bluuebunny/crossref_metadata_2025_split huggingface dataset:
SNP analysis reveals an evolutionary acceleration of the human-specific microRNAs
Authors: Zhang Qipeng , Lu Ming , Cui Qinghua 
Published: July 2019

AbstractMicroRNAs are one class of important gene regulators at the post-transcriptional level by binding to the 3’UTRs of target mRNAs. It has been reported that human microRNAs are evolutionary conserved and show lower single nucleotide polymorphisms (SNPs) than their flanking regions. However, in this study, we report that the human-specific microRNAs show a higher SNP density than both the conserved microRNAs and other control regions, suggesting rapid evolution and positive selection has occurred in these regions. Furthermore, we observe that the human-specific microRNAs show greater SNPs minor allele frequency and the SNPs in the human-specific microRNAs show fewer effects on the stability of the microRNA secondary structure, indicating that the SNPs in the human-specific microRNAs tend to be less deleterious. Finally, two microRNAs hsa-mir-423 (SNP: rs6505162), hsa-mir-608 (SNP: rs4919510) and 288 target genes that have apparently been under recent positive selection are identified. These findings will improve our understanding of the functions, evolution, and population disease susceptibility of human microRNAs.
Emerging challenges: Massive green algae blooms in the Yellow Sea
Authors: Sun Song , Wang Fan , Li Chaolun , Qin Song , Zhou Mingjiang , Ding Lanping , Pang Shaojun , Duan Delin , Wang Guangce , Yin Baoshu , Yu Rencheng , Jiang Peng , Liu Zhiliang , Zhang Guang-Tao , Fei Xiugen , Zhou Meng 
Published: July 2019

AbstractThe massive green algae (Enteromorpha prolifera) bloom in a coastal area of Qingdao between May and July 2008 prior to the sailing competition of the 29th Olympic Games has raised great concerns in local and regional communities and governmental agencies on environmental deterioration, causes and mitigation of such massive algal blooms. Results from field and laboratory studies during the bloom and post-bloom periods revealed that the bloom was originated from an offshore area 150 km south of Qingdao, and caused by complex coupled land-ocean and natural-human processes associated with increases in nutrient and organic matter loadings to the coastal ocean due to rapid expansions of agriculture, aquaculture and urbanization, behavior of algae, seasonal wind and coastal currents, and transport of nutrients and biota. This environmental disaster has brought us emerging challenges on how to integrate monitoring, analysis and prediction of complex coupled natural and human processes, environmental regulations, and management in land-ocean uses for the sustainable socioeconomic development.
Dielectric Constant of Liquids (Fluids) Shown to be Simple Fundamental Relation of Density over Extreme Ranges from - 50^o^ to + 600^o^C, Believed Universal
Authors: Marshall William L. 
Published: July 2019

AbstractExaminations of past complex theoretical equations describing isothermal dielectric constants ([epsilon]) of liquids show that none describe experiments throughout and that only a two-constant equation of density is required. The dielectric susceptibility ([epsilon] – 1) as a simple exponential function of density is shown here to describe [epsilon] for both polar and non-polar organic liquids over all available experimental ranges from 0.50 to 1.2 g cm^-3^ and temperatures to 400^o^C. For water above 0.25 g cm^-3^, the equation describes the excellent dielectric-constant formulation of Fernández, et al., (1997) throughout its experimental range [-35 to +600^o^C; to 1000 MPa (10000 Atm)] and even when diluted by "inert" solvents (Marshall, 2008). At lower densities at all temperatures, water susceptibilities converge to an even more simple unit proportionality to density below 0.003 g cm^-3^, not yet verified for organics without experiment. While the past Born, Tait, Clausius-Mossotti, and Owen-Brinkley theories describe [epsilon] equally well over a limited 10% change in density, all are shown to fail over greater ranges. The simple density relation presented here should be useful in clarifying and reducing complexity of theory applied to liquid structure.
Frizzled Proteins are bona fide G Protein-Coupled Receptors
Authors: Katanaev Vladimir , Buestorf Silke 
Published: July 2019

