bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prediction of high anti-angiogenic activity peptides in silico using a generalized linear model and feature selection
Authors: Blanco Jose Liñares , Porto-Pazos Ana B. , Pazos Alejandro , Fernandez-Lozano Carlos 
Published: October 2018

AbstractScreening and in silico modeling are critical activities for the reduction of experimental costs. They also speed up research notably and strengthen the theoretical framework, thus allowing researchers to numerically quantify the importance of a particular subset of information. For example, in fields such as cancer and other highly prevalent diseases, having a reliable prediction method is crucial. The objective of this paper is to classify peptide sequences according to their anti-angiogenic activity to understand the underlying principles via machine learning. First, the peptide sequences were converted into three types of numerical molecular descriptors based on the amino acid composition. We performed different experiments with the descriptors and merged them to obtain baseline results for the performance of the models, particularly of each molecular descriptor subset. A feature selection process was applied to reduce the dimensionality of the problem and remove noisy features – which are highly present in biological problems. After a robust machine learning experimental design under equal conditions (nested resampling, cross-validation, hyperparameter tuning and different runs), we statistically and significantly outperformed the best previously published anti-angiogenic model with a generalized linear model via coordinate descent (glmnet), achieving a mean AUC value greater than 0.96 and with an accuracy of 0.86 with 200 molecular descriptors, mixed from the three groups. A final analysis with the top-40 discriminative anti-angiogenic activity peptides is presented along with a discussion of the feature selection process and the individual importance of each molecular descriptors According to our findings, anti-angiogenic activity peptides are strongly associated with amino acid sequences SP, LSL, PF, DIT, PC, GH, RQ, QD, TC, SC, AS, CLD, ST, MF, GRE, IQ, CQ and HG.
Culture conditions and nutrition requirements for the mycelial growth of Isaria farinosa (Hypocreales: Cordycipitaceae) and the altitude effect on its growth and metabolome
Authors: Liu Fei , Xiang Meichun , Guo Yanlei , Wu Xiaoli , Lu Guangxin , Yang Yong , Liu Xingzhong , Chen Shijiang , Zhang Guozhen , Shi Wangpeng 
Published: October 2018

AbstractIsaria farinosa is a pathogen of alpine Thitarodes larvae that are hosts for the Chinese medicinal fungus, Ophiocordyceps sinensis. A matrix analysis indicated that the optimal culture conditions for the mycelial growth of I. farinosa are a 50-mL liquid broth in a 250-mL flask at more than 100-rpm rotation and 15–25 °C. Illumination does not affect the mycelial growth. The optimal nutrition requirements are D-(+)-galactose and D-(−)-fructose as carbon resources and D-cysteine as well as yeast powder, peptone, and beef extract as nitrogen resources at a carbon-to-nitrogen ratio of 1:1 to 1:7. The mineral component and vitamins also significantly increase the mycelial growth of I. farinosa. Based on the optimal culture conditions and nutrition requirements for the mycelial growth of I. farinosa, the effects of altitude on mycelial growth and its metabolome were evaluated using quadrupole-time-of-flight/mass spectrometry, principal component analysis and partial least squares discriminant analysis. The altitude did not affect the mycelial production but significantly regulated its metabolome. The study presents a new approach to better select a method for producing more useful metabolites and highlights the necessity of establishing standards for culturing methods related to altitude to preserve fungal quality; additionally, the results indicate that the use of a fermenter may meet the demands of large-scale mycelial production.
Attenuated lipopolysaccharide-induced inflammatory bladder hypersensitivity in mice deficient of transient receptor potential ankilin1
Authors: Kamei Jun , Aizawa Naoki , Nakagawa Takayuki , Kaneko Shuji , Kume Haruki , Homma Yukio , Igawa Yasuhiko 
Published: October 2018

