bluuebunny/crossref_metadata_2025 huggingface dataset:
A Mathematical Model of a Neuron with Synapses based on Physiology
Authors: Zhang Xiaolin
Published: July 2019

The neuron, when considered as a signal processing device, itsinputs are the frequency of pulses received at the synapses, and its output is the frequency of action potentials generated- in essence, a neuron is a pulse frequency signal processing device. In comparison, electrical devices use either digital or analog signals for communication or processing, and the mathematics behind these subjects is well understood. However, in regards to pulse frequency processing devices, there has not yet been a clear and persuasive mathematical model to describe the functions of neurons. It goes without saying that such a model is very important, not only for understanding neuron and neural system behavior, but also for undeveloped potential applications in industry. This paper proposes a method for obtaining the mathematical relationship between the input and output signals of a neuron based on physiological facts. The proposed method focuses on the currents across the postsynaptic membrane of each synapse, and the key is to recognize that the net charge across the whole membrane of a neuron over each action potential cycle must equal to zero. By analyzing the relationship between the input of a synapse and the currents across the postsynaptic membranes, a dynamic pulse frequency model of the neuron can be obtained. Here, we show that the transfer function of a neuron depends on the function of thepostsynaptic current of each synapse in resting state, which can be found by detecting the postsynaptic current when a pulse is received at the synapse. The transfer function of a typical neuron generally includes addition and subtraction of feedthrough terms and/or first order lag functions. To focus on the most basic characteristics of a neuron, accommodation, adaptation, learning, etc. are not discussed in this paper.
Identifying Data Sharing in Biomedical Literature
Authors: Piwowar Heather , Chapman Wendy
Published: July 2019

Many policies and projects now encourage investigators to share their raw research data with other scientists. Unfortunately, it is difficult to measure the effectiveness of these initiatives because data can be shared in such a variety of mechanisms and locations. We propose a novel approach to finding shared datasets: using NLP techniques to identify declarations of dataset sharing within the full text of primary research articles. Using regular expression patterns and machine learning algorithms on open access biomedical literature, our system was able to identify 61% of articles with shared datasets with 80% precision. A simpler version of our classifier achieved higher recall (86%), though lower precision (49%). We believe our results demonstrate the feasibility of this approach and hope to inspire further study of dataset retrieval techniques and policy evaluation.
Identifying Data Sharing in Biomedical Literature
Authors: Piwowar Heather , Chapman Wendy
Published: July 2019

Many policies and projects now encourage investigators to share their raw research data with other scientists. Unfortunately, it is difficult to measure the effectiveness of these initiatives because data can be shared in such a variety of mechanisms and locations. We propose a novel approach to find shared datasets: using NLP techniques to identify declarations of dataset sharing within the full text of primary research articles. Using regular expression patterns and machine learning algorithms on open access biomedical literature, our system was able to identify 61% of articles with shared datasets with 80% precision. A simpler version of our classifier achieved higher recall (86%), though lower precision (49%). We believe our results demonstrate the feasibility of this approach and hope to inspire further study of dataset retrieval techniques and policy evaluation.
Human metabolic adaptations and prolonged expensive neurodevelopment: A review
Authors: Skoyles John
Published: July 2019

1. After weaning, human hunter-gatherer juveniles receive substantial (≈3.5-7 MJ day^-1^), extended (≈15 years) and reliable (kin and nonkin food pooling) energy provision.2. The childhood (pediatric) and the adult human brain takes a very high share of both basal metabolic rate (BMR) (child: 50-70%; adult: ≈20%) and total energy expenditure (TEE) (child: 30-50%; adult: ≈10%).3. The pediatric brain for an extended period (≈4-9 years-of-age) consumes roughly 50% more energy than the adult one, and after this, continues during adolescence, at a high but declining rate. Within the brain, childhood cerebral gray matter has an even higher 1.9 to 2.2-fold increased energy consumption. 4. This metabolic expensiveness is due to (i) the high cost of synapse activation (74% of brain energy expenditure in humans), combined with (ii), a prolonged period of exuberance in synapse numbers (up to double the number present in adults). Cognitive development during this period associates with volumetric changes in gray matter (expansion and contraction due to metabolic related size alterations in glial cells and capillary vascularization), and in white matter (expansion due to myelination). 5. Amongst mammals, anatomically modern humans show an unique pattern in which very slow musculoskeletal body growth is followed by a marked adolescent size/stature spurt. This pattern of growth contrasts with nonhuman primates that have a sustained fast juvenile growth with only a minor period of puberty acceleration. The existence of slow childhood growth in humans has been shown to date back to 160,000 BP. 6. Human children physiologically have a limited capacity to protect the brain from plasma glucose fluctuations and other metabolic disruptions. These can arise in adults, during prolonged strenuous exercise when skeletal muscle depletes plasma glucose, and produces other metabolic disruptions upon the brain (hypoxia, hyperthermia, dehydration and hyperammonemia). These are proportional to muscle mass.7. Children show specific adaptations to minimize such metabolic disturbances. (i) Due to slow body growth and resulting small body size, they have limited skeletal muscle mass. (ii) They show other adaptations such as an exercise specific preference for free fatty acid metabolism. (iii) While children are generally more active than adolescents and adults, they avoid physically prolonged intense exertion. 8. Childhood has a close relationship to high levels of energy provision and metabolic adaptations that support prolonged synaptic neurodevelopment.
Bird pollination of Canary Island endemic plants
Authors: Ollerton Jeff , Cranmer Louise , Stelzer Ralph , Sullivan Steve , Chittka Lars
Published: July 2019

