bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrative immunogenomic analysis of gastric cancer dictates novel immunological classification and the functional status of tumor‐infiltrating cells
Authors: Sato Yasuyoshi , Wada Ikuo , Odaira Kosuke , Hosoi Akihiro , Kobayashi Yukari , Nagaoka Koji , Karasaki Takahiro , Matsushita Hirokazu , Yagi Koichi , Yamashita Hiroharu , Fujita Masashi , Watanabe Shuichi , Kamatani Takashi , Miya Fuyuki , Mineno Junichi , Nakagawa Hidewaki , Tsunoda Tatsuhiko , Takahashi Shunji , Seto Yasuyuki , Kakimi Kazuhiro 
Published: October 2020

AbstractObjectivesA better understanding of antitumor immunity will help predict the prognosis of gastric cancer patients and tailor the appropriate therapies in each patient. Therefore, we propose a novel immunological classification of gastric cancer.MethodsWe performed whole‐exome sequencing (WES), RNA‐Seq and flow cytometry in 29 gastric cancer patients who received surgery. The TCGA data set of 323 gastric cancer patients and RNA‐Seq data of 45 patients who received pembrolizumab (Kim et al. Nat Med 2018; 24: 1449–1458) were also analysed.ResultsImmunogram analysis of cancer–immunity interaction of gastric cancer revealed immune signatures of four main types, designated Hot1, Hot2, Intermediate and Cold. Immunologically hot tumors displayed a dysfunctional T‐cell signature, while cold tumors had an exclusion signature. Ex vivo tumor‐infiltrating lymphocyte analysis documented T‐cell dysfunction with the expression of checkpoint molecules and impaired cytokine production. The T‐cell function was more profoundly damaged in Hot1 than Hot2 tumors. Patients in Hot2 subtypes had better survival in our cohort and TCGA cohort. Although these immunological subtypes overlapped to some degree with the molecular subtypes in the TCGA, intratumoral immune responses cannot be predicted solely based on histological or molecular subtyping of gastric cancer. Molecular and immunological classifications complement each other to predict the responses to anti‐PD‐1 therapy and have the potential to be a biomarker for the treatment of gastric cancer.ConclusionThe immunological classification of gastric cancer resulted in four subtypes. Hot tumors were further divided into two subtypes, between which the functional status of T cells was different.
Stabilization of Human Whole Blood Samples for Multicenter and Retrospective Immunophenotyping Studies
Authors: Rybakowska Paulina , Burbano Catalina , Van Gassen Sofie , Varela Nieves , Aguilar‐Quesada Rocío , Saeys Yvan , Alarcón‐Riquelme Marta E. , Marañón Concepción 
Published: October 2020

AbstractWhole blood is often collected for large‐scale immune monitoring studies to track changes in cell frequencies and responses using flow (FC) or mass cytometry (MC). In order to preserve sample composition and phenotype, blood samples should be analyzed within 24 h after bleeding, restricting the recruitment, analysis protocols, as well as biobanking. Herein, we have evaluated two whole blood preservation protocols that allow rapid sample processing and long‐term stability. Two fixation buffers were used, Phosphoflow Fix and Lyse (BD) and Proteomic Stabilizer (PROT) to fix and freeze whole blood samples for up to 6 months. After analysis by an 8‐plex panel by FC and a 26‐plex panel by MC, manual gating of circulating leukocyte populations and cytokines was performed. Additionally, we tested the stability of a single sample over a 13‐months period using 45 consecutive aliquots and a 34‐plex panel by MC. We observed high correlation and low bias toward any cell population when comparing fresh and 6 months frozen blood with FC and MC. This correlation was confirmed by hierarchical clustering. Low coefficients of variation (CV) across studied time points indicate good sample preservation for up to 6 months. Cytokine detection stability was confirmed by low CVs, with some differences between fresh and fixed conditions. Thirteen months regular follow‐up of PROT samples showed remarkable sample stability. Whole blood can be preserved for phenotyping and cytokine‐response studies provided the careful selection of a compatible antibody panel. However, possible changes in cell morphology, differences in antibody affinity, and changes in cytokine‐positive cell frequencies when compared to fresh blood should be considered. Our setting constitutes a valuable tool for multicentric and retrospective studies. © 2020 International Society for Advancement of Cytometry
Testosterone regulates the emission of ultrasonic vocalizations and mounting behavior during different developmental periods in mice
Authors: Kikusui Takefumi , Shima Yuichi , Sonobe Miku , Yoshida Yuuki , Nagasawa Miho , Nomoto Kensaku , Mogi Kazutaka 
Published: October 2020

