bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Paradigm for Biology's Next Revolution
Authors: Young Fredric 
Published: July 2019

AbstractA recent essay on biology's next revolution described attributes of a future theory of biology that would replace post hoc modeling with an interplay between quantitative prediction and experimental test, more characteristic of the physical sciences1. The article suggested that flux from the environment whether it be energy, chemicals metabolites, or genes is a defining characteristic of life. The essay also suggests that an interdisciplinary approach to collective phenomena centered on statistical mechanics and dynamical systems theory will be required to make use of this perspective. Over the last 30 years we have developed an approach to drug discovery and translational research that is based on a paradigm for complex systems modeling that fits the description in the essay. The approach is a new paradigm because it focuses on the control of non-equilibrium flux, rather than genes. It has now been used to identify potential therapies for unmet medical needs that are currently being tested in phase II clinical trials.
Implications of uncertainty for Canada’s commercial hunt of harp seals (Pagophilus groenlandicus)
Authors: Leaper Russell , Matthews Justin 
Published: July 2019

AbstractThe Canadian government's current management procedure for harp seals is described by Fisheries and Oceans Canada as using the Precautionary Approach. Employing a similar underlying population model, we simulated the effects of uncertainty involving bias in estimates of human induced mortality, natural mortality, and pup production estimates as a set of robustness trials. Our results indicated that for the range of annual total allowable catches (TAC) considered and set for Canada’s commercial harp seal hunt (250,000 – 350,000), there were plausible circumstances under which the government's management procedures failed to meet their own conservation objectives. By contrast, a precautionary management regime should be robust to such levels of uncertainty. For some scenarios the current management strategy, although not fully specified, is likely to maintain a high TAC despite a declining population. In particular, once a high TAC has been set, the assessments are unlikely to provide the necessary evidence that the TAC should be reduced until the population is at a low level. Hence there is a substantial risk that the population may be depleted below the ‘minimum’ (N50) and ‘critical’ (N30) population reference points. There is a need for a management procedure based on risk analysis to be fully specified and tested. In the interim, reducing TACs to within limits calculated from a well-established precautionary procedure, such as Potential Biological Removal, would be a step towards more precautionary management.
Intra- and inter-individual genetic differences in gene expression
Authors: Cowley Mark , Cotsapas Chris , Williams Rohan , Chan Eva , Pulvers Jeremy , Liu Michael , Luo Oscar , Nott David , Little Peter 
Published: July 2019

AbstractGenetic variation is known to influence the amount of mRNA produced by a gene. Given that the molecular machines control mRNA levels of multiple genes, we expect genetic variation in the components of these machines would influence multiple genes in a similar fashion. In this study we show that this assumption is correct by using correlation of mRNA levels measured independently in the brain, kidney or liver of multiple, genetically typed, mice strains to detect shared genetic influences. These correlating groups of genes (CGG) have collective properties that account for 40-90% of the variability of their constituent genes and in some cases, but not all, contain genes encoding functionally related proteins. Critically, we show that the genetic influences are essentially tissue specific and consequently the same genetic variations in the one animal may up-regulate a CGG in one tissue but down-regulate the same CGG in a second tissue. We further show similarly paradoxical behaviour of CGGs within the same tissues of different individuals. The implication of this study is that this class of genetic variation can result in complex inter- and intra-individual and tissue differences and that this will create substantial challenges to the investigation of phenotypic outcomes, particularly in humans where multiple tissues are not readily available.
The impact of Bt cotton on poor households in rural India
Authors: Subramanian Arjunan , Qaim Matin 
Published: July 2019

