bluuebunny/crossref_metadata_2025 huggingface dataset:
Unusual ultrastructural findings in dendrites of pyramidal neurons in the cerebral cortex of rabies-infected mice
Authors: Torres-Fernández Orlando , Monroy-Gómez Jeison , Sarmiento Ladys E
Published: January 2018

Previous studies using the Golgi technique have demonstrated alterations in the dendritic morphology of pyramidal neurons of the cerebral cortex of mice inoculated with the rabies virus. However, knowledge about the fine structure of dendrites in rabies infection is scarce. This work had the aim of studying the ultrastructure of dendrites in cortical pyramidal neurons of rabies-infected mice. Mice were inoculated intramuscularly with a street rabies virus of canine origin. The animals that showed an advanced stage of disease were fixed by perfusion with glutaraldehyde and paraformaldehyde. Brains were removed and cut on a vibratome to obtain coronal slices of 200 micrometers of thickness. Vibratome slices were subjected to the following treatment: postfixation, dehydration, embedding in epoxy resin and polymerization between glass slides. Ultrathin sections of oriented tissue fragments from the cerebral cortex were obtained and observed under electron microscope. The most significant ultrastructural findings were located within distal dendrites of cortical pyramidal neurons: loss of mitochondria, disorganization and loss of microtubules, formation of vacuoles interrupting the continuity of the cytoplasm and formation of myelin-like figures. These strange myelin figures, which apparently had not been reported in previous studies of rabies, were the most noticeable ultrastructural feature. They also differ from the best known myelin figures formed by concentric lamellae. The possible origin of these myelin figures as result of mitochondrial degeneration is discussed.
The first report of an archosaur from the Kayenta Formation of Washington County, Utah
Authors: Gay Robert J , Milner Andrew RC
Published: January 2018

The Kayenta Formation has yielded numerous tetrapod fossils, including, amphibians, theropods, prosauropods, ornithischians, crocodylomorphs, sphenodonts, tritylodonts, pterosaurs, turtles, and rare mammals. Despite the phylogenetic diversity of the preserved animals, virtually all of the vertebrate fossils have come from the Ward Terrace area of north-central Arizona, on the Navajo Nation Reservation. Here we describe the first remains of a tetrapod found in the Kayenta Formation of Washington County, Utah. Tetrapod body fossils from the Kayenta Formation in southwestern Utah are proving to be very rare however, in contrast to common vertebrate tracks. The specimen described herein is likely the remains of a sphenosuchian crocodylomorph.
Global priorities for an effective information basis of biodiversity distributions
Authors: Meyer Carsten , Kreft Holger , Guralnick Robert P , Jetz Walter
Published: January 2018

Severe gaps and biases in digital accessible information (DAI) of species distributions hamper prospects of safeguarding biodiversity and ecosystem services and reliably addressing central questions in ecology and evolution. Accordingly, governments have agreed on improving and sharing biodiversity knowledge by 2020 (United Nations Convention on Biological Diversity’s Aichi target 19). To achieve this target, gaps in DAI must be identified, and actions prioritized to address their root causes. We take terrestrial vertebrates, an iconic and comparatively well-studied group, as a model and present the first globally comprehensive assessment of patterns and drivers of gaps in DAI, based on an integration of 157 million validated point records with 21,170 expert-based distribution maps. We demonstrate that outside a few well-sampled regions, DAI provides a very limited and spatially highly biased inventory of actual biodiversity. Coarser spatial grains result in more complete inventories, but provide insufficient detail for conservation and resource management. Surprisingly, large emerging economies are particularly under-represented in global DAI, even more so than species-rich, developing countries in the tropics. Multi-model inference reveals that completeness is mainly limited by distance to researchers, locally available research funding, and political participation in data-sharing networks, rather than transportation infrastructure, or size and funding of Western data contributors as often assumed. Our study provides an empirical baseline to advance strategies of enhancing the global information basis of biodiversity. In particular, our results highlight the need for targeted data integration from non-Western data holders and intensified cooperation to more effectively address societal biodiversity information needs.
Is the matamata only one species? Morphological variation and color polymorphism in the South American turtle Chelus fimbriatus (Schneider, 1783) (Pleurodira: Chelidae)
Authors: Garbin Rafaella C , Caramaschi Ulisses
Published: January 2018

