bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamic interhemispheric coordination in face processing
Authors: Lu Zhengang , Guo Bingbing , Meng Ming 
Published: June 2017

AbstractOur conscious experience of the world is normally unified. The brain coordinates different processes from the left and right hemispheres into one experience. However, the neural mechanisms underlying interhemispheric coordination remain poorly understood. A mechanistic approach to understanding interhemispheric coordination is “communication through coherence” (Fries, 2005; 2015). Using a recently developed time-resolved psychophysics (Fiebelkorn, Saalmann, & Kastner, 2013; Landau & Fries, 2012; Song, Meng, Chen, Zhou, & Luo, 2014), combined with fMRI decoding method, we investigated the interhemispheric coordination through coherence, by focusing on a quintessential case of hemispheric lateralized brain function: face processing in the left and right fusiform face area (FFA). We observed coherent oscillatory fMRI multi-voxel patterns in the left and right FFA when two stimuli presented successively cross visual fields, either initiating coordination from the left hemisphere or right hemisphere. When interhemispheric coordination started from the dominant right hemisphere, a coherent 44° phase difference between the left and right FFA in 3-4 Hz was observed; whereas when interhemispheric coordination started from the non-dominant left hemisphere, a coherent −17° phase difference between the left and right FFA in 5.5-6.5 Hz was observed. These results suggest that different phase coherence might mediate the interhemispheric coordination of face perception, depending on whether the initiating hemisphere is dominant or non-dominant. Our findings provide compelling fMRI evidence for interhemispheric coordination through coherence. The time-resolved fMRI decoding approach would be a useful starting point for a more promising approach for future investigation in interhemispheric dynamic coordination with fine-grained spatial and temporal resolution.
Post-exercise cold-water immersion increases Na+,K+-ATPase α2-isoform mRNA content in parallel with elevated Sp1 expression in human skeletal muscle
Authors: Christiansen Danny , Murphy Robyn M. , Broatch James R. , Bangsbo Jens , McKenna Michael J. , Kuang Jujiao , Bishop David J. 
Published: June 2017

AbstractWe investigated the effect of a session of sprint-interval exercise on the mRNA content of NKA isoforms (α1-3, β1-3) and FXYD1 in human skeletal muscle. To explore some of the cellular stressors involved in this regulation, we evaluated the association between these mRNA responses and those of the transcription factors Sp1, Sp3 and HIF-1α. Given cold exposure perturbs muscle redox homeostasis, which may be one mechanism important for increases in NKA-isoform mRNA, we also explored the effect of post-exercise cold-water immersion (CWI) on the mRNA responses. Muscle was sampled from nineteen men before (Pre) and after (+0h, +3h) exercise plus passive rest (CON, n=10) or CWI (10°C; COLD, n=9). In COLD, exercise increased NKAα2and Sp1 mRNA (+0h, p<0.05). These genes remained unchanged in CON (p>0.05). In both conditions, exercise increased NKAα1, NKAβ3and HIF-1α mRNA (+3h; p <0.05), decreased NKAβ2mRNA (+3h; p<0.05), whereas NKAα3, NKAβ1, FXYD1 and Sp3 mRNA remained unchanged (p>0.05). These human findings highlight 1) sprint-interval exercise increases the mRNA content of NKA α1and β3, and decreases that of NKA β2, which may relate, in part, to exercise-induced muscle hypoxia, and 2) post-exercise CWI augments NKAα2mRNA, which may be associated with promoted Sp1 activation.
DNA isolation protocol effects on nuclear DNA analysis by microarrays, droplet digital PCR, and whole genome sequencing, and on mitochondrial DNA copy number estimation
Authors: Nacheva Elizabeth , Mokretar Katya , Soenmez Aynur , Pittman Alan M , Grace Colin , Valli Roberto , Ejaz Ayesha , Vattathil Selina , Maserati Emanuela , Houlden Henry , Taanman Jan-Willem , Schapira Anthony H , Proukakis Christos 
Published: June 2017

