bluuebunny/crossref_metadata_2025_split huggingface dataset:
Risk factors for the histologic discrepancy of gastric adenomatous lesions and long-term outcome
Authors: Joo Jong Seok , Park Jae Ho , Kim Ju Seok , Kang Sun Hyung , Moon Hee Seok , Sung Jae Kyu , Jeong Hyun Yong 
Published: November 2021

Abstract
Although endoscopic forceps biopsies (EFB) have a significant role in diagnosing gastric adenoma, there are still discrepancies between EFBs and finalized pathology results.
Therefore, the objective of this study was to find the risk factors that cause this discrepancy and to analyze the effects of this discrepancy on the long-term outcome.
In this study patients that had received endoscopic resection due to low-grade gastric adenoma diagnosis from EFB between January of 2011 and January of 2018 at the Chungnam National University Hospital were retrospectively analyzed. According to whether there was histological discrepancy the cumulative incidence of the metachronous lesions were analyzed.
A total of 745 lesions diagnosed as low-grade gastric adenoma at EFB were enrolled, and the final pathology results were confirmed to be non-neoplastic (n = 19), low-grade adenoma (n = 614), High-grade adenoma (n = 63), and carcinoma (n = 49), and with the exception of non-neoplastic lesion, the results confirmed 84.6% (n = 614) for the concordant group and 15.4% (n = 112) for the discordant. The results of the multivariate analysis confirmed that depressed lesion (odds ratio [OR]: 2.056; 95% confidence interval [CI]: 1.130–3.451; P = .011), erythema (OR: 2.546; 95% CI: 1.604–4.030; P = .004), and a size >1.5 cm (OR: 1.903; 95% CI: 1.102–3.172; P = .018) were risk factors for discrepancy. The results also confirmed that for the average observation period of (SD) 39.12 (12.31) months, the cumulative incidence of metachronous neoplasm had a higher significance (P = 0.001) in the discordant group when compared to that of the concordant group.
The factors related to the histologic discrepancy of low-grade gastric adenoma were depressed lesion, erythema and size >1.5 cm. In the groups with histological discrepancy, the cumulative incidence of the metachronous neoplasm was significantly higher and therefore closer observation of such patients after performing endoscopic resection is necessary.
The efficacy of 5 rehabilitation treatments after anterior cruciate ligament reconstruction
Authors: Wang Congxiao , Ji Zhonglei , Wang Luyi , Zhang Qiaorong , Wang Hujun , Qie Shuyan 
Published: November 2021

Abstract

Background:
The efficacy of traditional rehabilitation, proprioceptive training, and neuromuscular training after anterior cruciate ligament (ACL) reconstruction is also controversial. In order to help medical staff better choose the rehabilitation treatment plan after ACL reconstruction, we conducted this network meta-analysis.

Methods:
Chinese and English databases such as Wanfang, Weipu, China Zhiwang, and PubMed, Cochrane Library, Embase were retrieved. We collected clinical controlled trial papers on traditional rehabilitation therapy, proprioceptive training and neuromuscular training after ACL reconstruction for meta-analysis.

Results:
In this meta-analysis, 12 studies were included, including 486 patients who received rehabilitation treatment after ACL reconstruction. Based on network meta-analysis, it was found that 4 groups of direct comparison and 6 groups of indirect comparison were formed for 5 rehabilitation treatment schemes after ACL reconstruction. The curative effect of traditional rehabilitation training combined with proprioception training is better than that of traditional rehabilitation training (mean difference value of traditional rehabilitation training combined with proprioception training vs traditional rehabilitation training was 8.00, 95% confidence interval: 2.61,13.39). The efficacy of proprioceptive training is better than that of traditional rehabilitation training (mean difference value of proprioceptive training vs traditional rehabilitation training is 11.01, 95% confidence interval: 0.62,21.39). There was no statistical significance between the other rehabilitation trainings. According to the surface under cumulative ranking curve, the therapeutic effects of the 5 rehabilitation treatment programs after ACL reconstruction were ranked as follows: proprioceptive training (72%) > traditional rehabilitation training combined with neuromuscular training (70.8%) > traditional rehabilitation training combined with proprioception training (57.1%) > neuromuscular training (45.5%) > traditional rehabilitation training (4.6%). No publication bias was found in the funnel plot.

