bluuebunny/crossref_metadata_2025_split huggingface dataset:
BITACORA: A comprehensive tool for the identification and annotation of gene families in genome assemblies
Authors: Vizueta Joel , Sánchez-Gracia Alejandro , Rozas Julio 
Published: September 2019

AbstractGene annotation is a critical bottleneck in genomic research, especially for the comprehensive study of very large gene families in the genomes of non-model organisms. Despite the recent progress in automatic methods, the tools developed for this task often produce inaccurate annotations, such as fused, chimeric, partial or even completely absent gene models for many family copies, which require considerable extra efforts to be amended. Here we present BITACORA, a bioinformatics solution that integrates sequence similarity search tools and Perl scripts to facilitate both the curation of these inaccurate annotations and the identification of previously undetected gene family copies directly from DNA sequences. We tested the performance of the BITACORA pipeline in annotating the members of two chemosensory gene families of different sizes in seven available chelicerate genome drafts. Despite the relatively high fragmentation of some of these drafts, BITACORA was able to improve the annotation of many members of these families and detected thousands of new chemoreceptors encoded in genome sequences. The program generates an output file in the general feature format (GFF) files, with both curated and novel gene models, and a FASTA file with the predicted proteins. These outputs can be easily integrated in genomic annotation editors, greatly facilitating subsequent manual annotation and downstream evolutionary analyses.
The genome of Caenorhabditis bovis
Authors: Stevens Lewis , Rooke Stefan , Falzon Laura C , Machuka Eunice M , Momanyi Kelvin , Murungi Maurice K , Njoroge Samuel M , Odinga Christian O , Ogendo Allan , Ogola Joseph , Fèvre Eric M , Blaxter Mark 
Published: September 2019

AbstractThe free-living nematode Caenorhabditis elegans is a key laboratory model for metazoan biology. C. elegans is also used as a model for parasitic nematodes despite being only distantly related to most parasitic species. All ∼65 Caenorhabditis species currently in culture are free-living with most having been isolated from decaying plant or fungal matter. Caenorhabditis bovis is a particularly unusual species, having been isolated several times from the inflamed ears of Zebu cattle in Eastern Africa where it is believed to be the cause of bovine parasitic otitis. C. bovis is therefore of particular interest to researchers interested in the evolution of nematode parasitism and in Caenorhabditis diversity. However, as C. bovis is not in laboratory culture, it remains little studied and details of its prevalence, role in bovine parasitic otitis and relationships to other Caenorhabditis species are scarce. Here, by sampling livestock markets and slaughterhouses in Western Kenya, we successfully reisolate C. bovis from the ear of adult female Zebu. We sequence the genome of C. bovis using the Oxford Nanopore MinION platform in a nearby field laboratory and use the data to generate a chromosome-scale draft genome sequence. We exploit this draft genome to reconstruct the phylogenetic relationships of C. bovis to other Caenorhabditis species and reveal the changes in genome size and content that have occurred during its evolution. We also identify expansions in several gene families that have been implicated in parasitism in other nematode species, including those associated with resistance to antihelminthic drugs. The high-quality draft genome and our analyses thereof represent a significant advancement in our understanding of this unusual Caenorhabditis species.
Superior temporal sulcus hypoperfusion in children with autism spectrum disorder: an arterial spin-labeling magnetic resonance study
Authors: Saitovitch Ana , Rechtman Elza , Lemaitre Hervé , Tacchella Jean-Marc , Vinçon-Leite Alice , Douard Elise , Calmon Raphael , Grévent David , Philippe Anne , Chabane Nadia , Brunelle Francis , Boddaert Nathalie , Zilbovicius Monica 
Published: September 2019