AbstractTransient receptor potential ankyrin 1 (TRPA1) channel expressed by urothelial cells and bladder sensory nerve fibers might act as a bladder mechanosensor and nociceptive transducer. To disclose the role of TRPA1 in bladder function and inflammation-associated hypersensitivity, we evaluated in vitro and in vivo bladder function and inflammatory mechanosensory and nociceptive responses to intravesical lipopolysaccharide (LPS)-instillation in wild type (WT) and TRPA1-knock out (KO) mice. At baseline before treatment, no significant differences were observed in frequency volume variables, in vitro detrusor contractility, and cystometric parameters between the two groups in either sex. LPS-instillation significantly increased voiding frequency and decreased mean voided volume at 24–48 hours after instillation in WT but not in TRPA1-KO mice. LPS-instillation also significantly increased the number of pain-like behavior at 24 hours after instillation in WT mice, but not in TRPA1-KO mice. Cystometry 24 hours after LPS-instillation revealed shorter inter-contraction intervals in the WT mice compared with TRPA1-KO mice. In contrast, inflammatory cell infiltration in the bladder suburothelial layer was not significantly different between the two groups. These results indicate that TRPA1 channels are involved in bladder mechanosensory and nociceptive hypersensitivity accompanied with inflammation but not in physiological bladder function or development of bladder inflammation.
An open quantum system approach to the radical pair mechanism
Authors: Adams Betony , Sinayskiy Ilya , Petruccione Francesco 
Published: October 2018

AbstractThe development of the radical pair mechanism has allowed for theoretical explanation of the fact that magnetic fields are observed to have an effect on chemical reactions. The mechanism describes how an external magnetic field can alter chemical yields by interacting with the spin state of a pair of radicals. In the field of quantum biology, there has been some interest in the application of the mechanism to biological systems. This paper takes an open quantum systems approach to a model of the radical pair mechanism in order to derive a master equation in the Born-Markov approximation for the case of two electrons, each interacting with an environment of nuclear spins as well as the external magnetic field, then placed in a dissipative bosonic bath. This model is used to investigate two different cases relating to radical pair dynamics. The first uses a collective coupling approach to simplify calculations for larger numbers of nuclei interacting with the radical pair. The second looks at the effects of different hyperfine configurations of the radical pair model, for instance the case in which one of the electrons interact with two nuclei with different hyperfine coupling constants. The results of these investigations are analysed to see if they offer any insights into the biological application of the radical pair mechanism in avian magnetoreception.
Characterizing Deformability of Drug Resistant Patient-Derived Acute Lymphoblastic Leukemia (ALL) Cells Using Acoustic Tweezers
Authors: Liu Hsiao-Chuan , Gang Eun Ji , Kim Hye Na , Lim Hae Gyun , Jung Hayong , Chen Ruimin , Abdel-Azim Hisham , Shung K. Kirk , Kim Yong-Mi 
Published: October 2018

AbstractThe role of cell mechanics in cancer cells is a novel research area that has resulted in the identification of new mechanisms of therapy resistance. Single beam acoustic (SBA) tweezers are a promising technology for the quantification of the mechanical phenotype of cells. Our previous study showed that SBA tweezers can be used to quantify the deformability of adherent breast cancer cell lines. The physical properties of patient-derived (primary) pre-B acute lymphoblastic leukemia (ALL) cells involved in chemotherapeutic resistance have not been widely investigated. Here, we demonstrate the feasibility of analyzing primary pre-B ALL cells from four cases using SBA tweezers. ALL cells showed increased deformability with increasing acoustic pressure of the SBA tweezers. Moreover, ALL cells that are resistant to chemotherapeutic drugs were more deformable than were untreated ALL cells. We demonstrated that SBA tweezers can quantify the deformability of nonadherent leukemia cells and discriminate this mechanical phenotype in chemotherapy-resistant leukemia cells in a contact- and label-free manner.
Successful cryopreservation of coral larvae using vitrification and laser warming
Authors: Daly Jonathan , Zuchowicz Nikolas , Nuñez Lendo C. Isabel , Khosla Kanav , Lager Claire , Henley E. Michael , Bischof John , Kleinhans F. W. , Lin Chiahsin , Peters Esther C. , Hagedorn Mary 
Published: October 2018

