bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deep Learning for Quality Control of Subcortical Brain 3D Shape Models
Authors:   The ENIGMA Consortium, Petrov Dmitry , Gutman Boris A. , Kuznetsov Egor , van Erp Theo G.M. , Turner Jessica A. , Schmaal Lianne , Veltman Dick , Wang Lei , Alpert Kathryn , Isaev Dmitry , Zavaliangos-Petropulu Artemis , Ching Christopher R.K. , Calhoun Vince , Glahn David , Satterthwaite Theodore D. , Andreassen Ole Andreas , Borgwardt Stefan , Howells Fleur , Groenewold Nynke , Voineskos Aristotle , Radua Joaquim , Potkin Steven G. , Crespo-Facorro Benedicto , Tordesillas-Gutirrez Diana , Shen Li , Lebedeva Irina , Spalletta Gianfranco , Donohoe Gary , Kochunov Peter , Rosa Pedro G.P. , James Anthony , Dannlowski Udo , Baune Bernhard T. , Aleman Andr , Gotlib Ian H. , Walter Henrik , Walter Martin , Soares Jair C. , Ehrlich Stefan , Gur Ruben C. , Doan N. Trung , Agartz Ingrid , Westlye Lars T. , Harrisberger Fabienne , Riecher-Rössler Anita , Uhlmann Anne , Stein Dan J. , Dickie Erin W. , Pomarol-Clotet Edith , Fuentes-Claramonte Paola , Canales-Rodrguez Erick Jorge , Salvador Raymond , Huang Alexander J. , Roiz-Santiaez Roberto , Cong Shan , Tomyshev Alexander , Piras Fabrizio , Vecchio Daniela , Banaj Nerisa , Ciullo Valentina , Hong Elliot , Busatto Geraldo , Zanetti Marcus V. , Serpa Mauricio H. , Cervenka Simon , Kelly Sinead , Grotegerd Dominik , Sacchet Matthew D. , Veer Ilya M. , Li Meng , Wu Mon-Ju , Irungu Benson , Walton Esther , Thompson Paul M. ,   for the ENIGMA consortium
Published: August 2018

AbstractWe present several deep learning models for assessing the morphometric fidelity of deep grey matter region models extracted from brain MRI. We test three different convolutional neural net architectures (VGGNet, ResNet and Inception) over 2D maps of geometric features. Further, we present a novel geometry feature augmentation technique based on parametric spherical mapping. Finally, we present an approach for model decision visualization, allowing human raters to see the areas of subcortical shapes most likely to be deemed of failing quality by the machine. Our training data is comprised of 5200 subjects from the ENIGMA Schizophrenia MRI cohorts, and our test dataset contains 1500 subjects from the ENIGMA Major Depressive Disorder cohorts. Our final models reduce human rater time by 46-70%. ResNet outperforms VGGNet and Inception for all of our predictive tasks.
Superresolution architecture of pluripotency guarding adhesions
Authors: Stubb Aki , Guzmán Camilo , Närvä Elisa , Aaron Jesse , Chew Teng-Leong , Saari Markku , Miihkinen Mitro , Jacquemet Guillaume , Ivaska Johanna 
Published: August 2018

AbstractHuman pluripotent stem cells (hPSC) can generate almost all adult cell lineages. While it is clear that key transcriptional programmes are important elements for maintaining pluripotency, the equally essential requirement for cell adhesion to specific extracellular matrix components remains poorly defined. Our recent observation that hPSC colonies form unusually large “cornerstone” focal adhesions (FA), distinct from parental somatic cells, that are lost following differentiation, emphasises the potential of these atypical FA as gatekeepers of pluripotency. Here, using nanopatterns, we further demonstrate that physical restriction of adhesion size, in hPSC colonies, is sufficient to trigger differentiation. Using superresolution two-colour interfero-metric photo-activated localization microscopy (iPALM), we examined the three-dimensional architecture of these cornerstone adhesions and report vertical lamination of FA proteins with three main structural peculiarities: 1) integrin β5 and talin are present at high density, at the edges of cornerstone FA, adjacent to a vertical kank-rich protein wall. 2) Vinculin localises higher than expected with respect to the substrata and displays a head-above-tail orientation, and 3) surprisingly, actin and α-actinin are present in two discrete layers, a previously undescribed localisation for these proteins. Finally, we report that depletion of kanks diminishes FA patterning, and actin organisation within the colony, indicating a key role for kanks in hPSC colony architecture.
Eco-evolutionary agriculture: a study in crop rotations
Authors: Bargués-Ribera Maria , Gokhale Chaitanya S. 
Published: August 2018