AbstractAdvances in neuroimaging techniques have significantly improved our understanding of the neural basis of autism spectrum disorder (ASD). Several attempts have been made to label the main neuroimaging phenotype of ASD, mostly by anatomical and functional activation studies, but none of the frameworks have been without controversy. Over the past decade, a renewed interest for rest brain functioning has emerged in the scientific community, reflected on a large number of resting state fMRI (rs-fMRI) studies, but results remain heterogeneous. It is possible today to investigate rest brain functioning by measuring rest cerebral blood flow (CBF) with MRI using arterial spin labeling (ASL). Here, we investigated rest CBF abnormalities using non-invasive ASL-MRI in 18 children with ASD without cognitive delay (10.4 ± 2.8 y) and 30 typically developing children (10.6 ± 3.0 y). Following quality control, images from a final sample of 12 children with ASD (11.2 ± 2.9 y) and 28 typically developing children (10.1 ± 2.5 y) were analyzed. Whole brain voxel-by-voxel analysis showed significant rest CBF decrease in temporal regions, mainly in the superior temporal sulcus (STS), in children with ASD. This hypoperfusion was individually detected in 83% of children with ASD. Finally, negative correlation was observed between ASD severity scores and rest CBF in the right posterior STS. Strikingly, despite the small sample studied here, our results are extremely similar to previous PET and SPECT findings describing decreased rest CBF in the same superior temporal regions at group and individual levels, as well as correlation with symptoms severity. The congruence between these results, with different methods and in different ASD profiles, reinforce the strength of rest functional abnormalities within these superior temporal regions in ASD and strongly indicates it might be a core characteristic of the disorder. Identifying a core dysfunctional region in ASD bears direct implications to the development of novel therapeutic interventions, such as transcranial magnetic stimulation. In addition, if confirmed in a larger sample, rest temporal hypoperfusion could become a reliable brain imaging biomarker in ASD.
Light-Activated Nanoscale Gas Vesicles Selectively Kill Tumor Cells
Authors: Fernando Ann , Gariépy Jean 
Published: September 2019

AbstractProtein-based nanobubbles such as halophilic archaeabacterial gas vesicles (GVs) represent a new class of stable, homogeneous nanoparticles with acoustic properties that allow them to be visualized by ultrasound (US) waves. To design GVs as theranostic agents, we modified them to respond to light, with a view to locally generate reactive oxygen species that can kill cancer cells. Specifically, up to 60,000 photoreactive chlorine6 (Ce6) molecules were chemically attached to lysine ε-amino groups present on the surface of each purifiedHalobacterium sp.NRC-1 GV. The resulting fluorescent NRC-1 Ce6-GVs have dimensions comparable to that of native GVs and were efficiently taken up by human breast [MCF-7] and human hypopharyngeal [FaDu-GFP] cancer cells as monitored by confocal microscopy and flow cytometry. When exposed to light, internalized Ce6-GVs were 200-fold more effective on a molar basis than free Ce6 at killing cells. These results demonstrate the potential of Ce6-GVs as novel and promising nanomaterials for image-guided photodynamic therapy.
State Space Methods for Phase Amplitude Coupling Analysis
Authors: Soulat Hugo , Stephen Emily P. , Beck Amanda M. , Purdon Patrick L. 
Published: September 2019

AbstractPhase Amplitude Coupling (PAC) is thought to play a fundamental role in the dynamic coordination of brain circuits and systems. There are however growing concerns that existing methods for PAC analysis are prone to error and misinterpretation. Improper frequency band selection can render true PAC undetectable, while non-linearities or abrupt changes in the signal can produce spurious PAC. Current methods require substantial amounts of data and lack formal statistical inference tools. We describe here a novel approach for PAC analysis that substantially addresses these problems. We use a state space model to estimate the component oscillations, avoiding problems with frequency band selection, nonlinearities, and sharp signal transitions. We represent cross-frequency coupling in parametric and time-varying forms to further improve statistical efficiency and estimate the posterior distribution of the coupling parameters to derive their credible intervals. We demonstrate the method using simulated data, rat LFP data, and human EEG data.
Direct detection of molecular intermediates from first-passage times
Authors: Thorneywork Alice L. , Gladrow Jannes , Qing Yujia , Rico-Pasto Marc , Ritort Felix , Bayley Hagan , Kolomeisky Anatoly B. , Keyser Ulrich F. 
Published: September 2019

