bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inferring decoding strategy from choice probabilities in the presence of noise correlations
Authors: Haefner Ralf , Gerwinn Sebastian , Macke Jakob , Bethge Matthias 
Published: July 2019

AbstractThe activity of cortical neurons in sensory areas covaries with perceptual decisions, a relationship often quantified by choice probabilities. While choice probabilities have been measured extensively, their interpretation has remained fraught with difficulty. Here, we derive the mathematical relationship between choice probabilities, read-out weights and noise correlations within the standard neural decision making model. Our solution allows us to prove and generalize earlier observations based on numerical simulations, and to derive novel predictions. Importantly, we show how the read-out weight profile, or decoding strategy, can be inferred from experimentally measurable quantities. Furthermore, we present a test to decide whether the decoding weights of individual neurons are optimal, even without knowing the underlying noise correlations. We confirm the practical feasibility of our approach using simulated data from a realistic population model. Our work thus provides the theoretical foundation for a growing body of experimental results on choice probabilities and correlations.
A novel predicted calcium-regulated kinase family implicated in neurological disorders
Authors: Dudkiewicz Małgorzata , Lenart Anna , Pawłowski Krzysztof 
Published: July 2019

AbstractProtein kinases are essential effectors of cellular signaling. Surprisingly, using bioinformatics tools, we predicted protein kinase structure and function for proteins of unknown function (FAM69 family) coded by five related human genes and their Metazoan homologues. Analysis of three-dimensional structure models and conservation of the classic catalytic motifs of protein kinases in four of human FAM69 proteins suggests they might have retained catalytic phosphotransferase activity. The FAM69 genes, FAM69A, FAM69B, FAM69C, C3ORF58 and CXORF36, are by large uncharacterized molecularly, yet linked to several neurological disorders in genetics studies. An EF-hand Ca2+-binding domain in FAM69A and FAM69B proteins, inserted within the structure of the kinase domain, suggests they function as Ca2+-dependent kinases.
Structural Analysis of Outer Membrane Beta-stranded Porins using Temperature Factor
Authors: Kumar Abhishek 
Published: July 2019

AbstractComputational and statistical analysis has formed a large component of the biophysical efforts put forth to understand protein structure and function, due to the diversity and complexity of their structure. Outer membrane proteins form a diverse and complex set of proteins. Of these, porins which allow passage of molecules across the membrane interface have been analyzed here from a biophysical and structural perspective. The objective of this study is to analyze the structural organization of porins using atomic temperature factor as a parameter. Generally atomic temperature factors of molecules from crystal structures indicate the degree of mobility or disorder seen in the crystal structure. As good crystal structures have fewer possibilities of errors so there is less chance that errors are playing roles in temperature factors. Structures of six porins (four 16 stranded beta barrel porins and two 8 stranded beta barrel porins) were taken from the PDB for the analysis based on resolution and R-factor. Programs and scripts were written for extracting the temperature factors for the beta strands, loops and turns so that the analysis could be done for different atom-types and residue-types. The residue distribution and mobility distribution was found to be characteristic of each of the porins. The mobility and residue distribution amongst the secondary structural elements were found to follow the level of homology at the sequence and structural level. The loops that had defined functional roles in structural terms were found to have lower temperature factors than the other loops. The turn regions that are thought to face the periplasmic region in the cell, showed higher temperature factors. For both the 16 stranded and the 8 stranded barrels it was found one part of the barrel (the lower wall or ‘inner’ wall comprising the trimer interface in the case of the 16 stranded barrels) was more rigid and the other half of the barrel (the higher or ‘outer’ wall) showed more mobility as seen from the temperature factors. This seems to be an intrinsic structural component of the beta barrels.
Can bacteria adapt to starvation-free environment?
Authors: Kitahara Kei 
Published: July 2019

AbstractBacteria will experience starvation-free environment if infinite nutrition is supplied continuously for a long period. In this study, an evolutionary experiment was performed for 118 days where bacteria adapted to starvation-free environment and reduced their doubling time. It is anticipated that this finding will help to select bacterial strains that can grow more rapidly in rich media.
Category of Metabolic-Replication Systems in Biology and Medicine
Authors: Baianu I. 
Published: July 2019

