bluuebunny/crossref_metadata_2025_split huggingface dataset:
Consensus clustering with missing labels (ccml): a consensus clustering tool for multi-omics integrative prediction in cohorts with unequal sample coverage
Authors: Li Chuan-Xing , Chen Hongyan , Zounemat-Kermani Nazanin , Adcock Ian M , Sköld C Magnus , Zhou Meng , Wheelock Åsa M ,   U-BIOPRED study group
Published: January 2024

Abstract
Multi-omics data integration is a complex and challenging task in biomedical research. Consensus clustering, also known as meta-clustering or cluster ensembles, has become an increasingly popular downstream tool for phenotyping and endotyping using multiple omics and clinical data. However, current consensus clustering methods typically rely on ensembling clustering outputs with similar sample coverages (mathematical replicates), which may not reflect real-world data with varying sample coverages (biological replicates). To address this issue, we propose a new consensus clustering with missing labels (ccml) strategy termed ccml, an R protocol for two-step consensus clustering that can handle unequal missing labels (i.e. multiple predictive labels with different sample coverages). Initially, the regular consensus weights are adjusted (normalized) by sample coverage, then a regular consensus clustering is performed to predict the optimal final cluster. We applied the ccml method to predict molecularly distinct groups based on 9-omics integration in the Karolinska COSMIC cohort, which investigates chronic obstructive pulmonary disease, and 24-omics handprint integrative subgrouping of adult asthma patients of the U-BIOPRED cohort. We propose ccml as a downstream toolkit for multi-omics integration analysis algorithms such as Similarity Network Fusion and robust clustering of clinical data to overcome the limitations posed by missing data, which is inevitable in human cohorts consisting of multiple data modalities. The ccml tool is available in the R language (https://CRAN.R-project.org/package=ccml, https://github.com/pulmonomics-lab/ccml, or https://github.com/ZhoulabCPH/ccml).
Reactions of neutral chromium silylyne complex with alkynes and butadiene: access to homoaromatic compounds and silacyclopentenyl complexes
Authors: Matsuoka Masahiro , Nagata Koichi , Ohno Ryoma , Matsuo Tsukasa , Hashimoto Hisako 
Published: January 2024

Abstract
Reactions of a chromium complex, featuring a Cr≡Si triple bond, with alkynes and butadiene were investigated. The former reaction yielded 4-membered metallasilacycles with a homoaromatic character through [2+2] cycloaddition, while the latter reaction afforded silacyclopentenyl complexes through [2+4] cycloaddition.
Frequency of screening for cardiac allograft vasculopathy: warranty period of initial low risk positron emission tomography
Authors: Abadie Bryan , Albert Chonyang , Bhat Pavan , Harb Serge , Jacob Miriam , Starling Randall C , Tang W H Wilson , Jaber Wael A 
Published: January 2024

Abstract

Aims
The short-term risk of moderate–severe cardiac allograft vasculopathy (CAV) after a low-risk positron emission tomography/computed tomography (PET/CT) is unknown, and therefore, there is no guidance on how frequently to perform screening. The aim of this study was to assess the rate of progression to moderate–severe CAV as part of an annual screening programme.

Methods and results
Patients with no history of CAV 2/3 and a low-risk result on initial screening PET/CT (CAV 0/1) were enrolled in the study. The primary outcome was the progression to CAV 2/3 as part of an annual screening programme (within 6–18 months of initial scan). PET CAV results were graded according to a published and externally validated diagnostic criterion for CAV. Over the study period, 231 patients underwent an initial PET/CT and had a subsequent evaluation for CAV. In this cohort, 4.3% of patients progressed to CAV 2/3 at a median of 374 days (interquartile range 363–433). Initial PET CAV grade was the most significant patient characteristic associated with the progression of CAV, with 17% of patients with PET CAV 1 progressing to CAV 2/3 compared with 1.6% with PET CAV 0 (odds ratio 12.4, 95% confidence interval 3.06–50.3).

