bluuebunny/crossref_metadata_2025_split huggingface dataset:
The largest reservoir of mitochondrial introns is a relic of an ancestral split gene
Authors: Ferandon Cyril , Moukha Serge , Callac Philippe , Benedetto Jean-Pierre , Castroviejo Michel , Barroso Gerard 
Published: July 2019

AbstractIn eukaryotes, introns are located in nuclear and organelle genes from several kingdoms (ref. 1-4). Large introns (0.1 to 5 kbp) are frequent in mitochondrial genomes of plant and fungi (ref. 1,5) but scarce in Metazoa, despite these organisms are grouped with fungi among Opisthokonts. Introns are classified in two main groups (I and II) according to their RNA secondary structure involved in the intron self-splicing mechanism (ref. 5,6). Most of the group I introns carry a "Homing Endonuclease Gene" (ref. 7-9) encoding a DNA endonuclease acting in the transfer and site specific integration "homing") and allowing the intron spreading and gain after lateral transfer even between species from different kingdoms (ref. 10,11). Opposite to this "late intron" paradigm, the "early intron" theory indicates that introns, which would have been abundant in the ancestral genes, would mainly evolve by loss (ref. 12,13).Here we report the sequence of the cox1 gene of the button mushroom Agaricus bisporus, the most worldwide cultivated mushroom. This gene is both the longest mitochondrial gene (29,902 nt) and the largest Group I intron reservoir reported to date. An analysis of the group I introns available in cox1 genes shows that they are ancestral mobile genetic elements, whose frequent events of loss (according to the "late theory") and gain by lateral transfer ("early theory") must be combined to explain their wide and patchy distribution extending on several kingdoms. This allows the conciliation of the "early" and "late intron" paradigms, which are still matters of much debate (ref. 14,15). The overview of the intron distribution indicates that they evolve towards elimination. In such a landscape of eroded and lost intron sequences, the A. bisporus largest intron reservoir, by its singular dynamics of intron keeping and catching, constitutes the most fitted relic of an early split gene.
Is severity of clinical manifestations following H. lepturus envenomation related to serum TNF-&alpha; level?
Authors: Jalali Amir , Pipelzadeh Mohammad , Taraz Mohammad , Khodadadi Ali , Makvandi Manoochr 
Published: July 2019

AbstractThirty six patients, with varying degrees of severity of envenomation, because of envenomation by Hemiscorpius lepturus scorpion, were systematically investigated. The serum levels (by double-ligand ELIZA kit) of interlukin-1 (IL-1), interlukin-6 (IL-6), interlukin-8 (IL-8) and tumor necrosis factor-&alpha; (TNF- &alpha;) were compared with 30 healthy controls and 10 age-matched patients envenomed by Mesobuthus eupeus scorpion. Blood samples from M. eupeus and H. lepturus victims were taken on admission and once more after 6 hr after serotherapy with multivalent antivenom from H. lepturus envenomed subjects. The results suggest that, unlike M. eupeus, the toxic manifestations observed following H lepturus may be associated with increase in serum TNF-&alpha; level and are positively correlated with its severity.
The model of proteolysis
Authors: Dittwald Piotr , Gambin Anna 
Published: July 2019

AbstractThis document presents the original approach for estimating parameters of proteolysis process. Data used to fit the model are taken from massspectrometric experiments. For parameters estimation the Levenberg-Marquadt algorithm is used. The motivation for model is a hypothesisthat discrimination between cancer patients and healthy donors can be based on activity of peptide cleaving enzymes (i.e. peptidases).
p53 Response to DNA Damage in S-phase
Authors: Reisman David , Takahashi Paula , Polson Amanda 
Published: July 2019