The Canary Islands are home to a guild of endemic, threatened bird pollinated plants. Previous work has suggested that these plants evolved floral traits as adaptations to pollination by flower specialist sunbirds, but subsequently they appear to be have co-opted passerine birds as sub-optimal pollinators. To test this idea we carried out a quantitative study of the pollination biology of three of the bird pollinated plants, Canarina canariensis (Campanulaceae), Isoplexis canariensis (Veronicaceae) and Lotus berthelotii (Fabaceae), on the island of Tenerife. Using colour vision models, we predicted the detectability of flowers to bird and bee pollinators. We measured pollinator visitation rates, nectar standing crops, as well as seed set and pollen removal and deposition. These data showed that the plants are effectively pollinated by non-flower specialist passerine birds that only occasionally visit flowers. The large nectar standing crops and extended flower longevities (>10days) of Canarina and Isoplexis suggests that they have evolved bird pollination system that effectively exploits these low frequency non-specialist pollen vectors and is in no way suboptimal. Seed set in two of the three species was high, and was significantly reduced or zero in flowers where pollinator access was restricted. In L. berthelotii, however, no fruit set was observed, probably because the plants were self incompatible horticultural clones of a single genet. We also show that, while all three species are easily detectable for birds, the orange Canarina and the red Lotus (but less so the yellow-orange Isoplexis) should be difficult to detect for insect pollinators without specialised red receptors, such as bumblebees. Contrary to expectations if we accept that the flowers are primarily adapted to sunbird pollination, the chiffchaff (Phylloscopus canariensis) was an effective pollinator of these species.
Effects of Cations and PH on Antimicrobial Activity of Thanatin and s-Thanatin against Escherichia coli ATCC25922 and B. subtilis ATCC 21332
Authors: Wu Guoqiu , Ding Jiaxuan , Li Hui , Li Linxian , Zhao Rui , Fan Xiaobo , Shen Zilong
Published: July 2019

Thanatin and s-thanatin were insect antimicrobial peptides which have shown potent antimicrobial activities on a variety of microbes. In order to investigate the effect of cations and pH on the activity of these peptides against Gram-negative bacteria and Gram-positive bacteria, the antimicrobial activities of both peptides were studied in increasing concentrations of monovalent cations (K^+^ and Na^+^), divalent cations (Ca^2+^ and Mg^2+^) and H^+^. The NCCLS broth microdilution method showed that both peptides were sensitive to the presence of cations. The divalent cations showed more antagonized effect on the activity against Gram-negative bacteria than the monovalent cations, since the two peptides lost the ability to inhibit bacterial growth at a very low concentration. In addition, the activities of both peptides tested were not significantly affected by pH. Comparing to studies of other antibacterial peptide activities, our data support a hypothesis that positive ions affect the sensitivity to cation peptides.
SNP analysis reveals an evolutionary acceleration of the human-specific microRNAs
Authors: Zhang Qipeng , Lu Ming , Cui Qinghua
Published: July 2019

MicroRNAs 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

The 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.
Regulating Nanomedicine: A European perspective
Authors: D’Silva Joel , Van Calster Geert
Published: July 2019

