bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extensive Viral mimicry of human proteins in AIDS, autoimmune disorders, late-onset and familial Alzheimer&apos;s disease and other genetic diseases
Authors: Carter Christopher 
Published: July 2019

AbstractPeptide stretches within HIV-1 proteins display homology to over 50 components from all compartments of the human immune defence network. The homologous peptides are in most cases immunogenic, suggesting that antibodies to HIV-1 proteins could mount an autoimmune attack against multiple components of the immune system itself. HIV-1 proteins are also homologous to autoantigens in Alzheimer&apos;s disease, chronic obstructive pulmonary disorder, multiple sclerosis, Myasthenia Gravis, Pemphigus Vulgaris, Sjogrens syndrome and systemic Lupus Erythematosus, all of which have been associated with HIV-1 infection. This mimicry suggests that HIV-1/AIDS has a major autoimmune component and that HIV-1 antibodies could selectively target the immune system and autoantigens in other autoimmune disorders. This could radically change our conception of how HIV-1 acts, and perhaps lead to novel therapeutic strategies, which, counter intuitively might even involve the use of immunosuppressants in the early stages of the disease. Autoantigens from the human autoimmune diseases mentioned above also align with peptides from other viruses implicated as risk factors in each disease. Mutant peptides from Huntington&apos;s disease and other polyglutamine disorders, and from cystic fibrosis also align with common viruses. The London APP717 V&x2192;I mutant in Familial Alzheimer&apos;s disease converts the surrounding peptide to matches with Rhinoviruses causing the common cold and to the Norovirus responsible for vomiting sickness. Viral mimicry related autoimmunity may thus play a role in many autoimmune and even human genetic disorders. It is possible that this is a near universal phenomenon, reflecting the idea that viruses are responsible for the origin of higher forms of life, leaving behind a deadly legacy of viral-derived human proteins with homology to antigenic proteins in the current virome that may be responsible for most of our ills.
Characteristics of Staphylococcus aureus infections to consider in designing an effective vaccine.
Authors: Romero-Pastrana Francisco , Hernández-Jáuregui Pablo , Baca Beatriz 
Published: July 2019

AbstractStaphylococcus aureus is a very versatile and adaptable microorganism. It can potentially infect virtually any host tissue. Given the appropriate conditions it can become a life-threatening pathogen, or a commensal colonizer of the nose. Extensive antibiotic use for infection control facilitated the rise of antibiotic resistance, stressing the need for alternate forms of control. Vaccine efforts in other pathogens have proved successful, but so far S. aureus candidate vaccines have not been as effective. Here we review S. aureus factors involved in pathogenesis that could help develop a successful vaccine, like host nasal colonization and immune evasion factors. An effective multicomponent vaccine could incorporate antigenic fragments from several S. aureus proteins, preferably involved in colonization, immune evasion and/or toxicity.
The Shape and Dimensionality of Phylogenetic Tree-Space Based on Mitochondrial Genomes
Authors: Wilgenbusch James , Huang Wen , Gallivan Kyle 
Published: July 2019

AbstractPhylogenetic analyses of large and diverse data sets generally result in large sets of competing phylogenetic trees. Consensus tree methods used to summarize sets of competing trees discard important information regarding the similarity and distribution of competing trees. A more fine grain approach is to use a dimensionality reduction method to project tree-to-tree distances in 2D or 3D space. In this study, we systematically evaluate the performance of several nonlinear dimensionality reduction (NLDR) methods on tree-to-tree distances obtained from independent nonparametric bootstrap analyses of genes from three mid- to large-sized mitochondrial genome alignments.
Isotope fractionation during impacts
Authors: Huang Hua 
Published: July 2019

AbstractEvaporation-condensation, a significant process, happens during impact events. Of special interest, this process can lead to significant isotope fractionations e.g. C, O, Mg, Si, S, Fe,and Cr.The nature of mass-independent fractionation of sulphur of the sulfur isotopes is that the fractionation of isotope is still mass dependent during impacts, which means the measured nonzero ⊿33S values of Archean sulfide- and sulfate-bearing minerals indicate that their different condensation sequences.
Free Will or Not: Causality Preserved but Access to Motor Decisions Obscured
Authors: Gorea Andrei , Grzeczkowski Lukasz , Rider Delphine 
Published: July 2019

