bluuebunny/crossref_metadata_2025_split huggingface dataset:
Insulin-induced Effects on the Subcellular Localization of AKT1, AKT2 and AS160 in Rat Skeletal Muscle
Authors: Zheng Xiaohua , Cartee Gregory D. 
Published: December 2016

AbstractAKT1 and AKT2, the AKT isoforms that are highly expressed in skeletal muscle, have distinct and overlapping functions, with AKT2 more important for insulin-stimulated glucose metabolism. In adipocytes, AKT2 versus AKT1 has greater susceptibility for insulin-mediated redistribution from cytosolic to membrane localization, and insulin also causes subcellular redistribution of AKT Substrate of 160 kDa (AS160), an AKT2 substrate and crucial mediator of insulin-stimulated glucose transport. Although skeletal muscle is the major tissue for insulin-mediated glucose disposal, little is known about AKT1, AKT2 or AS160 subcellular localization in skeletal muscle. The major aim of this study was to determine insulin’s effects on the subcellular localization and phosphorylation of AKT1, AKT2 and AS160 in skeletal muscle. Rat skeletal muscles were incubated ex vivo ± insulin, and differential centrifugation was used to isolate cytosolic and membrane fractions. The results revealed that: 1) insulin increased muscle membrane localization of AKT2, but not AKT1; 2) insulin increased AKT2 phosphorylation in the cytosol and membrane fractions; 3) insulin increased AS160 localization to the cytosol and membranes; and 4) insulin increased AS160 phosphorylation in the cytosol, but not membranes. These results demonstrate distinctive insulin effects on the subcellular redistribution of AKT2 and its substrate AS160 in skeletal muscle.
Hearing Loss and Cognitive-Communication Test Performance of Long-Term Care Residents With Dementia: Effects of Amplification
Authors: Hopper Tammy , Slaughter Susan E. , Hodgetts Bill , Ostevik Amberley , Ickert Carla 
Published: December 2016

Purpose
The study aims were (a) to explore the relationship between hearing loss and cognitive-communication performance of individuals with dementia, and (b) to determine if hearing loss is accurately identified by long-term care (LTC) staff. The research questions were (a) What is the effect of amplification on cognitive-communication test performance of LTC residents with early- to middle-stage dementia and mild-to-moderate hearing loss? and (b) What is the relationship between measured hearing ability and hearing ability recorded by staff using the Resident Assessment Instrument–Minimum Data Set 2.0 (RAI-MDS; Hirdes et al., 1999)?

Method
Thirty-one residents from 5 long-term care facilities participated in this quasiexperimental crossover study. Residents participated in cognitive-communication testing with and without amplification. RAI-MDS ratings of participants' hearing were compared to audiological assessment results.

Results
Participants' speech intelligibility index scores significantly improved with amplification; however, participants did not demonstrate significant improvement in cognitive-communication test scores with amplification. A significant correlation was found between participants' average pure-tone thresholds and RAI-MDS ratings of hearing, yet misclassification of hearing loss occurred for 44% of participants.

Conclusions
Measuring short-term improvement of performance-based cognitive communication may not be the most effective means of assessing amplification for individuals with dementia. Hearing screenings and staff education remain necessary to promote hearing health for LTC residents.
Function-theoretic solution to a class of dual integral equations and an application to diffraction theory
Authors: Schmeltzer Robert A. , Lewin Myrna 
Published: December 2016

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\int _0^\infty {{u^\lambda }f\left ( u \right ){J_\mu }\left ( {ru} \right )du = g\left ( r \right ),0 > r > 1, \\ \int _0^\infty u {{\left ( {{u^2} + {a^2}} \right )}^{ - 1/2}}f\left ( u \right ){J_v}\left ( {ru} \right )du = h\left ( r \right ),} 1 > r > \infty ,

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A general framework for association analysis of microbial communities on a taxonomic tree
Authors: Tang Zheng-Zheng , Chen Guanhua , Alekseyenko Alexander V , Li Hongzhe 
Published: December 2016