The potential impact of nanomedicine is foreseen to radically change health care; however it also challenges existing perceptions, dynamics and standards relating to ethics, safety and governance. This commentary briefly highlights aspects and approaches pertaining to nanomedical regulation in the European Union.
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

Examinations 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

Receptors 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

Discovery 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

HPLC 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

In 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

Fungi 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

*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

It 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

It 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

Interdisciplinary 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

Clinical 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

A 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

Anyone 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.
Chromobacterium violaceum ATCC12472: Multi-drug and ethidium bromide resistant
Authors: Dal'Molin Cristiana , Antônio Regina , Porto Luismar
Published: July 2019

Chromobacterium violaceum is an opportunistic human pathogen causing a range of gastric infections and occasionally septicemia. This Gram-negative bacillus is a common inhabitant of soil and water in tropical and subtropical areas of the world. Infection occurs after contamination of damaged skin exposed to soil or environmental water. Alternatively, systemic infection can follow the aspiration or ingestion of contaminated water. The major features of infections by C. violaceum are, in generally, rapid clinical course, multiple visceral abscesses, and high mortality. Genomic data on the type strain ATCC 12472 has provided a comprehensive basis for detailed studies of pathogenicity, virulence and drug resistance genes. In this study, the susceptibility of this organism was tested on a variety of drugs at different concentrations, in solid and liquid media. C. violaceum shown to be resistance to ampicilin, penicillin, rifampicin, erythromycin, vancomycin and also to ethidium bromide. The bacteria was susceptible to gentamicin, tetracycline, chloramphenicol, cotrimoxazole, kanamycin, streptomycin and nalidixic acid, at the tested concentrations.
Aboveground Net Primary Productivity in Grazed and Ungrazed pastures: Grazing Optimisation Hypothesis or Local Extinction of Vegetation Species
Authors: Otieno Silvanus , Njoka Jesse , Young Truman , Mureithi Stephen , Ngugi Robinson
Published: July 2019

The controversy that has surrounded herbivory studies in the last few decades prompted our investigation to establish the extent to which herbivore optimisation hypothesis or compensatory growth evidence is real. We used the traditional movable cage method to collect primary productivity data on herbage, functional groups and key individual grass species in various controlled large herbivore treatments in an east African savanna. The herbivore treatments in triplicate blocks included cattle, wild herbivores with and without mega herbivores and combinations of cattle and wild herbivores also with and without mega herbivores. The findings revealed that at herbage level, most grazed treatments (four out of five) had higher productivity than the ungrazed control and three showed grazing optimisation curve at sixth polynomial degree between monthly productivity and grazing intensity (1-g/ng). At functional group level forbs productivity was higher in the ungrazed control than in any of the grazed treatments while at individual grass species level Themeda triandra productivity was higher in all grazed treatments than in ungrazed control. We conclude against presence of herbivore optimisation hypothesis at herbage, functional group and species level because of lack of attributable grazing effect in grazed treatments that matches complex ecological effects in the ungrazed treatment.
The Bond Between a Horse and a Human
Authors: Crews Debbie
Published: July 2019

The bond that exists between a horse and human was examined using EEG from the horse and human simultaneously. Three volunteers ranging from novice to elite horse experience participated with an unfamiliar horse. The elite participant was also recorded with her own horse. A dose-response effect was tested using 6 conditions requiring increasing interaction between the horse and human (baseline - apart, standing together, petting, grooming, sitting, and riding). EEG was recorded from 10 locations on the horse and the human. EEG brain maps illustrated that increasing interaction between the horse and human showed more synchronous EEG. The elite horse person showed greater synchronization with her own familiar horse. Perhaps these findings illustrate the bond that exists between horses and humans.
Data Mining for Simple Sequence Repeats in Oil Palm Expressed Sequence Tags
Authors: Riju Aikkal , Arunachalam Vadivel
Published: July 2019

Expressed Sequence Tags or ESTs are small pieces of DNA sequence that are generated by sequencing either one or both ends of an expressed gene. ESTs provide researchers with a quick and inexpensive route for discovering new genes, for obtaining data on gene expression and regulation, and for constructing genome maps. Oil palm EST sequences as available in public domain are downloaded. They were grouped and made contigs using CAP3 and Phrap. Microsatellite repeats are located using 5 softwares (MISA, TRA, TROLL, SSRIT, SSR primer). Among the 5 methods MISA is found to be the best. It can elucidate the compound repeat also. Frequency and total number (202) of SSR were detected. Mononucleotide repeat is more abundant especially ‘A/T’ repeats in Oil palm. Flanking primers were designed using primer3, SSR primers. The results of the study are given as an online database ‘MEMCO’ to help Oil palm researchers.
Global warming is reducing thermal stability and mitigating the effects of eutrophication in Lake Victoria (East Africa)
Authors: Marshall Brian , Ezekiel Charles , Gichuki John , Mkumbo Oliva , Sitoki Lewis , Wanda Fred
Published: July 2019