AbstractAll natural phenomena are governed by energy landscapes. However, the direct measurement of this fundamental quantity remains challenging, particularly in complex systems involving intermediate states. Here, we uncover key details of the energy landscapes that underpin a range of experimental systems through quantitative analysis of first-passage time distributions. By combined study of colloidal dynamics in confinement, transport through a biological pore and the folding kinetics of DNA hairpins, we demonstrate conclusively how a short-time, power-law regime of the first-passage time distribution universally reflects the number of intermediate states associated with each process, irrespective of the lengthscales, timescales or interactions in the system. We thereby establish a powerful method for investigating the underlying mechanisms of complex molecular processes.
Extended snake venomics by top-down in-source decay: Investigating the newly discovered Anatolian Meadow viper subspecies,Vipera anatolica senliki
Authors: Hempel Benjamin-Florian , Damm Maik , Mrinalini  , Göçmen Bayram , Karış Mert , Nalbantsoy Ayse , Kini R. Manjunatha , Süssmuth Roderich D. 
Published: September 2019

AbstractHerein we report on the venom proteome ofVipera anatolica senliki,a recently discovered and hitherto unexplored subspecies of the critically endangered Anatolian Meadow viper endemic to the Antalya Province of Turkey. Integrative venomics, including venom gland transcriptomics as well as complementary bottom-up and top-down proteomic analyses, were applied to fully characterize the venom ofV. a. senliki. Furthermore, the classical top-down venomics approach was extended to elucidate the venom proteome by an alternative in-source decay (ISD) proteomics workflow using the reducing matrix 1,5-diaminonaphthalene (1,5-DAN). Top-down ISD proteomics allows for disulfide bond mapping as well as effectivede novoidentification of high molecular weight venom constituents, both of which are difficult to achieve by commonly established top-down approaches. Venom gland transcriptome analysis identified 42 venom transcript annotations from 13 venom toxin families. Relative quantitative snake venomics revealed snake venom metalloproteinases (svMP, 42.9%) as the most abundant protein family, followed by several less dominant toxin families. Online mass profiling and top-down venomics provide a detailed insight into the venom proteome ofV. a. senlikiand facilitates a comparative analysis of venom variability for the closely related subspecies,V. a. anatolica.TOC Figure
Selective loss of the GABAAα1subunit from Purkinje cells is sufficient to induce a tremor phenotype
Authors: Nietz Angela , Krook-Magnuson Chris , Gutierrez Haruna , Klein Julia , Sauve Clarke , Krook-Magnuson Esther 
Published: September 2019

AbstractBackgroundIncreased circuit level insights into Essential tremor, the most prevalent movement disorder, are needed. Previously, an Essential Tremor-like phenotype was noted in animals with a global knockout of the GABAAα1subunit. However, global knockout of the GABAAα1subunit has limitations, including potential early mortality and limited circuit level insights into the tremor.MethodsGiven the hypothesized role of the cerebellum in tremor, including Essential Tremor, we used transgenic mice to selectively knock out the GABAAα1subunit from cerebellar Purkinje cells. As previous work suggested background strain may influence phenotype in this model, we used two different background strains (a Black6 and a Mixed background). We examined the resulting phenotype regarding impacts on inhibitory postsynaptic currents, survival rates, gross motor abilities, and expression of tremor.ResultsWe found that GABAA-mediated synaptic currents are abolished in Purkinje cells from Purkinje cell specific knockout mice, while GABAA-mediated inhibition to cerebellar molecular layer interneurons remains intact. Selective loss of GABAAα1from Purkinje cells did not produce gross motor deficits, as measured by the accelerating rotarod, nor did it result in decreased survival rates. However, a tremor phenotype was apparent, regardless of sex or background strain. This tremor mimicked the tremor seen in animals with a global knockout of the GABAAα1subunit, and, like Essential Tremor in patients, was responsive to ethanol.ConclusionsThese findings indicate that reduced inhibition to Purkinje cells is sufficient to induce a tremor phenotype, highlighting the importance of the cerebellum, inhibition, and Purkinje cells, in tremor.
Aceclofenac Fast Dispersible Tablet Formulations: Effect of different concentration levels of Avicel PH102 on the compactional, mechanical and drug release characteristics
Authors: Yasmin Riffat , Shoaib Muhammad Harris , Ahmed Farrukh Rafiq , Qazi Faaiza , Ali Huma , Zafar Farya 
Published: September 2019

