bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proteins required for vacuolar function are targets of lysine polyphosphorylation in yeast
Authors: McCarthy Liam , Bentley-DeSousa Amanda , Denoncourt Alix , Tseng Yi-Chieh , Gabriel Matthew , Downey Michael 
Published: July 2019

ABSTRACTPolyphosphates (polyP) are long chains of inorganic phosphates that can be attached to lysine residues of target proteins as a non-enzymatic post-translational modification. This modification, termed polyphosphorylation, may be particularly prevalent in bacterial and fungal species that synthesize and store large quantities of polyP. In this study, we applied a proven screening strategy to evaluate the polyphosphorylation status of over 200 candidate targets in the budding yeastS. cerevisiae.We report 8 new polyphosphorylated proteins that interact genetically and physically with a previously identified network of targets implicated in ribosome biogenesis. The expanded target network includes vacuolar proteins Prb1 and Apl5, whose modification with polyP suggests a model for feedback regulation of polyP synthesis, while raising additional questions regarding the location of polyphosphorylationin vivo.
Emergence of consciousness and complexity amidst diffuse delta rhythms: the paradox of Angelman syndrome
Authors: Frohlich Joel , Bird Lynne M. , Dell’Italia John , Johnson Micah A. , Hipp Joerg F. , Monti Martin M. 
Published: July 2019

AbstractNumerous theories link consciousness to informationally rich, complex neural dynamics. This idea is challenged by the observation that children with Angelman syndrome (AS), while fully conscious, display a hypersynchronous electroencephalogram (EEG) phenotype typical of information-poor dynamics associated with unconsciousness. If informational complexity theories are correct, then sufficiently complex dynamics must still exist during wakefulness and exceed that observed in sleep despite pathological delta (1 – 4 Hz) rhythms in children with AS. As characterized by multiscale metrics, EEGs from 35 children with AS feature significantly greater complexity during wakefulness compared with sleep, even when comparing the most pathological segments of wakeful EEG to the segments of sleep EEG least likely to contain conscious experiences, and when factoring out delta power differences across states. These findings support theories linking consciousness with complexity and warn against reverse inferring an absence of consciousness solely on the basis of clinical readings of EEG.
A Survey and Systematic Assessment of Computational Methods for Drug Response Prediction
Authors: Chen Jinyu , Zhang Louxin 
Published: July 2019

AbstractDrug response prediction arises from both basic and clinical research of personalized therapy, as well as drug discovery for cancer and other diseases. With gene expression profiles and other omics data being available for over 1000 cancer cell lines and tissues, different machine learning approaches have been applied to solve drug response prediction problems. These methods appear in a body of literature and have been evaluated on different datasets with only one or two accuracy metrics. We systematically assessed 17 representative methods for drug response prediction, which have been developed in the past five years, on four large public datasets in nine metrics. This study provides insights and lessons for future research into drug response prediction.
Timescales of motor memory formation in dual-adaptation
Authors: Forano Marion , Franklin David W. 
Published: July 2019

AbstractThe timescales of adaptation to novel dynamics are well explained by a dual-rate model with slow and fast states. This model can predict interference, savings and spontaneous recovery, but cannot account for adaptation to multiple tasks, as each new task drives unlearning of the previously learned task. Nevertheless, in the presence of appropriate contextual cues, humans are able to adapt simultaneously to opposing dynamics. Consequently this model was expanded, suggesting that dual-adaptation occurs through a single fast process and multiple slow processes. However, such a model does not predict spontaneous recovery within dual-adaptation. Here we assess the existence of multiple fast processes by examining the presence of spontaneous recovery in two experimental variations of an adaptation-de-adaptation-error-clamp paradigm within dual-task adaptation in humans. In both experiments, evidence for spontaneous recovery towards the initially learned dynamics (A) was found in the error-clamp phase, invalidating the one-fast-two-slow dual-rate model. However, as adaptation is not only constrained to two timescales, we fit twelve multi-rate models to the experimental data. BIC model comparison again supported the existence of two fast processes, but extended the timescales to include a third rate: the ultraslow process. Even within our single day experiment, we found little evidence for decay of the learned memory over several hundred error-clamp trials. Overall, we show that dual-adaptation can be best explained by a two-fast-triple-rate model over the timescales of adaptation studied here. Longer term learning may require even slower timescales, explaining why we never forget how to ride a bicycle.Author SummaryRetaining motor skills is crucial to perform basic daily life tasks. However we still have limited understanding of the computational structure of these motor memories, an understanding that is critical for designing rehabilitation. Here we demonstrate that learning any task involves adaptation of independent fast, slow and ultraslow processes to build a motor memory. The selection of the appropriate motor memory is gated through a contextual cue. Together this work extends our understanding of the architecture of motor memories, by merging disparate computational theories to propose a new model.
MicroRNA-378 suppressed osteogenesis of mesenchymal stem cells and impaired bone formation via inactivating Wnt/β-catenin signaling
Authors: Feng Lu , Zhang Jin-fang , Shi Liu , Yang Zheng-meng , Wu Tian-yi , Wang Hai-xing , Lin Wei-ping , Lu Ying-fei , Lo Jessica Hiu Tung , Zhu Da-hai , Li Gang 
Published: July 2019

