bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evoregions: Mapping Shifts in Phylogenetic Turnover Across Biogeographic Regions
Authors: Maestri Renan , Duarte Leandro 
Published: May 2019

ABSTRACTBiogeographic regionalization offers context to the geographical evolution of clades. The positions of bioregions inform both the spatial location of clusters in species distribution and where their most important boundaries are. Nevertheless, defining bioregions based on species distribution alone only incidentally recovers regions that are important during the evolution of the focal group. The extent to which bioregions correspond to centers of independent diversification depends on how clusters of species composition naturally reflect the radiation of single clades, which is not the case when mixed colonization occurred. Here, we showed that using phylogenetic turnover based on fuzzy sets, instead of species composition, led to more adequate detection of evolutionary important bioregions, that is, regions that truly account for the independent diversification of lineages. Mapping those evoregions in the phylogenetic tree quickly reveals the timing and location of major shifts of biogeographic regions. Moreover, evolutionary transition zones are easily mapped, and permits the recognition of regions with high phylogenetic overlap. Our results using the global radiation of rats and mice (Muroidea) recovered four evoregions—three major evolutionary arenas corresponding to the Neotropics, a Nearctic-Siberian, and a Paleotropical-Australian evoregion, and a fourth and fuzzy Afro-Palearctic evoregion. In comparison, an analysis with a method considering species distribution alone found 52 bioregions. Evoregions is a useful framework whenever the question is related to the identification of the most important centers of a group’s diversification history and its evolutionary transitions zones.
Aberrant striatal oscillations after dopamine loss in parkinsonian non-human primates
Authors: Singh Arun , Papa Stella M. 
Published: May 2019

AbstractDopamine depletion in Parkinson’s disease (PD) is associated with abnormal oscillatory activity in the cortico-basal ganglia network. However, the oscillatory pattern of striatal neurons in PD remains poorly defined. Here, we analyzed the local field potentials in one untreated and five MPTP-treated non-human primates (NHP) to model advanced PD. Augmented oscillatory activity in the alpha (8-13 Hz) and low-beta (13-20 Hz) frequency bands was found in the striatum in parallel to the motor cortex and globus pallidus of the NHP-PD model. The coherence analysis showed increased connectivity in the cortico-striatal and striato-pallidal pathways at alpha and low-beta frequency bands, confirming the presence of abnormal 8-20 Hz activity in the cortico-basal ganglia network. The acute L-Dopa injection that induced a clear motor response normalized the amplified 8-20 Hz oscillations. These findings indicate that pathological striatal oscillations at alpha and low-beta bands are concordant with the basal ganglia network changes after dopamine depletion, and thereby support a key role of the striatum in the generation of parkinsonian motor abnormalities.
The advantages and disadvantages of short- and long-read metagenomics to infer bacterial and eukaryotic community composition
Authors: Pearman William S. , Freed Nikki E. , Silander Olin K. 
Published: May 2019

AbstractBackgroundThe first step in understanding ecological community diversity and dynamics is quantifying community membership. An increasingly common method for doing so is through metagenomics. Because of the rapidly increasing popularity of this approach, a large number of computational tools and pipelines are available for analysing metagenomic data. However, the majority of these tools have been designed and benchmarked using highly accurate short read data (i.e. illumina), with few studies benchmarking classification accuracy for long error-prone reads (PacBio or Oxford Nanopore). In addition, few tools have been benchmarked for non-microbial communities.ResultsHere we use simulated error prone Oxford Nanopore and high accuracy Illumina read sets to systematically investigate the effects of sequence length and taxon type on classification accuracy for metagenomic data from both microbial and non-microbial communities. We show that very generally, classification accuracy is far lower for non-microbial communities, even at low taxonomic resolution (e.g. family rather than genus).ConclusionsWe then show that for two popular taxonomic classifiers, long error-prone reads can significantly increase classification accuracy, and this is most pronounced for non-microbial communities. This work provides insight on the expected accuracy for metagenomic analyses for different taxonomic groups, and establishes the point at which read length becomes more important than error rate for assigning the correct taxon.
Transposable element dynamics are consistent across theDrosophilaphylogeny, despite drastically differing content
Authors: Hill Tom 
Published: May 2019