AbstractTestosterone masculinizes male sexual behavior by providing organizational and activational effects during the perinatal and peripubertal periods and during adulthood, respectively. We revealed that the emission of ultrasonic vocalizations (USVs) and mounting behavior was regulated by different neural circuits. However, the detailed testosterone effects on these two behaviors have not been fully elucidated. Here, we evaluated the time‐dependent effects of testosterone on USVs and mounting behavior in mice using a testosterone treatment model, in which females were treated with testosterone to assess the “gain‐of‐function” and a “loss‐of‐function” model. In the loss‐of‐function model, we used Ad4BP/SF‐1ΔFLC/‐ male mice, in which testosterone production was abolished in prenatal and postnatal stages, and Ad4BP/SF‐1ΔFLC/ΔFLC mice, in which testosterone production was markedly reduced only in prenatal stages. When testosterone was administered to female mice during the neonatal and peripubertal periods, but not during adulthood, USV emissions increased. Conversely, testosterone treatment in adult female mice increased the mounting behavior, but not USVs. In Ad4BP/SF‐1ΔFLC/‐ mice, USVs and mounting behavior was completely absent. Ad4BP/SF‐1ΔFLC/ΔFLC male mice displayed equivalent levels of USVs but less mounting behavior. Collectively, these results suggest that testosterone has dual regulatory roles in USV emissions and mounting behavior.
Potentially handicapped but otherwise functional: Malformations in prey capture tools show no impacts on octopus life
Authors: Fernández‐Álvarez Fernando Ángel , Farré Marc , Sánchez‐Márquez Antoni , Villanueva Roger , Escolar Oscar , Navarro Joan 
Published: October 2020

AbstractLarval mortality is a keystone ecological factor for many benthic octopus since it mostly occurs before their settlement in the sea bottom as benthic juveniles. The literature had revealed that records of adult animals with morphological abnormalities (teratologies) are fewer in species with complex life cycle than in those with direct development. This is a direct consequence of the morphological, physiological, and development challenges that the transition from the larval to the adult morphology represents. During a routine fishing sample, we found an immature female horned octopus with additional buccal structures in two suckers of its ventral arms, likely rendering these suckers as inefficient. Based on the literature about the natural history of octopus, we provide evidence that these abnormalities were present at the moment of hatch. We evaluated the impact of the teratologies by comparing the shape of the buccal beaks and the trophic niche of the individual with five normal conspecifics. Although the beaks showed a different shape than normal individuals, the trophic niche was similar. Surprisingly, the teratological condition of the individual likely had no severe impacts on its life, even though it likely represents a handicap for its survival during its planktonic life. We also comment on other previous records from the literature of teratological adult octopus to highlight the amazing adaptive capacity of octopus to deal with challenging morphologies.
Strong effects of a mutualism on freshwater community structure
Authors: Creed Robert P. , Skelton James , Farrell Kaitlin J. , Brown Bryan L. 
Published: October 2020