AbstractMetabolic-repair models, or (M,R)-systems were introduced in Relational Biology by Robert Rosen. Subsequently, Rosen represented such (M,R)-systems (or simply MRs)in terms of categories of sets, deliberately selected without any structure other than the discrete topology of sets. Theoreticians of life's origins postulated that Life on Earth has begun with the simplest possible organism, called the primordial. Mathematicians interested in biology attempted to answer this important question of the minimal living organism by defining the functional relations that would have made life possible in such a minimal system- a grandad and grandma of all living organisms on Earth.
Cancer Clinical Trials Optimization and Pharmacogenomics
Authors: Baianu I. 
Published: July 2019

AbstractA critical overview of recent clinical trials in cancer is presented focused on signaling pathways blockers or inhibitors with a view to developing successful clinical trials employing personalized cancer therapies. Rational, pharmacogenomic strategies in cancer trials should be adopted that include specific molecular targeting based on adequate data for, and detailed modeling of, cancer cell genomes, modifications of cancer signaling pathways and epigenetic mechanisms. Novel translational oncogenomics research is rapidly expanding through the application of highly sensitive and specific advanced technology, research findings and computational tools and complex models to both pharmaceutical and clinical problems. Multiple sample analyses from several recent clinical studies have shown that gene expression data for cancer cells can be employed to distinguish between tumor types as well as to predict outcomes. Potentially important applications of such results are individualized human cancer therapies or, in general,'personalized medicine' that will have to be validated through optimally designed clinical trials in cancer. A Human Cancer Genomes and Epigenetics Project is proposed that can provide the essential data required for the optimal design of clinical trials with the goal of achieving significant improvements of the survival rates of cancer patients participating in clinical trials for advanced cancer stages. The results of such a six-year Human Cancer Genomes and Epigenetics Project should also greatly aid with the accelerated, rational development of effective anti-cancer medicines and the chemoprevention of cancers.
Mind over chatter: plastic up-regulation of the fMRI alertness network by EEG neurofeedback
Authors: Lanius Ruth , Ros Tomas , Theberge Jean , Frewen Paul , Kluetsch Rosemarie , Densmore Maria , Calhoun Vince 
Published: July 2019

AbstractEEG neurofeedback (NFB) is a brain-computer interface (BCI) approach used to shape brain oscillations by means of real-time feedback from the electroencephalogram (EEG), which is known to reflect neural activity across cortical networks. Although NFB is being evaluated as a novel tool for treating brain disorders, evidence is scarce on the mechanism of its impact on brain function. In this study with 34 healthy participants, we examined whether, during the performance of an attentional auditory oddball task, the functional connectivity strength of distinct fMRI networks would be plastically altered after a 30-min NFB session of alpha-band reduction (n=17) versus a sham-feedback condition (n=17). Our results reveal that compared to sham, NFB induced a specific increase of functional connectivity within the alertness/salience network (dorsal anterior and mid cingulate), which was detectable 30 minutes after termination of training. Crucially, these effects were significantly correlated with reduced mind-wandering 'on-task' and were coupled to NFB-mediated resting state reductions in the alpha-band (8-12 Hz). No such relationships were evident for the sham condition. Although group default-mode network (DMN) connectivity was not significantly altered following NFB, we observed a positive association between modulations of resting alpha amplitude and precuneal connectivity, both correlating positively with frequency of mind-wandering. Our findings demonstrate a temporally direct, plastic impact of NFB on large-scale brain functional networks, and provide promising neurobehavioral evidence supporting its use as a noninvasive tool to modulate brain function in health and disease.
Comments on “Assessing future risk: quantifying the effects of sea level rise on storm surge risk for the southern shores of Long Island, New York”
Authors: Burton David 
Published: July 2019

