bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exotic plants accumulate and share herbivores yet dominate communities via rapid growth
Authors: Allen Warwick J. , Waller Lauren P. , Barratt Barbara I. P. , Dickie Ian A. , Tylianakis Jason M. 
Published: May 2021

AbstractHerbivores may facilitate or impede exotic plant invasion, depending on their direct and indirect interactions with exotic plants relative to co-occurring natives. However, previous studies investigating direct effects have mostly used pairwise native-exotic comparisons with few enemies, reached conflicting conclusions, and largely overlooked indirect interactions such as apparent competition. Here, we ask whether native and exotic plants differ in their interactions with invertebrate herbivores. We manipulate and measure plant-herbivore and plant-soil biota interactions in 160 experimental mesocosm communities to test several invasion hypotheses. We find that compared with natives, exotic plants support higher herbivore diversity and biomass, and experience larger proportional biomass reductions from herbivory, regardless of whether specialist soil biota are present. Yet, exotics consistently dominate community biomass, likely due to their fast growth rates rather than strong potential to exert apparent competition on neighbors. We conclude that polyphagous invertebrate herbivores are unlikely to play significant direct or indirect roles in mediating plant invasions, especially for fast-growing exotic plants.
Disruption of FOXO3a-miRNA feedback inhibition of IGF2/IGF-1R/IRS1 signaling confers Herceptin resistance in HER2-positive breast cancer
Authors: Luo Liyun , Zhang Zhijie , Qiu Ni , Ling Li , Jia Xiaoting , Song Ying , Li Hongsheng , Li Jiansheng , Lyu Hui , Liu Hao , He Zhimin , Liu Bolin , Zheng Guopei 
Published: May 2021

AbstractResistance to Herceptin represents a significant challenge for successful treatment of HER2-positive breast cancer. Here, we show that in Herceptin-sensitive cells, FOXO3a regulates specific miRNAs to control IGF2 and IRS1 expression, retaining basic IGF2/IGF-1R/IRS1 signaling. The basic activity maintains expression of PPP3CB, a subunit of the serine/threonine-protein phosphatase 2B, to restrict FOXO3a phosphorylation (p-FOXO3a), inducing IGF2- and IRS1-targeting miRNAs. However, in Herceptin-resistant cells, p-FOXO3a levels are elevated due to transcriptional suppression of PPP3CB, disrupting the negative feedback inhibition loop formed by FOXO3a and the miRNAs, thereby upregulating IGF2 and IRS1. Moreover, we detect significantly increased IGF2 in blood and IRS1 in the tumors of breast cancer patients with poor response to Herceptin-containing regimens. Collectively, we demonstrate that the IGF2/IGF-1R/IRS1 signaling is aberrantly activated in Herceptin-resistant breast cancer via disruption of the FOXO3a-miRNA negative feedback inhibition. Such insights provide avenues to identify predictive biomarkers and effective strategies overcoming Herceptin resistance.
Protein-based antigen presentation platforms for nanoparticle vaccines
Authors: Nguyen Brian , Tolia Niraj H. 
Published: May 2021

AbstractModern vaccine design has sought a minimalization approach, moving to the isolation of antigens from pathogens that invoke a strong neutralizing immune response. This approach has created safer vaccines but may limit vaccine efficacy due to poor immunogenicity. To combat global diseases such as COVID-19, malaria, and AIDS there is a clear urgency for more effective next-generation vaccines. One approach to improve the immunogenicity of vaccines is the use of nanoparticle platforms that present a repetitive array of antigen on its surface. This technology has been shown to improve antigen presenting cell uptake, lymph node trafficking, and B-cell activation through increased avidity and particle size. With a focus on design, we summarize natural platforms, methods of antigen attachment, and advancements in generating self-assembly that have led to new engineered platforms. We further examine critical parameters that will direct the usage and development of more effective platforms.
Mangrove roots model suggest an optimal porosity to prevent erosion
Authors: Kazemi Amirkhosro , Castillo Luciano , Curet Oscar M. 
Published: May 2021

