bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploiting Nonlinear Recurrence and Fractal Scaling Properties for Voice Disorder Detection
Authors: Little Max , McSharry Patrick , Roberts Stephen , Costello Declan , Moroz Irene 
Published: July 2019

Abstract
Background:
Voice disorders affect patients profoundly, and acoustic tools can potentially measure voice function objectively. Disordered sustained vowels exhibit wide-ranging phenomena, from nearly periodic to highly complex, aperiodic vibrations, and increased "breathiness". Modelling and surrogate data studies have shown significant nonlinear and non-Gaussian random properties in these sounds. Nonetheless, existing tools are limited to analysing voices displaying near periodicity, and do not account for this inherent biophysical nonlinearity and non-Gaussian randomness, often using linear signal processing methods insensitive to these properties. They do not directly measure the two main biophysical symptoms of disorder: complex nonlinear aperiodicity, and turbulent, aeroacoustic, non-Gaussian randomness. Often these tools cannot be applied to more severe disordered voices, limiting their clinical usefulness.

Methods:
This paper introduces two new tools to speech analysis: recurrence and fractal scaling, which overcome the range limitations of existing tools by addressing directly these two symptoms of disorder, together reproducing a "hoarseness" diagram. A simple bootstrapped classifier then uses these two features to distinguish normal from disordered voices.

Results:
On a large database of subjects with a wide variety of voice disorders, these new techniques can distinguish normal from disordered cases, using quadratic discriminant analysis, to overall correct classification performance of 91.8% plus or minus 2.0%. The true positive classification performance is 95.4% plus or minus 3.2%, and the true negative performance is 91.5% plus or minus 2.3% (95% confidence). This is shown to outperform all combinations of the most popular classical tools.

Conclusions:
Given the very large number of arbitrary parameters and computational complexity of existing techniques, these new techniques are far simpler and yet achieve clinically useful classification performance using only a basic classification technique. They do so by exploiting the inherent nonlinearity and turbulent randomness in disordered voice signals. They are widely applicable to the whole range of disordered voice phenomena by design. These new measures could therefore be used for a variety of practical clinical purposes.
ProbCD: enrichment analysis accounting for categorization uncertainty
Authors: Vêncio Ricardo , Shmulevich Ilya 
Published: July 2019

AbstractAs in many other areas of science, systems biology makes extensive use of statistical association and significance estimates in contingency tables, a type of categorical data analysis known in this field as enrichment (also over-representation or enhancement) analysis. In spite of efforts to create probabilistic annotations, especially in the Gene Ontology context, or to deal with uncertainty in high throughput-based datasets, current enrichment methods largely ignore this probabilistic information since they are mainly based on variants of the Fisher Exact Test. We developed an open-source R package to deal with probabilistic categorical data analysis, ProbCD, that does not require a static contingency table. The contingency table forthe enrichment problem is built using the expectation of a Bernoulli Scheme stochastic process given the categorization probabilities. An on-line interface was created to allow usage by non-programmers and is available at: http://xerad.systemsbiology.net/ProbCD/. We present an analysis framework and software tools to address the issue of uncertainty in categorical data analysis. In particular, concerning the enrichment analysis, ProbCD can accommodate: (i) the stochastic nature of the high-throughput experimental techniques and (ii) probabilistic gene annotation.
The Freezing Rotation Illusion
Authors: Dürsteler Max 
Published: July 2019

AbstractThe freezing rotation illusion arises when a figure is continuously rotating in front of a back and forth rotating ground. The term “freezing rotation” designates the decrease in the perceived rotation speed of a figure when the figure and the ground are turning in equal directions. Subjects had to estimate the rotation speed of a continuously turning figure while the ground was either turning opposite to or with the figure. Their estimations of the figure’s speed were significantly lower, when the ground was moving in the same direction as the figure. In control experiments subjects had to estimate the ground’s speed while the figure was turning opposite to or with the ground. Overall, their estimations of the rotational speed of the ground were not significantly influenced by the rotational direction of the figure.
Allosteric modulation of beta1 integrin function induces lung repair in animal model of emphysema.
Authors: Al-Jamal Rehab , Wilson Linda , Armit Chris J. , McIntyre Susan , Marsden Mark , Shapiro Steven D. , Harrison David J. 
Published: July 2019

