bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ozone Generation from a Germicidal Ultraviolet Lamp with Peak Emission at 222 nm
Authors: Link Michael F. , Shore Andrew , Hamadani Behrang H. , Poppendieck Dustin 
Published: May 2023

AbstractRecent interest in commercial devices containing germicidal ultraviolet lamps with a peak emission wavelength at 222 nm (GUV222) has focused on mitigating virus transmission indoors and disinfecting indoor spaces while posing minimum risk to human tissue. However, 222 nm light can produce ozone (O3) in air. O3is an undesirable component of indoor air because of health impacts from acute to chronic exposure and its ability to degrade indoor air quality through oxidation chemistry. We measured the total irradiance of one GUV222 lamp at a distance of 5 cm away from the source to be 27.0 W m-2± 4.6 W m-2in the spectral range of 210 nm to 230 nm, with peak emission centered at 222 nm and evaluated the potential for the lamp to generate O3in a 31.5 m3stainless steel chamber. In seven four-hour experiments average O3mixing ratios increased from levels near the detection limit of the instrument to 48 ppbv± 1 ppbv(94 μg m-3± 2 μg m-3). We determined an average constant O3generation rate for this lamp to be 1.10 mg h-1± 0.15 mg h-1. Using a radiometric method and chemical actinometry, we estimate effective lamp fluences that allow prediction of O3generation by the GUV222 lamp, at best, within 10 % of the measured mixing ratios. Because O3can react with gases and surfaces indoors leading to the formation of other potential by-products, future studies should evaluate the production of O3from GUV222 air cleaning devices.TOC
Reversible expansion of tissue macrophages in response to macrophage colony-stimulating factor (CSF1) transforms systemic metabolism to fuel liver growth
Authors: Keshvari Sahar , Masson Jesse J.R. , Ferrari-Cestari Michelle , Bodea Liviu-Gabriel , Nooru-Mohamed Fathima , Tse Brian W.C. , Sokolowski Kamil A. , Batoon Lena , Patkar Omkar L. , Sullivan Mitchell A. , Ebersbach Hilmar , Stutz Cian , Parton Robert G. , Summers Kim M. , Pettit Allison R. , Hume David A. , Irvine Katharine M. 
Published: May 2023

AbstractBackground and AimMacrophages regulate metabolic homeostasis in health and disease. Macrophage colony-stimulating factor (CSF1)-dependent macrophages contribute to homeostatic control of the size of the liver. This study aimed to determine the systemic metabolic consequences of elevating circulating CSF1.Methods and ResultsAcute administration of a CSF1-Fc fusion protein led to monocytosis, increased resident tissue macrophages in the liver and all major organs, and liver growth. These effects were associated with increased hepatic glucose uptake and extensive mobilisation of body fat. The impacts of CSF1 on macrophage abundance, liver size and body composition were rapidly reversed to restore homeostasis. CSF1’s effects on metabolism were independent of several known endocrine regulators and did not impact the physiological fasting response. Analysis using implantable telemetry in metabolic cages revealed progressively reduced body temperature and physical activity with no change in diurnal food intake.ConclusionThese results demonstrate the existence of a dynamic equilibrium between CSF1, the mononuclear phagocyte system, metabolic regulation and homeostatic control of liver:body weight ratio.
Pan-cancer mutational signature analysis of 111,711 targeted sequenced tumors using SATS
Authors: Lee Donghyuk , Hua Min , Wang Difei , Song Lei , Zhang Tongwu , Hua Xing , Yu Kai , Yang Xiaohong R. , Chanock Stephen J. , Shi Jianxin , Landi Maria Teresa , Zhu Bin 
Published: May 2023

AbstractTumor mutational signatures are informative for cancer diagnosis and treatment. However, targeted sequencing, commonly used in clinical settings, lacks specialized analytical tools and a dedicated catalogue of mutational signatures. Here, we introduce SATS, a scalable mutational signature analyzer for targeted sequencing data. SATS leverages tumor mutational burdens to identify and quantify signatures in individual tumors, overcoming the challenges of sparse mutations and variable gene panels. Validations across simulated data, pseudo-targeted sequencing data, and matched whole-genome and targeted sequencing samples show that SATS can accurately detect common mutational signatures and estimate their burdens. Applying SATS to 111,711 tumors from the AACR Project GENIE, we created a pan-cancer mutational signature catalogue specific to targeted sequencing. We further validated signatures in lung, breast and colorectal cancers using an additional 16,774 independent samples. This signature catalogue is a valuable resource for estimating signature burdens in individual targeted sequenced tumors, facilitating the integration of mutational signatures with clinical data.
A Simple Score to Predict New-onset Atrial Fibrillation After Ablation of Typical Atrial Flutter
Authors: Gu Zhoushan , Jiao Jincheng , Ding Xiangwei , Zhu Chao , Li Mingfang , Chen Hongwu , Ju Weizhu , Gu Kai , Yang Gang , Liu Hailei , Kojodjojo Pipin , Chen Minglong 
Published: May 2023

