bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automated yeast cultivation control using a biosensor and flow cytometry
Authors: Foncillas Raquel Perruca , Magnusson Sara , Al-Rudainy Basel , Wallberg Ola , Gorwa-Grauslund Marie F , Carlquist Magnus 
Published: October 2024

Abstract

Effective microbial bioprocessing relies on maintaining ideal cultivation conditions, highlighting the necessity for tools that monitor and regulate cellular performance and robustness. This study evaluates a fed-batch cultivation control system based on at-line flow cytometry monitoring of intact yeast cells having a fluorescent transcription factor-based redox biosensor. Specifically, the biosensor assesses the response of an industrial xylose-fermenting Saccharomyces cerevisiae strain carrying the TRX2p-yEGFP biosensor for NADPH/NADP+ ratio imbalance when exposed to furfural. The developed control system successfully detected biosensor output and automatically adjusted furfural feed rate, ensuring physiological fitness at high furfural levels. Moreover, the single-cell measurements enabled the monitoring of subpopulation dynamics, enhancing control precision over traditional methods. The presented automated control system highlights the potential of combining biosensors and flow cytometry for robust microbial cultivations by leveraging intracellular properties as control inputs.

One-Sentence Summary
An automated control system using flow cytometry and biosensors enhances microbial bioprocessing by regulating cellular performance in response to the environmental stressor furfural.
Optimal timing for initiating androgen receptor signaling inhibitor therapy in patients with nonmetastatic castration-resistant prostate cancer: a multicenter collaborative study
Authors: Hara Shuhei , Urabe Fumihiko , Tashiro Kojiro , Goto Yuma , Iwamoto Yuya , Ohtsuka Takashi , Fukuokaya Wataru , Imai Yu , Iwatani Kosuke , Atsuta Mahito , Mori Keiichiro , Igarashi Taro , Aikawa Koichi , Yanagisawa Takafumi , Kimura Shoji , Murakami Masaya , Tsuzuki Shunsuke , Yanada Brendan A , Hata Kenichi , Furuta Akira , Yamada Hiroki , Miki Jun , Kimura Takahiro ,   JIKEI-YAYOI Collaborative Group, Urabe Fumihiko , Hara Shuhei 
Published: October 2024

Abstract

Objective
We determined the optimal timing for initiating androgen receptor signaling inhibitor (ARSI) therapy in patients with nonmetastatic castration-resistant prostate cancer (nmCRPC) and assessed its impact on oncological outcomes.

Materials and methods
This retrospective study included 145 nmCRPC patients who received enzalutamide, apalutamide or darolutamide at the Jikei University Hospital or its affiliated institutions between May 2014 and November 2022. Patients were stratified based on prostate-specific antigen (PSA) doubling time (PSADT) at CRPC diagnosis and PSA levels at ARSI initiation. Oncological outcomes, including progression-free survival (PFS), metastasis-free survival (MFS), cancer-specific survival and overall survival, were assessed using the Kaplan–Meier curve and Cox regression analysis.

Results
The median age of the patients was 73 (interquartile range [IQR]: 52–88) years, and the median follow-up duration was 36 (IQR: 2–104) months. The median PSA level at ARSI initiation was 5.4 (IQR: 2.2–48) ng/ml, and 44.8% of patients had a PSADT &lt;3 months. Multivariate analysis revealed that PSADT and PSA levels at ARSI initiation were independent MFS predictors. Patients with a PSADT ≤3 months and a PSA level ≥5.4 ng/ml experienced significantly reduced PFS and MFS. Notably, ARSI initiation at a PSA level ≥5.4 ng/ml was associated with worse outcomes, suggesting the potential benefit of earlier intervention.

Conclusions
Patients with rapid PSADT are at increased risk of early disease progression, suggesting that immediate treatment may be warranted. In addition, initiating therapy at a PSA level &lt;5.4 ng/ml may be associated with improved patient outcomes in patients with low PSADT.
Religion, secularism, and postsecularism in Chinese internet literature
Authors: Ni Zhange 
Published: October 2024

Abstract
Internet literature emerged in China in the 1990s and became commercialized in the early 2000s, with readers paying an access fee, which is split between literary platforms and their contracted writers, to access popular novels. While the most popular genre is fantasy, a type of imaginative literature devoted to invoking magic beyond the limits of empirical reality and scientific rationality, the primary source of magic for Chinese fantasy is traditional Chinese cosmology and its concrete applications in everyday practices. These ideas and practices, the onto-epistemic-practical foundation of Chinese religion before the twentieth century, were considered superstitious and targeted for elimination in modernizing and secularization processes. However, they have not only survived but taken up a new life in fantasy novels, which depict them as the antecedents of, alternatives to, or more advanced forms than modern scientific endeavors at engineering natural environments and enhancing human bodies. This is why I see online fantasy literature as a palimpsest bearing the traces of Chinese religion, Chinese secularism, and the social conditions of contemporary China. In bearing such traces, this literature exemplifies the postsecular.
Immunoglobulin A nephropathy and IgA vasculitis
Authors: Cheung Chee Kay , Barratt Jonathan 
Published: October 2024