AbstractBackgroundThe evolutionary dynamics of transposable elements (TEs) vary across the tree of life and even between closely related species with similar ecologies. InDrosophila, most of the focus on TE dynamics has been completed inDrosophila melanogasterand the overall pattern indicates that TEs show an excess of low frequency insertions, consistent with their frequent turn over and high fitness cost in the genome. Outside ofD. melanogaster, insertions in the speciesDrosophila algonquin, suggests that this situation may not be universal, even withinDrosophila. Here we test whether the pattern observed inD. melanogasteris similar across fiveDrosophilaspecies that share a common ancestor more than fifty million years ago.ResultsFor the most part, TE family and order insertion frequency patterns are broadly conserved between species, supporting the idea that TEs have invaded species recently, are mostly costly and dynamics are conserved in orthologous regions of the host genomeConclusionsMost TEs retain similar activities and fitness costs across theDrosophilaphylogeny, suggesting little evidence of drift in the dynamics of TEs across the phylogeny, and that most TEs have invaded species recently.
SolXplain: An Explainable Sequence-Based Protein Solubility Predictor
Authors: Mall Raghvendra 
Published: May 2019

AbstractMotivationProtein solubility is a property associated with protein expression and is a critical determinant of the manufacturability of therapeutic proteins. It is thus imperative to design accurate in-silico sequence-based solubility predictors.MethodsIn this study, we propose SolXplain, an extreme gradient boosting machine based protein solubility predictor which achieves state-of-the-art performance using physio-chemical, sequence and novel structure derived features from protein sequences. Moreover, SolXplain has a unique attribute that it can provide explanation for the predicted class label for each test protein based on its corresponding feature values using SHapley Additive exPlanations (SHAP) method.ResultsBased on an independent test set, SolXplain outperformed other sequence-based methods by at least 2% in accuracy and 2% in Matthew’s correlation coefficient, with an overall accuracy of 78% and Matthew’s correlation coefficient of 0.56. Additionally, for fractions of exposed residues (FER) at various residual solvent accessibility (RSA) cutoffs, we observed higher fractions to associate positively with protein solubility, and tripeptide stretches that contain one isoleucine and one or more histidines, to associate negatively with solubility. The improved prediction accuracy of SolXplain enables it to predict protein solubility with greater consistency and screen for sequences with enhanced manufacturability.
Terminal neuron localization to the upper cortical plate is controlled by the transcription factor NEUROD2
Authors: Guzelsoy Gizem , Akkaya Cansu , Atak Dila , Dunn Cory D. , Kabakcioglu Alkan , Ozlu Nurhan , Ince-Dunn Gulayse 
Published: May 2019

AbstractExcitatory neurons of the mammalian cerebral cortex are organized into six functional layers characterized by unique patterns of connectivity, as well as distinctive physiological and morphological properties. Cortical layers appear after a highly regulated migration process in which cells move from the deeper, proliferative zone toward the superficial layers. Importantly, defects in this radial migration process have been implicated in neurodevelopmental and psychiatric diseases. Here we report that during the final stages of migration, transcription factor Neurogenic Differentiation 2 (Neurod2) contributes to terminal cellular localization within the cortical plate. In mice, in utero knockdown of Neurod2 results in reduced numbers of neurons localized to the uppermost region of the developing cortex, also termed the primitive cortical zone. Our ChIP-Seq and RNA-Seq analyses of genes regulated by NEUROD2 in the developing cortex identify a number of key target genes with known roles in Reelin signaling, a critical regulator of neuronal migration. Our focused analysis of regulation of the Reln gene, encoding the extracellular ligand REELIN, uncovers NEUROD2 binding to conserved E-box elements in multiple introns. Furthermore, we demonstrate that knockdown of NEUROD2 in primary cortical neurons results in a strong increase in Reln gene expression at the mRNA level, as well as a slight upregulation at the protein level. These data reveal a new role for NEUROD2 during the late stages of neuronal migration, and our analysis of its genomic targets offer new genes with potential roles in cortical lamination.
The Early Sociocognitive Battery: a clinical tool for early identification of children at risk for social communication difficulties and ASD?
Authors: Roy Penny , Chiat Shula 
Published: May 2019