AbstractMangrove swamps are extremely productive ecosystems providing many ecological services in coastal regions. The hydrodynamic interactions of mangrove roots and water flow have been proposed as a key element to mitigate erosion. Several studies reveal that precise prediction of the morphological evolution of coastal areas, in the face of global warming and the consequent sea-level rise, requires an understanding of interactions between root porosity (the fraction of the volume of void space over the total volume), water flows, and sediment transport. Water flows around the mangrove prop roots create a complex energetic process that mixes up sediments and generates a depositional region posterior to the roots. In this work, we investigated the boundary layer behind permeable arrays of cylinders (patch) that represent the mangrove roots to explore the impact of patch porosity on the onset of sediment transport. The flow measurements were performed in a vertical plane along the water depth downstream of the mangrove root models. A high-resolution Particle Image Velocimetry (PIV) was used in a flume to observe the impact of porosity on the mean flow, velocity derivatives, skin friction coefficient, and production of turbulent kinetic energy for Reynolds number of 2500 (based on patch diameter length-scale). Here, we proposed a predictive model for critical velocity for incipient motion that takes into account the mangrove roots porosity and the near-bed turbulence effect. It is found that the patch with the $$\phi =47\%$$

ϕ
=
47
%

porosity, has the maximum critical velocity over which the sediment transport initiates. We found the optimum porosity has the minimum sediment erosion and creates negative vorticity sources near the bed that increases the critical velocity. This signifies an optimum porosity for the onset of sediment transport consistent with the porosity of mangroves in nature. The phenomenological model is elucidated based on an analysis of the vorticity evolution equation for viscous incompressible flows. For the optimum porous patch, a sink of vorticity was formed which yielded to lower the near-bed turbulence and vorticity. The minimum velocity fluctuations were sufficient to initiate the boundary layer transition, however, the viscous dissipation dominated the turbulence production to obstruct the sediment transport. This work identified the pivotal role of mangrove root porosity in sediment transport in terms of velocity and its derivatives in wall-bounded flows. Our work also provides insight into the sediment transport and erosion processes that govern the evolution of the shapes of shorelines.
IDH2 mutations in patients with normal karyotype AML predict favorable responses to daunorubicin, cytarabine and cladribine regimen
Authors: Libura Marta , Bialopiotrowicz Emilia , Giebel Sebastian , Wierzbowska Agnieszka , Roboz Gail J. , Piatkowska-Jakubas Beata , Pawelczyk Marta , Gorniak Patryk , Borg Katarzyna , Wojtas Magdalena , Florek Izabella , Matiakowska Karolina , Jazwiec Bozena , Solarska Iwona , Noyszewska-Kania Monika , Piechna Karolina , Zawada Magdalena , Czekalska Sylwia , Salamanczuk Zoriana , Karabin Karolina , Wasilewska Katarzyna , Paluszewska Monika , Urbanowska Elzbieta , Gajkowska-Kulik Justyna , Semenczuk Grazyna , Rybka Justyna , Wrobel Tomasz , Ejduk Anna , Kata Dariusz , Grosicki Sebastian , Robak Tadeusz , Pluta Agnieszka , Kominek Agata , Piwocka Katarzyna , Pyziak Karolina , Sroka-Porada Agnieszka , Wrobel Anna , Przybylowicz Agnieszka , Wojtaszewska Marzena , Lewandowski Krzysztof , Gil Lidia , Piekarska Agnieszka , Knopinska Wanda , Bolkun Lukasz , Warzocha Krzysztof , Kuliczkowski Kazimierz , Sacha Tomasz , Basak Grzegorz , Jedrzejczak Wieslaw Wiktor , Holowiecki Jerzy , Juszczynski Przemysław , Haus Olga 
Published: May 2021