AbstractThe impact of genetically modified (GM) crops on the poor in developing countries is still the subject of controversy. While previous studies have examined direct productivity effects of Bacillus thuringiensis (Bt) cotton and other GM crops, little is known about wider socioeconomic outcomes. We develop a microeconomic modeling approach and use comprehensive survey data from India to analyze welfare and distribution effects in a typical village economy. Bt cotton adoption increases aggregate employment with interesting gender implications. Likewise, aggregate household incomes rise, including for poor and vulnerable farmers, suggesting that Bt cotton contributes to poverty reduction and rural development.
Selective insectivory in Nymphaea nouchali Burm. f.
Authors: Tetali Pundarikakshudu , Sutar Shrikant , Tetali Sujata 
Published: July 2019

AbstractCarnivorous plants comprise roughly 0.24 percent of the flowering plants, or 640 species represented in 12 families. Yet they are regarded as miracula naturae. Over fifty percent of these taxa are represented in a single family, namely Lentibulariaceae. Carnivorous plants are generally insectivorous, and carnivory in flowering plants is generally found in taxa that are adapted to nutrient-deficient habitats. The extra nutrients such plants acquire by special ways serve merely as supplements. The origin and evolution of carnivorous plants is a mystery in the phylogenetic tree of angiosperms, they often appear without a clear linkage. Here, we report that Nymphaea nouchali Burm. f. (a cultivar of var. cernua), a large aquatic member of the family Nymphaeaceae, indulges in a primitive form of insectivory and represents the missing evolutionary link. To the best of our knowledge, an insectivorous flower was not reported in flowering plants before.
The unique mouse pollination in an orchid species
Authors: Wang Yong , Zhang Yang , Ma Xiao-Kai , Dong Li 
Published: July 2019

AbstractThe Chinese orchid, Cymbidium serratum, is pollinated by the wild mountain mouse Rattus fulvescens. The flowers use both odor and colour as attractants, and provide labellum as food reward for the pollinators. The mice pollinate the flowers during their endeavour to eat the labellums.
Affymetrix probes containing runs of contiguous guanines are not gene-specific
Authors: Upton Graham , Langdon William , Harrison Andrew 
Published: July 2019

AbstractHigh Density Oligonucleotide arrays (HDONAs), such as the Affymetrix HG-U133A GeneChip, use sets of probes chosen to match specified genes, with the expectation that if a particular gene is highly expressed then all the probes in the designated probe set will provide a consistent message signifying the gene's presence. However, we demonstrate by data mining thousands of CEL files from NCBI's GEO database that 4G-probes (defined as probes containing sequences of four or more consecutive guanine (G) bases) do not react in the intended way. Rather, possibly due to the formation of G-quadruplexes, most 4G-probes are correlated, irrespective of the expression of the thousands of genes for which they were separately intended. It follows that 4G-probes should be ignored when calculating gene expression levels. Furthermore, future microarray designs should make no use of 4G-probes.
Systems biology of energetic and atomic costs in the yeast transcriptome, proteome, and metabolome
Authors: Barton Michael , Papp Balazs , Delneri Daniel , Oliver Stephen , Rattray Magnus , Bergman Casey 
Published: July 2019

AbstractProteins vary in their cost to the cell and natural selection may favour the use of proteins that are cheaper to produce. We develop a novel approach to estimate the amino acid biosynthetic cost based on genome-scale metabolic models, and directly investigate the effects of biosynthetic cost on transcriptomic, proteomic and metabolomic data in Saccharomyces cerevisiae. We find that our systems approach to formulating biosynthetic cost produces a novel measure that explains similar levels of variation in gene expression compared with previously reported cost measures. Regardless of the measure used, the cost of amino acid synthesis is weakly associated with transcript and protein levels, independent of codon usage bias. In contrast, energetic costs explain a large proportion of variation in levels of free amino acids. In the economy of the yeast cell, there appears to be no single currency to compute the cost of amino acid synthesis, and thus a systems approach is necessary to uncover the full effects of amino acid biosynthetic cost in complex biological systems that vary with cellular and environmental conditions.
A reassessment of the Carnot cycle and the concept of entropy
Authors: Chandrasekhar Sosale 
Published: July 2019