Background. Studies on the geographic variation of the matamata, Chelus fimbriatus, have previously demonstrated differences between carapace shape, plastral pigmentation and the ventral coloration of the neck between populations from the Amazon and Orinoco river basins, but did not discuss whether these populations should be considered different species. The aim of this study is to evaluate the taxonomic status of C. fimbriatus and to describe its intraspecific and ontogenetic variability and sexual dimorphism based on morphology and osteology. Methods. We analyzed 277 morphological characters and 138 osteological characters of the skull and shell of 82 matamatas from the four known populations (Amazon, Orinoco, Guyana and Tocantins) and performed the Population Aggregation Analysis (PAA) species delimitation test in searching for character states that are exclusive to and fixed between populations. The t Student test was also performed in order to observe sexual dimorphism. Results. Considerable overlap in character states between different populations prevents the recognition of these populations as independent species. Chelus fimbriatus has a high level of polymorphism, particularly among morphological and color pattern characters. Unlike what have been stated on previous studies, we recognise four different carapace shapes, of which the anteriorly larger oval shape is the most common one. Two coloration patterns can be found both for the plastron and the carapace that are strongly correlated with one another, but no such correlation was observed with geographic distribution. We furthermore recognise three states of neck coloration pattern. Ontogenetic variability was observed in the coloration of the carapace, plastron, and the underside of the neck, in that juveniles have a stronger pigmentation than adults. Sexual dimorphism was established for six morphometric variables of the shell and 20 variables of the skull. As expected, females are significant larger than males for all these variables, such as carapace, plastron and skull length. New osteological characters, such as the presence of a serrated medial process in the palatine and a pair of anterolateral tubercles in the basioccipital were observed. Discussion. This is the first study to confirm the presence of sexual dimorphism in C. fimbriatus using morphological and morphometric variables and to document infraspecific variation in detail. The possible presence of two subspecies has been discussed since the 19th century based on alleged geographic variation in coloration patterns. However, this hypothesis could not be confirmed in the context of this study and the matamata should therefore still be considered a single species with a wide distribution range.
Diversification patterns based on the largest morphological phylogenetic analysis of Pleurodira
Authors: Ferreira Gabriel S , Sterli Juliana , Bronzati Filho Mario , Langer Max C
Published: January 2018

Background. Most studies on pleurodiran turtles are about the behavior and/or feeding habits analyzes, description of new taxa or specimens (both extinct and extant), or phylogenetic analyzes of one of its subclades with extant taxa: Chelidae, Pelomedusidae or Podocnemididae. With the exception of some molecular phylogenies, there are no phylogenetic analyses of extant and extinct representatives of Pleurodira including all of its lineages. A broader understanding of the evolutionary history of Pleurodira requires a phylogenetic hypothesis based on more extensive taxonomic and character samplings.Methods. We constructed a taxon-character matrix including 227 morphological characters and 87 taxa from all the Pleurodira lineages, plus one stem Pan-Pleurodira, Notoemys laticentralis, and one stem-Testudinata, Proganochelys quenstedti, as outgroups. The resulting matrix was analyzed using parsimony, Tree Bisection and Reconnection (TBR) algorithms, with 5000 replicates, and a hold of 20. The obtained strict consensus tree was used as the basis of a diversification analysis using topology-based methods. A nestedgrowing tree approach was employed to create a corresponding tree for different intervals of the geological history of the group. Six distinct time bins were created for periods in which members of Pleurodira occur: Early Cretaceous, Late Cretaceous, Paleocene, Eocene, Miocene, and Recent.

Results. All main pleurodiran clades were recovered in the strict consensus tree, but with some changes in their relationship compared to previous analyses, e.g. the inclusiveness of both Pelomedusoides and Bothremydidae. The diversification analysis shows that, after the establishment of the two major lineages (i.e. Chelidae and Pelomedusoides) in the Early Cretaceous, these subgroups diversified in distinct rates along their evolutionary history. Two main diversification shifts were identified: one at the early evolution of Podocnemoidea, during the Late Cretaceous, and another during the Miocene, deep nested in the Podocnemididae clade.

Discussion. The resulting strict consensus tree is the largest exclusive phylogenetic hypothesis for Pleurodira, including both extant and extinct taxa. Based on morphological data, it allows more inclusive inferences on the general morphological and diversification patterns of the group. The diversification pulses analysis suggests variation on the rates of diversification on the different pleurodiran clades. The first shift detected is related to the great radiation of Bothremydidae and Podocnemoidae in the Late Cretaceous; the second shift, detected in the Miocene, is related to a diversification within the Stereogenyina, a Podocnemididae clade. Ongoing analysis will determine which factors could enforce those different diversification rates in the evolution of Pleurodira.
A within-subject comparison of seizure duration with etomidate and methohexital in electroconvulsive therapy
Authors: Black Kevin J
Published: January 2018

Objective: To determine whether etomidate is associated with longer seizures than methohexital in ECT anesthesia. Methods: Retrospective chart review in 39 patients who were switched from one anesthetic to the other. We compared motor and EEG seizure duration in the last ECT session on one anesthetic and the first session on the other anesthetic. Results: Motor seizures were about 10 seconds longer with etomidate (p < 0.05). However, few of the increases in seizure duration had obvious clinical import. Conclusions: Etomidate can lengthen ECT seizure time compared with methohexital, but the clinical significance of this observation requires further study.
Sight or smell? Behavioural and heart rate responses in subordinate rainbow trout exposed to cues from dominant fish
Authors: Höjesjö Johan , Axelsson Michael , Dahy Ronja , Gustavsson Lena , Johnsson Jörgen I
Published: January 2018