AbstractNumerous mutualisms have been described from terrestrial and marine communities and many of these mutualisms have significant effects on community structure and function. In contrast, there are far fewer examples of mutualisms from freshwater habitats and there is no evidence that any mutualism has community‐wide or ecosystem‐level consequences. Northern hemisphere crayfish are host to a variety of ectosymbiotic worms called branchiobdellidans. The association between some of these “crayfish worms” and their hosts is a mutualism. The outcome of the association is context dependent and can be influenced by host size, symbiont number, and the environment. Here we document in two experiments that the mutualism between crayfish and these worms alters the effect of crayfish on stream community structure and sediment deposition, an important ecosystem variable. We enclosed crayfish stocked with 0 worms and intermediate (3–6) and high worm densities (12) in cages in streams in Boone, North Carolina and Clemson, South Carolina, United States. At both locations, there was a negative relationship between initial worm density and final macroinvertebrate abundance. There was a significant effect of worm treatment on macroinvertebrate community structure in both the Boone and Clemson experiments. In Boone, there were effects on both overall macroinvertebrate abundance and community composition, whereas in Clemson, changes to community structure were primarily driven by changes in total abundance. There was a negative relationship between benthic sediment volume and initial worm density in both experiments, primarily later in the experiments, though these effects were influenced by sediment deposition rates. Our results are the first to demonstrate strong effects of a mutualism on freshwater communities. Both members of this mutualism are found throughout the northern hemisphere, so similar impacts may occur in many other waterways. Given that various species in addition to crayfish function as keystone species and ecosystem engineers in freshwater systems throughout the world, mutualisms involving these strongly interacting species may be as important to the structure and functioning of freshwater systems as comparable mutualisms in marine and terrestrial systems.
Why P2X must be the part of the energy solution?
Authors: Erdem Emre 
Published: October 2020

AbstractIn this contribution, the terms “clean energy,” “green energy” has been revisited in terms of their toxic components. A state of art energy concept Power‐to‐X (P2X) technology and its prospects were discussed from a very general perspective. The problems, in particular, the limits of renewable energy technologies such as solar and wind have been introduced and the integration of P2X systems has been suggested as one of the promising solutions for not only the storage problems of renewables but also the key issue for overcoming the difficulties for decarbonization. Hence, low‐carbon processes and direct energy conversions can be achieved in industrial scales. The main advantage of P2X methods is their potential to create long term storage possibilities and that they can be replaced fossil fuels by H, CH4, or other useful chemicals. Also, the answer to two important questions has been found an answer in this contribution: (a) Can P2X technology be a promising alternative for replacing industrial combustion? (b) Which countries will be the key player for applying such technologies?
Contribution of total dry matter and harvest index to maize grain yield—A multisource data analysis
Authors: Liu Wanmao , Hou Peng , Liu Guangzhou , Yang Yunshan , Guo Xiaoxia , Ming Bo , Xie Ruizhi , Wang Keru , Liu Yuee , Li Shaokun 
Published: October 2020

AbstractUnderstanding the contribution of aboveground dry matter (DM) production and harvest index (HI) to maize grain yield is essential to further improve grain yield to ensure future food growing requirements. In this study, we collected 548 sets of data of DM, HI, and grain yield from a multisite (40 sites) and multiyear (2009–2016) experiment conducted in major maize‐growing regions across China and 615 sets of data from 40 published papers distributed from 1988 to 2018 to assess the performance of DM, HI, and their contributions to grain yield. It was found that the average contribution rate of DM was 73.71%, which was much higher than those of HI (26.28%) across China. For the five different modern hybrids, the contribution rates of DM to grain yield (ranged from 71.36% to 89.10%) were also significantly higher than those of HI (ranged from 10.79% to 28.64%) on a large spatial scale. The significant differences in grain yields between cultivars were mainly due to the differences in HI. Among the four maize‐growing regions, the contribution rates of DM in both NW (57.34%) and NM (64.46%) were higher than those of HI (42.66% and 35.54%, respectively). In contrast, the contribution rates of HI in HM (52.67%) and SW (50.92%) were slightly higher than those of DM (47.33% and 49.08%, respectively). The interregional differences in grain yield were mainly attributed to the differences in DM between regions. Additionally, combining the data of this study and data collected from previous studies, we found that the increase in maize grain yield under lower yield levels (<15 Mg/ha) was mainly attributed to the increase in both DM and HI, while that under higher yield levels (>15 Mg/ha) was mainly dependent on the increase in DM.
Improving gelatin‐based emulsion films with cold plasma using different gases
Authors: Ledari Shahrbanoo Ahmadi , Milani Jafar Mohammadzadeh , Lanbar Farshad Sohbatzadeh 
Published: October 2020

