bluuebunny/crossref_metadata_2025 huggingface dataset:
Hypofractioned radiotherapy versus conventional radiotherapy for the treatment of multiform glioblastoma in adults over 70 years old
Authors: Jiménez Cantero Adriana , Chávez Nogueda Jessica , Flores Vázquez Fabiola , Castillo de la Garza José Pablo , Hernández Montes de Oca Raymundo , Olmos Guzmán Alejandro
Published: July 2019

Aim:

Multiform glioblastoma (MG) represents 70% of all gliomas, with half of patients older than 65 years with median survival of 12–18 months, hypofractionation seeks to reduce the intensity and duration of treatment without impacting on survival rates. The objective was to determine the global survival and recurrence-free survival of adults over 70 years old with MG treated with hypofractionated radiotherapy and standard scheme. The review of patients older than 70 years treated with radiotherapy from 2013 to 2016 was performed.

Results:

Twenty-four patients were analysed, with a median follow-up of 239 days, and there is no difference in overall survival 12·3 versus 10·5 months (p = 0·55) and recurrence-free survival 8·3 versus 3·4 months (p = 0·48) between both schemes, conventional versus hypofractioanted, respectively.

Conclusion:

The results in this study show that hypofractionated scheme could be comparable in overall survival and recurrence-free survival to conventional fractionation, but a longer patients’ trial should be done.
Validation of the Brazilian version of the Shame and Stigma Scale (SSS-Br) for patients with head and neck cancers
Authors: Pirola William Eduardo , Paiva Bianca Sakamoto Ribeiro , de Oliveira Cleyton Zanardo , Lucchetti Giancarlo , Lucchetti Alessandra Lamas Granero , Kissane David , Paiva Carlos Eduardo
Published: July 2019

Objective

To evaluate the psychometric properties of the Brazilian version of the Shame and Stigma Scale (SSS) in a sample of patients with head and neck cancers (HNC).

Methods

This is a validation study carried out in a Brazilian cancer hospital. Patients over 18 years old who knew about their HNC diagnosis were consecutively recruited, answering the SSS, the Functional Assessment of Cancer Therapy (General and Head and Neck supplement) questionnaire, and the University of Washington Quality of Life Questionnaire. Internal consistency, test-retest procedure, convergent validity, and responsiveness analysis were the psychometric properties evaluated.

Results

A total of 122 HNC patients were included. The SSS showed appropriate internal consistency (alphas ranging from 0.71 to 0.86), test-retest reliability (higher than 0.92 with exception of the “Regret domain”), and convergent validity. The responsiveness analysis with 38 patients was able to discriminate the scores before and after prosthetic procedures.

Significance of the Results

The Brazilian Portuguese version of the SSS may be considered a valid and reliable instrument for the evaluation of Brazilian patients with HNC. Future SSS validation studies are welcome in other developing countries in order to make cancer health providers aware of these negative feelings in their HNC patients.
Gene-specific marker screening and disease reaction validation of blast resistant genes, Pid3, Pigm and Pi54 in Thai landrace rice germplasm and recommended rice varieties
Authors: Teerasan Wattanaporn , Srikaew Ing-on , Phaitreejit Kritkittisak , Kate-Ngam Sureeporn , Jantasuriyarat Chatchawan
Published: July 2019

Rice blast caused by the fungal pathogen Magnaporthe oryzae, is one of the most devastating diseases in rice production worldwide. Information on rice varieties with the blast disease resistance gene is important for rice cultivar development. This study identified rice blast resistant genes in 226 rice cultivars including 203 Thai landrace rice cultivars (19 upland rice cultivars from the North, 99 lowland rice cultivars from the Northeast, 45 floating rice cultivars from the Northeast and 40 cultivars from the South), 21 recommended rice varieties and two susceptible varieties ‘KDML105’ and ‘Nipponbare’ by using gene-specific markers for the blast resistant genes Pid3, Pi54 and Pigm. Results showed that 159 cultivars have at least one resistant gene and four cultivars have all three resistant genes. These results indicate that Thai landrace rice is a valuable source of rice blast resistant genes for rice breeding programmes.
Dynamic Response of Ionospheric Plasma Density to the Geomagnetic Storm of 22‐23 June 2015
Authors: Ngwira Chigomezyo M. , Habarulema John‐Bosco , Astafyeva Elvira , Yizengaw Endawoke , Jonah Olusegun F. , Crowley Geoff , Gisler Andrew , Coffey Victoria
Published: July 2019

On 21–22 June 2015, three consecutive interplanetary shocks slammed into the Earth's magnetosphere. Immediately after the third shock at 18:36 UT on 22 June, marked by an exceptional sudden storm commencement with an amplitude of ΔSYM‐H = ∼106 nT, a major geomagnetic storm commenced. In the present study, a multi‐instrument approach comprising observations, data analysis, and modeling is used to examine the global ionospheric response. Results show that enhanced storm time processes produced major total electron content (TEC) variations at different latitudes, longitudes, and phases of the storm. A closer inspection of the TEC observations reveals strong longitudinal and hemispherical asymmetry. In addition, multiple equatorward and poleward propagating traveling ionospheric disturbances (TIDs) were detected in the TEC data. Equatorward propagating TIDs are consistent with vertical neutral winds simulated from Thermosphere‐Ionosphere‐Electrodynamics General Circulation Model; however, poleward TIDs were not reproduced in the model. We find that a combination of driving processes including enhanced high‐latitude injection, prompt penetration electric fields, disturbance dynamo effect, neutral winds, and composition changes were acting at different stages of the storm.
Fault Slip and Exhumation History of the Willard Thrust Sheet, Sevier Fold‐Thrust Belt, Utah: Relations to Wedge Propagation, Hinterland Uplift, and Foreland Basin Sedimentation
Authors: Yonkee W. A. , Eleogram B. , Wells M. L. , Stockli D. F. , Kelley S. , Barber D. E.
Published: July 2019