AbstractIt is argued that the Carnot cycle is a highly inaccurate representation of a steam engine, and that the net work obtained in its operation would be zero. This conclusion is also supported by an elementary mathematical approach, which re-examines the work done in the four individual steps of the cycle. An important consequence of this is that the concept of entropy, originally proposed on the basis of the Carnot theorem, may not be a fundamentally valid thermodynamic quantity. Also, the experimental approach generally adopted in the determination of entropy is questionable, and the importance of increasing randomness in natural processes not universally valid. In fact, a more viable basis, at least vis-à-vis chemical reactions, appears to be the ratio of mass to energy, which is apparently maximized in the case of a spontaneous process.
Immunogenicity of human spermatozoa
Authors: Chatterjee Jhinuk 
Published: July 2019

AbstractInvestigation and experimental design of the study was basically aimed at developing insight into the antigenicity of spermatozoa-associated proteins. Apart from studying the natural antigenicity of washed whole spermatozoa, their immunogenicity was also demonstrated in vitro. The whole live spermatozoa were immobilized and agglutinated in vitro by the antibodies they induced in the laboratory model - a female rabbit. A regular immunization routine induced a high titre of antisperm polyclonal antibodies. To prepare a spermatozoa specific antigen which will not produce a cross-reacting antibody against other human tissues, only the motile and live spermatozoa were selected for antigen preparation. In investigation the laboratory-bred female rabbits were used as the bioactive system of production of antisperm antibody. Agglutination of whole spermatozoa has been observed on slides. The technique though simple is highly eloquent; clumping of spermatozoa confirms the existence of antisperm antibodies in the serum under examination. The results show that nature and pattern of immobilization of active motile spermatozoa are different as observed in different graphs of immobilization. The variation in spermatozoal population in antigen distribution on individual spermatozoa is reflected in different patterns of agglutination.
Immunogenicity of human spermatozoa
Authors: Chatterjee Jhinuk , Chattopadhyay Sukumar 
Published: July 2019

AbstractInvestigation and experimental design of the study was basically aimed at developing insight into the antigenicity of spermatozoa-associated proteins. Apart from studying the natural antigenicity of washed whole spermatozoa, their immunogenicity was also demonstrated in vitro. The whole live spermatozoa were immobilized and agglutinated in vitro by the antibodies they induced in the laboratory model - a female rabbit. A regular immunization routine induced a high titre of antisperm polyclonal antibodies. To prepare a spermatozoa specific antigen which will not produce a cross-reacting antibody against other human tissues, only the motile and live spermatozoa were selected for antigen preparation. In investigation the laboratory-bred female rabbits were used as the bioactive system of production of antisperm antibody. Agglutination of whole spermatozoa has been observed on slides. The technique though simple is highly eloquent; clumping of spermatozoa confirms the existence of antisperm antibodies in the serum under examination. The results show that nature and pattern of immobilization of active motile spermatozoa are different as observed in different graphs of immobilization. The variation in spermatozoal population in antigen distribution on individual spermatozoa is reflected in different patterns of agglutination.
Reduced contribution of the ipsilateral primary motor cortex to force modulation with short-term motor learning in humans: An NIRS study
Authors: Shibuya Kenichi , Iwadate Masako , Sadamoto Tomoko 
Published: July 2019

AbstractHow is muscle force modulated during hand exercise? Oxygenation in the contralateral primary motor cortex (M1) has been observed to vary considerably across trials of repetitive handgrip exercise. No linear relationship was observed between the average value of oxygenation determined by a block design study and the force of the handgrip. We found reduced oxygenation in the ipsilateral M1 and unchanged oxygenation in the contralateral M1 during repetitive static handgrip exercises (40% and 60% maximal voluntary contraction; 10 s exercise/75 s rest; 5 sets), which might be due to short-term motor learning. These results support the hypothesis that the ipsilateral M1 might functionally compensate for the contralateral M1 in force modulation during unilateral exercises.
A Study on the Origin of Peroxisomes: Possibility of Actinobacteria Symbiosis
Authors: Narendra Duhita , Satoshi Saruhashi , Kazuo Hamada , Daisuke Miyata , Tokumasa Horiike , Takao Shinozawa 
Published: July 2019