ABSTRACTObjective of this study was based on the formulation development of fast dispersible Aceclofenac tablets (100mg) and to evaluate the influence of pharmaceutical mixtures of directly compressible Avicel PH102 with Mannitol and Acdisol on the compressional, mechanical characteristics and drug release properties. Fifteen different aceclofenac formulations were developed by central composite rotatable design (CCRD). Among them best possible formulations (FA–FH) were selected on the basis of micromeritic properties, appropriate tablet weight and disintegration time for further study. Tablets were compressed by direct compression method using hand held hydraulic press with a compressional force ranging from 8 to 80 MN/m2 (MPa). Pre and post compression studies were performed and the compressed formulations (FA-FH) were assessed for different quality tests. The Heckel and Kawakita equations were applied for determination of compressional behavior of formulations. The quality attributes suggested that formulation (FB) containing avicel PH 102 (20%), mannitol (25%) and ac-di-sol (3%) as best optimized formulation showing better mechanical strength i.e. hardness 37.75 ± 0.14N, tensile strength 5.67MN/m2 and friability 0.34%. Furthermore, compressional analysis of FB showed lowest PY value 59.52 MN/m2 and Pk value 1.040 MN/m indicating plasticity of the material. Formulation FB disintegrated rapidly within 21 seconds and released 99.92 % drug after 45min in phosphate buffer pH 6.8. Results of drug release kinetics showed that formulations FA-FH followed Weibull and First-order models in three different dissolution media. Avicel based formulation mixture exhibit excellent compactional strength with rapid disintegration and drug release.
State-dependent differences in the frequency of TMS-evoked potentials
Authors: Stanfield Candice T. , Wiener Martin 
Published: September 2019

AbstractPrevious evidence suggests different cortical areas naturally oscillate at distinct frequencies, reflecting tuning properties of each region. The concurrent use of transcranial magnetic stimulation (TMS) and electroencephalography (EEG) has been used to perturb cortical regions, resulting in an observed post-stimulation response that is maximal at the natural frequency of that region. However, little is known about the spatial extent of TMS-induced activation differences in cortical regions when comparing resting state (passive) versus active task performance. Here, we employed TMS-EEG to directly perturb three cortical areas in the right hemisphere while measuring the resultant changes in maximal evoked frequency in healthy human subjects during a resting state (N=12) and during an active sensorimotor task (N=12). Our results revealed that the brain engages a higher dominant frequency mode when actively engaged in a task, such that the frequency evoked during a task is consistently higher across cortical regions, regardless of the region stimulated. These findings suggest that a distinct characteristic of active performance versus resting state is a higher state of natural cortical frequencies.
Trends of the Florida manatee (Trichechus manatus latirostris) rehabilitation admissions 1991-2017
Authors: Ball Ray L. , Malmi Markuu , Zgibor Janice 
Published: September 2019

AbstractA retrospective study of admission data of 401 West Indian manatees (Trichechus manatus latirostris) presented to the David A. Straz Jr. Manatee Critical Care Center at ZooTampa at Lowry Park (ZooTampa) for rehabilitation from August 1991 through October 2017. Causes of admittance, location of rescue, gender, and age class were all recorded for each manatee admitted. Admittance categories as defined by the Florida Fish and Wildlife Conservation Commission (FWC) included watercraft collisions, natural causes, entanglement, entrapment, orphaned calves, captive born, mothers of rescued calves, calves of rescued mothers, human, and other. The admitted population was primarily from the southwest and northwest coasts and related waterways of Florida. The gender difference was relatively equivocal (54% female) while the adults comprised 79% of the admissions. The overall total admissions increased steadily over the study period as did the admissions for each individual categories of admission. Watercraft collisions and natural causes combined were 71% of all admissions for the entire study period and are the dominant causes of admission. Watercraft collisions are more likely to occur during May through October, whereas natural causes of admittance are more likely to occur between December and March. Rehabilitated manatees may reduce overall manatee mortality and can provide insight into population-based health concerns if evaluated appropriately. Future efforts can incorporate physical examination findings, hematology, biochemistry profiles, and ancillary diagnostic testing to continue to improve the individual welfare of this marine mammal in its natural range. Admissions data could also potentially serve the wider conservation and recovery efforts if it is proven that the data obtained is at least as informative as that obtained by the carcass salvage program. Limited conservation resources could then be re-directed as new challenges arise with the expanding population and potentially expanding range of this species.
Synergic action of Vitamin D3 and 17β-estradiol on behavioral impairments induced by unpredictable mild stress in the adult ovariectomized female rats
Authors: Baranenko Denis , Mironova Vera , Fedotova Julia , van den Tol Annemieke Johanna Maria 
Published: September 2019