AbstractEmphysema is a progressive lung disease characterised by loss of lung parenchyma with associated functional changes including decreased tissue elastance. Here we report beta1 integrin is a novel target for tissue repair and regeneration in emphysema. We show a single dose of a monoclonal antibody against beta1 integrin induced both functional and structural reversal of elastase-induced lung injury in vivo, and we found that similar matrix remodelling changes occurred in human lung tissue. We also identified a potential mechanism of action as this allosteric modulation of beta1 integrin inhibited elastase-induced caspase activation, F-actin aggregate formation and changes in cellular ATP levels. This was accompanied by maintenance of beta1?integrin levels and inhibition of caveolin-1 phosphorylation. We propose that allosteric modulation of beta1 integrin-mediated mechanosensing prevents cell death associated with lung injury and progressive emphysema, thus allowing cells to survive and for repair and regeneration to ensue.
Intact mitochondria migrate in membrane tubular network connections formed between human stem cells
Authors: Csordas Attila , Cselenyák Attila , Uher Ferenc , Murányi Marianna , Hennerbichler Simone , Redl Heinz , Kollai Márk , Lacza Zsombor 
Published: July 2019

AbstractThe hypothesis of mitochondrial transfer between eukaryotic animal cells is intriguing, although its route of action and physiological role is unknown. Our goal was to examine intercellular connections among several types of stem cells and to observe whether intact functional mitochondria may travel via these connections. Time-lapse laser scanning confocal microscopy has shown that human amnion-derived stem cells as well as bone marrow derived mouse and human mesenchymal stem cells form cell-to-cell connections via a tubular membrane network. The maximal length of these micrometer-thick tubes is around 180 ?m. Interestingly, freshly isolated amniotic epithelial stem cells did not form these connections, only after several passages when the morphology of the cells is significantly altered. Large area cell-cell contacts can be retained as long thin membrane bridges after the cells depart and de novo tube formation is also observed. Using MitoTracker red staining we observed that intact mitochondria are moving in these tubes by 20 – 60 nm/s velocity, suggesting that mitochondria can leave one cell via the membrane tubes and can enter into another cell. These results suggest that specific types of stem cells form comprehensive tubular networks among each other. One physiological role of these networks may be that mitochondria can migrate from one cell to the other, which may be a novel way of communication among stem cells.
Biological Activities of Extracts from Sumac (Rhus spp.): A Review
Authors: Rayne Sierra , Mazza Giuseppe 
Published: July 2019

AbstractSumac is the common name for a genus (Rhus) that contains over 250 individual species of flowering plants in the family Anacardiaceae. These plants are found in temperate and tropical regions worldwide, often grow in areas of marginal agricultural capacity, and have a long history of use by indigenous peoples for medicinal and other uses. The research efforts on sumac extracts to date indicate a promising potential for this plant family to provide renewable bioproducts with the following reported desirable bioactivities: antifibrogenic, antifungal, antiinflammatory, antimalarial, antimicrobial, antimutagenic, antioxidant, antithrombin, antitumorigenic, antiviral, cytotoxic, hypoglycaemic, and leukopenic. As well, the bioactive components can be extracted from the plant material using environmentally benign solvents that allow for both food and industrial end-uses. The favorable worldwide distribution of sumac also suggests that desirable bioproducts may be obtained at source, with minimal transportation requirements from the source through processing to end consumer. However, previous work has focussed on only a few members of this large plant family. In addition, not all of the species studied to date have been fully characterized for potential bioactive components and bioactivities. Thus, there remains a significant research gap spanning the range from lead chemical discovery through process development and optimization in order to better understand the full potential of the Rhus genus as part of global green technology based bioproduct and bioprocess research programs.
Trichoderma reesei derived cellulase activity in three N,N-dimethylethanolammonium akylcarboxylate ionic liquids
Authors: Rayne Sierra , Mazza Giuseppe 
Published: July 2019