AbstractMutations in isocitrate dehydrogenase 1 and 2 (IDH1/2) genes occur in about 20% patients with acute myeloid leukemia (AML), leading to DNA hypermethylation and epigenetic deregulation. We assessed the prognostic significance of IDH1/2 mutations (IDH1/2+) in 398 AML patients with normal karyotype (NK-AML), treated with daunorubicine + cytarabine (DA), DA + cladribine (DAC), or DA + fludarabine. IDH2 mutation was an independent favorable prognostic factor for 4-year overall survival (OS) in total NK-AML population (p = 0.03, censoring at allotransplant). We next evaluated the effect of addition of cladribine to induction regimen on the patients’ outcome according to IDH1/2 mutation status. In DAC group, 4-year OS was increased in IDH2+ patients, compared to IDH-wild type group (54% vs 33%; p = 0.0087, censoring at allotransplant), while no difference was observed for DA-treated subjects. In multivariate analysis, DAC independently improved the survival of IDH2+ patients (HR = 0.6 [0.37–0.93]; p = 0.024; censored at transplant), indicating that this group specifically benefits from cladribine-containing therapy. In AML cells with R140Q or R172K IDH2 mutations, cladribine restrained mutations-related DNA hypermethylation. Altogether, DAC regimen produces better outcomes in IDH2+ NK-AML patients than DA, and this likely results from the hypomethylating activity of cladribine. Our observations warrant further investigations of induction protocols combining cladribine with IDH1/2 inhibitors in IDH2-mutant.
Combining radiomic phenotypes of non-small cell lung cancer with liquid biopsy data may improve prediction of response to EGFR inhibitors
Authors: Yousefi Bardia , LaRiviere Michael J. , Cohen Eric A. , Buckingham Thomas H. , Yee Stephanie S. , Black Taylor A. , Chien Austin L. , Noël Peter , Hwang Wei-Ting , Katz Sharyn I. , Aggarwal Charu , Thompson Jeffrey C. , Carpenter Erica L. , Kontos Despina 
Published: May 2021

AbstractAmong non-small cell lung cancer (NSCLC) patients with therapeutically targetable tumor mutations in epidermal growth factor receptor (EGFR), not all patients respond to targeted therapy. Combining circulating-tumor DNA (ctDNA), clinical variables, and radiomic phenotypes may improve prediction of EGFR-targeted therapy outcomes for NSCLC. This single-center retrospective study included 40 EGFR-mutant advanced NSCLC patients treated with EGFR-targeted therapy. ctDNA data included number of mutations and detection of EGFR T790M. Clinical data included age, smoking status, and ECOG performance status. Baseline chest CT scans were analyzed to extract 429 radiomic features from each primary tumor. Unsupervised hierarchical clustering was used to group tumors into phenotypes. Kaplan–Meier (K–M) curves and Cox proportional hazards regression were modeled for progression-free survival (PFS) and overall survival (OS). Likelihood ratio test (LRT) was used to compare fit between models. Among 40 patients (73% women, median age 62 years), consensus clustering identified two radiomic phenotypes. For PFS, the model combining radiomic phenotypes with ctDNA and clinical variables had c-statistic of 0.77 and a better fit (LRT p = 0.01) than the model with clinical and ctDNA variables alone with a c-statistic of 0.73. For OS, adding radiomic phenotypes resulted in c-statistic of 0.83 versus 0.80 when using clinical and ctDNA variables (LRT p = 0.08). Both models showed separation of K–M curves dichotomized by median prognostic score (p < 0.005). Combining radiomic phenotypes, ctDNA, and clinical variables may enhance precision oncology approaches to managing advanced non-small cell lung cancer with EGFR mutations.
Hemiacetal-less rapamycin derivatives designed and produced by genetic engineering of a type I polyketide synthase
Authors: Kudo Kei , Nishimura Takehiro , Kozone Ikuko , Hashimoto Junko , Kagaya Noritaka , Suenaga Hikaru , Ikeda Haruo , Shin-ya Kazuo 
Published: May 2021

