bluuebunny/crossref_metadata_2025_split huggingface dataset:
Relationship between kinetic parameters of ultrafast dynamic contrast-enhanced (DCE) MRI and tumor-infiltrating lymphocytes (TILs) in breast cancer
Authors: Yamaguchi Ken , Nakazono Takahiko , Egashira Ryoko , Fukui Shuichi , Imaizumi Tsutomu , Maruyama Katsuya , Nickel Dominik , Hamamoto Takahiro , Yamaguchi Rin , Irie Hiroyuki 
Published: August 2024

Abstract
Purpose
To evaluate the relationship between kinetic parameters of ultrafast dynamic contrast-enhanced (DCE) magnetic resonance imaging (MRI) and tumor-infiltrating lymphocytes (TILs) in breast cancer.

Patients and methods
This retrospective study was approved by an institutional review board and included 76 women (median age: 60) with 76 surgically proven breast cancers who underwent DCE MRI including ultrafast sequence. Based on the TILs level, we classified the patients into the low-TILs (< 10%) group and the high-TILs (≥ 10%) group. Maximum slope (MS) and time to enhancement (TTE) derived from ultrafast DCE sequence were correlated in each TILs group. The percentages of six kinetic patterns (fast, medium, and slow from the early phase, washout, plateau, and persistent from the delayed phase) derived from the conventional DCE sequence were also correlated in each TILs group.

Results
Of the 76 breast cancers, 57 were in the low-TILs group and 19 comprised the high-TILs group. The median MS in the high-TILs group (32.4%/sec) was significantly higher than that in the low-TILs group (23.68%/s) (p = 0.037). In a receiver-operating characteristic (ROC) analysis, the area under the curve (AUC) for differentiating between the high- and low-TILs group was 0.661. The TTE in the high-TILs group was significantly shorter than that in the low-TILs group (p = 0.012). In the ROC analysis, the AUC was 0.685. There were no significant differences between the percentages of the six kinetic patterns from the conventional DCE sequence and the TILs level (p = 0.075–0.876).

Conclusion
Compared to the low-TILs group, the high-TILs group had higher MS and shorter TTE.
Towards an Epistemic Compass for Online Content Moderation
Authors: Tobi Abraham 
Published: August 2024

AbstractThe internet provides easy access to a wealth of information that can sometimes be false and harmful. This is most apparent on social media platforms. To combat this, platforms have implemented various methods of content moderation to flag or block content that is inaccurate or violates community standards. This approach has limitations – from the epistemic injustices that might occur due to content moderation practices to the concerns about the legitimacy of these for-profit platforms’ epistemic authority. In this paper, I highlight some of the epistemic challenges of online content moderation with a focus on how it harms internet users and moderators. If we are to moderate content effectively and ethically, we must attend to these challenges. Hence, I map out an epistemic compass for online content moderation that looks to attend to these challenges. I argue for a pluralistic model of content moderation that categorises content online and distributes the task of content moderation between human moderators, automated moderators, and community moderators in a way that plays to the strengths of each content moderation model. My compass is beneficial for two reasons: first, it allows room for the internet to realise its potential as a democratising force for knowledge, and second, it helps minimise the epistemic downsides of relying on profit-driven companies as epistemic authorities.
Key Uncertainties and Modeling Needs for Managing Living Marine Resources in the Future Arctic Ocean
Authors: Mason Julia G. , Bryndum‐Buchholz Andrea , Palacios‐Abrantes Juliano , Badhe Renuka , Morgante Isabella , Bianchi Daniele , Blanchard Julia L. , Everett Jason D. , Harrison Cheryl S. , Heneghan Ryan F. , Novaglio Camilla , Petrik Colleen M. 
Published: August 2024

