bluuebunny/crossref_metadata_2025 huggingface dataset:
Non-English Primary Language
Authors: Bakillah Emna , Sharpe James , Tong Jason K. , Goldshore Matthew , Morris Jon B. , Kelz Rachel R.
Published: May 2023

Objective:

To examine access to cholecystectomy and post-operative outcomes among non-English primary speaking patients.

Summary Background Data:

The population of U.S. residents with limited English proficiency is growing. Language affects health literacy and is a well-recognized barrier to healthcare in the U.SA. Historically marginalized communities are at greater risk of requiring emergent gallbladder operations. However, little is known about how primary language affects surgical access and outcomes of common surgical procedures such as cholecystectomy.

Methods:

We conducted a retrospective cohort study of adult patients following receipt of cholecystectomy in Michigan, Maryland, and New Jersey utilizing the Healthcare Cost and Utilization Project State Inpatient Database and State Ambulatory Surgery and Services Database (2016-2018). Patients were classified by primary spoken language: English or non-English. The primary outcome was admission type. Secondary outcomes included operative setting, operative approach, in-hospital mortality, post-operative complications, and length of stay. Multivariable logistic and Poisson regression were used to examine outcomes.

Results:

Among 122,013 cholecystectomy patients, 91.6% were primarily English speaking and 8.4% were non-English primary language speaking. Primary non-English speaking patients had a higher likelihood of emergent/urgent admissions (OR 1.22, 95% CI 1.04-1.44, P=0.015) and a lower likelihood of having an outpatient operation (OR 0.80, 95% CI 0.70-0.91, P=0.0008). There was no difference in use of minimally invasive approach or post-operative outcomes based on primary language spoken.

Conclusions:

Non-English primary language speakers were more likely to access cholecystectomy via the emergency department and less likely to receive outpatient cholecystectomy. Barriers to elective surgical presentation for this growing patient population needs to be further studied.
Neoadjuvant Chemotherapy versus Upfront Surgery for Resectable Pancreatic Adenocarcinoma
Authors: Sugawara Toshitaka , Rodriguez Franco Salvador , Sherman Samantha , Torphy Robert J. , Colborn Kathryn , Franklin Oskar , Ishida Jun , Grandi Samuele , Al-Musawi Mohammed H. , Gleisner Ana , Schulick Richard D. , Del Chiaro Marco
Published: May 2023

Objective:

To assess the association of survival with neoadjuvant chemotherapy (NAC) in resectable pancreatic adenocarcinoma (PDAC).

Summary Background Data:

The early control of potential micrometastases and patient selection using NAC has been advocated for patients with PDAC. However, the role of NAC for resectable PDAC remains unclear.

Methods:

Patients with clinical T1 and T2 PDAC were identified in the National Cancer Database from 2010 to 2017. Kaplan-Meier estimates and Cox regression models were used to compare survival. To address immortal time bias, landmark analysis was performed. Interactions between preoperative factors and NAC were investigated in subgroup analyses. A propensity score analysis was performed to compare survival between multiagent NAC and upfront surgery.

Results:

In total, 4,041 patients were treated with upfront surgery and 1,175 patients treated with NAC (79.4% multiagent NAC, 20.6% single-agent NAC). Using a landmark time of 6 months after diagnosis, patients treated with multiagent NAC had longer median overall survival, compared to upfront surgery and single-agent NAC. (35.8 vs. 27.1 vs. 27.4 mo). Multiagent NAC was associated with lower mortality rates compared to upfront surgery (adjusted HR, 0.77; 95% CI, 0.70–0.85), whereas single-agent NAC was not. The association of survival with multiagent NAC were consistent in analyses using the matched data sets. Interaction analysis revealed that multiagent NAC was associated with lower mortality rates across age, facility type, CA 19-9 levels, and clinical T/N stages, except in patients with body/tail tumors.