AbstractBackgroundA substantial proportion of preschool children referred to speech and language therapy (SLT) services have social communication difficulties and/or autistic spectrum disorders (SC&/ASD) that are not identified until late childhood. These ‘late’ diagnosed children miss opportunities to benefit from earlier targeted interventions. Prior evidence from a follow‐up clinical sample showed that preschool performance on the Early Sociocognitive Battery (ESB) was a good predictor of children with social communication difficulties 7–8 years later.AimsThe aims were three‐fold: (1) to determine the impact of child/demographic factors on ESB performance in a community sample of young children; (2) to assess the ESB's concurrent validity and test–retest reliability; and (3) to use cut‐offs for ‘low’ ESB performance derived from the community sample data to evaluate in a clinical sample the predictiveness of the ESB at 2–4 years for outcomes at 9–11 years, including parent‐reported SC&/ASD diagnosis.Methods & ProceduresA community sample of 205 children aged 2–4 years was assessed on the ESB and a receptive vocabulary test. A subsample (n = 20) was retested on the ESB within 2 weeks. Parents completed a questionnaire providing background child/demographic information. The clinical sample from our previous study comprised 93 children assessed on the ESB at 2;6 to < 4;0 whose parents completed the Social Responsiveness Scale (SRS), our measure of social communication, when the children were 9–11 years. Cut‐offs for ‘low’ ESB performance derived from the community sample were used to determine the predictive validity of ‘low’ ESB scores for social communication outcomes and parent‐reported SC&/ASD diagnosis according to age of ESB assessment.Outcome & ResultsFindings from the community sample confirmed the ESB as psychometrically robust, sensitive to age and language delay, and, in contrast to the receptive vocabulary measure, unaffected by bilingualism. While overall associations between ESB performance and later social communication difficulties in the clinical sample were particularly strong for the youngest age group (2;6 to < 3;0; r = .71, p < .001), ‘low’ ESB performance was equally predictive across age groups and overall identified 89% of children with ‘late’ SC&/ASD diagnoses (sensitivity), and 75% of those without (specificity).Conclusions & ImplicationsResults indicate that the ESB is a valid preschool assessment suitable for use with children from diverse language backgrounds. It identifies deficits in key sociocognitive skills and is predictive of social communication difficulties in school‐age children that had not been identified in preschool clinical assessment, supporting earlier targeted interventions for these children.
In Vitro Digestibility and Quality of an Emulsified Meat Product Formulated With Animal Fat Encapsulated With Pectin
Authors: Santiaguín‐Padilla Aarón Jonary , Peña‐Ramos Etna Aida , Pérez‐Gallardo Alfonso , Rascón‐Chu Agustin , González‐Ávila Marisela , González‐Ríos Humberto , González‐Noriega Julio A , Islava‐Lagarda Thalia 
Published: May 2019

AbstractAnimal fat plays a key role in the structure, quality, and acceptability of emulsified meat products. However, a high consumption of saturated fat has been related to several health problems. Fat encapsulation with a nondigestible carbohydrate, such as pectin, may offer a promising alternative to reduce fat intake from a meat product, by preventing its digestion and absorption. The objective of this study was to develop a meat sausage with pectin‐encapsulated‐fat (PEF) to decrease its lipid digestibility, without compromising its acceptability. Pork fat particles encapsulation by emulsification with a 4% pectin solution, and also stability during meat processing and cooking, was confirmed by confocal microscopy. No changes (P > 0.05) compared to Control (C) were found on thermal stability and composition of sausages formulated with direct addition of pectin (T1) and with incorporation of PEF (T2). However, in comparison with C, pH, color, and texture of T1 and T2 samples were affected (P < 0.05). Nevertheless, these changes had no influence (P > 0.05) on sensory acceptability of treated samples, and actually improved (P < 0.05) their texture acceptance. In vitro digestive degradation of triacylglycerols was decreased (P < 0.05) by 20% on T2 samples compared to control and it was superior (P < 0.05) to T1 (8%). Confocal images confirmed lipid digestibility reduction of T2 samples. Incorporation of PEF in a meat sausage offers a better protection against the hydrolytic action of lipases over triaclyglycerides, than a direct addition of pectin, without affecting its sensory acceptability. Therefore, it can be a potential strategy to reduce fat intake from meat products.Practical ApplicationReduction or replacement strategies tested to modify or decrease fat content in meat products usually leads to nondesirable sensory attributes. However, decreasing lipid digestibility by encapsulating animal fat with nondigestible pectin offers a new approach to reduce fat intake from full‐animal‐fat meat products, without affecting their sensory acceptability.
Change in Chemical Composition of Simmental Crossbred Cattle Milk Improved its Physicochemical, Nutritional, and Processed Properties
Authors: Li Xin , Ma Xin , Xiao Na , Long Wei , Wu Yong , Tong Ping , Chen Hongbing 
Published: May 2019

