bluuebunny/crossref_metadata_2025_split huggingface dataset:
Elucidating Signal Transduction Modulatory Drug Target Network of Colon Cancer: A Network Biology Approach
Authors: Sethi Deepak Ranjan , Kundu Sanjay , Hassan Ibnul , Bhattacharjee Biplab , R.M Jayadeepa , Middha Sushil Kumar 
Published: July 2019

AbstractLatest evaluation and validation of cancer drugs and their targets has demonstrated the lack and inadequate development of new and better drugs, based on available protocols. Even though the specificity of drug targets is a great challenge in the pharmaco-proteomics field of cancer biology, for eradicating such hurdles and paving the way for the drugs of future, a novel step has been envisaged here to study the relation between drug target network and the corresponding drug network using the advanced concepts of proteomics and network biology. The literature mining was done for the collection of receptors and the ligands. About 1000 natural compounds were collected and out of those 300 molecules showed anti-cancer activity against colon cancer. Ligand Vs multiple receptor docking was done using the software Quantum 3.3.0; the results were further used for the designing of a well connected Protein Ligand Interaction (PLI) network of colon cancer. The obtained network is then extrapolated to sort out the receptors expressed in the specific cancer type. The network is then statistically analyzed and represented by the graphical interpretation, in order to ascertain the hub nodes and their locally parsed neighbours. Based on the best docking scores, the graphs obtained from the docking analysis are statistically validated with the help of VisANT. In the network three hub nodes Neutrophil cytosol factor 2, UV excision repair protein RAD23 homolog A, & Receptor-type tyrosine-protein phosphatase eta were identified, which showed the highest interaction with the ligands. Butyrate and Farnesol showed highest interaction as ligands. Multiple Sequence Alignment was done of the binding site sequence of the drug targets to find out the evolutionary closeness of the binding sites. The phylogenetic tree was also constructed to further validate the observation. Further in-vitro and in-vivo studies needs to be done to analyse the receptor specificity and anti tumor activity of these compounds in Colon cancer.
Evidence of mature adipocyte proliferation regulated by proliferin
Authors: Kajita Kazuo , Mori Ichiro , Hanamoto Takayuki , Zhiliang Wu , Ikeda Takahide , Fujioka Kei , Yamauchi Masahiro , Okada Hideyuki , Minami Aki , Kajita Toshiko , Uno Yoshihiro , Morita Hiroyuki , Nagano Isao , Takemura Masao , Seishima Mitsuru , Takahashi Yuzo , Ishizuka Tatsuo 
Published: July 2019

AbstractDespite much research, whether mature adipocytes proliferate remains controversial. Here, we examined 5-bromo-2&x2032;-deoxyuridine (BrdU)-labelling of mature adipocytes. Although BrdU incorporation into subcutaneous adipocytes was less than that in visceral adipocytes, pioglitazone (Pio) treatment increased BrdU incorporation in subcutaneous, but not visceral, adipocytes in rats. Fully differentiated 3T3-L1 adipocytes exhibited an increase in cell number and BrdU incorporation with time, with this increase enhanced by Pio treatment. We therefore screened for genes that encode growth factors regulated by Pio, and selected proliferin (PLF). Both gene silencing of PLF by small interfering RNA and treatment with anti-PLF antibody suppressed proliferation in 3T3-L1 adipocytes. In adipocytes isolated from Pio-treated rats, the tissue-specific pattern of PLF expression was similar to that of BrdU incorporation. Administration of an anti-PLF antibody to mice reduced BrdU incorporation into adipocytes. Mature adipocytes thus have the ability to replicate, and this proliferation is positively regulated by PLF.
Overexpression of the leukotriene C4 synthase gene in mice reproduces human aspirin-induced asthma
Authors: Hirata Hirokuni , Honda Kyoko , Fukushima Yasutsugu , Arima Masafumi , Tokuhisa Takeshi , Fukuda Takeshi 
Published: July 2019