Zircon (U‐Th)/He (ZHe) and zircon fission track thermochronometric data for 47 samples spanning the areally extensive Willard thrust sheet within the western part of the Sevier fold‐thrust belt record enhanced cooling and exhumation during major thrust slip spanning approximately 125–90 Ma. ZHe and zircon fission track age‐paleodepth patterns along structural transects and age‐distance relations along stratigraphic‐parallel traverses, combined with thermo‐kinematic modeling, constrain the fault slip history, with estimated slip rates of ~1 km/Myr from 125 to 105 Ma, increasing to ~3 km/Myr from 105 to 92 Ma, and then decreasing as major slip was transferred onto eastern thrusts. Exhumation was concentrated during motion up thrust ramps with estimated erosion rates of ~0.1 to 0.3 km/Myr. Local cooling ages of approximately 160–150 Ma may record a period of regional erosion, or alternatively an early phase of limited (<10 km) thrust slip. Propagation of the Sevier wedge front and major thrust slip during the late Early to mid‐Cretaceous were synchronous with increasing subsidence and deposition of thick synorogenic strata in the foreland, crustal thickening in the hinterland, growing igneous activity in the Sierran magmatic arc, and increasing plate convergence rates. Along‐strike, other parts of the Cordilleran retroarc fold‐thrust belt also experienced major shortening during the late Early to mid‐Cretaceous, following a period of earlier Cretaceous quiescence. Late Jurassic shortening was concentrated nearer the arc, and thus mostly in the hinterland at the latitude of northern Utah, related to width and location of the passive‐margin sedimentary wedge relative to the plate margin.
The When and Where of Mesospheric Bores Revealed
Authors: Shultz David
Published: July 2019

In a new study, the enigmatic gravity waves were seen most frequently at equatorial latitudes and propagating from the winter to the summer hemisphere.
Detection of a Climate Change Signal in Extreme Heat, Heat Stress, and Cold in Europe From Observations
Authors: Lorenz Ruth , Stalhandske Zélie , Fischer Erich M.
Published: July 2019

In the last two decades Europe experienced a series of high‐impact heat extremes. We here assess observed trends in temperature extremes at ECA&D stations in Europe. We demonstrate that on average across Europe the number of days with extreme heat and heat stress has more than tripled and hot extremes have warmed by 2.3 °C from 1950–2018. Over Central Europe, the warming exceeds the corresponding summer mean warming by 50%. Days with extreme cold temperatures have decreased by a factor of 2–3 and warmed by more than 3 °C, regionally substantially more than winter mean temperatures. Cold and hot extremes have warmed at about 94% of stations, a climate change signal that cannot be explained by internal variability. The clearest climate change signal can be detected in maximum heat stress. EURO‐CORDEX RCMs broadly capture observed trends but the majority underestimates the warming of hot extremes and overestimates the warming of cold extremes.
Developing and Testing Physically Based Triggering Thresholds for Runoff‐Generated Debris Flows
Authors: Tang Hui , McGuire Luke A. , Rengers Francis K. , Kean Jason W. , Staley Dennis M. , Smith Joel B.
Published: July 2019

Runoff in steep channels is capable of transitioning into debris flows with hazardous implications for downstream communities and infrastructure, particularly in alpine landscapes with minimal vegetation and areas recently disturbed by wildfire. Here, we derive thresholds for the initiation of runoff‐generated debris flows based on critical values of dimensionless discharge and Shields stress. These thresholds are derived by using a numerical model to estimate the hydrodynamic conditions coinciding with the timing of debris flow activity in a recently burned basin. A benefit of hydrodynamic thresholds is that they can be used to assess debris flow likelihood based on measurable hydrologic and geomorphic parameters and therefore provide more universal criteria for quantifying the runoff‐to‐debris flow transition in landscape evolution studies and hazard assessments. We then demonstrate how hydrodynamic thresholds can be used to estimate rainfall intensity‐duration thresholds for runoff‐generated debris flows without the need for historic debris flow observations.
Interrogating a Surging Glacier With Seismic Interferometry
Authors: Aster Richard C.
Published: July 2019

Seismic interferometry can be spectacularly sensitive to temporal changes within the Earth. Zhan (2019, https://doi.org/10.1029/2019GL082411) analyzed 12 years of data from seismic stations situated near Bering Glacier, Alaska, that spanned a 2008–2011 surge. Interferometrically isolated glacier‐crossing surface waves revealed an anisotropic seismic wave speed decrease during the surge. 1‐D and 3‐D modeling suggests pressurized englacial water flow being stored and guided by a network of basal crevasses, thereby sustaining high water pressure at the bed and supporting the high surge velocities. This result is demonstrative of the potential for seismic interferometry and other cryoseismological methods to continuously monitor and reveal changes within dynamic glacial‐hydrological systems.
Statistical Distribution of Whistler Mode Waves in the Radiation Belts With Large Magnetic Field Amplitudes and Comparison to Large Electric Field Amplitudes
Authors: Tyler E. , Breneman A. , Cattell C. , Wygant J. , Thaller S. , Malaspina D.
Published: July 2019