AbstractPotential bias introduced during DNA isolation is inadequately explored, although it could have significant impact on downstream analysis. To investigate this in human brain, we isolated DNA from cerebellum and frontal cortex using spin columns under different conditions, and salting-out. We first analysed DNA using array CGH, which revealed a striking wave pattern suggesting primarily GC-rich cerebellar losses, even against matched frontal cortex DNA, with a similar pattern on a SNP array. The aCGH changes varied with the isolation protocol. Droplet digital PCR of two genes also showed protocol-dependent losses. Whole genome sequencing showed GC-dependent variation in coverage with spin column isolation from cerebellum. We also extracted and sequenced DNA from substantia nigra using salting-out and phenol / chloroform. The mtDNA copy number, assessed by reads mapping to the mitochondrial genome, was higher in substantia nigra when using phenol / chloroform. We thus provide evidence for significant method-dependent bias in DNA isolation from human brain, as reported in rat tissues. This may contribute to array “waves”, and could affect copy number determination, particularly if mosaicism is being sought, and sequencing coverage. Variations in isolation protocol may also affect apparent mtDNA abundance.
simExTargId: An R package for real-time LC-MS metabolomic data analysis, instrument failure/drift notification and MS2 target identification
Authors: Edmands William M. B. , Rappaport Stephen M. 
Published: June 2017

AbstractThe simExTargId R package provides real-time, autonomous, within-laboratory data analysis during a metabolomic LC-MS1-profiling experiment. Of concern to metabolomic investigators are instrumentation failure (especially for precious samples), outlier identification, instrument signal attenuation and pre-emptive feature identification for MS2 fragmentation.SimExTargId allows observation of an experiment in progress with PCA plot and peak table outputs and also two shiny applications targetId for MS2 target identification and peakMonitor for signal attenuation monitoring. SimExTargId is ideally utilised on a (temporarily) dedicated workstation or server which is networked to a LC-MS data directory. Features include: email notification for instrument stoppage/drift, file format conversion, peak-picking, pre-processing, PCA-based outlier identification and statistical analysis. Additional MS1/MS2 experiments can be concatenated to a worklist or cleaning/recalibration undertaken if instrument drift is observed.All source code and a vignette with example data are available on GitHubhttps://github.com/WMBEdmands/simExTargId/.Contact:edmandsw@berkeley.edu
High-qualityde novogenome assembly of theDekkera bruxellensisUMY321 yeast isolate using Nanopore MinION sequencing
Authors: Fournier Téo , Gounot Jean-Sébastien , Freel Kelle , Cruaud Corinne , Lemainque Arnaud , Aury Jean-Marc , Wincker Patrick , Schacherer Joseph , Friedrich Anne 
Published: June 2017

AbstractGenetic variation in natural populations represents the raw material for phenotypic diversity. Species-wide characterization of genetic variants is crucial to have a deeper insight into the genotype-phenotype relationship. With the advent of new sequencing strategies and more recently the release of long-read sequencing platforms, it is now possible to explore the genetic diversity of any non-model organisms, representing a fundamental resource for biological research. In the frame of population genomic surveys, a first step is evidently to obtain the complete sequence and high quality assembly of a reference genome. Here, we completely sequenced and assembled a reference genome of the non-conventionalDekkera bruxellensisyeast. While this species is a major cause of wine spoilage, it paradoxically contributes to the specific flavor profile of some Belgium beers. In addition, an extreme karyotype variability is observed across natural isolates, highlighting thatD. bruxellensisgenome is very dynamic. The whole genome of theD. bruxellensisUMY321 isolate was sequenced using a combination of Nanopore long-read and Illumina short-read sequencing data. We generated the most complete and contiguousde novoassembly ofD. bruxellensisto date and obtained a first glimpse into the genomic variability within this species by comparing the sequences of several isolates. This genome sequence is therefore of high value for population genomic surveys and represents a reference to study genome dynamic in this yeast species.
Evolution of human, chicken, alligator, frog and zebrafish mineralocorticoid receptors: Allosteric influence on steroid specificity
Authors: Katsu Yoshinao , Oka Kaori , Baker Michael E. 
Published: June 2017

