bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Bayesian Framework for Parameter Estimation in Dynamical Models with Applications to Forecasting
Authors: Coelho Flávio Codeço , Codeço Claudia 
Published: July 2019

AbstractMathematical models in Biology are powerful tools for the study and exploration of complex dynamics. Nevertheless, bringing theoretical results to an agreement with experimental observations involves acknowledging a great deal of uncertainty intrinsic to our theoretical representation of a real system.Proper handling of such uncertainties, is key to the successful usage of models to predict experimental or field observations. This problem has been addressed over the years by many tools for model calibration an parameter estimation. In this article we present a general framework for uncertainty analysis and parameter estimation which is designed to handle uncertainties associated with the modeling of dynamic biological systems while remaining agnostic as to the type of model used. We apply the framework to two Influenza transmission models: one deterministic and the other stochastic. The results show that the framework can be applied without modifications to the two types of models and that it performs equally well on both. We also discuss the application of the framework to calibrate models for forecasting purposes.
Association of autoimmune diseases to allele 2 of the 3&apos; immuno-globulines HS1.2 enhancer bearing an NF-&x03BA;B binding site.
Authors: Frezza Domenico , Gremese Elisa , Giambra Vincenzo , Mattioli Claudia , Tolusso Barbara , Bosello Silvia , DeSantis Maria , Birshtein Barbara , Ferraccioli Gianfranco 
Published: July 2019

AbstractWe identified allele *2 in the HS1.2 enhancer of the Igh 3&apos; regulatory region (3&apos;RR-1) as a risk factor for systemic lupus erythematosus (SLE), rheumatoid arthritis (RA) and systemic sclerosis (SSc) (scleroderma). An NF-&x03BA;B binding site specific to allele *2 may contribute to the association of this allele with chronic inflammatory autoimmune diseases.
An RNA cis-element upstream of the HMGA1a binding site affects exon exclusion caused by HMGA1a
Authors: Ohe Kenji , Manabe Takayuki , Katayama Taiichi , Tohyama Masaya , Mayeda Akila 
Published: July 2019

AbstractIn addition to its characteristics as a DNA binding transcription factor, HMGA1a is known to bind RNA, sequence specifically and regulate aberrant splicing of the Presenilin-2 gene in sporadic Alzheimer’s disease^1,2^. We show here that an RNA cis-element, immediately upstream the HMGA1a binding site, induces exon inclusion upon mutating a GU sequence to CA. Psoralen mediated UV crosslinking showed U1 snRNP did not bind this sequence but oligonucleotide-mediated RNase H digestion showed it important for U1 snRNP to recognize the authentic 5’ splice site. This sequence (5’-AAGUAC-3’) was tested for hnRNPA1 binding and function. Coimmunoprecipitation of endogenous HMGA1a and hnRNPA1 in HeLa nuclear extract, implicated hnRNPA1 to be involved in HMGA1a mediated dysfunction of U1 snRNP. Though hnRNPA1 binding was weak, there was decreased binding when GU was mutated to CA. hnRNPA1 alone had no effect of splicing of a 5’ splice site adjacently downstream the HMGA1a binding site, but significantly attenuated HMGA1a mediated splicing suppression of this 5’ splice site. Thus, hnRNPA1, known as the human homolog of hrp48 in the PSI model, attenuates HMGA1a mediated U1 snRNP dysfunction.
Application of a periodic table for the genetic code of the influenza A/H3N2 virus
Authors: Morimoto Susumu 
Published: July 2019

AbstractThe progress of life sciences would be greatly enhanced if biological data were available in a manner similar to the periodic table of the elements. Currently, the mutation rules for influenza viruses remain ambiguous. In light of the threat of Avian Influenza there is an urgent need to understand the governing principles behind influenza virus mutations. Here, the applicability of a periodic table for the genetic code of influenza A/H3N2 virus is explored. In addition, two rules regarding single point mutations of the hemagglutinin gene are presented. The first rule states that non-synonymous single point mutations are intimately associated with the first or second base replacements between two congener codons of four groups (5, 6, 9, and 10) in the proposed periodic table. The second rule involves the use of a new index (inversion number) that describes a mutation. This paper will take the first step toward developing an approach for indexing different types of mutations in the influenza genome.
Extending Astrobiology: Consciousness and Culture
Authors: Wallace Rodrick 
Published: July 2019