Abstractp53 induces the transcription of genes that negatively regulate progression of the cell cycle in response to DNA damage or other cellular stressors, and thus participates in maintaining genome stability. Under stress conditions, p53 must be activated to prohibit the replication of cells containing damaged DNA. However, in normal, non-stressed cells, p53 activity must be inhibited. Previous studies have demonstrated that p53 transcription is activated before or during early S-phase in cells progressing from G0/G1 into S-phase. In that this is not what would be predicted from a gene involved in growth arrest and apoptosis, in this study, we provide evidence that this induction occurs to provide available p53 mRNA in order to prepare the cell for DNA damage in S-phase, ensuring a rapid response to DNA damage before exiting this stage. When comparing exponential to synchronized Swiss3T3 cells upon Camptothecin-induced DNA damage, we found that in synchronized cells, p53 protein levels increased earlier, Bax and p21 transcription was activated earlier and to a greater extent and apoptosis occurred earlier and to a greater extent. These findings are consistent with p53 transcription being induced in S-phase to provide for a rapid DNA-damage response during S-phase of the cell cycle.
Genome Structural-Functional Peculiarities Affecting Plant Epigenetic Variability and Evolution
Authors: Levites Evgenii 
Published: July 2019

AbstractThere is an attempt to explain some evolutionary processes in plants such as saltatory changes on the base of multidimensionality of plant inherited information coding. According to the suggested hypothesis, inherited information is coded by not only a nucleotide sequence but also by chromosome differential endoreduplication. It is supposed that chromosomes compete among each other for the contact with the nuclear membrane, but a change in the endoreduplication degree of various chromosome sites can result in a change of a competition ability for the contact with a nuclear membrane. A simultaneous increase of chromosome endoreduplication degree of many sites can lead to an increase of nuclear membrane surface and to a change in chromosome competitive interrelations and, respectively, to a change of activity of many genes. Phenotypicaly it may manifest itself as a saltatory change of many traits.
Prolonged maturation of prefrontal white matter in chimpanzees
Authors: Sakai Tomoko , Hirai Daichi , Mikami Akichika , Suzuki Juri , Hamada Yuzuru , Tomonaga Masaki , Tanaka Masayuki , Miyabe-Nishiwaki Takako , Makishima Haruyuki , Nakatsukasa Masato , Matsuzawa Tetsuro 
Published: July 2019

AbstractDelayed maturation in the prefrontal cortex, a brain region associated with complex cognitive processing, has been proposed to be specific to humans. However, we found, using a longitudinal design, that prefrontal white matter volume in chimpanzees increased gradually with age, and the increase appears to continue beyond the onset of puberty, as in humans. This provides the first evidence for a prolonged period of prefrontal connection elaboration in great apes.
Defective FoxP3+ Treg cell differentiation in the gut of Type 1 Diabetic patients
Authors: Badami Ester , Sorini Chiara , Coccia Margherita , Molteni Laura , Bolla Andrea Mario , Scavini Marina , Mariani Alberto , Bosi Emanuele , Falcone Marika 
Published: July 2019

AbstractEnvironmental factors that act at the intestinal level such as diet, drugs, and microflora have a high impact on the pathogenesis of autoimmune Type 1 Diabetes (T1D), but it is still unclear how the gut milieu affects autoimmunity outside the intestine. Here we show that peripheral FoxP3+ Treg cell differentiation, a mechanism that takes place in the gut and is crucial to maintain systemic immune tolerance, is impaired in T1D patients. These results provide the first evidence that gut mucosa alteration could predispose to autoimmune T1D by affecting systemic immune regulation.
Resveratrol Increases Intracellular NAD+ Levels Through Up regulation of The NAD+ Synthetic Enzyme Nicotinamide Mononucleotide Adenylyltransferase
Authors: Grant Ross 
Published: July 2019

AbstractResveratrol is a polyphenol with major health benefits that is thought to operate through direct activation of the &apos;anti-aging&apos; enzyme SIRT1. However recent reports have challenged this &apos;direct-activation&apos; hypothesis, suggesting the mechanism by which resveratrol increases SIRT1 function is still unknown. We report for the first time that resveratrol induces a dose dependent increase in activity of the NAD+ synthetic enzyme nicotinamide mononucleotide adenylyl transferase (NMNAT1). Activation of NMNAT1 by resveratrol in cultured primary human astrocytes and neurons increased NAD+ levels by up to 5 fold. As SIRT1 requires NAD+ as a substrate to perform its gene silencing function, higher NAD+ levels will enhance SIRT1 activity. This finding suggests that resveratrol may promote SIRT1 function by enhancing NAD+ synthesis in whole cell systems without requiring direct activation.
Ediacaran Macro Body Fossils
Authors: Huang Timothy , Shaw Jei-Fu , Zheng Liang , Huang Chun-Lan , Chang YiLung , Yang ChuanWei 
Published: July 2019

