bluuebunny/crossref_metadata_2025_split huggingface dataset:
Outcome of stenting in central venous obstruction of benign	etiology
Authors: Jalaie Houman , Gombert Alexander , Grommes Jochen , Schleimer Karina , Kurstjens Ralph L. M. , de Graaf Rick , Wittens Cees H. A. , Razavi Mahmood , Barbati Mohammad Esmaeil 
Published: October 2020

Summary: Background: The aim of this study is to evaluate long term outcome in patients treated for benign superior vena cava (SVC) syndrome by endovascular techniques. Patients and methods: Between 2015 and 2018, 62 patients suffering from central venous obstruction of benign etiology underwent balloon angioplasty with stent placement for venous obstruction in our department. Patency was assessed clinically, using duplex ultrasound in all patients or with CT-phlebography in selected cases. Results: Median age was 60 years (23–83), forty-one patients (66%) had central venous devices. Swelling of the arm and face were the main symptoms (71%). During the median follow up of 22 months (9–38), cumulative primary patency was 71% after venous stenting. The cumulative assisted primary and the secondary patency were 85% and 92%, respectively. Conclusions: Recanalization and stenting of central vein obstruction has turned out to be the technique of reference and provides satisfactory mid-term patency rates. After adjusting for the risk factors, presence of AV-fistula remained a significant risk factor for recurrent stenosis or loss of patency after intervention.
Sulfur Cycling During Progressive Burial in Sulfate‐Rich Marine Carbonates
Authors: Jiang Lei , Fakhraee Mojtaba , Cai Chunfang , Worden Richard H. 
Published: October 2020

AbstractThe isotopic composition of sulfate in the rock record has been frequently used to track the changes in the Earth's surface environments. By considering isotopic fractionation imparted by microbial sulfate reduction (MSR) and thermochemical sulfate reduction (TSR), in this study, we aim to develop a holistic understanding of the mixed effects of MSR and TSR on δ34S signals in sulfate‐rich carbonate systems. We report the occurrence of various types of sulfur‐bearing components from the Cambrian‐Ordovician carbonate system in the Tarim Basin, NW China, coupled with a well‐established diagenesis framework for these rocks. Our results indicate that most of the sulfur‐bearing species possess δ34S values slightly lower than both the source sulfate and the sulfide generated by TSR, yet these sulfur‐bearing species have substantially higher δ34S values than sulfide that resulted from MSR. Hence, a combination of sulfides sourced from MSR and TSR can adequately explain the sulfur isotope data in the studied interval. Building upon this hypothesis, we developed a new sulfur diagenesis model in order to quantify the accumulated H2S from the combined effects of MSR and TSR. Our new model can be used to explain the origin of sulfur‐bearing species in many other deep burial carbonate systems, including the Sichuan Basin, China, and the Gulf of Mexico, USA. We propose that greater attention should be paid to isotopic modulation through mixed diagenetic processes in order to gain a better mechanistic understanding of the primary geochemistry signals (e.g., δ34S) in marine carbonates.
A Recharge Oscillator Model for Interannual Variability in Venus’ Clouds
Authors: Kopparla Pushkar , Seshadri Ashwin , Imamura Takeshi , Lee Yeon Joo 
Published: October 2020

AbstractSulfur dioxide is a radiatively and chemically important trace gas in the atmosphere of Venus and its abundance at the cloud tops has been observed to vary on interannual to decadal timescales. This variability is thought to come from changes in the strength of convection which transports sulfur dioxide to the cloud tops, although the dynamics behind such convective variability are unknown. Here, we propose a new conceptual model for convective variability that links the radiative effects of water abundance at the cloud‐base to convective strength within the clouds, which in turn affects water transport within the cloud. The model consists of two coupled equations which are identified as a recharge‐discharge oscillator. The solutions of the coupled equations are finite amplitude sustained oscillations in convective strength and cloud‐base water abundance on 3–9 years timescales. The characteristic oscillation timescale is given by the geometric mean of the radiative cooling time and the eddy mixing time near the base of the convective clouds.
Riverine Dissolved Organic Carbon and Freshwater Export in the Eastern Gulf of Alaska
Authors: Edwards Rick T. , D'Amore David V. , Biles Frances E. , Fellman Jason B. , Hood Eran W. , Trubilowicz Joel W. , Floyd William C. 
Published: October 2020