AbstractEngineering polyketide synthases is one of the most promising ways of producing a variety of polyketide derivatives. Exploring the undiscovered chemical space of this medicinally important class of middle molecular weight natural products will aid in the development of improved drugs in the future. In previous work, we established methodology designated ‘module editing’ to precisely manipulate polyketide synthase genes cloned in a bacterial artificial chromosome. Here, in the course of investigating the engineering capacity of the rapamycin PKS, novel rapamycin derivatives 1–4, which lack the hemiacetal moiety, were produced through the heterologous expression of engineered variants of the rapamycin PKS. Three kinds of module deletions in the polyketide synthase RapC were designed, and the genetically engineered vectors were prepared by the in vitro module editing technique. Streptomyces avermitilis SUKA34 transformed with these edited PKSs produced new rapamycin derivatives. The planar structures of 1–4 established based on 1D and 2D NMR, ESI–TOF–MS and UV spectra revealed that 2 and 3 had skeletons well-matched to the designs, but 1 and 4 did not. The observations provide important insights into the mechanisms of the later steps of rapamycin skeletal formation as well as the ketone-forming oxygenase RapJ.
Delineating visual, auditory and motor regions in the human brain with functional neuroimaging: a BrainMap-based meta-analytic synthesis
Authors: Heckner Marisa K. , Cieslik Edna C. , Küppers Vincent , Fox Peter T. , Eickhoff Simon B. , Langner Robert 
Published: May 2021

AbstractMost everyday behaviors and laboratory tasks rely on visual, auditory and/or motor-related processes. Yet, to date, there has been no large-scale quantitative synthesis of functional neuroimaging studies mapping the brain regions consistently recruited during such perceptuo-motor processing. We therefore performed three coordinate-based meta-analyses, sampling the results of neuroimaging experiments on visual (n = 114), auditory (n = 122), or motor-related (n = 251) processing, respectively, from the BrainMap database. Our analyses yielded both regions known to be recruited for basic perceptual or motor processes and additional regions in posterior frontal cortex. Comparing our results with data-driven network definitions based on resting-state functional connectivity revealed good overlap in expected regions but also showed that perceptual and motor task-related activations consistently involve additional frontal, cerebellar, and subcortical areas associated with “higher-order” cognitive functions, extending beyond what is captured when the brain is at “rest.” Our resulting sets of domain-typical brain regions can be used by the neuroimaging community as robust functional definitions or masks of regions of interest when investigating brain correlates of perceptual or motor processes and their interplay with other mental functions such as cognitive control or affective processing. The maps are made publicly available via the ANIMA database.
A new approach to radon temporal correction factor based on active environmental monitoring devices
Authors: Dicu T. , Burghele B. D. , Botoş M. , Cucoș A. , Dobrei G. , Florică Ș. , Grecu Ș. , Lupulescu A. , Pap I. , Szacsvai K. , Țenter A. , Sainz C. 
Published: May 2021

AbstractThe present study aims to identify novel means of increasing the accuracy of the estimated annual indoor radon concentration based on the application of temporal correction factors to short-term radon measurements. The necessity of accurate and more reliable temporal correction factors is in high demand, in the present age of speed. In this sense, radon measurements were continuously carried out, using a newly developed smart device accompanied by CR-39 detectors, for one full year, in 71 residential buildings located in 5 Romanian cities. The coefficient of variation for the temporal correction factors calculated for combinations between the start month and the duration of the measurement presented a low value (less than 10%) for measurements longer than 7 months, while a variability close to 20% can be reached by measurements of up to 4 months. Results obtained by generalized estimating equations indicate that average temporal correction factors are positively associated with CO2 ratio, as well as the interaction between this parameter and the month in which the measurement took place. The impact of the indoor-outdoor temperature differences was statistically insignificant. The obtained results could represent a reference point in the elaboration of new strategies for calculating the temporal correction factors and, consequently, the reduction of the uncertainties related to the estimation of the annual indoor radon concentration.
Proteome and transcriptome analyses of wheat near isogenic lines identifies key proteins and genes of wheat bread quality
Authors: Lv Liangjie , Zhao Aiju , Zhang Yelun , Li Hui , Chen Xiyong 
Published: May 2021

