bluuebunny/crossref_metadata_2025_split huggingface dataset:
Induction of Stress Granule Assembly is Essential for the Orchestration of DNA Damage Response
Authors: Verkaik Nicole , Persengiev Stephan 
Published: July 2019

AbstractDNA damage provokes several responses including DNA repair, cell cycle regulation and apoptosis that collectively represent the DNA damage response (DDR). Here, we demonstrate that the DDR incorporates the activation of stress granule (SG) formation pathway as a mechanism to process destabilized RNAs. UV irradiation induced the assembly of SGs during the G2 phase and newly formed SGs appeared exclusively in the early G1 phase. SG assembly pathway was activated within the first hours after DNA damage, suggesting that the processing of destabilized RNAs is activated at an early stage. The induction of SGs and RNAi effector protein Argonaute 2 recruitment after UV exposure was independent of ATM and ATR signaling cascades. Apoptosis occurred only in SG-negative cells indicating that SGs promote cell survival after genotoxic stress. Analysis of several DNA damage/repair deficient MEFs revealed that the SG accumulation remained unaltered after UV exposure. Our results show that SGs are an essential component of DDR that is activated in parallel to the DNA damage kinase response networks.
Increased risk and benefit simultaneously alter the outcome of territorial fights
Authors: Koga Tsunenori , Ikeda Satoshi 
Published: July 2019

AbstractCompetition for resource, including territories is seen in a broad range of taxa. There has been much research on factors that determine the intensity and outcome of competitions (e.g. resource holding potentials: RHP, and resource value: RV). No research, however, has shown how different factors can simultaneously alter the intensity and outcome of contests. We investigated the effects of RV on fighting behavior and success in inter-tidal, territorial male crabs. Under natural conditions the larger rival won contests irrespective of whether he was the resident or intruder (i.e. there was no residency effect). We then motivated intruders to fight hard by subjecting them to the threat of predation, and found that they were more likely to win contests. When we also motivated residents to fight hard by placing a female in his burrow (i.e. both rivals were simultaneously motivated to fight due to the perceived increase in resource value), we found that the contests escalated more and that resident males had a slightly increased chance of winning. This is the first report of two factors simultaneously affecting motivation and therefore altering the escalation and outcome of a contest.
Trigohexagonite: A Rare Quaternary Stoichiometry Network
Authors: Bucknum Michael , Wen Bin , Castro E.A. , Szebenyi Doletha 
Published: July 2019

AbstractA rare quaternary stoichiometry network of high hexagonal symmetry (P-6m2) is described. A set of hexagonal fractional crystallographic coordinates, for both an idealized network, and optimized boron and carbon allotropic realizations are described along with their band structures. Both should be metallic phases.
Selfish and Altruistic Bacterial Populations Maximize Fitness Under Stress by Local Segregation
Authors: Keymer Juan , Galajda Peter , Malinverni Juliana , Kolter Roberto , Lambert Guillaume , Liao David , Austin Robert 
Published: July 2019

AbstractLandscapes in ecology have a profound influence on the adaption and evolution of competing populations for resources. We are interested in how altruistic populations survive in the presence of selfish individuals in a non-stirred, closed and complex nutrient landscape. Well-stirred (landscape-free) but closed environments have a depressing future when selfish individuals arise in a population, a fate known as the tragedy of the Commons. Over-exploitation of a well-stirred communal habitat by selfish individuals which do not follow rules of communal self-regulation ends up in the elimination (extinction) of both the original altruistic inhabitants and the selfish population. In the context of bacterial population, the Commons tragedy that occurs is the consumption of limited resources by the individuals, resulting in metabolic stressing of the bacteria and growth advantages to be gained by defection from a ``social contract" of altruistic cooperation. There is no avoidance of this tragedy and the collapse of an original altruistic wild-type population by an emergent selfish population in a well-stirred but closed environment is inevitable. However, there is a fundamental difference between resource exploitation in a well-stirred homogenous commons and in a heterogenous landscape of nutrients which is not stirred. We show here using a non-stirred nanofabricated habitat landscape that altruists and selfish bacteria can in fact coexist, that they can maintain phenotype diversity and avoid the tragedy of the Commons. This emergent spatial segregation of competing populations under stress greatly changes, we believe, our perception of the true sophistication of bacterial response to stress and competition, and has broad implications for the adaptive strategies of higher organisms under stress in complex environments.
The genetic equidistance result of molecular evolution is independent of mutation rates
Authors: Huang Shi 
Published: July 2019

