bluuebunny/crossref_metadata_2025_split huggingface dataset:
Correlation Between Apparent Diffusion Coefficient Values of the Renal Parenchyma and Estimated Glomerular Filtration Rates on 3-T Diffusion-Weighted Echo-Planar Magnetic Resonance Imaging
Authors: Thiravit Shanigarn , Suwanchatree Paphatsanan , Skulratanasak Peenida , Thiravit Phakphoom , Suvannarerg Voraparee 
Published: July 2019

Objective
To evaluate the relationship between the apparent diffusion coefficient (ADC) values of renal parenchyma and estimated glomerular filtration rates (eGFR).

Methods
Data on 216 patients examined by 3-T magnetic resonance imaging for various reasons were retrospectively collected.

Results
There was a significant linear correlation between the ADC values and eGFRs (r = 0.254, P < 0.001). The ADC values in patients with an eGFR of less than 60 mL/min per 1.73 m2 were significantly lower than those with an eGFR of 60 mL/min per 1.73 m2 or greater. The mean ADC value of patients with grouped stage 2 disease was significantly higher than those with grouped stage 3 of chronic kidney disease (P < 0.01).

Conclusions
The ADC value of renal parenchyma may be a promising marker for the determination of patients with normal to mild reduction in renal function (eGFR ≥60 mL/min per 1.73 m2) versus those with a moderate to severe reduction in renal function (eGFR <60 mL/min per 1.73 m2).
Recent research on the social network concept and cancer
Authors: Jones Eric C. , Storksdieck Martin 
Published: July 2019

Purpose of review
This review covers articles in 2018 and early 2019 that employed the concept of networks and social interactions in research on how patients with cancer cope, receive and respond to medical treatment and allied support. The use of social aspects, and more formally the method of social network analysis for research on social aspects of cancer is quite new. Although we paid special attention to articles that used formal social network analysis, we noted that those articles cover just over a quarter of the material we reviewed. Most articles that incorporated social aspects of cancer did not intend to formalize those aspects but treated the network concept as a way to characterize social support, social influence, or social responsibilities.

Recent findings
We identified 74 recent articles that mentioned the network concept for research about cancer, excluding gene interaction networks. Of those 74 articles, 21 measured specific relationships between individuals or organizations and/or attributes of those individuals or organizations connected to participants or to others. Primary foci of the network analysis and nonnetwork analysis studies were breast cancer, social support for patients, and they usually at least considered sex and age of the cancer patients/survivors. Social media received some attention, and there were some studies considering quality of life and mental health. Among network analysis studies, size of network and number of people providing emotional/informational/instrumental support occurred in more than a couple studies but not the majority. There was little similarity among studies – whether using network analysis or not – suggesting that theory building and methodological development are in early stages.

Summary
Implications of the review include opportunities for more systematic research using the network concept to understand people's experience of cancer as well as research on cancer. Researchers can make considerable contributions at this stage in the field's development, and practitioners can help develop interventions that make fuller use of the insights of social network analysis.
Framework for rational donor selection in fecal microbiota transplant clinical trials
Authors: Duvallet Claire , Zellmer Caroline , Panchal Pratik , Budree Shrish , Osman Majdi , Alm Eric 
Published: July 2019

AbstractEarly clinical successes are driving enthusiasm for fecal microbiota transplantation (FMT), the transfer of healthy gut bacteria through whole stool, as emerging research is linking the microbiome to many different diseases. However, preliminary trials have yielded mixed results and suggest that heterogeneity in donor stool may play a role in patient response. Thus, clinical trials may fail because an ineffective donor was chosen rather than because FMT is not appropriate for the indication. Here, we describe a conceptual framework to guide rational donor selection to increase the likelihood that FMT clinical trials will succeed. We argue that the mechanism by which the microbiome is hypothesized to be associated with a given indication should inform how healthy donors are selected for FMT trials, categorizing these mechanisms into four disease models and presenting associated donor selection strategies. We next walk through examples based on previously published FMT trials and ongoing investigations to illustrate how donor selection might occur in practice. Finally, we show that typical FMT trials are not powered to discover individual taxa mediating patient responses, suggesting that clinicians should develop targeted hypotheses for retrospective analyses and design their clinical trials accordingly. Moving forward, developing and applying novel clinical trial design methodologies like rational donor selection will be necessary to ensure that FMT successfully translates into clinical impact.
The effectiveness of digital technology interventions to reduce loneliness in adult people: A protocol for a systematic review and meta-analysis
Authors: Shah Syed Ghulam Sarwar , Nogueras David , van Woerden Hugo Cornelis , Kiparoglou Vasiliki 
Published: July 2019