AbstractWe studied the response to aldosterone, 11-deoxycorticosterone, 11-deoxycortisol, cortisol, corticosterone, progesterone, 19-norprogesterone and spironolactone of human, chicken, alligator, frog and zebrafish full-length mineralocorticoid receptors (MRs) and truncated MRs, lacking the N-terminal domain (NTD) and DNA-binding domain (DBD), in which the hinge domain and ligand binding domain (LBD) were fused to a GAL4-DBD. Compared to full-length MRs, some vertebrate MRs required higher steroid concentrations to activate GAL4-DBD-MR-hinge/LBD constructs. For example, 11-deoxycortisol activated all full-length vertebrate MRs, but did not activate truncated terrestrial vertebrate MRs and was an agonist for truncated zebrafish MR. Progesterone, 19-norProgesterone and spironolactone did not activate full-length and truncated human, alligator and frog MRs. However, at 10 nM, these steroids activated full-length chicken and zebrafish MRs; at 100 nM, these steroids had little activity for truncated chicken MRs, while retaining activity for truncated zebrafish MRs, evidence that regulation of progestin activation of chicken MR resides in NTD/DBD and of zebrafish MR in hinge-LBD. Zebrafish and chicken MRs contain a serine corresponding to Ser810 in human MR, required for its antagonism by progesterone, suggesting novel regulation of progestin activation of chicken and zebrafish MRs. Progesterone may be a physiological activator of chicken and zebrafish MRs.
Antimicrobial susceptibility and phylogenetic analysis ofPropionibacterium acnesisolated from acne patients in Japan between 2013 and 2015
Authors: Nakase Keisuke , Hayashi Nobukazu , Akiyama Yui , Aoki Sae , Noguchi Norihisa 
Published: June 2017

AbstractThe prevalence of antimicrobial‐resistantPropionibacterium acnesstrains isolated from acne patients has been increasing in Japan. Here, to estimate the current resistance rate, we tested antimicrobial susceptibility amongP. acnesfrom acne patients having visited a specialized dermatology clinic between 2013 and 2015. Rates of resistance to macrolides and clindamycin were 44.3 (31/70) and 38.6% (27/70), respectively.erm(X), which confers high‐level clindamycin resistance (minimum inhibitory concentration ≥256 μg/mL), was detected in six isolates, whereas no resistance determinants were identified in eight strains showing high‐level resistance to clindamycin. Using single‐locus sequence typing, theP. acnesisolates were classified into five clades (A, E, F, H and K), with all high‐level clindamycin‐resistant strains lacking known clindamycin resistance determinants being grouped together (in clade F).P. acnesisolates from patients previously treated with macrolides and clindamycin showed a macrolide resistance rate (55.3%) significantly higher than that of those from patients not having received these treatments (21.7%,P< 0.05). Furthermore, strains of clade F, which were very rarely isolated from healthy individuals, were more frequently recovered from patients with severe acne (40.0%) than those with mild acne (23.3%). Our data showed an increase in macrolide‐resistantP. acnesprevalence in Japan due to the use of antimicrobial agents for acne treatment. Furthermore, we identified strains of specific phylogenetic groups frequently associated with severe acne patients.
Linear immunoglobulin A/G bullous dermatosis associated with ulcerative colitis
Authors: Onoe Asuka , Matsuura Daisuke , Terui Tadashi , Ishii Norito , Hashimoto Takashi , Ochiai Toyoko 
Published: June 2017

AbstractLinear immunoglobulin (Ig)A/G bullous dermatosis (LAGBD) is an autoimmune bullous disease characterized by formation of subepidermal blisters and linear deposition of IgA and IgG antibodies along the basement membrane zone (BMZ). The association between linear IgA bullous dermatosis and ulcerative colitis (UC) is well recognized, but reports of UC‐associated LAGBD are lacking. We have reported a 24‐year‐old man suffering from LAGBD associated with UC, which occurred before exacerbations of skin rash. A skin biopsy indicated a subepidermal blister with an infiltration of primarily neutrophils and eosinophils in the dermis. Direct immunofluorescence (IF) studies showed a linear deposition of IgA, IgG and C3c. Indirect IF of human skin revealed IgA and IgG anti‐BMZ autoantibodies. Indirect IF of 1 M NaCl‐split human skin demonstrated reactivity of IgA and IgG antibodies at the epidermal side. Immunoblotting showed that IgG antibodies reacted to the BP180 NC16a domain and 120‐kDa linear IgA dermatosis‐1, and enzyme‐linked immunoassay detected IgG anti‐BP230 antibodies. Administration of prednisolone and diaminodiphenyl sulfone (DDS) via the p.o. route improved skin lesions and bowel conditions. These results suggest that the bowel inflammation observed in UC may have a causative effect of initiation of the immune response to the skin and development of the bullous skin lesions in LAGBD. A combination of DDS and corticosteroid could be a recommended therapeutic option for patients with LAGBD with UC.
Frusemide aids diagnostic interpretation of 68Ga‐PSMA positron emission tomography/CT in men with prostate cancer
Authors: Fennessy Niall , Lee Jonathan , Shin Jane , Ho Bao , Ali Syed Aman , Paschkewitz Royce , Emmett Louise 
Published: June 2017