AbstractThe pathogenesis of aspirin-induced asthma (AIA) is presumed to involve the aspirin /non-steroidal anti-inflammatory drug (NSAID)-induced abnormal metabolism of arachidonic acid, resulting in an increase in 5-lopoxygenase (5-LO) metabolites, particularly leukotriene C4 (LTC4)&x3000;which is a highly potent bronchial constrictor. However, the role of LTC4 in the development of AIA has yet to be conclusively demonstrated. To elucidate the effect of LTC4 on the development of AIA, we generated LTC4 synthase (Ltc4s) gene transgenic (LTC4S-Tg) mice. In contrast to wild-type (WT) mice, LTC4S-Tg mice displayed NSAID-induced airway obstruction that was associated with increases of LTC4 and Th2 cytokines in lung tissue. This is the first study to demonstrate clearly that a balance shift towards the 5-LO pathway contributes to the pathogenesis of AIA in the presence of elevated levels of LTC4S.
City rats: From rat behaviour to human spatial cognition in urban environments
Authors: Eilam David , Portugali Juval , Yaski Osnat 
Published: July 2019

AbstractThe structure and shape of an urban environment influence our ability to find our way about in the city^1-2^. Indeed, urban designers who face the challenge of planning environments that facilitate wayfinding^3^, have a consequent need to understand the relations between the urban environment and spatial cognition^4^. Previous studies have suggested that certain qualities of city elements, such as a distinct contrast with the background (e.g. The Eiffel Tower in Paris), or a clear morphology (e.g. the grid layout of Manhattan's streets) affect spatial behaviour and cognition^1,5-7^. However, only a few empirical studies have examined the relations between the urban environment and spatial cognition. Here we suggest that testing rats in experimental environments that simulate certain facets of urban environment can provide an insight into human spatial behaviour in urban environments with a similar layout. Specifically, we simulated two city layouts: (1) a grid street layout such as that of Manhattan; and (2) an irregular street layout such as that of Jerusalem. We found that the rats that were tested in the grid layout covered more ground and visited more locations, compared with the restricted movement demonstrated by the rats tested in the irregular layout. This finding in rats is in accordance with previous findings that urban grids conduce to high movement flow throughout the city, compared to low movement flow in irregular urban layouts^8-9^. Previous studies revealed that the spatial behaviour of rats and humans is controlled by the same underlying mechanisms^10-11^. In the same vein, we show that rats demonstrate spatial movement patterns that recall those of humans in similar urban environments. Rat behaviour may thus offer an in-vivo means for testing and analyzing the spatial cognitive principles of specific urban designs and for inferring how humans may perceive a particular urban environment and orient in it.
∆N-p63 functions as an invasion, migration, and metastasis suppressor
Authors: Boominathan Lakshmanane 
Published: July 2019

AbstractThe tumor suppressor p53 homologues, TA-p73, and p63 have been shown to function as tumor suppressors. However, how they function as tumor suppressors remains elusive. Expression of p63 is controlled by two distinct promoters. Consequently, this results in two different gene products such as TA-(transactivation domain containing NH2 terminus) p63 and ∆N-(lacks NH2 terminus) p63. It is generally thought that the TA-p63 functions as a tumor suppressor, while the ∆N-p73 functions as a proto-oncogene. However, careful interpretation of the data concerning ∆N-p63 suggests that it could function as an invasion and metastasis/tumor suppressor in a cell context dependent manner.
Increased regeneration efficiency of Brassica napus L. cultivars Star, Westar and Cyclone from hypocotyle and cotyledonary explants
Authors: Khan Israr , Ali Waqar , Takar Zahir Ali , Farooqi Arfa , Khan Sikandar , Akhtar Muhammadwaheed 
Published: July 2019

AbstractThe comparative organogenesis of Brassica napus L cultivars Cyclone, Star and Westar was studied. The cotyledonary explants gave a higher response to all the combinations of 0.5 mg/L 2,4-D and BAP (0.5, 1.0,1.5 and 2.0 mg/L} used for optimizing the conditions for callus induction. The best mean weight and mean length of callus was obtained at 0.5 mg/L 2,4-D and 1.5mg/L BAP for Star cotyledonary explants. For the complete plant regeneration the new method of exposing the explants culture to Growth regulator free medium was performed. The method was applicable to both hypocotyl and cotyledonary explants. The Shoot Induction Frequency for hypocotyl (6-34%) in the three cultivars is higher than the cotyledonary explants (3-23%). The method is speedy and almost all of the shoots and some unshooted calli (78%) form roots on the same media without prior transfer to rooting medium.
PhyloCSF: a comparative genomics method to distinguish protein-coding and non-coding regions
Authors: Lin Michael , Jungreis Irwin , Kellis Manolis 
Published: July 2019