AbstractMotivationAssociation analysis of microbiome composition with disease-related outcomes provides invaluable knowledge towards understanding the roles of microbes in the underlying disease mechanisms. Proper analysis of sparse compositional microbiome data is challenging. Existing methods rely on strong assumptions on the data structure and fail to pinpoint the associated microbial communities.ResultsWe develop a general framework to: (i) perform robust association tests for the microbial community that exhibits arbitrary inter-taxa dependencies; (ii) localize lineages on the taxonomic tree that are associated with covariates (e.g. disease status); and (iii) assess the overall association of the whole microbial community with the covariates. Unlike existing methods for microbiome association analysis, our framework does not make any distributional assumptions on the microbiome data; it allows for the adjustment of confounding variables and accommodates excessive zero observations; and it incorporates taxonomic information. We perform extensive simulation studies under a wide-range of scenarios to evaluate the new methods and demonstrate substantial power gain over existing methods. The advantages of the proposed framework are further demonstrated with real datasets from two microbiome studies. The relevant R package miLineage is publicly available.Availability and ImplementationmiLineage package, manual and tutorial are available at https://medschool.vanderbilt.edu/tang-lab/software/miLineage.Supplementary informationSupplementary data are available at Bioinformatics online.
Openness and Closure in the Later Medieval Village*
Authors: Mileson Stephen 
Published: December 2016

Abstract
There is a growing scholarly interest in the daily life and perceptions of ordinary medieval people, yet there has been little attempt to conceptualise the social space of the rural settlements in which the great majority of the population lived. This article examines how a village or hamlet in England might have been used and perceived in the later Middle Ages (c.1200 to 1500), especially in terms of access and permeability—in other words how open or closed (or, more crudely, ‘public’ or ‘private’) the components of a settlement were, and how the spatial relationships between these components affected their use and social significance. The data are drawn mainly from lowland England, with a special focus on Ewelme hundred in Oxfordshire, an area of mixed countryside including open-field villages and dispersed wood-pasture settlements. It will be argued that differences in openness and closure across space and time supply a guide to rural social interaction as a whole.
Local Zinc Chloride Release From a Calcium Sulfate Carrier Enhances Fracture Healing
Authors: Krell Ethan S. , Ippolito Joseph A. , Montemurro Nicholas J. , Lim Phillip H. , Vincent Richard A. , Hreha Jeremy , Cottrell Jessica , Sudah Suleiman Y. , Muñoz Maximilian F. , Pacific Kristen P. , Benevenia Joseph , O'Connor J. Patrick , Lin Sheldon S. 
Published: December 2016

Background:
This study examined the efficacy of calcium sulfate (CaSO4) as a carrier for intramedullary delivery of zinc chloride (ZnCl2) to treat fracture healing in a BB Wistar rat model. A non–carrier-mediated injection of 3.0 mg/kg of ZnCl2 has previously been shown to enhance fracture healing.

Methods:
A heterogeneous mixture of ZnCl2 and CaSO4 was administered into the intramedullary femoral canal and a mid-diaphyseal femur fracture was created unilaterally. Early and late parameters of fracture healing were assessed using biomechanical testing, radiographic scoring, quantitative histomorphometry (for percentage of new cartilage and bone within the fracture callus), and long-term histologic evaluation.

Results:
Fractures treated with 1.0 mg/kg of ZnCl2/CaSO4 demonstrated a significantly higher maximum torque to failure compared with both CaSO4 (P = 0.048) and saline (P = 0.005) controls at 4 weeks postfracture (396.4 versus 251.3 versus 178.7 N mm, respectively). Statistically significant increases in torsional rigidity, effective shear modulus, and effective shear stress were also found, as well as a 3.5 times increase in radiographic score (based on bone union). Histologic examination of the fracture callus indicated enhanced chondrogenesis at day 14 postfracture, with increased percent cartilage for the ZnCl2/CaSO4 group compared with saline (P = 0.0004) and CaSO4 (P = 0.0453) controls. Long-term radiographic and histologic evaluation revealed no abnormal bone formation or infection up to 12 weeks postoperatively.