Abstract
Immunoglobulin A nephropathy (IgAN) is the commonest pattern of glomerulonephritis identified in areas of the world where kidney biopsy is widely practised. It is defined pathologically by IgA deposition in the glomerular mesangium accompanied by a mesangial proliferative glomerulonephritis which may vary greatly in severity. Aetiology is uncertain, but abnormalities of IgA1 hinge-region O-glycosylation are consistently found. Clinical features—IgAN can present with (1) visible haematuria, typically in children and young adults, developing within a day or two of an upper respiratory tract infection (‘synpharyngitic’); (2) asymptomatic nonvisible haematuria/proteinuria; (3) nephrotic syndrome (&lt;5% of cases); (4) acute kidney injury (uncommon); and (5) chronic kidney disease with up to 75% of patients reaching kidney failure within 20 years of diagnosis. IgA vasculitis (previously known as Henoch–Schönlein purpura (HSP)) is a small vessel systemic vasculitis characterized by small blood vessel deposition of IgA that predominantly affects the skin, joints, gut, and kidney, with nephritis that may be histologically indistinguishable from IgA nephropathy. Management—current first-line treatment options for most patients with IgAN are directed at optimizing supportive care, by controlling blood pressure and limiting proteinuria through blockade of the renin–angiotensin–aldosterone axis. With the introduction of novel disease-modifying therapies this is likely to change over the coming 5 years with a focus on treating the IgAN, rather than the downstream consequences of IgAN-induced nephron loss. In the rare patient presenting with a rapidly progressive glomerulonephritis (RPGN), a regimen such as those used for vasculitis and other forms of RPGN should be considered, for example, cyclophosphamide in combination with oral prednisolone.
Thin membrane nephropathy
Authors: Topham Peter , Gale Daniel 
Published: October 2024

Abstract
Thin membrane nephropathy is a common autosomal dominant glomerular disorder that results in persistent nonvisible haematuria and is pathologically characterized by the presence of diffuse and uniform thinning of the glomerular basement membrane. Recent genetic studies have identified mutations in the COL4A3 and COL4A4 genes in 40% of affected families. There is no specific treatment. Prognosis is excellent for most people, but in some cases proteinuria and progressive renal impairment occur.
Close binary fractions in accreted and in situ halo stars
Authors: Bashi Dolev , Belokurov Vasily , Hodgkin Simon 
Published: October 2024

ABSTRACT
The study of binary stars in the Galactic halo provides crucial insights into the dynamical history and formation processes of the Milky Way. In this work, we aim to investigate the binary fraction in a sample of accreted and in situ halo stars, focusing on short-period binaries. Utilizing data from Gaia Data Release 3 (DR3), we analysed the radial velocity uncertainty $\sigma _{\mathrm{RV}}$ distribution of a sample of main-sequence stars. We used a novel Bayesian framework to model the dependence in $\sigma _{\mathrm{RV}}$ of single and binary systems allowing us to estimate binary fractions F in a sample of bright ($G_{\mathrm{RVS}}$ &lt; 12) Gaia sources. We selected the samples of in situ and accreted halo stars based on estimating the 6D phase space information and affiliating the stars to the different samples on an action angle versus energy ($L_{\mathrm{z}}{\!-\!}E$) diagram. Our results indicate a higher, though not significant, binary fraction in accreted stars compared to the in situ halo sample. We further explore binary fractions using cuts in E and $L_z$, and find a higher binary fraction in both high-energy and prograde orbits that might be explained by differences in metallicity. By cross-matching our Gaia sample with APOGEE DR17 catalogue, we confirm the results of previous studies on higher binary fractions in metal-poor stars and find the fractions of accreted and in situ halo stars consistent with this trend. Our finding provides new insights into binary stars’ formation processes and dynamical evolution in the primordial Milky Way Galaxy and its accreted dwarf Galaxies.
Wide Area VISTA Extra-galactic Survey (WAVES): unsupervised star-galaxy separation on the WAVES-Wide photometric input catalogue using UMAP and hdbscan
Authors: Cook Todd L , Bandi Behnood , Philipsborn Sam , Loveday Jon , Bellstedt Sabine , Driver Simon P , Robotham Aaron S G , Bilicki Maciej , Kaur Gursharanjit , Tempel Elmo , Baldry Ivan , Gruen Daniel , Longhetti Marcella , Iovino Angela , Holwerda Benne W , Demarco Ricardo 
Published: October 2024