We present a statistical analysis with 100% duty cycle and non‐time‐averaged amplitudes of the prevalence and distribution of high‐amplitude >50‐pT whistler mode waves in the outer radiation belt using 5 years of Van Allen Probes data. Whistler mode waves with high magnetic field amplitudes are most common above L=4.5 and between magnetic local time of 0–14 where they are present approximately 1–6% of the time. During high geomagnetic activity, high‐amplitude whistler mode wave occurrence rises above 25% in some regions. The dayside population are more common during quiet or moderate geomagnetic activity and occur primarily >5° from the magnetic equator, while the night‐to‐dawn population are enhanced during active times and are primarily within 5° of the magnetic equator. These results are different from the distribution of electric field peaks discussed in our previous paper covering the same time period and spatial range. Our previous study found large‐amplitude electric field peaks were common down to L=3.5 and were largely absent from afternoon and near noon. The different distribution of large electric and magnetic field amplitudes implies that the low‐L component of whistler mode waves observed previously are primarily highly oblique, while the dayside and high‐L populations are primarily field aligned. These results have important implications for modeling radiation belt particle interactions with chorus, as large‐amplitude waves interact nonlinearly with electrons, resulting in rapid energization, de‐energization, or pitch angle scattering. This also may provide clues regarding the mechanisms which can cause significant whistler mode wave growth up to more than 100 times the average wave amplitude.
Along‐Strike and Downdip Segmentation of the Pamir Frontal Thrust and Its Association With the 1985Mw6.9 Wuqia Earthquake
Authors: Li Tao , Chen Zhuxin , Chen Jie , Thompson Jobe Jessica A. , Burbank Douglas W. , Li Zhigang , He Xiaohui , Zheng Wenjun , Zhang Peizhen , Zhang Boxuan
Published: July 2019

The Pamir Frontal Thrust along the leading edge of the northern Pamir is characterized by multiple earthquakes with moment magnitudes of 6.5–7.1. Geometric characteristics of the Pamir Frontal Thrust corresponding to these earthquakes and to future seismic hazards, however, remain largely unexplored. This study focuses on the easternmost segment of the Pamir Frontal Thrust, where theMw6.9 Wuqia earthquake occurred in 1985. Through interpretation of available two‐dimensional seismic reflection profiles and surface mapping data, we develop a three‐dimensional geometric model for the fault plane. Our results illustrate that, at depth, the fault plane is separated by a subhorizontal detachment horizon into upper and lower ramps, and both ramps are significantly segmented, along strike, by transfer faults or lateral ramps as well. Such along‐strike and downdip segmentation of the thrust sheet apparently plays a significant control on seismic rupture process of the Wuqia earthquake and can well explain why the region is characterized by moderate‐magnitude (Mw6.5–7.1) events. Additionally, our study helps quantify key constraints on the Cenozoic deformation and evolution of the northeastern Pamir and, specifically, determines a total shortening of ≤43 km at the Pamir front: accommodating about 15% of the total indentation of the Pamir range into central Asia.
Systems Biology Graphical Notation: Process Description language Level 1
Authors: Moodie Stuart , Le Novere Nicolas , Demir Emek , Mi Huaiyu , Schreiber Falk
Published: July 2019

Standard graphical representations have played a crucial role in science and engineering throughout the last century. Without electrical symbolism, it is very likely that our industrial society would not have evolved at the same pace. Similarly, specialised notations such as the Feynmann notation or the process flow diagrams did a lot for the adoption of concepts in their own fields. With the advent of Systems Biology, and more recently of Synthetic Biology, the need for precise and unambiguous descriptions of biochemical interactions has become more pressing. While some ideas have been advanced over the last decade, with a few detailed proposals, no actual community standard has emerged. The Systems Biology Graphical Notation (SBGN) is a graphical representation crafted over several years by a community of biochemists, modellers and computer scientists. Three orthogonal and complementary languages have been created, the Process Diagrams, the Entity Relationship Diagrams and the Activity Flow Diagrams. Using these three idioms a scientist can represent any network of biochemical interactions, which can then be interpreted in an unambiguous way. The set of symbols used is limited, and the grammar quite simple, to allow its usage in textbooks and its teaching directly in high schools. The first level of the SBGN Process Diagram has been publicly released. Software support for SBGN Process Diagram was developed concurrently with its specification in order to speed-up public adoption. Shared by the communities of biochemists, genomicians, theoreticians and computational biologists, SBGN languages will foster efficient storage, exchange and reuse of information on signalling pathways, metabolic networks and gene regulatory maps.
Mitigation of GHGs Emission From Soils by a Catalyzed In-Situ Photo-Oxidative Polymerization of Soil Organic Matter
Authors: Piccolo Alessandro , Spaccini Riccardo
Published: July 2019