AbstractReceptors of the Frizzled family initiate Wnt ligand-dependent signaling controllingmultiple steps in organism development and highly conserved in evolution.Misactivation of the Wnt/Frizzled signaling is cancerogenic. Frizzled receptorslaunch several signaling cascades: the canonical pathway regulating beta-catenin-dependent transcription; the planar cell polarity pathway polarizing thecytoskeleton within the epithelial plane; and the calcium pathway. Frizzledreceptors possess seven transmembrane domains and their signaling depends ontrimeric G proteins in various organisms. However, Frizzleds constitute adistinct group within the G protein-coupled receptors (GPCR) superfamily, andFrizzled signaling can be G protein-independent in some experimental setups, which led to concerns about the GPCR nature of Frizzled. Here we demonstratethat human Frizzled receptors can directly bind the trimeric Go protein in apertussis toxin-sensitive manner. Furthermore, addition of Wnt ligands elicitsFrizzled-dependent guanine nucleotide exchange on Go. An excess of secretedFrizzled-related protein (a Wnt antagonist) prevents Go activation, as doespretreatment of Go with pertussis toxin. These experiments provide a biochemicalproof of the GPCR activities of Frizzled receptors and establish an in vitro assay tomonitor Frizzled activation by Wnt ligands, applicable for the high-throughputagonist/antagonist screening.
Events of reclaiming marshes for rice fields between 7000BP and 4500 BP in east China
Authors: Zheng Yunfei , Sun Guoping , Qin Ling , Li Chunhai , Wu Xiaohong , Chen Xugao 
Published: July 2019

AbstractDiscovery of the oldest rice fields at the Tianluoshan site in east China has provided data of recovering reclaimation, cultivation, and the ecological system of rice fields between 7000BP and 4500 BP. People opened up marshes of dense reeds with fire and wooden or bone spades, in order to create rice fields. In the rice fields, there was not only rice, but a lot of weeds as well. The excavations proved that little or even no weeding or irrigation was adopted. However, tilling soil by wooden and bone tools was evidenced. The yields are estimated to have been about 8.3 kg for the early period and 9.5 kg per acre for the later period. The cultivation system was low-level. Although the Tianluoshan people cultivated rice, they still obtained a great deal of food by gathering and hunting.
Genome-wide association study identifies FUT8 and ESR2 as co-regulators of a bi-antennary N-linked glycan A2 (GlcNAc~2~Man~3~GlcNAc~2~) in human plasma proteins
Authors: Lauc Gordan , Huffman Jennifer , Hayward Caroline , Knezevic Ana , Polasek Ozren , Gornik Olga , Vitart Veronique , Kolcic Ivana , Biloglav Zrinka , Zgaga Lina , Hastie Nicholas , Wright Alan , Campbell Harry , Rudd Pauline , Rudan Igor 
Published: July 2019

AbstractHPLC analysis of N-glycans quantified levels of the biantennary glycan (A2) in plasma proteins of 924 individuals. Subsequent genome-wide association study (GWAS) using 317,503 single nucleotide polymorphysms (SNP) identified two genetic loci influencing variation in A2: FUT 8 and ESR2. We demonstrate that human glycans are amenable to GWAS and their genetic regulation shows sex-specific effects with FUT 8 variants explaining 17.3% of the variance in pre-menopausal women, while ESR2 variants explained 6.0% of the variance in post-menopausal women.
Evolutionary descent of prion genes from a ZIP metal ion transport ancestor
Authors: Schmitt-Ulms Gerold , Ehsani Sepehr , Watts Joel , Westaway David , Wille Holger 
Published: July 2019

AbstractIn the more than 20 years since its discovery, both the phylogenetic origin and cellular function of the prion protein (PrP) have remained enigmatic. Insights into the function of PrP may be obtained through a characterization of its molecular neighborhood. Quantitative interactome data revealed the spatial proximity of a subset of metal ion transporters of the ZIP family to mammalian prion proteins. A subsequent bioinformatic analysis revealed the presence of a prion-like protein sequence within the N-terminal, extracellular domain of a phylogenetic branch of ZIPs. Additional structural threading and ortholog sequence alignment analyses consolidated the conclusion that the prion protein gene family is phylogenetically derived from a ZIP-like ancestor molecule. Our data explain structural and functional features found within mammalian prion proteins as elements of an ancient involvement in the transmembrane transport of divalent cations. The connection to ZIP proteins is expected to open new avenues to elucidate the biology of the prion protein in health and disease.
A stable backbone for the fungi
Authors: Ebersberger Ingo , Gube Matthias , Strauss Sascha , Kupczok Anne , Eckart Martin , Voigt Kerstin , Kothe Erika , von Haeseler Arndt 
Published: July 2019

