bluuebunny/crossref_metadata_2025_split huggingface dataset:
Survey of commercial Rhodiola products revealed species diversity and potential safety issues
Authors: Xin Tianyi , Li Xiaojin , Yao Hui , Lin Yulin , Ma Xiaochong , Cheng Ruiyang , Song Jingyuan , Ni Lianghong , Fan Congzhao , Chen Shilin 
Published: February 2015

AbstractThe adulteration of herbal products is a threat to consumer safety. Here we surveyed the species composition of commercial Rhodiola products using DNA barcoding as a supervisory method. A Rhodiola dietary supplement DNA barcode database was successfully constructed using 82 voucher samples from 10 Rhodiola species. Based on the DNA barcoding standard operating procedure (SOP), we used this database to identify 100 Rhodiolae Crenulatae Radix et Rhizoma decoction piece samples that were purchased from drug stores and hospitals. The results showed that only 36 decoction piece sequences (40%) were authentic R. crenulata, which is recorded in Chinese Pharmacopeia, whereas the other samples were all adulterants and may indicate a potential safety issue. Among the adulterants, 35 sequences (38.9%) were authenticated as R. serrata, nine sequences (10%) were authenticated as R. rosea, which is documented in the United States Pharmacopeia and the remaining samples were authenticated as other three Rhodiola species. This result indicates decoction pieces that are available in the market have complex origins and DNA barcoding is a convenient tool for market supervision.
Animal feed formulation: mathematical programming techniques.
Authors: Pratiksha Saxena Pratiksha Saxena , Neha Khanna Neha Khanna 
Published: February 2015

Abstract
Animal feed models have been derived by mathematical programming techniques and are used for the purpose of optimizing weight gain and animal yield. This paper reviews the mathematical models for the animal feed formulation on the basis of programming techniques. It describes various programming techniques for feed formulation, shortcomings and their removal by improvement of techniques.
Knockdown of the host cellular protein transportin 3 attenuates prototype foamy virus infection
Authors: Ali Md Khadem , Kim Jinsun , Hamid Faysal Bin , Shin Cha-Gyun 
Published: February 2015

AbstractTransportin 3 (TNPO3) is a member of the importin-ß superfamily proteins. Despite numerous studies, the exact molecular mechanism of TNPO3 in retroviral infection is still controversial. Here, we provide evidence for the role and mechanism of TNPO3 in the replication of prototype foamy virus (PFV). Our findings revealed that PFV infection was reduced 2-fold by knockdown (KD) of TNPO3. However, late stage of viral replication including transcription, translation, viral assembly, and release was not influenced. The differential cellular localization of PFV integrase (IN) in KD cells pinpointed a remarkable reduction of viral replication at the nuclear import step. We also found that TNPO3 interacted with PFV IN but not with Gag, suggesting that IN-TNPO3 interaction is important for nuclear import of PFV pre-integration complex. Our report enlightens the mechanism of PFV interaction with TNPO3 and support ongoing research on PFV as a promising safe vector for gene therapy.
Edge effects in game theoretic dynamics of spatially structured tumours
Authors: Kaznatcheev Artem , Scott Jacob G. , Basanta David 
Published: February 2015

AbstractBackgroundAnalysing tumour architecture for metastatic potential usually focuses on phenotypic differences due to cellular morphology or specific genetic mutations, but often ignore the cell’s position within the heterogeneous substructure. Similar disregard for local neighborhood structure is common in mathematical models.MethodsWe view the dynamics of disease progression as an evolutionary game between cellular phenotypes. A typical assumption in this modeling paradigm is that the probability of a given phenotypic strategy interacting with another depends exclusively on the abundance of those strategies without regard local heterogeneities. We address this limitation by using the Ohtsuki-Nowak transform to introduce spatial structure to the go vs. grow game.ResultsWe show that spatial structure can promote the invasive (go) strategy. By considering the change in neighbourhood size at a static boundary – such as a blood-vessel, organ capsule, or basement membrane – we show an edge effect that allows a tumour without invasive phenotypes in the bulk to have a polyclonal boundary with invasive cells. We present an example of this promotion of invasive (EMT positive) cells in a metastatic colony of prostate adenocarcinoma in bone marrow.InterpretationPathologic analyses that do not distinguish between cells in the bulk and cells at a static edge of a tumour can underestimate the number of invasive cells. We expect our approach to extend to other evolutionary game models where interaction neighborhoods change at fixed system boundaries.
Linked annotations: a middle ground for manual curation of biomedical databases and text corpora
Authors: Goldberg Tatyana , Vinchurkar Shrikant , Cejuela Juan Miguel , Jensen Lars Juhl , Rost Burkhard 
Published: February 2015