AbstractThe coastal zone of southeast Alaska contains thousands of streams and rivers that drain one of the wettest, carbon‐rich, and most topographically varied regions in North America. Watersheds draining temperate rainforests, peatlands, glaciers, and three large rivers that flow from the drier interior of the Yukon Territory and British Columbia discharge water and dissolved organic carbon (DOC) into southeast Alaskan coastal waters. This area, which we have designated the southeast Alaska drainage basin (SEAKDB), discharges about twice as much water as the Columbia or Yukon Rivers. An understanding of the timing, location, and source of water and DOC guides research to better understand the influence of terrestrial outputs on the adjacent marine systems. Additionally, a spatially extensive understanding of riverine DOC flux will improve our understanding of lateral losses related to terrestrial carbon cycling. We estimate 1.17 Tg C yr−1 of DOC enters the adjacent marine system along with 430 km2 of freshwater that influences estuary, shelf, and Gulf of Alaska hydrology. We estimate that 23% to 66% of the DOC entering coastal waters is bioavailable and may influence metabolism and productivity within the marine system. The combination of the large and spatially distributed water and DOC input, long and complex shoreline, large enclosed estuarine volume, and bounded nearshore coastal currents suggests that the physiographic structure of southeast Alaska may have a significant impact on the metabolism of riverine DOC in coastal marine ecosystems.
Sempervirine inhibits RNA polymerase I transcription independently from p53 in tumor cells
Authors: Caggiano Cinzia , Guida Eugenia , Todaro Federica , Bielli Pamela , Mori Mattia , Ghirga Francesca , Quaglio Deborah , Botta Bruno , Moretti Fabiola , Grimaldi Paola , Rossi Pellegrino , Jannini Emmanuele A. , Barchi Marco , Dolci Susanna 
Published: October 2020

AbstractIn the search of small molecules that can target MDM2/p53 pathway in testicular germ cell tumors (TGCTs), we identified sempervirine (2,3,4,13-tetrahydro-1H-benz[g]indolo[2,3-a]quinolizin-6-ium), an alkaloid of Gelsemium sempervirens, that has been previously proposed as an inhibitor of MDM2 that targets p53-wildtype (wt) tumor cells. We found that sempervirine not only affects cell growth of p53-wt cancer cells, but it is also active in p53-mutated and p53-null cells by triggering p53-dependent and independent pathways without affecting non-transformed cells. To understand which mechanism/s could be activated both in p53-wt and -null cells, we found that sempervirine induced nucleolar remodeling and nucleolar stress by reducing protein stability of RPA194, the catalytic subunit of RNA polymerase I, that led to rRNA synthesis inhibition and to MDM2 block. As shown for other cancer cell models, MDM2 inhibition by nucleolar stress downregulated E2F1 protein levels both in p53-wt and p53-null TGCT cells with the concomitant upregulation of unphosphorylated pRb. Finally, we show that sempervirine is able to enter the nucleus and accumulates within the nucleolus where it binds rRNA without causing DNA damage. Our results identify semperivirine as a novel rRNA synthesis inhibitor and indicate this drug as a non-genotoxic anticancer small molecule.
The caspase-3/GSDME signal pathway as a switch between apoptosis and pyroptosis in cancer
Authors: Jiang Mingxia , Qi Ling , Li Lisha , Li Yanjing 
Published: October 2020

AbstractApoptosis has long been recognized as a mechanism that kills the cancer cells by cytotoxic drugs. In recent years, studies have proved that pyroptosis can also shrink tumors and inhibit cells proliferation. Both apoptosis and pyroptosis are caspase-dependent programmed cell death pathways. Cysteinyl aspartate specific proteinase-3 (Caspase-3) is a common key protein in the apoptosis and pyroptosis pathways, and when activated, the expression level of tumor suppressor gene Gasdermin E (GSDME) determines the mechanism of tumor cell death. When GSDME is highly expressed, the active caspase-3 cuts it and releases the N-terminal domain to punch holes in the cell membrane, resulting in cell swelling, rupture, and death. When the expression of GSDME is low, it will lead to the classical mechanism of tumor cell death, which is apoptosis. More interestingly, researchers have found that GSDME can also be located upstream of caspase-3, connecting extrinsic, and intrinsic apoptotic pathways. Then, promoting caspase-3 activation, and forming a self-amplifying feed-forward loop. GSDME-mediated pyroptosis is correlated with the side effects of chemotherapy and anti-tumor immunity. This article mainly reviews the caspase-3/GSDME signal pathway as a switch between apoptosis and pyroptosis in cancer, to provide new strategies and targets for cancer treatment.
Nuclear gene proximity and protein interactions shape transcript covariations in mammalian single cells
Authors: Tarbier Marcel , Mackowiak Sebastian D. , Frade João , Catuara-Solarz Silvina , Biryukova Inna , Gelali Eleni , Menéndez Diego Bárcena , Zapata Luis , Ossowski Stephan , Bienko Magda , Gallant Caroline J. , Friedländer Marc R. 
Published: October 2020