AbstractFungi are abundant in the biosphere. They have fascinated mankind as far as written history goes and have considerably influenced our culture. In biotechnology, cell biology, genetics, and life sciences in general fungi constitute relevant model organisms. Once the phylogenetic relationships of fungi are stably resolved individual results from fungal research can be combined into a holistic picture of biology. However, and despite recent progress, the backbone of the fungal phylogeny is not yet fully resolved. Especially the early evolutionary history of fungi and the order or below-order relationships within the ascomycetes remain uncertain. Here we present the first phylogenomic study for a eukaryotic kingdom that merges all publicly available fungal genomes and expressed sequence tags (EST) to build a data set comprising 128 genes and 146 taxa. The resulting tree provides a stable phylogenetic backbone for the fungi. Moreover, we present the first formal supertree based on 161 fungal taxa and 128 gene trees. The combined evidences from the trees support the deep-level stability of the fungal groups towards a comprehensive natural system of the fungi. They indicate that the classification of the fungi, especially their alliance with the Microsporidia, requires careful revision. Our analysis is also an inventory of present day sequence information for the fungi. It provides insights into which phylogenenetic conclusions can and which cannot be drawn from the current data and may serve as a guide to direct further sequencing initiatives. Together with a comprehensive animal phylogeny, we provide the second of three pillars to understand the evolution of the multicellular eukaryotic kingdoms, fungi, metazoa, and plants, in the past 1.6 billion years.
Prevalence of sarcopenia and sarcopenic obesity in Korean adults: The Korean Sarcopenic Obesity Study (KSOS)
Authors: Kim Tae Nyun , Yang Sae Jeong , Yoo Hye Jin , Lim Kang Il , Kang Hyun Joo , Song Wook , Seo Ji A , Kim Sin Gon , Kim Nan Hee , Baik Sei Hyun , Choi Dong Seop , Choi Kyung Mook 
Published: July 2019

Abstract*Context:* Sarcopenic obesity (SO), a combination of excess weight and reduced muscle mass and/or strength, is suggested to be associated with an increased risk of adverse health outcomes.
*Objectives:*
To examine the prevalence and characteristics of Sarcopenic and SO defined by using different indices such as Appendicular Skeletal muscle Mass (ASM)/height^2^ and Skeletal Muscle Index (SMI (%): skeletal muscle mass (kg)/weight (kg) × 100) for Korean adults. *Methods:* 591 participants were recruited from the Korean Sarcopenic Obesity Study (KSOS) which is an ongoing prospective observational cohort study. Analysis was conducted in 526 participants (328 women, 198 men) who had complete data on body composition using Dual X-ray absorptiometry and computed tomography.

*Results:*
The prevalence of sarcopenia and SO increases with aging. Using two or more standard deviations (SD) of ASM/height^2^ below reference values from young, healthy adults as a definition of sarcopenia, the prevalence of sarcopenia and SO was 6.3% and 1.3% in men and 4.1% and 1.7% in women over 60 years of age. However, using two or more SD of SMI, the prevalence of sarcopenia and SO was 5.1% and 5.1% respectively in men and 14.2% and 12.5% respectively in women. As defined by SMI, subjects with SO had 3 times the risk of metabolic syndrome (OR = 3.03, 95% confidence interval (CI) = 1.26-7.26) and subjects with non-sarcopenic obesity had approximately 2 times the risk of metabolic syndrome (OR = 1.89, 95% CI = 1.18-3.02) compared with normal subjects. *Conclusion:* Obese subjects with relative sarcopenia were associated with a greater likelihood for metabolic syndrome. As Koreans were more obese and aging, the prevalence of SO and its impact on health outcomes are estimated to be rapidly grow. Further research is requested to establish the definition, cause and consequences of SO.
Aging as a consequence of misrepair -- A novel theory of aging
Authors: Wang Jicun , Michelitsch Thomas , Wunderlin Arne , Mahadeva Ravi 
Published: July 2019