AbstractThe well-established genetic equidistance result shows that sister species are approximately equidistant to a simpler outgroup as measured by DNA or protein dissimilarity. The equidistance result is the most direct evidence, and remains the only evidence, for the constant mutation rate interpretation of this result, known as the molecular clock. However, data independent of the equidistance result have steadily accumulated in recent years that often violate a constant mutation rate. Many have automatically inferred non-equidistance whenever a non-constant mutation rate was observed, based on the unproven assumption that the equidistance result is an outcome of constant mutation rate. Here it is shown that the equidistance result remains valid even when different species can be independently shown to have different mutation rates. A random sampling of 50 proteins shows that nearly all proteins display the equidistance result despite the fact that many proteins have non-constant mutation rates. Therefore, the genetic equidistance result does not necessarily mean a constant mutation rate. Observations of different mutation rates do not invalidate the genetic equidistance result. New ideas are needed to explain the genetic equidistance result that must grant different mutation rates to different species and must be independently testable.
Gender Differential in the Association of Body Mass Index and Abdominal Obesity with Prehypertension and Hypertension in Iranian Adults
Authors: Janghorbani Mohsen , Amini Masoud , Gouya Mohammad Mehdi , Delavari Alireza , Alikhani Siamak , Mahdavi Alireza 
Published: July 2019

Abstract
*Objective:*
The aim of this study was to determine the gender differential in the relationship of body mass index (BMI) and abdominal obesity with blood pressure (BP) and prevalence of hypertension (HTN) and prehypertension (Pre-HTN) among the adult population of Iran.*Design:* A nationwide cross-sectional survey was conducted from December 2004 to February 2005. The selection was conducted by stratified probability cluster sampling through household family members in Iran.*Subjects and Measurements:* Weight, height, waist circumference (WC), and systolic and diastolic BP of 45,082 men and 44,322 women aged 15-65 (mean 39.2) were measured.

*Results:*
The prevalence of HTN was 25.2% in men and 24.8% in women; and 50.1% of men and 39.1% of women were pre-hypertensive. WC and BMI were strongly associated with BP in both genders. Multivariate analysis revealed that both WC and BMI had the stronger association with HTN and Pre-HTN in men than women. Compared to men and women with normal weight, the multivariate-adjusted odds ratio (OR) (95% confidence interval) of HTN was 5.75 (5.13, 6.44) for men and 4.29 (3.95, 4.66) for women with BMI ≥ 30. The multivariate OR of prevalence HTN in men with abdominal obesity compared with men without was 3.76 (3.41, 4.22) and in women, 2.92 (2.73, 3.13).*Conclusion:* These data indicate that both BMI and WC had the stronger association with HTN and Pre-HTN in men than women.
The Effect of a Reduced-Calorie Diet on alpha-2 Adrenergic Receptor Responsiveness in Abdominal Adipose Tissue in Obese Men During Exercise
Authors: Estrada Roy , Schmelz Joseph , Turbow David , Neumann Edith 
Published: July 2019

AbstractThere is at present an imperfect understanding of the effect of diet on availability of inhibitory receptors in fat cells during exercise among obese men.
*Objective:*
The purpose of this study was to determine whether diet results in downregulation of alpha-2 adrenergic receptor ([alpha]~2-AR~) messenger RNA (mRNA), improving metabolism in exercise in obese men. *Design:* One group, pre-test, post-test design.*Measurements:* Subcutaneous abdominal adipose tissue was tested for physiologic response, such as changes in catecholamines and other markers of lipolysis measured during periods of exercise, before and after a 12-week diet. Plasma markers of lipolysis/antilipolytic activity (catecholamines [adrenaline and noradrenaline], NEFA, lactate, glucose, hematocrit, or insulin levels) were analyzed at four points in time in order to determine the effect of exercise on [alpha]~2-AR~ and [beta]-AR responsiveness to sympathetic stimulation.*Subjects:* Otherwise healthy 18 to 45 year old obese men (defined as a body mass index (BMI) over 33 kg/m^2^).