AbstractSingle-cell RNA sequencing studies on gene co-expression patterns could yield important regulatory and functional insights, but have so far been limited by the confounding effects of differentiation and cell cycle. We apply a tailored experimental design that eliminates these confounders, and report thousands of intrinsically covarying gene pairs in mouse embryonic stem cells. These covariations form a network with biological properties, outlining known and novel gene interactions. We provide the first evidence that miRNAs naturally induce transcriptome-wide covariations and compare the relative importance of nuclear organization, transcriptional and post-transcriptional regulation in defining covariations. We find that nuclear organization has the greatest impact, and that genes encoding for physically interacting proteins specifically tend to covary, suggesting importance for protein complex formation. Our results lend support to the concept of post-transcriptional RNA operons, but we further present evidence that nuclear proximity of genes may provide substantial functional regulation in mammalian single cells.
ACE2 localizes to the respiratory cilia and is not increased by ACE inhibitors or ARBs
Authors: Lee Ivan T. , Nakayama Tsuguhisa , Wu Chien-Ting , Goltsev Yury , Jiang Sizun , Gall Phillip A. , Liao Chun-Kang , Shih Liang-Chun , Schürch Christian M. , McIlwain David R. , Chu Pauline , Borchard Nicole A. , Zarabanda David , Dholakia Sachi S. , Yang Angela , Kim Dayoung , Chen Han , Kanie Tomoharu , Lin Chia-Der , Tsai Ming-Hsui , Phillips Katie M. , Kim Raymond , Overdevest Jonathan B. , Tyler Matthew A. , Yan Carol H. , Lin Chih-Feng , Lin Yi-Tsen , Bau Da-Tian , Tsay Gregory J. , Patel Zara M. , Tsou Yung-An , Tzankov Alexandar , Matter Matthias S. , Tai Chih-Jaan , Yeh Te-Huei , Hwang Peter H. , Nolan Garry P. , Nayak Jayakar V. , Jackson Peter K. 
Published: October 2020

AbstractThe coronavirus SARS-CoV-2 is the causative agent of the ongoing severe acute respiratory disease pandemic COVID-19. Tissue and cellular tropism is one key to understanding the pathogenesis of SARS-CoV-2. We investigate the expression and subcellular localization of the SARS-CoV-2 receptor, angiotensin-converting enzyme 2 (ACE2), within the upper (nasal) and lower (pulmonary) respiratory tracts of human donors using a diverse panel of banked tissues. Here, we report our discovery that the ACE2 receptor protein robustly localizes within the motile cilia of airway epithelial cells, which likely represents the initial or early subcellular site of SARS-CoV-2 viral entry during host respiratory transmission. We further determine whether ciliary ACE2 expression in the upper airway is influenced by patient demographics, clinical characteristics, comorbidities, or medication use, and show the first mechanistic evidence that the use of angiotensin-converting enzyme inhibitors (ACEI) or angiotensin II receptor blockers (ARBs) does not increase susceptibility to SARS-CoV-2 infection through enhancing the expression of ciliary ACE2 receptor. These findings are crucial to our understanding of the transmission of SARS-CoV-2 for prevention and control of this virulent pathogen.
The misuse of colour in science communication
Authors: Crameri Fabio , Shephard Grace E. , Heron Philip J. 
Published: October 2020

AbstractThe accurate representation of data is essential in science communication. However, colour maps that visually distort data through uneven colour gradients or are unreadable to those with colour-vision deficiency remain prevalent in science. These include, but are not limited to, rainbow-like and red–green colour maps. Here, we present a simple guide for the scientific use of colour. We show how scientifically derived colour maps report true data variations, reduce complexity, and are accessible for people with colour-vision deficiencies. We highlight ways for the scientific community to identify and prevent the misuse of colour in science, and call for a proactive step away from colour misuse among the community, publishers, and the press.
Efficient separation of xylene isomers by a guest-responsive metal–organic framework with rotational anionic sites
Authors: Cui Xili , Niu Zheng , Shan Chuan , Yang Lifeng , Hu Jianbo , Wang Qingju , Lan Pui Ching , Li Yijian , Wojtas Lukasz , Ma Shengqian , Xing Huabin 
Published: October 2020

