bluuebunny/crossref_metadata_2025_split huggingface dataset:
Silent Spring - the lost call
Authors: Quinn Michael , Ottinger Mary Ann 
Published: July 2019

AbstractThe "silence" in Rachel Carson's Silent Spring1 alludes to the demise of bird populations through reproductive problems and death resulting from exposure to the pesticides of that time, many of which are endocrine active. Endocrine disrupting chemicals (EDCs) are compounds which may interfere with the endocrine system, producing effects that may disrupt the physiologic function of hormones. Early research on EDC exposure in humans and wildlife has focused mainly on reproductive effects of estrogenic chemicals, however recent studies have revealed that effects of estrogenic as well as non-estrogen active chemicals are often more far reaching than the reproductive system, and even mild exposures experienced early in development may have detrimental effects that are maintained throughout adulthood. Here we show trenbolone acetate, an androgen active environmental contaminant used as a growth promoter for cattle, to cause a literal silence in Japanese quail (Coturnix japonica) chicks following a one time embryonic exposure. Vocalizations were not merely lessened; this is the first study to demonstrate an environmental contaminant to cause a complete abolishment of the ability to vocalize. Since many reasons for vocalization in birds are directly linked to survival of the individual and species, the potential for detrimental population effects is a grave possibility for many avian species that may encounter androgen active chemicals in the environment. Many androgen active EDCs are persistent and ubiquitous in distribution, thereforechances for exposure to these chemicals in birds may be high. We hope that powerful, yet subtle effects like the ones presented here will encourage further research with EDCs to expand beyond the traditional focus of reproductive effects of estrogenic chemicals.
On the reliability of Bayesian posterior clade probabilities in phylogenetic analysis
Authors: Jones Graham 
Published: July 2019

AbstractThis article discusses possible reasons why posterior clade probabilities obtained from Bayesian phylogenetic analyses might be inaccurate. It attempts to list all possible sources of uncertainty and error in Bayesian phylogenetic analysis. The choice of priors on trees has been suggested by several authors as a cause of inaccurate posterior clade probabilities. I argue strongly for using priors based on biological knowledge. Two possible sources of bias which do not seem to have been published before are also discussed. One is a computational problem and the other related to majority rule consensus trees.
Tendril, adhesive disc and super adhesive effect of climbing plant
Authors: Deng Wenli 
Published: July 2019

AbstractUnderstanding the super adhesion mechanism of biological system is of great scientific interest and a prerequisite for bioinspired design of adhesive systems. To investigate the versatile climbing plant requires the development of new methods. Here I present strategies to fully study the super adhesive effect of climbing plant Parthenocissus tricuspidata by the first time measuring the mass and the attached area of single adhesive disc, by further determining the microscopic structure and the adhesive strength of single adhesive disc and by finally elucidating the adhesion mechanism in cellular and molecular level using the classical theories and the proposed new hypothesis and model. I have measured that a single mature adhesive disc has an average mass of only about 0.0005 g, an average attached area of about 1.22 sq mm and an adhesive force of about 13.7 N. I have found that a single adhesive disc can on average support a weight produced together by the stem, leaf, branchlet and tendril which is 260 times greater than its own weight during the growing, and can sustain the maximum pulling force which is 2,800,000 times higher than that produced by its own weight. Microscopic experiments show some new microstructures which have never been reported and reveal that the adhesive disc has super adhesive property which inspires us to fabricate a lot of mimic adhesives that have potential applications in biomedical science, bioelectronics and space science and technology.
Eukaryotic translation initiation machinery can operate in a prokaryotic-like mode without eIF2
Authors: Shatsky Ivan , Terenin Ilya , Dmitriev Sergey , Andreev Dmitri 
Published: July 2019