AbstractMicroRNAs (miRNAs) have been reported to serve as silencers to repress gene expression at post-transcriptional level. Multiple miRNAs have been demonstrated to play important roles in osteogenesis. MiR-378, a conserved miRNA, was reported to mediate bone metabolism and influence bone development, but the detailed function and underlying mechanism remain obscure. In this study, the miR-378 transgenic (TG) mouse was developed to study the role of miR-378 in osteogenic differentiation as well as bone formation. The abnormal bone tissues and impaired bone quality were displayed in the miR-378 TG mice, and a delayed healing effect was observed during bone fracture of the miR-378 TG mice. The osteogenic differentiation of MSCs derived from this TG mouse was also inhibited. We also found that miR-378 mimics suppressed while anti-miR-378 promoted osteogenesis of human MSCs. Two Wnt family members Wnt6 and Wnt10a were identified as bona fide targets of miR-378, and their expression were decreased by this miRNA, which eventually induced the inactivation of Wnt/β-catenin signaling. Finally, the sh-miR-378 modified MSCs were locally injected into the fracture sites in an established mouse fracture model. The results indicated that miR-378 inhibitor therapy could promote bone formation and stimulate healing process in vivo. In conclude, miR-378 suppressed osteogenesis and bone formation via inactivating Wnt/β-catenin signaling, suggesting miR-378 may be a potential therapeutic target for bone diseases.
JBrowse Connect: A server API to connect JBrowse instances and users
Authors: Yao Eric , Buels Robert , Sen Taner Z. , Stein Lincoln , Holmes Ian 
Published: July 2019

AbstractWe describe JBrowse Connect, an optional expansion to JBrowse that allows live messaging via WebSockets, notifications for new annotation tracks, heavy-duty analyses initiated by the user from within the browser, and other dynamic features. We present JBlast, an example application of JBrowse Connect that allows users to specify and execute BLAST searches, managed by a Galaxy instance, as well as tracking job progress and viewing results, all in the context of the browser.
The structural quality of maternal health services in primary health care facilities in Tanzania: Findings from a baseline study
Authors: Kapologwe Ntuli A. , Kalolo Albino , Isanzu Naomi H. , Borghi Josephine , Kibusi Stephen M. 
Published: July 2019