AbstractThe separation of xylene isomers (para-, meta-, orth-) remains a great challenge in the petrochemical industry due to their similar molecular structure and physical properties. Porous materials with sensitive nanospace and selective binding sites for discriminating the subtle structural difference of isomers are urgently needed. Here, we demonstrate the adaptively molecular discrimination of xylene isomers by employing a NbOF52−-pillared metal–organic framework (NbOFFIVE-bpy-Ni, also referred to as ZU-61) with rotational anionic sites. Single crystal X-ray diffraction studies indicate that ZU-61 with guest-responsive nanospace/sites can adapt the shape of specific isomers through geometric deformation and/or the rotation of fluorine atoms in anionic sites, thereby enabling ZU-61 to effectively differentiate xylene isomers through multiple C–H···F interactions. ZU-61 exhibited both high meta-xylene uptake capacity (3.4 mmol g−1) and meta-xylene/para-xylene separation selectivity (2.9, obtained from breakthrough curves), as well as a favorable separation sequence as confirmed by breakthrough experiments: para-xylene elute first with high-purity (≥99.9%), then meta-xylene, and orth-xylene. Such a remarkable performance of ZU-61 can be attributed to the type anionic binding sites together with its guest-response properties.
Identification of a myotropic AAV by massively parallel in vivo evaluation of barcoded capsid variants
Authors: Weinmann Jonas , Weis Sabrina , Sippel Josefine , Tulalamba Warut , Remes Anca , El Andari Jihad , Herrmann Anne-Kathrin , Pham Quang H. , Borowski Christopher , Hille Susanne , Schönberger Tanja , Frey Norbert , Lenter Martin , VandenDriessche Thierry , Müller Oliver J. , Chuah Marinee K. , Lamla Thorsten , Grimm Dirk 
Published: October 2020

AbstractAdeno-associated virus (AAV) forms the basis for several commercial gene therapy products and for countless gene transfer vectors derived from natural or synthetic viral isolates that are under intense preclinical evaluation. Here, we report a versatile pipeline that enables the direct side-by-side comparison of pre-selected AAV capsids in high-throughput and in the same animal, by combining DNA/RNA barcoding with multiplexed next-generation sequencing. For validation, we create three independent libraries comprising 183 different AAV variants including widely used benchmarks and screened them in all major tissues in adult mice. Thereby, we discover a peptide-displaying AAV9 mutant called AAVMYO that exhibits superior efficiency and specificity in the musculature including skeletal muscle, heart and diaphragm following peripheral delivery, and that holds great potential for muscle gene therapy. Our comprehensive methodology is compatible with any capsids, targets and species, and will thus facilitate and accelerate the stratification of optimal AAV vectors for human gene therapy.
Murine interfollicular epidermal differentiation is gradualistic with GRHL3 controlling progression from stem to transition cell states
Authors: Lin Ziguang , Jin Suoqin , Chen Jefferson , Li Zhuorui , Lin Zhongqi , Tang Li , Nie Qing , Andersen Bogi 
Published: October 2020

AbstractThe interfollicular epidermis (IFE) forms a water-tight barrier that is often disrupted in inflammatory skin diseases. During homeostasis, the IFE is replenished by stem cells in the basal layer that differentiate as they migrate toward the skin surface. Conventionally, IFE differentiation is thought to be stepwise as reflected in sharp boundaries between its basal, spinous, granular and cornified layers. The transcription factor GRHL3 regulates IFE differentiation by transcriptionally activating terminal differentiation genes. Here we use single cell RNA-seq to show that murine IFE differentiation is best described as a single step gradualistic process with a large number of transition cells between the basal and spinous layer. RNA-velocity analysis identifies a commitment point that separates the plastic basal and transition cell state from unidirectionally differentiating cells. We also show that in addition to promoting IFE terminal differentiation, GRHL3 is essential for suppressing epidermal stem cell expansion and the emergence of an abnormal stem cell state by suppressing Wnt signaling in stem cells.
Integrative transcriptome and chromatin landscape analysis reveals distinct epigenetic regulations in human memory B cells
Authors: Moroney Justin B. , Vasudev Anusha , Pertsemlidis Alexander , Zan Hong , Casali Paolo 
Published: October 2020