Conclusion
The rate of progression to moderate–severe CAV at 1 year after the lowest-risk PET/CT is low, but approximately 1/6 patients with PET CAV 1 progress to CAV 2/3. Annual screening with PET/CT for select patients with PET CAV 0 may not be warranted. The optimal screening interval awaits confirmation of our findings in multi-centre registries.
In vitro effects of selective serotonin reuptake inhibitors on Cryptococcus gattii capsule and biofilm
Authors: Viveiro Letícia Rampazzo da Gama , Rehem Amanda Rodrigues , Santos Evelyn Luzia De Souza , Carmo Paulo Henrique Fonseca do , Junqueira Juliana Campos , Scorzoni Liliana 
Published: January 2024

Abstract
Infections caused by Cryptococcus gattii mainly affect immunocompetent individuals and the treatment presents important limitations. This study aimed to validate the efficacy of selective serotonin reuptake inhibitors (SSRI), fluoxetine hydrochloride (FLH), and paroxetine hydrochloride (PAH) in vitro against C. gattii. The antifungal activity of SSRI using the microdilution method revealed a minimal inhibitory concentration (MIC) of 31.25 µg/ml. The combination of FLH or PAH with amphotericin B (AmB) was analyzed using the checkerboard assay and the synergistic effect of SSRI in combination with AmB was able to reduce the SSRI or AmB MIC values 4–8-fold. When examining the effect of SSRI on the induced capsules, we observed that FLH and PAH significantly decreased the size of C. gattii capsules. In addition, the effects of FLH and PAH were evaluated in biofilm biomass and viability. The SSRI were able to reduce biofilm biomass and biofilm viability. In conclusion, our results indicate the use of FLH and PAH exhibited in vitro anticryptococcal activity, representing a possible future alternative for the cryptococcosis treatment.
Machine Learning Made Easy (MLme): a comprehensive toolkit for machine learning–driven data analysis
Authors: Akshay Akshay , Katoch Mitali , Shekarchizadeh Navid , Abedi Masoud , Sharma Ankush , Burkhard Fiona C , Adam Rosalyn M , Monastyrskaya Katia , Gheinani Ali Hashemi 
Published: January 2024

Abstract

Background
Machine learning (ML) has emerged as a vital asset for researchers to analyze and extract valuable information from complex datasets. However, developing an effective and robust ML pipeline can present a real challenge, demanding considerable time and effort, thereby impeding research progress. Existing tools in this landscape require a profound understanding of ML principles and programming skills. Furthermore, users are required to engage in the comprehensive configuration of their ML pipeline to obtain optimal performance.

Results
To address these challenges, we have developed a novel tool called Machine Learning Made Easy (MLme) that streamlines the use of ML in research, specifically focusing on classification problems at present. By integrating 4 essential functionalities—namely, Data Exploration, AutoML, CustomML, and Visualization—MLme fulfills the diverse requirements of researchers while eliminating the need for extensive coding efforts. To demonstrate the applicability of MLme, we conducted rigorous testing on 6 distinct datasets, each presenting unique characteristics and challenges. Our results consistently showed promising performance across different datasets, reaffirming the versatility and effectiveness of the tool. Additionally, by utilizing MLme’s feature selection functionality, we successfully identified significant markers for CD8+ naive (BACH2), CD16+ (CD16), and CD14+ (VCAN) cell populations.

Conclusion
MLme serves as a valuable resource for leveraging ML to facilitate insightful data analysis and enhance research outcomes, while alleviating concerns related to complex coding scripts. The source code and a detailed tutorial for MLme are available at https://github.com/FunctionalUrology/MLme.
A multiscale magma system beneath the Tengchong volcano in western Yunnan revealed by ambient noise tomography
Authors: Lin Ye , Liu Shaolin , Yang Dinghui , Xu Xiwei , Yang Shuxin , Wang Wenshuai 
Published: January 2024