Agricultural lands under food and bio-energy crops, managed grass and permanent crops including agro-forestry, occupy about 40-50% of the Earth's land surface^1^. In 2005, agriculture accounted for an estimated emission of 5.1 to 6.1 GtCO2-eq/yr (10-12% of total global anthropogenic emissions of greenhouse gases (GHGs))^1^. However, measures to mitigate GHGs emission from agricultural soils are limited to improved cropland practices such as crop rotation, nutrient management, tillage/residue management, agroforestry, and return to natural vegetation^2^. These practices are not only far from substantially reducing GHGs emissions from soils or permanentlystabilizing soil organic matter^1-4^, but are also predicted to hardly match more than amaximum of 25% of the GHGs reductions required by the Kyoto Protocol within 2050^5^.Despite the knowledge that GHGs release from soil largely derives from biochemicaltransformations of plant litter and soil organic matter (SOM)^6-8^, no new and much wished biotechnological measures are adopted so far to augment mitigation^1^. Here we propose an innovative approach to mitigate GHGs emissions from soils based on the insitu photo-polymerization of SOM under biomimetic catalysis. Three Mediterranean soils of different physical and chemical properties were added with a synthetic watersolubleiron-porphyrin, irradiated by solar light, and subjected to 15, and 30 wetting and drying cycles. We found that the in situ catalysed photo-polymerization of SOM increased soil physical aggregation, shifted OC into larger soil aggregates, and reduced CO~2~ released by microbial respiration. Our findings suggest that "green" catalytic technologies can become viable soil management practices to enhance mitigation of GHGs emission from arable soils and contribute to match the expectations of the post-Kyoto Protocol in the agricultural sector.
Using Metaneva for Structuring, Managing and Retrieving Animal Data in the Cognitive Neurosciences
Authors: Derom Dirk , Schmidt Randall , McLeod Ian , Hewitt Bruce
Published: July 2019

Contemporary cognitive neuroscience data sets are characterized by a lack of a standardized ontology, leading to shortcomings in data reports and data sharing along with possibly outdated modular models of functional brain mechanisms. Neuroinformatics is actively addressing these hiatuses, developing detailed and more powerful workbenches. However, the structuring of data is largely neglected due to the intrinsically different data sets in the neurosciences. Here we present a workbench called Metaneva addressing the need of data structures for the improvement of both data storage and data retrieval. We hereby present both our data structuring approach and the system developed specifically for the storage and retrieval of this Metaneva specific data structures.
Interaction of the TNFR-Receptor Associated Factor TRAF1 with I-kappa B Kinase-2 and TRAF2 Indicates a Regulatory Function for NF-kappa B Signaling
Authors: Sughra Kalsoom , Birbach Andreas , de Martin Rainer , Schmid Johannes
Published: July 2019

Background

I-kappa B kinase 2 (IKK2 or IKK-beta) is one of the most crucial signaling kinases for activation of NF-kappa B, a transcription factor that is important for inflammation, cell survival and differentiation. Since many NF-kappa B activating pathways converge at the level of IKK2, molecular interactions of this kinase are pivotal for regulation of NF-kappa B signaling.*Methodology/Principal Findings*We searched for proteins interacting with IKK2 using the C-terminal part (amino acids 466-756) as bait in a yeast two-hybrid system and identified the N-terminal part (amino acids 1-228) of the TNF-receptor associated factor TRAF1 as putative interaction partner. The interaction was confirmed in human cells by mammalian two-hybrid and coimmunoprecipitation experiments. The IKK2/TRAF1 interaction seemed weaker than the interaction between TRAF1 and TRAF2, an important activating adapter molecule of NF-kappa B signaling. Reporter gene and kinase assays using ectopic expression of TRAF1 indicated that it can both activate and inhibit IKK2 and NF-kappa B. Co-expression of fluorescently tagged TRAF1 and TRAF2 at different ratios implied that TRAF1 can affect clustering and presumably the activating function of TRAF2 in a dose dependent manner.

Conclusions/Significance

The observation that TRAF1 can either activate or inhibit the NF-kappa B pathway and the fact that it influences the oligomerization of TRAF2 indicates that relative levels of IKK2, TRAF1 and TRAF2 may be important for regulation of NF-kappa B activity. Since TRAF1 is an NF-kappa B induced gene, it might act as a feedback effector molecule.
Immunogenic Modulations Induced by Prospective Anti-Malarial Herbal Extracts in Murine Model
Authors: Chakraborty Sudipta , Chhetri Swapna , Ray Sajal , Gupta Shyamal Das , Mukherjee Suman , Bhunia Niladri Sekhar , Das Manoj , Biswas Sanat , Sarkar Sreemayee , Mandal Guruprasad , Singha Dipankar , Karjee Chinmoy
Published: July 2019

Keeping in view the ever increasing problem of drug resistance and affordability of the antimalarial drugs by the poor mass, herbal medicines can become an important and alternative sustainable strategy for malaria treatment. Aqueous extracts of three Himalayan herbs― Equisetum ravense, Artemisia vulgaris and Centella asiatica, with reported antimalarial property were screened for clinical efficacy against a local strain of Plasmodium vivax antigen in murine model. E. arvense extract was consistent in boosting phagocytic activity, nitric oxide generation, acid phosphatase and alkaline phosphatase activities in the peritoneal macrophages. The effectiveness of the rest herbals was discrete. A need for further detailed investigation to evaluate the clinical efficacy of these herbals seems essential.
Neuron impairment or loss in brain may be responsible for type 2 diabetes and essential hypertension
Authors: Zheng Xiang , Zhou Xue
Published: July 2019