AbstractBackgroundStructural quality of maternal health services remains a key indicator of highly performing health care system. Evidence attest to the fact that introduction of the new interventions in the health care system does not necessarily lead into improvement of the target outcome, such as quality of health services delivered. This study aimed at assessing the structural quality of maternal health services prior to introduction of Direct Health Facility Financing (DHFF) program.MethodsThis was a cross-sectional study, conducted in 42 public primary health facilities between January and mid February 2018. Observational were used to collect the data from health facilities. The collected information was on privacy, hygiene and sanitation, obstetric emergences, sterilization, maternal death audit reviews and waste management. Collected data were analyzed by using SPSS.ResultsAll 42 (100%) primary health facilities that were assessed were public primary health facilities, of which 14 (33.3%) were health centers and 28 were dispensaries. The furthest primary health facilities from the district head office were 140 Kms and the nearest 2 Kms. Focusing on; - privacy, hygiene and sanitation, obstetric emergences, sterilization, maternal death audit reviews and waste management assessed eight areas of Structural qualities. Majority (68.9%) of Health Centers has less than 39 skilled staff while some of them they have up to 129 health service providers and majority (92.8%) of Dispensaries have less than 15 staff and some have 1 staff.By comparing Dispensary and Health center performances on structural quality indicated relatively low differences among the attributes assessed. Specifically, they did not show statistical significant differences except for obstetric emergencies (p < .005), sterilization (p=. 034) and overall structural quality (p=. 018). With regard to rural-urban performance on structural quality, there was no statistical significant difference on total performance. Similarly, there was no significant differences between rural and urban health facilities on other assessed attributes of structural quality (p >.05) except for sterilization in which urban facilities performed significantly higher than the rural facilities [M=41.2, SD=27.7, 61.3, SD=28.4, respectively (p= .028)]. On the other hand, marginal differences were observed on individual assessed attributes. For examples, rural facilities performed relatively higher than urban ones on privacy (41.2 and 32.0), maternal death reviews (31.4 and 30.7) and waste management (49.0 and 47.3) respectively.ConclusionGenerally facilities performed low on the structural quality indicators of maternal health services provision however; they had high performance on sterilization and emergence obstetric care.
Virtual screening identifies novel high-affinity σ1 receptor ligands
Authors: Greenfield Daniel A. , Schmidt Hayden R. , Sliz Piotr , Kruse Andrew C. 
Published: July 2019

AbstractThe σ1 receptor is a transmembrane protein implicated in several pathophysiological conditions, including neurodegenerative disease1, drug addiction2, cancer3, and pain4. However, there are no high-throughput functional assays for σ1 receptor drug discovery. Here, we assessed high-throughput structure-based computational docking for discovery of novel ligands of the σ1 receptor. We screened a library of over 6 million compounds using the Schrödinger Glide package, followed by experimental characterization of top-scoring candidates. 77% of tested candidates bound σ1 with high affinity (10-550 nM). These include compounds with high selectivity for the σ1 receptor compared to the genetically unrelated but pharmacologically similar σ2 receptor, as well as compounds with substantial cross-reactivity between the two receptors. These results establish structure-based virtual screening as a highly effective platform for σ1 receptor ligand discovery.
Aging Skeletal Muscle Proteomics Finds Changes in Spliceosome, Immune factors, Proteostasis and Mitochondria
Authors: Ubaida-Mohien Ceereena , Lyashkov Alexey , Gonzalez-Freire Marta , Tharakan Ravi , Shardell Michelle , Moaddel Ruin , Semba Richard D. , Chia Chee W. , Gorospe Myriam , Sen Ranjan , Ferrucci Luigi 
Published: July 2019

AbstractA progressive decline of skeletal muscle strength with aging is a primary cause of mobility loss and frailty in older persons, but the molecular mechanisms of such decline are not fully understood. Here, using quantitative discovery proteomic data from skeletal muscle specimens collected from 58 healthy persons aged 20 to 87 years show that ribosomal proteins and proteins related to energetic metabolism, including those related to the TCA cycle, mitochondria respiration, and glycolysis were underrepresented in older persons. Proteins with important roles in innate and adaptive immunity, involved in proteostasis and regulation of alternative splicing were all overrepresented in muscle from older persons. Changes with aging of alternative splicing were confirmed by RNA-seq. Overall, older muscle has a profound deficit of energetic metabolism, a pro-inflammatory environment and increased proteostasis. Upregulation of the splicing machinery maybe an attempt to compensate for these changes and this could be tested in future studies.
A novel method for merging academic social network ontologies using formal concept analysis and hybrid semantic similarity measure
Authors: Priya M. , Ch. Aswani Kumar 
Published: July 2019

Purpose
The purpose of this paper is to merge the ontologies that remove the redundancy and improve the storage efficiency. The count of ontologies developed in the past few eras is noticeably very high. With the availability of these ontologies, the needed information can be smoothly attained, but the presence of comparably varied ontologies nurtures the dispute of rework and merging of data. The assessment of the existing ontologies exposes the existence of the superfluous information; hence, ontology merging is the only solution. The existing ontology merging methods focus only on highly relevant classes and instances, whereas somewhat relevant classes and instances have been simply dropped. Those somewhat relevant classes and instances may also be useful or relevant to the given domain. In this paper, we propose a new method called hybrid semantic similarity measure (HSSM)-based ontology merging using formal concept analysis (FCA) and semantic similarity measure.