AbstractIntroduction68Ga‐PSMA positron emission tomography–computed tomography (PET/CT) is useful for both staging and assessment of biochemical relapse in men with prostate cancer. Renal excretion of 68Ga‐PSMA can lead to difficulties in scan interpretation, particularly in the pelvis. We evaluated if intravenous Frusemide at the time of 68Ga‐PSMA injection reduces excreted activity artefact and improves diagnostic certainty.MethodsSixty‐two men with prostate cancer undergoing clinically indicated 68Ga‐PSMA PET/CT were prospectively included, 30 men receiving Frusemide at the time of radiotracer injection. Clinical information and reasons for the scan were documented. Intensity of excreted activity was assessed semi quantitatively for each patient (SUV max). PET/CT images were interpreted by two experienced readers for image quality, and presence/absence of PSMA‐positive disease.ResultsTwenty‐nine percent (18/62) were staging scans, and 71% (44/62) re‐staging. PSMA‐positive findings were identified in 95% (59/62). Staging scans had PSMA‐positive findings within the prostate in 100% (18/18) and re‐staging scans, 50% (22/44) in the prostate fossa, 64% (28/44) in lymph nodes and 21% (9/44) in viscera and bone. Administration of Frusemide had a significant impact on intensity of excreted activity in the ureters and bladder. Impaired image quality was noted in 33% (10/30) of men not given Frusemide, compared to only 3% (1/32) in men given Frusemide (P = 0.002). Reporter confidence on the presence/absence of PSMA avid disease in the prostate fossa improved from 63% (19/30) without Frusemide, to 91% (29/32) with Frusemide (P < 0.015).ConclusionIntravenous Frusemide given with 68Ga‐PSMA reduces excretion artefact, and improves diagnostic certainty. Frusemide should be considered for all 68Ga‐PSMA PET/CT imaging protocols.
Toxicity after post‐prostatectomy image‐guided intensity‐modulated radiotherapy using Australian guidelines
Authors: Chin Stephen , Aherne Noel J , Last Andrew , Assareh Hassan , Shakespeare Thomas P 
Published: June 2017

AbstractIntroductionWe evaluated single institution toxicity outcomes after post‐prostatectomy radiotherapy (PPRT) via image‐guided intensity‐modulated radiation therapy (IG‐IMRT) with implanted fiducial markers following national eviQ guidelines, for which late toxicity outcomes have not been published.MethodsProspectively collected toxicity data were retrospectively reviewed for 293 men who underwent 64–66 Gy IG‐IMRT to the prostate bed between 2007 and 2015.ResultsMedian follow‐up after PPRT was 39 months. Baseline grade ≥2 genitourinary (GU), gastrointestinal (GI) and sexual toxicities were 20.5%, 2.7% and 43.7%, respectively, reflecting ongoing toxicity after radical prostatectomy. Incidence of new (compared to baseline) acute grade ≥2 GU and GI toxicity was 5.8% and 10.6%, respectively. New late grade ≥2 GU, GI and sexual toxicity occurred in 19.1%, 4.7% and 20.2%, respectively. However, many patients also experienced improvements in toxicities. For this reason, prevalence of grade ≥2 GU, GI and sexual toxicities 4 years after PPRT was similar to or lower than baseline (21.7%, 2.6% and 17.4%, respectively). There were no grade ≥4 toxicities.ConclusionsPost‐prostatectomy IG‐IMRT using Australian contouring guidelines appears to have tolerable acute and late toxicity. The 4‐year prevalence of grade ≥2 GU and GI toxicity was virtually unchanged compared to baseline, and sexual toxicity improved over baseline. This should reassure radiation oncologists following these guidelines. Late toxicity rates of surgery and PPRT are higher than following definitive IG‐IMRT, and this should be taken into account if patients are considering surgery and likely to require PPRT.
Deriving low‐risk gambling limits from longitudinal data collected in two independent Canadian studies
Authors: Currie Shawn R. , Hodgins David C. , Casey David M. , el‐Guebaly Nady , Smith Garry J. , Williams Robert J. , Schopflocher Don P. 
Published: June 2017