AbstractIn this research, the effects of cold plasma treatment on the properties of gelatin‐based emulsion films (GEFs) using different gases were investigated. The gases used include O2, N2, air, Ar, and ethanol‐argon (EtOH‐Ar). Surface hydrophobicity, morphology, water vapor permeability (WVP), and mechanical, thermal, and antifungal properties after plasma application on the film were analyzed. The results revealed that surface hydrophilicity significantly increased after cold plasma, while the contact angle significantly decreased (p < .05). Furthermore, atomic force microscopy results showed that the argon gas plasma significantly increased roughness of the GEFs surface. Besides, plasma did not decrease WVP. Different gases had no significant effect on the mechanical properties of the GEFs (p > .05). Oxygen permeability after plasma application was significantly different from the control sample; consequently, the permeability after plasma application decreased and the lowest level 55.7 (cm3μm m−2 day−1 Pa−1) was seen for oxygen gas. Plasma treatment caused etching effects and lessened the surface moisture of the polymer film. Antimicrobial activity was observed in the cold plasma‐treated samples, especially under air and nitrogen atmosphere. Cold plasma treatment is an effective method for surface modification, expanding the application of emulsion films in the packing industry with improved performance properties.
Effect of foliar application of selenium on morphological and physiological indices of savory (Satureja hortensis) under cadmium stress
Authors: Azizi Iraj , Esmaielpour Behrooz , Fatemi Hamideh 
Published: October 2020

AbstractCadmium is a heavy metal that pollutes the environment and affects plants physiologically and morphologically. Selenium is considered as a beneficial element, with effective roles in increasing plant tolerance to environmental stresses. A greenhouse factorial pot experiment was conducted to study the impact of selenium on traits of Savory plants under Cd stress. Experimental factors included soil contamination with cadmium (0, 75, 100, and 150 μM) and foliar spraying of selenium (0, 10, 20, and 40 μM of Sodium Selenate). Biomass, photosynthetic pigments including chlorophyll a, chlorophyll b, total chlorophyll, proline, total soluble solids, cell membrane leakage, relative water content of leaves antioxidant enzymes, and Cd and Zn concentration in shoot and root were recorded. Results revealed that Cd stress decreased vegetative growth criteria, photosynthetic pigments include chlorophyll a, chlorophyll b, total chlorophyll, and carotenoid almost, 55%, 57%, 57%, and 68%, respectively, while poline, cell membrane leakage, peroxidase (POD), and catalase (CAT) antioxidant enzymes were increased with increasing Cd concentrations. Foliar spray of selenium reduced the toxic effects of Cd stress on savory plants via enhancing of proline content and stimulation of CAT and POD enzymes and limitation of cell membrane leakage. Also, selenium foliar spray improved chlorophyll content under Cd stress condition and decreased cadmium accumulation 29% in root, respectively. In general, these results suggest that foliar application of selenium could mitigate Cd toxicity and improve growth and antioxidant capacity of savory under different level of cadmium heavy metal stress.
Beaver dam analogues drive heterogeneous groundwater–surface water interactions
Authors: Wade Jeffrey , Lautz Laura , Kelleher Christa , Vidon Philippe , Davis Julianne , Beltran Julio , Pearce Casey 
Published: October 2020

AbstractBeaver dam analogues (BDAs) are a cost‐effective stream restoration approach that leverages the recognized environmental benefits of natural beaver dams on channel stability and local hydrology. Although natural beaver dams are known to exert considerable influence on the hydrologic conditions of a stream system by mediating geomorphic processes, nutrient cycling, and groundwater–surface water interactions, the impacts of beaver‐derived restoration methods on groundwater–surface water exchange are poorly characterized. To address this deficit, we monitored hyporheic exchange fluxes and streambed porewater biogeochemistry across a sequence of BDAs installed along a central Wyoming stream during the summer of 2019. Streambed fluxes were quantified by heat tracing methods and vertical hydraulic gradients. Biogeochemical activity was evaluated using major ion porewater chemistry and principal component analysis. Vertical fluxes of approximately 1.0 m/day were observed around the BDAs, as was the development of spatially heterogeneous zones of nitrate production, groundwater upwelling, and anaerobic reduction. Strong contrasts in hyporheic zone processes were observed across BDAs of differing sizes. This suggests that structures may function with size‐dependent behaviour, only altering groundwater–surface water interactions after a threshold hydraulic step height is exceeded. Patterns of hyporheic exchange and biogeochemical cycling around the studied BDAs resemble those around natural beaver dams, suggesting that BDAs may provide comparable benefits to channel complexity and near‐stream function over a 1‐year period.
Attendance at early recall and colposcopy in routine cervical screening with human papillomavirus testing
Authors: Green Leonardo I. , Mathews Christopher S. , Waller Jo , Kitchener Henry , Rebolj Matejka ,   The HPV Pilot Steering Committee
Published: October 2020

