bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Diagnostic Accuracy of Magnetic Resonance Imaging in Restaging of Rectal Cancer After Preoperative Chemoradiotherapy: A Meta-Analysis and Systematic Review
Authors: Wei Ming-Zhu , Zhao Zhen-Hua , Wang Jian-Yun 
Published: January 2020

Objective
To evaluate the overall diagnostic value of magnetic resonance imaging (MRI) in restaging of rectal cancer after preoperative chemoradiotherapy based on qualified studies.

Methods
PubMed, Cochrane, and EMBASE database were searched by the index words to identify the qualified studies, and relevant literature sources were also searched. The latest research was done in April 2019. Heterogeneity of the included studies was tested, which was used to select proper effect model to calculate pooled weighted sensitivity, specificity, and diagnostic odds ratio (DOR). Summary receiver operating characteristic (SROC) analyses were also performed.

Result
Nineteen studies with 1262 patients were involved in the meta-analysis exploring the diagnostic accuracy of MRI for rectal cancer. The diagnostic accuracy of MRI in T3–T4 rectal cancer was as follows: sensitivity, 81% (95% confidence interval [CI], 67%–90%); specificity, 67% (95% CI, 51%–80%); positive likelihood ratio, 2.48 (95% CI, 1.57–3.91); negative likelihood ratio, 0.28 (95% CI, 0.15–0.52); global DOR, 6.86 (95% CI, 3.07–15.30); the area under the SROC was high (0.81; 95% CI, 0.78–0.84). The diagnostic accuracy of MRI in lymphatic metastasis of rectal cancer was as follows: sensitivity, 77% (95% CI, 65%–86%); specificity, 77% (95% CI, 63%–87%); positive likelihood ratio, 3.40 (95% CI, 2.07–5.59); negative likelihood ratio, 0.30 (95% CI, 0.20–0.45); DOR, 10.81 (95% CI, 4.99–23.39); area under the SROC was high (0.84; 95% CI, 0.80–0.87).

Conclusions
This study provides a systematic review and meta-analysis of diagnostic accuracy studies of MRI for rectal cancer. The results indicate that MRI is a highly accurate diagnostic tool for rectal cancer T3–T4 staging and N staging but sensitivity and specificity are not high.
Magnetic Resonance Imaging Texture Analysis in Differentiating Benign and Malignant Breast Lesions of Breast Imaging Reporting and Data System 4: A Preliminary Study
Authors: Wang Yanfang , Liao Xing , Xiao Feng , Zhang Hanfei , Li Jianyu , Liao Meiyan 
Published: January 2020

Rationale and Objectives
This novel study aims to investigate texture parameters in distinguishing malignant and benign breast lesions classified as Breast Imaging Reporting and Data System 4 in dynamic contrast-enhanced magnetic resonance imaging (MRI).

Materials and Methods
This retrospective study included 203 patients with 136 breast cancer and 67 benign lesions who underwent breast MRI between November 23, 2016, and August 27, 2018. Co-occurrence matrix-based texture features were extracted from each lesion on T1-weighted contrast-enhanced MRI using MatLab software. The association between texture parameters and breast lesions was analyzed, and the diagnostic model for breast cancer was created. Classification performance was evaluated by the area under the receiver operating characteristic curve, sensitivity, and specificity.

Results
Significant differences were seen between malignant and benign lesions for a number of textural features, including contrast, correlation, autocorrelation, dissimilarity, cluster shade, and cluster performance (P < 0.05). After the analysis of the multicollinearity, 5 texture features (contrast, correlation, dissimilarity, cluster shade, and cluster performance) were included for the next principal component analysis. The differentiation accuracy of breast cancer based on the diagnostic model was 0.948 (95% confidence interval, 0.908–0.974).

Conclusions
Texture features that measure randomness, heterogeneity, or homogeneity may reflect underlying growth patterns of breast lesions and show great difference in malignant and benign lesions. Therefore, texture analysis may be a valuable assisted tool for diagnostic analysis on breast.
Usefulness of Virtual Monochromatic Dual-Layer Computed Tomographic Imaging for Breast Carcinoma
Authors: Inoue Taihei , Nakaura Takeshi , Iyama Ayumi , Kidoh Masafumi , Nagayama Yasunori , Uetani Hiroyuki , Oda Seitaro , Utsunomiya Daisuke , Yamashita Yasuyuki 
Published: January 2020

Objective
This study aimed to evaluate virtual monochromatic images (VMIs) obtained using dual-layer dual-energy computed tomography (CT) for breast carcinoma.

