bluuebunny/crossref_metadata_2025 huggingface dataset:
Emergence of macroscopic simplicity from the Tumor Necrosis Factor-alpha signaling dynamics
Authors: Hayashi Kentaro , Piras Vincent , Tomita Masaru , Tsuchiya Masa , Selvarajoo Kumar
Published: July 2019

The Tumor Necrosis Factor-α (TNF-α), a cytokine produced during the innate immune response to invading pathogens, is involved in numerous fundamental cellular processes. Here, to understand the temporal activation profiles of the TNF-α regulated signaling network, we developed a dynamic computational model based on the perturbation-response approach and the law of information (signaling flux) conservation. Our simulations show that the temporal average population response of the TNF-α stimulated transcription factors NF-κB and AP-1, and 3 groups of 180 downstream gene expressions follow first-order equations. Using the model, in contrast to a well-known previous study, our model suggests that the continuous activation of the third group of genes is not mainly due to the poor rate of mRNA decay process, rather, the law of signaling flux conservation stipulates the presence of secondary signaling, such as feedback mechanism or autocrine signaling, is crucial. Although the living system is perceived as sophisticated and complex, notably, our work reveals the presence of simple governing principles in cell population dynamics.
Accelerated Macromolecular Solution Structure Recovery
Authors: Zwart Petrus , Liu Haiguang
Published: July 2019

Small Angle X-ray Scattering (SAXS) is a standard technique for the determination of low-resolution shapes of macromolecules and their complexes, adding important insights in understanding biological function. We present a novel and computationally efficient method for shape reconstruction from SAXS data. High-quality molecular shapes are calculated in less than two minutes, providing real-time feedback during SAXS experiments.
Invasive monitoring of the clinical effects of high intra-abdominal pressure for insertion of the first trocar.
Authors: Miyahira Susana , Miguel Gustavo , Azevedo Glicia , Marigliani Bianca , Borborema José , Hypolito Octavio , Azevedo Joao-Luiz , Gama Fernanda , Azevedo Otavio , Becker Junior Otavio , Bernardes Linda , Machado Afonso
Published: July 2019

Background:

To analyze the effects of transitory, high intra-abdominal pressure on clinical, hemodynamic, blood gas and metabolic parameters.Methods: Sixty-seven laparoscopic patients were divided into groups P12 (n = 30, maximum intra-abdominal pressure of 12 mmHg) and P20 (n = 37, maximum intra-abdominal pressure of 20 mmHg). Through radial artery cannulation, mean arterial pressure (MAP) was assessed and blood gas analysis – pH, arterial oxygen tension (PaO2), arterial carbon dioxide tension (PaCO2), bicarbonate (HCO3) and base excess (BE) – was performed. These parameters were evaluated in both groups at time point zero, before CO2 insufflation; at time point one (TP1), when intra-abdominal pressure of 12 mmHg was reached in both groups; at time point two (TP2), 5 minutes after reaching intra-abdominal pressure of 12 mmHg in group P12 and of 20 mmHg in group P20; and at time point three (TP3), 10 minutes after reaching intra-abdominal pressure of 12 mmHg in group P12 and 10 minutes after TP1 in group P20, when intra-abdominal pressure decreased from 20 mmHg to 12 mmHg. Values out of the normal range or the occurrence of atypical phenomena suggestive of organic disease indicated clinical changes.

Results:

Significant variations in MAP, pH, HCO3 and BE were observed in group P20; these changes, however, were within normal limits. Clinical changes were also within normal limits, and no pathological phenomena were observed.

Conclusions:

Brief, intra-abdominal hypertension for the insertion first trocar insertion causes variations in MAP, pH, HCO3 and BE without adverse effects, and it may protect from iatrogenic injury.
Relationship of arterial and exhaled CO2 during elevated artificial pneumoperitoneum pressure for introduction of the first trocar.
Authors: Hypolito Octavio , Azevedo Joao-Luiz , Miyahira Susana , Scarpelli Fabiana , Becker Junior Otavio , Machado Afonso , Azevedo Otavio , Azevedo Glicia , Marigliani Bianca , Borborema Jose , Bernardes Linda , Miguel Gustavo
Published: July 2019

The present study evaluated the correlation between arterial CO2 and exhaled CO2 during brief high-pressure pneumoperitoneum. Patients were randomly distributed into two groups: P12 group (n=30) received a maximum intraperitoneal pressure of 12mmHg, and P20 group (n=37) received a maximum intraperitoneal pressure of 20mmHg. Arterial CO2 was evaluated by radial arterial catheter and exhaled CO2 was measured by capnometry at the following time points: before insufflation, once intraperitoneal pressure reached 12mmHg , 5 minutes after intraperitoneal pressure reached 12mmHg for the P12 group or 20mmHg for the P20 group, and 10 minutes after intraperitoneal pressure reached 12mmHg for the P12 group or when intraperitoneal pressure had decreased from 20mmHg to 12mmHg, for the P20 group. During brief durations of very high intraperitoneal pressure (20mmHg), there was a strong correlation between arterial CO2 and exhaled CO2. Capnometry can be effectively used to monitor patients during transient increases in artificial pneumoperitoneum pressure.
Density alteration in non-physiological cells
Authors: Wang Ming , Li Hai-Cheng , Li Lin-Na , Li Ju-Xiang , Liu Yu , Zhu Yuan-Chang , Wu Bin-Bin , Wu Xiao-Hua , Lan Fei-Fei , Fei Jia , Wei Jian-Ge
Published: July 2019