AbstractEmerging fishing activity due to melting ice and poleward species distribution shifts in the rapidly‐warming Arctic Ocean challenges transboundary management and requires proactive governance. A 2021 moratorium on commercial fishing in the Arctic high seas provides a 16‐year runway for improved scientific understanding. Given substantial knowledge gaps, characterizing areas of highest uncertainty is a key first step. Marine ecosystem model ensembles that project future fish distributions could inform management of future Arctic fisheries, but Arctic‐specific variation has not yet been examined for global ensembles. We use the Fisheries and Marine Ecosystem Intercomparison Project ensemble driven by two Earth System Models (ESMs) under two Shared Socioeconomic Pathways (SSP1‐2.6 and SSP5‐8.5) to illustrate the current state of and uncertainty among biomass projections for the Arctic Ocean over the duration of the moratorium. The models generally project biomass increases in more northern Arctic ecosystems and decreases in southern ecosystems, but wide intra‐model variation exceeds projection means in most cases. The two ESMs show opposite trends for the main environmental drivers. Therefore, these projections are currently insufficient to inform policy actions. Investment in sustained monitoring and improving modeling capacity, especially for sea ice dynamics, is urgently needed. Concurrently, it will be necessary to develop frameworks for making precautionary decisions under continued uncertainty. We conclude that researchers should be transparent about uncertainty, presenting these model projections not as a source of scientific “answers,” but as bounding for plausible, policy‐relevant questions to assess trade‐offs and mitigate risks.
New Insights Into the Sources of Atmospheric Organic Aerosols in East China: A Comparison of Online Molecule‐Level and Bulk Measurements
Authors: Ge Dafeng , Nie Wei , Liu Yuliang , Huang Dan Dan , Yan Chao , Wang Jinbo , Li Yuanyuan , Liu Chong , Wang Lei , Wang Jiaping , Chi Xuguang , Ding Aijun 
Published: August 2024

AbstractOrganic aerosols (OA) significantly contribute to haze pollution, threaten human health, and affect the radiation balance. However, real‐time tracking of OA evolution at the molecular level is limited, hindering a comprehensive understanding of their origins and behaviors. In this study, we investigated wintertime OA in a megacity in East China by combining simultaneous measurements from an extractive electrospray ionization time‐of‐flight mass spectrometer (EESI‐TOF) and a high‐resolution time‐of‐flight aerosol mass spectrometer (AMS) (HR‐TOF‐AMS). AMS results indicate that OA accounts for about 27% of non‐refractory submicron particulate matter (NR‐PM1) on average. EESI‐TOF data reveal that CxHyOz and CxHyN1–2Oz are the predominant OA components, contributing over 70% and 20%, respectively. Factorization analysis shows that while traffic, cooking, and biomass burning are major primary sources, most OA (>70% for EESI‐TOF, >55% for AMS) originate from secondary production. EESI‐TOF, although missing hydrocarbon‐like OA, excels in providing molecular information on oxygenated OA, identifying aromatics and aliphatics as possible key precursors. It further differentiates less oxidized secondary organic aerosols (SOA) into two factors with distinct molecular compositions, likely due to diverse source regions. Importantly, EESI‐TOF identifies two additional factors: one possibly related to plasticizers and another representing SOA formation from monoterpene oxidation by NO3 radicals. In conclusion, EESI‐TOF complements AMS by offering valuable molecular insights into the chemical processes underlying OA formation, especially in complex urban environments.
Ultra-broadband diffractive imaging with unknown probe spectrum
Authors: Chen Chuangchuang , Gu Honggang , Liu Shiyuan 
Published: August 2024

AbstractStrict requirement of a coherent spectrum in coherent diffractive imaging (CDI) architectures poses a significant obstacle to achieving efficient photon utilization across the full spectrum. To date, nearly all broadband computational imaging experiments have relied on accurate spectroscopic measurements, as broad spectra are incompatible with conventional CDI systems. This paper presents an advanced approach to broaden the scope of CDI to ultra-broadband illumination with unknown probe spectrum, effectively addresses the key challenges encountered by existing state-of-the-art broadband diffractive imaging frameworks. This advancement eliminates the necessity for prior knowledge of probe spectrum and relaxes constraints on non-dispersive samples, resulting in a significant extension in spectral bandwidth, achieving a nearly fourfold improvement in bandlimit compared to the existing benchmark. Our method not only monochromatizes a broadband diffraction pattern from unknown illumination spectrum, but also determines the compressive sampled profile of spectrum of the diffracted radiation. This superiority is experimentally validated using both CDI and ptychography techniques on an ultra-broadband supercontinuum with relative bandwidth exceeding 40%, revealing a significantly enhanced coherence and improved reconstruction with high fidelity under ultra-broadband illumination.
Schnurri-3 inhibition rescues skeletal fragility and vascular skeletal stem cell niche pathology in the OIM model of osteogenesis imperfecta
Authors: Li Na , Shi Baohong , Li Zan , Han Jie , Sun Jun , Huang Haitao , Yallowitz Alisha R. , Bok Seoyeon , Xiao Shuang , Wu Zuoxing , Chen Yu , Xu Yan , Qin Tian , Huang Rui , Zheng Haiping , Shen Rong , Meng Lin , Greenblatt Matthew B. , Xu Ren 
Published: August 2024