AbstractTide gauge and satellite data indicate that the rate of sea level rise has not increased significantly in response to the last 3/4 century of CO2 emissions, so there is no reason to expect that it will do so in response to the next 3/4 century of CO2 emissions. The best prediction for sea level in the future is simply a linear projection of the history of sea level at the same location in the past. For Long Island, that is about 7-8 inches by 2080.
Music can reduce cognitive dissonance
Authors: Masataka Nobuo , Perlovsky Leonid 
Published: July 2019

AbstractThe fundamental cognitive functions of music in the brain have not been known and evolutionary reasons for musical abilities seem mysterious. A recent hypothesis suggested that a fundamental function of music has been to help mitigating cognitive dissonances. A cognitive dissonance is "a discomfort caused by holding conflicting cognitions" simultaneously; it usually leads to devaluation of conflicting knowledge. Since every concept implies some degree of contradictions to other knowledge, unmitigated cognitive dissonances could prevent evolution of cognition. Thus music might be fundamental for the evolution of cognition. Here we provide experimental confirmation of this hypothesis using a classical paradigm known to induce a cognitive dissonance and devaluation of a dissonant object; in presence of music devaluation has not occurred.
Quantum Genetics and Quantum Automata Models of Quantum-Molecular Evolution Involved in the Evolution of Organisms and Species
Authors: Baianu I. 
Published: July 2019

AbstractPrevious theoretical or general approaches to the problems of Quantum Genetics and Molecular Evolution are considered in this article from the point of view of Quantum Automata Theory first published by the author in 1971 and further developed in several recent articles. The representation of genomes and Interactome networks in categories of many-valued logic LMn –algebras that are naturally transformed during biological evolution, or evolve through interactions with the environment provide a new insight into the mechanisms of molecular evolution, as well as organismal evolution, in terms of sequences of quantum automata. Phenotypic changes are expressed only when certain environmentally-induced quantum-molecular changes are coupled with an internal re-structuring of major submodules of the genome and Interactome networks related to cell cycling and cell growth. Contrary to the commonly held view of 'standard’ Darwinist models of evolution, the evolution of organisms and species occurs through coupled multi-molecular transformations induced not only by the environment but actually realized through internal re-organizations of genome and interactome networks. The biological, evolutionary processes involve certain epigenetic transformations that are responsible for phenotypic expression of the genome and Interactome transformations initiated at the quantum-molecular level. It can thus be said that only quantum genetics can provide correct explanations of evolutionary processes that are initiated at the quantum--multi-molecular levels and propagate to the higher levels of organismal and species evolution.Biological evolution should be therefore regarded as a multi-scale process which is initiated by underlying quantum (coupled) multi-molecular transformations of the genomic and interactomic networks, followed by specific phenotypic transformations at the level of organism and the variable biogroupoids associated with the evolution of species which are essential to the survival of the species. The theoretical framework introduced in this article also paves the way to a Quantitative Biology approach to biological evolution at the quantum-molecular, as well as at the organismal and species levels. This is quite a substantial modification of the 'established’ modern Darwinist, and also of several so-called `molecular evolution’ theories.
Double burden of malnutrition among urban Bengalee adolescent boys in Midnapore, West Bengal, India
Authors: Bisai S , Khongsdier R , Bose K , Mahalanabis D 
Published: July 2019

AbstractMalnutrition is an important public health problem worldwide. Therefore a study was undertaken to assess the prevalence of adolescent thinness, overweight and obesity in Midnapore town, West Bengal, India. A total of 974 adolescent boys aged 10-18 years were selected following multistage cluster sampling method from three higher secondary schools. Data was collected using pretested questionnaire following standard technique. Presence of thinness was evaluated using the cut-off values of international survey as suggested by Cole et al (2007). While overweight and obesity was determine by using international cut-off values develop by Cole et al (2000) based on international surveys as recommended by IOTF. Overall the prevalence of thinness, overweight and obesity were 20.8%, 14.9% and 3.8%, respectively. This study developed age specific smooth BMI percentile values using LMS method. Moreover, the study also developed BMI cut-off values to define thinness, overweight and obesity. In conclusion, the present analyses indicated that the prevalence of adolescent undernutrition is still a major problem. In addition, there was also an emerging trend for overweight/obesity, thereby indicating a double burden of malnutrition as observed in other developing countries.
Strong and weak competitors can coexist in the same niche
Authors: Kalmykov Lev , Kalmykov Vyacheslav 
Published: July 2019