In the present study an important phenomenon of cells was discovered: the change of intracellular density in cell's response to drug and environmental factors. For convenience, this phenomenon is named as "density alteration in non-physiological cells" ( DANCE). DANCE was determined by discontinuous sucrose gradient centrifugation (DSGC), in which cells were separated into several bands. The number and position of the bands in DSGC varied with the change of cell culture conditions, drugs, and physical process, indicating that cell's response to these factors was associated with alteration of intracellular density. Our results showed that the bands of cells were molecularly different from each other, such as the expression of some mRNAs. For most cells tested, intracellular density usually decreased when the cells were in bad conditions, in presence of drugs, or undergoing pathological changes. However, unlike other tissue cells, brain cells showed increased intracellular density in 24 hrs after the animal death. In addition, DANCE was found to be related to drug resistance, with higher drug-resistance in cells of lower intracellular density. Further study found that DANCE also occurred in microorganisms including bacteria and fungus, suggesting that DANCE might be a sensitive and general response of cells to drugs and environmental change. The mechanisms for DANCE are not clear. Based on our study the following causes were hypothesized: change of metabolism mode, change of cell membrane function, and pathological change. DANCE could be important in medical and biological sciences. Study of DANCE might be helpful to the understanding of drug resistance, development of new drugs, separation of new subtypes from a cell population, forensic analysis, and importantly, discovery of new physiological or pathological properties of cells.
Down-regulation of serotonergic genes expression in the raphe nuclei of midbrain under chronic social defeat stress in male mice
Authors: Boyarskikh Ul’yana , Bondar Natalya , Filipenko Maxim , Kudryavtseva Natalia
Published: July 2019

Background:

There is ample experimental evidence supporting the hypothesis that the brain serotonergic system is involved in the control of chronic social defeat stress (CSDS), depression and anxiety. The study aimed to analyze mRNA levels of the serotonergic genes in the raphe nuclei of the midbrain that may be associated with chronic social defeats consistently shown by male mice in special experimental settings.Methodology/Principal Findings:The serotonergic genes were the Tph2, Sert, Maoa and Htr1a. The Bdnf, Creb, Cphn, Gapdh, Hprt, B2M, 18S and Actb genes were also studied. The experimental groups were composed of male mice with experience of defeats in 21 daily encounters and male mice with the same track record of defeats followed by a no-defeat period without agonistic interactions (relative rest for 14 days). It has been shown that mRNA levels of the Tph2, Maoa, Sert, Htr1a, Bdnf and Creb genes in the raphe nuclei of defeated mice are decreased as compared with the controls. Under CSDS the Cphn, Gapdh, Hprt, B2M, 18S, Actb genes are also down-regulated. The expression of the serotonergic genes as well as the Cphn and Creb genes is not restored to the control level after the 2 weeks of relative rest. mRNA levels of other genes are not recovered to the control levels, although some up-regulation was observed in rested losers. Significant positive correlations were found between the total time of avoidance behavior demonstrated by the 21-day defeaters in agonistic interactions and Sert, Maoa, Bdnf, Gapdh and 18S mRNA levels.

Conclusions:

CSDS experience inducing the development of mixed anxious/depression-like state in male mice down-regulates the serotonergic genes expression associated with the synthesis, inactivation and reception of serotonin. The Bdnf and Creb genes as well as the cell and metabolic Cphn, Gapdh, Hprt, B2M, Actb and 18S genes in the midbrain raphe nuclei are also down-regulated under CSDS. Period of relative rest is not enough for most genes to recover expression to the control levels.
Combining Transfer of TTF-1 and Pax-8 Gene: a Potential Strategy to Promote Radioiodine Therapy of Thyroid Carcinoma
Authors: Mu Da , Huang Rui , Ma Xiaojuan , Li Suping , Kuang Anren
Published: July 2019

Cotransfer of TTF-1 and Pax-8 gene to tumor cells, resulting in the reexpression of iodide metabolism-associated proteins, such as sodium iodide symporter (NIS), thyroglobulin (Tg), thyroperoxidase (TPO), offers the possibility of radioiodine therapy to non-iodide-concentrating tumor because the expression of iodide metabolism-associated proteins in thyroid are mediated by the thyroid transcription factors TTF-1 and Pax-8. The human TTF-1 and Pax-8 gene were transducted into the human thyroid carcinoma (K1 and F133) cells by the recombinant adenovirus, AdTTF-1 and AdPax-8. Reexpression of NIS mRNA and protein, but not TPO and Tg mRNA and protein, was detected in AdTTF-1-infected F133 cells, following with increasing radioiodine uptake (6.1~7.4 times), scarcely iodide organification and rapid iodide efflux (t1/2≈8 min in vitro, t1/2≈4.7 h in vivo).In contrast, all of the reexpression of NIS, TPO and Tg mRNA and proteins in F133 cells were induced by the synergetic effect of TTF-1 and Pax-8. AdTTF-1 and AdPax-8 coinfected K1 and F133 cells could effectively accumulate radioiodine (6.6-7.5 times) and obviously retarded radioiodine retention (t1/2≈25-30 min in vitro, t1/2≈12 h in vivo) (p<0.05).Accordingly, the effect of radioiodine therapy of TTF-1 and Pax-8 cotransducted K1 and F133 cells (21-25% survival rate in vitro) was better than that of TTF-1-transducted cells(40% survival rate in vitro) (p<0.05). These results indicate that single TTF-1 gene transfer may have limited efficacy of radioiodine therapy because of rapid radioiodine efflux. The cotransduction of TTF-1 and Pax-8 gene, with resulting NIS-mediated radioiodine accumulation and TPO and Tg-mediated radioiodine organification and intracellular retention, may lead to effective radioiodine therapy of thyroid carcinoma.
The Semantic Automated Discovery and Integration (SADI) Web service Design-Pattern, API and Reference Implementation
Authors: Wilkinson Mark , Vandervalk Benjamin , McCarthy Luke
Published: July 2019

Background.