ABSTRACTIntroductionLoneliness is an emerging public health problem, which is associated with social, emotional, mental and physical health issues. The application of digital technology (DT) interventions to reduce loneliness has increased in recent years. The effectiveness of DT interventions needs to be assessed systematically.Methods and analysisAimTo undertake a systematic review and meta-analysis on the effectiveness of digital technology interventions to reduce loneliness among adult people.Designsystematic review and meta-analysis.Data sourcesFive leading online bibliographic databases: PubMed, Medline, CINAHL, EMBASE, and Web of Science.Publication period1 January 2010 to 30 April 2019.Inclusion criteriaPrimary studies involving the application of digital technology interventions to reduce loneliness, involving adult participants (aged 18 years and more) and published in the English language.Search strategyLiterature searches using a priory list of keywords, involvement of two independent researchers in article screening, short listing and data extraction using a predefined template based on the population, intervention(s), comparator(s) and outcome(s) (PICO) framework.Synthesis and meta-analysisA narrative summary of the characteristics of included studies, findings by the type of DT intervention, and the age, gender and ethnicity of participants. A meta-analysis by the type of DT intervention and determination of effect sizes.Quality of evidence and biasQuality of evidence assessed the RoB 2.0 (revised tool for Risk of Bias in randomized trials) and ROBINS-I (Risk Of Bias in Non-randomized Studies - of Interventions) tools for randomized control trials and non-randomized studies respectively. Heterogeneity between studies determined by the I2 and Cochran’s Q statistics and publication bias checked with funnel plots and the Egger’s test.Patients and public involvementNoneEthics and disseminationEthics approval was not required for writing this protocol. The findings will be disseminated through the publication of research articles and conference presentations.PROSPERO Registration NumberCRD42019131524.Article SummaryStrengths and limitations of this studyThe main strength of this study includes a systematic assessment of evidence on the effectiveness of digital technology interventions to reduce loneliness, which is imperative from the health and social care and public health perspectives.Another strength of the study is the involvement of two independent researchers (and a third researcher as an arbitrator) involved in the identification, screening, inclusion and extraction of on a predefined template using the PICO framework.Limitations may include missing identification of additional relevant studies due to the application of selection filters such as the publication years and English as the publication language.
Robotic middle ear access for cochlear implantation: first in man
Authors: Caversaccio Marco , Wimmer Wilhelm , Anso Juan , Mantokoudis Georgios , Gerber Nicolas , Rathgeb Christoph , Schneider Daniel , Hermann Jan , Wagner Franca , Scheidegger Olivier , Huth Markus , Anschuetz Lukas , Kompis Martin , Williamson Tom , Bell Brett , Gavaghan Kate , Weber Stefan 
Published: July 2019

ABSTRACTTo demonstrate the feasibility of robotic middle ear access in a clinical setting, nine adult patients with severe-to-profound hearing loss indicated for cochlear implantation were included in this clinical trial. A keyhole access tunnel to the tympanic cavity and targeting the round window was planned based on preoperatively acquired computed tomography image data and robotically drilled to the level of the facial recess. Intraoperative imaging was performed to confirm sufficient distance of the drilling trajectory to relevant anatomy. Robotic drilling continued toward the round window. The cochlear access was manually created by the surgeon. Electrode arrays were inserted through the keyhole tunnel under microscopic supervision via a tympanomeatal flap. All patients were successfully implanted with a cochlear implant. In 9 of 9 patients the robotic drilling was planned and performed to the level of the facial recess. In 3 patients, the procedure was reverted to a conventional approach for safety reasons. No change in facial nerve function compared to baseline measurements was observed. Robotic keyhole access for cochlear implantation is feasible. Further improvements to workflow complexity, duration of surgery, and usability including safety assessments are required to enable wider adoption of the procedure.
The chromatin remodeler SMARCD3 regulates cell cycle progression and its expression predicts survival outcome in ER+ breast cancer
Authors: Tropée Romain , de la Peña Avalos Bárbara , Gough Madeline , Snell Cameron , Duijf Pascal H.G. , Dray Eloïse 
Published: July 2019