AbstractThe origin of peroxisomes as having developed from the endoplasmic reticulum (ER) was proposed on the basis of the similarity between some peroxisomal proteins and ER proteins, and the localization of some peroxisomal proteins on the ER. To study the evolutionary distance between peroxisomes and ER and Prokaryotes, we carried out a phylogenetic analysis of CDC48 (cell division control 48) and its homologs, including ER-localized CDC48, CDC48 homologs in Prokaryotes and peroxisome-localized PEX1 and PEX6. A similarity search analysis of peroxisomal protein sequences to prokaryotic protein sequences using BLAST at several thresholds (E-values) was also done. We propose Actinobacteria symbiosis for the origin of peroxisomes based on the following evidence: (1) PEX1 and PEX6 are close in distance to CDC48 homologs in Actinobacteria, and these distances are closer than to ER-localized CDC48. (2) Actinobacteria proteins show the highest degree of similarity to peroxisomal proteins compared with other prokaryotes.
The non-obligatory role of endothelial cells in the relaxation of arterial smooth muscle by acetylcholine
Authors: Buchwalow Igor , Cacanyiova Sona , Neumann Joachim , Samoilova Vera , Boecker Werner , Kristek Frantisek 
Published: July 2019

AbstractThe concept of Endothelium Derived Relaxing Factor (EDRF), put forward by Furchgott in the earlier 80s of the past century, implies that nitric oxide (NO) produced by NO synthase (NOS) in the endothelium in response to acetylcholine (ACh) passively diffuses to the underlying vascular smooth muscle cells (VSMC) thereby reducing vascular tension. It was thought that VSMC do not express NOS by themselves, but to the time of those studies immunohistochemical techniques were not what they are now. State-of-the-art immunohistochemistry permits nowadays to localize NOS both to the endothelium and to VSMC. However, the principal question remained unanswered, is the NO generation by VSMC physiologically relevant? We hypothesized that the destruction of the vascular wall anatomical integrity by rubbing the blood vessel intimal surface may increase vascular superoxides that, in turn, reduce NO bioactivity. To address this issue, we examined ACh-induced vasorelaxation in endothelium-deprived blood vessels under protection against oxidative stress and found that superoxide scavengers - tempol and N-acetyl-L-cysteine - restored vasodilatory responses to ACh in endothelium-deprived blood vessels without influencing the vascular wall tension in intact blood vessels. Herewith we provided the first evidence that VSMC can release NO in amounts sufficient to account for the vasorelaxatory response to ACh. In contrast to the commonly accepted concept of the obligatory role of endothelial cells in the relaxation of arterial smooth muscle, the local NO generation by VSMC can modulate vascular functions in an endothelium-independent manner.
A novel regulator of the p53-mediated mitochondrial apoptotic pathway
Authors: Ahn Bo Young , Trinh Diane , Zajchowski Laura , Kim Sung-Woo 
Published: July 2019

AbstractThe p53 tumor suppressor protein induces apoptosis in response to genotoxic and environmental stress. Recent studies have revealed the existence of a transcription-independent mitochondrial p53 apoptosis pathway, however the mechanism regulating p53 translocation to mitochondria and subsequent initiation of apoptosis was not known. Here, we show that Tid1, also known as mtHsp40 or Dnaja3, interacts with p53 and directs its translocation to mitochondria in cells exposed to hypoxia. Overexpression of Tid1 in tumor cells promoted mitochondrial localization of both wildtype and mutant forms of p53 and was able to restore the pro-apoptotic activity of mutant p53 proteins that were otherwise unable to induce apoptosis. Tid1&apos;s mitochondrial signal sequence and DnaJ domain were both required for the movement of the p53-Tid1 complex from the cytosol to the mitochondria. Our findings establish Tid1 as a novel regulator of p53 localization and apoptotic function.
Satellite Images Show the Movement of Floating Sargassum in the Gulf of Mexico and Atlantic Ocean
Authors: Gower Jim , King Stephanie 
Published: July 2019