AbstractOsteogenesis imperfecta (OI) is a disorder of low bone mass and increased fracture risk due to a range of genetic variants that prominently include mutations in genes encoding type I collagen. While it is well known that OI reflects defects in the activity of bone-forming osteoblasts, it is currently unclear whether OI also reflects defects in the many other cell types comprising bone, including defects in skeletal vascular endothelium or the skeletal stem cell populations that give rise to osteoblasts and whether correcting these broader defects could have therapeutic utility. Here, we find that numbers of skeletal stem cells (SSCs) and skeletal arterial endothelial cells (AECs) are augmented in Col1a2oim/oim mice, a well-studied animal model of moderate to severe OI, suggesting that disruption of a vascular SSC niche is a feature of OI pathogenesis. Moreover, crossing Col1a2oim/oim mice to mice lacking a negative regulator of skeletal angiogenesis and bone formation, Schnurri 3 (SHN3), not only corrected the SSC and AEC phenotypes but moreover robustly corrected the bone mass and spontaneous fracture phenotypes. As this finding suggested a strong therapeutic utility of SHN3 inhibition for the treatment of OI, a bone-targeting AAV was used to mediate Shn3 knockdown, rescuing the Col1a2oim/oim phenotype and providing therapeutic proof-of-concept for targeting SHN3 for the treatment of OI. Overall, this work both provides proof-of-concept for inhibition of the SHN3 pathway and more broadly addressing defects in the stem/osteoprogenitor niche as is a strategy to treat OI.
Radiation-induced YAP/TEAD4 binding confers non-small cell lung cancer radioresistance via promoting NRP1 transcription
Authors: Wang Mingwei , Yi Junxuan , Gao Hui , Wei Xinfeng , Xu Weiqiang , Zhao Mingqi , Zhao Mengdie , Shen Yannan , Wang Zhicheng , Wu Ning , Wei Wei , Jin Shunzi 
Published: August 2024

AbstractDespite the importance of radiation therapy as a non-surgical treatment for non-small cell lung cancer (NSCLC), radiation resistance has always been a concern, due to poor patient response and prognosis. Therefore, it is crucial to uncover novel targets to enhance radiotherapy and investigate the mechanisms underlying radiation resistance. Previously, we demonstrated that NRP1 was connected to radiation resistance in NSCLC cells. In the present study, bioinformatics analysis of constructed radiation-resistant A549 and H1299 cell models revealed that transcription coactivator YAP is a significant factor in cell proliferation and metastasis. However, there has been no evidence linking YAP and NRP1 to date. In this research, we have observed that YAP contributes to radiation resistance in NSCLC cells by stimulating cell proliferation, migration, and invasion. Mechanistically, YAP dephosphorylation after NSCLC cell radiation. YAP acts as a transcription co-activator by binding to the transcription factor TEAD4, facilitating TEAD4 to bind to the NRP1 promoter region and thereby increasing NRP1 expression. NRP1 has been identified as a new target gene for YAP/TEAD4. Notably, when inhibiting YAP binds to TEAD4, it inhibits NRP1 expression, and Rescue experiments show that YAP/TEAD4 influences NRP1 to regulate cell proliferation, metastasis and leading to radiation resistance generation. According to these results, YAP/TEAD4/NRP1 is a significant mechanism for radioresistance and can be utilized as a target for enhancing radiotherapy efficacy.
Fatty acid metabolism constrains Th9 cell differentiation and antitumor immunity via the modulation of retinoic acid receptor signaling
Authors: Nakajima Takahiro , Kanno Toshio , Ueda Yuki , Miyako Keisuke , Endo Takeru , Yoshida Souta , Yokoyama Satoru , Asou Hikari K. , Yamada Kazuko , Ikeda Kazutaka , Togashi Yosuke , Endo Yusuke 
Published: August 2024