SUMMARY
The western Yunnan is located in the SE Tibetan Plateau, and is characterized by the active Tengchong volcano (TCV), complex crust–mantle coupling and intense earthquakes. To elucidate tectonism in the western Yunnan, we construct a 3-D S-wave velocity model to 80 km depth via ambient noise tomography using dense seismic stations. Our model shows significant low-velocity anomalies at different depths in the crust and uppermost mantle. Compared with the results of previous regional tomography, we image low-velocity anomalies consistent with a large-scale source of partial melts in the uppermost mantle beneath the Tengchong and Baoshan blocks, rather than just below the Tengchong block. Our results also reveal a magma chamber extending from the shallow subsurface to the lower crust beneath the TCV, which is fed by the mantle source. Based on these findings, we propose that the mantle source and crustal magma chamber form a multiscale magma system. Moreover, the mantle source is potentially resulted from asthenospheric upwelling, which is related to the subduction of the Indian slab. In addition, our model shows that the 1976 M7.4 and M7.3 Longling earthquakes occurred near a magma chamber. Thus, fluids from the magma chamber likely reduced the frictional coefficient on the seismogenic fault and caused the Longling earthquakes.
Preterm Birth and in Utero Exposure to Corticosteroids Are Associated With Increased Infection Risk in Children of Mothers With IBD
Authors: Vestergaard Thea , Holm Meiltoft Ida , Julsgaard Mette , Bek Helmig Rikke , Friedman Sonia , Kelsen Jens 
Published: January 2024

Abstract

Background
Corticosteroids, thiopurines, and biologics may come into play during pregnancy in women with inflammatory bowel disease and potentially impact the developing fetal immune system. We aimed to assess the risk of serious infections in children stratified by in utero exposure to biologics and immunomodulators or concomitant treatment with corticosteroids.

Methods
All singleton IBD pregnancies between 2008 and 2022 at a tertiary IBD center in Denmark were included. Maternal and offspring demographics, maternal disease activity, antenatal medical treatment, and infant infections resulting in hospital admission were recorded after review of medical records.

Results
In 602 live births (99.0%), we registered exposure to antenatal treatment as follows: biological monotherapy (n = 61, 10.2%), thiopurines (n = 110, 17.9%), biologics and concomitant thiopurines (n = 63, 10.3%), and controls (ie, no treatment with biological and/or thiopurines; n = 369, 60.6%). Preterm delivery (&lt;37 gestational weeks) and systemic steroid administration during the third trimester were associated with an increased risk of serious infection in the offspring immediately after birth (relative risk = 17.5; 95% confidence interval, 7.8-39.8; P &lt; .001, and relative risk = 4.8; 95% confidence interval, 1.5-12.7; P = 0.003, respectively).
Intra-uterine exposure to biologics or combination treatment were not associated with a statistically significant higher risk of serious infections compared with controls; however, combination treatment showed an inclination towards an increased risk across analyses.

Conclusion
Preterm birth and systemic corticosteroid administration late in pregnancy are significant risk factors for serious infections in the offspring of IBD mothers.
SARS-CoV-2 inactivation on hard non-porous airplane cabin material surfaces was limited after exposure to far UV-C (222 nm) radiation
Authors: Wilson Mark E , Quigley Wes W C , Davis Angela C , Critchlow Nyle K , Madonna Angelo J , Hogan Jeffery N , Rogers Adam Z , Olson Nels A 
Published: January 2024

Abstract

Aims
To test the efficacy of 222 nm far UV-C for surface disinfection of SARS-CoV-2 on inanimate surfaces from airplane cabins.

Methods and results
Two far ultraviolet (UV-C) irradiation light systems were evaluated for disinfection of SARS-CoV-2. Materials used for carriers (test surfaces) included polished stainless steel and used airplane materials, including seat belt latches, window dust covers, sidewall laminates, and tray tables.

