bluuebunny/crossref_metadata_2025_split huggingface dataset:
Racial Differences in the Association of Endometriosis and Uterine Leiomyomas With the Risk of Ovarian Cancer
Authors: Harris Holly R. , Peres Lauren C. , Johnson Courtney E. , Guertin Kristin A. , Beeghly Alicia , Bandera Elisa V. , Bethea Traci N. , Joslin Charlotte E. , Wu Anna H. , Moorman Patricia G. , Ochs-Balcom Heather M. , Petrick Jessica L. , Setiawan Veronica W. , Rosenberg Lynn , Schildkraut Joellen M. , Myers Evan 
Published: May 2023

OBJECTIVE:
To evaluate associations between endometriosis and uterine leiomyomas with ovarian cancer risk by race and the effect of hysterectomy on these associations.

METHODS:
We used data from four case–control studies and two case–control studies nested within prospective cohorts in the OCWAA (Ovarian Cancer in Women of African Ancestry) consortium. The study population included 3,124 Black participants and 5,458 White participants, of whom 1,008 Black participants and 2,237 White participants had ovarian cancer. Logistic regression was used to calculate odds ratios (ORs) and 95% CIs for the associations of endometriosis and leiomyomas with ovarian cancer risk, by race, stratified by histotype and hysterectomy.

RESULTS:
The prevalences of endometriosis and leiomyomas were 6.4% and 43.2% among Black participants and 7.0% and 21.5% among White participants, respectively. Endometriosis was associated with an increased risk of endometrioid and clear-cell ovarian cancer in both racial groups (eg, OR for endometrioid tumors for Black and White participants 7.06 [95% CI 3.86–12.91] and 2.17 [95% CI 1.36–3.45], respectively, P
hetereogeneity=.003). The association between endometriosis and ovarian cancer risk in White participants was stronger in those without hysterectomy, but no difference was observed in Black participants (all P
interaction≥.05). Leiomyomas were associated with an elevated risk of ovarian cancer only in those without hysterectomy in both Black (OR 1.34, 95% CI 1.11–1.62) and White (OR 1.22, 95% CI 1.05–1.41) participants (all P
interaction≥.05).

CONCLUSIONS:
Black and White participants with endometriosis had a higher risk of ovarian cancer, and hysterectomy modified this association among White participants. Leiomyomas were associated with an increased risk of ovarian cancer in both racial groups, with hysterectomy modifying the risk in both groups. Understanding how racial differences in access to care and treatment options (eg, hysterectomy) may help guide future risk reduction strategies.
A case report of chylous ascites after cardiac surgery
Authors: Yuan Shuaishuai , Xie Pailing , Liu Xiantao , Li Peijun 
Published: May 2023

AbstractBackgroundChylous ascites (CA), an emulsion rich in triglycerides, is a rare type of ascites, especially after cardiac surgery. Also, there are few reports of the occurrence of CA after mitral valve replacement, aortic valve replacement, tricuspid valvuloplasty, and coronary artery bypass grafting.Case presentationWe report the case of a 53-year-old man who underwent surgery for a diagnosis of mitral incompetence, aortic incompetence, tricuspid incompetence, and coronary atherosclerotic heart disease. Fifteen days after surgery, 3000 mL of milky-yellow ascites appeared in the abdominal cavity, diagnosed as CA by laboratory examination. The ascites gradually disappeared after being drained, and the patients improved. The curative was objective, but the exact cause is not clear.ConclusionAlthough CA is rare, it may occur during the surgical intervention in cardiac surgery.
Microsurgical Resection of Vascular Malformations of the Upper Extremity
Authors: Horan Katelyn M. H. , Beijnen Usha E. A. , Upton Joseph , Taghinia Amir H. 
Published: May 2023

Background:
Vascular malformations that circumferentially surround end or near-end arteries are challenging to manage. Minimally invasive treatment options such as sclerotherapy can directly damage these vessels and cause ischemia. Surgical resection is desired without sacrificing or injuring a patent artery, especially in end organs like the upper limb. Microsurgical resection of these lesions provides a viable option for treatment.

Methods:
The records of nine patients who presented with vascular malformations that circumferentially surrounded an artery in the upper limb were reviewed. The main indications for surgical intervention were pain or persistent growth. In each case, microsurgical technique using a microscope and microsurgical instruments was used to dissect the lesions free from the affected end arteries. Four digital arteries, three radial arteries, one brachial artery and one palmar arch were involved.