Conclusion:

The findings suggest that multiagent NAC followed by resection is associated with improved survival compared to upfront surgery.
Genomic surveillance of multidrug-resistant Klebsiella in Wales reveals persistent spread of Klebsiella pneumoniae ST307 and adaptive evolution of pOXA-48-like plasmids
Authors: David Sophia , Mentasti Massimo , Sands Kirsty , Portal Edward , Graham Lee , Watkins Joanne , Williams Catie , Healy Brendan , Spiller Owen B. , Aanensen David M. , Wootton Mandy , Jones Lim
Published: May 2023

Rising rates of multidrug-resistant

Klebsiella

infections necessitate a comprehensive understanding of the major strains and plasmids driving spread of resistance elements. Here, we analysed 540 clinical, screen and environmental

Klebsiella

isolates recovered from across Wales between 2007 and 2020 using combined short- and long-read sequencing approaches. We identified resistant clones that have spread within and between hospitals including the high-risk strain sequence type (ST)307, which acquired the bla
OXA-244 carbapenemase gene on a pOXA-48-like plasmid. We found evidence that this strain, which caused an acute outbreak largely centred on a single hospital in 2019, had been circulating undetected across South Wales for several years prior to the outbreak. In addition to clonal transmission, our analyses revealed evidence for substantial plasmid spread, mostly notably involving bla
KPC-2 and bla
OXA-48-like (including bla
OXA-244) carbapenemase genes that were found among many species and strain backgrounds. Two thirds (20/30) of the bla
KPC-2 genes were carried on the Tn4401a transposon and associated with IncF plasmids. These were mostly recovered from patients in North Wales, reflecting an outward expansion of the plasmid-driven outbreak of bla
KPC-2-producing

Enterobacteriaceae

in North-West England. A total of 92.1 % (105/114) of isolates with a bla
OXA-48-like carbapenemase carried the gene on a pOXA-48-like plasmid. While this plasmid family is highly conserved, our analyses revealed novel accessory variation including integrations of additional resistance genes. We also identified multiple independent deletions involving the tra gene cluster among pOXA-48-like plasmids in the ST307 outbreak lineage. These resulted in loss of conjugative ability and signal adaptation of the plasmids to carriage by the host strain. Altogether, our study provides, to our knowledge, the first high resolution view of the diversity, transmission and evolutionary dynamics of major resistant clones and plasmids of

Klebsiella

in Wales, and forms an important basis for ongoing surveillance efforts. This article contains data hosted by Microreact.
Genomic epidemiology of Mycobacterium bovis infection in sympatric badger and cattle populations in Northern Ireland
Authors: Akhmetova Assel , Guerrero Jimena , McAdam Paul , Salvador Liliana C. M. , Crispell Joseph , Lavery John , Presho Eleanor , Kao Rowland R. , Biek Roman , Menzies Fraser , Trimble Nigel , Harwood Roland , Pepler P. Theo , Oravcova Katarina , Graham Jordon , Skuce Robin , du Plessis Louis , Thompson Suzan , Wright Lorraine , Byrne Andrew W. , Allen Adrian R.
Published: May 2023

Bovine tuberculosis (bTB) is a costly, epidemiologically complex, multi-host, endemic disease. Lack of understanding of transmission dynamics may undermine eradication efforts. Pathogen whole-genome sequencing improves epidemiological inferences, providing a means to determine the relative importance of inter- and intra-species host transmission for disease persistence. We sequenced an exceptional data set of 619

Mycobacterium bovis

isolates from badgers and cattle in a 100 km2 bTB ‘hotspot’ in Northern Ireland. Historical molecular subtyping data permitted the targeting of an endemic pathogen lineage, whose long-term persistence provided a unique opportunity to study disease transmission dynamics in unparalleled detail. Additionally, to assess whether badger population genetic structure was associated with the spatial distribution of pathogen genetic diversity, we microsatellite genotyped hair samples from 769 badgers trapped in this area. Birth death models and TransPhylo analyses indicated that cattle were likely driving the local epidemic, with transmission from cattle to badgers being more common than badger to cattle. Furthermore, the presence of significant badger population genetic structure in the landscape was not associated with the spatial distribution of

M. bovis

genetic diversity, suggesting that badger-to-badger transmission is not playing a major role in transmission dynamics. Our data were consistent with badgers playing a smaller role in transmission of

M. bovis

infection in this study site, compared to cattle. We hypothesize, however, that this minor role may still be important for persistence. Comparison to other areas suggests that

M. bovis

transmission dynamics are likely to be context dependent, with the role of wildlife being difficult to generalize.
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

Recent 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

Background and Aim

Macrophages 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 Results

Acute 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.

Conclusion

These 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

Tumor 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

Background

New-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 Results

From 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.

Conclusions

39.5% 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 Perspective

What 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

Pesticides 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.