AbstractThis paper, Ediacaran Macro Body Fossils, reports a new discovery of well preserved three dimensional macro body fossils of the Ediacaran Period in central YunNan province in the People's Republic of China. These body fossils will enable more detailed and in-depth exploration of the evolution of multi-cellular macro organisms on this planet, whereas in the past, researches could only rely on cast or imprint fossils.
Effect of p21Waf1 and p27Kip1 on centrosome replication and proliferation of breast cancer cell
Authors: Li Fu-Nian , Jiang Dan-Dan , Liu Xiang-Ping , Ge Yin-Lin , Cao Ming-Zhi , Wang Xin-Gang 
Published: July 2019

AbstractAberrant centrosome numbers are detected in virtually all cancersincreasing the risk for cell division errors and chromosomal instability. Deregulation of the centrosome duplication cycle is considered as the major contributing factor for abnormal amplification of centrosomes. p21Waf1 and p27Kip1, general CDK inhibitors by inhibiting cyclin-dependent kinase 2 (CDK2)/cyclin E and cyclin A complexes, controlled the initiation and progress of centrosome duplication . We transfected p21 Waf1, p27 Kip1 or p21 Waf1- p27 Kip1 genes into MCF-7 cells by lipofection to explore the effect of the genes on centrosome duplication and proliferation of breast cancer cell. The result shows that the cell growth was obviously inhibited after being transfected, resulting in an accumulation of cells in G1 and the proportion of cells which contained abnormal centrosomes was obviously decreased. Comparing with p21 Waf1or p27 Kip1, the effects of p21Waf1- p27 Kip1 genes are more significative. These results suggest that p21Waf1 and p27Kip1 genes could inhibit the growth of human breast cancer cells and reverse abnormal duplication of centrosomes. p21Waf1 and p27Kip1 cooperate to regulate centrosome duplication and cell cycle progress, indicating p21 Waf1- p27 Kip1 combined gene might be potential therapeutic agents of breast cancer which reveals suppressed p21Waf1 and p27Kip1 expression.
Cellular delivery of antibodies: effective targeted subcellular imaging and new therapeutic tool
Authors: Massignani Marzia , Canton Irene , Patikarnmonthon Nisa , Warren Nicholas , Armes Steven , Lewis Andrew , Battaglia Giuseppe 
Published: July 2019

AbstractIt is already more than a century since the pioneering work of the Nobel Laureate Ehrlich gave birth to the side chain theory1, which helped to define antibodies and their ability to target specific biological sites. However, the use of antibodies is still restricted to the extracellular space due to the lack of a suitable delivery vehicle for the efficient transport of antibodies into live cells without inducing toxicity. In this work, we report the efficient encapsulation and delivery of antibodies into live cells with no significant loss of cell viability or any deleterious affect on the cell metabolic activity. This delivery system is based on poly(2-(methacryloyloxy)ethyl phosphorylcholine)-block-(2-(diisopropylamino)ethyl methacrylate), (PMPC-PDPA), a pH sensitive diblock copolymer that self-assembles to form nanometer-sized vesicles, also known as polymersomes, at physiological pH. These polymersomes can successfully deliver relatively high antibody payloads within live cells. Once inside the cells, we demonstrate that these antibodies can target their epitope by immune-labelling of cytoskeleton, Golgi, and transcription factor proteins in live cells. We also demonstrate that this effective antibody delivery mechanism can be used to control specific subcellular events, as well as modulate cell activity and pro-inflammatory process.
Thermal signatures of human pheromones in sexual and reproductive behaviour
Authors: Mazzatenta Andrea , Romani Gian Luca , Tommasi Luca , Merla Arcangelo 
Published: July 2019