AbstractClimate change has increased the incidence of coral bleaching events, resulting in the loss of ecosystem function and biodiversity on reefs around the world. As reef degradation accelerates, the need for innovative restoration tools has become acute. Despite past successes with ultra-low temperature storage of coral sperm to conserve genetic diversity, cryopreservation of larvae has remained elusive due to their large volume, membrane complexity, and sensitivity to chilling injury. Here we show for the first time that coral larvae can survive cryopreservation and resume swimming after warming. Vitrification in a 3.5 M cryoprotectant solution (10% v/v propylene glycol, 5% v/v dimethyl sulfoxide, and 1 M trehalose in phosphate buffered saline) followed by warming at a rate of approximately 4,500,000 °C/min with an infrared laser resulted in up to 43% survival of Fungia scutaria larvae on day 2 post-fertilization. Surviving larvae swam and continued to develop for at least 12 hours after laser-warming. This technology will enable biobanking of coral larvae to secure biodiversity, and, if managed in a high-throughput manner where millions of larvae in a species are frozen at one time, could become an invaluable research and conservation tool to help restore and diversify wild reef habitats.
Haze smoke impacts survival and development of butterflies
Authors: Tan Yue Qian , Dion Emilie , Monteiro Antónia 
Published: October 2018

AbstractThe Southeast Asian transboundary haze contains a mixture of gases and particles from forest fires and negatively impacts people’s health and local economies. However, the effect of the haze on organisms other than humans has not yet been sufficiently studied. Insects are important members of food webs and environmental disturbances that affect insects may impact whole ecosystems. Here we studied how haze directly and indirectly affects the survival, growth, and development of insects by rearing Bicyclus anynana butterflies under artificially generated smoke as well as reared in clean air but fed on plants previously exposed to smoke. Direct haze exposure significantly increased the mortality of caterpillars, increased larval development time, and decreased pupal weight, while indirect haze exposure, via ingestion of haze-exposed food plants, also affected development time and pupal weight. No smoke particles were found in the tracheae of subjects from the smoke treatment suggesting that the increase in development time and mortality of B. anynana under smoke conditions might be due to toxic smoke gases and toxic food, rather than particulate matter. These results document significant deleterious effect of haze smoke to the development, adult size, and survival of insects, key players in food-webs.
Confidence is higher in touch than in vision in cases of perceptual ambiguity
Authors: Fairhurst Merle T. , Travers Eoin , Hayward Vincent , Deroy Ophelia 
Published: October 2018

AbstractThe inclination to touch objects that we can see is a surprising behaviour, given that vision often supplies relevant and sufficiently accurate sensory evidence. Here we suggest that this ‘fact-checking’ phenomenon could be explained if touch provides a higher level of perceptual certainty than vision. Testing this hypothesis, observers explored inverted T-shaped stimuli eliciting the Vertical-horizontal illusion in vision and touch, which included clear-cut and ambiguous cases. In separate blocks, observers judged whether the vertical bar was shorter or longer than the horizontal bar and rated the confidence in their judgments. Decisions reached by vision were objectively more accurate than those reached by touch with higher overall confidence ratings. However, while confidence was higher for vision rather than for touch in clear-cut cases, observers were more confident in touch when the stimuli were ambiguous. This relative bias as a function of ambiguity qualifies the view that confidence tracks objective accuracy and uses a comparable mapping across sensory modalities. Employing a perceptual illusion, our method disentangles objective and subjective accuracy showing how the latter is tracked by confidence and point towards possible origins for ‘fact checking’ by touch.
Genetic divergence of HIV-1 B subtype in Italy over the years 2003–2016 and impact on CTL escape prevalence
Authors: Alteri Claudia , Fabeni Lavinia , Scutari Rossana , Berno Giulia , Di Carlo Domenico , Gori Caterina , Bertoli Ada , Vergori Alessandra , Mastrorosa Ilaria , Bellagamba Rita , Mussini Cristina , Colafigli Manuela , Montella Francesco , Pennica Alfredo , Mastroianni Claudio Maria , Girardi Enrico , Andreoni Massimo , Antinori Andrea , Svicher Valentina , Ceccherini-Silberstein Francesca , Perno Carlo Federico , Santoro Maria Mercedes 
Published: October 2018

