bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single‐cell RNA sequencing reveals the multi‐cellular ecosystem in different radiological components of pulmonary part‐solid nodules
Authors: Li Yanmeng , Li Xiao , Chen Haiming , Sun Kunkun , Li Hao , Zhou Ying , Wang Jun , Bai Fan , Yang Fan 
Published: February 2022

AbstractBackgroundEarly‐stage lung adenocarcinoma that radiologically manifests as part‐solid nodules, consisting of both ground‐glass and solid components, has distinctive growth patterns and prognosis. The characteristics of the tumour microenvironment and transcriptional features of the malignant cells of different radiological phenotypes remain poorly understood.MethodsTwelve treatment‐naive patients with radiological part‐solid nodules were enrolled. After frozen pathology was confirmed as lung adenocarcinoma, two regions (ground‐glass and solid) from each of the 12 part‐solid nodules and 5 normal lung tissues from 5 of the12 patients were subjected to single‐cell sequencing by 10x Genomics. We used Seurat v3.1.5 for data integration and analysis.ResultsWe comprehensively dissected the multicellular ecosystem of the ground‐glass and solid components of part‐solid nodules at the single‐cell resolution. In tumours, these components had comparable proportions of malignant cells. However, the angiogenesis, epithelial‐to‐mesenchymal transition, KRAS, p53, and cell‐cycle signalling pathways were significantly up‐regulated in malignant cells within solid components compared to those within ground‐glass components. For the tumour microenvironment, the relative abundance of myeloid and NK cells tended to be higher in solid components than in ground‐glass components. Slight subtype composition differences existed between the ground‐glass and solid components. The T/NK cell subsets’ cytotoxic function and the macrophages’ pro‐inflammation function were suppressed in solid components. Moreover, pericytes in solid components had a stronger communication related to angiogenesis promotion with endothelial cells and tumour cells.ConclusionThe cellular landscape of ground‐glass components is significantly different from that of normal tissue and similar to that of solid components. However, transcriptional differences exist in the vital signalling pathways of malignant and immune cells within these components.
An asymmetric CPW‐fed modified bow tie‐shaped antenna with parasitic elements for ultra‐wideband applications
Authors: Alam Md. Mottahir , Azim Rezaul , Sobahi Nebras M. , Khan Asif Irshad , Islam Mohammad Tariqul 
Published: February 2022

SummaryIn this paper, a modified bow tie‐shaped antenna for ultra‐wideband (UWB) communication applications is presented. The anticipated antenna consists of a CPW‐fed modified bow tie‐shaped patch and two asymmetric ground planes with dual parasitic elements. Electromagnetic computation on the antenna demonstrates that the patch and grounds are strongly linked, and the designed antenna can exhibit multiple resonances which overlap to reveal the UWB working spectrum. Experimental verification of the presented antenna shows that the antenna achieved a working band of 3.2–11.0 GHz, with a fractional bandwidth of 109.9%. The antenna also attained a peak gain of 4.32 dBi at 7.3 GHz and peak efficiency of 87.3% at 6.8 GHz and reveals excellent time‐domain behavior and omnidirectional radiation patterns throughout the operating band. A small‐size, large operating band, high gain and efficiency, high fidelity factor, omnidirectional radiation patterns, and very small group delay make the antenna ideal for portable communication devices in the UWB band.
Phylogeography and population genetic structure of the European roe deer in Switzerland following recent recolonization
Authors: Vasiljevic Nina , Morf Nadja V. , Senn Josef , Pérez‐Espona Sílvia , Mattucci Federica , Mucci Nadia , Moore‐Jones Gaia , Pisano Simone Roberto Rolando , Kratzer Adelgunde , Ogden Rob 
Published: February 2022

AbstractIn the early 1800s, the European roe deer (Capreolus capreolus) was probably extirpated from Switzerland, due to overhunting and deforestation. After a federal law was enacted in 1875 to protect lactating females and young, and limiting the hunting season, the roe deer successfully recovered and recolonized Switzerland. In this study, we use mitochondrial DNA and nuclear DNA markers to investigate the recolonization and assess contemporary genetic structure in relation to broad topographic features, in order to understand underlying ecological processes, inform future roe deer management strategies, and explore the opportunity for development of forensic traceability tools. The results concerning the recolonization origin support natural, multidirectional immigration from neighboring countries. We further demonstrate that there is evidence of weak genetic differentiation within Switzerland among topographic regions. Finally, we conclude that the genetic data support the recognition of a single roe deer management unit within Switzerland, within which there is a potential for broad‐scale geographic origin assignment using nuclear markers to support law enforcement.
Face‐off: Novel depredation and nest defense behaviors between an invasive and a native predator in the Greater Everglades Ecosystem, Florida, USA
Authors: Currylow Andrea F. , McCollister Matthew F. , Anderson Gretchen E. , Josimovich Jillian M. , Fitzgerald Austin L. , Romagosa Christina M. , Yackel Adams Amy A. 
Published: February 2022