AbstractThe Stanley Miller experiment suggests that amino acid-based life is ubiquitous in our universe, although its varieties are not likely to have followed the particular, highly contingent and path-dependent, evolutionary trajectory found on Earth. Are many alien organisms likely to be conscious in ways that we would recognize? Almost certainly. Will some develop high order technology? Less likely, but still fairly probable. If so, will we be able to communicate with them? Only on a basic level, and only with profound difficulty. The argument is fairly direct.
Remote preconditioning by aortic constriction: affords cardioprotection as classical or other remote ischemic preconditioning? Role of iNOS
Authors: Sharma Ashish , Munajjam Arshee , Vaishnav Bhawna , Sharma Richa , Kishore Kunal , Sharma Ashok , Sharma Akash , Sharma Divya , Kumari Rita , Tiwari Ashish , Srinivasan B.P. , Agarwal Shyam 
Published: July 2019

AbstractDose remote preconditioning by aortic constriction (RPAC) affords cardioprotection similar to classical or other remote ischemic preconditioning stimulus? Moreover study was also designed to investigate role of inducible nitric oxide synthase in remote preconditioning by aortic constriction. There are sufficient evidences that &quot;ischemic preconditioning&quot; has surgical applications and afford clinically relevant cardioprotection. Transient occlusion of circumflex artery, renal artery, limb artery or mesenteric artery preconditions the myocardium against ischemia reperfusion injury in case of ischemic heart disease leading to myocardial infraction. Here abdominal aorta was selected to produce RPAC. Four episodes of Ischemia-reperfusion of 5 min each to abdominal aorta produced RPAC by assessment of infract size, LDH and CK. These studies suggest RPAC produced acute (FWOP) and delayed (SWOP) cardioprotective effect. RPAC demonstrated a significant decrease in Ischemia-reperfusion induced release of LDH, CK and extent of myocardial infract size. L-NAME (10 mg/Kg i.v.), Aminoguanidine (150 mg/Kg s.c.), Aminoguanidine (300 mg/Kg s.c.), S-methyl isothiourea (3 mg/Kg i.v.), 1400W (1 mg/Kg i.v.) administered 10 min. before global ischemia reperfusion produced no marked effect. Aminoguanidine (150 mg/Kg s.c.), Aminoguanidine (300 mg/Kg s.c.), S-methyl isothiourea (3 mg/Kg i.v.), 1400W (1 mg/Kg i.v.) pretreatment after RPAC produced no significant effect on acute RPAC induced decrease in LDH, CK and infract size, whereas L-NAME (10 mg/Kg i.v.) increased RPAC induced decrease in LDH, CK and infract size. Most interesting observation is in delayed RPAC, where all NOS inhibitors pretreatment attenuate RPAC induced decrease in LDH, CK and infract size. In conclusions, &quot;Remote preconditioning by aortic constriction&quot; (RPAC) affords cardioprotection similar to classical or other remote ischemic preconditioning stimulus. Moreover, late or delayed phase of RPAC has been mediated by inducible nitric oxide synthase (iNOS) whereas it has not involved in acute RPAC.
Fuzzy logic as a decision-making support system for the indication of bariatric surgery based on an index (OBESINDEX) generated by the association between body fat and body mass index
Authors: Azevedo Joao , Miyahira Susana , Leal Lucas , Azevedo Glicia , Azevedo Otavio , Azevedo Joao , Miguel Gustavo 
Published: July 2019

Abstract
Background:
A Fuzzy Obesity Index (OBESINDEX) for use as an alternative in bariatric surgery indication (BSI) is presented. The search for a more accurate method to evaluate obesity and to indicate a better treatment is important in the world health context. BMI (body mass index) is considered the main criteria for obesity treatment and BSI. Nevertheless, the fat excess related to the percentage of Body Fat (%BF) is actually the principal harmful factor in obesity disease that is usually neglected. This paper presents a new fuzzy mechanism for evaluating obesity by associating BMI with %BF that yields a fuzzy obesity index for obesity evaluation and treatment and allows building up a Fuzzy Decision Support System (FDSS) for BSI.