AbstractEmpirical studies having addressed the free-will issue suffer from controversial methodologies and interpretations. We present a new paradigm involving a synchronization task where the time interval to synchronize with is randomly within and without subject's synchronization capabilities and ask subjects to retrospectively evaluate (Q1) which of the two occurred or (Q2) whether their motor response had had been reactive/speeded or delayed. Contrary to the non-FW view, Q1-judgments correlate with the actual duration of the synchronization interval rather than with subjects's motor response latencies. Instead of postidictively reshuffling their judgment to make it match the outcome of their actions, subjects preserve the causal chain of events having entailed them. When answering Q2 subjects' judgments also correlate with the synchronization interval, proof that they cannot decide on the intentionality of their actions. Hence the present results reveal the intrinsic duality of the free-will concept.
Critical Concentration Gradient Model of Bacterial Cell Division
Authors: Rashid Aijaz , Sing Perminder 
Published: July 2019

AbstractCritical concentration gradient model is helpful in understanding the mechanism of Z-ring formation. The distribution of positive and negative regulators of Z-ring formation in cell is not random but well programmed. The positive and negative regulators in cell lead to a critical concentration gradient from mid cell to the poles. The critical concentration of FtsZ required for Z-ring assembly at the centre of cell is less than that at the poles. So FtsZ starts polymerizing at cell centre and afterwards by cooperative association of more and more monomers leads to the Z-ring formation. Simultaneously during Z-ring formation the recruitment of other accessory proteins takes place, leading to the formation of a stable divisome complex.
Familial and late-onset Alzheimer&apos;s disease: Autoimmune disorders triggered by viral, microbial and allergen mimics of beta-amyloid and APP mutants ?
Authors: Carter Christopher 
Published: July 2019

AbstractBeta-amyloid (A[beta]) autoantibodies are common in Alzheimer's disease. Some may be derived from Herpes simplex and 68 other virus proteins matching an immunogenic and fibrillogenic VGGVV A[beta] sequence.Many other viral, microbial and allergenic proteins (particularly from dust mites) align with A[beta] as do proteins from C.Neoformans which has been associated with a rare but curable form of the disorder. Immune-related proteins are present in amyloid plaques and the complement membrane attack complex in neurones in Alzheimer's disease brains. Alzheimer's disease may thus be an autoimmune disorder triggered by pathogenic antigens homologous to A[beta], whose antibodies target and kill A[beta] containing neurones, via immune activation and complement-related lysis. This scenario explains many epidemiological observations in Alzheimer's disease, which is more common in women and Afro-Americans, as is HSV-2 seroprevalence; related to the number of pregnancies (exposure to childhood infections) and less severe in nuns (low exposure to sexually transmitted diseases). Atopy and autoimmune disorders are common in Alzheimer's disease in accord with allergen homology to A[beta], and anti-inflammatory agents reduce Alzheimer's disease risk. Cancer-causing, and plant viruses from Mediterranean diet components align with the A[beta] sequence targeted by catalytic autoantibodies, perhaps explaining the inverse association of diet and cancer with Alzheimer's disease. As a papillomavirus vaccine already exists, it may have a role to play in Alzheimer's disease. This scenario is also relevant to familial Alzheimer's disease. Mutant forms of APP~717~ and the Swedish mutant convert the surrounding peptide to matches with commensal bacteria (E.Coli, E. Faecalis, P.Gingivalis) and to viruses with very high seroprevalence (HHV-6, norovirus, influenza and the common cold). Late-onset and Familial Alzheimer's disease may both be autoimmune disorders caused by diverse common pathogens and allergens homologous to A[beta] or mutant APP fragments. Immunosuppressants, vaccination and pathogen elimination may be of benefit in both conditions.
The stroboscopic human vision
Authors: Bouman Maarten 
Published: July 2019