Many animals, including fish, can utilize both vision and the chemical senses in intra-specific communication. However, the relative influence of these sensory modalities on behavioral and physiological responses in social interactions is not well understood. The aim of this study was therefore to investigate the relative effects of visual and chemical stimuli from dominant individuals on the behavioral and physiological responses of subordinate rainbow trout (Oncorhynchus mykiss). External electrodes were used to detect ECG signals from free-swimming fish. This method allowed the simultaneous recording of behavioral and physiological responses, and possible sex differences in these responses were also investigated. The results suggest that, in this context, visual cues are more important than chemical cues in settling the social hierarchy in rainbow trout because a combination of chemical and visual exposure generally yielded a response in focal fish that was similar to the response elicited by visual exposure alone. Both activity and physiological responses were most pronounced during the first ten seconds after exposure, with subordinate fish moving closer to the dominant, accompanied by a strong bradycardic response. Furthermore, females acted more boldly and moved closer to the dominant fish than males, but here the effect of the modes was additive, with a stronger effect of the combined visual and chemical exposure. Overall, the extra information furnished to the fish in the form of chemical cues did not change either the behavioral or the physiological response. This result suggests that visual cues are more important than chemically mediated ones for social communication and individual recognition in rainbow trout.
The blurred line between form and process: a comparison of stream classification frameworks
Authors: Kasprak Alan , Hough-Snee Nate , Beechie Tim , Bouwes Nicolaas , Brierley Gary J. , Camp Reid , Fryirs Kirstie A. , Imaki Hiroo , Jensen Martha L. , O'Brien Gary , Rosgen David L. , Wheaton Joseph M.
Published: January 2018

Stream classification provides a means to understand the diversity and distribution of channels and floodplains that occur across a landscape while drawing linkages between geomorphic form and process. Accordingly, stream classification is frequently employed as a watershed planning, management, and restoration tool. At the same time, there has been intense debate and criticism of particular frameworks, on the grounds that these frameworks classify stream reaches based largely on their physical form, rather than direct measurements of the hydrogeomorphic processes operating therein. Despite this critical debate surrounding stream classifications, and their ongoing use in applied watershed management, direct comparisons of channel classification frameworks are rare. Here we apply four classification frameworks that contain a range of form- and process-based methods within a watershed of high conservation interest in the Columbia River Basin, U.S.A. We compare the results of the River Styles Framework, Natural Channel Classification, Rosgen Classification System, and a channel form-based statistical classification at 33 field-monitored sites. For stream network-based frameworks (Natural Channel Classification and River Styles) we compare classification outputs across the entire Middle Fork John Day Watershed. We found that the four frameworks consistently classified reach types into similar groups based on each reach or segment’s dominant hydrogeomorphic elements. Where divergence in classified channel types occurred, differences can be attributed to the (a) spatial scale of input data used, (b) the requisite metrics and their order in completing a framework’s decision tree and/or (c) whether the framework attempts to classify current or historic channel form. The relative agreement between frameworks indicates that criticism of classification based simply on whether a classification contains form-based measurements, devalues each framework’s relative merits. These form-based criticisms may also ignore the geomorphic tenet that channel form reflects formative hydrogeomorphic processes across a given landscape.
Multi-scale modelling of E. coli metabolism
Authors: Smallbone Kieran , Millard Pierre
Published: January 2018

In response to environmental and genetic perturbations, micro-organisms may regulate their metabolism both metabolically – via metabolite-enzyme interactions – and hierarchically – via modulating enzyme capacities. In this report, we develop a combined metabolic and genetic regulatory model of E. coli that may be used to test this multi-scale response.
Unique method for analysing pressure distribution accross the knuckles during boxing
Authors: Loosemore Mike , Lightfoot Joseph , Meswania Jay , Beardsley Chris
Published: January 2018

Objectives: The hand is commonly injured in boxing but it is not clear why some athletes sustain hand injuries while others do not. It is possible that there are differences in the distribution of impact forces at the knuckle during punching between athletes and that certain distribution patterns may be predictive of increased injury risk. We developed a method of analysing the distribution of impact forces at the knuckle during punching using pressure film. Pressure film allows a calculation of the distribution and magnitude of pressure and force between any two surfaces that come into contact. Methods: Pressure film was inserted into the gloves of three male subjects prior to punching a stationary target. After each punch, the pressure film was removed and analysed to determine the distribution of the impact force during each punch across each of the four knuckles. Punches were repeated multiple times for each subject. The proportional distribution of the impact force during punches was compared between knuckles and within subjects. Results: The proportional distribution of the impact force exerted during punches was significantly different between knuckles and within subjects (p < 0.05). Knuckle 2 displayed the largest proportion of impact forces while knuckle 3 displayed the smallest proportion of impact forces. Conclusions: Pressure film inserted into boxing gloves can be used to analyse the distribution of impact forces across the knuckles during punching. Further work is needed to confirm the reliability and validity of the technique and establish whether there is an association between the impact forces at the individual knuckles and hand injury risk during boxing.
Predicting the oligomeric states of fluorescent proteins
Authors: Simeon Saw , Shoombuatong Watshara , Preeyanon Likit , Prachayasittikul Virapong , Nantasenamat Chanin
Published: January 2018