ABSTRACTBackgroundNew-onset atrial fibrillation (NeAF) is common after cavotricuspid isthmus-dependent counterclockwise atrial flutter (CCW-AFL) ablation. This study aimed to investigate a simple predictive model of NeAF after CCW-AFL ablation.Methods and ResultsFrom January 2013 to December 2017, consecutive patients receiving CCW-AFL ablation were enrolled from three centers. Clinical, echocardiographic, and electrocardiographic data were collected and followed. Patients from two centers and another center were assigned into the derivation and validation cohorts, respectively. In the derivation cohort, logistic regression was performed to evaluate the ability of parameters to discriminate those with and without NeAF. A score system was developed and then validated. Two hundred seventy-one patients (mean 59.7±13.6 age; 205 male) were analyzed. During follow-up (73.0±6.5 months), 107 patients (39.5%) had NeAF. 190 and 81 patients were detected in the derivation and validation cohorts, respectively. Hypertension, age ≥70 years, left atrial diameter ≥42 mm, P wave duration ≥120 ms and the negative component of flutter wave in lead II ≥120 ms were selected as the final parameters. A weighted score was used to develop the HAD-AF score ranging from 0 to 9. In the derivation cohort, area under the receiver operating characteristic curve (AUC) was 0.938 (95% CI 0.902-0.974), superior to those of currently used CHA2DS2-VASC(0.679, 95% CI 0.600-0.757) and HATCH scores (0.651, 95% CI 0.571-0.730) (P<0.001). Performance maintained in the validation cohort.Conclusions39.5% of patients developed NeAF in 6 years after CCW-AFL ablation. HAD-AF score can reliably identify patients likely to develop NeAF after CCW-AFL ablation.Clinical PerspectiveWhat Is New?During a follow-up period of more than 6 years after CCW-AFL ablation, 107 of 271 (39.5%) patients developed NeAF.HAD-AF score, based on easily obtainable clinical, echocardiographic and electrocardiographic parameters, could better predict development of NeAF after CCW-AFL ablation (area under the receiver operating characteristics curve [AUC], 0.938), compared with currently used HATCH score (AUC, 0.651) and CHA2DS2-VASCscore (AUC, 0.679) (P<0.001).What Are the Clinical Implications?In CCW-AFL patients with a HAD-AF score >4, close postoperative follow-up for earlier detection of AF should be recommended, or the option of concomitant AF ablation could be considered during the shared decision-making process.
Synergistic effects of multiple pesticides on the flight ability of honey bees (Apis ceranaF.)
Authors: Ma Changsheng , Shi Xiaoyu , Chen Sihao , Han Jincai , Bai Haodong , Yu Haitao , Li Zuren , Li-Byarlay Hongmei , Bai Lianyang 
Published: May 2023

AbstractPesticides cause risks in the environment for Asian honey bees (Apis cerana). Imidacloprid (I), chlorpyrifos (C) and glyphosate (G) are among the most-widely used pesticides in the world. It is not clear on how these pesticides and combination of them affect the flight ability ofA. cerana. Here we utilized flight mills to show new results that acute treatment of individual pesticides, such as 0.2 ng/bees imidacloprid (20 μL, 10 ng/g), 0.6 ng/bees chlorpyrifos (20 μL, 30 ng/g) and 1.2 ng/bees glyphosate (20 μL, 60 ng/g), had no effect on the flight ability of bees. However, forager bees showed a significantly decrease in the flying duration and flying distance when oral exposed to two or three these pesticides. This evidence indicated that two or three pesticides can produce synergistic changes in the flight ability and behavior of honeybees. Results showed a light on new understandings of complex effects and potential risks of these three pesticide on bee behavior including homing ability and food-collecting ability. Our results are key information to understand new synergistic potential among pesticide formulations and how they impair bee behavior.Table of Contents Graphic
Shortcut barcoding and early pooling for scalable multiplex single-cell reduced-representation CpG methylation sequencing at single nucleotide resolution
Authors: Mai Liyao , Wen Zebin , Zhang Yulong , Gao Yu , Lin Guanchuan , Lian Zhiwei , Yang Xiang , Zhou Jingjing , Lin Xianwei , Luo Chaochao , Peng Wanwan , Chen Caiming , Liu Duolian , Zhang Junxiao , Marjani Sadie L. , Tao Qian , Wu Xuedong , Weissman Sherman M. , Pan Xinghua 
Published: May 2023