Design/methodology/approach
The HSSM categorizes the relevancy into three classes, namely highly relevant, moderate relevant and least relevant classes and instances. To achieve high efficiency in merging, HSSM performs both FCA part and the semantic similarity part.

Findings
The experimental results proved that the HSSM produced better results compared with existing algorithms in terms of similarity distance and time. An inconsistency check can also be done for the dissimilar classes and instances within an ontology. The output ontology will have set of highly relevant and moderate classes and instances as well as few least relevant classes and instances that will eventually lead to exhaustive ontology for the particular domain.

Practical implications
In this paper, a HSSM method is proposed and used to merge the academic social network ontologies; this is observed to be an extremely powerful methodology compared with other former studies. This HSSM approach can be applied for various domain ontologies and it may deliver a novel vision to the researchers.

Originality/value
The HSSM is not applied for merging the ontologies in any former studies up to the knowledge of authors.
Trichophyton tonsurans‐induced kerion celsi with decreased defensin expression and paradoxically increased interleukin‐17A production
Authors: Goto Yoshihiro , Suzuki Takahiro , Suzuki Yoko , Anzawa Kazushi , Mochizuki Takashi , Tamura Takashi , Makimura Koichi , Aoshima Masahiro , Ito Taisuke , Tokura Yoshiki 
Published: July 2019

AbstractWe report a case of kerion celsi due to Trichophyton tonsurans. An 18‐year‐old male student judo practitioner had alopecic patches, black dots and subcutaneous abscesses on the right temporal region. The damaged hair represented endothrix infection with T. tonsurans, as assessed by mycological examinations. He was treated with oral itraconazole without any therapeutic effect, followed by terbinafine with good effect. A skin biopsy showed neutrophil, lymphocyte and histiocyte infiltration into the dermis and subcutaneous tissue with abscesses around a number of dilated hair follicles. Immunostaining showed that the expression level of human β‐defensin 2 (HBD‐2) was decreased in the epidermis of the alopecic and adjacent skin. Because interleukin (IL)‐17A generally induces HBD‐2 production by epidermal keratinocytes, we also immunohistochemically investigated IL‐17A expression. Unexpectedly, many IL‐17A‐bearing cells were found around destructed hair follicles, indicating that IL‐17A expression was not attenuated, but rather increased in the skin lesion. Our case suggests that IL‐17A‐upregulated antimicrobial peptide expression is disordered in kerion celsi, and severe inflammation with IL‐17A may cause tissue damage and resultant scar.
Effects of forest windstorm disturbance on invasive plants in protected areas of southern Illinois, USA
Authors: Daniels Melissa K. , Larson Eric R. 
Published: July 2019

Abstract

Invasive plant populations respond positively to light increase from windstorm‐caused canopy damage, but are typically out‐competed over time as the tree canopy recovers. Some invasive plants have the ability to slow or even completely prevent canopy regrowth. It is important to understand invasive plant dynamics in windstorm blowdowns to inform effective forest management. We hypothesized that blowdown areas are more invaded than unaffected forest and that invadedness of a blowdown will decrease with increasing time since disturbance and increase with disturbance magnitude.

We used Landsat imagery to identify 31 blowdowns caused by one of three storms in southern Illinois of the United States: 2006 tornado, 2009 derecho or 2017 tornado. We statistically matched these blowdowns to areas of unaffected forest based on slope, aspect, elevation, distance to a road and distance to a trail. We surveyed blowdown and unaffected units for invasive plants in summer 2018. Disturbance magnitude was measured in two ways: per cent change in normalized difference vegetation index (NDVI) and area of blowdown.

Overall, blowdowns were more invaded than their statistically matched areas. Invadedness of blowdowns decreased with increasing time since disturbance, indicating that the blowdowns are recovering as tree canopy regrowth shades out invasive plants. Per cent change in NDVI was not a supported predictor of blowdown invadedness, but invadedness was strongly positively related to blowdown size. Larger blowdowns recover more slowly than smaller disturbances due to different recovery pathways, providing more time and opportunity for the spread and establishment of invasive plants.