The complexity and inter-related nature of biological data poses a difficult challenge for data and tool integration. There has been a proliferation of interoperability standards and projects over the past decade, none of which has been widely adopted by the bioinformatics community. Recent attempts have focused on the use of semantics to assist integration, and Semantic Web technologies are being welcomed by this community.Description.SADI – Semantic Automated Discovery and Integration – is a lightweight set of fully standards-compliant Semantic Web service design patterns that simplify the publication of services of the type commonly found in bioinformatics and other scientific domains. Using Semantic Web technologies at every level of the Web services “stack”, SADI services consume and produce instances of OWL Classes following a small number of very straightforward best-practices. In addition, we provide codebases that support these best-practices, and plug-in tools to popular developer and client software that dramatically simplify deployment of services by providers, and the discovery and utilization of those services by their consumers.

Conclusions.

SADI Services are fully compliant with, and utilize only foundational Web standards; are simple to create and maintain for service providers; and can be discovered and utilized in a very intuitive way by biologist end-users. In addition, the SADI design patterns significantly improve the ability of software to automatically discover appropriate services based on user-needs, and automatically chain these into complex analytical workflows. We show that, when resources are exposed through SADI, data compliant with a given ontological model can be automatically gathered, or generated, from these distributed, non-coordinating resources - a behavior we have not observed in any other Semantic system. Finally, we show that, using SADI, data dynamically generated from Web services can be explored in a manner very similar to data housed in static triple-stores, thus facilitating the intersection of Web services and Semantic Web technologies.
Milk is for Children, Colostrum silage is for calves.
Authors: Leivas Leite Fábio , Helena Saalfeld Mara , Brayer Pereira Daniela , Krüguer Silveira Kathleen , Gularte Marcia , Valente Julia , Schramm Renata
Published: July 2019

One sixth of the world population is starving. In the meantime, producers from all over the world daily disdain billions of liters of bovine colostrum, which is seen as rich in nutrients, immunoglobulin and bioactive substances. The milk is the most expensive component in the final costs of calves breeding. Considering the impossibility of substituting the milk to feed the calf, different ways to use the colostrum have been studied however with controversial results. We have developed colostrum silage. This product is economical and possible to store in the environment for up to eighteen months. Being efficient for calf breeding, yielding income and profit to the dairy business. The colostrum silage keeps the necessary physicochemical characteristics for the development of the calves. Calves fed with this product had a significant higher weight gain comparing to the ones fed with milk. Then the milk can be used for human consumption.
Levy flights are not evolved behavior
Authors: Willis Jay , Merckelbach Lucas
Published: July 2019

Tracks of moving animals have many short moves interspersed with longer moves, and frequencies of all moves together often indicate Levy flights (a type of power law)^1^. The Levy flight foraging hypothesis suggests that, 'since Levy flights and walks can optimize search efficiencies, therefore natural selection should have led to adaptations for Levy flight foraging^1^ and it has been apparently supported by several studies of large numbers of tracks of marine animals^234^. We show that Levy flights are caused by marine animals attempting to move in simple ways and they are unlikely to be evolved behavior. We do this by analyzing the tracks of autonomous underwater gliders which conform to Levy flights while they were programmed to perform simple directed movement. Gliders are autonomous underwater vehicles (AUV), propelled by a buoyancy engine^5^.The principle of operation is that by alternating positive and negative buoyancy, the winged AUV glides through the ocean in an undulating path, resurfacing after a pre-programmed number of undulations. During the periods at the surface, which typically last 15 minutes, GPS is used for positioning before and after transmission of data via a satellite link, whereas underwater the trajectory is deadreckoned from measured heading, pitch and pressure rate. Thus they are potentially a good analogy to a navigating animal which may also attempt to make directed movements using the best available (and often intermittent^6^) navigational information.
Sodium Benzoate as Promoter in the Soap Flotation of Phosphate Minerals
Authors: DM Mihir , P Vijay Kumar , Gowda Prabhulingaiah
Published: July 2019

In the present study we show that sodium benzoate substantially improves the efficiency of Soap LDO collector in the flotation of phosphate minerals.
A comparative study on the production of ethanol from lignocellulosic biomass by chemical and biological method
Authors: SM Shaheed , JP Rohit , R Madhan , K Selvakumar
Published: July 2019