ABSTRACTDNA methylation is essential for a wide variety of biological processes, yet the development of a highly efficient and robust technology remains a challenge for routine single-cell analysis. We developed a multiplex scalable single-cell reduced representation bisulfite sequencing (msRRBS) technology with off-the-shelf reagents and equipment. It allows cell-specific barcoded DNA fragments of individual cells to be pooled before bisulfite conversion, free of enzymatic modification or physical capture of the DNA ends, and achieves unparalleled read mapping rates of 62.51%, covering 59.95% of CpG islands and 71.62% of promoters in K562 cells on average. Its reproducibility is shown in duplicates of bulk cells with near perfect correlation (R=0.97-99). At a low 1 Mb of clean reads, msRRBS provides consistent coverage of CpG islands and promoters, outperforming the conventional methods with orders of magnitude reduction in cost. Here, we use this method to characterize the distinct methylation patterns and cellular heterogeneity of 6 cell lines, and leukemia and hepatocellular carcinoma models. Taking 4 hours of hands-on time, msRRBS offers a unique, highly efficient approach for dissecting methylation heterogeneity in a variety of multicellular systems.
A rigorous benchmarking of alignment-based HLA typing algorithms for RNA-seq data
Authors: Yu Dottie , Ayyala Ram , Sadek Sarah Hany , Chittampalli Likhitha , Farooq Hafsa , Jung Junghyun , Nahid Abdullah Al , Boldirev Grigore , Jung Mina , Park Sungmin , Nguyen Austin , Zelikovsky Alex , Mancuso Nicholas , Joo Jong Wha J. , Thompson Reid F. , Alachkar Houda , Mangul Serghei 
Published: May 2023

AbstractAccurate identification of human leukocyte antigen (HLA) alleles is essential for various clinical and research applications, such as transplant matching and drug sensitivities. Recent advances in RNA-seq technology have made it possible to impute HLA types from sequencing data, spurring the development of a large number of computational HLA typing tools. However, the relative performance of these tools is unknown, limiting the ability for clinical and biomedical research to make informed choices regarding which tools to use. Here we report the study design of a comprehensive benchmarking of the performance of 12 HLA callers across 682 RNA-seq samples from 8 datasets with molecularly defined gold standard at 5 loci, HLA-A, -B, -C, -DRB1, and -DQB1. For each HLA typing tool, we will comprehensively assess their accuracy, compare default with optimized parameters, and examine for discrepancies in accuracy at the allele and loci levels. We will also evaluate the computational expense of each HLA caller measured in terms of CPU time and RAM. We also plan to evaluate the influence of read length over the HLA region on accuracy for each tool. Most notably, we will examine the performance of HLA callers across European and African groups, to determine discrepancies in accuracy associated with ancestry. We hypothesize that RNA-Seq HLA callers are capable of returning high-quality results, but the tools that offer a good balance between accuracy and computational expensiveness for all ancestry groups are yet to be developed. We believe that our study will provide clinicians and researchers with clear guidance to inform their selection of an appropriate HLA caller.
Cell cycle plasticity underlies fractional resistance to palbociclib in ER+/HER2- breast tumor cells
Authors: Zikry Tarek M. , Wolff Samuel C. , Ranek Jolene S. , Davis Harris , Naugle Ander , Whitman Austin A. , Kosorok Michael R. , Spanheimer Philip M. , Purvis Jeremy E. 
Published: May 2023