Methods
We retrospectively enrolled 28 patients with breast cancer who were pathologically diagnosed using dual-layer dual-energy CT. Virtual monochromatic images (40–200 keV) were generated. We compared CT number, image noise, contrast, and contrast-to-noise ratio (CNR) between VMIs with the highest CNR and conventional CT images. We performed qualitative image analysis between VMIs at optimized energy and conventional CT images.

Results
Image noise of VMIs was not significantly different from that of the conventional CT images. As the x-ray energy decreased, CNR increased. The 40-keV VMIs were highest CNR and higher than that of the conventional CT images. In qualitative image analysis, the 40-keV images were significantly higher than conventional CT images.

Conclusion
Both qualitative and quantitative analyses showed that the image quality of VMIs at 40 keV was significantly higher than that of conventional CT images.
Role of Diffusional Kurtosis Imaging in Differentiating Neuromyelitis Optica–Related and Multiple Sclerosis–Related Acute Optic Neuritis: Comparison With Diffusion-Weighted Imaging
Authors: Lu Ping , Yuan Ting , Liu Xilan , Tian Guohong , Zhang Jibin , Sha Yan 
Published: January 2020

Purpose
The discrimination between neuromyelitis optica (NMO)– and multiple sclerosis (MS)–related acute optic neuritis (ON) after the first presentation is difficult in clinical practice. Through a comparison with diffusion-weighted imaging using readout-segmented echo-planar imaging (RESOLVE-DWI), our aim was to determine the feasibility of diffusional kurtosis imaging (DKI) for differential diagnosis.

Materials and Methods
Orbital DKI and RESOLVE-DWI in a 3.0-T scanner were performed on 37 patients with acute ON (15 NMO-related and 22 MS-related). The mean kurtosis (MK), axial kurtosis (AK), radial kurtosis (RK), mean diffusivity (MD), and apparent diffusion coefficient (ADC) were calculated for quantitative analyses, and receiver operating characteristic curve analyses were also performed to determine their abilities to differentiate the 2 conditions.

Results
The intraclass correlation coefficients among observers were 0.842, 0.885, 0.828, 0.871, and 0.942 for MK, RK, AK, MD, and ADC, respectively, in the affected nerve group and 0.890, 0.840, 0.832, 0.934, and 0.941 in the unaffected nerve group. Regarding the comparisons of the DKI and RESOLVE-DWI parameters among the groups, the mean MK, RK, AK, MD, and ADC values were significantly lower in the affected groups (all, P < 0.001). Furthermore, the MK, RK, MD, and ADC values were significantly lower in the NMO-ON group than in the MS-ON group (P = 0.001, 0.002, 0.013, and <0.001, respectively), and no significant differences were found in the AK values (P = 0.064). In addition, establishing MK ≤ 0.843 as the diagnostic criterion for NMO-related acute ON provided the highest sensitivity (90.5%), whereas the highest specificity (91.3%) was obtained using RK ≤ 0.784 as the diagnostic criterion.

Conclusions
Diffusional kurtosis imaging is helpful for differentiating NMO-related acute ON from MS-related acute ON, and it can achieve more agreeable sensitivity and specificity than RESOLVE-DWI in differential diagnosis.
Effectiveness of Preoperative Iron Supplementation in Major Surgical Patients With Iron Deficiency
Authors: Triphaus Chris , Judd Leonie , Glaser Patricia , Goehring Marie H. , Schmitt Elke , Westphal Sabine , Füllenbach Christoph , Lindau Simone , Zacharowski Kai , Meybohm Patrick , Choorapoikayil Suma 
Published: January 2020