Ethanol derived from non-edible biomass is renewable and a clean source of energy. It is independent of the food industry and it is economically feasible. The first generation biofuel or bioethanol is still not a very convenient source of energy as it prominently depends on the availability of grains. The main objective of this work is to develop an industrious efficient process to produce ethanol from lignocellulosic biomasses like wood and leaf in a lab scale. Two processes were compared. The first process involved an alkaline pre-treatment of the powdered biomass followed by dilute acid hydrolysis. The second process involved an alkaline treatment followed by direct hydrolysis of the biomass by use of a fungal species obtained from rotting wood. Following hydrolysis, fermentation was performed using Saccharomyces cerevisiae and ethanol produced was measured. The process methodologies performed here are liable to be scaled up easily. The final study determines factors such as temperature, strength of the reagents and retention time to maximize ethanol production.
Neural Basis of Motivation Lateralizes with Motor Control
Authors: Brookshire Geoffrey , Casasanto Daniel
Published: July 2019

According to decades of research on affective motivation in the human brain, approach motivational states are subserved by the left hemisphere and avoidance states by the right hemisphere. Here we show that hemispheric specialization for motivation reverses with handedness. This covariation provides initial support for the Sword and Shield Hypothesis, according to which hemispheric laterality of affective motivation is causally linked to motor control for the dominant and non-dominant hands.
A potential cyanobacterial ancestor of Viridiplantae chloroplasts
Authors: Ghosh Wriddhiman , Haldar Prabir , Bhattacharya Sabyasachi , Chatterjee Jaideb , Pyne Prosenjit , Alam Masrure
Published: July 2019

The theory envisaging the origin of plastids from endosymbiotic cyanobacteria is well-established but it is difficult to explain the evolution (spread) of plastids in phylogenetically diverse plant groups. It is widely believed that primordial endosymbiosis occurred in the last common ancestor of all algae^1^, which then diverged into the three primary photosynthetic eukaryotic lineages, viz. the Rhodophyta (red algae), Glaucocystophyta (cyanelle-containing algae) and Viridiplantae (green algae plus all land plants)^2^. Members of these three groups invariably have double membrane-bound plastids^3^, a property that endorses the primary endosymbiotic origin of the organelles. On the other hand, the three or four membrane-bound plastids of the evolutionary complicated Chromalveolates [chromista (cryptophytes, haptophytes, and stramenopiles) and alveolata (dinoflagellates, apicomplexans, and ciliates)] are inexplicable in the light of a single endosymbiosis event, thereby necessitating the postulation of the secondary^4,5^ and tertiary^6^ endosymbiosis theories where a nonphotosynthetic protist supposedly engulfed a red or a green alga^7^ and an alga containing a secondary plastid itself was engulfed^8^ respectively. In the current state of understanding, however, there is no clue about the taxonomic identity of the cyanobacterial ancestor of chloroplasts, even though there is a wide consensus on a single primordial endosymbiosis event. During our metagenomic investigation of a photosynthetic geothermal microbial mat community we discovered a novel order-level lineage of Cyanobacteria that - in 16S rRNA gene sequence-based phylogeny - forms a robust monophyletic clade with chloroplast-derived sequences from diverse divisions of Viridiplantae. This cluster diverged deeply from the other major clade encompassing all hitherto known groups of Cyanobacteria plus the chloroplasts of Rhodophyta, Glaucocystophyceae and Chromalveolates. Since this fundamental dichotomy preceded the origin of all chloroplasts, it appears that two early-diverging cyanobacterial lineages had possibly given rise to two discrete chloroplast descents via two separate engulfment events.
Identification of MHC Class II Binders/ Non-binders using Negative Selection Algorithm
Authors: Soam S.S. , Khan Feroz , Bhasker Bharat , Mishra B. N.
Published: July 2019

The identification of major histocompatibility complex (MHC) class-II restricted peptides is an important goal in human immunological research leading to peptide based vaccine design. These MHC class–II peptides are predominantly recognized by CD4+ T-helper cells, which when turned on, have profound immune regulatory effects. Thus, prediction of such MHC class-II binding peptides is very helpful towards epitope-based vaccine design. HLA-DR proteins were found to be associated with autoimmune diseases e.g. HLA-DRB1*0401 with rheumatoid arthritis. It is important for the treatment of autoimmune diseases to determine which peptides bind to MHC class II molecules. The experimental methods for identification of these peptides are both time consuming and cost intensive. Therefore, computational methods have been found helpful in classifying these peptides as binders or non-binders. We have applied negative selection algorithm, an artificial immune system approach to predict MHC class–II binders and non-binders. For the evaluation of the NSA algorithm, five fold cross validation has been used and six MHC class–II alleles have been taken. The average area under ROC curve for HLA-DRB1*0301, DRB1*0401, DRB1*0701, DRB1*1101, DRB1*1501, DRB1*1301 have been found to be 0.75, 0.77, 0.71, 0.72, and 0.69, and 0.84 respectively indicating good predictive performance for the small training set.
NIR Calibrations for Soybean Seeds and Soy Food Composition Analysis: Total Carbohydrates, Oil, Proteins and Water Contents
Authors: Baianu I. , Guo Jun
Published: July 2019

Conventional chemical analysis techniques are expensive, time consuming, and often destructive. The non-invasive Near Infrared (NIR) technology was introduced over the last decades for wide-scale, inexpensive chemical analysis of food and crop seed composition (see Williams and Norris, 1987; Wilcox and Cavins, 1995; Buning and Diller, 2000 for reviews of the NIR technique development stage prior to 1998, when Diode Arrays were introduced to NIR). NIR spectroscopic measurements obey Lambert and Beer’s law, and quantitative measurements can be successfully made with high speed and ease of operation. NIR has been used in a great variety of food applications. General applications of products analyzed come from all sectors of the food industry including meats, grains, and dairy products (Shadow, 1998).
Consortium Building For PEM MFC Using Synthetic Media As Substrate
Authors: Ayyappan Muralidharan , Parida Dimpal , Yadav Arti , Mohandass Ramya
Published: July 2019