Methods:
Seventy-two patients were evaluated for both BMI and %BF. These data are modified and treated as fuzzy sets. Afterwards, the BMI and %BF classes are aggregated yielding a new index (OBESINDEX) for input linguistic variable are considered the BMI and %BF, and as output linguistic variable is employed the OBESINDEX, an obesity classification with entirely new classes of obesity in the fuzzy context as well is used for BSI.

Results:
There is a gradual, smooth obesity classification and BSI when using the proposed fuzzy obesity index when compared with other traditional methods for dealing with obesity.

Conclusion:
The BMI is not adequate for surgical indication in all the conditions and fuzzy logic becomes an alternative for decision making in bariatric surgery indication based on the OBESINDEX.
The neural bases of distracter-resistant working memory
Authors: Wager Tor , Insler Rachel , Smith Edward 
Published: July 2019

AbstractA major difference between humans and other animals is our capacity to maintain information in working memory (WM) while performing secondary tasks, which enables sustained, complex cognition. A common assumption is that the lateral prefrontal cortex (PFC) is critical for WM performance in the presence of distracters, but direct evidence is scarce. We assessed the relationship between fMRI activity and WM performance within-subjects, with performance matched across Distracter and No-distracter conditions. Activity in ventrolateral PFC during WM encoding and maintenance positively predicted performance in both conditions, whereas activity in the pre-supplementary motor area (pre-SMA) predicted performance only under distraction. Other parts of dorsolateral and ventrolateral PFC predicted performance only in the No-distracter condition. These findings challenge a lateral PFC-centered view of distracter-resistance, and suggest that the lateral PFC supports a type of WM representation that is efficient for dealing with task-irrelevant input but is nonetheless easily disrupted by dual-task demands.
Basic emotions: Differences in time sequence and functional imaging with low resolution brain electrical tomography (LORETA)
Authors: Costa Tommaso , Crini Manuella 
Published: July 2019

AbstractThe aim of the present study is to investigate the relationship between the time course of brain activation during the observation of pictures depicting scenes associated with the four basic emotion of happiness, sadness, fear and disgust. Twenty-nine right-handed volunteers (17 male, 12 female; mean age 24.6 years) took part in the study. To study the time course of the affective processing the low resolution brain electromagnetic tomography (LORETA) has been used. Each emotional condition has shown specific activation patterns in different brain regions, changing over time. Our findings are in good agreement with other brain-imaging studies (PET/fMRI) but with the advantage to investigate the temporal evolution of the emotional process in the millisecond range. The results showed that the time sequence of activations is different and characteristic for each emotion conditions.
A sorites paradox in the conventional definition of amount of substance
Authors: Wheatley Nigel 
Published: July 2019

AbstractThe conventional definition of amount of substance n is as a quantity proportional to number of entities N. This implies that n is discrete for small N while n is considered to be continuous at the macroscopic scale, leading to a sorites paradox. A practical criterion is proposed for distinguishing between amount of substance and number of entities, and the implications for the conventional definition of amount of substance are discussed.
Unnatural Selection: A new formal approach to punctuated equilibrium in economic systems
Authors: Wallace Rodrick 
Published: July 2019

AbstractGeneralized Darwinian evolutionary theory has emerged as central to the description of economic process (e.g., Aldrich et. al., 2008). Here we demonstrate that, just as Darwinian principles provide necessary, but not sufficient, conditions for understanding the dynamics of social entities, in a similar manner the asymptotic limit theorems of information theory provide another set of necessary conditions that constrain the evolution of socioeconomic process. These latter constraints can, however, easily be formulated as a statistics-like analytic toolbox for the study of empirical data that is consistent with a generalized Darwinism, and this is no small thing.
Widespread Mitochondrial Disease in North American Bison
Authors: Pringle Thomas 
Published: July 2019