Type 2 diabetes and essential hypertension are both very common chronic diseases. Type 2 diabetes is often associated with hypertension, but the exact causes of them are unknown. Here, based on recent investigations, we will look at the pathogenesis of these two diseases in a new light.
The novel adiponectin-resistin (AR) and insulin resistance (IR~AR~) indexes
Authors: Lau Cia-Hin , Muniandy Sekaran
Published: July 2019

Serum hypoadiponectinemia and hyperrestinemia independently links insulin resistance to type 2 diabetes (T2DM) and metabolic syndrome (MS). Thus, the aim of this study was propose a novel adiponectin-resistin (AR) index by unifying the effect of adiponectin and resistin. Then, a novel insulin resistance (IR~AR~) index was proposed by taking into account the AR index. Serum adiponectin and resistin levels as well as other insulin resistance, T2DM and MS risk factors were tested. Experimental results showed the AR index was more stronger correlated with insulin resistance risk factors and had stronger association (df=5; F=51.154; P<0.001) with T2DM and MS susceptibility rather than the serum adiponectin (df=5; F=15.680; P<0.001) and resistin (df=5; F=40.648; P<0.001) levels alone. Therefore, the AR index looks very strongly links insulin resistance to T2DM and MS. Meanwhile, the IR~AR~ index (df=5; F=78.396; P<0.001) is a potent useful index of insulin sensitivity in subjects with T2DM and MS.
Inflammation targets specific organs for cancer in carriers of BRCA1/2 pathway mutations
Authors: Friedenson Bernard
Published: July 2019

Women who inherit a defective BRCA1 or BRCA2 gene have risks for breast/ovarian cancer that are so high and apparently so selective that many mutation carriers choose to have the most likely targets for cancer surgically removed. Recent research has focused on better methods of treating such seemingly unavoidable hereditary cancers. Prevention has received much less attention so a positive test result for a cancer gene leaves carriers with very limited options. In order to prevent BRCA1/2 related cancers, it may be important to understand why they seem to occur only in certain characteristic organs. Results here show that mutations in a pathway depending on BRCA1/2 gene products magnify cancer risks from chronic infection and inflammation, making them especially important in selecting the site where hereditary cancer develops. Controlling chronic infections and inflammation may be a helpful option to prevent or delay cancers in mutation carriers.
The Symmetrical Immune Network Theory and a New HIV Vaccine Concept
Authors: Hoffmann Geoffrey
Published: July 2019

The symmetrical immune network theory is based on Jerne’s network hypothesis. An improved version of the theory is presented. The theory is characterized by symmetrical stimulatory, inhibitory and killing interactions between idiotypic and antiidiotypic immune system components. In this version killing is ascribed to IgM antibodies, while IgG antibodies are stimulatory. In the symmetrical immune network theory T cells make specific T cell factors, that have a single V region, and are cytophilic for non-specific accessory cells (A cells, including macrophages and monocytes) and play a role in the system switching between stable steady states. A recurring theme in the theory is the concept of co selection. Co-selection is the mutual positive selection of individual members from within two diverse populations, such that selection of members within each population is dependent on interaction with (recognition of) one or more members within the other population. Prior to exposure to an antigen, antigen-specific and antiidiotypic T cells are equally diverse. This equality is a form of symmetry. Immune responses with the production of IgG involve co selection of the antigen-specific and antiidiotypic classes with the breaking of this diversity symmetry, while induction of unresponsiveness involves co-selection without the breaking of diversity symmetry. The theory resolves the famous I-J paradox of the 1980s, based on co selection of helper T cells with some affinity for MHC class II and suppressor T cells that are anti-anti-MHC class II. The theory leads to three experimentally testable predictions concerning I-J. The theory includes a model for HIV pathogenesis, and suggests that polyclonal IgG from many donors given in immunogenic form may be an effective vaccine for protection against infection with HIV. Surprisingly, a mathematical model that simulates the autonomous dynamics of the system is the same as one that models a previously described neural network.
Phosphatidylserine polarization is required for proper Cdc42 localization and for development of cell polarity.
Authors: Fairn Gregory , Grinstein Sergio
Published: July 2019

We used genetically-encoded fluorescent probes to visualize the distribution of phosphatidylserine (PS) in live S. cerevisiae. The majority of the PS was found to reside in the cytosolic leaflet of the plasma membrane. Remarkably, PS was polarized, accumulating in bud necks, the bud cortex and the tips of mating projections. Polarization required vectorial delivery of PS-enriched secretory and recycling vesicles. Rapid dissipation of the PS gradient is prevented by the slow diffusion of lipids along the plasmalemmal inner leaflet, estimated by photobleaching recovery measurements to be over an order of magnitude slower than in mammalian cells. In mutants lacking PS-synthase the absence of PS was associated with, and likely responsible for impaired polarization of the Cdc42 complex, leading to inhibition of bud emergence, diminished growth rate and abolishment of mating. The results indicate that PS polarization is required for optimal Cdc42 targeting and activation during cell division and mating.
Higher accuracy protein Multiple Sequence Alignment by Stochastic Algorithm
Authors: Jeevitesh M. , Behera Narayan , Jose Justin , Kant Krishna , Dey Alpana
Published: July 2019