Microbial production of electricity is an important form of bioenergy since Microbial Fuel cells (MFC) offer the possibility of extracting electric current from a wide range of organic wastes and renewable biomass. Factors affecting the MFC operational effectiveness are the MFC design and the bacterial metabolism and electron transfer. The purpose of this study is to identify species which are responsible for electricity generation so as to build a suitable consortium and to investigate the relative efficiencies between the microbial consortiums. Enrichment by repeated transfer of a bacterial consortium harvested from the anode compartment of a MFC with synthetic media as a substrate increased the output from an initial level of 34 mA to a maximal level of 363 mA. Scanning electron microscope image indicated the enhanced microbial biofilm deposition over the electrode which were not initially detected in the community.
Pramipexole protective effect on rotenone induced neurotoxicity in mice
Authors: Gad-Elhak Seham , Salama Mohamed , El-Tantawy Dina , El-Dakroury Sahar , Abd-Elghaffar Hasan , El-Dosouky Sara , Ghanem Abdelaziz
Published: July 2019

Introduction:Pramipexole is a new dopaminergic drug which has been approved for PD treatment. However, we tried to find a new capacity for this drug rather than symptomatic effect.

Materials and Methods:

A chronic rotenone model with daily oral dose of 30mg/kg was induced in mice. Pramipexole was tried in a new approach where the treatment began in the middle of rotenone course with oral dose 1mg/kg/day of pramipexole.

Results:

Further analysis of behavioral tests and immunohistochemistry revealed success of pramipexole in improving the rotenone intoxicated mice.

Conclusion:

These results showed possible beneficial effects of pramipexole against rotenone-induced neurotoxicity.
The Olfactory Nervous System Of Terrestrial And Aquatic Vertebrates
Authors: Hussain Ashiq
Published: July 2019

Animals in their natural milieu are surrounded by odors. These odors are rich source of information, and are perceived by sophisticated olfactory systems, that have evolved over time. The sense of smell helps species to localize prey, evade predators, explore food and recognize viable mates. In humans, memoirs, thoughts, emotions, and associations are more readily reached through the sense of smell than through any other channel. This suggests that olfactory processing is imperative and may differ fundamentally from processing in other sensory modalities. The molecular age in olfaction initiated in 1991 with the significant discovery of a large, multigene family of olfactory receptors in rat by Linda Buck and Richard Axel (Buck and Axel, 1991). The first cloned olfactory receptors consisted of a diverse repertoire of G-protein coupled receptors (GPCRs) with seven-trans membrane topology, and they were sparsely expressed in the olfactory epithelium. This Nobel Prize worthy pioneering discovery, together with availability of modern techniques and numerous completely sequenced genomes opened the way to characterize the gene families of olfactory receptors through exhaustive computational data mining in different species genome as well as by in vitro biology. In this review, I will explain about the two main model organism of olfactory perceptions, zebrafish and mouse.
Finite Predation Rate: a Novel Parameter for the Quantitative Measurement of Predation Potential of Predator at Population Level
Authors: Farhadi Roya , Gholizadeh Majid , Chi Hsin , Mou De-Fen , Allahyari Hossein , Yu Jih-Zu , Huang Yu-Bing , Yang Ta-Chi
Published: July 2019

Demography and population growth are the most important subjects of population ecology and economics. Finite and intrinsic growth rates have been used as standard parameters for describing and comparing growth potentials of populations. The predation potentials of predator populations or consumption potentials of consumer populations cannot be properly described using these growth rates alone. A standard parameter is needed for the description of the predation or consumption potential, as well as for the quantitative evaluation of a predator population in an ecosystem or biological control program. We show that the finite predation rate can be the standard parameter by linking the finite rate, the stable age-stage distribution, and the age-stage specific predation rate. The finite predation rate can be used to describe and compare the predation potentials of natural enemies used in biological control and in predicting the damage potential of different pest populations to crops.
Evolution signatures in genome network properties
Authors: Dalmolin Rodrigo , de Almeida Rita , Brunnet Leonardo , Rybarczyk-Filho José Luiz , Ferreira Ricardo , Moreira Jose Claudio , Castro Mauro
Published: July 2019

Genomes maybe organized as networks where protein-protein association plays the role of network links. The resulting networks are far from being random and their topological properties are a consequence of the underlying mechanisms for genome evolution. Considering data on protein-protein association networks from STRING database, we present experimental evidence that degree distribution is not scale free, presenting an increased probability for high degree nodes. We also show that the degree distribution approaches a scale invariant state as the number of genes in the network increases, although real genomes still present finite size effects. Based on the experimental evidence unveiled by these data analyses, we propose a simulation model for genome evolution, where genes in a network are either acquired de novo using a preferential attachment rule, or duplicated, with a duplication probability that linearly grows with gene degree and decreases with its clustering coefficient. The results show that topological distributions are better described than in previous genome evolution models. This model correctly predicts that, in order to produce protein-protein association networks with number of links and number of nodes in the observed range, it is necessary 90% of gene duplication and 10% of de novo gene acquisition. If this scenario is true, it implies a universal mechanism for genome evolution.
Distinct cytokine patterns in Occult Hepatitis C and Chronic Hepatitis C Virus Infection
Authors: Mousa Nasser , Abousamra Nashwa , Azza Abdel-Aziz Azza , Gad Yahia , Elhadidy Mona , Abd-elmaksoud Mohamed
Published: July 2019