AbstractAnnotators of text corpora and biomedical databases carry out the same labor-intensive task to manually extract structured data from unstructured text. Tasks are needlessly repeated because text corpora are widely scattered. We envision that alinked annotation resourceunifying many corpora could be a game changer. Such an open forum will help focus on novel annotations and on optimally benefiting from the energy of many experts. As proof-of-concept, we annotated protein subcellular localization in 100 abstracts cited by UniProtKB. The detailed comparison between our new corpus and the original UniProtKB annotations revealed sustained novel annotations for 42% of the entries (proteins). In a unified linked annotation resource these could immediately extend the utility of text corpora beyond the text-mining community. Our example motivates the central idea that linked annotations from text corpora can complement database annotations.
Intrinsic coupling modes reveal the functional architecture of cortico-tectal networks
Authors: Stitt Iain , Galindo-Leon Edgar , Pieper Florian , Engler Gerhard , Fiedler Eva , Stieglitz Thomas , Engel Andreas K 
Published: February 2015

SummaryIn the absence of sensory stimulation or motor output, the brain exhibits complex spatiotemporal patterns of intrinsically generated neural activity. However, little is known about how such patterns of activity are correlated between cortical and subcortical brain areas. Here, we investigate the large-scale correlation structure of ongoing cortical and superior colliculus (SC) activity across multiple spatial and temporal scales. Cortico-tectal interaction was characterized by correlated fluctuations in the amplitude of delta, spindle, low gamma and high frequency oscillations (> 100 Hz). Of these identified coupling modes, topographical patterns of high frequency coupling were the most consistent with anatomical connectivity, and reflected synchronized spiking in cortico-tectal networks. Ongoing high frequency cortico-tectal coupling was temporally governed by the phase of slow cortical oscillations. Collectively, our findings show that cortico-tectal networks can be resolved through the correlation structure of ongoing neural activity, and demonstrate the rich information conveyed by high frequency electrocorticographic signals.
Long-range functional coupling predicts performance: oscillatory EEG networks in multisensory processing
Authors: Wang Peng , Göschl Florian , Friese Uwe , König Peter , Engel Andreas K. 
Published: February 2015

AbstractThe integration of sensory signals from different modalities requires flexible interaction of remote brain areas. One candidate mechanism to establish communication in the brain is transient synchronization of oscillatory neural signals. Although there is abundant evidence for the involvement of cortical oscillations in brain functions based on the analysis of local power, assessment of the phase dynamics among spatially distributed neuronal populations and their relevance for behavior is still sparse. In the present study, we investigated the interaction between remote brain areas by analyzing high-density electroencephalogram (EEG) data obtained from human participants engaged in a visuotactile pattern matching task. We deployed an approach for purely data-driven clustering of neuronal phase coupling in source space, which allowed imaging of large-scale functional networks in space, time and frequency without defining a priori constraints. Based on the phase coupling results, we further explored how brain areas interacted across frequencies by computing phase-amplitude coupling. Several networks of interacting sources were identified with our approach, synchronizing their activity within and across the theta (~5 Hz), alpha (~10 Hz), and beta (~ 20 Hz) frequency bands and involving multiple brain areas that have previously been associated with attention and motor control. We demonstrate the functional relevance of these networks by showing that phase delays – in contrast to spectral power – were predictive of task performance. The data-driven analysis approach employed in the current study allowed an unbiased examination of functional brain networks based on EEG source level connectivity data. Showcased for multisensory processing, our results provide evidence that large-scale neuronal coupling is vital to long-range communication in the human brain and relevant for the behavioral outcome in a cognitive task.
Disturbance opens recruitment sites for bacterial colonization in activated sludge
Authors: Vuono David C. , Munakata-Marr Junko , Spear John R. , Drewes Jörg E. 
Published: February 2015