AbstractChromatin remodeling plays an essential role in regulating transcriptional networks and timing of gene expression. Chromatin remodelers such as SWItch/Sucrose Non-Fermentable (SWI/SNF) harbor many protein components, with the catalytic subunit providing ATPase activity to displace histones along or from the DNA molecules, and associated subunits ensuring tissue specificity and transcriptional or co-transcriptional activities. Mutations in several of the SWI/SNF subunits have been linked to cancer. Here, we describe how SMARCD3/Baf60c expression is associated with hormone positive (ER+) breast cancer. The level SMARCD3, as detected by immunohistochemistry in breast cancer patient samples, is correlated with differential long-term disease-free survival. In contrast, the expression level of SMARCD1/Baf60a and SMARCD2/Baf60b, which are mutually exclusive within the SWI/SNF complex and have a partially redundant function, lacks predictive value in breast cancer patient samples. Lower proliferation rates are observed in SMARCD3 depleted cells, which reflects a failure to fully progress through G2/M, and an increase in endoreplication. In the absence of SMARCD3, p21 accumulates in cells but does not halt the cell cycle, and DNA damage accumulates and remains unrepaired. Taken together, our data begin to explain why ER+ breast cancer patients with low SMARCD3 expressing tumors exhibit reduced survival rates compared to patients expressing normal or higher levels of SMARCD3. SMARCD3 might act as a tumor suppressor role through regulation of cell cycle checkpoints and could be a reliable and specific breast cancer prognostic biomarker.SignificanceMutations in chromatin remodelers are a leading cause of cancer. Estrogen Receptor positive (ER+) breast cancers represent approximately 80% of all cases diagnosed. Although these tumors can be treated with hormone therapy, most breast cancer fatalities occur in ER+ breast cancer patients, due to metastasis. Low expression of SMARCD3 in ER+ cancer is associated with diminished survival rates. As such, SMARCD3 could be used as a predictive biomarker for survival. In addition, we have identified a role for SMARCD3 in the cell cycle, which could at least partially explain its protective role in breast cancer. While catalytic subunits are often viewed as the major components in chromatin remodeling function, we show here new evidence that mutations or silencing of SMARCD3 may also contribute to genomic instability and thus development of breast cancer.
Conformity to Bergmann’s rule in birds depends on nest design and migration
Authors: Mainwaring Mark C. , Street Sally E. 
Published: July 2019

AbstractSpecies’ geographic ranges and range limits are thought to be determined by climate, and across climatic gradients the morphology of populations varies non-randomly. Ecogeographic rules seek to characterise such variation, with Bergmann’s rule positing that organisms inhabiting colder environments are typically larger-bodied than those inhabiting warmer environments. While Bergmann’s rule has been supported across a range of taxonomic groups, how organisms’ behaviour may moderate its effect remains unclear. Here we investigate whether conformity to Bergmann’s rule among birds of the Western Palearctic varies in relation to nest design and migratory behaviour, using phylogenetic comparative analyses. We test predictions using data on nest structure and location, migration, body mass, latitudinal distribution, annual mean temperature and phylogenetic relatedness for a sample of >500 species. We find that conformity to Bergmann’s rule depends strongly on migratory behaviour: non-migratory species breeding at colder, more northerly latitudes are larger-bodied, while body mass is unaffected by climate in short- and long-distance migrants. Among non-migratory species, conformity to Bergmann’s rule depends, further, on nest design: species with more open nests, who are thus most exposed to adverse climatic conditions while breeding, conform most strongly to Bergmann’s rule. Our findings suggest that enclosed nesting and migration allow smaller bodied species to breed in colder environments than their body size would otherwise allow. Therefore, we conclude that organisms’ behaviour can strongly affect exposure to environmental selection pressures.
IsoSeq transcriptome assembly of C3panicoid grasses provides tools to study evolutionary change in the Panicoideae
Authors: Carvalho Daniel S. , Schnable James C. 
Published: July 2019

AbstractThe number of plant species with genomic and transcriptomic data has been increasing rapidly. The grasses – Poaceae – have been well represented among species with published reference genomes. However, as a result the genomes of wild grasses are less frequently targeted by sequencing efforts. Sequence data from wild relatives of crop species in the grasses can aid the study of domestication, gene discovery for breeding and crop improvement, and improve our understanding of the evolution of C4photosynthesis. Here we used long read sequencing technology to characterize the transcriptomes of three C3panicoid grass species:Dichanthelium oligosanthes, Chasmanthium laxum, andHymenachne amplexicaulis. Based on alignments to the sorghum genome we estimate that assembled consensus transcripts from each species capture between 54.2 and 65.7% of the conserved syntenic gene space in grasses. Genes co-opted into C4were also well represented in this dataset, despite concerns that, because these genes might play roles unrelated to photosynthesis in the target species, they would be expressed at low levels and missed by transcript-based sequencing. A combined analysis using syntenic orthologous genes from grasses with published reference genomes and consensus long read sequences from these wild species was consistent with previously published phylogenies. It is hoped that this data, targeting under represented classes of species within the PACMAD grasses – wild species and species utilizing C3photosynthesis – will aid in futurue studies of domestication and C4evolution by decreasing the evolutionary distance between C4and C3species within this clade, enabling more accurate comparisons associated with evolution of the C4pathway.
Poincaré Maps for Analyzing Complex Hierarchies in Single-Cell Data
Authors: Klimovskaia Anna , Lopez-Paz David , Bottou Léon , Nickel Maximilian 
Published: July 2019