AbstractThis study aimed to evaluate a new milk resource from Simmental crossbred cattle, which could be an alternative raw milk for dairy products. In the experiment, physicochemical characterization of raw milk was evaluated according to the Standards. In addition, Simmental crossbred cattle milk (SHCM) samples had the higher contents of total amino acid than those of Chinese Holstein cow milk (HCM) samples, especially for Leu, Lys, Met, and Phe. We also observed the contents of protein, fat, and lactose in SHCM samples changed during 12 months, where in milk fat content was mostly affected by the season, followed by the lactose and protein contents. Moreover, texture profile analysis showed that yoghurt made from SHCM had stronger structures, which especially reflected in hardness and chewiness. The G’ of yoghurt made from SHCM during storage time was always higher than that made from HCM, indicating that SHCM yoghurt showed higher apparent viscosity values. Logically, the milk from Simmental crossbred cattle has desirable physicochemical characteristics and nutritional value, which could be a new better resource of dairy products.Practical ApplicationCompared with Chinese Holstein cattle, Simmental crossbred cattle have strong resistance to moist weather and better performance in disease resistance, which are particularly important for lactating cows persisting in south of China. We evaluated the nutritional values of SHCM and HCM, and compared the seasonal variation on chemical composition of SHCM sample. All the data could be used to produce different dairy products using raw milk from different seasons. In addition, textural properties of yoghurt made from two milks were also determined, and we suggested that SHCM could be used as a new resource candidate for developing dairy product in the future.
Retrogradation and Digestibility of Rice Starch Gels: The Joint Effect of Degree of Gelatinization and Storage
Authors: Denchai Naree , Suwannaporn Prisana , Lin Jenshinn , Soontaranon Siriwat , Kiatponglarp Worawikunya , Huang Tzou‐Chi 
Published: May 2019

AbstractRetrogradation affects acceptability of starchy foods; however, it is preferred in some products such as rice noodles. Amylose content, gelatinization temperature, and storage condition were reported to affect retrogradation but with disputed data. The joint effects of these parameters were interested in this study. Rice starch was gelatinized using different temperatures (77, 81, 95, and 121 °C) and stored isothermally with temperature cycles for 10 days. Results showed that the most important parameter that affected retrogradation was storage time followed by storage condition and gelatinization temperature. The recrystallization rate constant (k) and Avrami exponent (n) of retrograded starches stored under temperature cycle were higher than isothermal storage. All samples showed similar polymorphs of a mixture of B and V types. High‐temperature gelatinized starch gel stored under temperature cycle condition produced higher yield of resistant starch. The study provided useful information on how to apply these parameters to control the retrogradation of starchy foods, especially rice noodle.Practical ApplicationRetrogradation is found to be more prominent at higher gelatinization temperature and longer storage time. Resistant starch produced from retrograded starch depended largely on storage time than storage condition. This finding can be applied to improve rice noodle qualities (by increasing retrogradation) with lower digestibility (by producing higher resistant starch).
A Natural Peanut Edible Coating Enhances the Chemical and Sensory Stability of Roasted Peanuts
Authors: Martín María Paula , Riveros Cecilia Gabriela , Paredes Alejandro Javier , Allemandi Daniel Alberto , Nepote Valeria , Grosso Nelson Rubén 
Published: May 2019