AbstractSince its origins, thousands of years ago, agriculture has been challenged by the presence of evolving plant pathogens. In response, current practices have started relying on computational tools to design efficient prospective planning, but further efforts for multi-criteria assessment are needed. Here, we present a methodology for developing cultivation strategies optimal for control or eradication of pathogens. This approach can integrate both, traditionally used criteria in crop rotations and the analysis of host-pathogen coevolution systems where hosts are artificially selected. Our analysis shows that prospective planning can maximise cash yield in the long run by investing consecutively in soil quality during initial sea-sons. Importantly, rational application of crop rotation patterns can minimise yield loss in infected fields, despite the evolution of pathogen virulence. Our results provide strategies for optimal resource investment for increased food production and lead to further insights into minimisation of pesticide use in a society demanding efficient agriculture.
Pat1 promotes processing body assembly by enhancing the phase separation of the DEAD-box ATPase Dhh1 and RNA
Authors: Sachdev Ruchika , Hondele Maria , Linsenmeier Miriam , Vallotton Pascal , Mugler Christopher F. , Arosio Paolo , Weis Karsten 
Published: August 2018

AbstractProcessing bodies (PBs) are cytoplasmic mRNP granules that assemble via liquid-liquid phase separation and are implicated in the decay or storage of mRNAs. How PB assembly is regulated in cells remains unclear. We recently identified the ATPase activity of the DEAD-box protein Dhh1 as a key regulator of PB dynamics and demonstrated that Not1, an activator of the Dhh1 ATPase and member of the CCR4-NOT deadenylase complex inhibits PB assemblyin vivo[Mugler et al., 2016]. Here, we show that the PB component Pat1 antagonizes Not1 and promotes PB assembly via its direct interaction with Dhh1. Intriguingly,in vivoPB dynamics can be recapitulatedin vitro, since Pat1 enhances the phase separation of Dhh1 and RNA into liquid droplets, whereas Not1 reverses Pat1-Dhh1-RNA condensation. Overall, our results uncover a function of Pat1 in promoting the multimerization of Dhh1 on mRNA, thereby aiding the assembly of large multivalent mRNP granules that are PBs.
The effect of community dialogues and sensitization on patient reporting of adverse events in rural Uganda: uncontrolled before-after study
Authors: Ndagije Helen Byomire , Manirakiza Leonard , Kajungu Dan , Galiwango Edward , Kusemererwa Donna , Olsson Sten , Spinewine Anne , Speybroeck Niko 
Published: August 2018

AbstractBackgroundThe patients that experience adverse events are in the best position to report them, only if they were empowered to do so. Systematic community engagement and support to patients in a rural setting to monitor any potential harm from medicines should provide evidence for patient safety.MethodsThis paper describes an uncontrolled before and after study aimed at assessing the effect of a community engagement strategy, the Community Dialogues and Sensitization (CDS) intervention between January and April 2017, on the knowledge, attitude and practice of reporting adverse drug events by community members in the two eastern Ugandan districts. A representative cross-sectional baseline household survey was done prior to the intervention in September 2016 (n=1034) and the end-line survey (n=827) in July 2017.ResultsAfter implementation of the CDS intervention, there was an overall 20% (95% CI=16- 25) increase in awareness about adverse drug events in the community. The young people (15- 24 years) demonstrated a 41% (95% CI =31-52) increase and the un-educated showed a 50% (95% CI=37-63) increase in awareness about adverse drug events. The attitudes towards reporting increased overall by 5% in response to whether there was a need to report ADEs (95% CI =3-7). An overall 115% (95% CI =137-217) increase in the population that had ever experienced ADEs was also reported.ConclusionOur evaluation shows that the CDS intervention increases knowledge, improves attitudes by catalyzing discussions among community members and health workers on health issues and monitoring safety of medicines.
Biogeography of the savanna-like vegetation in hot dry valleys in southwestern China with reference to their floristic origin and evolution
Authors: Zhu Hua , Yan Lichun 
Published: August 2018