AbstractUnlike prokaryotes, a specialized eukaryotic initiation factor 2 (eIF2), in the form of the ternary complex eIF2*GTP*Met-tRNAiMet is utilized to deliver the initiator tRNA to the ribosome within all eukaryotic cells1. Phosphorylation of eIF2 is known to be central to the global regulation of protein synthesis under stress conditions and infection2. Another distinctive feature of eukaryotic translation is scanning of mRNA 5'-leaders, whose origin in evolution may be relevant to the appearance of eIF2 in eukaryotes. Translation initiation on the hepatitis C virus (HCV) internal ribosome entry site (IRES) occurs without scanning3,4. Whether these unique features of the HCV IRES account for the formation of the final 80S initiation complex is unknown. Here we show that the HCV IRES-directed translation can occur without either eIF2 or its GTPase activating protein eIF5. In addition to the general eIF2- and eIF5-dependent pathway of 80S complex assembly, the HCV IRES makes use of a prokaryotic-like pathway which involves eIF5B, the analogue of bacterial IF25,6, instead of eIF2. This switch from a eukaryotic-like mode of AUG selection to a "bacterial" one occurs when eIF2 is inactivated by phosphorylation, a way with which host cells counteract infection. The relative resistance of HCV IRES-directed translation to eIF2 phosphorylation may represent one more line of defense used by this virus against host antiviral responses and can contribute to the well known resistance of HCV to interferon based therapy.
Shelling the Voronoi interface of protein-protein complexes predicts residue activity and conservation
Authors: Bouvier Benjamin , Grünberg Raik , Nilges Michael , Cazals Frederic 
Published: July 2019

AbstractThe accurate description of protein-protein interfaces remains a challenging task. Traditional criteria, based on atomic contacts or changes in solvent accessibility, tend to over or underpredict the interface itself and cannot discriminate active from less relevant parts. A recent simulation study by Mihalek and co-authors (2007, JMB 369, 584-95) concluded that active residues tend to be `dry', that is, insulated from water fluctuations. We show that patterns of `dry' residues can, to a large extent, be predicted by a fast, parameter-free and purely geometric analysis of protein interfaces. We introduce the shelling order of Voronoi facets as a straightforward quantitative measure of an atom's depth inside an interface. We analyze the correlation between Voronoi shelling order, dryness, and conservation on a set of 54 protein-protein complexes. Residues with high shelling order tend to be dry; evolutionary conservation also correlates with dryness and shelling order but, perhaps not surprisingly, is a much less accurate predictor of either property. Voronoi shelling order thus seems a meaningful and efficient descriptor of protein interfaces. Moreover, the strong correlation with dryness suggests that water dynamics within protein interfaces may, in first approximation, be described by simple diffusion models.
Shelling the Voronoi interface of protein-protein complexes predicts residue activity and conservation
Authors: Bouvier Benjamin , Grünberg Raik , Nilges Michael , Cazals Frederic 
Published: July 2019

AbstractThe accurate description and analysis of protein-protein interfaces remains a challenging task. Traditional definitions, based on atomic contacts or changes in solvent accessibility, tend to over- or underpredict the interface itself and cannot discriminate active from less relevant parts.We here extend a fast, parameter-free and purely geometric definition of protein interfaces and introduce the shelling order of Voronoi facets as a novel measure for an atom's depth inside the nterface. Our analysis of 54 protein-protein complexes reveals a strong correlation between Voronoi Shelling Order (VSO) and water dynamics. High Voronoi Shelling Order coincides with residues that were found shielded from bulk water fluctuations in a recent molecular dynamics study. Yet, VSO predicts such "dry" residues at dramatically reduced cost and without consideration of forcefields or dynamics. More central interface positions are often also increasingly enriched for hydrophobic residues. Yet, this hydrophobic centering is not universal and does not mirror the far stronger geometric bias of water fluxes. The seemingly complex water dynamics at protein interfaces appears thus largely controlled by geometry. Sequence analysis supports the functional relevance of both dry residues and residues with high VSO, both of which tend to be more conserved. However, upon closer inspection, the spatial distribution of conservation argues against the arbitrary dissection into core or rim and thus refines previous results. Voronoi Shelling Order reveals clear geometric patterns in protein interface composition, function and dynamics and facilitates the comparative analysis of protein-protein interactions.
Sensitivity Analysis of Self-Identified Race and Ethnicity (SIRE): Screening for Single Nucleotide Polymorphisms.
Authors: Miles Toni , Hanson Stephen , Kidd LaCreis , Connor Avonne , Jortani Saeed 
Published: July 2019