AbstractChemically mediated sexual communication in humans has been largely neglected due to its non-conscious and relatively concealed nature. However, menstrual cycle synchronisation, puberty onset in young pre-pubertal girls exposed to their stepfather, and consanguinity avoidance suggest a function in the physiological regulation of sexual and reproductive behaviour in humans. These phenomena are related to activation of the limbic system by pheromones. On the basis of sexually dimorphic activation of brain hypothalamic areas and the control of body temperature via the hypothalamus, our hypothesis is that human sexual pheromones can induce thermal effects that can be revealed by high-resolution thermal infrared imaging. Here we show that in women, male sexual pheromones induce thermal effects that are linked to the ovarian cycle. These findings suggest a dramatic influence of pheromones on human sexual and reproductive behaviour through neuroendocrine brain control, established on the plesiomorphic nature of chemical communication across species.
Laboratory and field evaluation for the resistance of commonly used woods against Coptotermes heimi (Wasmann).
Authors: Manzoor Farkhanda , Sheikh Nadeem , Zawar Asma 
Published: July 2019

AbstractThe current study was conducted to evaluate the resistance of four wood species (Azadirachta indica, Pinus roxberghii, Dalbergia sissoo and Populus deltoides) against subterranean termite species Coptotermes heimi by choice and no choice field and laboratory trials. Of these four wood species P. roxberghii and D. sissoo proved to be most resistant to termite attack. Taken together these results we can conclude that D. sissoo is the least preferred and P. deltoides is the most preferred wood by the C. heimi. The data obtained from the field choice and no-choice the woods are arranged in order of preference DS>PR>AI>PD whereas in laboratory choice and no-choice trials the order of preference was PD>AI>PR>DS.
Extending the Modern Synthesis: The evolution of ecosystems
Authors: Wallace Rodrick 
Published: July 2019

AbstractThe Modern Evolutionary Synthesis formalizes the role of variation, heredity, differential reproduction and mutation in population genetics. Here we explore a mathematical structure, based on the asymptotic limit theorems of information theory, that instantiates the punctuated dynamic relations of organisms and their embedding environments. The mathematical overhead is considerable, and we conclude that the model must itself be extended even further to allow the possibility of the transfer of heritage information between different classes of organisms. In essence, we provide something of a formal roadmap for the modernization of the Modern Synthesis.
Extending the Modern Synthesis: The evolution of ecosystems
Authors: Wallace Rodrick 
Published: July 2019

AbstractThe Modern Evolutionary Synthesis formalizes the role of variation, heredity, differential reproduction, and mutation in population genetics. Here we explore a mathematical structure, based on the asymptotic limit theorems of communication theory, that instantiates the punctuated dynamic relations of organisms with their embedding environments, including the possibility of the transfer of heritage information between different classes of organisms. In essence, we provide something of a formal roadmap for the modernization of the Modern Synthesis, making application to both relatively rapid evolutionary punctuated equilibrium and to the conservation of ecological interactions across deep evolutionary time.
Global Network Alignment
Authors: Kuchaiev Oleksii , Przulj Natasa 
Published: July 2019

AbstractMotivation: High-throughput methods for detecting molecular interactions have lead to a plethora of biological network data with much more yet to come, stimulating the development of techniques for biological network alignment. Analogous to sequence alignment, efficient and reliable network alignment methods will improve our understanding of biological systems. Network alignment is computationally hard. Hence, devising efficient network alignment heuristics is currently one of the foremost challenges in computational biology. Results: We present a superior heuristic network alignment algorithm, called Matching-based GRAph ALigner (M-GRAAL), which can process and integrate any number and type of similarity measures between network nodes (e.g., proteins), including, but not limited to, any topological network similarity measure, sequence similarity, functional similarity, and structural similarity. This is efficient in resolving ties in similarity measures and in finding a combination of similarity measures yielding the largest biologically sound alignments. When used to align protein-protein interaction (PPI) networks of various species, M-GRAAL exposes the largest known functional and contiguous regions of network similarity. Hence, we use M-GRAAL’s alignments to predict functions of un-annotated proteins in yeast, human, and bacteria C. jejuni and E. coli. Furthermore, using M-GRAAL to compare PPI networks of different herpes viruses, we reconstruct their phylogenetic relationship and our phylogenetic tree is the same as sequenced-based one.
Generalised and abdominal adiposity are important risk factors for chronic disease in older people: results from a nationally representative survey
Authors: Hirani Vasant 
Published: July 2019