AbstractNorth American bison have rebounded from near-extinction in the nineteenth century but from such small inbred founding populations that once-rare deleterious nuclear gene alleles and mitochondrial haplotypes are now at high frequencies. The initial bottleneck was compounded by decades of unnatural selection affecting bison conservation genomics and undercutting restoration initiatives. The genomics era began in late 2010 for bison and sister species yak with the release of 102 whole mitochondrial genomes, displacing earlier control region and microsatellite data not extending to coding regions. This allows detection of both sporadic and sub-clade level mutations in mitochondrially encoded proteins and tRNAs by comparative genomics methods: deleterious mutations in both cytochrome b (V98A) and ATP6 (I60N) occur within a single common bison haplotype. Since similar mutations in human and dog cause clinical impairment of mitochondrial oxidative phosphorylation, these bison are predicted to be significantly impaired in aerobic capacity, disrupting highly evolved cold tolerance, winter feeding behaviors, escape from predators and competition for breeding. Because Yellowstone National Park bison are subjected to genetically uninformed culls and surplus animals used to seed new conservation herds, mutational status has significant implications. Continuing take of the remaining bison with wildtype mitochondria may recapitulate errors of nineteenth century bison stewardship bringing bison conservation to the point of no return.
Molecular Bio-imprinting of Biocatalysts
Authors: Khan Israr , Akhtar Muhammad Waheed 
Published: July 2019

AbstractEnergy conservation is the cry of the day. Attempts are made all over the world to occupy and use energy reserves. Increased industrialization and mechanization has led to the depletion of natural energy reserves. Its unavoidable to search for renewable sources of energy, which may be not used now but can be used by future generations. We are using the expertise of our ancestors. Thus exploiting the nature and newer techniques in this area would yield the best results. Bio-imprinting is one of those techniques whereby chemical modification is done in order to achieve highly expressed protein which can be stored in its highly active form in the specific solvent.
Why not &quot;do simple things in a simple way&quot;: Use of the Pap test as the first step in screening genetic stability for human cultured stem cell therapy?
Authors: Carvalho Katherine Athayde Teixeira de , Irioda Ana Carolina , Zocche Larissa , Souza Carolina Maria Costa de Oliveira , Ferreira Reginaldo J. , Aliprandini Eduardo , Cunha Ricardo C , Francisco Julio C , Guarita-Souza Luiz Cesar , Malvezzi Mariester , Beltrame Miriam , Mesquita Lismary , Kuczera Diogo , Vargas Rafael 
Published: July 2019

AbstractThe aim of this study was to analyze adipose tissue-derived mesenchymal stem cells (AT-MSCs) using the Pap test as a first screening step to evaluate genetic stability. Human adipose tissue from six healthy female donors was obtained from elective liposuction procedures. The cells were isolated, cultivated at P2/P3, characterized by flow cytometric analysis, and differentiation induced. The AT-MSCs were stained by Papanicolaou staining and analyzed according to the Bethesda classification, and viability-apoptosis relationships were evaluated. The results of the Pap test for Sample I indicated high-grade alterations consistent with genetic instability; for Samples II-V, atypical cells of undetermined significance; and for Sample VI, normal cells. These results demonstrate the potential of using the Pap test as an initial screening step to evaluate the genetic stability of cultured AT-MSCs and also suggest its use for other adherent cells such as embryonic stem cells or induced pluripotent stem cells.
Biodiversity Conservation Of The Irtysh River
Authors: Kulikov Yevgeniy , Kirichenko Olga 
Published: July 2019

AbstractOne of the basic principles of environmental protection is the conservation of biological diversity of natural objects. In addressing this issue plays an important role the Red Book of Kazakh-stan, which is one of the main effective instruments for the preservation and restoration of rare and declining in numbers and endangered species. Red Books are the main weapon of environmental education tool for the inventory of rare and endangered species, scientifically sound foundation for their protection. Studies of fish that are listed and recommended for inclusion in the Red Book, is a priority and is evidenced not only on the state of study of the securities and small fish species, but also to demonstrate the quality of protection and conservation of biodiversity. Prioritize the conservation of genetic resources for sustainable development is enshrined in the Convention on Biological Diversity. Government of the Republic of Kazakhstan in 2001 approved a national program &quot;Conservation and sustainable use of rare and valuable species of farm animals&quot;, under which the task to preserve the gene pool of valuable species and breeds of fish.
`The frozen accident' as an evolutionary adaptation: A rate distortion theory perspective on the dynamics and symmetries of genetic coding mechanisms
Authors: Glazebrook James , Wallace Rodrick 
Published: July 2019