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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

DNA 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

Accurate 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

The 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

Natural 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.
Narwhal (Monodon monoceros) echolocation click rates to support cue counting passive acoustic density estimation
Authors: Marques Carolina S. , Marques Diana A. , Blackwell Susanna B. , Heide-Jørgensen Mads Peter , Malinka Chloe E. , Marques Tiago A.
Published: May 2023

Estimating animal abundance is fundamental for effective management and conservation. It is increasingly done by combining passive acoustics with knowledge about rates at which animals produce cues (cue rates). Narwhals (Monodon monoceros) are elusive marine mammals for which passive acoustic density estimation might be plausible, but for which cue rates are lacking. Clicking rates in narwhals were investigated using a pre-existing dataset from sound and movement tag records collected in August 2013-2016 and 2019 in East Greenland. Clicking rates were quantified for∼1200 one-second-long systematic random samples from 8 different whales. Generalized Additive Models were used to model (1) the probability of being in a clicking state versus depth; and (2) the clicking rate while in a clicking state, versus time and depth. The probability of being in a clicking state increased with depth, reaching∼1.0 at∼500 meters, while the number of clicks per second (while in a clicking state) increased with depth. The mean cue production rate, weighted by tag duration, was 1.28 clicks per second (se= 0.13, CV= 0.10). This first cue rate for narwhals may be used for cue counting density estimation, but care should be taken if applying it to other geographical areas or seasons.
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

Nociceptive 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

In 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

Herein 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

In 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.
Environmental stiffness restores mechanical homeostasis in vimentin-depleted cells
Authors: Grolleman Janine , Engeland Nicole C.A. van , Raza Minahil , Rasthi Sepinoud Azimi , Conte Vito , Sahlgren Cecilia M. , Bouten Carlijn V.C.
Published: May 2023

Recent experimental evidence indicates a role for the intermediate filament vimentin in regulating cellular mechanical homeostasis, but its precise contribution remains to be discovered. Mechanical homeostasis requires a balanced bi-directional interplay between the cell’s microenvironment and the cellular morphological and mechanical state – this balance being regulated via processes of mechanotransduction and mechanoresponse, commonly referred to as mechanoreciprocity. Here, we systematically analyze vimentin-expressing and vimentin-depleted cells in a swatch ofin vitrocellular microenvironments varying in stiffness and/or ECM density. We find that vimentin-expressing cells maintain mechanical homeostasis by adapting cellular morphology and mechanics to micromechanical changes in the microenvironment. However, vimentin-depleted cells lose this mechanoresponse ability on short timescales, only to reacquire it on longer time scales. Indeed, we find that the morphology and mechanics of vimentin-depleted cell in stiffened microenvironmental conditions can get restored to the homeostatic levels of vimentin-expressing cells. Additionally, we observed vimentin-depleted cells increasing collagen matrix synthesis and its crosslinking, a phenomenon which is known to increase matrix stiffness, and which we now hypothesize to be a cellular compensation mechanism for the loss of vimentin. Taken together, our findings provide further insight in the regulating role of intermediate filament vimentin in mediating mechanoreciprocity and mechanical homeostasis.
G6PC2 controls glucagon secretion by defining the setpoint for glucose in pancreatic α-cells
Authors: Bahl Varun , Waite Eric , Rifkind Reut , Hamdan Zenab , May Catherine Lee , Manduchi Elisabetta , Voight Benjamin F. , Lee Michelle Y.Y. , Tigue Mark , Manuto Nicholas ,   the HPAP Consortium, Glaser Benjamin , Avrahami Dana , Kaestner Klaus H.
Published: May 2023

Impaired glucose suppression of glucagon secretion (GSGS) is a hallmark of type 2 diabetes. A critical role for α-cell intrinsic mechanisms in regulating glucagon secretion was previously established through genetic manipulation of the glycolytic enzyme glucokinase (GCK) in mice. Genetic variation at theG6PC2locus, encoding an enzyme that opposes GCK, has been reproducibly associated with fasting blood glucose and hemoglobin A1c levels. Here, we find that trait-associated variants in theG6PC2promoter are located in open chromatin not just in β− but also in α-cells, and document allele-specificG6PC2expression of linked variants in human α– cells. Using α-cell specific gene ablation ofG6pc2in mice, we show that this gene plays a critical role in controlling glucagon secretion independent of alterations in insulin output, islet hormone content, or islet morphology; findings we confirmed in primary human α-cells. Collectively, our data demonstrate thatG6PC2impacts glycemic control via its action in α-cells and suggest thatG6PC2inhibitors could help control blood glucose through a novel, bi-hormonal mechanism.
Full-length single-cell BCR sequencing paired with RNA sequencing reveals convergent responses to vaccination
Authors: Morgan Duncan M. , Zhang Yiming , Kim Jin-Hwan , Murillo MaryAnn , Singh Suddham , Loschko Jakob , Surendran Naveen , Patil Sarita U. , Kanevsky Isis , Chorro Laurent , Love J. Christopher
Published: May 2023