AbstractAs high-throughput transcriptome sequencing provides evidence for novel transcripts in many species, there is a renewed need for accurate methods to classify small genomic regions as protein-coding or non-coding. We present PhyloCSF, a novel comparative genomics method that analyzes a multi-species nucleotide sequence alignment to determine whether it is likely to represent a conserved protein-coding region, based on a formal statistical comparison of phylogenetic codon models. We show that PhyloCSF's classification performance in 12-species Drosophila genome alignments exceeds all other methods we compared in a previous study, and we provide a software implementation for use by the community. We anticipate that this method will be widely applicable as the transcriptomes of many additional species, tissues, and subcellular compartments are sequenced, particularly in the context of ENCODE and modENCODE.
The role of acute inflammation at the peritoneal cavity-enhanced adhesion formation
Authors: Corona Roberta , Mailova Karina , Binda Maria Mercedes , Schonman Ron , Verguts Jasper , Koninckx Philippe Robert 
Published: July 2019

Abstract
Objective:
To investigate the role of acute inflammation of the peritoneal cavity in adhesion formation. Design: Prospective randomized, controlled trial Setting: University laboratory research centerAnimals: 9-10 weeks old BALB/c female mice Interventions: In our laparoscopic mouse model acute inflammation of the peritoneal cavity and adhesion formation were evaluated in a control group with CO2 pneumoperitoneum (PP)-enhanced adhesions, in CO2 PP plus manipulation-enhanced adhesions and in the latter group + dexamethasone-reduced adhesions. Adhesions and acute inflammation were assessed by neoangiogenesis, diapedesis and leukocytes accumulation on the 2nd day after surgery. Main outcome measure(s): Qualitative and quantitative adhesion scores and an acute inflammation score.Results: Adhesions were enhanced by the CO2 PP (p=0.007), further enhanced by manipulation (p&lt;0.0001 versus CO2 PP) and decreased by the administration of dexamethasone (p&lt;0.0001 versus CO2 PP+manipulation ). Acute inflammation scores strongly correlated with total adhesion score whether assessed as total inflammation score (p&lt;0.0001) or as neoangiogenesis (p&lt;0.0002), diapedesis (p&lt;0.03) or leukocyte accumulation (p&lt;0.0002). Inflammation scores, moreover, were strikingly similar at the surgical lesion and at the parietal peritoneum.

Conclusions:
These data strongly suggest that acute inflammation in the entire peritoneum cavity is the driving mechanism of adhesion formation at the lesion site.
To be resistant or tolerant: the evolution of mixed defence strategies
Authors: Garrido Etzel , Fornoni Juan 
Published: July 2019

AbstractTheory predicts that resistance and tolerance represent mutually exclusive strategies of host defence. However, empirical evidence reveals that individual hosts simultaneously allocate resources to both mechanisms. Understanding the maintenance of this defence pattern remains controversial because empirical evidence is at odds with theoretical assumptions. Here, we present a novel host-enemy dynamic that considers: the differential effect of each defence strategy upon the evolutionary response of natural enemies; the process of local adaptation of the natural enemies to their hosts and the effect of negative and positive frequency-dependent selection acting on resistance and tolerance respectively. Our analysis suggests that a mixed pattern of defence allocation could be evolutionary stable because of the differential dynamic that each strategy has in the interaction with natural enemies.
Microstructural Correlates of Resilience against Major Depressive Disorder: Epigenetic Mechanisms?
Authors: Frodl Thomas , Ferguson Yolande , Fagan Andrew , Lisiecka Danusia , Carballedo Angela , Daly Ian , Meaney James , Kelleher Dermot 
Published: July 2019