AbstractWe describe several photo‐documented novel interactions between intraguild predators in southern Florida—the native bobcat (Lynx rufus) and the invasive Burmese python (Python bivittatus). Over several days we documented a bobcat's depredation of an unguarded python nest and subsequent python nest defense behavior following the return of both animals to the nest. This is the first documentation of any animal in Florida preying on python eggs, and the first evidence or description of such antagonistic interactions at a python nest.
Competition and disturbance affect elevational distribution of two congeneric conifers
Authors: Takahashi Koichi , Ikeda Keigo , Okuhara Isao , Kurasawa Rintaro , Kobayashi Suguru 
Published: February 2022

AbstractClimatic change will affect elevational vegetation distribution because vegetation distribution is related to thermal conditions. However, how elevational species distributions are determined by biotic and abiotic factors is not clear. The long‐term plot census along an elevational gradient is indispensable to clarify mechanisms of elevational distribution of tree species. Two congeneric conifers, the less shade‐tolerant Abies veitchii and shade‐tolerant A. mariesii, dominate at low and high elevations, respectively, in the subalpine zone in Japan. This study investigated the population dynamics of the two species at three elevations (low, middle, high) for 13 years to examine why the two species dominated the different elevations from the viewpoints of competition and disturbance. This study showed that growth and survival rates were not highest at the most dominant elevations for each species. At the high elevation where A. mariesii dominated and small disturbances frequently occurred, the recruitment rate of A. mariesii was highest among the three elevations and that of A. veitchii was largely decreased by tree competition. However, A. veitchii was dominant earlier than A. mariesii at the low elevation after large disturbances by the high growth rate of individual trees. Therefore, A. mariesii was superior to A. veitchii at the high elevation because of its high recruitment rate and large reduction of recruitment of A. veitchii due to competition, while A. veitchii was superior to A. mariesii at the low elevation after large disturbances because of higher growth rate than A. mariesii. It is suggested that the elevational distributions of the two species were determined by elevational changes in population dynamics in relation to competition and disturbance. Long‐term observational studies of forest dynamics among various elevations are indispensable to predict the effects of climatic change on vegetation distribution.
Metapopulation dynamics of multiple species in a heterogeneous landscape
Authors: Pantel Jelena H. , Lamy Thomas , Dubart Maxime , Pointier Jean‐Pierre , Jarne Philippe , David Patrice 
Published: February 2022

AbstractCharacterizing the diversity of demographic strategies among species can inform research in topics such as trait syndromes, community stability, coexistence, and ecological succession. However, this diversity can depend on the spatial scale considered: at the landscape scale, species often form metapopulations, that is sets of local, sometimes short‐lived, populations, inhabiting discrete habitat patches. Metapopulation dynamics are most frequently analyzed in individual species or pairs of interacting species because of the large amount of data required for multiple species, and because species vary in their perceptions of what constitutes a favorable or unfavorable habitat. Here we evaluate, using a case study, whether a metapopulation model can be used to generate accurate estimates of demographic parameters and to describe the diversity of dynamics, responses to environment, and prospects of long‐term persistence in a guild of species inhabiting a common fragmented landscape. We applied this approach to a guild of 22 mollusk species that inhabit freshwater habitats on two islands of Guadeloupe, to compare metapopulation dynamics among species. We analyzed a 15‐year time series of occupancy records for 278 sites using a multistate occupancy model that estimated colonization and extinction rates as a function of site‐specific and year‐specific environmental covariates, then used model results to simulate future island metapopulation dynamics. Despite the diverse array of metapopulation trajectories—a mix of species with either stable, increasing, declining, or fluctuating metapopulations—and the inherent challenges associated with such data (e.g., imperfect detection, spatial and temporal heterogeneity), our model accurately captured among‐patch variation in suitability for many mollusk taxa. The dynamics of rare species or species with habitat preferences not fully captured by the retained set of covariates were less well described. For several species, we detected a negative correlation between extinction and colonization. This variation in habitat suitability created species‐specific extinction‐resistant pockets in the landscape. Our comparative analysis also revealed that species had distinct strategies for metapopulation dynamics, such as “fast‐turnover” species with both a high proportion of occupied sites and a high rate of site extinction in the landscape.
Organic fluorescent nanoprobes with NIR‐IIb characteristics for deep learning
Authors: Wanderi Kevin , Cui Zongqiang 
Published: February 2022