Background & Aim:

The immunopathogenesis of chronic hepatitis C virus (HCV) infection is a matter of great controversy. The imbalance of T-helper lymphocyte cell cytokine production was believed to play an important pathogenic role in chronic viral hepatitis. Occult hepatitis C infection is regarded as a new entity that should be considered when diagnosing patients with a liver disease of unknown origin. The aim of this study was to determine serum T-helper 1 and T-helper 2 cytokine production in patients with occult HCV infection and its role in pathogenesis versus chronic viral hepatitis C infection.

Methods:

Serum levels of cytokines of T-helper 1 (IL-2, IFN-[gamma]) and T-helper 2 (IL-4) were measured in 27 patients with occult HCV infection and 50 patients with chronic hepatitis C infection.

Results:

The levels of the T-helper 1 cytokines, IL-2 and IFN-[gamma], were highly and significantly increased in patients with chronic HCV infection as compared with occult HCV infection (p<0.001). The T-helper 2 cytokine IL-4 was highly and significantly increased in occult HCV infection as compared with chronic HCV infection (p<0.001). Necroinflammation (P<0.001) fibrosis (P<0.001) and cirrhosis (P =0.03) were significantly increased in chronic HCV than occult HCV.

Conclusion:

Patients with occult HCV infection exhibited distinct immunoregulatory cytokine patterns, favoring viral persistence in the liver in spite of its absence from peripheral blood and explaining the less aggressive course of this disease entity than chronic hepatitis C virus infection.
A Biomimetic Model of the Outer Plexiform Layer by Incorporating Memristive Devices
Authors: Gelencser Andras , Prodromakis Themistoklis , Toumazou Christofer , Roska Tamas
Published: July 2019

In this paper we present a biorealistic model for the first part of the early vision processing by incorporating memristive nanodevices. The architecture of the proposed network is based on the organisation and functioning of the outer plexiform layer (OPL) in the vertebrate retina. We demonstrate that memristive devices are indeed a valuable building block for neuromorphic architectures, as their highly non-linear and adaptive response could be exploited for establishing ultra-dense networks with similar dynamics to their biological counterparts. We particularly show that hexagonal memristive grids can be employed for faithfully emulating the smoothing-effect occurring at the OPL for enhancing the dynamic range of the system. In addition, we employ a memristor-based thresholding scheme for detecting the edges of grayscale images, while the proposed system is also evaluated for its adaptation and fault tolerance capacity against different light or noise conditions as well as distinct device yields.
Design of RNAi reagents for invertebrate model organisms and human disease vectors
Authors: Horn Thomas , Boutros Michael
Published: July 2019

RNAi has become an important tool to silence gene expression in a variety of organisms, in particular when classical genetic methods are missing. However, application of this method in functional studies has raised new challenges in the design of RNAi reagents in order to minimize false positive and false negative results. Since the performance of reagents can be rarely validated on a genome-wide scale, improved computational methods are required that consider experimentally derived design parameters. Here, we describe computational methods for the design of RNAi reagents for invertebrate model organisms and human disease vectors, such as Anopheles. We describe procedures on how to design short and long double-stranded RNAs for single genes, and evaluate their predicted specificity and efficiency. Using a bioinformatics pipeline we also describe how to design a genome-wide RNAi library for Anopheles gambiae.
The Rise of Consortia
Authors: Caporaso Neil , Bennett Siiri
Published: July 2019

We provide some observations on the role of consortia in GWAS. We include 2 surveys (addressed to GWAS Investigators and to GWAS Consortia) sent to GWAS investigators in the spring of 2011. Tables and figures derived from the data are included. We also provide a summary table with some basic data on 110 consortia. We invite the community to visit the WikiGene site (http://www.wikigenes.org/GWAS/consortia.html) where this data may be further corrected and updated.
Assessment Of Response To Heart Failure Therapy: Ventricular Volume Changes Versus Shape Changes
Authors: Adhyapak Srilakshmi , Parachuri V.Rao
Published: July 2019

The prolate ellipsoid left ventricular geometry is crucial for its unique contraction and relaxation patterns. Perturbations in optimal cardiac function preceding overt heart failure ensue when this ellipsoid shape assumes a more spherical configuration. This stage of spherical configuration, prior to overt dilatation, is when therapy should be intensified. The dynamic shape changes during the cardiac cycle of systole and diastole in valvular regurgitations when ventricular volumes are within normal range have proved that shape changes are clearly dissociated from volume changes in the early stages. In the scenario of advanced heart failure, several therapeutic interventions have been tried with variable success. These therapies aim at decreasing the ventricular equator, and hence its volume. However, the ventricular shape may still be spherical leading to suboptimal function. The aim in any therapy for heart failure should be therefore to achieve near normal left ventricular anatomy and physiology, with shape assessment as the surrogate marker of therapeutic success.
Limitation of F1 hybrids uniformity law
Authors: Levites Evgenii
Published: July 2019