Currently, monomeric fluorescent proteins (FP) are ideal markers for protein tagging. The prediction of oligomeric states is helpful for enhancing live biomedical imaging. Computational prediction of FP oligomeric states can accelerate the effort of protein engineering to create monomeric FPs by saving time and money. To the best of our knowledge, this study represents the first computational model for predicting and analyzing FP oligomerization directly from their amino acid sequences. An exhaustive dataset consisting of 397 unique FP oligomeric states was compiled from the literature. FP were described by 3 classes of protein descriptors including amino acid composition, dipeptide composition and physicochemical properties. The oligomeric states of FP was predicted using decision tree (DT) algorithm and results demonstrated that DT provided robust performance with accuracies in ranges of 79.97-81.72% and 80.76-82.63% for the internal (e.g. 10-fold cross-validation) and external sets, respectively. This approach was also benchmarked with other common machine learning algorithms such as artificial neural network, support vector machine and random forest. A thorough analysis of amino acid sequence features was conducted to provide informative insights into FP oligomerization, which may aid in engineering novel monomeric fluorescent proteins. The following differentiating characteristics of monomeric and oligomeric fluorescent proteins were derived from DT: (i) substitution of any amino acid to Glu led to the reduction of aggregated proteins and (ii) oligomerization of FP appears to be stabilized by several hydrophobic contacts. Datasets and R source code are available at http://dx.doi.org/10.6084/m9.figshare.1348575.
Fading sight of endemic Zapornia bicolor (Walden, 1872) in Eastern Himalayan Hotspot
Authors: Pradhan Prakash
Published: January 2018

A biosurvey was conducted in Samendu Lake and its surroundings wetlands of Eastern Himalayan Hill region of Mirik in Darjeeling in West Bengal, India. In the study, endemic and locally rare species of Zapornia bicolor (Walden, 1872) was studied with point transect method regarding its population and habitat. Very low population (only 21 individuals) and habitat degradation (encroachment, pollution, invasive plant species etc.) has been observed at the study sites. Conservation measures for this species have been suggested.
”Gait-&Balance-Box”
Authors: Daumer Martin , Müller Karl
Published: January 2018

The ”Gait-&Balance-Box” suggests a standardization for clinical walk and balance tests with the aim to improve quality, applicability and comparability. Heart of the patient monitoring is the actibeltblue, an autonomous wireless accelerometer that is worn like a belt. The actibelt sends the acceleration data via blue-tooth to a tablet that provides direct analysis of the human motion. The box can be quickly unfolded into a mobile gait lab using 2 light barriers to perform walking test. The acceleration measurement plus the duration for the fixed walking distance are combined to an enhanced 4-meter walk test.
The impact of the fossils in molecular clocks: an example using chelid turtles
Authors: Holley Juan Alfredo , Basso Néstor Guillermo , Sterli Juliana
Published: January 2018

Background. The clade Chelidae (Testudines, Pleurodira) is a group of fresh water turtles with representatives in Australasia and South America. Its diversity of extant and fossil species is characterized by two recognized morphotypes: the long-necked and the short-necked chelids. So far, the phylogenies constructed over Chelidae differ depending on the information source. While morphology recovers one monophyletic group of long-necked chelids (with South American and Australasian species), the molecular data split the group into South American and Australasian chelids, both as monophyletic sister groups and containing long-necked species. The consequences of this conflict imply the emergence of long-necked chelids (i) one time before the final breakup of Southern Gondwana (≅ 35 Mya) or (ii) independently after this event.

Methods. Using BEAST, a set of molecular clock analyses was performed. Seven of these analyses correspond to the molecular hypothesis and thirteen to the morphological hypothesis. So, ten fossils were used as calibration points in different combinations for each hypothesis. The results were statistically compared performing ANOVA and the global similarity was inspected by a hierarchical cluster analysis (HCA).

Results. Molecular hypothesis: all the analyses produced an age of the origin of Chelidae, and rising of long neck, older than 35 Mys. Divergence times in the South American clade were generally older than the observed in the Australasian clade. The result of the HCA was: analyses 2, 4 and 5 form a group and the analyses 3, 6 and 7 form another group; the analysis 1 is close related to this last. Morphological hypothesis: the origin of the clade of long-necked chelids predated the 35 Mys in all the analyses except one; however the Chelodina group resulted younger than this age in all the analyses. The HCA yielded two main groups of molecular clock analyses (1, 3, 7, 8, 9, 13 and 2, 4, 6, 10, 11, 12) and one analysis (5) clearly separated of these two. The ANOVA resulted in significant differences for all estimated nodes in both phylogenetic hypotheses.

Discussion. Our set of molecular clock analyses suggests an early diversification of the chelid turtles and the raising of the long-necked chelids before the final breakup of Southern Gondwana. However, the appearance of this trait one time or as evolutionary convergence still depends on which phylogenetic scenario is taken into account. Furthermore, our results indicate that the number of calibration points not necessarily improve the precision of estimated nodes. Instead the “quality” of the fossils used as calibrations and its position in the phylogeny, have appreciable impact not only over this parameter, but also over the global evolutionary rate along the tree.
Is grazing exclusion effective in restoring vegetation in degraded alpine grasslands in Tibet, China?
Authors: Yan Yan , Lu Xuyang
Published: January 2018