Synthesis. Our findings suggest that although blowdowns contained higher cover of invasive plants than forest unaffected by windstorms, invasive plants were responding negatively to canopy regrowth. Land managers should prioritize treatment of invasive plants in larger and more recent blowdowns.
The impact of supplementing goats' milk with quinoa extract on some properties of yoghurt
Authors: El‐Shafei Samah M S , Sakr Sally S , Abou‐Soliman Nagwa H I 
Published: July 2019

This study investigated the impact of supplementing goats' milk with quinoa extracts, in the range of 5, 10 and 15 g/100 g on the milk fermentation. The properties of yoghurt produced from this milk, which include viscosity, microstructure and sensory acceptability, were assessed. The supplementation of goats' milk with quinoa extracts, particularly permeate extract, reduced the fermentation time and enhanced the viability of lactic acid bacteria. Supplementation of yoghurt with increased levels of quinoa extracts increased the apparent viscosity and changed the yoghurt protein matrix. Panellists highly accepted the yoghurt that contained quinoa permeate extract.
A Review of Hot Beverage Temperatures—Satisfying Consumer Preference and Safety
Authors: Abraham John , Diller Kenneth 
Published: July 2019

AbstractHot beverages are served ubiquitously in the food‐service industry as well as at residences and other venues. Coffee and tea beverages, in particular, are brewed at temperatures that are sufficiently high to cause immediate and serious risk for scald injuries. On the other hand, numerous research studies have been performed to identify the preferred consumption temperatures for hot beverages. The outcome of these mutually reinforcing studies is that the preferred drinking temperatures are significantly below the often‐encountered brewing temperatures (∼200 °F). Consequently, there is great need to distinguish brewing temperatures from serving temperatures. Serving consumers beverages at very high temperatures is not only unnecessary (from a preference standpoint) but also unsafe. An appropriate range for service temperatures is (130 to 160 °F).Practical ApplicationOften times, hot beverages are served at temperatures near their brewing temperature; far hotter than preferred by consumers. This practice creates unnecessary risk to the consumer. A more rationale recommended range of service temperatures is 130 to 160 °F. This recommendation balances a range of consumer preferences and safety.
Blue–green opponency and trichromatic vision in the greenhouse whitefly (Trialeurodes vaporariorum) explored using light emitting diodes
Authors: Stukenberg Niklas , Poehling Hans‐Michael 
Published: July 2019

AbstractVisual orientation in the greenhouse whitefly (Trialeurodes vaporariorum Westwood, Hemiptera: Aleyrodidae) is the result of “wavelength‐specific behaviours.” Green–yellow elicits “settling behaviour” while ultraviolet (UV) radiation initiates “migratory behaviour.” The only available physiological study of the photoreceptors' spectral efficiency showed peaks in the green and the UV range and whitefly vision was said to be dichromatic so far. In order to study the visual behaviour of T. vaporariorum, 19 narrow‐bandwidth light emitting diodes (LEDs) covering the UV‐A and visible range were used in combination with light scattering acrylic glass screens in a small‐scale choice arena under greenhouse conditions. Multiple‐choice and dual‐choice assays were performed, resulting in LED‐based behavioural action spectra of settling (green) and migratory behaviour (UV). A potential inhibitory blue–green chromatic mechanism was studied by combining yellow with different bluish LEDs. Intensity dependencies were illustrated by changing LED intensities. Regarding the “settling response,” highest attraction was achieved by a green LED with a centroid wavelength of 550 nm, while a blue LED with 469 nm proved to be most inhibitory. Besides this inhibitory interaction, an intensity dependence was observed within the action spectrum in the green–yellow range. “Migratory behaviour” was elicited the most by the UV LED with the shortest available wavelength of 373 nm. The results provide compelling behavioural evidence for the presence of a green and a yet undescribed blue sensitive photoreceptor and a blue–green opponent mechanism. Furthermore, empirical colour choice models were built and receptor peaks were estimated around 510–520 nm (green), 480–490 nm (blue) and 340–370 nm (UV). Consequently, a trichromatic receptor setup is suggested for T. vaporariorum.