Conclusions:
The effective dose of ZnCl2 augmentation for the enhancement of fracture healing in rats was reduced 3-fold in this study compared with previous findings. Furthermore, CaSO4 acted synergistically with ZnCl2 to increase the mechanical strength and stability at the fracture site.
A Novel Reconstructive Procedure for the Divided Nevus of the Eyelids Using a Tissue Expander
Authors: Yamamichi Kosaku , Kosaka Masaaki 
Published: December 2016

Summary:
Expanded local flaps and skin grafts (expanded/nonexpanded) are a common approach for reconstructing medium (1.5–20 cm) and large (>20 cm) divided nevi of the eyelids. However, this approach does not often provide a satisfactory cosmetic result, particularly in Asian patients, because of different skin types. We recently devised a new surgical procedure using an extended cheek flap and tissue expander for the medium-sized divided nevus of the eyelids. The upper and lower eyelids are concurrently reconstructed by divided flaps. This method is an effective treatment method for the medium-sized divided nevus of the eyelids and can be applied in total reconstruction of the eyelids in the future. This article presents our novel technique and is illustrated using a brief case report.
STRUCTURAL AND FUNCTIONAL MONITORING OF EXTRAMACULAR CYSTOID SPACES IN A CASE OF X-LINKED RETINOSCHISIS TREATED WITH ACETAZOLAMIDE
Authors: Collison Frederick T. , Fishman Gerald A. 
Published: December 2016

Background:
Carbonic anhydrase inhibitors (CAIs) have been shown to have a beneficial effect on cystoid macular edema in X-linked retinoschisis (XLRS) and other inherited retinal conditions. The effect of CAIs outside the macula has been less well studied.

Methods:
Snellen visual acuity, spectral-domain optical coherence tomography (SD-OCT), kinetic visual field, and dark-adapted single-flash full-field electroretinogram (ERG) testing were all done at baseline and at least one follow-up visit. A 55-year-old male diagnosed with XLRS exhibited extensive macular and extramacular cystoid splitting in the right eye and was treated with oral extended-release acetazolamide 500 mg/day.

Results:
By 6 months of follow-up on acetazolamide treatment, SD-OCT demonstrated resolution of cystoid spaces both within the macula and out to the midperiphery. Visual acuity improved from 20/70 to 20/30. The full-field ERG was distinctly electronegative at both baseline and at a follow-up visit, with oscillatory potentials becoming more apparent at the follow-up visit. Peripheral visual field boundaries did not change significantly.

Conclusion:
This report demonstrates structural resolution of cystoid spaces throughout much of the retina in a patient with XLRS, adding to a published case report in which we first noted that extramacular cystoid spaces observed in XLRS may respond to CAI treatment. To our knowledge, this is the first reported study of follow-up functional studies (ERG and perimetry) in a CAI treatment responder with XLRS.
Unusual Presentations of Childhood Systemic Lupus Erythematosus to the Emergency Department
Authors: Gültekingil Keser Ayşe , Ertuğrul İlker , Tekşam Özlem , Konuşkan Bahadir , Özkutlu Süheyla , Özen Seza 
Published: December 2016

Introduction
Systemic lupus erythematosus (SLE) is a multisystemic autoinflammatory disease that can involve any organ system; therefore, diagnosis can be challenging. Hereby, we present 4 cases that presented to pediatric emergency department with unusual clinical pictures of SLE.

Cases
Case 1 presented with inability to walk or talk for the last 1 week as well as intermittent pain and swelling in her joints. Case 2 presented with generalized edema and severe dyspnea. Case 3 and 4 presented to pediatric emergency department with rashes on the legs.

Discussion
Systemic lupus erythematosus may mimic many clinical entities, and differential diagnosis may be difficult, especially if presentation is atypical. In every emergency physician, right diagnosis and prompt treatment are very important especially in life-threatening conditions such as cardiac involvement in SLE.
Quantitative Analysis of Dopamine Neuron Subtypes Generated from Mouse Embryonic Stem Cells
Authors: Dingle Yu-Ting L. , Xiong Katherine B. , Machan Jason T. , Seymour Kimberly A. , Ellisor Debra , Hoffman-Kim Diane , Zervas Mark 
Published: December 2016