Overgrazing is considered one of the key disturbance factors that results in alpine grassland degradation in Tibet. Grazing exclusion by fencing has been widely used as an approach to restore degraded grassland s in Tibet since 2004. Is the grazing exclusion management strategy effective for the vegetation restoration of degraded alpine grasslands? Three alpine grassland types were selected in Tibet to investigate the effect of grazing exclusion on plant community structure and biomass. Our results showed that species biodiversity indicators, including the Pielou evenness index, the Shannon-Wiener diversity index, and the Simpson dominance index, did not significantly change under grazing exclusion conditions. In contrast, the total vegetation cover, the mean vegetation height of the community, and the aboveground biomass were significantly higher in the grazing exclusion grasslands than in the free grazed grasslands. These results indicated that grazing exclusion is an effective measure for maintaining community stability and improving aboveground vegetation growth in alpine grasslands. However, the statistical analysis showed that the alpine grassland type plays a more important role than grazing exclusion in which influence on vegetation in alpine grasslands because the alpine grassland type had a significant effect on vegetation indicators but grazing exclusion not. In addition, because the results of the present study come from short term (5-7 years) grazing exclusion, it is still uncertain whether these improvements will be continuable if grazing exclusion is continuously implemented. Therefore, the assessments of the ecological effects of the grazing exclusion management strategy on degraded alpine grasslands in Tibet are still need long term continued research.
A standardized, extensible framework for optimizing classification improves marker-gene taxonomic assignments
Authors: Bokulich Nicholas A , Rideout Jai Ram , Kopylova Evguenia , Bolyen Evan , Patnode Jessica , Ellett Zach , McDonald Daniel , Wolfe Benjamin , Maurice Corinne F , Dutton Rachel J , Turnbaugh Peter J , Knight Rob , Caporaso J Gregory
Published: January 2018

Background: Taxonomic classification of marker-gene (i.e., amplicon) sequences represents an important step for molecular identification of microorganisms.

Results: We present three advances in our ability to assign and interpret taxonomic classifications of short marker gene sequences: two new methods for taxonomy assignment, which reduce runtime up to two-fold and achieve high-precision genus-level assignments; an evaluation of classification methods that highlights differences in performance with different marker genes and at different levels of taxonomic resolution; and an extensible framework for evaluating and optimizing new classification methods, which we hope will serve as a model for standardized and reproducible bioinformatics methods evaluations.

Conclusions: Our new methods are accessible in QIIME 1.9.0, and our evaluation framework will support ongoing optimization of classification methods to complement rapidly evolving short-amplicon sequencing and bioinformatics technologies. Static versions of all of the analysis notebooks generated with this framework, which contain all code and analysis results, can be viewed at http://bit.ly/srta-012 .
Parents' and children's emotions spanning the HIV disclosure process in Kenya
Authors: Gachanja Grace , Burkholder Gary J , Ferraro Aimee
Published: January 2018

Background: HIV disclosure from parent to child is challenging. While disclosure is expected to be emotional for parents and children, the total disclosure experience has not been described. The purpose of this study was to understand the lived experiences of HIV-positive parents and their children in Kenya during the disclosure process. Methods: Phenomenological qualitative data were collected using in-depth semistructured interviews. Thirty four participants consisting of HIV-positive parents, children (infected and uninfected), and healthcare professionals (HCPs) were enrolled. Data analysis was performed using NVivo 8 and the Van Kaam method. Results: Pre-disclosure, parents were plagued with fear/worry of stigma, judgment, rejection, blame; and the reaction/consequences of disclosure on their children. Guilt and shame for bringing the illness into the home abounded. Children sensed, wondered, and worried about secrets within their homes. During disclosure, parents experienced catharsis, guilt, confusion, and panic when children reacted negatively. Children experienced shock, disbelief, anger, sadness, worry, depression, confusion, and catharsis from finally knowing what was wrong. Post-disclosure parents alternated between relief, guilt, and depression as their children’s behavior changed due to disclosure. Children experienced unhappiness, depression, hopelessness, self-hate, and withdrawal. Recovery time varied lasting from a few hours to four months later; some children ultimately felt relief and self-acceptance. However, stress exposure caused disclosure emotions to reappear. Conclusion: HIV disclosure process is accompanied by alternating negative and positive feelings for both parents and children. To ease the process, HCPs should provide support services such as disclosure practice sessions/training, counseling, peer support groups, and stress management.
Efficient "pythonic" access to FASTA files using pyfaidx
Authors: Shirley Matthew D , Ma Zhaorong , Pedersen Brent S , Wheelan Sarah J
Published: January 2018

The pyfaidx Python module provides memory and time-efficient indexing, subsetting, and in-place modification of subsequences of FASTA files. pyfaidx provides Python classes that expose a dictionary interface where sequences from an indexed FASTA can be accessed by their header name and then sliced by position without reading the full file into memory. pyfaidx includes an extensive test suite to ensure correct and reproducible behavior. A command-line program (faidx) is also provided as an alternative interface, with significant enhancements to functionality, while maintaining full index file compatibility with samtools. The pyfaidx module is installable from PyPI (https://pypi.python.org/pypi/pyfaidx), and development versions can be found at Github (https://github.com/mdshw5/pyfaidx).
Analgesia effects of lappaconitine in leukemia bone pain in a mouse model
Authors: Zhu Xiao-Cui , Ge Chen-Tao , Pan Wang , Zhang Jia-Li , Yu Yuan-Yang , Fu Cai-Yun
Published: January 2018