Conclusion:
Combined with the results of meta-analysis and surface under cumulative ranking efficacy sequence diagram, it can be seen that traditional rehabilitation training combined with proprioceptive training and traditional rehabilitation training combined with neuromuscular training have significant efficacy. Due to the limitations of this study, the conclusions of this network meta-analysis still need to be further confirmed by a large sample size and well-designed randomized controlled trials.
Posterior fossa transient ischemic attack in the setting of bilateral persistent hypoglossal arteries
Authors: Ren Xiaolu 
Published: November 2021

Abstract

Rationale:
Persistent hypoglossal artery (PHA) is the second rare abnormal anastomosis of the internal carotid and vertebrobasilar arteries, and bilateral persistent hypoglossal arteries in particular have rarely been reported. This is the first case of bilateral persistent hypoglossal arteries presenting with posterior fossa transient ischemic attack (TIA).

Patient concerns:
We reported a 54-year old female with posterior fossa TIA due to the coexisting bilateral persistent hypoglossal arteries and left internal carotid artery stenosis.

Diagnosis:
The patient was diagnosed with posterior fossa TIA, bilateral persistent hypoglossal arteries and left internal carotid artery stenosis.

Interventions:
The patient was given aspirin 100 mg/qd and advised to avoid excessive neck movement.

Outcomes:
Symptoms of intermittent subjective dizziness accompanied by nausea were relieved.

Lessons:
Although requires no special treatment, PHA could be accompanied by hypoplasia of vertebral arteries and posterior communicating arteries and becomes the main blood supply pathway for the posterior circulation. Accurate identification and evaluation of PHA is important of ensuring the safety of carotid interventions and identifying specific types of stroke.
Genome-wide selection signatures reveal widespread synergistic effects of culture conditions and temperature stress in Drosophila melanogaster
Authors: Claire Burny , Viola Nolte , Marlies Dolezal , Christian Schlötterer 
Published: November 2021

ABSTRACTExperimental evolution combined with whole-genome sequencing is a powerful approach to study the adaptive architecture of selected traits, in particular when replicated experimental populations evolving in opposite selective conditions (e.g. hot vs. cold temperature) are compared. Nevertheless, such comparisons could be affected by environmental effects shared between selective regimes (e.g. laboratory adaptation), which complicate the interpretation of selection signatures. Here, we used an experimental design, which takes advantage of the simplicity of selection signatures from founder populations with reduced variation, to study the fitness consequences of the laboratory environment (culture conditions) at two temperature regimes. After 20 generations of adaptation at 18°C and 29°C, strong genome-wide selection signatures were observed. About one third of the selection signatures can be either attributed to temperature effects, laboratory adaptation or the joint effects of both. The fitness consequences reflecting the combined effects of temperature and laboratory adaptation were more extreme in the hot environment for 83% of the affected genomic regions, fitting the pattern of larger expression differences between founders at 29°C. We propose that evolve and resequence (E&R) with reduced genetic variation allows to study genome-wide fitness consequences driven by the interaction of multiple environmental factors.
Improving Neural Networks for Genotype-Phenotype Prediction Using Published Summary Statistics
Authors: Cui Tianyu , Mekkaoui Khaoula El , Havulinna Aki , Marttinen Pekka , Kaski Samuel 
Published: November 2021

AbstractPhenotype prediction is a necessity in numerous applications in genetics. However, when the size of the individual-level data of the cohort of interest is small, statistical learning algorithms, from linear regression to neural networks, usually fail due to insufficient data. Fortunately, summary statistics from genome-wide association studies (GWAS) on other large cohorts are often publicly available. In this work, we propose a new regularization method, namely, main effect prior (MEP), for making use of GWAS summary statistics from external datasets. The main effect prior is generally applicable for machine learning algorithms, such as neural networks and linear regression. With simulation and real-world experiments, we show empirically that MEP improves the prediction performance on both homogeneous and heterogeneous datasets. Moreover, deep neural networks with MEP outperform standard baselines even when the training set is small.
Nitrate fertilization may delay autumn leaf senescence, while amino acid treatments do not
Authors: Fataftah Nazeer , Edlund Erik , Lihavainen Jenna , Bag Pushan , Björkén Lars , Näsholm Torgny , Jansson Stefan 
Published: November 2021