Multiple Sequence Alignment gives insight into evolutionary, structural and functional relationships among the proteins. Here, a novel Protein Alignment by Stochastic Algorithm (PASA) is developed. Evolutionary operators of a genetic algorithm, namely, mutation and selection are utilized in combining the output of two most important sequence alignment programs and then developing an optimized new algorithm. Efficiency of protein alignments is evaluated in terms of Total Column score which is equal to the number of correctly aligned columns between a test alignment and the reference alignment divided by the total number of columns in the reference alignment. The PASA optimizer achieves, on an average, significant better alignment over the well known individual bioinformatics tools. This PASA is statistically the most accurate protein alignment method today. It can have potential applications in drug discovery processes in the biotechnology industry.
Formulating MEDLINE queries for article retrieval based on PubMed exemplars
Authors: Garnett Alexander , Piwowar Heather , Rasmussen Edie , Illes Judy
Published: July 2019

Bibliographic search engines allow endless possibilities for building queries based on specific words or phrases in article titles and abstracts, indexing terms, and other attributes. Unfortunately, deciding which attributes to use in a methodologically sound query is a non-trivial process. In this paper, we describe a system to help with this task, given an example set of PubMed articles to retrieve and a corresponding set of articles to exclude. The system provides the users with unigram and bigram features from the title, abstract, MeSH terms, and MeSH qualifier terms in decreasing order of precision, given a recall threshold. From this information and their knowledge of the domain, users can formulate a query and evaluate its performance. We apply the system to the task of distinguishing original research articles of functional magnetic resonance imaging (fMRI) of sensorimotor function from fMRI studies of higher cognitive functions.
A Rate Distortion approach to protein symmetry
Authors: Wallace Rodrick
Published: July 2019

A spontaneous symmetry breaking argument is applied to the problem of protein form, via a Rate Distortion analysis of the relation between genome coding and the final condensation of the protein 'molten globule'. The Rate Distortion Function, under coding constraints, serves as a temperature analog, so that low values act to drive proteins to simple symmetries. The Rate Distortion Function itself is significantly constrained by the availability of metabolic free energy. This work extends Tlusty's (2007) elegant exploration of the evolution of the genetic code, suggesting that rate distortion considerations may play a critical role across a broad spectrum of molecular expressions of evolutionary process.
Versatile Control System for Automated Single-Molecule Optical Tweezers Investigations
Authors: Koch Steven , Yeh Richard
Published: July 2019

We present a versatile control system to automate single-molecule biophysics experiments. This method combines low-level controls into various functional, user-configurable modules, which can be scripted in a domain-specific instruction language. The ease with which the high-level parameters can be changed accelerates the development of a durable experiment for the perishable single-molecule samples. Once the experimental parameters are tuned, the control system can be used to repeatedly manipulate other single molecules in the same way, which is necessary to accumulate the statistics needed to report results from single-molecule studies. This system has been implemented for an optical tweezers instrument for single-molecule manipulations, with real-time point-by-point feedback at a loop rate of 10-20 kHz.
Phagocytic Activity and Hexose Monophosphate Shunt Activity of Cultured Human Kupffer Cells upon Zymosan, Erythrocytes, Amoebic Trophozoits, Latex Beads and Nitroimidazole
Authors: Sharma Rakesh , Singh Vijay
Published: July 2019

Phagocytic function of human Kupffer cells was altered by the addition of nitroimidazole and amoebic trophozoits. The hypothesis was that phagocytic activity was dependent on the nature of additives in culture. The Kupffer cells were fractionated and lysosomes were isolated for enzyme estimations in presence of additives. Phagocytic activity function of human Kupffer cells was altered by the addition of nitroimidazole and amoebic trophozoits in Kupffer cell culture. The human Kupffer cells showed take up of zymosan particles larger than 1 micron in diameter and inert interaction with latex particles. The liver endothelial cells or phagocytes constitute a second line of defense in the liver for the phagoctosis function. The nitroimidazole slowed down the Kupffer cells phagocytosis activity of engulfing beads, trophozoits and removing the foreign materials from the vicinity while Kupffer cell phagocytic function remained totally intact. The potential role of Kupffer cells was phagocytosis and nitroimidazole slowed down the further activated Kupffer cells under physiologic conditions when Kupffer cells are active in clearing foreign substance from the circulation. In conclusion, theses first Kupffer cell and trophozoits interaction in the presence of nitroimidazole suggested the synergistic interaction and this cellular interaction in liver.
A war-prone tribe migrated out of Africa to populate the world.
Authors: Moreno Eduardo
Published: July 2019

Of the tribal hunter gatherers still in existence today, some lead lives of great violence, whereas other groups live in societies with no warfare and very little murder^1,2,3,4,5^. Here I find that hunter gatherers that belong to mitochondrial haplotypes L0, L1 and L2 do not have a culture of ritualized fights. In contrast to this, almost all L3 derived hunter gatherers have a more belligerent culture that includes ritualized fights such as wrestling, stick fights or headhunting expeditions. This appears to be independent of their environment, because ritualized fights occur in all climates, from the tropics to the arctic. There is also a correlation between mitochondrial haplotypes and warfare propensity or the use of murder and suicide to resolve conflicts. This, in the light of the “recent out of Africa” hypothesis”^6,7^, suggests that the tribe that left Africa 80.000 years ago performed ritualized fights. In contrast to the more pacific tradition of non-L3 foragers, it may also have had a tendency towards combat. The data implicate that the entire human population outside Africa is descended from only two closely related sub-branches of L3 that practiced ritual fighting and probably had a higher propensity towards warfare and the use of murder for conflict resolution. This may have crucially influenced the subsequent history of the world.
Regulation of Phosphatase Homologue of Tensin Protein Expression by Bone Morphogenetic Proteins in Prostate Epithelial Cells
Authors: Jerde Travis , Wu Zhong , Theodorescu Dan , Bushman Wade
Published: July 2019