Bone pain is a common and severe symptom in cancer patients. The present study employed a mouse model of leukemia bone pain by injection K562 cells into tibia of mouse to evaluate the analgesia effects of Lappaconitine. Our results showed that the lappaconitine treatment at day 15, 17 and 19 could effectively reduce the spontaneous pain scoring values, restore reduced degree in the inclined-plate test induced by injection of K562 cells, as well as restore paw mechanical withdrawal threshold and paw withdrawal thermal latency induced by injection of K562 cells to normal group levels. Additionally, the molecular mechanisms of lappaconitine’s analgesia effects may be related to affect the expressive levels of endogenous opioid system genes (POMC, PENK and MOR), as well as apoptosis-related genes (Xiap, Smac, Bim, NF-κB and p53). Our present results indicated that lappaconitine may become a new analgesia agent for pain management induced by leukemia cells.
Staphylococcus Aureus carriage and long-term Rituximab treatment for Granulomatosis with polyangiitis
Authors: Besada Emilio , Koldingsnes Wenche , Nossent Johannes C
Published: January 2018

Objective: Chronic nasal carriage of Staphylococcus aureus (SA) increases the risk of relapse while Rituximab (RTX) is an effective agent for inducing and maintaining remission in patients with Granulomatosis with polyangiitis (GPA). We investigated whether B cell depletion and hypogammaglobulinemia that occur during RTX treatment increase the risk of chronic SA nasal carriage and subsequent disease flares, in GPA patients on long-term RTX maintenance therapy. Methods: Retrospective cohort study from a disease registry involving 29 GPA patients receiving RTX maintenance (median RTX dose of 9 g) during a median period of 49 months. Nasal swabs were collected prior and during RTX for a median of 3 and 9 swabs respectively. Persistent SA nasal carriage was defined with the presence of SA in more than 75 % of nasal swabs. Results: SA nasal carriage did not change during RTX (p=0.297). Persistent SA nasal carriage did not increase the risk of relapses (p=0.844) and of severe infections (p=0.144), but reduced the risk of chronic infections (p=0.044). Non-SA carriers were more prone to discontinue RTX due to hypogammaglobulinemia (p=0.122), since they had more profound decline of serum total Ig both after the first 2 g of RTX (p=0.079) and during RTX maintenance (p=0.063). Conclusion: Long-term RTX maintenance therapy in GPA patients did not significantly influence SA nasal carriage status. Persistent SA carriage during long-term RTX treatment did not increase the risk of relapses and was associated with a lower risk of hypogammaglobulinemia associated chronic infections.
Prediction of deleterious nonsynonymous SNPs by integrating multiple classifiers – An application to neurodegenerative diseases
Authors: Mesbah-Uddin Md
Published: January 2018

In this study, we propose a logistic regression model to classify deleterious missense mutation from a list of nonsynonymous SNPs (nsSNPs) – where multiple features (i.e. rank scores of 18 classifiers e.g. SIFT, PolyPhen2, MutationTaster, MutationAssessor, FATHMM, VEST 3.0, RadialSVM, LR, CADD, etc. from dbNSFP v2.5) are combined for 44,702 UniProt human polymorphisms and disease mutations (19,033 disease and 25,669 neutral). The model is trained and validated on 80% of the data (15,226 disease + 20,535 neutral nsSNPs), and tested on remaining 20% (3,807 disease + 5134 neutral nsSNPs); and finally applied to a neurodegenerative disease-specific dataset (NeuroTest) from UniProt. The ROC AUC of the model is 0.97 on test set and 0.92 on NeuroTest dataset, with an accuracy of 0.91 and 0.86, respectively. Our model outperforms SIFT, PolyPhen2, MutationTaster, MutationAssessor, and the two ensemble classifiers of dbNSFP v2.5, on both the testing sets.
The Shake Stick
Authors: Wilson Alex , Hindle Abram
Published: January 2018

We present a new embedded instrument, with discussion on the challenges of developping embedded instruments, and the practice and theory of NIME evaluation and design. The Shake Stick is a Raspberry Pi-based embedded instrument using SuperCollider for granular synthesis. In our analysis and design, we explore the MINUET design framework, dimension space analysis for inter-instrument comparison, and learning curves. Furthermore, we discuss lessons learned from using the instrument in group improvisation, as well as challenges and prospects for the creation of sound palettes used in the granular synthesis.
Detection of human disease conditions by single-cell morpho-rheological phenotyping of blood
Authors: Toepfner Nicole , Herold Christoph , Otto Oliver , Rosendahl Philipp , Jacobi Angela , Kräter Martin , Stächele Julia , Menschner Leonhard , Herbig Maik , Ciuffreda Laura , Ranford-Cartwright Lisa , Grzybek Michal , Coskun Ünal , Reithuber Elisabeth , Garriss Geneviève , Mellroth Peter , Henriques-Normark Birgitta , Tregay Nicola , Suttorp Meinolf , Bornhäuser Martin , Chilvers Edwin R , Berner Reinhard , Guck Jochen
Published: January 2018