AbstractSavanna-like vegetation and dry thickets occur in hot dry valleys across southwestern China. Here, the flora and biogeography of these vegetations are studied. Native seed plants of 3,217 species from 1,038 genera in 163 families are recorded from the hot dry valleys in SW China. The biogeographical elements with a tropical distribution contribute 57.18%, but the ones with a temperate distribution contribute 36.45% of the total genera of the flora. This shows that the flora has proliferated by temperate elements via their evolution, although the flora occur in tropical habitats in the hot dry valleys. Floristic divergence across these hot dry valleys is obvious. The floras in the Yuanjiang (the upper reaches of the Red River) and the Nujiang (the upper reaches of the Salween River) valleys are dominated by tropical elements (77.26% and 74.49 of the total genera, respectively), but the flora of the Jinshajiang (the upper reaches of the Yangtze River) valley is composed of half tropical (47.27%) and half temperate (44.96%) genera. Regarding floristic similarities, the Jinshajiang shows the highest similarity to the Yuanjiang although these river valleys are located a great distance from each other. Our results could be well explained from the geological events since the Cenozoic, such as the uplift of Himalayas, the extrusion of Indochina, the river capture of the Jinshajiang separating from the Yuanjiang, and the northward movement of the Burma Plate. Further floristic comparison between the flora in hot dry valleys of SW China and southern Africa supports the consideration that the flora of savanna-like vegetations of SW China could have floristic affinity to African savannas over the course of its evolutionary history by the Indian Plate from southern Africa colliding with Eurasia in the Cenozoic.
Electrical Fields Induced Inside the Rat Brain with Skin, Skull, and Dural Placements of the Current Injection Electrode
Authors: Asan Ahmet S. , Gok Sinan , Sahin Mesut 
Published: August 2018

AbstractTranscranial electrical stimulation (tES) is rapidly becoming an indispensable clinical tool with its different forms. Animal data are crucially needed for better understanding of the underlying mechanisms of tES. For reproducibility of results in animal experiments, the electric fields (E-Fields) inside the brain parenchyma induced by the injected currents need to be predicted accurately. In this study, we measured the electrical fields in the rat brain perpendicular to the brain surface, i.e. vertical electric field (VE-field), when the stimulation electrode was placed over the skin, skull, or dura mater through a craniotomy hole. The E-field attenuation through the skin was a few times larger than that of the skull and the presence of skin substantially reduced the VE-field peak at the cortical surface near the electrode. The VE-field declined much quicker in the gray matter underneath the pial surface than it did in the white matter, and thus the large VE-fields were contained mostly in the gray matter. The transition at the gray/white matter border caused a significant peak in the VE-field, as well as at other local inhomogeneties. A conductivity value of 0.57 S/m is predicted as a global value for the whole brain by matching our VE-field measurements to the field profile given by analytical equations for volume conductors. Finally, insertion of the current return electrode into the shoulder, submandibular, and hind leg muscles had virtually no effects on the measured E-field amplitudes in the cortex underneath the epidural electrodes.
Over-expression of the photoperiod response regulatorZmCCT10modifies plant architecture, flowering time and inflorescence morphology in maize
Authors: Stephenson Elizabeth , Estrada Stacey , Meng Xin , Ourada Jesse , Muszynski Michael G. , Habben Jeffrey E. , Danilevskaya Olga N. 
Published: August 2018

AbstractMaize originated as a tropical plant that required short days to transition from vegetative to reproductive development.ZmCCT10[CO, CONSTANS, CO-LIKEandTIMING OF CAB1(CCT) transcription factor family] is a photoperiod regulator and was identified as a major QTL controlling photoperiod sensitivity in maize. We modulated expression ofZmCCT10in transgenic maize using two constitutive promoters which cause differing expression levels. Transgenic plants over expressingZmCCT10with either promoter was delayed in their transition from vegetative to reproductive development but were not affected in their change from juvenile-to-adult vegetative growth. Strikingly, transgenic plants containing the stronger expressing construct had a very prolonged period of vegetative growth accompanied with dramatic modifications to plant architecture that impacted both vegetative and reproductive traits. These plants did not produced ears, but tassels were heavily branched, and more than half of the transgenic plants showed conversion of shoot apices into “bushy tops”, which were composed of vegetative reversion plantlets. Analysis of expression modules controlling the floral transition and meristem identity linked these networks to photoperiod dependent regulation, whereas phase change modules appeared to be photoperiod independent. Results from this study clarified the influence of the photoperiod pathway on vegetative and reproductive development and allowed to fine-tune the flowering time model for maize.
Temporally varying isotopic niche overlap of the invasive ctenophore Mnemiopsis leidyi with other zooplanktivores in the western Dutch Wadden Sea
Authors: Walraven Lodewijk van , Looijengoed Wouter van , Sarina Jung A. , Langenberg Victor T. , van der Veer Henk W. 
Published: August 2018