Results:
There were six venous malformations, two fibro-adipose vascular anomalies, and one lymphatic malformation. There were no cases of distal ischemia, bleeding, or functional compromise. Two patients experienced delayed wound healing. After a minimum follow-up of 1 year, only one patient experienced a small area of recurrence but had no pain.

Conclusions:
Microsurgical dissection using a microscope and microsurgical instruments is a viable technique for resection of difficult vascular malformations that surround major arterial channels in the upper limb. This technique allows preservation of maximum blood supply while treating problematic lesions.
Deep Infantile Hemangioma in the Involuting Phase That Was Difficult to Diagnose before Surgery
Authors: Sakai Yuki , Tsuge Itaru , Kataoka Masako , Takeuchi Yasuhide , Katayama Yasuhiro , Yamanaka Hiroki , Katsube Motoki , Sowa Yoshihiro , Sakamoto Michiharu , Morimoto Naoki 
Published: May 2023

Summary:
Infantile hemangioma (IH) is a common pediatric vascular tumor and is easily diagnosed in most cases based on the clinical course and appearance, but deep IHs are difficult to diagnose based on external appearance alone. Clinical and imaging findings are therefore important clues to the diagnosis of soft tissue tumors; however, a definitive diagnosis is decided based on the pathological examination of biopsy or resection specimens. A 1-year-old girl with a subcutaneous mass on her glabella was referred to our hospital. At 3 months of age, her mother noticed a tumor that swelled when she cried. It gradually enlarged, and ultrasonography and magnetic resonance imaging were performed at 12 months of age. Doppler ultrasonography showed a hypo-vascular mass. Magnetic resonance imaging revealed a subcutaneous mass with low-intensity on T1-weighted image and slightly high-intensity on T2-weighted image, with tiny flow voids. Computed tomography showed no frontal bone defect. The soft tissue tumor could not be diagnosed based on these imaging findings; thus, we decided to perform total resection under general anesthesia. A histopathological examination showed a highly cellular tumor with capillaries with opened small vascular channels and glucose transporter 1 positivity. Thus, it was diagnosed as deep IH transitioning from the proliferative phase to the involuting phase. Deep IHs are difficult to diagnose because characteristic imaging findings disappear during the involuting phase. We emphasize the importance of performing Doppler ultrasonography in the early phase (eg, at 6 months of age) for soft tissue tumors of infancy.
The role of the Southern Ocean in the global climate response to carbon emissions
Authors: Williams Richard G. , Ceppi Paulo , Roussenov Vassil , Katavouta Anna , Meijers Andrew J. S. 
Published: May 2023

The effect of the Southern Ocean on global climate change is assessed using Earth system model projections following an idealized 1% annual rise in atmospheric CO2. For this scenario, the Southern Ocean plays a significant role in sequestering heat and anthropogenic carbon, accounting for 40% ± 5% of heat uptake and 44% ± 2% of anthropogenic carbon uptake over the global ocean (with the Southern Ocean defined as south of 36°S). This Southern Ocean fraction of global heat uptake is however less than in historical scenarios with marked hemispheric contrasts in radiative forcing. For this idealized scenario, inter-model differences in global and Southern Ocean heat uptake are strongly affected by physical feedbacks, especially cloud feedbacks over the globe and surface albedo feedbacks from sea-ice loss in high latitudes, through the top-of-the-atmosphere energy balance. The ocean carbon response is similar in most models with carbon storage increasing from rising atmospheric CO2, but weakly decreasing from climate change with competing ventilation and biological contributions over the Southern Ocean. The Southern Ocean affects a global climate metric, the transient climate response to emissions, accounting for 28% of its thermal contribution through its physical climate feedbacks and heat uptake, and so affects inter-model differences in meeting warming targets.This article is part of a discussion meeting issue 'Heat and carbon uptake in the Southern Ocean: the state of the art and future priorities'.
Sailing through the southern seas of air–sea CO
2
flux uncertainty
Authors: Landschützer Peter , Tanhua Toste , Behncke Jacqueline , Keppler Lydia 
Published: May 2023

The Southern Ocean is among the largest contemporary sinks of atmospheric carbon dioxide on our planet; however, remoteness, harsh weather and other circumstances have led to an undersampling of the ocean basin, compared with its northern hemispheric counterparts. While novel data interpolation methods can in part compensate for such data sparsity, recent studies raised awareness that we have hit a wall of unavoidable uncertainties in air–sea