AbstractIllumination of biological events with near‐infrared II sub‐channel (NIR‐IIb, 1500–1700 nm) enhances the transparency of biological tissues, which is very attractive for deep imaging. Due to the long‐wavelength, which reduces optical damage, suppresses autofluorescence, and obviates light scattering, NIR‐IIb nanoprobes afford deep tissue penetration with unprecedented spatiotemporal resolution. Hence, NIR‐IIb imaging facilitates deep learning and decipherment of biological proceedings in living organisms with astounding high clarity. In comparison to its predecessors in the visible‐near‐infrared spectrum, imaging in the NIR‐IIb has shown great potential for tissue imaging and extrapolating imaging applications for clinical studies. However, the use of organic fluorescent nanoprobes (OFNPs) in the NIR‐IIb region is still rare since it is in its early stages. Thus, herein we aim to survey the recent development of different organic fluorescent nanomaterials with NIR‐IIb characteristics, their unique photophysical properties, and their utilization in deep imaging in animal models. Further, practical researches on organic fluorescent nanoprobes with NIR‐IIb emission and their transition to clinical applications are highlighted.
Urban Households’ Biomass Energy Fuel Stacking and Its Implications for Sustainable Development Goal Seven: The Case of Jimma Town, Ethiopia
Authors: Tucho Gudina Terefe , Deti Mulunesh , Dadi Dessalegni , Teshome Tizita 
Published: February 2022

AbstractSustainable development goal seven aims to provide access to affordable, reliable, sustainable, and modern energy for all by 2030, but its progress and energy stacking conditions have not been evaluated. This study aims to assess the urban household energy profile and link its state to sustainable development goals. This study employs a cross‐sectional study design on 265 households selected by systematic random sampling from a town called Jimma in Ethiopia and collects the data using interview‐based semi‐structured questionnaires. The study obtains information from all the selected households. The results show that more than 80% of the households have a grid electricity connection, but more than 85% of the households regularly use firewood and charcoal for cooking. On average, households use about 1236 kg of firewood and 630 kg of charcoal per year. Most households report power interruption, inability to afford electricity costs, and personal preferences for relying on biomass energy for cooking. Over 98% of the households use electricity for lighting, but few use it for appliances. This shows an inherent challenge attributed to the cooking energy services provided by biomass energy sources despite the accessibility of electricity. This shows the significant impacts of biomass energy stacking which connection to electricity alone cannot solve.
Hypoxia‐driven immunosuppression by Treg and type‐2 conventional dendritic cells in HCC
Authors: Suthen Sheena , Lim Chun Jye , Nguyen Phuong H. D. , Dutertre Charles‐Antoine , Lai Hannah L. H. , Wasser Martin , Chua Camillus , Lim Tony K. H. , Leow Wei Qiang , Loh Tracy Jiezhen , Wan Wei Keat , Pang Yin Huei , Soon Gwyneth , Cheow Peng Chung , Kam Juinn Huar , Iyer Shridhar , Kow Alfred , Tam Wai Leong , Shuen Timothy W. H. , Toh Han Chong , Dan Yock Young , Bonney Glenn K. , Chan Chung Yip , Chung Alexander , Goh Brian K. P. , Zhai Weiwei , Ginhoux Florent , Chow Pierce K. H. , Albani Salvatore , Chew Valerie 
Published: February 2022

Abstract

Background and Aims
Hypoxia is one of the central players in shaping the immune context of the tumor microenvironment (TME). However, the complex interplay between immune cell infiltrates within the hypoxic TME of HCC remains to be elucidated.