AbstractWhen the frequency of seeing light from a pair of point flashes is beyond the probability summation of the separate flashes, the surplus is due to the successful interaction of subliminal responses from the different flashes. Experiments with various distances and various periods of the pair show thet successful interaction occurs when in each of two successive time-quanta of 0.04 seconds and in each of two adjacent distinct receptor groups at least one subliminal receptor response occurs. An autonomous source produces the time-quanta. It serves the time-processing of the central nervous system and of the motor system. Posdsibly, action potentials from the purkinje cells of the myocardium play a role. Hyper acuity in direction and in depth, flicker fusion, perceptual rivalry and ather phenomena follow from the quantized spatiotemporal signal processing.
Two 'protein folding codes' can be inferred from empirical classifications using Tlusty's topological approach
Authors: Wallace Rodrick 
Published: July 2019

AbstractTlusty's topological arguments regarding the genetic code are applied to the classification of tertiary irregular protein symmetries. Unlike the genetic case, two protein folding codes are found, a 'normal' globular and a 'pathological' amyloid version. The underlying normal 'protein folding code error network' is found to have one major, highly dominant, 'spherical' component, a minor attachment handle in the Morse Theory sense, and as many as three additional subminor handles. The basic amyloid folding code error network appears to be more complicated, of genus two, giving the eightfold symmetry of the steric zipper. Like many before us, we conjecture that the elaborate cellular regulatory machinery associated with the endoplasmic reticulum and heat shock proteins is needed to prevent transition between these two thermodynamically 'natural' sets of protein conformations, and that its corrosion by aging accounts for the subsequent onset of many protein folding disorders. These results suggest markedly different evolutionary trajectories for the genetic and protein folding codes.
Many in vivo 'protein folding codes' can be inferred from empirical classifications using Tlusty's topological approach
Authors: Wallace Rodrick 
Published: July 2019

AbstractTlusty's topological rate distortion approach to the genetic code is applied to the problem of protein symmetries and to the analysis of protein folding rates. Unlike the genetic case, numerous 'protein folding codes' can be identified from empirical classifications. Protein folding rates follow from a topologically-driven rate distortion argument. These results imply markedly different evolutionary trajectories for the genetic and protein folding codes, and suggest that the 'protein folding code' is, in fact, a complicated composite, distributed across protein production and a cellular, or higher, regulatory apparatus acting as a canalizing catalyst that drives the system to converge on particular transitive components within a significantly larger 'protein folding groupoid'.
Prebiotic Organic Globules
Authors: Bassez Marie-Paule , Takano Yoshinori 
Published: July 2019

AbstractAnalogs of organic globules observed in carbonaceous chondrite meteorites and in interplanetary dust particles and of rod to spherical structures observed in terrestrial archean microstructures have been synthesized in our experiments conducted with proton irradiation on a mixture of simple inorganic constituants, CO, N2 and H2O. Our analyses of these laboratory organic globules show that the proton irradiation residue contains proteinous and non-proteinous amino acid precursors. On the basis of morphology, of hydrothermal and mineral environment, we suggest that the meteoritic organic globules and the archean carbon microstructures could be composed of amino acid precursors.
TLR-9 Expression in Human Bronchial Epithelial Cells induced with Lipopolysaccharide
Authors: Dharmalingam Sangeetha , Saravanabhavan Shanmuga 
Published: July 2019

AbstractThe study conducted here was to investigate the gene and protein expression of Toll like receptor 9 when human bronchial epithelial cells were induced by lipopolysaccharide. TLRs are pattern recognition receptor (PRR) which plays a key role in innate immunity. They recognise the molecules that are shared by pathogens but distinguishes from the host which is referred to as pathogen associated molecular patterns (PAMPs). The HBECs were first cultured and once it becomes confluent they were induced with 10ng/ml of LPS. In order to find out whether the gene was expressed in the cells, the RNA was isolated and RT-PCR was carried out. Before carrying out the RT-PCR, RNA gel electrophoresis was carried out to show the 28S and 18S bands. Once the gene expression was analysed protein expression was carried out by extracting the protein using RIPA buffer and running the SDS-PAGE followed by staining. Silver staining and western blotting results revealed clear bands at 116kDa illustrating that the TLR9 protein had been expressed. RT-PCR results showed that a smear of bands for TLR9 and the in protein expression bands were seen in TLR9 protein region which indicates that TLR9 was expressed in the HBEC by LPS.
Obesity care pathway
Authors: Hobson Phillipa , Mangoud Abdallah 
Published: July 2019