CO

2

flux reconstructions. Here, we present results from autonomous observing campaigns using a novel platform to observe remote ocean regions: sailboats. Sailboats are at present a free of charge environmentally friendly platform that recurrently pass remote ocean regions during round-the-globe racing events. During the past 5 years, we collected

>

350

000

measurements of the sea surface partial pressure of

CO

2

(p

CO

2

) around the globe including the Southern Ocean throughout an Antarctic circumnavigation during the Vendée Globe racing event. Our analysis demonstrates that the sailboat tracks pass regions where large uncertainty in the air–sea

CO

2

flux reconstruction prevails, with regional oversaturation or undersaturation of the sea surface p

CO

2

. Sailboat races provide an independent cross-calibration platform for autonomous measurement devices, such as Argo floats, ultimately strengthening the entire Southern Ocean observing system.

This article is part of a discussion meeting issue ‘Heat and carbon uptake in the Southern Ocean: the state of the art and future priorities’.
New insights into air-sea fluxes and their role in Subantarctic Mode Water formation
Authors: Tamsitt V. 
Published: May 2023

The formation of Subantarctic Mode Water SAMW in the Southern Ocean plays a key role in the global oceanic uptake and storage of anthropogenic heat and carbon. Wintertime ocean surface heat loss is a dominant driver of Subantarctic Mode Water formation and variability, but wintertime air-sea flux observations in the Southern Ocean are extremely sparse. Recent advances in our understanding of the role of air-sea fluxes in Subantarctic Mode Water Formation from novel ocean observations are summarized here, particularly the role of synoptic atmospheric extreme events, and the drivers of interannual variations in SAMW. These advances in understanding have important implications for variability in Southern Ocean heat and carbon uptake, and can inform future Southern Ocean observing system design.
This article is part of a discussion meeting issue ‘Heat and carbon uptake in the Southern Ocean: the state of the art and future priorities’.
Tracing the impacts of recent rapid sea ice changes and the A68 megaberg on the surface freshwater balance of the Weddell and Scotia Seas
Authors: Meredith Michael P. , Povl Abrahamsen E. , Alexander Haumann F. , Leng Melanie J. , Arrowsmith Carol , Barham Mark , Firing Yvonne L. , King Brian A. , Brown Peter , Alexander Brearley J. , Meijers Andrew J. S. , Sallée Jean-Baptiste , Akhoudas Camille , Tarling Geraint A. 
Published: May 2023

The Southern Ocean upper-layer freshwater balance exerts a global climatic influence by modulating density stratification and biological productivity, and hence the exchange of heat and carbon between the atmosphere and the ocean interior. It is thus important to understand and quantify the time-varying freshwater inputs, which is challenging from measurements of salinity alone. Here we use seawater oxygen isotopes from samples collected between 2016 and 2021 along a transect spanning the Scotia and northern Weddell Seas to separate the freshwater contributions from sea ice and meteoric sources. The unprecedented retreat of sea ice in 2016 is evidenced as a strong increase in sea ice melt across the northern Weddell Sea, with surface values increasing approximately two percentage points between 2016 and 2018 and column inventories increasing approximately 1 to 2 m. Surface meteoric water concentrations exceeded 4% in early 2021 close to South Georgia due to meltwater from the A68 megaberg; smaller icebergs may influence meteoric water at other times also. Both these inputs highlight the importance of a changing cryosphere for upper-ocean freshening; potential future sea ice retreats and increases in iceberg calving would enhance the impacts of these freshwater sources on the ocean and climate.
This article is part of a discussion meeting issue ‘Heat and carbon uptake in the Southern Ocean: the state of the art and future priorities’.
Inhibition of Proliferation of Acute Lymphocytic Leukemia (ALL) by frequency-specific Oscillating Pulsed Electric Fields (OPEF) broadcast by an enclosed gas plasma antenna
Authors: Holland Anthony , Bare James 
Published: May 2023

ABSTRACTFrequency-specific Oscillating Pulsed Electric Fields (OPEF) broadcast by an enclosed gas plasma antenna with a frequency of 160kHz from a distance of 18 inches inhibited the proliferation of Acute Lymphocytic Leukemia cells in vitro by up to 44%.
The temporal progression of immune remodeling during metastasis
Authors: McGinnis Christopher S. , Miao Zhuang , Reticker-Flynn Nathan E. , Winker Juliane , Satpathy Ansuman T. 
Published: May 2023