Blood is arguably the most important bodily fluid and its analysis provides crucial health status information. A first routine measure to narrow down diagnosis in clinical practice is the differential blood count, determining the frequency of all major blood cells. What is lacking to advance initial blood diagnostics is an unbiased and quick functional assessment of blood that can narrow down the diagnosis and generate specific hypotheses. To address this need, we introduce the continuous, cell-by-cell morpho-rheological (MORE) analysis of diluted whole blood, without labeling, enrichment or separation, at rates of 1000 cells/sec. In a drop of blood we can identify all major blood cells and characterize their pathological changes in several disease conditions in vitro and in patient samples. This approach takes previous results of mechanical studies on specifically isolated blood cells to the level of application directly in blood and adds a functional dimension to conventional blood analysis.
The synaptic ribbon is critical for sound encoding at high rates and with temporal precision
Authors: Jean Philippe , Lopez de la Morena David , Michanski Susann , Jaime Tobón Lina María , Chakrabarti Rituparna , Picher Maria Magdalena , Neef Jakob , Jung SangYong , Gültas Mehmet , Maxeiner Stephan , Neef Andreas , Wichmann Carolin , Strenzke Nicola , Grabner Chad , Moser Tobias
Published: January 2018

We studied the role of the synaptic ribbon for sound encoding at the synapses between inner hair cells (IHCs) and spiral ganglion neurons (SGNs) in mice lacking RIBEYE (RBEKO/KO). Electron and immunofluorescence microscopy revealed a lack of synaptic ribbons and an assembly of several small active zones (AZs) at each synaptic contact. Spontaneous and sound-evoked firing rates of SGNs and their compound action potential were reduced, indicating impaired transmission at ribbonless IHC-SGN synapses. The temporal precision of sound encoding was impaired and the recovery of SGN-firing from adaptation indicated slowed synaptic vesicle (SV) replenishment. Activation of Ca2+-channels was shifted to more depolarized potentials and exocytosis was reduced for weak depolarizations. Presynaptic Ca2+-signals showed a broader spread, compatible with the altered Ca2+-channel clustering observed by super-resolution immunofluorescence microscopy. We postulate that RIBEYE disruption is partially compensated by multi-AZ organization. The remaining synaptic deficit indicates ribbon function in SV-replenishment and Ca2+-channel regulation.
The presynaptic ribbon maintains vesicle populations at the hair cell afferent fiber synapse
Authors: Becker Lars , Schnee Michael E , Niwa Mamiko , Sun Willy , Maxeiner Stephan , Talaei Sara , Kachar Bechara , Rutherford Mark A , Ricci Anthony J
Published: January 2018

The ribbon is the structural hallmark of cochlear inner hair cell (IHC) afferent synapses, yet its role in information transfer to spiral ganglion neurons (SGNs) remains unclear. We investigated the ribbon’s contribution to IHC synapse formation and function using KO mice lacking RIBEYE. Despite loss of the entire ribbon structure, synapses retained their spatiotemporal development and KO mice had a mild hearing deficit. IHCs of KO had fewer synaptic vesicles and reduced exocytosis in response to brief depolarization; a high stimulus level rescued exocytosis in KO. SGNs exhibited a lack of sustained excitatory postsynaptic currents (EPSCs). We observed larger postsynaptic glutamate receptor plaques, potentially compensating for the reduced EPSC rate in KO. Surprisingly, large-amplitude EPSCs were maintained in KO, while a small population of low-amplitude slower EPSCs was increased in number. The ribbon facilitates signal transduction at physiological stimulus levels by retaining a larger residency pool of synaptic vesicles.
A revised cranial description ofMassospondylus carinatusOwen (Dinosauria: Sauropodomorpha) based on computed tomographic scans and a review of cranial characters for basal Sauropodomorpha
Authors: Chapelle Kimberley E.J. , Choiniere Jonah N.
Published: January 2018

Massospondylus carinatusis a basal sauropodomorph dinosaur from the early Jurassic Elliot Formation of South Africa. It is one of the best-represented fossil dinosaur taxa, known from hundreds of specimens including at least 13 complete or nearly complete skulls. Surprisingly, the internal cranial anatomy ofM. carinatushas never been described using computed tomography (CT) methods. Using CT scans and 3D digital representations, we digitally reconstruct the bones of the facial skeleton, braincase, and palate of a complete, undistorted cranium ofM. carinatus(BP/1/5241). We describe the anatomical features of the cranial bones, and compare them to other closely related sauropodomorph taxa such asPlateosaurus erlenbergiensis,Lufengosaurus huenei,Sarahsaurus aurifontanalisandEfraasia minor. We identify a suite of character states of the skull and braincase forM. carinatusthat sets it apart from other taxa, but these remain tentative due to the lack of comparative sauropodomorph braincase descriptions in the literature. Furthermore, we hypothesize 27 new cranial characters useful for determining relationships in non-sauropodan Sauropodomorpha, delete five pre-existing characters and revise the scores of several existing cranial characters to make more explicit homology statements. All the characters that we hypothesized or revised are illustrated. Using parsimony as an optimality criterion, we then test the relationships ofM. carinatus(using BP/1/5241 as a specimen-level exemplar) in our revised phylogenetic data matrix.
FastViromeExplorer: a pipeline for virus and phage identification and abundance profiling in metagenomics data
Authors: Tithi Saima Sultana , Aylward Frank O. , Jensen Roderick V. , Zhang Liqing
Published: January 2018