SummaryLittle is known about the role of immigration in shaping bacterial communities or the factors that may dictate success or failure of colonization by bacteria from regional species pools. To address these knowledge gaps, the influence of bacterial colonization into an ecosystem (activated sludge bioreactor) was measured through a disturbance gradient (successive decreases in the parameter solids retention time) relative to stable operational conditions. Through a DNA sequencing approach, we show that the most abundant bacteria within the immigrant community have a greater probability of colonizing the receiving ecosystem, but mostly as low abundance community members. Only during the disturbance do some of these bacterial populations significantly increase in abundance beyond background levels and in few cases become dominant community members post-disturbance. Two mechanisms facilitate the enhanced enrichment of immigrant populations during disturbance: 1) the availability of resources left unconsumed by established species and 2) the increased availability of niche space for colonizers to establish and displace resident populations. Thus, as a disturbance decreases local diversity, recruitment sites become available to promote colonization. This work advances our understanding of microbial resource management and diversity maintenance in complex ecosystems.
A Single Gene Causes an Interspecific Difference in Pigmentation inDrosophila
Authors: Ahmed-Braimah Yasir H. , Sweigart Andrea L. 
Published: February 2015

AbstractThe genetic basis of species differences remains understudied. Studies in insects have contributed significantly to our understanding of morphological evolution. Pigmentation traits in particular have received a great deal of attention and several genes in the insect pigmentation pathway have been implicated in inter- and intraspecific differences. Nonetheless, much remains unknown about many of the genes in this pathway and their potential role in understudied taxa. Here we genetically analyze the puparium color difference between members of the Virilis group ofDrosophila. The puparium ofDrosophila virilisis black, while those ofD. americana, D. novamexicana, andD. lummeiare brown. We used a series of backcross hybrid populations betweenD. americanaandD. virilisto map the genomic interval responsible for the difference between this species pair. First, we show that the pupal case color difference is caused by a single Mendelizing factor, which we ultimately map to an ~11kb region on chromosome 5. The mapped interval includes only the first exon and regulatory region(s) of the dopamineN-acetyltransferase gene (Dat). This gene encodes an enzyme that is known to play a part in the insect pigmentation pathway. Second, we show that this gene is highly expressed at the onset of pupation in light-brown taxa (D. americanaandD. novamexicana) relative toD. virilis, but not in the dark-brownD. lummei. Finally, we examine the role ofDatinadultpigmentation betweenD. americana(heavily melanized) andD. novamexicana(lightly melanized) and find no discernible effect of this gene in adults. Our results demonstrate that a single gene is entirely or almost entirely responsible for a morphological difference between species.
Generators and connectivity of the early auditory evoked gamma band response
Authors: Polomac Nenad , Leicht Gregor , Nolte Guido , Andreou Christina , Schneider Till R. , Steinmann Saskia , Engel Andreas K. , Mulert Christoph 
Published: February 2015