Using isozymes as markers, data indicative of polymorphisms in the progeny produced from crossing two beet plants, homozygous on contrastive alleles of enzyme loci, were obtained.
Determination of linkage disequilibrium region suggests association of the ancient haplotype, hX with neural function
Authors: Shimada Makoto , Kanasashi Tsutomu
Published: July 2019

Modern human populations are known to contain "ancient haplotypes" that originated from archaic humans by hybridization. Some of them had been reported before the development of human genomic diversity databases, such as HapMap. Consequently, some of them have no information about linkage disequilibrium (LD) regions. Because genetic information within LD is tightly linked, to know LD region containing ancient haplotypes will be useful to estimate basic parameters of admixture events, and to infer biological functions that linked with the ancient haplotypes. One of these ancient haplotypes, haplotype X (hX) was found in a 10.1 kb-region located on Xp11.22, which diverged at 1.4 M years ago, with low diversity within the cluster in gene genealogy and worldwide distribution in low frequency. We determined the LD region around the ancient haplotypes using LD information obtained in the HapMap project. The LD determination presents that the LD region surrounding the hX is stable and contains genic regions that may associate with neural and brain functions.
The genomic landscape of Epstein-Barr virus-associated pulmonary lymphoepithelioma-like carcinoma
Authors: Hong Shaodong , Liu Dongbing , Luo Shuzhen , Fang Wenfeng , Zhan Jianhua , Fu Sha , Zhang Yaxiong , Wu Xuan , Zhou Huaqiang , Chen Xi , Chen Gang , Zhang Zhonghan , Zheng Qiufan , Li Xiaobo , Chen Jinghao , Liu Xingmin , Lei Mengyue , Ye Chen , Wang Jian , Yang Huanming , Xu Xun , Zhu Shida , Yang Yunpeng , Zhao Yuanyuan , Zhou Ningning , Zhao Hongyun , Huang Yan , Zhang Lanjun , Wu Kui , Zhang Li
Published: July 2019

Pulmonary lymphoepithelioma-like carcinoma (LELC) is a rare and distinct subtype of primary lung cancer characterized by Epstein-Barr virus (EBV) infection. Herein, we reported the mutational landscape of pulmonary LELC using whole-exome sequencing, targeted deep sequencing and single-nucleotide polymorphism arrays. We identify a low degree of somatic mutation but widespread existence of copy number variations. We reveal predominant signature 2 mutations and frequent loss of type I interferon genes that are involved in the host-virus counteraction. Integrated analysis shows enrichment of genetic lesions affecting several critical pathways, including NF-κB, JAK/STAT, and cell cycle. Notably, multi-dimensional comparison unveils that pulmonary LELC resemble NPC but are clearly different from other lung cancers, natural killer/T-cell lymphoma or EBV-related gastric cancer in terms of genetic features. In all, our study illustrates a distinct genomic landscape of pulmonary LELC and provides a road map to facilitate genome-guided personalized treatment.
High density oilfield wastewater disposal causes deeper, stronger, and more persistent earthquakes
Authors: Pollyea Ryan M. , Chapman Martin C. , Jayne Richard S. , Wu Hao
Published: July 2019

Oilfield wastewater disposal causes fluid pressure transients that induce earthquakes. Here we show that, in addition to pressure transients related to pumping, there are pressure transients caused by density differences between the wastewater and host rock fluids. In northern Oklahoma, this effect caused earthquakes to migrate downward at ~0.5 km per year during a period of high-rate injections. Following substantial injection rate reductions, the downward earthquake migration rate slowed to ~0.1 km per year. Our model of this scenario shows that the density-driven pressure front migrates downward at comparable rates. This effect may locally increase fluid pressure below injection wells for 10+ years after substantial injection rate reductions. We also show that in north-central Oklahoma the relative proportion of high-magnitude earthquakes increases at 8+ km depth. Thus, our study implies that, following injection rate reductions, the frequency of high-magnitude earthquakes may decay more slowly than the overall earthquake rate.
Microbial spatial footprint as a driver of soil carbon stabilization
Authors: Kravchenko A. N. , Guber A. K. , Razavi B. S. , Koestel J. , Quigley M. Y. , Robertson G. P. , Kuzyakov Y.
Published: July 2019

Increasing the potential of soil to store carbon (C) is an acknowledged and emphasized strategy for capturing atmospheric CO2. Well-recognized approaches for soil C accretion include reducing soil disturbance, increasing plant biomass inputs, and enhancing plant diversity. Yet experimental evidence often fails to support anticipated C gains, suggesting that our integrated understanding of soil C accretion remains insufficient. Here we use a unique combination of X-ray micro-tomography and micro-scale enzyme mapping to demonstrate for the first time that plant-stimulated soil pore formation appears to be a major, hitherto unrecognized, determinant of whether new C inputs are stored or lost to the atmosphere. Unlike monocultures, diverse plant communities favor the development of 30–150 µm pores. Such pores are the micro-environments associated with higher enzyme activities, and greater abundance of such pores translates into a greater spatial footprint that microorganisms make on the soil and consequently soil C storage capacity.
Systematic allelic analysis defines the interplay of key pathways in X chromosome inactivation
Authors: Nesterova Tatyana B. , Wei Guifeng , Coker Heather , Pintacuda Greta , Bowness Joseph S. , Zhang Tianyi , Almeida Mafalda , Bloechl Bianca , Moindrot Benoit , Carter Emma J. , Alvarez Rodrigo Ines , Pan Qi , Bi Ying , Song Chun-Xiao , Brockdorff Neil
Published: July 2019