AbstractThis paper recognises that obesity is a growing problem within the UK with Britain with one of the highest rates for overweight children in Europe and with one in three adults predicted to be obese by 2012. Within the UK, nearly 25 per cent of men and women are now obese which has created enormous implications for health service providers (NICE, 2006). This paper focuses specifically on North East Lincolnshire where life expectancy is less than the national average with males (76) and females (80.8). Within North East Lincolnshire we developed an evidence-based adult obesity care pathway based on the NICE obesity guidance, incorporating local referral criteria and input. The pathway is benefiting patients by helping to reduce obesity through an increase in lifestyle referrals. Since the pathway was developed we have seen a reduction in referrals for unnecessary bariatic surgery which is reducing the cost to the NHS. This paper shares our learning and best practice from stakeholder engagement, partnership working, successfully implementing and evaluating the adult obesity care pathway across all general practices.
A dynamical model of genetic networks describes cell differentiation
Authors: Serra Roberto , Marco Villani , Barbieri Alessia 
Published: July 2019

AbstractCell differentiation is a complex phenomenon whereby a stem cell becomes progressively more specialized and eventually gives rise to a specific cell type. Differentiation can be either stochastic or, when appropriate signals are present, it can be driven to take a specific route. Induced pluripotency has also been recently obtained by overexpressing some genes in a differentiated cell. Here we show that a stochastic dynamical model of genetic networks can satisfactorily describe all these important features of differentiation, and others. The model is based on the emergent properties of generic genetic networks, it does not refer to specific control circuits and it can therefore hold for a wide class of lineages. The model points to a peculiar role of cellular noise in differentiation, which has never been hypothesized so far, and leads to non trivial predictions which could be subject to experimental testing.
Rapid antigen detection using the liquid sample as a lens and self-mixer for light scattering detection
Authors: Garcia Antonio , Schneider John 
Published: July 2019

AbstractSuperhydrophobic surfaces, both natural and artificial, cause aqueous drops to bead on them. The most water-repellent surfaces produce nearly perfect spheres with very little contact between water, solutes, and surface due to the roughness of the surface ^1^. However, a related phenomenon that has not been well appreciated until recently, is that colloidal particles in the aqueous drop remain highly mobile, and smaller-sized colloids migrate to the drop surface due to both the driving force of evaporation and the expanded liquid/air interface ^2-3^. A newly identified, third useful optical property resulting from the suspension of an aqueous drop by the superhydrophobic surface is that a spheroidal lens is created. Without any additional energy or instrumentation, the simple placement of an aqueous sample on a superhydrophobic surface followed by the placement of a reagent drop results in very rapid mixing and a means to detect and monitor antigens via agglutination.
The interplay of descriptor-based computational analysis with pharmacophore modeling builds the basis for a novel classification scheme for feruloyl esterases
Authors: Udatha D.B.R.K. Gupta , Kouskoumvekaki Irene , Olsson Lisbeth , Panagiotou Gianni 
Published: July 2019