AbstractThe activity and denaturation extent of cellulase from Trichoderma reesei (E.C. 3.2.1.4) was investigated in three representative N,N-dimethylethanolammonium akylcarboxylate ionic liquids. Significant cellulase activity and absence of enzyme unfolding was found in all concentrations of N,N-dimethylethanolammonium acetate (DMEAA), including the pure liquid. Activities in 20% and 40% (v/v) solutions of DMEAA were equal to citrate buffer controls. Lower enzymatic activities and denaturation were observed in solutions of the corresponding formate and octanoate ionic liquids, although cellulose hydrolysis still proceeded at a substantial rate. The results provide the first proof-of-principle that cellulose can be enzymatically hydrolyzed in the presence of high ionic liquid concentrations.
Solvent Induced Disulfide Bond Formation in 2,5-dimercapto-1,3,4-thiadiazole
Authors: Kalimuthu Palanisamy , Kalimuthu Palraj , Abraham John S. 
Published: July 2019

AbstractDisulfide bond formation is the decisive event in the protein folding to determine the conformation and stability of protein. To achieve this disulfide bond formation in vitro, we took 2,5-dimercapto-1,3,4-thiadiazole (DMcT) as a model compound. We found that disulfide bond formation takes place between two sulfhydryl groups of DMcT molecules in methanol. UV-Vis, FT-IR and mass spectroscopic as well as cyclic voltammetry were used to monitor the course of reaction. We proposed a mechanism for the solvent induced disulfide bond formation on the basis of the results we obtained.
Computer simulations on the sympatric speciation modes for the Midas cichlid species complex
Authors: Luz-Burgoa Karen , Moss de Oliveira Suzana , de Sá Martins Jorge 
Published: July 2019

AbstractCichlid fishes are one of the best model system for the study of evolution of the species. Inspired by them, in this paper we simulated the splitting of a single species into two separate ones via random mutations, with both populations living together in sympatry, sharing the same habitat. We study the ecological, mating and genetic conditions needed to reproduce the polychromatism and polymorphism of three species of the Midas Cichlid species complex. Our results show two scenarios for the A. Citrinellus speciation process, one with and the other without disruptive natural selection. In the first scenario, the ecological and genetic conditions are sufficient to create two new species, while in the second the mating and genetic conditions must be synchronized in order to control the velocity of genetic drift.
CARE1, a TY3-gypsy long terminal repeat retrotransposon in the food legume chickpea (Cicer arietinum L)
Authors: Rajput Manoj , Upadhyaya Kailash 
Published: July 2019

AbstractWe report a novel Ty3-gypsy long terminal repeat retrotransposon CARE1 (Cicer arietinum retro-element 1) in chickpea. This 5920-bp AT-rich (63%) element carries 723-bp 5' and 897-bp 3' LTRs respectively flanking an internal region of 4300-bp. The LTRs of CARE1 show 93.9% nucleotide identity to each other and have 4-bp (ACTA) terminal inverted repeats. A 17-bp potential tRNAmet primer binding site downstream to 5' LTR and a 13-bp polypurine tract upstream to 3' LTR have been identified. The order of domains (Gag-proteinase-reverse transcriptase-RNaseH-integrase) in the deduced amino acid sequence and phylogenetic tree constructed using reverse transcriptase sequences places CARE1 in the gypsy group of retrotransposons. Homologues of a number of cis-elements including CCAAT, TATA and GT-1 have been detected in the regulatory region or the 5' LTR of CARE1. Transgenic tobacco plants containing 5' LTR:GUS construct show that its 5'-LTR is inactive in a heterologous system under normal as well as tissue culture conditions. Genomic Southern blot experiments using 5’LTR of the element as a probe show that CARE1 or its related elements are present in the genomes of various chickpea accessions from various geographic regions.
Pregnancy Obstructs Involution Stage II of the Mammary Gland in Cows: General Biological Implications
Authors: Silanikove Nissim , Leitner Gabriel , Anug Ana-Maria , Merin Uzi 
Published: July 2019

Abstract
*Background*
Repeated research findings over the last 4 decades show that involution of mammary glands in dairy cows did not regress to same extend as that noticed in other mammalian species.*Methodology/Principal Findings*We took an advantage of a rare event in the normal modern dairy farming: A cow that was false-positively identified as being pregnant was "dried up" (i.e., induced into involution) conventionally about 60 before her expected parturition. This cow was culled, and samples of her mammary gland tissue were examined for gross histology. In this study we demonstrate for the first time that modern dairy cow may undergo extensive obliteration of the lobular-alveolar structure, as expected in involution stage II.