Single-cell RNA sequencing can to resolve transcriptional features from large numbers of individual immune cells, but techniques capable of resolving the variable regions of B cell receptors (BCR) – defining features that confer antigen specificity to B cells – remain limited, especially from widely-used 3′-barcoded libraries. Here, we report a method that for recovering paired, full-length variable region sequences of the BCRs from 3′-barcoded single-cell whole transcriptome libraries. We first verified this method could produce accurate, full-length BCR sequences. We then applied this method to profile antigen-specific B cell responses elicited against the capsular polysaccharide ofStreptococcus pneumoniaeserotype 3 (ST3) by glycoconjugate vaccines in infant rhesus macaques. Using our method, we defined features of the BCR associated with specificity for the ST3 antigen and showed that these sequence characteristics are present in multiple vaccinated monkeys, indicating a convergent response to vaccination. These results demonstrate the utility of our method to resolve key features of the B cell repertoire and for profiling antigen-specific responses elicited by vaccination.
Converging evidence that left extrastriate body area supports visual sensitivity to social interactions
Authors: Gandolfo Marco , Abassi Etienne , Balgova Eva , Downing Paul E. , Papeo Liuba , Koldewyn Kami
Published: May 2023

Navigating our complex social world requires processing the interactions we observe. Recent psychophysical and neuroimaging studies provide parallel evidence that the human visual system may be attuned to efficiently perceive dyadic interactions. This work implies, but has not yet demonstrated, that activity in body-selective cortical regions causally supports efficient visual perception of interactions. We adopt a multi-method approach to close this important gap. First, using a large fMRI dataset (N=92), we found that the left-hemisphere Extrastriate Body Area (EBA) responds more to face-to-face than non-facing dyads. Second, we replicated a behavioural marker of visual sensitivity to interactions: categorisation of facing dyads is more impaired by inversion than non-facing dyads. Third, in a pre-registered experiment, we used fMRI-guided transcranial magnetic stimulation to show that online stimulation of the left EBA, but not a nearby control region, abolishes this selective inversion effect. Activity in left EBA, thus, causally supports the efficient perception of social interactions.
Model-X knockoffs reveal data-dependent limits on regulatory network identification
Authors: Kernfeld Eric , Keener Rebecca , Cahan Patrick , Battle Alexis
Published: May 2023

Computational biologists have long sought to automatically infer transcriptional regulatory networks (TRNs) from gene expression data, but such approaches notoriously suffer from false positives. Two points of failure could yield false positives: faulty hypothesis testing, or erroneous assumption of a classic criterion calledcausal sufficiency. We show that a recent statistical development, model-X knockoffs, can effectively control false positives in tests of conditional independence in mouse andE. colidata, which rules out faulty hypothesis tests. Yet, benchmarking against ChIP and other gold standards reveals highly inflated false discovery rates. This identifies the causal sufficiency assumption as a key limiting factor in TRN inference.
The digestive system of a cricket pulverizes polyethylene microplastics
Authors: Ritchie Marshall W. , Provencher Jennifer F. , Allison Jane E. , Muzzatti Matthew J. , MacMillan Heath A.
Published: May 2023

Microplastics (MPs; <5 mm) are a growing concern and a poorly understood threat to biota. Despite a recent spike in research on MPs, most of this work has focused on marine systems, and less is known about interactions between terrestrial organisms. We used a generalist insect (a cricket;Gryllodes sigillatus) to examine whether individuals would ingest and physically degrade MPs in their food. We fed crickets a range of concentrations (0, 2.5, 5, and 10% w/w) of fluorescent MPs mixed into a standard diet and dissected the gut regions to isolate the MPs within. Comparing plastic content and fragment size within gut regions, we sought to identify whether and where crickets can fragment ingested MP particles. Given the digestive tract morphology of this species, we expected that the crickets would both ingest and egest the MPs. We also predicted that the MPs would be fragmented into smaller pieces during this digestive process. We found thatG. sigillatusegested much smaller pieces than they ingested (likely into the nanoplastic range), and this fragmentation occurs early in the digestive process of this insect. These findings suggest that generalist insects can act as agents of plastic transformation in their environment if/when encountering MPs.
Sex differences in music perception are negligible
Authors: Bertolo Mila , Müllensiefen Daniel , Peretz Isabelle , Woolley Sarah C. , Sakata Jon T. , Mehr Samuel A.
Published: May 2023