AbstractThe invasive ctenophore Mnemiopsis leidyi can be a major predator of zooplankton in areas where it has been introduced. In this study, the possible competition of M. leidyi with native macroplankton and nekton in the western Dutch Wadden Sea was investigated in March–August, 2011 by determining and comparing isotopic niches of zooplanktivores. Stable carbon and nitrogen isotope signatures were determined from tissue samples of fish, scyphozoa, hydromedusa, ctenophores, crustaceans and cephalopods. δ15N of M. leidyi was positively related to ctenophore size, suggesting that small ctenophores occupied a lower trophic level than large ones. A cluster analysis showed that in the spring and early summer period, when M. leidyi densities are low, average δ13C and δ15N ratios of the invasive M. leidyi were similar to those of most other gelatinous zooplankton and pelagic fish species sampled. At the beginning of the bloom period in August there was no overlap in isotopic niche of M. leidyi with that of any other pelagic zooplanktivore. During this month the population consisted mainly of larvae and juveniles with lower δ15N ratios. At present, M. leidyi appears not to be a significant competitor for other gelatinous zooplankton and fish species because the period of high diet overlap with other consumers was also the period in which M. leidyi was least abundant.
Access to and use of preventive intermittent treatment for Malaria during pregnancy: a qualitative study in Chókwè district, Southern Mozambique
Authors: Arnaldo Paulo , Cambe Isabel , Magasso Amílcar , Chicumbe Sérgio , Rovira-Vallbona Eduard , Rosanas-Urgell Anna , Enosse Sónia M. 
Published: August 2018

AbstractBackgroundMalaria remains a significant health problem in Mozambique, particularly to pregnant women and children less than five years old. Intermittent preventive treatment is recommended for malaria prevention in pregnancy (IPTp). Despite the widespread use and cost-effectiveness of this intervention, the coverage remains low. In this study, we aimed to explore the factors limiting the access and use of IPTp-SP in Chókwè district.Methods and findingsWe used qualitative research methods through semi-structured interviews to collect data from 46 pregnant women and four health care staff from Chókwè, a rural area of southern Mozambique. Data were transcribed, manually coded and analysed using content and thematic method. Participants were not aware of pregnancy-related risks of malaria infection or the benefit of malaria prevention in pregnancy. Late and infrequently antenatal care (ANC) attendance, concerns about the long waiting time at ANC consultations,plus reluctance to disclose the pregnancy early, emerged as driving factors for inadequate IPTp delivery.ConclusionsPregnant women experience substantial barriers to receive adequate IPTp-SP dosing for malaria prevention. Poor awareness, non-compliance with ANC attendance and poor attitude of health care staff were main barriers to IPTp-SP delivery. There is a need to strengthen actions that improve awareness about malaria and prevention among pregnant women, as well as quality services across the ANC services in order to increase IPTp-SP uptake.
A natural history model for planning prostate cancer testing: calibration and validation using Swedish registry data
Authors: Karlsson Andreas , Jauhiainen Alexandra , Gulati Roman , Eklund Martin , Grönberg Henrik , Etzioni Ruth , Clements Mark 
Published: August 2018