AbstractWithin the realm of medical care, Self-Identified Race and Ethnicity (SIRE) categories are promoted as an inexpensive tool to identify underlying genotypic diversity. Scientific opinion is divided about the adequacy of SIRE to serve this function. If genetic diversity can guide medical decisions, it is important to know the effectiveness of genetic screening via SIRE. Proper development of self-reported measures such as SIRE requires sensitivity and specificity studies. These types of formal evaluation are largely absent for SIRE. To begin this formal process, we estimate the sensitivity of SIRE in screening for variant Single Nucleotide Polymorphism (SNP). Our results indicate that the current use of SIRE is inadequate to screen for selected biotransformation related SNP in the N-Acetyl Transferase pathway. The widespread usage of SIRE to screen for genotypic diversity could promote erroneous assignment of patients to disease risk or therapeutic categories.
Isoprene Emission and Carbon Dioxide Protect Aspen Leaves from Heat Stress
Authors: Darbah Joseph , Sharkey Thomas , Karnosky David 
Published: July 2019

AbstractHigh temperature, especially above 35oC, is known to reduce leaf photosynthetic rate in many tree species. This study investigated the effect of high temperature on isoprene-emitting (aspen) and non- emitting (birch) trees under ambient and elevated CO2 under open field conditions. Aspen trees tolerate heat better than birch trees and elevated CO2 protects both species against moderate heat stress. The increased thermotolerance in aspen trees compared to the birch trees may result from the aspen's ability to produce isoprene. Elevated CO2 increased carboxylation capacity, photosynthetic electron transport capacity and triose phosphate use in both birch and aspen trees. High temperature decreased all of these parameters in birch regardless of CO2 treatment but only photosynthetic electron transport and triose phosphate use at ambient CO2 were reduced in aspen. As temperature rises, non-isoprene-emitting trees will be at a disadvantage and biological diversity and species richness might be lost in some ecosystems. Our results indicate that isoprene emitting tree species will have an advantage over non-isoprene emitting ones under high temperatures.
Tumor-associated EGFR over-expression specifically activates Stat3 and Smad7 resulting in desensitization of TGF-β signaling
Authors: Luwor Rodney , Taylor Lauren , Wang Bo , Zhu Hong-Jian 
Published: July 2019

AbstractTransforming Growth Factor-[beta] (TGF-[beta]) and Epidermal Growth Factor (EGF) signaling pathways are both independently implicated as key regulators in tumor formation and progression. Here, we demonstrate that activation of the tumor-associated and over-expressed EGFR desensitizes TGF-[beta] signaling and its cytostatic regulation through specific Stat3 activation and Smad7 induction. In normal and tumor human cell lines, reduction of TGF-[beta]-mediated Smad2 phosphorylation, nuclear translocation and Smad3 target gene activation were observed where EGFR is over-expressed, but not in cells which expressed EGFR at normal levels. The EGFR downstream signaling molecules phosphatidyinositol-3 Kinase (PI3K) or mitogen-activated protein kinase/ERK kinase (MEK) are not responsible for the down-regulation of TGF-[beta] signaling since blockade of them by specific pharmacological inhibitors LY294002 and U0126 had little effects on the sensitivity of TGF-[beta] signaling. We identified Stat3 as a signaling molecule activated specifically and persistently by over-expressed EGFR, but not by normal levels. Importantly, Stat3 is responsible for the reduced TGF-[beta] sensitivity, since its knockdown by siRNA restored TGF-[beta] signaling sensitivity. Furthermore, over-expressed EGFR, through Stat3 activates Smad7 promoter activity, increasing its protein levels, which is a negative regulator of TGF-[beta] signaling. Consequently, cells were re-sensitized to TGF-[beta] when Smad7 expression was reduced using siRNA. Therefore we establish a novel EGFR-Stat3-Smad7-TGF-[beta] signaling molecular axis where tumor-associated over-expression of EGFR in epithelial cells results in hyperactivation of Stat3, which activates Smad7 expression, compromising the TGF-[beta]'s cytostatic regulation of epithelium and consequent tumor formation.
New Spontaneous Model of Fibrodysplasia Ossificans Progressiva
Authors: Rothschild Bruce , Martin Larry , Timm Robert 
Published: July 2019