*Results:*
The 12-week reduced calorie diet did not result in improved metabolism. Instead, upregulation of alpha-2 adrenergic receptor ([alpha]~2-AR~) messenger RNA (mRNA) was observed. On average, [alpha]~2-AR~ mRNA levels (ratio of [alpha]~2-AR~ to cyclophilin) in subjects increased by 0.022-0.023 after the diet. The average differences in of [alpha]~2-AR~ mRNA and [beta]-AR mRNA measured before and after diet were both insignificant (M = 0.015) t(4) = -0.911; P > 0.05; (M = 0.0139; t(4) = 0.077; P > 0.05). *Conclusion:* The observed direction of change in [alpha]~2-AR~ mRNA levels, when viewed together with the stability of [beta]-AR mRNA levels, suggests that upregulation of [alpha]~2-AR~ rather than downregulation occurred. Downregulation would account for decreased lipolytic activity during exercise, future study is needed.
14-3-3ζ is Amplified, Overexpressed and Possesses Oncogenic Activities in Head and Neck Squamous Cell Carcinoma
Authors: Lin Mauting , Morrison Carl , Jones Susie , Mohamed Nehad , Bacher Jason , Plass Christoph 
Published: July 2019

AbstractGene amplification, a common mechanism for oncogene activation in cancers, has been used in the discovery of novel oncogenes. DNA amplification is frequently observed in head and neck squamous cell carcinomas (HNSCCs) where numerous amplification events and potential oncogenes have already been reported. Recently, we applied restriction landmark genome scanning (RLGS) to study gene amplifications in HNSCC and located novel amplified and uncharacterized regions in primary tumor samples. DNA amplification on 8q22.3, the location of 14-3-3[zeta] (YWHAZ, KCIP-1) is found in 30-40% HNSCC cases. Data obtained from fluorescent in-situ hybridization (FISH) and immunohistochemistry on HNSCC tissue microarrays confirmed frequent low-level 14-3-3[zeta] copy number gains and protein overexpression. 14-3-3[zeta] mRNA was frequently upregulated in patients' tumor tissues. Furthermore, 14-3-3[zeta] RNAi significantly suppressed the growth rate of HNSCC cell lines, and overexpression of 14-3-3[zeta] in HaCaT immortalized human skin keratinocytes promotes its growth, as well as morphological changes. Reduced 14-3-3[zeta] levels increased the G1/G0-phase proportion, decreased the S-phase proportion and the rate of DNA synthesis. Based on this evidence, we suggest that 14-3-3[zeta] is a candidate proto-oncogene and deserves further investigations into its role in HNSCC carcinogenesis.
Peptides as potent antimicrobials tethered to a solid surface: Implications for medical devices
Authors: Gonzalez Ivan , Wong XiXi , DeAlmeida Dilhari , Yurko Raymond , Watkins Simon , Islam Kazi , Montelaro Ronald , El-Ghannam Ahmed , Mietzner Timothy 
Published: July 2019

AbstractMedical devices are an integral part of therapeutic management; despite their importance, they carry a significant risk of microbial infection. Bacterial attachment to a medical device is established by a single, multiplying organism, leading to subsequent biofilm formation. To date, no preventative measures have impacted the incidence of device-related infection. We report the bidirectional covalent coupling of an engineered cationic antimicrobial peptide (eCAP), WLBU2, to various biological surfaces is accomplished. These surfaces included (i) a carbohydrate-based gel matrix, (ii) a complex polymeric plastic bead, and (iii) a silica-calcium phosphate nanocomposite associated with bone reconstruction. WLBU2-conjugated surfaces are shown to retain potent antimicrobial activity related to bacterial surface adhesion. This study provides proof of principle that covalently coating laboratory and bone-regenerating materials with eCAPs has the potential for decreasing infection rates of implanted devices. These findings have important consequences to the patient management component of our current health care technology.
CD14 Modulates PI3K/AKT/p38-MAPK Licensing of Negative Regulators of TLR Signaling to Restrain Chronic Inflammation
Authors: Sahay Bikash , Patsey Rebeca , Whatley Nicole , Nayak Sasmita , Eggers Christian , Radolf Justin , Sellati Timothy 
Published: July 2019