AbstractHIV-1 is characterized by high genetic variability, with implications for spread, and immune-escape selection. Here, the genetic modification of HIV-1 B subtype over time was evaluated on 3,328poland 1,152V3sequences belonging to B subtype and collected from individuals diagnosed in Italy between 2003 and 2016. Sequences were analyzed for genetic-distance from consensus-B (Tajima-Nei), non-synonymous and synonymous rates (dN and dS), CTL escapes, and intra-host evolution over four time-spans (2003–2006, 2007–2009, 2010–2012, 2013–2016). Genetic-distance increased over time for bothpolandV3sequences (P < 0.0001 and 0.0003). Similar results were obtained for dN and dS. Entropy-value significantly increased at 16poland twoV3amino acid positions. Seven of them were CTL escape positions (protease: 71; reverse-transcriptase: 35, 162, 177, 202, 207, 211). Sequences with ≥3 CTL escapes increased from 36.1% in 2003–2006 to 54.0% in 2013–2016 (P < 0.0001), and showed better intra-host adaptation than those containing ≤2 CTL escapes (intra-host evolution: 3.0 × 10−3[2.9 × 10−3–3.1 × 10−3] vs. 4.3 × 10−3[4.0 × 10−3–5.0 × 10−3], P[LRT] < 0.0001[21.09]). These data provide evidence of still ongoing modifications, involving CTL escape mutations, in circulating HIV-1 B subtype in Italy. These modifications might affect the process of HIV-1 adaptation to the host, as suggested by the slow intra-host evolution characterizing viruses with a high number of CTL escapes.
A striking new species of leaf warbler from the Lesser Sundas as uncovered through morphology and genomics
Authors: Ng Nathaniel. S. R. , Prawiradilaga Dewi. M. , Ng Elize. Y. X. , Suparno  , Ashari Hidayat , Trainor Colin , Verbelen Philippe , Rheindt Frank. E. 
Published: October 2018

AbstractLeaf warblers (Aves; Phylloscopidae) are a diverse clade of insectivorous, canopy-dwelling songbirds widespread across the Old World. The taxonomy of Australasian leaf warblers is particularly complex, with multiple species-level divergences between island taxa in the region requiring further scrutiny. We use a combination of morphology, bioacoustics, and analysis of thousands of genome-wide markers to investigate and describe a new species of Phylloscopus leaf warbler from the island of Rote in the Lesser Sundas, Indonesia. We show that this new Rote Leaf Warbler is morphologically and genomically highly distinct from its congenerics, but do not find vocal differentiation between different island taxa. We discuss the behaviour and ecology of this highly distinctive new species, and make recommendations about its conservation status. We believe this constitutes the first description of a novel bird species that is partly based on insights from massive amounts of genome-wide DNA markers.
A role for calcium in resistin transcriptional activation in diabetic hearts
Authors: Singh Rajvir , Moreno Pedro , Hajjar Roger J. , Lebeche Djamel 
Published: October 2018

AbstractThe adipokine resistin has been proposed to link obesity, insulin resistance and diabetes. We have previously reported that diabetic hearts express high levels of resistin while overexpression of resistin in adult rat hearts gives rise to a phenotype resembling diabetic cardiomyopathy. The transcriptional regulation of resistin in diabetic cardiac tissue is currently unknown. This study investigated the mechanism of resistin upregulation and the role of Serca2a in its transcriptional suppression. We demonstrate that restoration of Ca2+ homeostasis in diabetic hearts, through normalization of Serca2a function genetically and pharmacologically, suppressed resistin expression via inhibition of NFATc. H9c2 myocytes stimulated with high-glucose concentration or Ca2+ time-dependently increased NFATc and resistin expression while addition of the Ca2+ chelator BAPTA-AM attenuated this effect. NFATc expression was enhanced in hearts from ob/ob diabetic and from cardiac-specific Serca2a−/− mice. Similarly, NFATc increased resistin expression in myocytes cultured in low glucose while the NFATc inhibitor VIVIT blocked glucose-induced resistin expression, suggesting that hyperglycemia/diabetes induces resistin expression possibly through NFATc activation. Interestingly, overexpression of Serca2a or VIVIT mitigated glucose-stimulated resistin and NFATc expression and enhanced AMPK activity, a downstream target of resistin signaling. NFATc direct activation of resistin was verified by resistin promoter luciferase activity and chromatin-immunoprecipitation analysis. Interestingly, activation of Serca2a by a novel agonist, CDN1163, mirrored the effects of AAV9-Serca2a gene transfer on resistin expression and its promoter activity and AMPK signaling in diabetic mice. These findings parse a role for Ca2+ in resistin transactivation and provide support that manipulation of Serca2a-NFATc-Resistin axis might be useful in hyper-resistinemic conditions.
Argonaute2 attenuates active transcription by limiting RNA Polymerase II elongation in Drosophila melanogaster
Authors: Nazer Ezequiel , Dale Ryan K. , Palmer Cameron , Lei Elissa P. 
Published: October 2018