AbstractThe question of the origin, distribution and fate of the floating seaweed Sargassum has fascinated sailors and scientists from the time of Columbus. Observations from ships are hampered by the large and variable area over which Sargassum is dispersed. Here we use satellite imagery to present the first mapping of the full distribution and movement of the population of Sargassum in the Gulf of Mexico and western Atlantic in the years 2002 to 2008. For the first time, we show a seasonal pattern in which Sargassum originates in the northwest Gulf of Mexico in spring of each year, is advected into the Atlantic in about July, appearing east of Cape Hatteras as a "Sargassum jet", and ending northeast of the Bahamas in February of the following year. This pattern appears consistent with historical surveys. Future satellite observations will show whether this pattern repeats in all or most years.
Natural evidence for garnet-spinel transition (GST) in the Earth's mantle
Authors: Su BenXun 
Published: July 2019

AbstractThis study based on compiled world-wide garnet peridotite data confirms the GST in high P and T conditions, which was obtained from Al-free experimental system (MgO-Cr~2~O~3~-SiO~2~) by Klemme (2004). A new spinel-phase peridotite zone, garnet peridotite discontinuous zone, is defined, and another GST, although no experimental data, is principally and presumably proposed to exist. The garnet inclusion-bearing spinel harzburgite from Lashaine (Tanzania) provides the first evidence for the existence of ultra-high spinel zone and is explained as recrystallized minerals hosting the interacted residue of ancient oceanic lithosphere subducted into the great depth of more than 220km. These previously unexpected findings are generating great challenges to phase transition in extreme conditions and to our understanding of layered-structure of the Earth. In addition, coexistent five-phase peridotite is suggested to be naturally useful tool to constrain the GST.
New Evidence for Early Silk in the Indus Civilization
Authors: Good Irene , Kenoyer Jonathan Mark , Meadow Richard 
Published: July 2019

AbstractSilk is an important economic fiber, and is generally considered to have been the exclusive cultural heritage of China. Silk weaving is evident from the Shang period, though the earliest evidence for silk textiles in ancient China dates to more than a millennium earlier. New study of fibers from Harappan bronze artifacts reveals surprising early evidence for knowledge of silkworking in South Asia, the earliest evidence in the world for any silk outside China, and roughly contemporaneous with the earliest Chinese evidence for silk. This important new finding brings into question the traditional historical notion of sericulture as being an exclusively Chinese invention.
Effects of processes at the population and community level on carbon dynamics of an ecosystem model
Authors: Sierra Carlos , Harmon Mark 
Published: July 2019

AbstractEcological processes at the population and community level are often ignored in biogeochemical models, however, the effects of excluding these processes at the ecosystem level is uncertain. In this study we analyzed the set of behaviors that emerge after introducing population and community processes into an ecosystem carbon model. We used STANDCARB, a hybrid model that incorporates population, community, and ecosystem processes to predict carbon dynamics over time. Our simulations showed that at the population level, colonization and mortality rates can limit the maximum biomass achieved during a successional sequence. Specifically, colonization rates control temporal lags in the initiation of carbon accumulation, and mortality rates can have important effects on annual variation in live biomass. At the community level, differences in species traits and changes in species composition over time introduced significant changes in carbon dynamics. Species with different set of parameters, such as growth and mortality rates, introduce patterns of carbon accumulation that could not be reproduced using a single species with the average of parameters of multiple species or by simulating the most abundant species (strategies commonly employed in terrestrial biogeochemical models). We conclude that omitting population and community processes from biogeochemical models introduces an important source of uncertainty that can impose important limitations for predictions of future carbon balances.