AbstractT helper 9 (Th9) cells are interleukin 9 (IL-9)-producing cells that have diverse functions ranging from antitumor immune responses to allergic inflammation. Th9 cells differentiate from naïve CD4+ T cells in the presence of IL-4 and transforming growth factor-beta (TGF-β); however, our understanding of the molecular basis of their differentiation remains incomplete. Previously, we reported that the differentiation of another subset of TGF-β–driven T helper cells, Th17 cells, is highly dependent on de novo lipid biosynthesis. On the basis of these findings, we hypothesized that lipid metabolism may also be important for Th9 cell differentiation. We therefore investigated the differentiation and function of mouse and human Th9 cells in vitro under conditions of pharmacologically or genetically induced deficiency of the intracellular fatty acid content and in vivo in mice genetically deficient in acetyl-CoA carboxylase 1 (ACC1), an important enzyme for fatty acid biosynthesis. Both the inhibition of de novo fatty acid biosynthesis and the deprivation of environmental lipids augmented differentiation and IL-9 production in mouse and human Th9 cells. Mechanistic studies revealed that the increase in Th9 cell differentiation was mediated by the retinoic acid receptor and the TGF-β–SMAD signaling pathways. Upon adoptive transfer, ACC1-inhibited Th9 cells suppressed tumor growth in murine models of melanoma and adenocarcinoma. Together, our findings highlight a novel role of fatty acid metabolism in controlling the differentiation and in vivo functions of Th9 cells.
Risk factors for reoperation of inflatable penile prosthesis among an ethnically diverse urban population in a high-volume center
Authors: Hawks-Ladds Noah , Babar Mustufa , Labagnara Kevin , Loloi Justin , Patel Rutul D. , Aalami Harandi Arshia , Zhu Michael , Salami Azizou , Maria Pedro 
Published: August 2024

AbstractInflatable penile prosthesis (IPP) is a surgical treatment for erectile dysfunction refractory to medical therapy or for those who desire permanent treatment. Complications like mechanical failure and infection may necessitate reoperation, and patients with certain risk factors remain predisposed to reoperation. We retrospectively analyzed 530 patients undergoing primary IPP implantation at a large, urban, multiethnic hospital with a high volume of IPP implantations. Primary outcomes were reoperation due to any reason and reoperation due to infection. Patient characteristics and intraoperative factors were compared between those requiring reoperation and those not requiring reoperation. Overall, 12.1% of patients underwent reoperation, primarily due to infection, with a median time to reoperation of 4 months. Analysis revealed an increased likelihood of reoperation with Peyronie’s disease (OR = 2.47), hemoglobin A1c over 8 (OR = 2.25), active smoking (OR = 2.75), and estimated blood loss (EBL) ≥ 25cc (OR = 2.45). A decreased likelihood of reoperation was observed when Arista™ powder was used intraoperatively (OR = 0.38). Reoperation specifically due to infection was associated with an infrapubic approach (OR = 2.56) and hypertension (OR = 9.12). Our findings confirm smoking and diabetes as risk factors for reoperation, while also providing insights into factors like estimated blood loss and Arista™ powder use. However, long-term survival rates were limited by loss to follow-up. (Clinical trial registration N/A).
Subducted carbon weakens the forearc mantle wedge in a warm subduction zone
Authors: Oyanagi Ryosuke , Okamoto Atsushi 
Published: August 2024

AbstractSubducting oceanic plates carry large amounts of carbon into the Earth’s interior. The subducted carbon is mobilized by fluid and encounters ultramafic rocks in the mantle wedge, resulting in changes to the mineral assemblage and mechanical properties of the mantle. Here, we use thermodynamic modeling of interactions between carbon-bearing multi-component fluids and mantle rocks to investigate the down-dip variation in mineral assemblage in the forearc mantle along subduction megathrusts. We found that fluids rich in aqueous carbon are preferentially generated in a warm subduction zone (e.g., Nankai, SW Japan), causing a change in mineral assemblage from serpentine-rich at the mantle wedge corner to talc + carbonate-rich at greater depths. The transition caused by the infiltration of aqueous carbon may influence the depth of the boundary between the seismogenic and aseismic zones, and the down-dip limit of episodic tremor and slip.
Systematic discovery of gene-environment interactions underlying the human plasma proteome in UK Biobank
Authors: Hillary Robert F. , Gadd Danni A. , Kuncheva Zhana , Mangelis Tasos , Lin Tinchi , Ferber Kyle , McLaughlin Helen , Runz Heiko ,   Biogen Biobank Team, Marshall Eric , Marioni Riccardo E. , Foley Christopher N. , Sun Benjamin B. 
Published: August 2024