AbstractRecent prostate cancer screening trials have given conflicting results and it is unclear how to reduce prostate cancer mortality while minimising overdiagnosis and overtreatment. Prostate cancer testing is a partially observable process, and planning for testing requires either extrapolation from randomised controlled trials or, more flexibly, modelling of the cancer natural history.An existing US prostate cancer natural history model (Gulati et al, Biostatistics 2010;11:707-719) did not model for differences in survival between Gleason 6 and 7 cancers and predicted too few Gleason 7 cancers for contemporary Sweden. We re-implemented and re-calibrated the US model to Sweden. We extended the model to more finely describe the disease states, their time to biopsy-detectable cancer and prostate cancer survival. We first calibrated the model to the incidence rate ratio observed in the European Randomised Study of Screening for Prostate Cancer (ERSPC) together with age-specific cancer staging observed in the Stockholm PSA (prostate-specific antigen) and Biopsy Register; we then calibrated age-specific survival by disease states under contemporary testing and treatment using the Swedish National Prostate Cancer Register.After calibration, we were able to closely match observed prostate cancer incidence trends in Sweden. Assuming that patients detected at an earlier stage by screening receive a commensurate survival improvement, we find that the calibrated model replicates the observed mortality reduction in a simulation of ERSPC.Using the resulting model, we predicted incidence and mortality following the introduction of regular testing. Compared with a model of the current testing pattern, organised 8 yearly testing for men aged 55–69 years was predicted to reduce prostate cancer incidence by 0.11% with no increase in the mortality rate. The model is open source and suitable for planning for effective prostate cancer screening into the future.Author summaryA naïve perspective is that cancer screening is simple: people are screened, some cancers are detected early, and cancer mortality rates decline. However, the mathematics for screening becomes difficult quickly, it is hard to infer causation from observational data, and even large randomised screening studies provide limited evidence. Simulations are therefore important for planning cancer screening.We found an older US prostate cancer natural history model to be poorly suited for contemporary Sweden. We therefore re-implemented and re-calibrated the US model using data from Swedish registries.Our revised model, the Stockholm “Prostata” model, provides predictions similar to those observed in the detailed Swedish registers on prostate cancer incidence and mortality. By modelling the mechanisms of the screening effect, we can predict the benefits and harms under a range of screening interventions.
Limits to the rate of information transmission through MAPK pathway
Authors: Grabowski Frederic , Czyż Paweł , Kochańczyk Marek , Lipniacki Tomasz 
Published: August 2018

AbstractTwo important signaling pathways of NF-κB and ERK transmit merely one bit of information about the level of extracellular stimulation. It is thus unclear how such systems can coordinate complex cell responses to external cues. Here, we analyze information transmission in the MAPK/ERK pathway that features relaxation oscillations and responds to EGF by pulses of activated ERK. Based on an experimentally verified computational model of the MAPK/ERK pathway, we demonstrate that when input sequences of EGF pulses are transcoded to output sequences of ERK activity pulses, transmitted information increases nearly linearly with time. Moreover, the information channel capacity C (defined as the upper limit of information that can be transmitted over a sufficiently long time t, divided by t), is not limited by the bandwidth B = 1/τ, where τ ≈ 1 hour is the relaxation time. Specifically, when input is provided in the form of sequences of short binary EGF pulses separated by varying intervals that are multiples of τ/n (but are not shorter than τ), then for n = 2, C ≈ 1.39 bit/hour; and for n = 4, C ≈ 1.86 bit/hour. We hypothesize that the primary mode of operation of the MAPK pathway is to translate extracellular growth factor “bursts” into precisely timed intracellular ERK “spikes” of a predefined amplitude. Such pulse-interval transcoding allows to relay more information than the amplitude–amplitude transcoding considered previously for the ERK and NF-κB pathways.Author summaryTo coordinate their actions, cells communicate with each other by sending, receiving, and interpreting cytokine signals. Cells recognize chemical identity of signaling molecules and process quantitative and temporal properties of stimulation: amplitude, duration, or frequency. Previous studies indicated that the MAPK pathway transmits about one bit of information about the amplitude (concentration) of a stimulating cytokine, EGF. Sending more information may be enabled by temporal signal modulation. Here, we use the conceptual framework of information theory to support a hypothesis that the MAPK pathway, analyzed as a noisy information channel, reaches maximum information transmission rate when receiving sequences of EGF pulses that are transcoded to sequences of activity pulses of an effector kinase of the pathway, ERK. Since the pathway resetting time is about 1 hour, one could expect that—when sending EGF pulses of “0” or “1” amplitude every hour—the pathway is able transmit up to 1 bit per hour. We show, however, that when EGF pulses are separated by intervals that are not shorter than 1 hour and are multiples of 15 min (60, 75, 90 min, etc.), information rate can be nearly 2 bits per hour. We hypothesize that high information rate is necessary to control cell proliferation and motility.