AbstractIt is now increasingly realized that the underlying mechanisms which govern aging is a complex interplay of genetic regulation and damage accumulation. Aging as a result of accumulation of ‘faults’ on cellular and molecular levels, has been proposed in the damage (fault)-accumulation theory by Kirkwood 2006. However, this theory fails to explain some aging phenotypes such as fibrosis and premature aging, since terms such as ‘damage’ and ‘fault’ are not specified. Therefore we introduce here a specification of the underlying mechanism and arrive at a novel theory: aging of the body is a result of the accumulation of Misrepair of tissue. It emphasizes: a) it is Misrepair, not the original damage, that accumulates and leads to aging; and b) aging can occur at different levels, however aging of the body takes place at least on the tissue level, but not necessarily on cellular/molecular level. The novel concept of Misrepair which is introduced here unifies the understanding of the roles of environmental damage, repair, gene regulation, and multicellular structure in the aging process. The Misrepair-accumulation theory which is introduced here gives also explanations for the aging phenotypes, premature aging, and the difference of longevity in different species and is consistent with the point of view of physical theory of complex systems.
Aging as a consequence of misrepair -- A novel theory of aging
Authors: Wang Jicun , Michelitsch Thomas , Wunderlin Arne , Mahadeva Ravi 
Published: July 2019

AbstractIt is now increasingly realized that the underlying mechanisms which govern aging is a complex interplay of genetic regulation and damage accumulation. Aging as a result of accumulation of ‘faults’ on cellular and molecular levels, has been proposed in the damage (fault)-accumulation theory by Kirkwood 2006. However, this theory fails to explain some aging phenotypes such as fibrosis and premature aging, since terms such as ‘damage’ and ‘fault’ are not specified. Therefore we introduce here a specification of the underlying mechanism of aging and arrive at a novel theory: aging of the body is a result of the accumulation of Misrepair of tissue. It emphasizes: a) it is Misrepair, not the original damage, that accumulates and leads to aging; and b) aging can occur at different levels, however aging of the body takes place at least on the tissue level, but not necessarily on cellular/molecular level. The novel concept of Misrepair introduced here unifies the understanding of the roles of environmental damage, repair, gene regulation, and multicellular structure in the aging process. The Misrepair-accumulation theory introduced in the present paper gives explanations for the aging phenotypes, premature aging, and the difference of longevity in different species, and is consistent with the point of view of physical theory of complex adaptive systems.
Memristance can explain Spike-Time-Dependent-Plasticity in Neural Synapses
Authors: Linares-Barranco Bernabé , Serrano-Gotarredona Teresa 
Published: July 2019

AbstractInterdisciplinary research broadens the view of particular problems yielding fresh and possibly unexpected insights. This is the case of neuromorphic engineering where technology and neuroscience cross-fertilize each other. For example, consider on one side the recently discovered memristor, postulated in 1974, thanks to research in nanotechnology electronics. On the other side, consider the mechanism known as Spike-Time-Dependent-Plasticity (STDP) which describes a neuronal synaptic learning mechanism that outperforms the traditional Hebbian synaptic plasticity proposed in 1949. STDP was originally postulated as a computer learning algorithm, and is being used by the machine intelligence and computational neuroscience community. At the same time its biological and physiological foundations have been reasonably well established during the past decade. If memristance and STDP can be related, then (a) recent discoveries in nanophysics and nanoelectronic principles may shed new lights into understanding the intricate molecular and physiological mechanisms behind STDP in neuroscience, and (b) new neuromorphic-like computers built out of nanotechnology memristive devices could incorporate the biological STDP mechanisms yielding a new generation of self-adaptive ultra-high-dense intelligent machines. Here we show that by combining memristance models with the electrical wave signals of neural impulses (spikes) converging from pre- and post-synaptic neurons into a synaptic junction, STDP behavior emerges naturally. This result serves to understand how neural and memristance parameters modulate STDP, which might bring new insights to neurophysiologists in searching for the ultimate physiological mechanisms responsible for STDP in biological synapses. At the same time, this result also provides a direct mean to incorporate STDP learning mechanisms into a new generation of nanotechnology computers employing memristors.
Objective dysphonia quantification in vocal fold paralysis: comparing nonlinear with classical measures
Authors: Little Max , Costello Declan , Harries Meredydd 
Published: July 2019