Conclusions
While demonstrating reasonable efficacy under some experimental conditions, the data indicated that 222 nm far UV-C disinfection alone does not reliably provide a 3 log10 or 99.9% reduction of SARS-CoV-2 on inanimate surfaces from an airplane cabin. An Ushio (Cypress, CA) 1.7″ × 2.3″ Care222® 12 W 222 nm BI lamp module tested in triplicate at a low (⁓1.5 mJ cm−2), medium (⁓3.0 mJ cm−2), and high (⁓6–9 mJ cm−2) fluence did not provide a ≥3 log10 or 99.9% reduction of SARS-CoV-2. The reduction of SARS-CoV-2 was greatest on stainless steel. The result was a log10 reduction of 2.83, 1.33, 2.58, and 2.21 logs for virus samples containing saline, saline with 2.5 mg BSA, saline with 0.25 mg BSA, and artificial saliva, respectively, at a dosage of 5–9 mJ cm−2. The log10 reduction of SARS-CoV-2 in saline with 2.5 mg bovine serum albumin was lowest with 1.33 for stainless steel, 0.93 for belt latch, and 0.61 for tray table at a dosage of 5–6 mJ cm−2. The second UV lighting system tested was a prototype mobile wand with a built-in short-pass filtered krypton-chloride cylindrical lamp. One pass of the wand over a tray holding carriers inoculated with SARS-CoV-2 in artificial saliva at a rate of ∼1 foot (1′) per second exposed the carriers to 7.3 mJ cm−2. The log10 reductions determined for the single pass were 2.97, 3.75, 1.78, 1.91, and 1.28 logs for stainless steel, belt latch, dust cover, sidewall, and tray table, respectively. Two passes of the wand generated 17.2 mJ cm−2 and resulted in log10 reductions of 4.04, 3.74, 4.24, 3.68, and 1.66 logs for stainless steel, belt latch, dust cover, sidewall, and tray table, respectively. The combination of higher fluence from multiple passes of the wand, the close proximity (10 cm wand to the carrier), the exposure to elevated temperatures up to 35°C, and ozone from the bulb being blown directly onto the carriers contributed to effective viral inactivation on all surfaces except the airplane tray table. The impact of temperature and ozone on viral inactivation should be determined for future testing of the 222 nm UV-C wand.
Hypoxia rewires glucose and glutamine metabolism in different sources of skeletal stem and progenitor cells similarly, except for pyruvate
Authors: Loopmans Shauni , Tournaire Guillaume , Stockmans Ingrid , Stegen Steve , Carmeliet Geert 
Published: January 2024

Abstract
Skeletal stem and progenitor cells (SSPCs) are crucial for bone development, homeostasis, and repair. SSPCs are considered to reside in a rather hypoxic niche in the bone, but distinct SSPC niches have been described in different skeletal regions, and they likely differ in oxygen and nutrient availability. Currently it remains unknown whether the different SSPC sources have a comparable metabolic profile and respond in a similar manner to hypoxia. In this study, we show that cell proliferation of all SSPCs was increased in hypoxia, suggesting that SSPCs can indeed function in a hypoxic niche in vivo. In addition, low oxygen tension increased glucose consumption and lactate production, but affected pyruvate metabolism cell-specifically. Hypoxia decreased tricarboxylic acid (TCA) cycle anaplerosis and altered glucose entry into the TCA cycle from pyruvate dehydrogenase to pyruvate carboxylase and/or malic enzyme. Finally, a switch from glutamine oxidation to reductive carboxylation was observed in hypoxia, as well as cell-specific adaptations in the metabolism of other amino acids. Collectively, our findings show that SSPCs from different skeletal locations proliferate adequately in hypoxia by rewiring glucose and amino acid metabolism in a cell-specific manner.
Treatment of waxborne honey bee (Hymenoptera: Apidae) viruses using time, temperature, and electron-beam irradiation
Authors: Colwell Megan J , Pernal Stephen F , Currie Robert W 
Published: January 2024

Abstract
Viruses are one of many serious threats to honey bee (Apis mellifera L.) health. There are many transmission routes for honey bee viruses, and there is potential for wax comb to act as a reservoir for transmission of viruses. Some work has been done on treating viruses on wax, focusing on irradiation as a potential treatment. However, irradiation is not universally available or economically viable for beekeepers in many regions. With increased colony deaths over winter beekeepers potentially risk further loss from reusing contaminated equipment from dead colonies. Here we explored the use of storage time and temperature on the reduction of waxborne virus levels from winter loss colony wax over 30 days and at −20, 5, and 20 °C. Furthermore, because irradiation has previously worked against waxborne viruses, we performed a dosage experiment with electron-beam irradiation. Winter loss wax was again used, and exposed to 10, 25, 35, and 45 kGy irradiation, including a nonirradiated transport control. Storage time decreased abundance of black queen cell virus and deformed wing virus at times equal or greater than 30 days but temperatures had no significant effect on virus levels. All irradiation doses decreased virus abundance and prevalence, yet only 35 and 45 kGy did so at a greater rate than the effect of transport alone.
The use of Nafs ‘soul’ for self-referencing in al-Maqqarī’s Nafḥ al-ṭīb and the evolution of the ‘divided self’
Authors: Jreis-Navarro Laila M 
Published: January 2024