Abstract
Objective:
To look at the trends in prevalence of generalised (body mass index (BMI)&8805; 25 kg/m2) and abdominal obesity (waist circumference (WC) &gt;102cm, men; &gt;88cm, women) among older people from 1993 to 2008, prevalence of chronic disease by overweight/obesity and waist circumference categories in England 2005 and evaluate the association of these measures with chronic diseases. Methods: Analyses of nationally representative cross-sectional population surveys, the Health Survey for England (HSE), including non-institutionalised men and women aged &8805;65years.

Results:
Generalised obesity and abdominal obesity increased among men and women from 1993 to 2008. In 2005, the HSE 2005 focussed on older people. 72% of men and 68% of women aged over 65 were either overweight or obese. Prevalence of raised WC was higher in women (58%) than in men (46%). Multivariate analysis confirmed that generalised and abdominal obesity were independently associated with risk of hypertension, diabetes and arthritis in both men and women. In women only, there was an association between generalised obesity and having a fall in the last year (OR: 1.5), and between abdominal obesity and having a joint replacement (OR: 1.9, p=0.01) Conclusion: Complications of obesity such as diabetes, hypertension and arthritis, are more common in men and women aged over 65 who are overweight or obese, as well as in those with a raised waist circumference. These conditions impact on morbidity, mortality and have cost implications for the health service and are known to improve with weight loss even in old age. Treatment strategies to address these conditions such as weight management and prevention of overweight and obesity are important even in older people. There is a need to ensure that older people are given appropriate advice about keeping physically active and eating sensibly.
Aqueous phase hydration and hydrate acidity of perfluoroalkyl and n:2 fluorotelomer aldehydes
Authors: Rayne Sierra , Forest Kaya 
Published: July 2019

AbstractPerfluoroalkyl aldehydes (PFAlds) and n:2 fluorotelomer aldehydes (FTAlds) are degradation products of precursor compounds that include fluorotelomer alcohols, iodides, acrylates, phosphate esters, and other derivatives, as well as hydrofluorocarbons and hydrochlorofluorocarbons. The SPARC software program and comparative density functional theory (DFT) calculations were used to investigate the aqueous phase hydration equilibrium constants (K~hyd~) of PFAlds and FTAlds. DFT studies suggest that all PFAlds will be dominantly present as the hydrated form in aqueous solution. While SPARC correctly estimates the K~hyd~ for the C~1~ PFAld, it appears to incorrectly predict a large decline in K~hyd~ (particularly between C~1~ and C~2~) with increasing perfluoroalkyl chain length for this class of compounds. Both SPARC and DFT investigations suggest that FTAlds will not likely be substantially hydrated in aquatic systems or in vivo. Using corrected SPARC estimates, PFAld hydrates are expected to have pK~a~ values in the range of phenols (ca. 9 to 10), whereas n:2 FTAld hydrates are expected to have pK~a~ values ca. 2 to 3 units higher (ca. 12 to 13). Where relevant, the molecular and/or dissociated hydrate forms of PFAlds and FTAlds need to be explicitly considered in environmental, toxicological, and waste treatment investigations.
Calming down the seas: the near collapse of an Atlantic coastal fishery
Authors: Pita Pablo , Freire Juan 
Published: July 2019

AbstractFor years now the estimates of the consequences of overfishing for marine ecosystems have differed greatly within the scientific community^1^. The use of commercial catch statistics to estimate tendencies has been much criticised^2^, but alternative information sources with long time series are rare. Here we employ the historic archive (1953-2007) of the recreational spearfishery in Galicia (NW Spain), which does not have the problems common to other fishery registers, to estimate long-term changes in coastal ecosystems. Using generalized additive regression models (GAM) we estimated decreases of around 83% in the abundances of coastal fish over the last 50 years. In the same period the average body size decreased by 36%. In addition, the relative catch frequency has decreased for the most valuable commercial species. Commercial overfishing has brought these ecosystems so close to the brink of collapse that it is necessary to implement measures that ensure their recovery.