AbstractIncreasing lines of evidence support that Argonaute2 (AGO2) harbors several nuclear functions in metazoa. In particular, Drosophila AGO2 modulates transcription of developmentally regulated genes; however, the molecular mechanisms behind AGO2 recruitment into chromatin and its function in transcription have not been deeply explored. In this study, we show that Drosophila AGO2 chromatin association depends on active transcription. In order to gain insight into how AGO2 controls transcription, we performed differential ChIP-seq analysis for RNA Polymerase II (Pol II) upon depletion of AGO2. Remarkably, we find specific accumulation of the elongating but not initiating form of Pol II after AGO2 knockdown, suggesting that AGO2 impairs transcription elongation. Finally, AGO2 also affects Negative Elongation Factor (NELF) chromatin association but not the Cyclin Dependent Kinase 9 (CDK9). Altogether, these results provide key insights into the molecular role of AGO2 in attenuating elongation of certain actively transcribed genes.
Readily Functionalizable and Stabilizable Polymeric Particles with Controlled Size and Morphology by Electrospray
Authors: Lee Hoik , An Sol , Kim Sukjoo , Jeon Bokyoung , Kim Myungwoong , Kim Ick Soo 
Published: October 2018

AbstractElectrospraying is an effective and facile technique for the production of micro- or nanoparticles with tailored sizes, shapes, morphologies, and microstructures. We synthesized functionalizable poly(styrene-random-glycidyl methacrylate) copolymers and used them to fabricate microparticles via the electrospray technique. The sizes and morphologies of the electrosprayed particles are controlled by altering the process parameters (feed rate and applied voltage), and the composition and thermodynamic properties of the polymer (i.e., compatibility of the polymer with the solvent). We further investigated modifying the surfaces of the electrosprayed particles with 3-mercaptopropionic acid by a simple and efficient thiol-epoxy “click” reaction as a proof-of-concept demonstration that desired functionality can be introduced onto the surfaces of these particles; the outcome was confirmed by various spectroscopic techniques. In addition, the epoxides within the particles easily undergo crosslinking reactions, enabling further effective particle stabilization. The results reveal that the structure and properties of the polymer can be used to fine-tune the structural parameters of the electrosprayed particles, such as their sizes and morphologies, which opens up the possibility of imparting a variety of desired chemical functionalities into the structures of stable organic materials via post-electrospray modification processes.
Pore geometry control of apparent wetting in porous media
Authors: Rabbani Harris Sajjad , Zhao Benzhong , Juanes Ruben , Shokri Nima 
Published: October 2018

AbstractWettability, or preferential affinity of a fluid to a solid substrate in the presence of another fluid, plays a critical role in the statics and dynamics of fluid-fluid displacement in porous media. The complex confined geometry of porous media, however, makes upscaling of microscopic wettability to the macroscale a nontrivial task. Here, we elucidate the contribution of pore geometry in controlling the apparent wettability characteristics of a porous medium. Using direct numerical simulations of fluid-fluid displacement, we study the reversal of interface curvature in a single converging-diverging capillary, and demonstrate the co-existence of concave and convex interfaces in a porous medium—a phenomenon that we also observe in laboratory micromodel experiments. We show that under intermediate contact angles the sign of interface curvature is strongly influenced by the pore geometry. We capture the interplay between surface chemical properties and pore geometry in the form of a dimensionless quantity, the apparent wettability number, which predicts the conditions under which concave and convex interfaces co-exist. Our findings advance the fundamental understanding of wettability in confined geometries, with implications to macroscopic multiphase-flow processes in porous media, from fuel cells to enhanced oil recovery.