AbstractUnderstanding how gene-environment interactions (GEIs) influence the circulating proteome could aid in biomarker discovery and validation. The presence of GEIs can be inferred from single nucleotide polymorphisms that associate with phenotypic variability - termed variance quantitative trait loci (vQTLs). Here, vQTL association studies are performed on plasma levels of 1463 proteins in 52,363 UK Biobank participants. A set of 677 independent vQTLs are identified across 568 proteins. They include 67 variants that lack conventional additive main effects on protein levels. Over 1100 GEIs are identified between 101 proteins and 153 environmental exposures. GEI analyses uncover possible mechanisms that explain why 13/67 vQTL-only sites lack corresponding main effects. Additional analyses also highlight how age, sex, epistatic interactions and statistical artefacts may underscore associations between genetic variation and variance heterogeneity. This study establishes the most comprehensive database yet of vQTLs and GEIs for the human proteome.
Formation of the Atlantic Meridional Overturning Circulation lower limb is critically dependent on Atlantic-Arctic mixing
Authors: Dey Dipanjan , Marsh Robert , Drijfhout Sybren , Josey Simon A. , Sinha Bablu , Grist Jeremy , Döös Kristofer 
Published: August 2024

AbstractDeep-water formation in the eastern Subpolar North Atlantic Ocean (eSPNA) and Nordic Seas is crucial for maintaining the lower limb of the Atlantic Meridional Overturning Circulation (AMOC), of consequence for global climate. However, it is still uncertain which processes determine the deep-water formation and how much Atlantic and Arctic waters respectively contribute to the lower limb. To address this, here we used Lagrangian trajectories to diagnose a global eddy-resolving ocean model that agrees well with recent observations highlighting the eSPNA as a primary source of the AMOC lower limb. Comprised of 72% Atlantic waters and 28% Arctic waters, the density and depth of the AMOC lower limb is critically dependent on Atlantic-Arctic mixing, primarily in the vicinity of Denmark Strait. In contrast, Atlantic waters gaining density through air-sea interaction along the eastern periphery of Nordic Seas and not entering the Arctic Ocean make a negligible contribution to the lower limb.
Epidemiology and antibiotic resistance of staphylococci on commercial pig farms in Cape Town, South Africa
Authors: Ocloo Remous , Newton-Foot Mae , Chabuka Lucious , Ziebuhr Wilma , Whitelaw Andrew Christopher 
Published: August 2024

AbstractStaphylococci are responsible for a wide range of infections in animals. The most common species infecting animals include Staphylococcus aureus, Staphylococcus epidermidis and Staphylococcus intermedius. Recent increases in antibiotic use and antibiotic resistance in animals highlight the need to understand the potential role of commercial livestock as a reservoir of staphylococci and antibiotic resistance genes. Nasal swabs were collected from 143 apparently healthy pigs and 21 pig farm workers, and 45 environmental swabs of feed and water troughs, from two commercial pig farms in the Western Cape, South Africa. Staphylococci were isolated, identified using mass-spectrometry, and antimicrobial susceptibility testing and Illumina whole genome sequencing were performed. One hundred and eighty-five (185) Staphylococcus spp. isolates were obtained, with Mammalicoccus sciuri (n = 57; 31%) being the most common, followed by S. hyicus (n = 40; 22%) and S. aureus (n = 29; 16%). S. epidermidis was predominantly identified in the farm workers (n = 18; 86%). Tetracycline resistance was observed across all species, with rates ranging from 67 to 100%. Majority of M. sciuri isolates (n = 40; 70%) were methicillin resistant, with 78% (n = 31) harbouring mecA. M. sciuri isolates had genes/elements which were associated with SCCmec_type_III (3A) and SCCmec_type_VIII(4A) and were mostly observed in ST61 strains. ST239 strains were associated with SCCmec_type_III(3A). High rates of tetracycline resistance were identified among staphylococci in the pig farms in Western Cape, South Africa. This highlights the need for policy makers to regulate the use of this antibiotic in pig farming.