AbstractMemory B cells (MBCs) are long-lived and produce high-affinity, generally, class-switched antibodies. Here, we use a multiparameter approach involving CD27 to segregate naïve B cells (NBC), IgD+ unswitched (unsw)MBCs and IgG+ or IgA+ class-switched (sw)MBCs from humans of different age, sex and race. Conserved antibody variable gene expression indicates that MBCs emerge through unbiased selection from NBCs. Integrative analyses of mRNAs, miRNAs, lncRNAs, chromatin accessibility and cis-regulatory elements uncover a core mRNA-ncRNA transcriptional signature shared by IgG+ and IgA+ swMBCs and distinct from NBCs, while unswMBCs display a transitional transcriptome. Some swMBC transcriptional signature loci are accessible but not expressed in NBCs. Profiling miRNAs reveals downregulated MIR181, and concomitantly upregulated MIR181 target genes such as RASSF6, TOX, TRERF1, TRPV3 and RORα, in swMBCs. Finally, lncRNAs differentially expressed in swMBCs cluster proximal to the IgH chain locus on chromosome 14. Our findings thus provide new insights into MBC transcriptional programs and epigenetic regulation, opening new investigative avenues on these critical cell elements in human health and disease.
Reprogramming bacterial protein organelles as a nanoreactor for hydrogen production
Authors: Li Tianpei , Jiang Qiuyao , Huang Jiafeng , Aitchison Catherine M. , Huang Fang , Yang Mengru , Dykes Gregory F. , He Hai-Lun , Wang Qiang , Sprick Reiner Sebastian , Cooper Andrew I. , Liu Lu-Ning 
Published: October 2020

AbstractCompartmentalization is a ubiquitous building principle in cells, which permits segregation of biological elements and reactions. The carboxysome is a specialized bacterial organelle that encapsulates enzymes into a virus-like protein shell and plays essential roles in photosynthetic carbon fixation. The naturally designed architecture, semi-permeability, and catalytic improvement of carboxysomes have inspired rational design and engineering of new nanomaterials to incorporate desired enzymes into the protein shell for enhanced catalytic performance. Here, we build large, intact carboxysome shells (over 90 nm in diameter) in the industrial microorganism Escherichia coli by expressing a set of carboxysome protein-encoding genes. We develop strategies for enzyme activation, shell self-assembly, and cargo encapsulation to construct a robust nanoreactor that incorporates catalytically active [FeFe]-hydrogenases and functional partners within the empty shell for the production of hydrogen. We show that shell encapsulation and the internal microenvironment of the new catalyst facilitate hydrogen production of the encapsulated oxygen-sensitive hydrogenases. The study provides insights into the assembly and formation of carboxysomes and paves the way for engineering carboxysome shell-based nanoreactors to recruit specific enzymes for diverse catalytic reactions.
Auditory information enhances post-sensory visual evidence during rapid multisensory decision-making
Authors: Franzen Léon , Delis Ioannis , De Sousa Gabriela , Kayser Christoph , Philiastides Marios G. 
Published: October 2020

AbstractDespite recent progress in understanding multisensory decision-making, a conclusive mechanistic account of how the brain translates the relevant evidence into a decision is lacking. Specifically, it remains unclear whether perceptual improvements during rapid multisensory decisions are best explained by sensory (i.e., ‘Early’) processing benefits or post-sensory (i.e., ‘Late’) changes in decision dynamics. Here, we employ a well-established visual object categorisation task in which early sensory and post-sensory decision evidence can be dissociated using multivariate pattern analysis of the electroencephalogram (EEG). We capitalize on these distinct neural components to identify when and how complementary auditory information influences the encoding of decision-relevant visual evidence in a multisensory context. We show that it is primarily the post-sensory, rather than the early sensory, EEG component amplitudes that are being amplified during rapid audiovisual decision-making. Using a neurally informed drift diffusion model we demonstrate that a multisensory behavioral improvement in accuracy arises from an enhanced quality of the relevant decision evidence, as captured by the post-sensory EEG component, consistent with the emergence of multisensory evidence in higher-order brain areas.