Since Darwin1, researchers have proposed that human musicality evolved in a reproductive context in which males produce music to signal their mate quality to females. Sexually selected traits involve tradeoffs in the costs of high-quality signal production and high-fidelity signal detection2, leading to observable sexual dimorphisms across many species3,4. If musicality is a sexually selected trait in humans, males and females should then differ in their music perception ability, music production ability, or both. The evidence for this possibility is unclear, because previous reports of sex differences in human auditory perception are restricted in scope and inconsistent in direction5–15. Here, we report a test of music processing ability in 360,009 men and 194,291 women from 208 countries. In contrast to other non-musical human traits16–19, and in contrast to music-related traits in non-human animals20–23, we found no consistent advantage for either sex. The sex differences we did observe were negligible (Cohen’sdrange: 0.009-0.111) and Bayesian analyses indicated evidence in favor of the null hypothesis of no sex difference in general musical ability (Bayes Factor = 0.6). These results suggest that it is unlikely that music evolved in the context of sexual selection.
A systemic approach allows to identify the pedoclimatic conditions most critical in the susceptibility of a grapevine cultivar to esca/Botryosphaeria dieback
Authors: Monod Vinciane , Zufferey Vivian , Wilhelm Matthieu , Viret Olivier , Gindro Katia , Croll Daniel , Hofstetter Valérie
Published: May 2023

Esca and/or Botryosphaeria dieback (esca-BD) are two of the most destructive grapevine trunk diseases in the world, disease complex which remains poorly understood. As some vine cultivars show highly variable susceptibility to esca-BD, we designed a four-year experiment to identify which environmental factors influence the expression of the disease. We collected epidemiological and physiological data once a year for four consecutive years in 19 vineyard plots located in four wine-growing regions of Western Switzerland. We compared these data with climatic data obtained from weather stations for these same plots for four years and over the long term. We also estimated the soil water holding capacity of each plot. Confounding factors were minimal because all vineyards were planted in 2003 with the same cultivar and all plants grafted in the same nursery with genetically homogeneous grafting material. Principal component and regression analyses of combined epidemiological, biotic and pedoclimatic data identified a positive correlation between soil water retention capacity and plant mortality due to esca-BD. These analyses also showed that leaf disease symptoms and apoplexy are more frequent when cold, wet periods are followed - or alternate with - hot, dry periods, and that apoplexy occurs more frequently when weather conditions change abruptly (cold, wet May followed by a hot June) and deviate significantly from long-term climatic conditions. Regression analyses show that the soil water holding capacity impacts less the disease expression when the climate is warm and dry, both at the regional and at year-specific levels. Having identified the most important environmental factors towards expression of esca-BD, this study allows recommendations to be given to the winegrowers for the cultivar studied but can also be used as a model to identify the environmental factors that influence the expression of fungal diseases in other grapevine cultivars, other grapevine trunk diseases and even in other woody plants.
Increased bleeding and thrombosis in myeloproliferative neoplasms mediated through altered expression of inherited platelet disorder genes
Authors: Mitchell Alan , Frontini Mattia , Islam Serajul , Sivapalaratnam Suthesh , Krishnan Anandi
Published: May 2023

An altered thrombo-hemorrhagic profile has long been observed in patients with myeloproliferative neoplasms (MPNs). We hypothesized that this observed clinical phenotype may result from altered expression of genes known to harbor genetic variants in bleeding, thrombotic, or platelet disorders. Here, we identify 32 genes from a clinically validated gene panel that were also significantly differentially expressed in platelets from MPN patients as opposed to healthy donors.

This work begins to unravel previously unclear mechanisms underlying an important clinical reality in MPNs. Knowledge of altered platelet gene expression in MPN thrombosis/bleeding diathesis opens opportunities to advance clinical care by: (1) enabling risk stratification, in particular, for patients undergoing invasive procedures, and (2) facilitating tailoring of treatment strategies for those at highest risk, for example, in the form of antifibrinolytics, desmopressin or platelet transfusions (not current routine practice). Marker genes identified in this work may also enable prioritization of candidates in future MPN mechanistic as well as outcome studies.