AbstractDopamine (DA) neuron subtypes modulate specific physiological functions and are involved in distinct neurological disorders. Embryonic stem cell (ESC) derived DA neurons have the potential to aid in the study of disease mechanisms, drug discovery, and possibly cell replacement therapies. DA neurons can be generated from ESCs in vitro, but the subtypes of ESC-derived DA neurons have not been investigated in detail despite the diversity of DA neurons observed in vivo. Due to cell culture heterogeneity, sampling methods applied to ESC-derived cultures can be ambiguous and potentially biased. Therefore, we developed a quantification method to capture the depth of DA neuron production in vitro by estimating the error associated with systematic random sampling. Using this method, we quantified calbindin+ and calretinin+ subtypes of DA neurons generated from mouse ESCs. We found a higher production of the calbindin+ subtype (11−27%) compared to the calretinin+ subtype (2-13%) of DA neuron; in addition, DA neurons expressing neither subtype marker were also generated. We then examined whether exogenous sonic hedgehog (SHH) and fibroblast growth factor 8 (FGF8) affected subtype generation. Our results demonstrate that exogenous SHH and FGF8 did not alter DA neuron subtype generation in vitro. These findings suggest that a deeper understanding DA neuron derivation inclusive of mechanisms that govern the in vitro subtype specification of ESC-derived DA neurons is required.NoteAll research was planned and conducted while members were at Brown UniversityResearch fundingNIH/NCRR/NIGMS RI Hospital COBRE Center for Stem Cell Biology (8P20GM103468-04) (MZ) Brown Institute for Brain Science Pilot Grant (4-63662) (MZ/DHK)
The triple-flash illusion reveals a driving role of alpha-band reverberations in visual perception
Authors: Gulbinaite Rasa , İlhan Barkin , VanRullen Rufin 
Published: December 2016

ABSTRACTThe modulatory role of spontaneous brain oscillations on perception of threshold-level stimuli is well established. Here, we provide evidence that alpha-band (7-14 Hz) oscillations not only modulate but also can drive perception. We used the “triple-flash” illusion: Occasional perception of three flashes when only two spatially-coincident veridical ones are presented, separated by ~100 ms. The illusion was proposed to result from superposition of two hypothetical oscillatory impulse response functions (IRF) generated in response to each flash (Bowen, 1989). In Experiment 1, we varied stimulus onset asynchrony (SOA) and validated Bowen's theory: the optimal SOA for illusion to occur was correlated, across subjects, with the subject-specific IRF period. Experiment 2 revealed that pre-stimulus parietal alpha EEG phase and power, as well as post-stimulus alpha phase-locking, together determine the occurrence of the illusion on a trial-by-trial basis. Thus, oscillatory reverberations create something out of nothing – a third flash where there are only two.
CONTINUATION: Evaluation of adaptive somatic models in a gold standard whole genome somatic dataset
Authors: Campagne Fabien 
Published: December 2016

ABSTRACTInhttp://dx.doi.org/10.1101/079087, we presented adaptive models for calling somatic mutations in high-throughput sequencing data. These models were developed by training deep neural networks with semi-simulated data. In this continuation, I evaluate how such models can predict known somatic mutations in a real dataset. To address this question, I tested the approach using samples from the International Cancer Genome Consortium (ICGC) and the previously published ground-truth mutations (GoldSet). This evaluation revealed that training models with semi-simulation does produce models that exhibit strong performance in real datasets. I found a linear relationship between the performance observed on a semi-simulated validation set and independent ground-truth in the gold set (R2= 0.952,P< 2−16). I also found that semi-simulation can be used to pre-train models before continuing training with true labels and that this pre-training improves model performance substantially on the real dataset compared to training models only with the real dataset. The best model pre-trained with semi-simulation achieved an AUC of 0.969 [0.957-0.982] (95% confidence interval) compared to 0.911 [0.890-0.932] when training with real labels only. These data demonstrate that semi-simulation can be a very effective approach to training filtering and ranking probabilistic models.
Cultivation and genomics of the first freshwater SAR11 (LD12) isolate
Authors: Henson Michael W. , Lanclos V. Celeste , Faircloth Brant C. , Thrash J. Cameron 
Published: December 2016