SUMMARYTumor metastasis requires systemic remodeling of distant organ microenvironments which impacts immune cell phenotypes, population structure, and intercellular communication networks. However, our understanding of immune phenotypic dynamics in the metastatic niche remains incomplete. Here, we longitudinally assayed lung immune cell gene expression profiles in mice bearing PyMT-driven metastatic breast tumors from the onset of primary tumorigenesis, through formation of the pre-metastatic niche, to the final stages of metastatic outgrowth. Computational analysis of these data revealed an ordered series of immunological changes that correspond to metastatic progression. Specifically, we uncovered a TLR-NFκB myeloid inflammatory program which correlates with pre-metastatic niche formation and mirrors described signatures of CD14+ ‘activated’ MDSCs in the primary tumor. Moreover, we observed that cytotoxic NK cell proportions increased over time which illustrates how the PyMT lung metastatic niche is both inflammatory and immunosuppressive. Finally, we predicted metastasis-associated immune intercellular signaling interactions involvingIgf1andCcl6which may organize the metastatic niche. In summary, this work identifies novel immunological signatures of metastasis and discovers new details about established mechanisms that drive metastatic progression.Graphical abstractIn briefMcGinnis et al. report a longitudinal scRNA-seq atlas of lung immune cells in mice bearing PyMT-driven metastatic breast tumors and identify immune cell transcriptional states, shifts in population structure, and rewiring of cell-cell signaling networks which correlate with metastatic progression.HighlightsLongitudinal scRNA-seq reveals distinct stages of immune remodeling before, during, and after metastatic colonization in the lungs of PyMT mice.TLR-NFκB inflammation correlates with pre-metastatic niche formation and involves both tissue-resident and bone marrow-derived myeloid cell populations.Inflammatory lung myeloid cells mirror ‘activated’ primary tumor MDSCs, suggesting that primary tumor-derived cues induceCd14expression and TLR-NFκB inflammation in the lung.Lymphocytes contribute to the inflammatory and immunosuppressive lung metastatic microenvironment, highlighted by enrichment of cytotoxic NK cells in the lung over time.Cell-cell signaling network modeling predicts cell type-specificCcl6regulation and IGF1-IGF1R signaling between neutrophils and interstitial macrophages.
Inferring secretory and metabolic pathway activity from omic data with secCellFie
Authors: Masson Helen O. , Samoudi Mojtaba , Robinson Caressa M. , Kuo Chih-Chung , Weiss Linus , Ud Doha Km Shams , Campos Alex , Tejwani Vijay , Dahodwala Hussain , Menard Patrice , Voldborg Bjorn G. , Sharfstein Susan T. , Lewis Nathan E. 
Published: May 2023

AbstractUnderstanding protein secretion has considerable importance in the biotechnology industry and important implications in a broad range of normal and pathological conditions including development, immunology, and tissue function. While great progress has been made in studying individual proteins in the secretory pathway, measuring and quantifying mechanistic changes in the pathway’s activity remains challenging due to the complexity of the biomolecular systems involved. Systems biology has begun to address this issue with the development of algorithmic tools for analyzing biological pathways; however most of these tools remain accessible only to experts in systems biology with extensive computational experience. Here, we expand upon the user-friendly CellFie tool which quantifies metabolic activity from omic data to include secretory pathway functions, allowing any scientist to infer protein secretion capabilities from omic data. We demonstrate how the secretory expansion of CellFie (secCellFie) can be used to predict metabolic and secretory functions across diverse immune cells, hepatokine secretion in a cell model of NAFLD, and antibody production in Chinese Hamster Ovary cells.
Connecting higher order interactions with ecological stability in experimental aquatic food webs
Authors: Shen Chenyu , Lemmen Kimberley , Alexander Jake , Pennekamp Frank 
Published: May 2023

AbstractCommunity ecology is built on theories that represent the strength of interactions between species as pairwise links. Higher order interactions occur when the presence of a third (or more) species changes the pairwise interaction between a focal pair. Recent theoretical work has highlighted the stabilizing role of higher order interactions for large, simulated communities, yet it remains unclear how important higher order effects are in real communities. Here we used experimental communities of aquatic protists to examine the relationship between higher-order interactions and community stability (as measured by the persistence of species in a community). We cultured a focal pair of consumers in the presence of additional competitors and a predator and collected time series data of their abundances. We then fitted competition models with and without HOIs to measure interaction strength between the focal pair across different community compositions. We used survival analysis to measure the persistence of individual species. We found evidence that additional species positively affected persistence of the focal species and that HOIs were present in most of our communities. However, persistence was only linked to HOIs for one of the focal species. Our results vindicate community ecology theory positing that species interactions may deviate from assumptions of pairwise interactions, opening avenues to consider possible consequences for coexistence and community stability.
Analytical performance and concordance with next-generation sequencing of a rapid multiplexed dPCR panel for the detection of actionable DNA and RNA biomarkers in non-small cell lung cancer
Authors: Cabrera Kerri , Gole Jeffery , Leatham Bryan , Jacky Lucien , Brown Bradley A. 
Published: May 2023