AbstractFertilization with nitrogen (N)-rich compounds leads to increased growth, but may compromise phenology and winter survival of trees in boreal regions. During autumn, N is remobilized from senescing leaves and stored in other parts of the tree to be used in the next growing season. However, the mechanism behind the N fertilization effect on winter survival is not well understood and it is unclear how N levels or forms modulate autumn senescence. We performed fertilization experiments and showed that treatingPopulussaplings with high or low levels of inorganic nitrogen resulted in a delay in senescence. In addition, by using precise delivery of solutes into the xylem stream ofPopulustrees in their natural environment, we found that delay of autumn senescence was dependent on the form of N administered: inorganic N (NO3−1) delayed senescence but amino acids (Arg, Glu, Gln, and Leu) did not. Metabolite profiling of leaves showed that the levels of tricarboxylic acids (TCA), arginine catabolites (ammonium, ornithine), glycine, glycine-serine ratio and overall carbon-to-nitrogen (C/N) ratio were affected differently by the way of applying NO3−1and Arg treatments. In addition, the onset of senescence did not coincide with soluble sugar accumulation in any of the treatments. Taken together, metabolomic rearrangement under different N forms or experimental setups could modulate senescence process, but not initiation and progression inPopulus. We propose that the different regulation of C and N status through direct molecular signaling of NO3−1could account for the contrasting effects of NO3−1and Arg on senescence.One sentence summaryNitrate, administered by precision fertilization through injection into the trunk, may delay autumn senescence and change metabolism inPopulusleaves, while the same amount of amino acids does not have the same effect.
Contribution of linear and nonlinear mechanisms to predictive motion estimation
Authors: Liu Belle , Hong Arthur , Rieke Fred , Manookin Michael B. 
Published: November 2021

ABSTRACTSuccessful behavior relies on the ability to use information obtained from past experience to predict what is likely to occur in the future. A salient example of predictive encoding comes from the vertebrate retina, where neural circuits encode information that can be used to estimate the trajectory of a moving object. Predictive computations should be a general property of sensory systems, but the features needed to identify these computations across neural systems are not well understood. Here, we identify several properties of predictive computations in the primate retina that likely generalize across sensory systems. These features include calculating the derivative of incoming signals, sparse signal integration, and delayed response suppression. These findings provide a deeper understanding of how the brain carries out predictive computations and identify features that can be used to recognize these computations throughout the brain.
4DPhenoMVS: A Low-Cost 3D Tomato Phenotyping Pipeline Using a 3D Reconstruction Point Cloud Based on Multiview Images
Authors: Zhai Ruifang , Wang Yinghua , Hu Songtao , Yang Wanneng 
Published: November 2021

AbstractManual phenotyping of tomato plants is time consuming and labor intensive. Due to the lack of low-cost and open-access 3D phenotyping tools, the dynamic 3D growth of tomato plants during all growth stages has not been fully explored. In this study, based on the 3D structural data points generated by employing structures from motion algorithms on multiple-view images, we proposed a dynamic 3D phenotyping pipeline, 4DPhenoMVS, to calculate and analyze 14 phenotypic traits of tomato plants covering the whole life cycle. The results showed that the R2 values between the phenotypic traits and the manual measurements stem length, plant height, and internode length were more than 0.8. In addition, to investigate the environmental influence on tomato plant growth and yield in the greenhouse, eight tomato plants were chosen and phenotyped during 7 growth stages according to different light intensities, temperatures, and humidities. The results showed that stronger light intensity and moderate temperature and humidity contribute to a higher growth rate and higher yield. In conclusion, we developed a low-cost and open-access 3D phenotyping pipeline for tomato plants, which will benefit tomato breeding, cultivation research, and functional genomics in the future.HighlightsBased on the 3D structural data points generated by employing structures from motion algorithms on multiple-view images, we developed a low-cost and open-access 3D phenotyping tool for tomato plants during all growth stages.
High-frequency changes in single-trial visual evoked potentials for unattended stimuli in chronic schizophrenia
Authors: Kipiński Lech , Maciejowski Andrzej , Małyszczak Krzysztof , Pilecki Witold 
Published: November 2021