AbstractThis study aims to assess the enhancement of the chemical and sensory properties of roasted peanuts during storage, through the application of high‐protein defatted peanut flour (DPF) coatings incorporated with and without antioxidants. The control sample without coating, packed in normal atmosphere (control), showed the highest conjugated dienes (CD) increment (from 1.17 on day 0 to 3.60 on day 180). Roasted peanuts without coating, packed in high barrier bags under vacuum, reached the lowest CD at day 180 (1.92). Conjugated trienes and peroxide values were analogous to CD. The control exhibited the greatest decrease in α‐tocopherol (from 27.65 mg/100 g on day 0 to 21.32 mg/100 g on day 180) and γ‐tocopherol (from 21.91 mg/100 g on day 0 to 14.99 mg/100 g on day 180). 3‐Methylpyridine and 2,5‐dimethylpyrazine decreased with storage time only for the control, which had the highest increase in oxidized flavor (from 0 on day 0 to 13.30 on day 180), cardboard (from 7.67 on day 0 to 15.23 on day 180), and astringency. The lowest decreases in roasted peanutty scores were seen in coated samples. DPF coatings delayed roasted peanuts oxidation, enhancing their sensory properties and shelf life compared with the control sample.Practical ApplicationDefatted peanut flour (DPF) is a byproduct obtained during peanut oil extraction and is a possible material for edible film preparation. This strategy adds value to the peanut industry by transforming a by‐product into a material with the potential to develop biodegradable and economical films. The application of this DPF‐based edible coating on the surface of roasted peanuts may have contributed to extent product's shelf life, allowing for coated products to be packaged in lower barrier and less expensive materials. Use of peanut material to coat peanuts avoids the risk of allergen protein cross contamination, which would be highly valuable for the food industry.
Managing Regional Conflict: The Gulf Cooperation Council and the Embargo of Qatar
Authors: Miller Rory 
Published: May 2019

AbstractThis article will explore the arrangement of and relations between states inside ROs as they move from conflict to negotiation, as well as the different types of negotiations that they choose – bilateral, mediated, multiparty, or hybrid. In doing so, it will illuminate the opportunities that exist at the regional level to develop inclusive regional frameworks for mediation and negotiation and, in the right circumstances, effective security communities. Broadly defined, a security community exists when sovereign states can overcome a lack of mutual trust and difficult regional environments to develop new forms of cooperative security that prioritize self‐restraint and the peaceful resolution of differences and reduce the expectation of the need to resort to organized violence to settle interstate disputes (Adler and Barnett, 1988; Adler and Greve, 2009).
Administration of melatonin for prevention of preterm birth and fetal brain injury associated with premature birth in a mouse model
Authors: Lee Ji Yeon , Song Haengseok , Dash Oyunbileg , Park Mira , Shin Na E. , McLane Michael W. , Lei Jun , Hwang Jong Yun , Burd Irina 
Published: May 2019

AbstractProblemMaternal inflammation leads to preterm birth and perinatal brain injury. Melatonin, through its anti‐inflammatory effects, has been shown to be protective against inflammation‐induced perinatal adverse effects. However, the immunomodulatory effects of melatonin on preterm birth and prematurity‐related morbidity remain unknown. We wanted to investigate the effects of maternally administered melatonin on preterm birth and perinatal brain injury in a mouse model of maternal inflammation.Method of studyA model of maternal inflammation employing lipopolysaccharide (LPS) was used to mimic the most common clinical scenario of preterm birth, that of maternal inflammation. Mice were randomly divided into the following groups: control, LPS, and LPS with melatonin pre‐treatment. Doppler ultrasonography was used to obtain fetal and maternal hemodynamic measurements in utero. Placenta and fetal brains were harvested and analyzed for proinflammatory markers and signs of perinatal brain injury, respectively. Surviving offspring were assessed for neuromotor outcomes.ResultsMelatonin pre‐treatment lowered the level of proinflammatory cytokines in the uterus and the placenta, significantly improved LPS‐induced acute fetal neuroinflammation and perinatal brain injury, as well as significantly upregulated the SIRT1/Nrf2 signaling pathway to reduce LPS‐induced inflammation. Melatonin also prevented adverse neuromotor outcomes in offspring exposed to maternal inflammation.ConclusionMaternally administered melatonin modulated immune responses to maternal inflammation and decreased preterm birth and perinatal brain injury. These results suggest that melatonin, a safe treatment during pregnancy, may be used as an experimental therapeutic in clinical trials.