AbstractBackground:High frequency oscillations in the gamma range are known to be involved in early stages of auditory information processing in terms of synchronization of brain regions, e.g., in cognitive functions. It has been shown using EEG source localisation, as well as simultaneously recorded EEG-fMRI, that the auditory evoked gamma-band response (aeGBR) is modulated by attention. In addition to auditory cortex activity a dorsal anterior cingulate cortex (dACC) generator could be involved. In the present study we investigated aeGBR magnetic fields using magnetoencephalography (MEG). We aimed to localize the aeGBR sources and its connectivity features in relation to mental effort.Methods:We investigated the aeGBR magnetic fields in 13 healthy participants using a 275-channel CTF-MEG system. The experimental paradigms were two auditory choice reaction tasks with different difficulties and demands for mental effort. We performed source localization with eLORETA and calculated the aeGBR lagged phase synchronization between bilateral auditory cortices and frontal midline structures.Results:The eLORETA analysis revealed sources of the aeGBR within bilateral auditory cortices and in frontal midline structures of the brain including the dACC. Compared to the control condition the dACC source activity was found to be significantly stronger during the performance of the cognitively demanding task. Moreover, this task involved a significantly stronger functional connectivity between auditory cortices and dACC.Conclusion:In accordance with previous EEG and EEG-fMRI investigations, our study confirms an aeGBR generator in the dACC by means of MEG and suggests its involvement in the effortful processing of auditory stimuli.
Mediated pleiotropy between psychiatric disorders and autoimmune disorders revealed by integrative analysis of multiple GWAS
Authors: Wang Qian , Yang Can , Gelernter Joel , Zhao Hongyu 
Published: February 2015

AbstractEpidemiological observations and molecular-level experiments have indicated that brain disorders in the realm of psychiatry may be influenced by immune dysregulation. However, the degree of genetic overlap between immune disorders and psychiatric disorders has not been well established. We investigated this issue by integrative analysis of genome-wide association studies (GWAS) of 18 complex human traits/diseases (five psychiatric disorders, seven autoimmune disorders, and others) and multiple genomewide annotation resources (Central nervous system genes, immune-related expressionquantitative trait loci (eQTL) and DNase I hypertensive sites from 98 cell-lines). We detected pleiotropy in 24 of the 35 psychiatric-autoimmune disorder pairs, with statistical significance as strong asp=3.9e-285 (schizophrenia-rheumatoid arthritis). Strong enrichment (>1.4 fold) of immune-related eQTL was observed in four psychiatric disorders. Genomic regions responsible for pleiotropy between psychiatric disorders and autoimmune disorders were detected. The MHC region on chromosome 6 appears to be the most important (and it was indeed previously noted (1-3) as a confluence between schizophrenia and immune disorder risk regions), with many other regions, such as cytoband 1p13.2. We also found that most alleles shared between schizophrenia and Crohn’s disease have thesameeffect direction, with similar trend found for other disorder pairs, such as bipolar-Crohn’s disease. Our results offer a novel bird’s-eye view of the genetic relationship and demonstrate strong evidence for mediated pleiotropy between psychiatric disorders and autoimmune disorders. Our findings might open new routes for prevention and treatment strategies for these disorders based on a new appreciation of the importance of immunological mechanisms in mediating risk.
Predictability of Autism, Schizophrenic and Obsessive Spectra Diagnosis: Toward a Damage Network Approach
Authors: Cauda Franco , Costa Tommaso , Fava Luciamo , Palermo Sara , Bianco Francesca , Duca Sergio , Geminiani Giuliano , Tatu Karina , Keller Roberto 
Published: February 2015

ABSTRACTSchizophrenia, obsessive-compulsive and autistic disorders are traditionally considered as three separate psychiatric conditions each with specific symptoms and pattern of brain alterations. This view can be challenged since these three conditions have the same neurobiological origin, stemming from a common root of a unique neurodevelopmental tree.The aim of this meta-analytic study was to determine, from a neuroimaging perspective, whether i) white matter and gray matter alterations are specific for the three different spectrum disorders, and the nosographical differentiation of three spectra is supported by different patterns of brain alterations. ii) it might be possible to define new spectra starting from specific brain damage. iii) it is possible to detect a “brain damage network” (a connecting link between the damaged areas that relates areas constantly involved in the disorder).Three main findings emerged from our meta-analysis:The three psychiatric spectra do not appear to have their own specific damage.It is possible to define two new damage clusters. The first includes substantial parts of the salience network, and the second is more closely linked to the auditory-visual, auditory and visual somatic areas.It is possible to define a "Damage Network" and to infer a hierarchy of brain substrates in the pattern of propagation of the damage.These results suggest the presence of a common pattern of damage in the three pathologies plus a series of variable alterations that, rather than support the sub-division into three spectra, highlight a two-cluster parcellation with an input-output and more cognitive clusters.
An exon-capture system for the entire class Ophiuroidea
Authors: Hugall Andrew F. , O’Hara Timothy D. , Hunjan Sumitha , Nilsen Roger , Moussalli Adnan 
Published: February 2015