The impacts of global warming have been reported from several deep lakes in the African Rift Valley and in each thermal gradients within the water column have increased thus strengthening already existing oxyclines, below which the water is permanently anoxic^1,2,3,4^. The temperature of Lake Victoria rose by 0.9°C between 1960 and 1990 raising fears that thermal stability would increase resulting in more extensive and severe anoxia in the deeper waters^5^. This is of concern because of the eutrophication of the lake, which began in the 1960s,^6,7^ and led to dense blooms of sometimes toxic cyanobacteria, increased deoxygenation of the bottom waters, and fish kills in some parts of the lake^8,9,10^. Here we show that thermal gradients in the water column have weakened over the last decade and that deoxygenation of deeper waters is less pronounced than expected. Since 1927 the temperature of the deeper waters has risen by 1.3°C compared to only 1.0°C in the surface layers, thereby decreasing thermal and density differentials in the water column. This contradicts the view that eutrophication would increase deoxygenation of the water column perhaps to the point where fish production could not be sustained^11^. Our results suggest that the impacts of global warming on tropical lakes are likely to highly variable and may not, in the short term at least, be uniformly detrimental.
CO2 Enhancement of Forest Productivity Constrained by Limited Nitrogen Availability
Authors: Norby Richard , Warren Jeffrey , Iversen Colleen , Garten Charles , Medlyn Belinda , McMurtrie Ross
Published: July 2019

Stimulation of terrestrial productivity by rising CO~2~ concentration is projected to reduce the airborne fraction of anthropogenic CO~2~ emissions; coupled climate-carbon (C) cycle models, including those used in the IPCC Fourth Assessment Report (AR4), are sensitive to this negative feedback on atmospheric CO~2~^1^. The representation of the so-called CO~2~ fertilization effect in the 11 models used in AR4 and subsequent models^2,3^ was broadly consistent with experimental evidence from four free-air CO~2~ enrichment (FACE) experiments, which indicated that net primary productivity (NPP) of forests was increased by 23 +/- 2% in response to atmospheric CO~2~ enrichment to 550 ppm^4^. Substantial uncertainty remains, however, because of the expectation that feedbacks through the nitrogen (N) cycle will reduce the CO~2~ stimulation of NPP^5,6^; these feedbacks were not included in the AR4 models and heretofore have not been confirmed by experiments in forests^7^. Here, we provide new evidence from a FACE experiment in a deciduous Liquidambar styraciflua (sweetgum) forest stand in Tennessee, USA, that N limitation has significantly reduced the stimulation of NPP by elevated atmospheric CO~2~ concentration (eCO~2~). Isotopic evidence and N budget analysis support the premise that N availability in this forest ecosystem has been declining over time, and declining faster in eCO~2~. Model analyses and evidence from leaf- and stand-level observations provide mechanistic evidence that declining N availability constrained the tree response to eCO2. These results provide a strong rationale and process understanding for incorporating N limitation and N feedback effects in ecosystem and global models used in climate change assessments.
Iron (FeSO4) Bioavailability in Obese Subjects Submitted to Bariatric Surgery
Authors: Bueno Luciana , Pizzo Juliana , dos Santos José Ernesto , Marchini Julio Sérgio , Dutra de Oliveira José Eduardo
Published: July 2019

Objective:

To determine iron bioavailability in obese subjects after the ingestion of a nutritional supplement containing multiple nutrients. Methods: Fourteen persons were studied before and after bariatric surgery after the ingestion of a nutritional formulation containing 25 mg iron, 25 g fiber and 800 mg calcium. Serum iron levels were measured basally and every hour after the ingestion of 200 mL of the formulation, and serum ferritin, unsaturated iron binding capacity (UIBC), hemoglobin, albumin, total proteins, total triglycerides, total cholesterol and fractions (LDL-cholesterol and HDL-cholesterol) sere determined at the same time points.