Approach and Results
We analyzed the immune landscapes of hypoxia‐low and hypoxia‐high tumor regions using cytometry by time of light, immunohistochemistry, and transcriptomic analyses. The mechanisms of immunosuppression in immune subsets of interest were further explored using in vitro hypoxia assays. Regulatory T cells (Tregs) and a number of immunosuppressive myeloid subsets, including M2 macrophages and human leukocyte antigen–DR isotype (HLA‐DRlo) type 2 conventional dendritic cell (cDC2), were found to be significantly enriched in hypoxia‐high tumor regions. On the other hand, the abundance of active granzyme Bhi PD‐1lo CD8+ T cells in hypoxia‐low tumor regions implied a relatively active immune landscape compared with hypoxia‐high regions. The up‐regulation of cancer‐associated genes in the tumor tissues and immunosuppressive genes in the tumor‐infiltrating leukocytes supported a highly pro‐tumorigenic network in hypoxic HCC. Chemokine genes such as CCL20 (C‐C motif chemokine ligand 20) and CXCL5 (C‐X‐C motif chemokine ligand 5) were associated with recruitment of both Tregs and HLA‐DRlo cDC2 to hypoxia‐high microenvironments. The interaction between Tregs and cDC2 under a hypoxic TME resulted in a loss of antigen‐presenting HLA‐DR on cDC2.

Conclusions
We uncovered the unique immunosuppressive landscapes and identified key immune subsets enriched in hypoxic HCC. In particular, we identified a potential Treg‐mediated immunosuppression through interaction with a cDC2 subset in HCC that could be exploited for immunotherapies.
Quality of biomarker defined subgroups in FDA approvals of PD‐1/PD‐L1 inhibitors 2014 to 2020
Authors: Kim Myung S. , Xu Alexander , Haslam Alyson , Prasad Vinay 
Published: February 2022

AbstractPD‐L1 expression is associated with differential response in cancers treated with checkpoint inhibitors. Clinical trials for Food and Drug Administration (FDA) approvals of programmed death receptor‐1 (PD‐1)/programmed death ligand‐1 (PD‐L1) inhibitors include limited subgroup analyses based on PD‐L1 expression. We aimed to define the characteristics of PD‐L1 defined subgroups of clinical trials leading to FDA approvals for new indications of PD‐1/PD‐L1 inhibitors. FDA approvals for PD‐1/PD‐L1 inhibitors from January 2014 to December 2020 were identified and the clinical trials leading to each drug approval were reviewed. We collected key variables from publicly available information on FDA website and peer‐reviewed publications of clinical trials. We assessed regulatory characteristics (approval date, approved drug[s], cancer type, line of therapy and biomarker‐restricted approval criteria) of each approval. Clinical trials leading to approvals were reviewed for trial design (RCT vs single arm study, primary endpoint) and PD‐L1 defined subgroup design (no subgroup analysis, single threshold 2‐group analysis, nested subgroups and adjacent subgroups). We then compared regulatory and trials characteristics (trial design, primary endpoint and biomarker approval criteria) between studies with nested and adjacent subgroups. There were 60 approvals for PD‐1/PD‐L1 inhibitors between January 2014 and December 2020. Twelve of 60 (20%) did not include any PD‐L1 subgroups. Twenty‐five of 60 (42%) approvals reported only two subgroups, 14 (23%) included adjacent subgroups and 9 (15%) had nested subgroups. Twenty‐five of 60 trials (42%) are single arm studies. Comparison of characteristics between trials with nested subgroup design and adjacent subgroup design did not show differences. We conclude that approvals for new indications of PD‐1/PD‐L1 inhibitors are based on studies that do not include comprehensive reporting of outcomes by PD‐L1 biomarker subgroups.
Regulatory networks and 5′ partner usage of miRNA host gene fusions in breast cancer
Authors: Hafstað Völundur , Søkilde Rolf , Häkkinen Jari , Larsson Malin , Vallon‐Christersson Johan , Rovira Carlos , Persson Helena 
Published: February 2022