Xist RNA, the master regulator of X chromosome inactivation, acts in cis to induce chromosome-wide silencing. Whilst recent studies have defined candidate silencing factors, their relative contribution to repressing different genes, and their relationship with one another is poorly understood. Here we describe a systematic analysis of Xist-mediated allelic silencing in mouse embryonic stem cell-based models. Using a machine learning approach we identify distance to the Xist locus and prior gene expression levels as key determinants of silencing efficiency. We go on to show that Spen, recruited through the Xist A-repeat, plays a central role, being critical for silencing of all except a subset of weakly expressed genes. Polycomb, recruited through the Xist B/C-repeat, also plays a key role, favouring silencing of genes with pre-existing H3K27me3 chromatin. LBR and the Rbm15/m6A-methyltransferase complex make only minor contributions to gene silencing. Together our results provide a comprehensive model for Xist-mediated chromosome silencing.
Superior Photo-thermionic electron Emission from Illuminated Phosphorene Surface
Authors: Madas S. , Mishra S. K. , Kahaly S. , Kahaly M. Upadhyay
Published: July 2019

This work demonstrates that black phosphorene, a two dimensional allotrope of phosphorus, has the potential to be an efficient photo-thermionic emitter. To investigate and understand the novel aspects we use a combined approach in which ab initio quantum simulation tools are utilized along with semiclassical description for the emission process. First by using density functional theory based formalism, we study the band structure of phosphorene. From the locations of electronic bands, and band edges, we estimate the Fermi level and work function. This leads us to define a valid material specific parameter space and establish a formalism for estimating thermionic electron emission current from phosphorene. Finally we demonstrate how the emission current can be enhanced substantially under the effect of photon irradiation. We observe that photoemission flux to strongly dominate over its coexisting counterpart thermionic emission flux. Anisotropy in phosphorene structure plays important role in enhancing the flux. The approach which is valid over a much wider range of parameters is successfully tested against recently performed experiments in a different context. The results open up a new possibility for application of phosphorene based thermionic and photo-thermionic energy converters.
A Pilot Proof-Of-Principle Analysis Demonstrating Dielectrophoresis (DEP) as a Glioblastoma Biomarker Platform
Authors: Lewis Jean , Alattar Ali A. , Akers Johnny , Carter Bob S. , Heller Michael , Chen Clark C.
Published: July 2019

Extracellular vesicles (EVs) are small, membrane-bound particles released by all cells that have emerged as an attractive biomarker platform. We study the utility of a dielectrophoretic (DEP) micro-chip device for isolation and characterization of EVs derived from plasma specimens from patients with brain tumors. EVs were isolated by DEP chip and subjected to on-chip immunofluorescence (IF) staining to determine the concentration of glial fibrillary acidic protein (GFAP) and Tau. EVs were analyzed from the plasma samples isolated from independent patient cohorts. Glioblastoma cell lines secrete EVs enriched for GFAP and Tau. These EVs can be efficiently isolated using the DEP platform. Application of DEP to clinical plasma samples afforded discrimination of plasma derived from brain tumor patients relative to those derived from patients without history of brain cancer. Sixty-five percent (11/17) of brain tumor patients showed higher EV-GFAP than the maximum observed in controls. Ninety-four percent (16/17) of tumor patients showed higher EV-Tau than the maximum observed in controls. These discrimination thresholds were applied to plasma isolated from a second, independent cohort of 15 glioblastoma patients and 8 controls. For EV-GFAP, we observed 93% sensitivity, 38% specificity, 74% PPV, 75% NPV, and AUC of 0.65; for EV-Tau, we found 67% sensitivity, 75% specificity 83% PPV, 55% NPV, and AUC of 0.71 for glioblastoma diagnosis. This proof-of-principle study provides support for DEP-IF of plasma EVs for diagnosis of glioblastoma.
Observation of treated iris neovascularization by swept-source-based en-face anterior-segment optical coherence tomography angiography
Authors: Shiozaki Daiki , Sakimoto Susumu , Shiraki Akihiko , Wakabayashi Taku , Fukushima Yoko , Oie Yoshinori , Usui Shinichi , Sato Shigeru , Sakaguchi Hirokazu , Nishida Kohji
Published: July 2019

We evaluated regression of iris neovascularization (INV) using en-face anterior-segment optical coherence tomography angiography (AS-OCTA) after anti-vascular endothelial growth factor (VEGF) therapy. Seven consecutive eyes with INV were examined before and after anti-VEGF therapy, and all AS-OCTA scans were obtained using a swept-source OCTA system with an anterior-segment lens adapter. Slit-lamp microscopy photography and anterior indocyanine green angiography also were performed. Quantitative analyses of the vascular density, vascular lacunarity, and fractal dimension on AS-OCTA images were performed. AS-OCTA visualized the INV as signals around the pupillary margin, which corresponded to the vasculature confirmed by slit-lamp microscopy. After anti-VEGF drug injection, regression of INV was observed by AS-OCTA in all eyes (100%). The vascular density decreased and vascular lacunarity increased significantly after anti-VEGF therapy. This pilot study demonstrated the ability of AS-OCTA not only to detect but also to evaluate INV. Further study is warranted to improve the algorithm for delineating the iris vasculature to decrease artifacts.