*Conclusions/Significance*
We conclude that lack of histological evidence for the appearance of involution stage II in the vast majority of modern cow's population is related to the peculiar modern dairy husbandry, in which dairy cows are induced into involution still pregnant. Because retardation of involution stage II in pregnant mammals is most likely a general physiological phenomena, it might occurs in other mammals, particularly in lactating humans. Thus, based on basic comparative physiology considerations, we suggest that concurrent lactation and pregnancy should be considered as an independent risk factor for breast cancer.
Homologous self-organising scale-invariant properties characterise long range species spread and cancer invasion
Authors: Marco Diana , Cannas Sergio , Montemurro Marcelo , Hu Bo , Cheng Shi-Yuan 
Published: July 2019

AbstractOccupancy of new habitats through dispersion is a central process in nature. In particular, long distance dispersal is involved in the spread of species and epidemics, although it has not been previously related with cancer invasion, a process that involves cell spreading to tissues far away from the primary tumor.Using simulations and real data we show that the early spread of cancer cells is similar to the species individuals spread and that both processes are represented by a common spatio-temporal signature of long-distance dispersal and subsequent local proliferation. This signature is characterized by a particular fractal geometry of the boundaries of patches generated, and a power law-scaled, disrupted patch size distribution. In contrast, invasions involving only dispersal but not subsequent proliferation (“physiological invasions”) like trophoblast cells invasion during normal human placentation did not show the patch size power law pattern. Our results are robust to temporal and spatial scales, and to the resolution level of analysis.We conclude that the scaling properties are a hallmark and a direct result of long-distance dispersal and proliferation, and that they reflect homologous ecological processes of population self-organization during cancer and species spread. Our results are significant for the detection of processes involving long-range dispersal and proliferation like cancer metastasis, biological invasions and epidemics, and for the formulation of new cancer therapeutical approaches.
Keratinocytes from human skin respond as typical immune cells after the stimulation with Trichophyton rubrum
Authors: Islas-Rodríguez Alfonso , García-Madrid Luz 
Published: July 2019

AbstractTrichophyton rubrum is the main agent causing dermatophytosis (1). Keratinocytes areconsidered to be the first physical barrier of defense against pathogens (2). But notonly a physical barrier. They recognize antigens through Toll like receptors (TLR) (3).The activation of this TLR, present on the surface of the keratinocytes, induce theexpression of different pro-inflammatory cytokines, co-stimulatory molecules andantimicrobial peptides such as [beta]-defensins (4).The main objective of this work is to determine if lipopolysaccharides of G – bacteria(LPS), lipotheichoic acid from G+ bacteria (LTA), and conidias, isolated from T. rubrumwere able to activate the expression of TLR2 and TLR6 on the cell surface of a primaryculture of human keratinocytes through Flow cytometry. Furthermore we are looking forthe presence of [beta]-defensins 1 and 2, IL-1b and IL-8 in the supernatant, of the abovementioned culture of cells, by Western blot.From the flow cytometry data, the preliminary results showed an important dispersionin terms of proliferation, increase in size and granularity of keratinocytes, from primarycultures of skin from healthy donors, stimulated 6 hours with conidias of T. rubrum, andLTA, but not when non stimulated, or stimulated with LPS (Fig 1).When keratinocytes from primary cultures of skin from healthy donors were cultivated48 hours, it was found dispersion in terms of proliferation, increase in size andgranularity when stimulated with conidias of T. rubrum, and LPS but not when nonstimulated, or stimulated with LTA (Fig 2).The keratinocytes expressed increased levels of TLR2 and TLR6 when werestimulated with LTA and less to T. rubrum, in the 6 hours cultures, but this last cells stillshowed increased size (Fig 3).The Keratinocytes expressed increased levels of TLR2 in the 48 hours cultures whenwere stimulated with LPS and T. rubrum.(Fig 4)Besides, [beta]-defensin-2 was detected in the supernatant of cultures of keratinocytesstimulated with LPS (Fig 5).It can preliminary be concluded that keratinocytes from primary cultures of human skin from healthy donors, are cells that respond as typical immune cells, after stimulationwith T. rubrum, LTA and LPS in different conditions, and that this mechanism may bevery important, for the protection of local environment. References1.- Arenas R., Dermatofitosis en México. Rev Iberoam Micol 2002; 19: 63-67.2.- Kupper T. and Fuhlbrigge R. Immune surveillance in the skin: mechanims and clinical consecuences.Nat Rev Immunol 2004; 4: 211-2223.- Kôllish G., Naderi B., Voelcker V., Wallich R., Behrendt H., Ring J., Bauer S., Jacob T., Mempel M. andOlelrt M. Various members of the Toll-Like receptor family contribute to the innate immune response ofhuman epidermal keratinocytes. Immunology 2005; 114: 531-541.4.- Akira, S. and Takeda K. 2004. Toll-like Receptor Signalling. Nature Reviews Immunology 4:499-511.
The Normal Fetal Heart Rate Study: Analysis Plan
Authors: Daumer Martin , Scholz Michael , Boulesteix Anne-Laure , Pildner von Steinburg Stephanie , Schiermeier Sven , Hatzmann Wolfgang , Schneider K T M 
Published: July 2019