AbstractBackgroundPatients with schizophrenia reveal changes in information processing associated with external stimuli, which is reflected in the measurements of brain evoked potentials. We discuss actual knowledge on electro- (EEG) and magnetoencephalographic (MEG) changes in schizophrenia.New methodThe commonly used averaging technique entails the loss of information regarding the generation of evoked responses. We propose a methodology to describe single-trial (non-averaged) visual evoked potentials (VEP) using spectral and statistical analyses. We analysed EEG data registered in the O1-Cz and O2-Cz leads during unattended pattern-reversal stimulation, collected from a group of adult patients with chronic schizophrenia, and compared them to those of healthy individuals. Short-time single-trial VEP were transformed to the frequency domain using the FFT algorithm. Changes of the spectral power were visualized using spectrograms which were created by stacking single-trial spectra across all trials. Measures of the absolute and the relative spectral power were calculated and compared statistically.ResultsIn schizophrenia, the energy density of VEP oscillations is shifted towards higher (gamma) frequencies, compared to healthy individuals. These differences are statistically significant in all analysed frequency bands for the relative power. This indicates distorted early processing of visual stimuli in schizophrenia.Comparison with existing methodsThe main advantage of the presented methodology is its simplicity and ease of interpretation of obtained results. The presented observations complement the knowledge on gamma oscillations acquired from computationally more complex methods of time–frequency analysis.ConclusionsHigh-frequency changes for single-trial VEPs are detected in chronic schizophrenia.
Reliability of quantitative multiparameter maps is high for MT and PD but attenuated for R1 and R2* in healthy young adults
Authors: Wenger Elisabeth , Polk Sarah E. , Kleemeyer Maike M. , Weiskopf Nikolaus , Bodammer Nils C. , Lindenberger Ulman , Brandmaier Andreas M. 
Published: November 2021

AbstractWe investigate the reliability of individual differences of four quantities measured by magnetic resonance imaging based multiparameter mapping (MPM): magnetization transfer (MT), proton density (PD), longitudinal relaxation rate (R1), and effective transverse relaxation rate (R2*). A total of four MPM datasets, two on each of two consecutive days, were acquired in healthy young adults. On Day 1, no repositioning occurred; on Day 2, participants were repositioned between MPM datasets. Using intra-class correlation effect decomposition (ICED), we assessed the contributions of session-specific, day-specific, and residual sources of measurement error. For whole-brain gray and white matter, all four MPM parameters showed high reproducibility and high reliability, as indexed by the coefficient of variation (CoV) and the intra-class correlation (ICC). However, MT, PD, R1, and R2* differed markedly in the extent to which reliability varied across brain regions. MT and PD showed high reliability in almost all regions. In contrast, R1 and R2* showed low reliability in some regions outside the basal ganglia, such that the sum of the measurement error estimates in our structural equation model was higher than estimates of between-person differences. In sum, in this sample of healthy young adults, the four MPM parameters showed very little variability over four measurements over two days but differed in how well they could assess between-person differences. We conclude that R1 and R2* might carry only limited person-specific information in samples of healthy young adults, and, by implication, might be of restricted utility for studying associations to between-person differences in behavior.
The roles of distinct Ca2+ signaling mediated by Piezo and inositol triphosphate receptor (IP3R) in the remodeling of E-cadherin during cell dissemination
Authors: Cabrera Alejandra J.H. , Gumbiner Barry M. , Kwon Young V. 
Published: November 2021