AbstractOne of the most intriguing groups of enzymes, the feruloyl esterases (FAEs), is ubiquitous in both simple and complex organisms. FAEs have gained importance in biofuel, medicine and food industries due to their capability of acting on a large range of substrates for cleaving ester bonds and synthesizing high-added value molecules through esterification and transesterification reactions. During the past two decades extensive studies have been carried out on the production and partial characterization of FAEs from fungi, while much less is known about FAEs of bacterial or plant origin. Initial classification studies on FAEs were restricted on sequence similarity and substrate specificity on just four model substrates and considered only a handful of FAEs belonging to the fungal kingdom. This study centers on the descriptor-based classification and structural analysis of experimentally verified and putative FAEs; nevertheless, the framework presented here is applicable to every poorly characterized enzyme family. 365 FAE-related sequences of fungal, bacterial and plantae origin were collected and they were clustered using Self Organizing Maps followed by k-means clustering into distinct groups based on amino acid composition and physico-chemical composition descriptors derived from the respective amino acid sequence. A Support Vector Machine model was subsequently constructed for the classification of new FAEs into the pre-assigned clusters. The model successfully recognized 98.2% of the training sequences and all the sequences of the blind test. The underlying functionality of the 12 proposed FAE families was validated against a combination of prediction tools and published experimental data. Another important aspect of the present work involves the development of pharmacophore models for the new FAE families, for which sufficient information on known substrates existed. Knowing the pharmacophoric features of a small molecule that are essential for binding to the members of a certain family opens a window of opportunities for tailored applications of FAEs.
A Micropropagation, Molecular and Physiochemical Analysis of Canola Brassica napus L. From Seeds
Authors: Khan Israr , Shuaib Muhammad , Khan Sikandar , Zia Muhammad Amir , Akbar Haji 
Published: July 2019

AbstractCanola is important for its oil, anticarcinogenic phytochemicals and low saturated fat content and has wide scope for further improvement through genetic transformations. Micropropagation is the practice of rapidly multiplying stock plant material to produce a large number of disease free progeny plants, using modern asceptic plant tissue culture methods and also to conserve germ plasm. A combination of auxin and cytikinin and a shock on growth regulator free medium is used for micropropagation. Molecular and physiochemical analysis done to know variation in seeds protein content and electric conductivity.
Transcriptional coupling of neighbouring genes and gene expression noise: evidence that gene orientation and non-coding transcripts are modulators of noise
Authors: Wang Guang-Zhong , Lercher Martin , Hurst Laurence 
Published: July 2019

AbstractFor some genes, notably essential genes, expression when expression is needed is vital hence low noise in expression is favourable. For others noise is necessary for coping with stochasticity or for providing dice-like mechanisms to control cell fate. But how is noise in gene expression modulated? We hypothesise that gene orientation may be crucial, as for divergently organized gene pairs expression of one gene could affect chromatin of a neighbour thereby reducing noise. Transcription of antisense non-coding RNA from a shared promoter is similarly argued to be a noise-reduction mechanism. Stochastic simulation models confirm the expectation. The model correctly predicts: that protein coding genes with bi-promoter architecture, including those with a ncRNA partner, have lower noise than other genes; divergent gene pairs uniquely have correlated expression noise; distance between promoters predicts noise; ncRNA divergent transcripts are associated with genes that a priori would be under selection for low noise; essential genes reside in divergent orientation more than expected; bi-promoter pairs are rare subtelomerically, cluster together and are enriched in essential gene clusters. We conclude that gene orientation and transcription of ncRNAs, even if unstable, are candidate modulators of noise levels.
Immunogens and Antigen Processing: Report from a Global HIV Vaccine Enterprise Working Group
Authors: Mascola John , King Richter , Steinman Ralph , Working Group convened by the Globa the 
Published: July 2019

AbstractThe Global HIV Vaccine Enterprise convened a meeting of a Working Group in July 2009 to discuss recent progress in rational design of the components of an HIV vaccine, such as inserts, vectors and adjuvants,and in understanding antigen processing and presentation to T and B cells. This Report summarizes the key points of that discussion, and subsequent discussions with the Chairs of the other Enterprise Working Groups, the Enterprise Science Committee, the Enterprise Council and the broader scientific community during open sessions at scientific conferences.
Novel approaches, including systems biology, to HIV vaccine research and development: Report from a Global HIV Vaccine Enterprise Working Group
Authors: Pulendran Bali , Rappuoli Rino , Aderem Alan , Working Group convened by the Globa the 
Published: July 2019

AbstractThe Global HIV Vaccine Enterprise convened a two-day workshop on August 10-11 2009, at the Fred Hutchison Cancer Research Center offices in Seattle, WA, to discuss the application of novel approaches,including systems biology, to HIV vaccine research and development. The goals of this Working Group were to identify key scientific issues and opportunities that have emerged since the Enterprise Scientific Strategic Plan1 was published in 2005, and to make recommendations to Enterprise stakeholders.