AbstractThe regulation of wheat protein quality is a highly complex biological process involving multiple metabolic pathways. To reveal new insights into the regulatory pathways of wheat glutenin synthesis, we used the grain-filling period wheat grains of the near-isogenic lines NIL-723 and NIL-1010, which have large differences in quality, to perform a combined transcriptome and proteome analysis. Compared with NIL-1010, NIL-723 had 1287 transcripts and 355 proteins with significantly different abundances. Certain key significantly enriched pathway were identified, and wheat quality was associated with alanine, aspartate and glutamate metabolism, nitrogen metabolism and alpha-linolenic acid metabolism. Differentially expressed proteins (DEPs) or Differentially expressed genes (DEGs) in amino acid synthesis pathways were upregulated primarily in the glycine (Gly), methionine (Met), threonine (Thr), glutamic acid (Glu), proline (proC), cysteine (Cys), and arginine (Arg) synthesis and downregulated in the tryptophan (trpE), leucine (leuC), citrulline (argE), and ornithine (argE) synthesis. Furthermore, to elucidate changes in glutenin in the grain synthesis pathway, we plotted a regulatory pathway map and found that DEGs and DEPs in ribosomes (RPL5) and the ER (HSPA5, HYOU1, PDIA3, PDIA1, Sec24, and Sec31) may play key roles in regulating glutenin synthesis. The transcriptional validation of some of the differentially expressed proteins through real-time quantitative PCR analysis further validated the transcriptome and proteomic results.
Morpho-molecular signal correlation between optical coherence tomography and Raman spectroscopy for superior image interpretation and clinical diagnosis
Authors: Schie Iwan W. , Placzek Fabian , Knorr Florian , Cordero Eliana , Wurster Lara M. , Hermann Gregers G. , Mogensen Karin , Hasselager Thomas , Drexler Wolfgang , Popp Jürgen , Leitgeb Rainer A. 
Published: May 2021

AbstractThe combination of manifold optical imaging modalities resulting in multimodal optical systems allows to discover a larger number of biomarkers than using a single modality. The goal of multimodal imaging systems is to increase the diagnostic performance through the combination of complementary modalities, e.g. optical coherence tomography (OCT) and Raman spectroscopy (RS). The physical signal origins of OCT and RS are distinctly different, i.e. in OCT it is elastic back scattering of photons, due to a change in refractive index, while in RS it is the inelastic scattering between photons and molecules. Despite those diverse characteristics both modalities are also linked via scattering properties and molecular composition of tissue. Here, we investigate for the first time the relation of co-registered OCT and RS signals of human bladder tissue, to demonstrate that the signals of these complementary modalities are inherently intertwined, enabling a direct but more importantly improved interpretation and better understanding of the other modality. This work demonstrates that the benefit for using two complementary imaging approaches is, not only the increased diagnostic value, but the increased information and better understanding of the signal origins of both modalities. This evaluation confirms the advantages for using multimodal imaging systems and also paves the way for significant further improved understanding and clinically interpretation of both modalities in the future.
Radiomics-based neural network predicts recurrence patterns in glioblastoma using dynamic susceptibility contrast-enhanced MRI
Authors: Shim Ka Young , Chung Sung Won , Jeong Jae Hak , Hwang Inpyeong , Park Chul-Kee , Kim Tae Min , Park Sung-Hye , Won Jae Kyung , Lee Joo Ho , Lee Soon-Tae , Yoo Roh-Eul , Kang Koung Mi , Yun Tae Jin , Kim Ji-Hoon , Sohn Chul-Ho , Choi Kyu Sung , Choi Seung Hong 
Published: May 2021

AbstractGlioblastoma remains the most devastating brain tumor despite optimal treatment, because of the high rate of recurrence. Distant recurrence has distinct genomic alterations compared to local recurrence, which requires different treatment planning both in clinical practice and trials. To date, perfusion-weighted MRI has revealed that perfusional characteristics of tumor are associated with prognosis. However, not much research has focused on recurrence patterns in glioblastoma: namely, local and distant recurrence. Here, we propose two different neural network models to predict the recurrence patterns in glioblastoma that utilizes high-dimensional radiomic profiles based on perfusion MRI: area under the curve (AUC) (95% confidence interval), 0.969 (0.903–1.000) for local recurrence; 0.864 (0.726–0.976) for distant recurrence for each patient in the validation set. This creates an opportunity to provide personalized medicine in contrast to studies investigating only group differences. Moreover, interpretable deep learning identified that salient radiomic features for each recurrence pattern are related to perfusional intratumoral heterogeneity. We also demonstrated that the combined salient radiomic features, or “radiomic risk score”, increased risk of recurrence/progression (hazard ratio, 1.61; p = 0.03) in multivariate Cox regression on progression-free survival.