With the increase in the availability of metagenomic data generated by next generation sequencing, there is an urgent need for fast and accurate tools for identifying viruses in host-associated and environmental samples. In this paper, we developed a stand-alone pipeline called FastViromeExplorer for the detection and abundance quantification of viruses and phages in large metagenomic datasets by performing rapid searches of virus and phage sequence databases. Both simulated and real data from human microbiome and ocean environmental samples are used to validate FastViromeExplorer as a reliable tool to quickly and accurately identify viruses and their abundances in large datasets.
Urban heat island effect on cicada densities in metropolitan Seoul
Authors: Nguyen Hoa Q. , Andersen Desiree K. , Kim Yuseob , Jang Yikweon
Published: January 2018

Background

Urban heat island (UHI) effect, the ubiquitous consequence of urbanization, is considered to play a major role in population expansion of numerous insects. Cryptotympana atrata and Hyalessa fuscata are the most abundant cicada species in the Korean Peninsula, where their population densities are higher in urban than in rural areas. We predicted a positive relationship between the UHI intensities and population densities of these two cicada species in metropolitan Seoul.

Methods

To test this prediction, enumeration surveys of cicada exuviae densities were conducted in 36 localities located within and in the vicinity of metropolitan Seoul. Samples were collected in two consecutive periods from July to August 2015. The abundance of each species was estimated by two resource-weighted densities, one based on the total geographic area, and the other on the total number of trees. Multiple linear regression analyses were performed to identify factors critical for the prevalence of cicada species in the urban habitat.

Results

C. atrata and H. fuscata were major constituents of cicada species composition collected across all localities. Minimum temperature and sampling period were significant factors contributing to the variation in densities of both species, whereas other environmental factors related to urbanization were not significant. More cicada exuviae were collected in the second rather than in the first samplings, which matched the phenological pattern of cicadas in metropolitan Seoul. Cicada population densities increased measurably with the increase in temperature. Age of residential complex also exhibited a significantly positive correlation to H. fuscata densities, but not to C. atrata densities.

Discussion

Effects of temperature on cicada densities have been discerned from other environmental factors, as cicada densities increased measurably in tandem with elevated temperature. Several mechanisms may contribute to the abundance of cicadas in urban environments, such as higher fecundity of females, lower mortality rate of instars, decline in host plant quality, and local adaptation of organisms, but none of them were tested in the current study.

Conclusions

In sum, results of the enumeration surveys of cicada exuviae support the hypothesis that the UHI effect underlies the population expansion of cicadas in metropolitan Seoul. Nevertheless, the underlying mechanisms for this remain untested.
Resilient Design: ‘Systems Thinking’ as a Response to Climate Change
Authors: Weisz Claire
Published: January 2018

Design thinking is not enough. For resilient architecture and urbanism to meet the challenges of global warming head on, what is needed is systems thinking: an in‐depth, interdisciplinary approach which recognises that change is constant. Claire Weisz – founding partner of New York urban design, planning and architecture practice WXY – highlights a number of small, innovative US firms that are leading the way, and describes some of their ventures to date.
Naphthalene Derivatives and Quinones from Ventilago denticulata and Their Nitric Oxide Radical Scavenging, Antioxidant, Cytotoxic, Antibacterial, and Phosphodiesterase Inhibitory Activities
Authors: Molee Wannapha , Phanumartwiwath Anuchit , Kesornpun Chatchai , Sureram Sanya , Ngamrojanavanich Nattaya , Ingkaninan Kornkanok , Mahidol Chulabhorn , Ruchirawat Somsak , Kittakoop Prasat
Published: January 2018

New naphthalene derivatives (1 and 2) and a new isomer (3) of ventilagolin, together with known anthraquinones, chrysophanol (4), physcion or emodin 3‐methyl ether (5), and emodin (6), were isolated from vines of Ventilago denticulata. The isolated compounds exhibited cytotoxic activity with IC50 values of 1.15 – 40.54 μg/ml. Compounds 1 – 3 selectively exhibited weak antibacterial activity (MIC values of 200.0 – 400.0 μg/ml), while emodin (6) displayed moderate antibacterial activity with MIC value of 25.0 μg/ml. The isolated compounds showed nitric oxide and DPPH radical scavenging activities. Compounds 1 – 3 and 6 exhibited weak xanthine oxidase inhibitory activity, while emodin (6) acted as an aromatase inhibitor with the IC50 value of 10.1 μm. Compounds 1 and 2 exhibited phosphodiesterase 5 inhibitory activity with IC50 values of 8.28 μm and 6.48 μm, respectively.
Selectivity of Nanoporous MnO2 and TiO2 Membranes for Residual Contaminants in Treated Wastewater
Authors: Giwa Adewale , Jung Sung M. , Ahmed Menatalla , Fang Wenjing , Kong Jing , Hasan Shadi W.
Published: January 2018

Treated effluent from an electrically enhanced membrane bioreactor (eMBR) was filtered through MnO2 or TiO2 nanoporous membranes for the removal of residual heavy metals, bacteria, and biological oxygen demand (BOD). The fresh and spent membranes were characterized via energy‐dispersive X‐ray spectroscopy (EDAX), zeta potential analysis, and thermogravimetric analysis (TGA). Water analysis was performed by means of UV/Vis spectrophotometry. For most contaminants, eMBR‐TiO2 showed highest removal efficiency compared to MnO2 because of the combined adhesion and photocatalytic effects of TiO2. Meanwhile, eMBR‐MnO2 provided higher removal efficiency for Fe.