AbstractClinical acoustic voice recording analysis is usually performed using classical perturbation measures including jitter, shimmer and noise-to-harmonic ratios. However, restrictive mathematical limitations of these measures prevent analysis for severely dysphonic voices. Previous studies of alternative nonlinear random measures addressed wide varieties of vocal pathologies. Here, we analyze a single vocal pathology cohort, testing the performance of these alternative measures alongside classical measures.We present voice analysis pre- and post-operatively in unilateral vocal fold paralysis (UVFP) patients and healthy controls, patients undergoing standard medialisation thyroplasty surgery, using jitter, shimmer and noise-to-harmonic ratio (NHR), and nonlinear recurrence period density entropy (RPDE), detrended fluctuation analysis (DFA) and correlation dimension. Systematizing the preparative editing of the recordings, we found that the novel measures were more stable and hence reliable, than the classical measures, on healthy controls.RPDE and jitter are sensitive to improvements pre- to post-operation. Shimmer, NHR and DFA showed no significant change (p > 0.05). All measures detect statistically significant and clinically important differences between controls and patients, both treated and untreated (p < 0.001, AUC > 0.7). Pre- to post-operation, GRBAS ratings show statistically significant and clinically important improvement in overall dysphonia grade (G) (AUC = 0.946, p < 0.001).Re-calculating AUCs from other study data, we compare these results in terms of clinical importance. We conclude that, when preparative editing is systematized, nonlinear random measures may be useful UVFP treatment effectiveness monitoring tools, and there may be applications for other forms of dysphonia.
Projected Climate Change Impacts on Grape Growing in the Okanagan Valley, British Columbia, Canada
Authors: Rayne Sierra , Forest Kaya , Friesen Ken 
Published: July 2019

AbstractA statistical analysis was conducted on long-term climate records in the Okanagan Valley wine grape growing region of British Columbia, Canada. No observable trends for average annual temperatures were found in the region. Analyses of monthly mean and extreme temperatures show wide spatial and temporal heterogeneity, indicating that future studies using downscaling of global climate models for this region will require resolutions on the order of several kilometers. Mean winter temperatures are increasing throughout the valley, and extreme minimum temperatures are also increasing during the winter at the central and northern sites which have historically presented the most risk of winter damage to grapevines. Only the most southern and northern sub-regions are expected to see significant changes in their heat unit accumulations during the growing season. Over the coming century, the southern end of the valley will likely move from Winkler heat unit region 1 to 2. All regions of the Okanagan will continue to have latitude-temperature indices among the lowest of the world's fine table wine producing regions over the coming century. Growing season and dormant season average temperatures are expected to change by only a modest amount by 2100. Current climate maturity groupings for ripening grape varieties will likely stay constant at cool (central and southern areas) and intermediate (south-central) for all sites except Osoyoos (south). The climate trendings at Osoyoos suggest it will transition from an intermediate to a warm grouping by about 2050. The early to mid-season ripening capacity of the region may improve due to climate changes, but there is a risk of the asymmetric late season increases in minimum daily temperatures lowering the daily temperature range at some sites, possibly leading to difficulties in maintaining a balanced between sugar and sensory profiles as wine grapes approach maturity. The projected warming at the southern end of the valley should favor improved and increased Merlot production, will require Chardonnay production to shift northwards, and will allow growing of warmer climate wine grape varieties currently inaccessible because of low winter temperatures and a lack of growing season heat units. Increasing winter temperatures throughout the region are expected to result in increased risk of pests such as Pierce’s disease.
Reflect: Augmented Browsing for the Life Scientist
Authors: Pafilis Evangelos , O'Donoghue Seán , Jensen Lars , Horn Heiko , Kuhn Michael , Brown Nigel , Schneider Reinhard 
Published: July 2019

AbstractAnyone who regularly reads life science literature often comes across names of genes, proteins, or small molecules that they would like to know more about. To make this process easier, we have developed a new, free service called Reflect ("http://reflect.ws":http://reflect.ws) that can be installed as a plug-in to Firefox or Internet Explorer. Reflect tags gene, protein, and small molecule names in any web page, typically within a few seconds, and without affecting document layout. Clicking on a tagged gene or protein name opens a popup showing a concise summary that includes synonyms, database identifiers, sequence, domains, 3D structure, interaction partners, subcellular location, and related literature. Clicking on a tagged small molecule name opens a popup showing 2D structure and interaction partners. The popups also allow navigation to commonly used databases. In the future we plan to add further entity types to Reflect, including outside the life sciences.