AbstractThe aim of the present study was study changes in antidepressant-like responses to Vitamin D3 (VD3) supplementation in three different doses (1.0, 2.5, and 5.0 mg/kg, s.c.) in long-term ovariectomized (OVX) rats treated with low dose of 17β-E2 (0.5 μg/rat, s.c.) during chronic unpredictable mild stress (CUMS). Sucrose preference (SPT), forced swimming (FST), and open-field (OFT) tests were administered to measure depression-like behavior. Brain-derived neurotrophic factor (BDNF), and serotonine (5-HT) and 5-hydroxyindoleacetic acid (5-HIAA) levels in the hippocampus were measured by ELISA, western blotting analysis, and by using high performance liquid chromatography (HPLC), respectively.The findings demonstrated that VD3 (5.0 mg/kg, s.c.) in a combination with low dose of 17β-E2 increased sucrose consumption in the SPT and decreased depression-like in the FST of the long-term OVX rats exposed to CUMS. VD3 (5.0 mg/kg) resulted in significant elevated levels of hippocampal BDNF protein expression, as well as to the normalization of 5-HT and 5-HIAA levels in long-term OVX rats plus 17β-E2 compared to the OVX rats plus solvent or 17β-E2 submitted to CUMS. There were no significant effects of VD3 (1.0 and 2.5 mg/kg) treatment on both BDNF protein levels and 5-HT turnover in the hippocampus of the long-term OVX rats treated with 17β-E2 exposed to CUMS compared to the long-term OVX with CUMS rats plus solvent.In conclusion, VD3 (5.0 mg/kg, s.c.) in a combination with low dose of 17β-E2 had a synergic antianhedonic- and antidepressant-like effects in the adult female rats following long-term ovariectomy submitted to CUMS. This is the first study in long-term OVX female rats showing beneficial effects of VD3 on depression-like behavior that are depended on the presence/absence of stressful factors.
Unexpected predicted length variation for the coding sequence of the sleep related gene,BHLHE41in gorilla amidst strong purifying selection across mammals
Authors: Unadkat Krishna , Whittall Justen B. 
Published: September 2019

AbstractThere is a molecular basis for many sleep patterns and disorders involving circadian clock genes. In humans, “short-sleeper” behavior has been linked to specific amino acid substitutions inBHLHE41(DEC2), yet little is known about variation at these sites and across this gene in mammals. We compareBHLHE41coding sequences for 27 mammals. The coding sequence alignment length was 1794bp, of which 55.0% of base pairs were invariant among the sampled mammals. The mean pairwise nucleotide identity was 92.2%. Of the 598 residue amino acid alignment for mammals, 71.7% of amino acids were identical. The pairwise percent identity for amino acids was 94.8%. No other mammals had the same “short-sleeper” amino acid substitutions previously described from humans. Phylogenetic analyses based on the nucleotides of the coding sequence alignment are consistent with established mammalian relationships. Significant purifying selection was detected in 66.2% of variable codons. No codons exhibited significant signs of positive selection. Unexpectedly, the gorillaBHLHE41sequence has a 318 bp insertion at the 5’ end of the coding sequence and a deletion of 195 bp near the 3’ end of the coding sequence (including the two short sleeper variable sites). Given the strong signal of purifying selection across this gene, phylogenetic congruence with expected relationships and generally conserved function among mammals investigated thus far, we suggest the unexpected indels predicted in the gorillaBHLHE41may represent an annotation error and warrant experimental validation.