES1-network is potentially important for integrating growth-related responses with physiological adjustments and defenses through the protection of photosynthetic machinery and maintenance of stomatal aperture, oxidative defenses, and osmotic adjustment. Equivalent physiological processes are functional in O. sativa but their genetic mechanisms are under the direct control of ABA-dependent, DREB-dependent and/or oxidative-mediated networks uncoupled to BES1. While O. officinalis and O. sativa represent long periods of speciation and domestication, their comparable cold tolerance potentials involve equivalent physiological processes but distinct genetic networks. BES1-network represents a novel attribute of O. officinalis with potential applications in diversifying or complementing other mechanisms in the cultivated germplasm.
Multiplex real-time PCR assay to detect illegal trade of CITES-listed shark species
Authors: Cardeñosa Diego , Quinlan Jessica , Shea Kwok Ho , Chapman Demian D. 
Published: October 2018

AbstractThe Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) is a multilateral environmental agreement to ensure that the international trade of threatened species is either prohibited (Appendix I listed species) or being conducted legally, sustainably, and transparently (Appendix II listed species). Twelve threatened shark species exploited for their fins, meat, and other products have been listed under CITES Appendix II. Sharks are often traded in high volumes, some of their products are visually indistinguishable, and most importing/exporting nations have limited capacity to detect illicit trade and enforce the regulations. High volume shipments often must be screened after only a short period of detainment (e.g., a maximum of 24 hours), which together with costs and capacity issues have limited the use of DNA approaches to identify illicit trade. Here, we present a reliable, field-based, fast (<4 hours), and cost effective ($0.94 USD per sample) multiplex real-time PCR protocol capable of detecting nine of the twelve sharks listed under CITES in a single reaction. This approach facilitates detection of illicit trade, with positive results providing probable cause to detain shipments for more robust forensic analysis. We also provide evidence of its application in real law enforcement scenarios in Hong Kong. Adoption of this approach can help parties meet their CITES requirements, avoiding potential international trade sanctions in the future.
Breed Differences in Pig Liver Esterase (PLE) between Tongcheng (Chinese Local Breed) and Large White Pigs
Authors: Xiao Qiling , Zhou Qiongqiong , Yang Lu , Tian Zhongyuan , Wang Xiliang , Xiao Yuncai , Shi Deshi 
Published: October 2018

AbstractHuman carboxylesterases has been proven to be age and race-related and a sound basis of clinical medication. PLE involve in signal transduction and highly catalyze hydrolysis. Therefore, the expression level of PLE most probably exist age and breed difference and lead to significant differences of pharmacology and physiology. Four age groups of Tongcheng (TC) and Large White (LW) pigs were selected to explore PLE breed and age differences, and it was found that PLE mRNA was most abundant in liver in both breeds. In liver, PLE levels and hydrolytic activities increased with age, and PLE levels (except for 3 month) and the hydrolytic activities were higher in LW than in TC across all age groups. Abundance of PLE isoenzymes was obvious different between breeds and among age groups. The most abundant PLE isoenzyme in LW and TC pigs was PLE-A1 (all age groups) and PLE-B9 (three early age groups) or PLE-G3 (adult groups), respectively. 103 new PLE isoenzymes were found, and 55 high-frequency PLE isoenzymes were accordingly classified into seven categories (A-G). The results of this research provide a necessary basis not only for clinical medication of pigs but also for pig breeding purposes.