Objective:To evaluate the effectiveness of routine intravenous iron in surgical patients with iron deficiency anemia (IDA).Background:Anemia is the most common medical disease in the world and is an independent risk factor for morbidity and mortality. Iron deficiency (ID) is the main cause for anemia and constitutes a potentially preventable condition with great impact on surgical outcome.Methods:In this prospective single-center observational study, surgical patients were screened for the presence of anemia and ID. Patients were assigned to 1 of 4 study groups: A−(no anemia); A−, ID+, T+(no anemia, iron-deficient, iron supplementation); A+(anemia); and A+, ID+, T+(anemia, iron-deficient, iron supplementation) according to hemoglobin level, iron status, and supplementation with iron.Results:Among 1728 patients, 1028 were assigned to A−; 55 to A−, ID+, T+; 461 to A+; and 184 to A+, ID+, T+. While all iron-supplemented IDA patients required less red blood cell (RBC) transfusion during the postoperative period (A+42.5% vs A+, ID+, T+31.5%), a reduced intraoperative transfusion rate was observed for ID and IDA patients only if iron was supplemented >7 days before surgery. Hospital stay was significantly reduced by 2.8 days in iron-supplemented patients (P< 0.01 comparing 13.9 ± 0.8 days for A+, ID+, T+vs. 16.7 ± 0.7 days for A+).Conclusion:Preoperative IDA management with intravenous iron is effective in improving hemoglobin level, thereby reducing intraoperative RBC transfusion rate particular if iron is administrated >7 days before surgery. Hospital length of stay was reduced in all preoperatively iron-supplemented IDA patients.
Anellovirus Dynamics Are Associated With Primary Graft Dysfunction in Lung Transplantation
Authors: Blatter Joshua A. , Takahashi Tsuyoshi , Mittler Brigitte , Nava Ruben G. , Puri Varun , Kreisel Daniel , Wang David 
Published: January 2020

Background.
Primary graft dysfunction (PGD) is the leading cause of early death in lung transplant. Anelloviruses are small circular DNA viruses that have been noted to be present at elevated levels in immunosuppressed patients. They have been associated with both short- and long-term outcomes in lung transplant, and we hypothesized that anellovirus dynamics might be associated with the development of PGD.

Methods.
We analyzed alphatorquevirus (ie, an anellovirus genus) levels in whole blood samples from 64 adult lung transplant recipients.

Results.
Patients with a relatively rapid rise in alphatorquevirus levels in the week following transplant were less likely to develop higher-grade PGD over the first 3 days following transplant (P = 0.031).

Conclusions.
This study is the first to establish an association between the development of PGD and a component of the blood virome. While it is not known whether anelloviruses directly affect outcomes in lung transplant, they may serve as a biomarker of immune status in lung transplant recipients.
The Camouflage Machine: Optimising protective colouration using deep learning with genetic algorithms
Authors: Fennell J. G. , Talas L. , Baddeley R. J. , Cuthill I. C. , Scott-Samuel N. E. 
Published: January 2020

AbstractThe essential problem in visual detection is separating an object from its background. Whether in nature or human conflict, camouflage aims to make the problem harder, while conspicuous signals (e.g. for warning or mate attraction) require the opposite. Our goal is to provide a reliable method for identifying the hardest and easiest to find patterns, for any given environment. The problem is challenging because the parameter space provided by varying natural scenes and potential patterns is vast. Here we successfully solve the problem using deep learning with genetic algorithms and illustrate our solution by identifying appropriate patterns in two environments. To show the generality of our approach, we do so for both trichromatic and dichromatic visual systems. Patterns were validated using human participants; those identified as the best camouflage were significantly harder to find than a widely adopted military camouflage pattern, while those identified as most conspicuous were significantly easier than other patterns. Our method, dubbed the ‘Camouflage Machine’, will be a useful tool for those interested in identifying the most effective patterns in a given context.
Different ecological processes drive the assembly of dominant and rare root-associated bacteria in a promiscuous legume
Authors: Ramoneda Josep , Le Roux Jaco , Frossard Emmanuel , Frey Beat , Gamper Hannes Andres 
Published: January 2020

AbstractUnderstanding how plant-associated microbial communities assemble and the roles they play in plant performance are major goals in microbial ecology. For nitrogen-fixing rhizobia, assemblages are mostly determined by filtering by the host as well as abiotic soil conditions. However, for legumes adapted to highly variable environments and nutrient-poor soils, filtering out rhizobial partners may not be an effective strategy to ensure symbiotic benefits. As a consequence, this can lead to net increases in rhizobial diversity driven by stochastic (neutral) assembly processes. Here, we addressed whether symbiotic promiscuity of rooibos (Aspalathus linearisBurm. Dahlgren), reflects increases in rhizobial diversity that are independent of the environmental conditions, following a neutral assembly. We performed a common garden experiment to assess whether root system size and location- and habitat-specific rhizobial propagule pools of rooibos affected rhizobial community diversity and composition. We found a dominance of drift in driving taxonomic turnover in the root nodule communities, but operating at different scales in the dominantMesorhizobiumsymbionts and the rest of bacterial taxa. Specifically, drift triggered differentiation between the core rhizobial symbionts of rooibos due to dispersal limitation on a regional scale, whereas it dominated the assembly of non-dominant rhizobial taxa at the root level. This suggests the existence of a significant neutral component in rhizobial community assembly when selectivity by the host plant is low. We conclude that in this promiscuous legume neutral processes govern bacterial community root nodule community assembly, but that these operate at different scales in dominant and rare rhizobial symbionts of the plant.
Unsupervised changes in core object recognition behavior are predicted by neural plasticity in inferior temporal cortex
Authors: Jia Xiaoxuan , Hong Ha , DiCarlo James J. 
Published: January 2020