AbstractAttendance at early recall and colposcopy is crucial to attaining the benefits of primary high‐risk human papillomavirus (HR‐HPV)‐based screening. Within the English HPV pilot, we analysed deprivation‐ and age‐related patterns of attendance at colposcopy and 12‐ and 24‐month early recall of HR‐HPV positive women screened in 2013 to 2015 (N = 36 466). We fitted logistic regression models for adjusted odds ratios (OR). Despite high overall attendance, area deprivation had a small but significant impact at both early recalls, for example, attendance at 24 months was 86.3% and 83.0% in less vs more deprived areas, respectively (ORadj: 0.76; 95% CI: 0.67‐0.87). Older women (≥30 years) were more likely to attend early recall than younger women (<30 years), for example, attendance at 24 months was 86.1% vs 82.3%, respectively (ORadj: 1.32, 95% CI: 1.16‐1.51). Most women attended colposcopy following a baseline referral, with 96.9% attendance among more deprived and 97.8% among less deprived areas (ORadj: 0.70; 95% CI: 0.55‐0.88). Differences in colposcopy attendance by deprivation level at 12 and 24 months were of approximately the same magnitude. In conclusion, attendance at early recall and colposcopy was reassuringly high. Although there were statistically significant differences by deprivation and age group, these were small in absolute terms.
Everolimus after failure of one prior VEGF‐targeted therapy in metastatic renal cell carcinoma: Final results of the MARC‐2 trial
Authors: Staehler Michael , Stöckle Michael , Christoph Daniel C. , Stenzl Arnulf , Potthoff Karin , Grimm Marc‐Oliver , Klein Dunja , Harde Johanna , Brüning Fabian , Goebell Peter J. , Augustin Marinela , Roos Frederik , Benz‐Rüd Iris , Marschner Norbert , Grünwald Viktor 
Published: October 2020

AbstractMARC‐2, a prospective, multicenter phase IV trial, aimed to investigate clinical outcomes in patients with metastatic renal cell carcinoma (mRCC) treated with everolimus after failure of one initial vascular endothelial growth factor receptor tyrosine kinase inhibitor (VEGFR‐TKI) therapy and to identify subgroups benefiting most, based on clinical characteristics and biomarkers. Patients with clear cell mRCC failing one initial VEGFR‐TKI received everolimus until progression or unacceptable toxicity. Primary endpoint was 6‐month progression‐free survival rate (6moPFS). Secondary endpoints were overall response rate (ORR), PFS, overall survival (OS), and safety. Between 2011 and 2015, 63 patients were enrolled. Median age was 65.4 years (range 43.3‐81.1). 6moPFS was 39.3% (95% confidence interval [CI], 27.0‐51.3) overall, 54.4% (95% CI, 35.2‐70.1) vs 23.7% (95% CI, 10.5‐39.9) for patients aged ≥65 vs <65 years and 51.4% (95% CI, 34.7‐65.7) vs 18.2% (95% CI, 5.7‐36.3) for patients with body mass index (BMI) >25 vs ≤25 kg/m2. A Cox proportional hazards model confirmed a longer PFS for patients aged ≥65 years (hazard ratio [HR] 0.46; 95% CI, 0.26‐0.80) and a longer OS for patients with BMI >25 kg/m2 (HR 0.36; 95% CI, 0.18‐0.71). Median PFS and median OS were 3.8 months (95% CI, 3.2‐6.2) and 16.8 months (95% CI, 14.3‐24.3). ORR was 7.9% and disease control rate was 60.3%. No new safety signals emerged. Most common adverse events were stomatitis (31.7%), fatigue (31.7%), and anemia (30.2%). One patient died from treatment‐related upper gastrointestinal hemorrhage. Everolimus remains a safe and effective treatment option for mRCC patients after one prior VEGFR‐TKI therapy. Patients aged ≥65 years and patients with BMI >25 kg/m2 benefited most.