AbstractRecording of fetal heart rate via CTG monitoring has been routinely performed as an important part of antenatal and subpartum care for several decades. The current guidelines of the FIGO (ref1) recommend a normal range of the fetal heart rate from 110 to 150 bpm. However, there is no agreement in the medical community whether this is the correct range (ref2). We aim to address this question by computerized analysis (ref 3) of a high quality database (HQDb, ref 4) of about one billion electronically registered fetal heart rate measurements from about 10,000 pregnancies in three medical centres over seven years. In the present paper, we lay out a detailed analysis plan for this evidence-based project in the vein of the validation policy of the Sylvia Lawry Centre for Multiple Sclerosis Research (ref 5) with a split of the database into an exploratory part and a part reserved for validation. We will perform the analysis and the validation after publication of this plan in order to reduce the probability of publishing false positive research findings (ref 6-7).
Screening of actinobacteria for antimicrobial activities by a modified "Cross-Streak" method
Authors: Kamat Nandkumar , Velho-Pereira Sonashia 
Published: July 2019

AbstractNew molecule discovery from natural sources, such as that of actinobacteria, has proved to be an interesting area in antibiotic research, as most of these antibiotics are difficult to synthesize. Out of 30 actinobacterial cultures screened for antimicrobial activity, 28 cultures were found to produce active products against various pathogenic microorganisms such as Gram-negative, Gram-positive bacteria and yeast, using a ‘modified cross streak method.' The modified method helped in easy quantification of results and also in ruling out probable mutual antibiosis. 53%, 13% and 10% of tested actinobacterial strains belonging to Streptomyces, Micromonospora and Actinomadura genera, respectively, showed the ability of producing antimicrobial compounds. Streptomyces sp. strain MMA-5 showed the highest percentage multispecific antibiosis efficiency score value. Broad antibiotic spectrum activity was exhibited by Streptomyces sp. strain MMA-2 and Micromonospora sp. strain MMA-8. The multidrug resistant human pathogenic yeast strain Candida albicans was inhibited by 18 actinobacterial strains.
Ligand induced cleavage and nuclear localization of the rice XA21 immune receptor
Authors: Park Chang-Jin , Ronald Pamela 
Published: July 2019

AbstractThe rice XA21 receptor confers immunity to the Gram-negative bacterial pathogen, Xanthomonas oryzae pv. oryzae (Xoo) upon recognition of the conserved microbial signature AxY^S^22. Here, we demonstrate that the intracellular kinase domain of XA21 translocates to the nucleus upon AxY^S^22-mediated perception and that this translocation event is required for XA21-mediated immunity.
The Diet of the Rhinolophidae in the “Kabylia of the Babors” Region, Northern Algeria
Authors: Mourad Ahmim , Aissa Moali 
Published: July 2019

AbstractMany bats of the Rhinolophidae family are currently threatened all over the world. In Algeria they are represented by six species listed in the IUCN red list and whose hunting habits and diet are, at best, poorly known. This paper describes the diet composition of four of these species (Rhinolophus ferrumequinum, R. hipposideros, R. euryale and R. blasii) in the Bejaia and Jijel districts, and in Kabylia of the Babors region, in northern Algeria. Between March 2007 and January 2008 guano was sampled every fortnight in the different sites used by the species and preys remains identified under microscope. Results show that these Algerian Rhinolophidae prey on three groups of Arthropodes (Insects, Chilopodes and Spiders) whose frequencies vary from one species to another.