AbstractTemporal continuity of object identity is a feature of natural visual input, and is potentially exploited -- in an unsupervised manner -- by the ventral visual stream to build the neural representation in inferior temporal (IT) cortex and IT-dependent core object recognition behavior. Here we investigated whether plasticity of individual IT neurons underlies human behavioral changes induced with unsupervised visual experience by building a single-neuron plasticity model combined with a previously established IT population-to-recognition-behavior linking model to predict human learning effects. We found that our model quite accurately predicted the mean direction, magnitude and time course of human performance changes. We also found a previously unreported dependency of the observed human performance change on the initial task difficulty. This result adds support to the hypothesis that tolerant core object recognition in human and non-human primates is instructed -- at least in part -- by naturally occurring unsupervised temporal contiguity experience.
Structure of the teneurin-latrophilin complex: Alternative splicing controls synapse specificity by a novel mechanism
Authors: Li Jingxian , Xie Yuan , Cornelius Shaleeka , Jiang Xian , Kordon Szymon P. , Sando Richard , Pan Man , Leon Katherine , Südhof Thomas C. , Zhao Minglei , Araç Demet 
Published: January 2020

SUMMARYThe trans-synaptic interaction of the cell-adhesion molecules teneurins (Tenm’s) with latrophilins (Lphn’s) promotes excitatory synapse formation when Lphn’s simultaneously interact with FLRTs. Insertion of a short alternatively-spliced region within Tenm’s abolishes the Tenm-Lphn interaction and switches Tenm function to specify inhibitory synapses. How Tenm’s bind to Lphn’s in a manner regulated by alternative splicing remains unclear. Here, we report the high-resolution cryo-EM structure of the Tenm2-Lphn3 complex, and describe the trimeric Tenm2-Lphn3-FLRT3 complex. The structure reveals that the N-terminal lectin-like domain of Lphn3 binds to the Tenm2 barrel at a site far away from the alternatively-spliced region. Alternative-splicing regulates the Tenm2-Lphn3 interaction by hindering access to the Lphn-binding surface rather than altering it. Strikingly, mutagenesis of the Lphn-binding surface of Tenm2 abolishes the Lphn3 interaction and impairs excitatory but not inhibitory synapse formation. These results suggest that a multi-level coincident binding mechanism mediated by a cryptic adhesion complex between Tenm’s and Lphn’s regulates synapse specificity.
Species coexistence in resource-limited patterned ecosystems is facilitated by the interplay of spatial self-organisation and intraspecific competition
Authors: Eigentler Lukas 
Published: January 2020

AbstractThe exploration of mechanisms that enable species coexistence under competition for a sole limiting resource is widespread across ecology. Two examples of such facilitative processes are intraspecific competition and spatial self-organisation. These processes determine the outcome of competitive dynamics in many resource-limited patterned ecosystems, classical examples of which include dryland vegetation patterns, intertidal mussel beds and Sub-alpine ribbon forests. Previous theoretical investigations have explained coexistence within patterned ecosystems by making strong assumptions on the differences between species (e.g. contrasting dispersal behaviours or different functional responses to resource availability). In this paper, I show that the interplay between the detrimental effects of intraspecific competition and the facilitative nature of self-organisation forms a coexistence mechanism that does not rely on species-specific assumptions and captures coexistence across a wide range of the environmental stress gradient. I use a theoretical model that captures the interactions of two generic consumer species with an explicitly modelled resource to show that coexistence relies on a balance between species’ colonisation abilities and their local competitiveness, provided intraspecific competition is sufficiently strong. Crucially, the requirements on species’ self-limitation for coexistence to occur differ on opposite ends of the resource input spectrum. For low resource levels, coexistence is facilitated by strong intraspecific dynamics of the species superior in its colonisation abilities, but for larger volumes of resource input, strong intraspecific competition of the locally superior species enables coexistence. Results presented in this paper also highlight the importance of hysteresis in understanding tipping points, in particular extinction events. Finally, the theoretical framework provides insights into spatial species distributions within single patches, supporting verbal hypotheses on co-existence of herbaceous and woody species in dryland vegetation patterns and suggesting potential empirical tests in the context of other patterned ecosystems.
sampbias, a method for quantifying geographic sampling biases in species distribution data
Authors: Zizka Alexander , Antonelli Alexandre , Silvestro Daniele 
Published: January 2020