Phosphatase homologue of tensin (PTEN) is the key endogenous inhibitor of phosphoinositide signaling and is the most commonly mutated gene in human prostate cancer. The bone morphogenetic proteins (BMPs) are secreted developmental signaling molecules known to promote differentiation in the prostate. BMP ligands have been shown to inhibit prostate cancer cell line proliferation and tumor growth and expression of BMPs, BMP ligands, receptors and signaling effectors are diminished in prostate cancer. A previous report in the colon led us to investigate the potential mechanistic relationship between PTEN and BMP signaling in prostate epithelial cells. We show here that BPM signaling positively regulates PTEN in normal and malignant prostate cells by increasing mRNA expression and stabilizing PTEN protein. Further, we show that BMP attenuates prostate cell growth at least in part through its effects on PTEN. BMP treatment did not further inhibit the growth of conditional PTEN over-expressing cells, and stable shRNA-PTEN transfectants were refractory to BMP-mediated growth inhibition. Loss-of-function of PTEN in prostate cancer cells may render them insensitive to the normal differentiating and growth-inhibitory effects of BMPs. These data are the first to identify a mechanistic linkage between BMP signaling and PTEN in normal prostate epithelial cells and to suggest coordinate dysregulation in prostate cancer.
Understanding Consciousness: An Online Workshop on Contemporary Theories
Authors: Pereira Jr Alfredo , Edwards Jonathan , Lehmann Dietrich , Nunn Chris , Trehub Arnold , Velmans Max
Published: July 2019

An invited workshop on ‘Theories of Consciousness’ was organized in the format of a Nature Network closed group during the second semester of 2009. There were presentations by each of 15 authors active in the field, followed by debate with other presenters and invitees. A week was allocated to each of the theories proposed; general discussion threads were also opened from time to time, as seemed appropriate. We (who had been participants in the workshop) offer here an account of the principal outcomes. It can be regarded as a contemporary, ‘state of the art’ snapshot of thinking in this field.
Improving cellular cancer vaccines
Authors: Lokhov Petr
Published: July 2019

Immunization with cancer cells is of great demand in anti-cancer therapy. However, current cellular vaccines are inefficient and there are questions regarding their overall safety. We report a simple and straightforward approach for improving of cellular cancer vaccines. Through treatment of cancer cell cultures with purified protease, it is possible to make preparations of cell-surface antigens that are free of intracellular content and contain two orders-of-magnitude less protein than the whole lysate of an equivalent number of cancer cells. Despite this difference in total protein content, protease-generated preparations stimulate anti-cancer responses from immune cells better those stimulated with cancer cells themselves. The composition of collected cell-surface antigens, prior to vaccination, can be directly compared with antigenic profile of target cancer cells by the proteomic footprinting. Any contaminates (cell parasites, viruses, toxins, prions, etc.) are easily separated from antigens by means of ultrafiltration. Thus, current cellular vaccines may be improved by replacing whole cancer cells with their isolated cell-surface antigens. Vaccines prepared in this manner are potentially more qualified, purer, and safer.
Simulation of Two Dimensional Ultraviolet (2DUV) Spectroscopy of Amyloid Fibrils
Authors: Jiang Jun , Abramavicius Darius , Falvo Cyril , Bulheller Benjamin , Hirst Jonathan , Mukamel Shaul
Published: July 2019

Revealing the structure and aggregation mechanism of amyloid fibrils is essential for the treatment of over 20 diseases related to protein misfolding. Coherent two dimensional (2D) infrared spectroscopy is a novel tool that provides a wealth of new insight into the structure and dynamics of biomolecular systems. Recently developed ultrafast laser sources are extending multidimensional spectroscopy into the ultraviolet (UV), and this opens up new opportunities for probing fibrils. In a simulation study, we show that 2DUV spectra of the backbone of a 32-residue &x03B2;-amyloid (A&x03B2;(9-40)) fibril associated with Alzheimer's disease, and two intermediate prefibrillar structures carry characteristic signatures of fibril size and geometry that could be used to monitor its formation kinetics. The dominant features of the &x03B2;-amyloid fibril spectra are determined by intramolecular interactions within a single A&x03B2;(9-40), while intermolecular interactions at the "external interface" have clear signatures in the fine details of these signals.
Studies of Histidine, Phenylalanine Complexes of Oxovanadium(IV) Derived from Acetylacetone
Authors: Singh Yadav Rajeev
Published: July 2019

Schiff base complexes of oxovanadium(IV) with amino acids and acetylacetone were synthesized and characterized by elemental analysis, conductivity measurements, spectral and magnetic data. The complexes were found to be non-electrolytes and stoichiometry shown 1:1. The spectral and magnetic data were suggesting the square pyramidal geometry
The architecture of predator-prey and the relationship between complexity and stability
Authors: Burgoa Rosso Karen Luz , Nogales Vera Jose Alberto , Faria Lucas , Charret Iraziet , Paixao Chrystian
Published: July 2019