AbstractWe report the first known example of spontaneous, naturally occurring fibrodysplasia ossificans progressiva (FOP) in a mammal. The Southeast Asian mouse deer of the genus Tragulus (Artiodactyla: Tragulidae) have an osseous sheath covering the lower back and upper thigh region consistent with the clinical definition of FOP. This heterotophic bone deposition is sex related apparently with a genetic basis - it only occurs in males and is lacking in females; it is present in all adults males, including both wild obtained and zoo bred animals. Tragulus may offer the opportunity to examine many of the disease's most significant attributes experimentally.
Role and immunomodulatory profile of histamine receptors by H1 and H2 antagonists
Authors: Tripathi Trivendra , Shahid Mohd. , Siddiqui Mashiatullah , Khan Rahat 
Published: July 2019

AbstractThe present study was designed to delineate the immunomodulatory role of histamine receptors (H1- and H2-) on induction of antibody response to sheep red blood cells (SRBC), as well as the antibody generation profile, in rabbit system, systemically. The rabbits in two groups received pheniramine (H1-receptor antagonist) and ranitidine (H2-receptor antagonist), respectively, via intramuscular route and were immunized with SRBC intravenously to evaluate suppression or enhancement of antibody responses in sem. A third, control group, received vehicle and were immunized in a similar manner. Histamine released from effector cells (mast cells and basophils) in vivo during inflammatory reactions could influence a detectable antibody response to SRBC as early as day 7-postimmunization (post-I), which lasted until day 28- post-I. Pheniramine-treated rabbits had significantly (&42;Pa &le; 0.05 and &42;&42;Pa &le; 0.01) more suppressed total serum antibody (IgM + IgG) to SRBC as compared to ranitidine-treated ad cotrol rabbits, while ranitidine-treated rabbits showed different pattern (suppressed or enhanced) during the whole study period. Ranitidine suppressed total antibody level at days 7- and 14- post-I, and enhanced at days 21- and 28- post-I. IgM suppression at day 7- and enhancement at days 14-, 21- and 28- post-I, while IgG suppression during whole study period, as compared to control group was significant (&42;Pa &le; 0.05 and &42;&42;Pa &le; 0.01) as assessed by direct hemagglutination assay&42; ad whole SBC-ELISA method&42;&42;. Here we report that histamine receptor type 2 (H2R)-antagonists have a dominant role on immunosuppression and in immunoregulation of humoral immune responses. Histamine receptor type 2 (H2R)-antagonists are mainly involved in B cell differentiation and proliferation over histamine receptor type 1 (H1R)-antagonists.
Dual expression recombinase based (DERB) single vector system for high throughput screening and verification of protein interactions in living cells
Authors: Lu JianPing , Beatty Laura , Pinthus Jehonathan 
Published: July 2019

AbstractIdentification of novel protein interactions and their mediators is fundamental in understanding cellular processes and is necessary for protein-targeted therapy. Evidently high throughput formatting of these applications in living cells would be beneficial, however no adequate system exists. We present a novel platform technology for the high throughput screening and verification of protein interactions in living cells. The platform's series of Dual Expression Recombinase Based (DERB) destiny vectors individually encode two sets of recombinase recognizable sequences for inserting the protein open reading frame (ORF) of interest, two sets of promoters and reporter tags in frame with the ORFs for detecting interactions. Introduction into living cells (prokaryotic and eukaryotic) enables the detection of protein interactions by fluorescence resonance energy transfer (FRET) or bimolecular fluorescence complementation (BiFC). The DERB platform shows advantages over current commercialized systems by DERB vectors validated through proof-of-principle experiments and the identification of an unknown interaction.
Posterior parietal cortex controls spatial attention through modulation of anticipatory alpha rhythms
Authors: Capotosto Paolo , Babiloni Claudio , Romani Gian Luca , Corbetta Maurizio 
Published: July 2019