AbstractGeo-referenced species occurrences from public databases have become essential to biodiversity research and conservation. However, geographical biases are widely recognized as a factor limiting the usefulness of such data for understanding species diversity and distribution. In particular, differences in sampling intensity across a landscape due to differences in human accessibility are ubiquitous but may differ in strength among taxonomic groups and datasets. Although several factors have been described to influence human access (such as presence of roads, rivers, airports and cities), quantifying their specific and combined effects on recorded occurrence data remains challenging. Here we presentsampbias, an algorithm and software for quantifying the effect of accessibility biases in species occurrence datasets.Sampbiasuses a Bayesian approach to estimate how sampling rates vary as a function of proximity to one or multiple bias factors. The results are comparable among bias factors and datasets. We demonstrate the use ofsampbiason a dataset of mammal occurrences from the island of Borneo, showing a high biasing effect of cities and a moderate effect of roads and airports.Sampbiasis implemented as a well-documented, open-access and user-friendly R package that we hope will become a standard tool for anyone working with species occurrences in ecology, evolution, conservation and related fields.
Abiotic and biotic drivers underly short- and long-term soil respiration responses to experimental warming in a dryland ecosystem
Authors: Dacal Marina , García-Palacios Pablo , Asensio Sergio , Gozalo Beatriz , Ochoa Victoria , Maestre Fernando T. 
Published: January 2020

AbstractSoil carbon losses to the atmosphere through soil respiration are expected to rise with ongoing temperature increases, but available evidence from mesic biomes suggests that such response disappears after a few years of experimental warming. However, there is lack of empirical basis for these temporal dynamics in soil respiration responses, and of the mechanisms underlying them, in drylands, which collectively form the largest biome on Earth and store 32% of the global soil organic carbon pool. We coupled data from a ten-year warming experiment in a biocrust-dominated dryland ecosystem with laboratory incubations to confront 0-2 years (short-term hereafter) vs. 8-10 years (long-term hereafter) soil respiration responses to warming. Our results showed that increased soil respiration rates with short-term warming observed in areas with high biocrust cover returned to control levels in the long-term. Warming-induced increases in soil temperature were the main driver of the short-term soil respiration responses, whereas long-term soil respiration responses to warming were primarily driven by thermal acclimation and warming-induced reductions in biocrust cover. Our results highlight the importance of evaluating short and long-term soil respiration responses to warming as a mean to reduce the uncertainty in predicting the soil carbon – climate feedback in drylands.
Evolutionary dynamics ofTomato spotted wilt viruswithin and between alternate plant hosts and thrips
Authors: Ruark-Seward Casey L. , Bonville Brian , Kennedy George , Rasmussen David A. 
Published: January 2020

AbstractTomato spotted wilt virus (TSWV) is a generalist pathogen with one of the broadest known host ranges among RNA viruses. To understand how TSWV adapts to different hosts, we experimentally passaged viral populations between two alternate hosts,Emilia sochifoliaandDatura stramonium, and an obligate vector in which it also replicates, western flower thrips (Frankliniella occidentalis). Deep sequencing viral populations at multiple time points allowed us to track the evolutionary dynamics of viral populations within and between hosts. High levels of viral genetic diversity were maintained in both plants and thrips between transmission events. Rapid fluctuations in the frequency of amino acid variants indicated strong host-specific selection pressures on proteins involved in viral movement (NSm) and replication (RdRp). While several genetic variants showed opposing fitness effects in different hosts, fitness effects were generally positively correlated between hosts indicating that positive rather than antagonistic pleiotropy is pervasive. These results suggest that high levels of genetic diversity together with the positive pleiotropic effects of mutations have allowed TSWV to rapidly adapt to new hosts and expand its host range.