Theoretical studies predict that the stability of an ecosystem is negatively correlated with its complexity, measured by the number of interacting species. On the other hand, empirical evidence indicates that food webs are highly interconnected. In this manuscript we present results on the stability two-level predator-prey food webs. We analyzed exhaustively all possible topologies of connections among species. Our findings show that those food webs fall into two classes with clearly distinct stability properties. In one of them stability is negatively correlated with complexity, and in the other group stability is positively correlated. For a positive relationship our results reveals highly structured food webs. The positive or negative relationship is related only to the topological structure of the food web. It is independent of the number of connections, strengths of predator-prey interactions or number of species. We review empirical evidence that corroborates our results.
Induced fit, conformational selection and independent dynamic segments: an extended view of binding events
Authors: Csermely Peter , Palotai Robin , Nussinov Ruth
Published: July 2019

Single molecule and NMR measurements of protein dynamics increasingly uncover the complexity of binding scenarios. Here we describe an extended conformational selection model which embraces a repertoire of selection and adjustment processes. Induced fit can be viewed as a subset of this repertoire, whose contribution is affected by the bond-types stabilizing the interaction and the differences between the interacting partners. We argue that protein segments whose dynamics are distinct from the rest of the protein (‘discrete breathers’) can govern conformational transitions and allosteric propagation that accompany binding processes, and as such may be more sensitive to mutational events. Additionally, we highlight the dynamic complexity of binding scenarios as they relate to events such as aggregation and signalling, and the crowded cellular environment.
In-Vivo Lipidomics using Single-Cell Raman Spectroscopy
Authors: Wu Huawen , Volponi Joanne , Oliver Ann , Parikh Atul , Simmons Blake , Singh Seema
Published: July 2019

We describe a method for direct, quantitative, in vivo lipid profiling of oil producing microalgae using single-cell laser-trapping Raman spectroscopy (LTRS). This approach is demonstrated in the quantitative determination of the degree of unsaturation and transition temperatures of constituent lipids within microalgae. These properties are important markers for determining engine compatibility and performance metrics of algal biodiesel. We show that these factors can be directly measured from a single living microalgal cell held in place with an optical trap while simultaneously collecting Raman data. Cellular response to different growth conditions is monitored in real time. Our approach circumvents the need for lipid extraction and analysis that is both slow and invasive. Furthermore, this technique yields real-time chemical information in a label-free manner, thus eliminating the limitations of impermeability, toxicity and specificity of the fluorescent probes used in other common protocols. Although the single-cell Raman spectroscopy demonstrated here is focused on the study of the microalgal lipids with biofuel applications, the analytical capability and quantitation algorithms demonstrated are applicable to many different organisms, and should prove useful for a diverse range of applications in lipidomics.
How and why physicists and chemists use blogs
Authors: Pikas Christina
Published: July 2019

This study examined how and why chemists and physicists blog. Two qualitative methods were used: content analysis of blog and “about” pages and in-depth responsive interviews with chemists and physicists who maintain blogs. Analysis of the data yielded several cross-cutting themes that provide a window into how physicists and chemists use their blogs and what value they receive from maintaining a blog and participating in a blogging community. The article concludes with a discussion of implications for supporting scientists’ work.
Graphs, Networks, Extinction and Paleocommunity Food Webs
Authors: Roopnarine Peter
Published: July 2019

Food webs represent the trophic interactions among species in communities. Those interactions both structure and are structured by species richness, ecological diversity, and evolutionary processes. Geological and macroevolutionary timescales are therefore important to the understanding of food web dynamics, and there is a need for proper reconstruction and analysis of paleocommunity food webs. The fossil record presents many challenges, but the problem may be approached with combinatoric analysis, and graph and network theories. This paper is a brief introduction to the aspects of those disciplines relevant to the study of paleo-food webs, and explores several probabilistic and numerical approaches.
EAG K+ channel joins the p53&x2212;miR-34&x2212;E2F1 signaling pathway as a terminal effecter component for its oncogenic overexpression and action
Authors: Wang Zhiguo , Chen Chang , Li Zhe , Luo Xiaobin , Xiao Jiening , Lin Huixian , Zhang Jianchun , Dong Deli , Lu Yanjie , Yang Baofeng
Published: July 2019

The human ether-&x00E0;-go-go-1 (h-eag1) voltage-dependent K+ channel is necessary for cell cycle progression and its overexpression stimulates tumorigenesis; specific inhibition of h-eag1 expression leads to a reduction in tumor cell proliferation in vitro and in vivo. On the other hand, the tumor-suppressor gene p53 and its downstream genes consist of a complex molecular signaling network and p53 is at the center of this network regulating diverse physiological responses to cancer-related stresses. We report here that h-eag1 expression is controlled by the p53&x2212;miR-34&x2212;E2F1 pathway through a negative feed-forward mechanism. We first established E2F1 as a transactivator of h-eag1 gene. We then revealed that miR-34, a known transcriptional target of p53, is an important negative regulator of h-eag1 through dual mechanisms by directly repressing h-eag1 at the post-transcriptional level and indirectly silencing h-eag1 at the transcriptional level via repressing E2F1. The antisense against h-eag1 antagonized the growth-stimulating effects and the upregulation of h-eag1 expression in SHSY5Y cells, induced by E2F1 overexpression, inhibition of p53 activity, or knockdown of miR-34. Thus, negative regulation of p53 causes oncogenic overexpression of h-eag1 by relieving the negative feed-forward regulation of the p53&x2212;miR-34&x2212;E2F1 pathway or overexpression of h-eag1 fulfills the oncogenic cell growth-stimulating effect of p53 inactivation.