AbstractThe competitive exclusion principle postulates that two trophically identical but fitness different species can not stably coexist in the same niche. However, this principle contradicts the observed nature's species richness. This fact is known as the biodiversity paradox. Here, using a simple cellular automaton model, we mechanistically show how two trophically identical, but fitness different species may stably coexist in the same niche. As environment is stable and any trade-offs are absent in this model, it strongly violates the competitive exclusion principle.
Visual Molecular Dynamics Investigations of the Impact of Hydrophobic Nanoparticles on Prognosis of Alzheimer’s Disease and Cancers
Authors: Baianu I. , Charles M , Prisecaru V. 
Published: July 2019

AbstractThe possible impact of hydrophobic lectin nanoparticles on the prognosis and progression of Alzheimer's disease (AD) and cancers was investigated by Visual Molecular Dynamics (VMD) computer modeling programs available from the Beckmann Advanced Research Institute at the University of Illinois at Urbana. Our results indicate the possibility of impeding pathological aggregation of certain proteins such as modified tau- or beta-amyloid that are currently being considered as possible causes of Alzheimer's disease. VMD programs serve as useful tools for investigation hydrophobic protein aggregation that may play a role in aging of human populations.
Angiogenesis in Chronic Obstructive Pulmonary Disease
Authors: Matarese Alessandro , Santulli Gaetano 
Published: July 2019

AbstractAngiogenesis is a crucial component of lung pathophysiology, not only in cancer but also in other disorders, such as chronic obstructive pulmonary disease (COPD). In COPD angiogenesis is definitely able to control and orchestrate the progression of airway remodeling. Herein, we provide several remarkable translational aspects of angiogenesis in COPD, exploring both basic and clinical research in this field. Indeed, we present a number of pro- and anti-angiogenic factors, which can be also used as potential biomarkers to monitor disease progression.This pre-print has subsequently been published at http://www.unisa.it/uploads/7100/06.pdf
Synchronized Mammalian Cells in Culture: A Comparison of Normal and KB Cancer Cell Growth
Authors: Baianu I. 
Published: July 2019

AbstractExperimentation and tests with cells in culture and cell synchronization or synchrony are important in order to be able to make both reliable and high-sensitivity measurements. This is also very important for mechanistic studies of cell division control, oncogenesis and tumor growth. A comparison is made in this article between the initially synchronized cell growth of rabbit and KB cells in synchronized cultures.
Micron-gap spacers with ultrahigh thermal resistance and mechanical robustness for direct energy conversion
Authors: Nicaise Samuel M. , Lin Chen , Azadi Mohsen , Bozorg-Grayeli Tara , Adebayo-Ige Promise , Lilley Drew E. , Pfitzer Yann , Cha Wujoon , Van Houten Kyana , Melosh Nicholas A. , Howe Roger T. , Schwede Jared W. , Bargatin Igor 
Published: July 2019