AbstractWe survey some interpretations and related issues concerning the frozen hypothesis due to F. Crick and how it can be explained in terms of several natural mechanisms involving error correction codes, spin glasses, symmetry breaking and the characteristic robustness of genetic networks. The approach to most of these questions involves using elements of Shannon's rate distortion theory incorporating a semantic system which is meaningful for the relevant alphabets and vocabulary implemented in transmission of the genetic code. We apply the fundamental homology between information source uncertainty with the free energy density of a thermodynamical system with respect to transcriptional regulators and the communication channels of sequence/structure in proteins. This leads to the suggestion that the frozen accident may have been a type of evolutionary adaptation.
Archon Genomics X PRIZE Validation Protocol
Authors: Kedes Larry , Sutton Granger , Liu Edison , Jongeneel Victor 
Published: July 2019

AbstractThis document is a collective assembly of techniques designed to test the quality and accuracy of 100 whole human genome sequences resulting from the $10 Million Archon Genomics X PRIZE (AGXP) competition. The purpose of this article is to enlist constructive criticism from the genomic and genetic community on the outlined approaches. The intent for the final version of this Validation Protocol is to become a useful standard by which to gauge the capabilities of whole genome sequencing technologies that emerge even after 2012.
Longitudinal Metagenomic Analysis of the Water and Soil from Gulf of Mexico Beaches Affected by the Deep Water Horizon Oil Spill
Authors: Widger William , Golovko Georgiy , Martinez Antonio , Ballesteros Efren , Howard Jesse , Xu Zhenkang , Pandya Utpal , Fofanov Viacheslav , Rojas Mark , Bradburne Christopher , Hadfield Ted , Olson Nels , Santarpia Joshua , Fofanov Yuriy 
Published: July 2019

AbstractEstimates of 7x105 cubic meters of crude oil were released into the Gulf of Mexico as a consequence of the April 20th, 2010 Deep Water Horizon drilling rig explosion, leaving thousands of square miles of earth&apos;s surface covered in crude oil. Dispersants were used on large slicks and injected at the well head, resulting in oil being suspended throughout the water column. Starting in June 2010, oil reached hundreds of miles of Louisiana, Alabama, Mississippi, and Florida shoreline disturbing the ecological balance and economic stability of the region. While visible damages are evident in the wildlife populations and marine estuaries, the most significant affect may be on the most basic level of the ecosystems: the bacterial and plankton populations.We present results from high throughput DNA sequencing of close-to-shore water and beach soil samples before and during the appearance of oil in Louisiana and Mississippi. Sixteen samples were taken over a two month period at approximately two week intervals from Grand Isle, LA and Gulfport, MS and were sequenced using the Illumina GAIIx platform. Significant genomic-based population fluctuations were observed in the soil and water samples. These included large spikes in the human pathogen Vibrio cholera, a sharp increase in Rickettsiales sp., and decrease of Synechococus sp. in water samples. Analysis of the contiguous de-novo assembled DNAs (contigs) from the samples also suggested the loss of biodiversity in water samples by the time oil appeared at the shores in both locations. Our observations lead us to the conclusion that oil strongly influenced microbial population dynamics, had a striking impact on the phytoplankton and other flora present prior to the appearance of oil, and that the microbial community had not recovered to pre-spill conditions by the end of our observational period.
In-vitro Antifungal Activity of Some 1,3,5-triazine Derivatives
Authors: Singh Udaya Pratap , Gahtori Prashant , Singh Ramendra K. 
Published: July 2019

AbstractA series of substituted phenylthiazolyl 1,3,5-triazine derivatives were screened for their in-vitro antifungal activity (MIC and MFC) against four fungi viz. Candida species (C. albicans NCIM-3102, C. glabrata NCIM-3266), Cryptococcus neoformans NCIM-3542, and Aspergillus niger NCIM-620 using modified broth microdilution method recommended by CLSI, with reference to fluconazole and amphotericin B.