AbstractMental disorders are a major cause of long-term disability and are a direct cause of mortality, with approximately 800.000 individuals dying from suicide every year worldwide - a high proportion of them related to major depressive disorder (MDD)^1^. Healthy relatives of patients with major depressive disorder (MDD) are at risk to develop the disease. This higher vulnerability is associated with structural^2-4^ and functional brain changes^5^. However, we found using high angular resolution diffusion imaging (HARDI) with 61 diffusion directions that neuron tracts between frontal cortices and limbic as well as temporal and parietal brain regions are characterized by better diffusion coefficients in unaffected relatives (UHR), who managed to stay healthy, compared to healthy volunteers without any family history for a psychiatric disease (HC). Moreover, those UHR with stronger fibre connections better managed incidences of adversity in early life without later developing depression, while in HC axonal connections were found to be decreased when they had early-life adversity. Altogether these findings indicate the presence of stronger neural fibre connections in UHR, which seem to be associated with resilience against environmental stressors, which we suggest occur through epigenetic mechanisms.
Men fear other men most: Gender specific brain activations in perceiving threat from dynamic faces and bodies. An fMRI study.
Authors: de Gelder Beatrice , Pichon Swann , Kret Mariska , Grezes Julie 
Published: July 2019

AbstractWe report a functional magnetic resonance imaging experiment showing different activation patterns as a function of threatening signals from facial or bodily expressions and these differed between male and female participants as a function of male and female actors. Male observers showed a clear motor preparation response to threatening male body language.
Motor fluency shapes abstract concepts
Authors: Casasanto Daniel , Chrysikou Evangelia 
Published: July 2019

AbstractPeople with different types of bodies tend to think differently in predictable ways, even about abstract ideas that seem far removed from bodily experience. Right- and left-handers implicitly associate positive ideas like goodness and honesty more strongly with their dominant side of space, the side on which they can interact with their environment more fluently, and negative ideas with their non-dominant side. This suggests a role for motor experience in shaping abstract thoughts. Yet, previous evidence is also consistent with an experience-independent account. Here we show that right-handers' tendency to associate 'good' with right and 'bad' with left can be reversed due to both long- and short-term changes in motor fluency. Among stroke patients who were right-handed prior to unilateral cerebrovascular accident (CVA), those with left-hemiparesis (following right CVA) associated good with right, but those with right-hemiparesis (following left CVA) associated good with left, like natural left-handers. A similar pattern was found in healthy right-handers whose right or left hand was temporarily handicapped in a laboratory training task. Motor experience influences judgments of good and bad, overriding any predispositions due to natural handedness. Even highly abstract ideas depend, in part, on how people interact with the physical world.
Designing L-Systems for making three and six open reading frames from the leading strand of a single DNA molecule
Authors: Goswami Arunava , Singh Rajneesh , Choudhury Pabitra , Hassan Sk. Sarif Hassan 
Published: July 2019

AbstractCurrent molecular biology dogma (except alternative splicing) suggests that leading strand of DNA produces mRNA and usually the leading strand gives one ORF (ORF) among the available six ORFs. We attempted to break this rule where three and six ORFs from the leading strand will be formed by designing L-Systems, originally proposed to study symmetry of biological world. We thought this would revolutionize the world of synthetic biology. While doing so, we found L-System containing A&rarr;T, T&rarr;G, C&rarr;A, and G&rarr;C, i.e., single nucleotide production rule will stop growing after one nucleotide. L-System containing either (a) A&rarr;TG, T&rarr;GC, C&rarr;GA, G&rarr;TC or (b) A&rarr;CTG, T&rarr;GAC, C&rarr;TAC, G&rarr;TGC will lead to generation of repetitive DNA sequence after few iteration. These repetitive sequences might become easy target for enzyme like restriction endonucleases and transposase or RNAse but may give repetitive DNA sequences which are normally found in the large non-coding region of the genome. Here we show that a number of L-Systems like with (Axiom: A) A&rarr;ATGC, C&rarr;CTCA, T&rarr;GCAG, G&rarr;CGAA and A&rarr;GTAC, C&rarr;TGCA, T&rarr; CTGG, G&rarr;ATAT if used to generate either a short (~ 2000 bp) or long (~ 16000 bp) can give rise to three ORFs and six ORFs per DNA molecule when conceptually translated through Expasy tools respectively. To our surprise we find that L-System production rule with only four letter codes (not one, two, three, five, six) can produce this miraculous results which nothing but follows Young Fibonacci graph. We find that production rule with higher order of magnitude like 10 bp also give similar results but not 20 bp containing production rules.
HTself2: Combining p-values to Improve Classification of Differential Gene Expression in HTself
Authors: Cortez Daniel , Tonon Angela , Colepicolo Pio , Vêncio Ricardo 
Published: July 2019