ABSTRACTThe CDK4/6 inhibitor palbociclib blocks cell cycle progression in ER+/HER2- breast tumor cells. Although these drugs have significantly improved patient outcomes in metastatic breast cancers, a small percentage of tumor cells continues to divide in the presence of palbociclib—a phenomenon we refer to as fractional resistance. It is critical to understand the cellular mechanisms underlying fractional resistance because the precise percentage of resistant cells in patient tissue is a strong predictor of clinical outcome. Here, we hypothesize that fractional resistance arises from cell-to-cell differences in core cell cycle regulators that allow a subset of cells to escape CDK4/6 inhibitor therapy. We used multiplex, single-cell imaging to identify fractionally resistant tumor cells both in a cell culture model of ER+/HER2- breast cancer as well as live primary tumor cells resected from a patient. We found that tumor cells capable of proliferating in the presence of palbociclib showed both expected (e.g., CDK2, E2F1) and unexpected (e.g., Cdt1, p21, cyclin B1) shifts in core cell cycle regulators. Notably, resistant cells in both tumor models showed premature enrichment of the G1 regulators E2F1 and CDK2 protein and, unexpectedly, the G2/M regulator cyclin B1 just before cell cycle entry, suggesting that resistant cells may use noncanonical mechanisms to overcome CDK4/6 inhibition. Using computational data integration and trajectory inference approaches, we show how plasticity in cell cycle regulators gives rise to alternate cell cycle “paths” that allow individual ER+/HER2- tumor cells to escape palbociclib treatment. Understanding drivers of cell cycle plasticity, and how to eliminate resistant cell cycle paths, could lead to improved cancer therapies targeting fractionally resistant cells to improve patient outcomes.
Expansion of novel biosynthetic gene clusters from diverse environments using SanntiS
Authors: Sanchez Santiago , Rogers Joel D. , Rogers Alexander B. , Nassar Maaly , McEntyre Johanna , Welch Martin , Hollfelder Florian , Finn Robert D. 
Published: May 2023

AbstractNatural products biosynthesised by microbes are an important component of the pharmacopeia with a vast array of biomedical and industrial applications, in addition to their key role in mediating many ecological interactions. One approach for the discovery of these metabolites is the identification of biosynthetic gene clusters (BGCs), genomic units which encode the molecular machinery required for producing the natural product. Genome mining has revolutionised the discovery of BGCs, yet metagenomic assemblies represent a largely untapped source of natural products. The imbalanced distribution of BGC classes in existing databases restricts the generalisation of detection patterns and limits the ability of mining methods to recognise a broader spectrum of BGCs. This problem is further intensified in metagenomic datasets, where BGC genes may be incomplete. This work presents SanntiS, a new machine learning-based tool for identifying BGCs. SanntiS achieved high precision and recall in both genomic and metagenomic datasets, effectively capturing a broad range of BGCs. Application of SanntiS to MGnify metagenomic assemblies led to a resource containing 1.9 million BGC predictions with associated contextual data from diverse biomes and demonstrates a significant fraction of novelty compared to equivalent isolate genomes datasets. Subsequent experimental validation of a novel antimicrobial peptide detected solely by SanntiS, further demonstrates the potential of this approach for uncovering novel bioactive compounds.
Mapping the Organization and Morphology of Calcitonin Gene-Related Peptide (CGRP)-IR Axons in the Whole Mouse Stomach
Authors: Ma Jichao , Nguyen Duyen , Madas Jazune , Bizanti Ariege , Mistareehi Anas , Kwiat Andrew M. , Chen Jin , Lin Mabelle , Christie Richard , Hunter Peter , Heal Maci , Baldwin Shane , Tappan Susan , Furness John B. , Powley Terry L. , Cheng Zixi (Jack) 
Published: May 2023