AbstractA dorsal fronto-parietal network, including regions in intra-parietal sulcus (IPS) and frontal eye field (FEF), has been hypothesized to control the allocation of spatial attention to environmental stimuli. One putative mechanism of control is the de-synchronization of electroencephalography (EEG) alpha rhythms (~8-12 Hz) in parieto-occipital cortex in anticipation of a visual target. We show that brief interference by transcranial magnetic stimulation (rTMS) with preparatory activity in right IPS or right FEF while subjects attend to a spatial location impairs identification of target stimuli ~2 seconds later. Moreover, the visual deficit relates to the disruption of anticipatory (pre-stimulus) alpha desynchronization and its topography in parieto-occipital cortex. After right IPS stimulation, the degree to which alpha desynchronization is suppressed predicts the speed of visual identification. These results demonstrate the causal role of posterior parietal cortex in the control of visuo-spatial attention exerted through the synchronization of visual neurons.
Altruism among relatives and non-relatives
Authors: Rachlin Howard , Jones Bryan 
Published: July 2019

AbstractThe amount of their own monetary reward that undergraduate participants claimed they were willing to forgo, in order to give $75 to another person, decreased hyperbolically as social distance increased between the participant and the other person. Relatives tended to be ranked at closer social distances than were non-relatives. However, even at the same social distance, participants were willing to forgo significantly more money for the benefit of relatives than for the benefit of non-relatives. These results imply that altruism is determined by factors in addition to social distance.
Chemical Physics of Phonons & Superconductivity: A Heuristic Approach
Authors: Bucknum Michael 
Published: July 2019

AbstractSeveral lines of thought are pursued in an attempt to further clarify the role played by phonons in the theory of superconductivity. The central results of BCS theory are examined in the context of anharmonicity in the phonon motion and the role that Badger's rule of spectroscopy can play in simplifying and making more chemically intuitive the nature of the mechanism of superconductivity.
Structural dynamics and divergence of the polygalacturonase gene family in land plants
Authors: Kwon Soon-Jae , Son Jae-Han , Park Kyong-Cheul , Oh Hae-Young , Kim Pyeung-Hyeun , Byeon Woo-Hyeon , Kim Nam-Soo 
Published: July 2019

AbstractA distinct feature of eukaryotic genomes is the presence of gene families. The polygalacturonase (PG) (EC3.2.1.15) gene family is one of the largest gene families in plants. PG is a pectin-digesting enzyme with a glycoside hydrolase 28 domain. It is involved in numerous plant developmental processes. The evolutionary processes accounting for the functional divergence and the specialized functions of PGs in land plants are unclear. Here, phylogenetic and gene structure analysis of PG genes in algae and land plants revealed that land plant PG genes resulted from differential intron gain and loss, with the latter event predominating. PG genes in land plants contained 15 homologous intron blocks and 13 novel intron blocks. Intron position and phase were not conserved between PGs of algae and land plants but conserved among PG genes of land plants from moss to vascular plants, indicating that the current introns in the PGs in land plants appeared after the split between unicellular algae and multicelluar land plants. These findings demonstrate that the functional divergence and differentiation of PGs in land plants is attributable to intronic loss. Moreover, they underscore the importance of intron gain and loss in genomic adaptation to selective pressure.
GESTATION LENGTH OF KARI SHEEP
Authors: Ahmad Sohail 
Published: July 2019

AbstractPreviously, the concept of a gestation period of sheep shorter than 121 days was unheard of in the field of sheep biology. Our findings during a farmers’ survey in the Lotkho area of Chitral, Pakistan, revealed that the sheep native to the region, locally called “Kari”, gestates for a period of only three months. This duration is 25-40% short of the usual gestation length and is shorter than ever recorded for the species. The mean and mode gestation length (GL) was 110 and 92 days respectively and was concentrated in three distinct clusters: day 87-95, 120-123 and 151-153, accounting for 52% of all observations. GL was influenced by location, season of conception and lambing and the interaction of location with season; had an estimated repeatability of zero. The mean lambing interval was 224.7 ±5.24 days, ranging between 109 and 467 days. During a trial conducted in a controlled environment, only three out of the 27 copulated ewes conceived, and gestated in 113, 125 and 145 days respectively. Gestation length during the trial supported field findings. The results suggest that GL in Kari sheep is unusual as many ewes gestated in three months, with variations of up to 5 months. Genotype by environment interaction is a possibility. However, reasons for the findings are still not clear and further controlled studies should be carried out to establish and further explore the factor(s) responsible for this unusual and unique manifestation of the Kari with regards to its gestation length.