AbstractAimsTo derive low‐risk gambling limits using the method developed by Currie et al. (2006) applied to longitudinal data.DesignSecondary analysis of data from the Quinte Longitudinal Study (n = 3054) and Leisure, Lifestyle and Lifecycle Project (n = 809), two independently conducted cohort studies of the natural progression of gambling in Canadian adults.SettingCommunity‐dwelling adults in Southeastern Ontario and Alberta, Canada.ParticipantsA total of 3863 adults (50% male; median age = 44) who reported gambling in the past year.MeasurementsGambling behaviours (typical monthly frequency, total expenditure and percentage of income spent on gambling) and harm (experiencing two or more consequences of gambling in the past 12 months) were assessed with the Canadian Problem Gambling Index.FindingsThe dose–response relationship was comparable in both studies for frequency of gambling (days per month), total expenditure and percentage of household income spent on gambling (area under the curve values ranged from 0.66 to 0.74). Based on the optimal sensitivity and specificity values, the low‐risk gambling cut‐offs were eight times per month, $75CAN total per month and 1.7% of income spent on gambling. Gamblers who exceeded any of these limits at time 1 were approximately four times more likely to report harm at time 2 [95% confidence interval (CI) = 2.9–6.6].ConclusionsLongitudinal data in Canada suggest low‐risk gambling thresholds of eight times per month, $75CAN total per month and 1.7% of income spent on gambling, all of which are higher than previously derived limits from cross‐sectional data. Gamblers who exceed any of the three low‐risk limits are four times more likely to experience future harm than those who do not.
Associations between anhedonia and marijuana use escalation across mid‐adolescence
Authors: Leventhal Adam M. , Cho Junhan , Stone Matthew D. , Barrington‐Trimis Jessica L. , Chou Chih‐Ping , Sussman Steven Y. , Riggs Nathaniel R. , Unger Jennifer B. , Audrain‐McGovern Janet , Strong David R. 
Published: June 2017

AbstractBackground and aimsAnhedonia—a transdiagnostic psychopathological trait indicative of inability to experience pleasure—could lead to and result from adolescent marijuana use, yet this notion has not been tested. This study aimed to estimate the association of: (1) anhedonia at age 14 with rate of change in marijuana use over an 18‐month follow‐up, and (2) marijuana use at age 14 with rate of change in anhedonia over follow‐up. Secondary aims were to test whether gender, baseline marijuana use history and peer marijuana use moderated these associations.DesignObservational longitudinal cohort repeated‐measures design, with baseline (age 14 years), 6‐month, 12‐month and 18‐month follow‐up assessments.SettingsTen public high schools in Los Angeles, CA, USA, 2013–15.ParticipantsStudents [n = 3394; 53.5% female, mean (standard deviation) age at baseline = 14.1 (0.42)].MeasurementsSelf‐report level of anhedonia on the Snaith–Hamilton Pleasure Scale and frequency of marijuana use in the past 30 days.FindingsParallel process latent growth curve models adjusting for confounders showed that baseline anhedonia level was associated positively with the rate of increase in marijuana use frequency across follow‐ups [β, 95% confidence interval (CI) = 0.115 (0.022, 0.252), P = 0.03]. Baseline marijuana use frequency was not related significantly to the rate of change in anhedonia across follow‐ups [β, 95% CI = −0.015 (−0.350, 0.321), P = 0.93]. The association of baseline anhedonia with faster marijuana use escalation was amplified among adolescents with (versus without) friends who used marijuana at baseline [β, 95% CI = 0.179 (0.043, 0.334) versus 0.064 (−0.071, 0.187), interaction P = 0.04], but did not differ by gender or baseline ever marijuana use.ConclusionsIn mid‐adolescence, anhedonia is associated with subsequent marijuana use escalation, but marijuana use escalation does not appear to be associated with subsequent anhedonia.
Changing predictions, stable recognition: Children's representations of downward incline motion
Authors: Hast Michael , Howe Christine 
Published: June 2017

Various studies to‐date have demonstrated children hold ill‐conceived expressed beliefs about the physical world such as that one ball will fall faster than another because it is heavier. At the same time, they also demonstrate accurate recognition of dynamic events. How these representations relate is still unresolved. This study examined 5‐ to 11‐year‐olds’ (N = 130) predictions and recognition of motion down inclines. Predictions were typically in error, matching previous work, but children largely recognized correct events as correct and rejected incorrect ones. The results also demonstrate while predictions change with increasing age, recognition shows signs of stability. The findings provide further support for a hybrid model of object representations and argue in favour of stable core cognition existing alongside developmental changes.
Statement of contribution

What is already known on this subject?

Children's predictions of physical events show limitations in accuracy

Their recognition of such events suggests children may use different knowledge sources in their reasoning

What the present study adds?

Predictions fluctuate more strongly than recognition, suggesting stable core cognition

But recognition also shows some fluctuation, arguing for a hybrid model of knowledge representation