AbstractNociceptive afferent axons innervate the stomach and send signals to the brain and spinal cord. Peripheral nociceptive afferents can be detected with a variety of markers [e.g., substance P (SP) and calcitonin gene-related peptide (CGRP)]. We recently examined the topographical organization and morphology of SP-immunoreactive (SP-IR) axons in the whole mouse stomach muscular layer. However, the distribution and morphological structure of CGRP-IR axons remain unclear. We used immunohistochemistry labeling and applied a combination of imaging techniques, including confocal and Zeiss Imager M2 microscopy, Neurolucida 360 tracing, and integration of axon tracing data into a 3D stomach scaffold to characterize CGRP-IR axons and terminals in the whole mouse stomach muscular layers. We found that: 1) CGRP-IR axons formed extensive terminal networks in both ventral and dorsal stomachs. 2) CGRP-IR axons densely innervated the blood vessels. 3) CGRP-IR axons ran in parallel with the longitudinal and circular muscles. Some axons ran at angles through the muscular layers. 4) They also formed varicose terminal contacts with individual myenteric ganglion neurons. 5) CGRP-IR occurred in DiI-labeled gastric-projecting neurons in the dorsal root and vagal nodose ganglia, indicating CGRP-IR axons were visceral afferent axons. 6) CGRP-IR axons did not colocalize with tyrosine hydroxylase (TH) or vesicular acetylcholine transporter (VAChT) axons in the stomach, indicating CGRP-IR axons were not visceral efferent axons. 7) CGRP-IR axons were traced and integrated into a 3D stomach scaffold. For the first time, we provided a topographical distribution map of CGRP-IR axon innervation of the whole stomach muscular layers at the cellular/axonal/varicosity scale.
Meta-omics analysis revealed structural and metabolic shifts of acidification communities after feeding with thermal hydrolysis pretreated food waste
Authors: Jiang Minxi , Chandran Kartik , Khunjar Wendell , Gilmore Kevin 
Published: May 2023

AbstractIn this study, a reduced total volatile fatty acid (VFA) yield (VFA/tCOD,P= .003) and accumulated fractions of butyric acid (BA) (BA/total VFA,P< 0.001) was observed after feeding the arrested anaerobic digestor with thermal hydrolysis pretreated food waste. Further analysis through meta-omics revealed a reduction in the diversity of acidification communities (Shannon index,P= .03), indicating a sterilization effect of THP on the indigenous microbes in the feedstock. Additionally, although both the community-level acidification genetic potential and transcriptional activities were reduced (DNA and mRNA RPKM log2 fold change = 1.77 and 0.11, respectively) after the inclusion of THP, the remaining microbial communities exhibited an elevated mRNA/DNA RPKM ratio in acidification-related genes, especially within the AA and BA metabolic networks. This suggested that the elevated BA fraction might stem from improved chain-elongation activities using AA as a precursor. Furthermore, the inclusion of THP in the feedstock changed the main functional microbial groups of BA production (via the genecrt-buk2) fromSelenomonasandBacteroidestoPrevotellaandMegasphaera. Overall, these results reveal a complex shift in the acidification community and provide new insights to evaluate THP technologies behind the formed black box of VFA production performance.
Sound-based assembly of three-dimensional cellularized and acellularized constructs
Authors: Tognato Riccardo , Parolini Romedi , Jahangir Shahrbanoo , Ma Junxuan , Florczak Sammy , Richards R. Goeff , Levato Riccardo , Alini Mauro , Serra Tiziano 
Published: May 2023

AbstractHerein we show an accessible technique based on Faraday waves that assist the rapid assembly osteoinductive β-TCP particles as well as human osteoblast pre-assembled in spheroids. The hydrodynamic forces originating at ’seabed’ of the assembly chamber can be used to tightly aggregate inorganic and biological entities at packing densities that resemble those of native tissues. Additionally, following a layer-by-layer assembly procedure, centimeter scaled osteoinductive three-dimensional and cellularised constructs have been fabricated. We showed that the intimate connection between biological building blocks is essential in engineering living system able of localized mineral deposition. Our results demonstrate, for the first time, the possibility to obtain three-dimensional cellularised and acellularised anisotropic constructs using Faraday waves.
Construction and optimization of multi-platform precision pathways for precision medicine
Authors: Tran Andy , Wang Andy , Mickaill Jamie , Strbenac Dario , Larance Mark , Vernon Steve , Grieve Stuart , Figtree Gemma , Patrick Ellis , Yang Jean Yee Hwa 
Published: May 2023

AbstractIn the enduring challenge against disease, advancements in medical technology have empowered clinicians with novel diagnostic platforms. Whilst in some cases, a single test may provide a confident diagnosis, often additional tests are required. However, to strike a balance between diagnostic accuracy and cost-effectiveness, one must rigorously construct the clinical pathways. Here, we developed a framework to build multi-platform precision pathways in an automated, unbiased way, recommending the key steps a clinician would take to reach a diagnosis. We achieve this by developing a confidence score, used to simulate a clinical scenario, where at each stage, either a confident diagnosis is made, or another test is performed. Our framework provides a range of tools to interpret, visualize and compare the pathways, improving communication and enabling their evaluation on accuracy and cost, specific to different contexts. This framework will guide the development of novel diagnostic pathways for different diseases, accelerating the implementation of precision medicine into clinical practice.