AbstractBackgroundOver the last ten years, the discovery and FDA approval of targeted therapies for lung cancer has significantly improved patient survival rates. However, despite these improved survival rates, only 68% of patients receive molecular testing that results in assignment of targeted therapy1,2. Barriers to timely access to biomarker information include no testing ordered3,high nucleic acid input requirements, and problematic turnaround time (TAT) by NGS (> 14 days)4.Here we report the analytical performance and concordance with next-generation sequencing (NGS) of a highly-multiplexed research use only (RUO) panel using digital PCR (dPCR). The HDPCR NSCLC panel reports the status for variants (SNV, indels, and fusions) in eight actionable genes using amplitude modulation and multi-spectral encoding in dPCR5.MethodsThe panel’s analytical sensitivity and reactivity were determined using DNA and RNA extracted from formalin-fixed paraffin-embedded (FFPE) tissue spiked with plasmid DNA or in-vitro transcribed RNA. Concordance was established on 106 FFPE samples previously characterized using the Oncomine Precision Assay® or pathology results. Discordant resolution was resolved with Archer Fusionplex® and Variantplex® panels.ResultsThe analytical sensitivity, reported as estimated mutant allele fraction (MAF), for DNA targets (EGFRexon 19 deletions,EGFRexon 20 insertions,EGFRS768I,EGFRL858R,EGFRT790M,EGFRL861Q,BRAFV600E,EGFRG719X,ERBB2exon 20 insertions andKRASG12C) ranged from 0.8% – 4.9% with 40 ng of DNA input, and 2.4% to 10.9% with 15 ng of DNA input. For RNA fusion targets (ALK, RET, ROS, NTRK1/2/3, andMETexon 14 skipping), the analytical sensitivity ranged from 24 - 150 copies with 5 ng of total RNA input. The population prevalence-based coverage ranged from 89.2% to 100.0% across targets and >99.0% in aggregate. The accuracy of the assay was >97% with respect to the comparator method.
Upscaling biodiversity monitoring: Metabarcoding estimates 31,846 insect species from Malaise traps across Germany
Authors: Buchner Dominik , Sinclair James S. , Ayasse Manfred , Beermann Arne , Buse Jörn , Dziock Frank , Enss Julian , Frenzel Mark , Hörren Thomas , Li Yuanheng , Monaghan Michael T. , Morkel Carsten , Müller Jörg , Pauls Steffen U. , Richter Ronny , Scharnweber Tobias , Sorg Martin , Stoll Stefan , Twietmeyer Sönke , Weisser Wolfgang W. , Wiggering Benedikt , Wilmking Martin , Zotz Gerhard , Gessner Mark O. , Haase Peter , Leese Florian 
Published: May 2023

AbstractMitigating ongoing losses of insects and their key functions (e.g., pollination) requires accurately tracking large-scale and long-term community changes. However, doing so has been notoriously hindered by uniquely high insect species diversity that requires prohibitively high investments of time, funding, and taxonomic expertise. Here, we show that these concerns can be addressed through a comprehensive, scalable and cost-efficient DNA metabarcoding workflow. We use 1,815 samples from 75 Malaise traps across Germany from 2019 and 2020 to demonstrate how metabarcoding can be incorporated into large-scale insect monitoring networks for less than 50 € per sample, including supplies, labor and maintenance. With on average 1.4M sequence reads per sample we uncovered 10,803 validated insect species, of which 83.9% were represented by a single OTU. We estimated another 21,403 plausible species, which likely either lack a reference barcode or are undescribed. The total of 31,846 species is similar to the number of insect species known for Germany (∼35,500). Because Malaise traps capture only a subset of insects, our approach identified many species likely unknown from Germany or new to science. Our reproducible workflow (∼80% OTU-similarity among years) provides a blueprint for large-scale biodiversity monitoring of insects and other biodiversity components in near real time.