AbstractGenomic rearrangements in cancer cells can create gene fusions where the juxtaposition of two different genes leads to the production of chimeric proteins or altered gene expression through promoter‐swapping. We have previously shown that fusion transcripts involving microRNA (miRNA) host genes contribute to deregulation of miRNA expression regardless of the protein‐coding potential of these transcripts. Many different genes can also be used as 5′ partners by a miRNA host gene in what we named recurrent miRNA‐convergent fusions. Here, we have explored the properties of 5′ partners in fusion transcripts that involve miRNA hosts in breast tumours from The Cancer Genome Atlas (TCGA). We hypothesised that firstly, 5′ partner genes should belong to pathways and transcriptional programmes that reflect the tumour phenotype and secondly, there should be a selection for fusion events that shape miRNA expression to benefit the tumour cell through the known hallmarks of cancer. We found that the set of 5′ partners in miRNA host fusions is non‐random, with overrepresentation of highly expressed genes in pathways active in cancer including epithelial‐to‐mesenchymal transition, translational regulation and oestrogen signalling. Furthermore, many miRNAs were upregulated in samples with host gene fusions, including established oncogenic miRNAs such as mir‐21 and the mir‐106b~mir‐93~mir‐25 cluster. To the list of mechanisms for deregulation of miRNA expression, we have added fusion transcripts that change the promoter region. We propose that this adds material for genetic selection and tumour evolution in cancer cells and that miRNA host fusions can act as tumour ‘drivers’.
Erythroid spectrin binding modulates peroxidase and catalase activity of heme proteins
Authors: Bose Dipayan , Aggarwal Shantanu , Das Debashree , Narayana Chandrabhas , Chakrabarti Abhijit 
Published: February 2022

AbstractHemoglobin oxidation due to oxidative stress and disease conditions leads to the generation of ROS (reactive oxygen species) and membrane attachment of hemoglobin in‐vivo, where its redox activity leads to peroxidative damage of membrane lipids and proteins. Spectrin, the major component of the red blood cell (RBC) membrane skeleton, is known to interact with hemoglobin and, here this interaction is shown to increase hemoglobin peroxidase activity in the presence of reducing substrate ABTS (2′, 2′‐Azino‐Bis‐3‐Ethylbenzothiazoline‐6‐Sulfonic Acid). It is also shown that in the absence of reducing substrate, spectrin forms covalently cross‐linked aggregates with hemoglobin which display no peroxidase activity. This may have implications in the clearance of ROS and limiting peroxidative damage. Spectrin is found to modulate the peroxidase activity of different hemoglobin variants like A, E, and S, and of isolated globin chains from each of these variants. This may be of importance in disease states like sickle cell disease and HbE‐β‐thalassemia, where increased oxidative damage and free globin subunits are present due to the defects inherent in the hemoglobin variants associated with these diseases. This hypothesis is corroborated by lipid peroxidation experiments. The modulatory role of spectrin is shown to extend to other heme proteins, namely catalase and cytochrome‐c. Experiments with free heme and Raman spectroscopy of heme proteins in the presence of spectrin show that structural alterations occur in the heme moiety of the heme proteins on spectrin binding, which may be the structural basis of increased enzyme activity.
Differential expression of HNF1A and HNF1A‐AS1 in colon cancer cells
Authors: Sepehri Zahra , Banerjee Archana , Vizeacoumar Frederick S. , Freywald Andrew , Vizeacoumar Franco J. , Dolinsky Vernon W. , Davie James R. 
Published: February 2022

AbstractThe human hepatocyte nuclear factor 1 homeobox A (HNF1A) gene loci express the protein‐coding HNF1A transcript and a long non‐coding RNA in the anti‐sense (HNF1A‐AS1) direction. HNF1A‐AS1 is expressed in numerous types of cancers and poor clinical outcomes such as higher mortality rates, greater metastatic capacity, and poor prognosis of the disease are the results of this expression. In this study, we determined the epigenetic features of the HNF1A gene loci, and expression and cellular localization of HNF1A‐AS1 RNA, HNF1A RNA, and HNF1A protein in colorectal cancer (HT‐29, HTC116, RKO, and SW480) and normal colon epithelial (CCD841) cells. The HT‐29 HNF1A gene had active histone marks (H3K4me3, H3K27ac) and DNase 1 accessible sites at the promoter regions of the HNF1A and HNF1A‐AS1 genes. These epigenetic marks were not observed in the other colorectal cancer cells or in the normal colon epithelial cells. Consistent with the active gene epigenetic signature of the HNF1A gene in HT‐29 cells, HNF1A protein, and HNF1A/HNF1A‐AS1 transcripts were detected in HT‐29 cells but poorly, if at all observed, in the other cell types. In HT‐29 cells, HNF1A‐AS1 localized to the nucleus and was found to bind to the enhancer of zeste homolog 2 (EZH2, a member of PRC2 complex) and potentially form RNA–DNA triplexes with DNase 1 accessible sites in the HT‐29 genome. These activities of HNF1A‐AS1 may contribute to the oncogenic properties of this long non‐coding RNA.