AbstractHTself is a web-based bioinformatics tool designed to deal with the classification of differential gene expression for low replication microarray studies. It is based on a statistical test that uses self-self experiments to derive intensity-dependent cutoffs. The method was previously described in Vêncio et al, (DNA Res. 12: 211- e 214, 2005). In this work we consider an extension of HTself by calculating p-values instead of using a fixed credibility level α. As before, the statistic used to compute single spots p-values is obtained from the gaussian Kernel Density Estimator method applied to self-self data. Different spots corresponding to the same biological gene (replicas) give rise to a set of independent p-values which can be combined by well known statistical methods. The combined p-value can be used to decide whether a gene can be considered differentially expressed or not. HTself2 is a new version of HTself that uses the idea of p-values combination. It was implemented as a user-friendly desktop application to help laboratories without a bioinformatics infrastructure.
Evolution of social behaviour
Authors: Nanjundiah Vidyanand 
Published: July 2019

AbstractNowak et al.1 wish to explain why the version of kin selection theory that is summarised by the formula R&gt;c/b (c=cost of performing &apos;altruistic&apos; act, b=benefit derived by recipient of act, R=relatedness between the two) is of little utility for understanding the evolution of eusociality. But in trying to do so they omit much that is relevant and risk misrepresenting the issue to anyone who is not familiar with the literature. A fairer account would include the following facts.
CDK2 and CKI targeting can significantly lower the cellular senescence bar - reveals a mathematical model of G1/S checkpoint pathway
Authors: Ling Hong , Samarasinghe Sandhya , Kulasiri Don 
Published: July 2019

AbstractCellular senescence, a mechanism employed by cells for thwarting proliferation, has shown to play an important role in protecting cells against cancer development in recent experimental observations, indicating that a deeper understanding of the cellular senescence pathway can help exploit its capacity for more effective cancer treatment. Furthermore, some experimental evidence points out that inhibition of CDK2 or Skp2 can be the critical trigger for cellular senescence. However, no mathematical model has been developed to highlight cellular senescence until now. In this study, we first implement a mathematical model of G1/S transition involving the DNA-damage pathway to highlight cellular senescence by lowering the critical trigger- CDK2. For this, we focus on the behaviour of two important proteins (E2F and CycE) for several reduced CDK2 levels under two DNA-damage conditions by calculating the probability (&x03B2;) of DNA-damaged cells passing the G1/S. Our recently published results from the same model indicated that a large percentage of damaged cells pass G1/S under normal CDK2 levels, reaching &x03B2; values of up to 65% under high level of DNA damage. The current study reveals that reduced CDK2 levels can significantly lower the percentage of damaged cells passing the G1/S; in particular, 50% reduction in CDK2 achieves 65% reduction in the passage of damaged cells. Furthermore, the model analyses the relationship between CDK2 and its CKIs in search of other effective ways to bring forward cellular senescence. Results show that the degradation rate of p21 and initial concentration of p27 can be effectively used to lower the senescence threshold. Specifically, p27 is the most effective, followed by CDK2 and p21. However, the combined effect of CDK2 and CKIs is dramatic with CDK2/p27 combination almost totally arresting the passage of damaged cells. Biologists may wish to validate the efficacy of these targets for treating cancer.
_Cavernularia malabarica_ Fowler, 1894 from the Bay coast of Visakhapatnam, Andhra Pradesh
Authors: Shettigar Veena , P Kaladharan 
Published: July 2019

AbstractMany initiatives have come up to investigate the fauna around India. Due to accidental sighting and dislocation caused due to fishing and forming a part of the trash brought ashore is how the organisms are located. During regular sampling carried out from Mangamaripeta fish landing centre of Visakhapatnam, delicate shallow-water sea pens were collected and investigated. No previous records are available pertaining to the presence of these animals from this area and the species have not been identified from these waters. This report identifies and describes the species as Cavernularia malabarica Fowler, 1894 for the first time from these waters.
Occurrence Of Ascidian Molgula Sp. From The Coastal Waters Of Visakhapatnam, India
Authors: Shettigar Veena , P Kaladharan 
Published: July 2019

AbstractA specimen of solitary ascidian Molgula sp., collected from seaweeds growing at Thotlakonda beach, Visakhapatnam is reported for the first time from Visakhapatnam coast of Indian waters.