ABSTRACTWe present an exon-capture system for an entire class of marine invertebrates, the Ophiuroidea, built upon a phylogenetically diverse transcriptome foundation. The system captures ~90 percent of the 1552 exon target, across all major lineages of the quarter-billion year old extant crown group. Key features of our system are: 1) basing the target on an alignment of orthologous genes determined from 52 transcriptomes spanning the phylogenetic diversity and trimmed to remove anything difficult to capture, map or align, 2) use of multiple artificial representatives based on ancestral states rather than exemplars to improve capture and mapping of the target, 3) mapping reads to a multi-reference alignment, and 4) using patterns of site polymorphism to distinguish among paralogy, polyploidy, allelic differences and sample contamination. The resulting data gives a well-resolved tree (currently standing at 417 samples, 275,352 bp, 91% data-complete) that will transform our understanding of ophiuroid evolution and biogeography.
Difference in the impacts of the neonicotinoid dinotefuran administered through sugar syrup from that through pollen paste on a honeybee colony in the long-term field experiment
Authors: Yamada Toshiro , Yamada Yasuhiro , Yamada Kazuko 
Published: February 2015

SummaryWe have previously examined the impact of neonicotinoid pesticides, dinotefuran and clothianidin, on honeybee Apis mellifera colonies in long-term field experiments when they were simultaneously administered through both vehicles of sugar syrup and pollen paste (Yamadaet al., 2012). The independent effect of a pesticide through two vehicles has not been studied in our previous work. In this paper, we investigated the independent impact of dinotefuran through each of the two vehicles. We confirmed that dinotefuran intake per bee until colony extinction due to administration through pollen paste (DF-TIPP) was roughly one-fifth as much as that through sugar syrup (DF-TISS). The intake was largely independent of dinotefuran concentration. We considered the possibility of DF-TIPP per bee as an indicator to assess the impact of persistent pesticide on a honeybee colony in a practical apiary.This work has replicated the finding that a honeybee colony has dwindled away to nothing after assuming an aspect of a colony collapse disorder (CCD) by administration of the neonicotinoids dinotefuran and clothianidin in our previous work, regardless of the vehicles. In addition, a failure in wintering was observed in case of administration of dinotefuran with the lowest concentration in this work even if the colony appeared vigorous before winter.We can infer that a CCD and a failure in wintering may have the same roots of chronic toxicity of neonicotinoids under conditions of low concentrations due to the persistency and high toxicity which are characteristic of them.
Molecular evolutionary consequences of island colonisation
Authors: James Jennifer E. , Lanfear Robert , Eyre-Walker Adam 
Published: February 2015

AbstractIsland endemics are likely to experience population bottlenecks; they also have restricted ranges. Therefore we expect island species to have small effective population sizes (Ne) and reduced genetic diversity compared to their mainland counterparts. As a consequence, island species may have inefficient selection and reduced adaptive potential. We used both polymorphisms and substitutions to address these predictions, improving on the approach of recent studies that only used substitution data. This allowed us to directly test the assumption that island species have small values ofNe. We found that island species had significantly less genetic diversity than mainland species; however, this pattern could be attributed to a subset of island species that had undergone a recent population bottleneck. When these species were excluded from the analysis, island and mainland species had similar levels of genetic diversity, despite island species occupying considerably smaller areas than their mainland counterparts. We also found no overall difference between island and mainland species in terms of effectiveness of selection or mutation rate. Our evidence suggests that island colonisation has no lasting impact on molecular evolution. This surprising result highlights gaps in our knowledge of the relationship between census and effective population size.