AbstractThe need to understand cell developmental processes spawned a plethora of computational methods for discovering hierarchies from scRNAseq data. However, existing techniques are based on Euclidean geometry, a suboptimal choice for modeling complex cell trajectories with multiple branches. To overcome this fundamental representation issue we propose Poincaré maps, a method that harness the power of hyperbolic geometry into the realm of single-cell data analysis. Often understood as a continuous extension of trees, hyperbolic geometry enables the embedding of complex hierarchical data in only two dimensions while preserving the pairwise distances between points in the hierarchy. This enables direct exploratory analysis and the use of our embeddings in a wide variety of downstream data analysis tasks, such as visualization, clustering, lineage detection and pseudo-time inference. When compared to existing methods —unable to address all these important tasks using a single embedding— Poincaré maps produce state-of-the-art two-dimensional representations of cell trajectories on multiple scRNAseq datasets. More specifically, we demonstrate that Poincaré maps allow in a straightforward manner to formulate new hypotheses about biological processes unbeknown to prior methods.Significance statementThe discovery of hierarchies in biological processes is central to developmental biology. We propose Poincaré maps, a new method based on hyperbolic geometry to discover continuous hierarchies from pairwise similarities. We demonstrate the efficacy of our method on multiple single-cell datasets on tasks such as visualization, clustering, lineage identification, and pseudo-time inference.
Large-scale hyperparameter search for predicting human brain responses in the Algonauts challenge
Authors: Jozwik Kamila M. , Lee Michael , Marques Tiago , Schrimpf Martin , Bashivan Pouya 
Published: July 2019

Image features computed by specific convolutional artificial neural networks (ANNs) can be used to make state-of-the-art predictions of primate ventral stream responses to visual stimuli.However, in addition to selecting the specific ANN and layer that is used, the modeler makes other choices in preprocessing the stimulus image and generating brain predictions from ANN features. The effect of these choices on brain predictivity is currently underexplored.Here, we directly evaluated many of these choices by performing a grid search over network architectures, layers, image preprocessing strategies, feature pooling mechanisms, and the use of dimensionality reduction. Our goal was to identify model configurations that produce responses to visual stimuli that are most similar to the human neural representations, as measured by human fMRI and MEG responses. In total, we evaluated more than 140,338 model configurations. We found that specific configurations of CORnet-S best predicted fMRI responses in early visual cortex, and CORnet-R and SqueezeNet models best predicted fMRI responses in inferior temporal cortex. We found specific configurations of VGG-16 and CORnet-S models that best predicted the MEG responses.We also observed that downsizing input images to ~50-75% of the input tensor size lead to better performing models compared to no downsizing (the default choice in most brain models for vision). Taken together, we present evidence that brain predictivity is sensitive not only to which ANN architecture and layer is used, but choices in image preprocessing and feature postprocessing, and these choices should be further explored.
Observing changes in human functioning during induced sleep deficiency and recovery periods
Authors: Ochab Jeremi K. , Szwed Jerzy , Oleś Katarzyna , Bereś Anna , Chialvo Dante R. , Domagalik Aleksandra , Fafrowicz Magdalena , Gudowska-Nowak Ewa , Marek Tadeusz , Nowak Maciej A. , Ogińska Halszka 
Published: July 2019

ABSTRACTThe duration of sleep, wakefulness and dynamic changes in human performance are determined by neural and genetic mechanisms. Sleep deprivation and chronic restriction of sleep cause perturbations of circadian rhythmicity and degradation of waking alertness as reflected in attention, cognitive efficiency and memory. In this work we report on multiple neurobehavioral correlates of sleep loss in healthy adults in an unprecedented study comprising 21 consecutive days divided into periods of 4 days of regular life (a baseline), 10 days of chronic partial sleep restriction and 7 days of recovery. Throughout the whole experiment we continuously measured the spontaneous locomotor activity by means of actigraphy with 1-minute resolution in two acquisition modes (frequency and intensity of movement). Moreover, on daily basis the subjects were undergoing EEG measurements (64-electrodes with 500 Hz sampling frequency): resting state with eyes open and closed (RS; 8 minutes long each) followed by Stroop task (ST; 22 minutes). Altogether we analyzed actigraphy (distributions of rest and activity durations), behavioral measures (accuracy and reaction times from Stroop task) and EEG (amplitudes, latencies and scalp maps of event-related potentials from Stroop task and power spectra from resting states). The actigraphy measures clearly indicate rapid changes after sleep restriction onset, confirming our former investigations — the novel insight is a slow and incomplete relaxation to the original locomotor behavior. The pattern of partial recovery appears also in accuracy (in ST) and power of delta rhythm (in RS). The impact of sleep loss is also evident in reaction times (in ST), yet followed by complete recovery, and finally in ERP amplitudes and latencies, which however did not return to the baseline at all. The results indicate that short periods (a few days) of recovery sleep subsequent to prolonged periods of sleep restriction are overall insufficient to recover fully.