AbstractGiven the role of E-cadherin (E-cad) in holding epithelial cells together, the inverse relationship between E-cad levels and cell invasion has been perceived as a principle underlying the invasiveness of tumor cells. In contrast, our study employing the Drosophila model of cell dissemination demonstrates that E-cad is necessary for the invasiveness of Rasv12-transformed cells in vivo. Drosophila E-cad/β-catenin disassembles at adherens junctions and assembles at invasive protrusions—the actin- and cortactin-rich invadopodia-like protrusions associated with breach of the extracellular matrix (ECM)—during cell dissemination. Loss of E-cad attenuates dissemination of Rasv12-transformed cells by impairing their ability to compromise the ECM. Strikingly, the remodeling of E-cad/β-catenin subcellular distribution is controlled by two discrete intracellular calcium signaling pathways: Ca2+ release from endoplasmic reticulum via the inositol triphosphate receptor (IP3R) disassembles E-cad at adherens junctions while Ca2+ entry via the mechanosensitive channel Piezo assembles E-cad at invasive protrusions. Thus, our study provides molecular insights into the unconventional role of E-cad in cell invasion during cell dissemination in vivo and describes the discrete roles of intracellular calcium signaling in the remodeling of E-cad/β-catenin subcellular localization.
Chromosome scale assembly of allopolyploid genome of the diatom Fistulifera solaris
Authors: Maeda Yoshiaki , Watanabe Kahori , Kobayashi Ryosuke , Yoshino Tomoko , Bowler Chris , Matsumoto Mitsufumi , Tanaka Tsuyoshi 
Published: November 2021

AbstractMicroalgae including diatoms are of interest for environmentally-friendly manufacturing such as biofuel production. However, only a very few of their genomes have been elucidated owing to their diversified and complex evolutionary history. The genome of the marine oleaginous diatom Fistulifera solaris, an allopolyploid diatom possessing two subgenomes, has been analyzed previously by pyrosequencing. However, many unsolved regions and unconnected scaffolds remained. Here we report the entire chromosomal structure of the genome of F. solaris strain JPCC DA0580 using a long-read nanopore sequencing platform. From just one single run using a MinION flow-cell, the chromosome scale assembly with telomere-to-telomere resolution was achieved for 41 out of 44 chromosomes. Centromere regions were also predicted from the chromosomes, and we discovered conserved motifs in the predicted regions. The function of the motifs was experimentally confirmed by successful transformation of the diatom via bacterial conjugation. This discovery provides insights into chromosome replication, facilitating the rational design of artificial chromosomes for large-scale metabolic engineering of diatoms. The chromosome scale assembly also suggests the potential existence of multi-copy mini-chromosomes and tandemly repeated lipogenesis genes related to the oleaginous phenotype of F. solaris. The nanopore sequencing also solved the sequential arrangement of the repeat region in the F. solaris mitochondrial genome. Findings of this study will be useful to understand and further engineer the oleaginous phenotype of F. solaris.
GutMicroNet: an interactive platform for gut microbiome interaction exploration
Authors: Arif Muhammad , Portlock Theo , Güngör Cem , Koç Elif , Özcan Berkay , Subaş Oğuzhan , Çakmak Buğra , Turkez Hassan , Uhlén Mathias , Mardinoglu Adil , Shoaie Saeed 
Published: November 2021

ABSTRACTThe human gut microbiome data has been proven to be a powerful tool to understand the human body in both health and disease conditions. However, understanding their complex interactions and impact on the human body remains a challenging task. Unravelling the species-level interactions could allow us to study the causality of the microbiome. Moreover, it could lead us to better understand the underlying mechanisms of complex diseases and, subsequently, the discovery of new therapeutic targets. Given these challenges and benefits, it has become evident that a freely accessible and centralized platform for presenting gut microbiome interaction is essential to untangle the complexity and open multiple new paths and opportunities in disease- and drug-related research. Here, we present GutMicroNet, an interactive visualization platform of human gut microbiome interaction networks. We generated 45 gut microbiome co-abundance networks from various geographical origins, gender, and diseases based on the data presented in the Human Gut Microbiome Atlas. This interactive platform includes more than 1900 gut microbiome species and allows users to query multiple species at the same time based on their interests and adjust it based on the statistical properties. Moreover, users can download publication-ready figures or network information for further analysis. The platform can be accessed freely onhttps://gutmicro.netwithout any login requirements or limitations, including access to the full networks data.