AbstractCurrent thinking emphasizes the primacy of CD14 in facilitating TLR recognition of microbes to initiate proinflammatory signaling events and the importance of p38-MAPK in augmenting such responses. Herein, this paradigm is challenged by demonstrating that recognition of Borrelia burgdorferi not only triggers an inflammatory response in the absence of CD14, but one that is uncontrolled as a consequence of impaired PI3K/AKT/p38-MAPK signaling and negative regulation of TLR2. CD14 deficiency results in hyperphosphorylation of AKT and reduced activation of p38. Such aberrant signaling leads to decreased negative regulation by SOCS1, SOCS3, and CIS thereby engendering a more severe and persistent inflammatory response to B. burgdorferi. Perturbation of this CD14/p38-MAPK-dependent mechanism of immune regulation may underlie development of infectious chronic inflammatory syndromes.
The effects of anti-sense interleukin-5 gene transferred by recombinant adeno-associated virus in allergic rats
Authors: Zeng Daxiong , Cao Yong , Song Qingfeng , Cao Chao , Liu Xiansheng , Xu Yongjian , Xiong Weining 
Published: July 2019

AbstractThe accumulation and infiltration of eosinophils in airways is one of the most important characteristics of asthma, and is mediated partly by secretion of IL-5 from Th2 lymphocytes. It is well known that interleukin-5 (IL-5) played an important role in the regulation of eosinophils. In this study, an anti-sense IL-5 gene transferred by recombinant adeno-associated virus (rAAV-ASIL-5) was prepared to transfect allergic rats. It was found that the expression of IL-5 protein in plasma and BALF were inhibited significantly. The rAAV-ASIL-5-mediated suppression of total cell counts in peripheral blood and BALF were also observed. Moreover, rAAV-ASIL-5 remarkably reduced the eosinophil counts in peripheral blood and BALF, as well as the expression of ECP protein in plasma and BALF. The inflammation in lungs of rAAV-ASIL-5 pretreated rats also became slighter when compared with allergic rats. Otherwise, no apparent pathological damage to vital organs of rats was found. In conclusion, recombinant adeno-associated virus-mediated delivery of anti-sense IL-5 gene inhibited the accumulation of eosinophils and the airways inflammation in rat model of allergic asthma via suppressing IL-5 expression. It suggested the feasibility of rAAV-ASIL-5 in the gene therapy for allergic asthma and other eosinophilic diseases.
Yeast surface 2-hybrid to detect protein-protein interactions via the secretory pathway as a platform for antibody discovery
Authors: Hu Xuebo , Kang Sungkwon , Chen Xiaoyue , Shoemaker Charles , Jin Moonsoo 
Published: July 2019

AbstractHigh throughput methods to measure protein-protein interactions will facilitate uncovering pairs of unknown interactions as well as designing new interactions. We have developed a platform to detect protein interactions on the surface of yeast, where one protein (bait) is covalently anchored to the cell wall and the other (prey) is expressed in secretory form. The prey is released either outside of the cells or remains on the cell surface by its binding to the bait. The strength of their interaction is measured by antibody binding to the epitope tag fused to the prey or direct readout of split fluorescence protein complementation. Our novel 'yeast surface 2-hybrid' system was found to differentiate 6-log difference in binding affinities between coiled coil associations and to measure specific interactions of antibodies and antigens. We demonstrate the use of YS2H in exploring activation allostery in integrins and isolating heavy chain only antibodies against botulinum neurotoxin.
Reductive Biotransformation of Ethyl Acetoacetate: A Comparative Studies using Free and Immobilized Whole Yeast Cells
Authors: Kumbhar Amit , Kulkarni Vaibhav , Pande Madhav , Laddha Sachin 
Published: July 2019

AbstractBioreduction of ethyl acetoacetate with free and immobilized yeast whole cell was achieved by using water and sucrose combination. After detachment from immobilized beads under basic condition, the corresponding ethyl(S)-(+)-3-hydroxybutanoate was isolated with 98 to 100% yield. Immobilized beads of yeast whole cell were prepared at different temperature which affects the morphology and physiology of the beads for the diffusion of the enzyme, which shown the maximum conversion of the substrate to products as compared to the free yeast whole cell.
Characteristics of oligonucleotide frequencies across genomes: Conservation versus variation, strand symmetry, and evolutionary implications
Authors: Zhang Shang-Hong , Huang Ya-Zhi 
Published: July 2019