AbstractIn thermionic energy converters, the absolute efficiency can be increased up to 40% if space-charge losses are eliminated by using a sub-10-µm gap between the electrodes. One practical way to achieve such small gaps over large device areas is to use a stiff and thermally insulating spacer between the two electrodes. We report on the design, fabrication and characterization of thin-film alumina-based spacers that provided robust 3–8 μm gaps between planar substrates and had effective thermal conductivities less than those of aerogels. The spacers were fabricated on silicon molds and, after release, could be manually transferred onto any substrate. In large-scale compression testing, they sustained compressive stresses of 0.4–4 MPa without fracture. Experimentally, the thermal conductance was 10–30 mWcm−2K−1and, surprisingly, independent of film thickness (100–800 nm) and spacer height. To explain this independence, we developed a model that includes the pressure-dependent conductance of locally distributed asperities and sparse contact points throughout the spacer structure, indicating that only 0.1–0.5% of the spacer-electrode interface was conducting heat. Our spacers show remarkable functionality over multiple length scales, providing insulating micrometer gaps over centimeter areas using nanoscale films. These innovations can be applied to other technologies requiring high thermal resistance in small spaces, such as thermophotovoltaic converters, insulation for spacecraft and cryogenic devices.
Toward point-of-care assessment of patient response: a portable tool for rapidly assessing cancer drug efficacy using multifrequency impedance cytometry and supervised machine learning
Authors: Ahuja Karan , Rather Gulam M. , Lin Zhongtian , Sui Jianye , Xie Pengfei , Le Tuan , Bertino Joseph R. , Javanmard Mehdi 
Published: July 2019

AbstractWe present a novel method to rapidly assess drug efficacy in targeted cancer therapy, where antineoplastic agents are conjugated to antibodies targeting surface markers on tumor cells. We have fabricated and characterized a device capable of rapidly assessing tumor cell sensitivity to drugs using multifrequency impedance spectroscopy in combination with supervised machine learning for enhanced classification accuracy. Currently commercially available devices for the automated analysis of cell viability are based on staining, which fundamentally limits the subsequent characterization of these cells as well as downstream molecular analysis. Our approach requires as little as 20 μL of volume and avoids staining allowing for further downstream molecular analysis. To the best of our knowledge, this manuscript presents the first comprehensive attempt to using high-dimensional data and supervised machine learning, particularly phase change spectra obtained from multi-frequency impedance cytometry as features for the support vector machine classifier, to assess viability of cells without staining or labelling.
Evolving concepts in bone infection: redefining “biofilm”, “acute vs. chronic osteomyelitis”, “the immune proteome” and “local antibiotic therapy”
Authors: Masters Elysia A. , Trombetta Ryan P. , de Mesy Bentley Karen L. , Boyce Brendan F , Gill Ann Lindley , Gill Steven R. , Nishitani Kohei , Ishikawa Masahiro , Morita Yugo , Ito Hiromu , Bello-Irizarry Sheila N. , Ninomiya Mark , Brodell James D. , Lee Charles C. , Hao Stephanie P. , Oh Irvin , Xie Chao , Awad Hani A. , Daiss John L. , Owen John R. , Kates Stephen L. , Schwarz Edward M. , Muthukrishnan Gowrishankar 
Published: July 2019

AbstractOsteomyelitis is a devastating disease caused by microbial infection of bone. While the frequency of infection following elective orthopedic surgery is low, rates of reinfection are disturbingly high.Staphylococcus aureusis responsible for the majority of chronic osteomyelitis cases and is often considered to be incurable due to bacterial persistence deep within bone. Unfortunately, there is no consensus on clinical classifications of osteomyelitis and the ensuing treatment algorithm. Given the high patient morbidity, mortality, and economic burden caused by osteomyelitis, it is important to elucidate mechanisms of bone infection to inform novel strategies for prevention and curative treatment. Recent discoveries in this field have identified three distinct reservoirs of bacterial biofilm including:Staphylococcalabscess communities in the local soft tissue and bone marrow, glycocalyx formation on implant hardware and necrotic tissue, and colonization of the osteocyte-lacuno canalicular network (OLCN) of cortical bone. In contrast,S. aureusintracellular persistence in bone cells has not been substantiated in vivo, which challenges this mode of chronic osteomyelitis. There have also been major advances in our understanding of the immune proteome againstS. aureus, from clinical studies of serum antibodies and media enriched for newly synthesized antibodies (MENSA), which may provide new opportunities for osteomyelitis diagnosis, prognosis, and vaccine development. Finally, novel therapies such as antimicrobial implant coatings and antibiotic impregnated 3D-printed scaffolds represent promising strategies for preventing and managing this devastating disease. Here, we review these recent advances and highlight translational opportunities towards a cure.