Abstract
This article will analyze the use of the noun nafs ‘soul’ with the first-person possessive pronominal suffix, through the corpus of Andalusi texts gathered in Nafḥ al-ṭīb by the North-African author Shihāb al-Dīn al-Maqqarī (d. 1632). The aim is threefold: one, to identify patterns of the use of nafsī in the Nafḥ, their semantic performance, and diachronic evolution; two, to compare the use of the term in this corpus with its use in lists of collocates in the macro corpora KSUCCA and arTenTen of Classical and Modern Standard Arabic; and three, to show that linguistically systematizing self-expression is adequate for the identification of highly subjective texts in a corpus. Analysis will show that the notions of the ‘divided self’, sacrificing oneself, and yearning change towards a closer relationship between the subject and the self over time.
The interplay between feedback, accretion, transport, and winds in setting gas-phase metal distribution in galaxies
Authors: Sharda Piyush , Ginzburg Omri , Krumholz Mark R , Forbes John C , Wisnioski Emily , Mingozzi Matilde , Zovaro Henry R M , Dekel Avishai 
Published: January 2024

ABSTRACT
The recent decade has seen an exponential growth in spatially resolved metallicity measurements in the interstellar medium (ISM) of galaxies. To first order, these measurements are characterized by the slope of the radial metallicity profile, known as the metallicity gradient. In this work, we model the relative role of star formation feedback, gas transport, cosmic gas accretion, and galactic winds in driving radial metallicity profiles and setting the mass–metallicity gradient relation (MZGR). We include a comprehensive treatment of these processes by including them as sources that supply mass, metals, and energy to marginally unstable galactic discs in pressure and energy balance. We show that both feedback and accretion that can drive turbulence and enhance metal-mixing via diffusion are crucial to reproduce the observed MZGR in local galaxies. Metal transport also contributes to setting metallicity profiles, but it is sensitive to the strength of radial gas flows in galaxies. While the mass loading of galactic winds is important to reproduce the mass–metallicity relation (MZR), we find that metal mass loading is more important to reproducing the MZGR. Specifically, our model predicts preferential metal enrichment of galactic winds in low-mass galaxies. This conclusion is robust against our adopted scaling of the wind mass-loading factor, uncertainties in measured wind metallicities, and systematics due to metallicity calibrations. Overall, we find that at z ∼ 0, galactic winds and metal transport are more important in setting metallicity gradients in low-mass galaxies whereas star formation feedback and gas accretion dominate setting metallicity gradients in massive galaxies.
eUDS: the SRG/eROSITA X-ray survey of the UKIDSS Ultra Deep Survey field. Catalogue of sources
Authors: Krivonos R , Gilfanov M , Medvedev P , Sazonov S , Sunyaev R 
Published: January 2024

ABSTRACT
The eROSITA X-ray telescope on board the Spectrum-Roentgen-Gamma (SRG) spacecraft observed the field of the UKIDSS Ultra-Deep Survey (UDS) in August–September 2019, during its flight to Sun–Earth L2 point. The resulting eROSITA UDS (or eUDS) survey was thus the first eROSITA X-ray imaging survey, which demonstrated the capability of the telescope to perform uniform observations of large sky areas. With a moderate single-camera exposure of 150 ks, eUDS covered ∼5 deg2 with the limiting flux ranging between 4 × 10−15 and 5 × 10−14 erg s−1 cm−2 in the 0.3–2.3 keV band. We present a catalogue of 647 sources detected at likelihood &gt;10 (∼4σ) during the eUDS. The catalogue provides information on the source fluxes in the main energy band 0.3–2.3 keV and forced photometry in a number of bands between 0.3 and 8 keV. Using the deeper 4XMM-DR12 catalogue, we have identified 22 strongly variable objects that have brightened or faded by at least a factor of ten during the eROSITA observations compared to previous observations by XMM–Newton. We also provide a catalogue of 22 sources detected by eROSITA in the hard energy band of 2.3–5 keV.