AbstractOne of the objectives of evolutionary genomics is to reveal the genetic information contained in the primordial genome (called the primary genetic information in this paper, with the primordial genome defined here as the most primitive nucleic acid genome for earth’s life) by searching for primitive traits or relics remained in modern genomes. As the shorter a sequence is, the less probable it would be modified during genome evolution. For that reason, some characteristics of very short nucleotide sequences would have considerable chances to persist during billions of years of evolution. Consequently, conservation of certain genomic features of mononucleotides, dinucleotides, and higher-order oligonucleotides across various genomes may exist; some, if not all, of these features would be relics of the primary genetic information. Based on this assumption, we analyzed the pattern of frequencies of mononucleotides, dinucleotides, and higher-order oligonucleotides of the whole-genome sequences from 458 species (including archaea, bacteria, and eukaryotes). Also, we studied the phenomenon of strand symmetry in these genomes. The results show that the conservation of frequencies of some dinucleotides and higher-order oligonucleotides across genomes does exist, and that strand symmetry is a ubiquitous and explicit phenomenon that may contribute to frequency conservation. We propose a new hypothesis for the origin of strand symmetry and frequency conservation as well as for the constitution of early genomes. We conclude that the phenomena of strand symmetry and the pattern of frequency conservation would be original features of the primary genetic information.
Secondary water pore formation for proton transport in a ClC exchanger revealed by an atomistic molecular dynamics simulation
Authors: Ko Youn Jo , Jo Won Ho 
Published: July 2019

AbstractSeveral prokaryotic ClC proteins have been demonstrated to function as exchangers that transport both chloride ions and protons simultaneously in opposite directions. However, the path of the proton through the ClC exchanger and how the protein brings about the coupled movement of both ions are still unknown. In the present work, we demonstrate that a previously unknown secondary water pore is formed inside a ClC exchanger by using an atomistic molecular dynamics (MD) simulation. From the systematic simulations, it was determined that the glutamate residue exposed to the intracellular solution, E203, plays an important role as a trigger for the formation of the secondary water pore. Based on our simulation results, we conclude that protons in the ClC exchanger are conducted via a water network through the secondary water pore and we propose a new mechanism for the coupled transport of chloride ions and protons.
High Resolution Imaging of the Fusiform Face Area (FFA) Using Nonlinear Classifiers Shows Diagnosticity for Nonface Categories
Authors: Hanson Stephen , Schmidt Arielle 
Published: July 2019

AbstractHow are objects represented in the human visual pathway? This question continues to elude the neuroimaging field due to at least two kinds of problems: first, the relatively low spatial resolution of fMRI and second, the bias inherent in prevailing statistical methods for analyzing the actual diagnosticity of cortical tissue. We collected high-resolution (1mm x 1mm) imaging data of the fusiform face area (FFA) from 4 subjects while they categorized images as &apos;animal&apos;, &apos;car&apos;, &apos;face&apos;, or &apos;sculpture.&apos; We performed exploratory analysis to determine the nature of the distributions over classes and the similarity structure between classes. The FFA was visualized using nonmetric multidimensional scaling revealing &quot;string-like&quot; sequences of voxels, which appeared in small non-contiguous clusters of categories, intertwined with other categories. Since the feature space appeared highly nonlinear, we trained various statistical classifiers on the class conditional distributions (labelled) and separated the four categories with 100% reliability (over replications) and generalized to out of sample cases with high significance (45% to 51%; p&lt;. 000001, chance=25%). The increased noise inherent in high-resolution neuroimaging data relative to standard resolution resisted any further gains in category performance above 60% (with &quot;FACE&quot; category often having the highest bias per category) even coupled with various feature extraction/selection methods. A sensitivity/diagnosticity analysis for each classifier per voxel showed: (1) reliable (with S.E.&lt;3%) sensitivity present throughout the FFA for all 4 categories, and (2) showed multi-selectivity, that is, many voxels were selective for one category but responded to all 4 categories with some high diagnosticity but at lower intensity. This work further verifies the hypothesis that the FFA is a distributed, object-heterogeneous similarity structure and bolsters the view that the FFA response to &quot;FACE&quot; stimuli in standard resolution may be primarily due to a linear bias, which has resulted from an averaging artifact.