Results:

The following ferremia values (median/minimum - maximum) were obtained before and after bariatric surgery, respectively: Fasting, 105 (70 - 364) &x00B5;g/dL and 198 (38 - 617) &x00B5;g/dL; 1 hour, 103 (63 - 305) &x00B5;g/dL and 160 (11 - 207) &x00B5;g/dL; 2 hours, 103 (62 - 150) &x00B5;g/dL and 141 (10 - 412) &x00B5;g/dL; 3 hours. 97 (63 - 190) &x00B5;g/dL and 153 (6 - 270) &x00B5;g/dL; 4 hours, 91 (58 - 163) &x00B5;g/dL and 156 (40 - 251) &x00B5;g/dL (p>0.05), with no association of serum iron levels with time. There was a difference in total triglycerides (95 &177; 29 mg/dL and 60 &177; 10 mg/dL) which were correlated with a decrease in serum ferritin levels (r = 0,926, p = 0.008), UIBC (r = 0.910, p = 0.01), total cholesterol (r = 0,918, p = 0.01) and LDL-c fraction (r = 0.830, p = 0.04), with an increase in HDL-c fraction (r = 0,807, p = 0.05). Conclusion: Iron bioavailability in obese subjects was affected by the ingestion of the nutritional formulation containing calcium and fiber and the serum ferritin and UIBC values involved in the body metabolism of iron were reduced by the surgery, a fact that may cause these patients to develop iron deficiency.
Limusaurus and bird digit identity
Authors: Vargas Alexander , Wagner Günter , Gauthier Jacques
Published: July 2019

Limusaurus is a remarkable herbivorous ceratosaur unique among theropods in having digits II, III and IV, with only a small metacarpal vestige of digit I. This raises interesting questions regarding the controversial identity of avian wing digits. The early tetanuran ancestors of birds had tridactyl hands with digital morphologies corresponding to digits I, II & III of other dinosaurs. In bird embryos, however, the pattern of cartilage formation indicates that their digits develop from positions that become digits II, III, & IV in other amniotes. Limusaurus has been argued to provide evidence that the digits of tetanurans, currently considered to be I, II and III, may actually be digits II, III, & IV, thus explaining the embryological position of bird wing digits. However, morphology and gene expression of the anterior bird wing digit specifically resemble digit I, not II, of other amniotes. We argue that digit I loss in Limusaurus is derived and thus irrelevant to understanding the development of the bird wing.
Earth History and the Evolution of Caribbean Bats
Authors: Dávalos Liliana
Published: July 2019

Although the natural history of the Caribbean is better understood now than ever before, a general biogeographic explanation for the peculiar faunal composition of the islands remains elusive. New molecular phylogenetic and divergence analyses presented here show that dispersal and diversification in Caribbean bats are synchronous with sea level drops during inter-stage transitions in the Miocene. The phylogenies indicate that several continental bat species descended from West Indian ancestors, as the exceptionally low sea level of the Miocene transitions allowed for two-way biotic exchange between the islands and the continent. These results suggest a common mechanism underlies colonization and subsequent speciation in the Caribbean, and underscore the importance of geological history in all biogeographic scenarios, including dispersal.
Accurate telemonitoring of Parkinson’s disease progression by non-invasive speech tests
Authors: Tsanas Athanasios , Little Max , McSharry Patrick , Ramig Lorraine
Published: July 2019

Tracking Parkinson's disease (PD) symptom progression often uses the Unified Parkinson’s Disease Rating Scale (UPDRS), which requires the patient's presence in clinic, and time-consuming physical examinations by trained medical staff. Thus, symptom monitoring is costly and logistically inconvenient for patient and clinical staff alike, also hindering recruitment for future large-scale clinical trials. Here, for the first time, we demonstrate rapid, remote replication of UPDRS assessment with clinically useful accuracy (about 7.5 UPDRS points difference from the clinicians’ estimates), using only simple, self-administered, and non-invasive speech tests. We characterize speech with signal processing algorithms, extracting clinically useful features of average PD progression. Subsequently, we select the most parsimonious model with a robust feature selection algorithm, and statistically map the selected subset of features to UPDRS using linear and nonlinear regression techniques, which include classical least squares and non-parametric classification and regression trees (CART). We verify our findings on the largest database of PD speech in existence (~6,000 recordings from 42 PD patients, recruited to a six-month, multi-centre trial). These findings support the feasibility of frequent, remote and accurate UPDRS tracking. This technology could play a key part in telemonitoring frameworks that enable large-scale clinical trials into novel PD treatments.