AbstractEvolutionary transitions between fresh and salt water happen infrequently among bacterioplankton. Within the ubiquitous and highly abundant heterotrophic Alphaproteobacteria orderPelagibacterales(SAR11), most members live in marine habitats, but the LD12 subclade has evolved as a unique freshwater lineage. LD12 cells occur as some of the most dominant freshwater bacterioplankton, yet this group has remained elusive to cultivation, hampering a more thorough understanding of its biology. Here, we report the first successful isolation of an LD12 representative, strain LSUCC0530, using high throughput dilution to extinction cultivation methods, and its complete genome sequence. Growth experiments corroborate ecological data suggesting active populations of LD12 in brackish water up to salinities of ~5. LSUCC0530 has the smallest closed genome thus far reported for a SAR11 strain (1.16 Mbp). The genome affirms many previous metabolic predictions from cultivation-independent analyses, like a complete Embden-Meyerhof-Parnas glycolysis pathway, but also provides novel insights, such as the first isocitrate dehydrogenase in LD12, a likely homologous recombination of malate synthase from outside of the SAR11 clade, and analogous substitutions of ion transporters with others that occur throughout the rest of the SAR11 clade. Growth data support metagenomic recruitment results suggesting temperature-based ecotype diversification within LD12. Key gene losses for osmolyte uptake provide a succinct hypothesis for the evolutionary transition of LD12 from salt to fresh water. For strain LSUCC0530, we propose the provisional nomenclatureCandidatusFonsibacter ubiquis.
Correlated Evolution of Metabolic Functions over the Tree of Life
Authors: Patterson Murray , Bernard Thomas , Kahn Daniel 
Published: December 2016

AbstractWe are interested in the structure and evolution of metabolism in order to better understand its complexity. We study metabolic functions in 1459 species within which several hundreds of thousands of families of homologous genes have been identified [17]. Given a protein sequence, PRIAM search [5] delivers probabilities of the presence of several thousand enzymes (ECs). This allows us to infer reaction sets and to construct a metabolic network for an organism, given its set of sequences.We then propagate these ECs to the ancestral nodes of the species tree using maximimum likelihood methods. These evolutionary scenarios are systematically compared using pairwise mutual information. We identify co-evolving enzyme sets from the graph of these relationships using community detection algorithms [1,3]. This sheds light on the structure of the metabolic networks in terms of co-evolving metabolic modules. These modules are also interpreted from a functional perspective using stoichiometric models of metabolic networks.
Openspritzer: an open hardware pressure ejection system for reliably delivering picolitre volumes
Authors: Forman C.J. , Tomes H. , Mbobo B. , Baden T. , Raimondo J.V. 
Published: December 2016

AbstractThe ability to reliably and precisely deliver picolitre volumes is an important component of biological research. Here we describe a high-performance, low-cost, open hardware pressure ejection system (Openspritzer), which can be constructed from off the shelf components. When connected to a standard micro-pipetteviasuitable pneumatic tubing, the device is capable of delivering minute doses of reagents to a wide range of biological and chemical systems. In this work, we characterise the performance of the device and compare it to a popular commercial system using two-photon fluorescence microscopy. We found that Openspritzer provides the same level of control over delivered reagent dose as the commercial system. Next, we demonstrate the utility of Openspritzer in a series of standard neurobiological applications. First, we used Openspritzer to deliver precise amounts of the neurotransmitters glutamate and GABA to hippocampal neurons to elicit time- and dose-precise excitatory and inhibitory responses, respectively. Second, we used Openspritzer to deliver infectious viral and bacterial agents to living tissue. Viral transfection of hippocampal interneurons with channelrhodopsin allowed for the optogenetic manipulation of hippocampal circuitry with light. Finally, we successfully used Openspritzer to infect organotypic hippocampal slice cultures with fluorescentMycobacterium bovisbacilli. We anticipate that due to its high performance and low cost Openspritzer will be of interest to a broad range of researchers working in the life and physical sciences.
A polymerisation-associated conformational switch in FtsZ that enables treadmilling
Authors: Wagstaff James M. , Tsim Matthew , Oliva María A. , García-Sanchez Alba , Kureisaite-Ciziene Danguole , Andreu José Manuel , Löwe Jan 
Published: December 2016

AbstractBacterial cell division in many organisms involves a constricting cytokinetic ring that is orchestrated by the tubulin-like protein FtsZ. FtsZ forms dynamic filaments close to the membrane at the site of division that have recently been shown to treadmill around the division ring, guiding septal wall synthesis.Here, using X-ray crystallography ofStaphylococcus aureusSaFtsZ we reveal how an FtsZ can adopt two functionally distinct conformations, open and closed. The open form is found in SaFtsZ filaments formed in crystals and also in soluble filaments ofE. coliFtsZ as deduced by cryoEM. The closed form is found within several crystal forms of two non-polymerising SaFtsZ mutants and corresponds to many previous FtsZ structures from other organisms.We argue that FtsZ undergoes a polymerisation-associated conformational switch. We show that such a switch provides explanations for both how treadmilling may occur within a single-stranded filament, and why filament assembly is cooperative.