ABSTRACT
Star-galaxy separation is a crucial step in creating target catalogues for extragalactic spectroscopic surveys. A classifier biased towards inclusivity risks including high numbers of stars, wasting fibre hours, while a more conservative classifier might overlook galaxies, compromising completeness and hence survey objectives. To avoid bias introduced by a training set in supervised methods, we employ an unsupervised machine learning approach. Using photometry from the Wide Area VISTA Extragalactic Survey (WAVES)-Wide catalogue comprising nine-band $u - K_s$ data, we create a feature space with colours, fluxes, and apparent size information extracted by ProFound. We apply the non-linear dimensionality reduction method UMAP (Uniform Manifold Approximation and Projection) combined with the classifier hdbscan (Hierarchical Density-Based Spatial Clustering of Applications with Noise) to classify stars and galaxies. Our method is verified against a baseline colour and morphological method using a truth catalogue from Gaia, SDSS (Sloan Digital Sky Survey), GAMA (Galaxy And Mass Assembly), and DESI (Dark Energy Spectroscopic Instrument). We correctly identify 99.75 per cent of galaxies within the AB magnitude limit of $Z=21.2$, with an F1 score of $0.9971 \pm 0.0018$ across the entire ground truth sample, compared to $0.9879 \pm 0.0088$ from the baseline method. Our method’s higher purity ($0.9967 \pm 0.0021$) compared to the baseline ($0.9795 \pm 0.0172$) increases efficiency, identifying 11 per cent fewer galaxy or ambiguous sources, saving approximately 70 000 fibre hours on the 4MOST (4-m Multi-Object Spectroscopic Telescope) instrument. We achieve reliable classification statistics for challenging sources including quasars, compact galaxies, and low surface brightness galaxies, retrieving 92.7 per cent, 84.6 per cent, and 99.5 per cent of them, respectively. Angular clustering analysis validates our classifications, showing consistency with expected galaxy clustering, regardless of the baseline classification.
From outskirts to core: the suppression and activation of radio AGN around galaxy clusters
Authors: de Vos K , Hatch N A , Merrifield M R 
Published: October 2024

ABSTRACT
To investigate how the radio-identified active galactic nuclei (AGN) fraction varies with cluster-centric radius, we present the projected and de-projected distributions of a large sample of Low-Frequency Array-identified radio AGN out to $30R_{500}$ around galaxy clusters. The AGN fraction experiences a ${\sim} 25~{{\ \rm per\ cent}}$ increase above the field fraction in the cluster outskirts at around $10R_{500}$, a ${\sim} 20~{{\ \rm per\ cent}}$ decrease around ${\sim} 0.5R_{500}$, and an increase of over three times the field fraction value in the very cluster core. We label these three radial windows the outer, intermediate, and inner regions respectively, and investigate how these radial trends might arise due to intrinsic properties of the AGN population. The only difference seen in host galaxy stellar mass is in the inner region, where there is a much higher fraction of massive host galaxies. Analysing AGN radio luminosity, regions with a higher AGN fraction tend to have more radio luminous AGN, and vice versa. We discuss the physical mechanisms that might be responsible for these results with reference to the literature.
A novel circRNA–miRNA–mRNA regulatory axis as a sex-specific biological variable in bronchopulmonary dysplasia
Authors: Das Pragnya , Shyamal Sharmishtha , Prahaladan Varsha M , Mishra Smruti S , Takada Xander , Chandran Srinarmadha , Addya Sankar , Agarwal Beamon , Andersson Sture , Panda Amaresh C , Bhandari Vineet 
Published: October 2024

Abstract
Babies born prematurely with gestational age &lt;28 weeks usually develop a severe pulmonary complication called Bronchopulmonary Dysplasia (BPD) in response to hyperoxia. BPD is a sexually dimorphic pediatric disease with no curative options. Several micro RNAs (miRNAs) are implicated in BPD and are expressed differentially in males and females. Circular (circ) RNAs serve as sponges for their dedicated miRNAs to influence transcription and translation. We tested the dimorphism of these circular RNAs in BPD to assess their biological significance and unravel a circRNA–miRNA–mRNA regulatory axis in response to hyperoxia. Our RNA-Sequencing assay identified approximately 33 000 circRNAs at the alveolar stage of development with only a handful of them being expressed differentially between males and females in the control room air (RA) and hyperoxia-treated (BPD) groups. One circRNA, i.e circNfix was found to be associated with miR204-5p that targets the downstream mRNA target Ntrk2. To prove that circNfix regulates Ntrk2, we silenced circNfix using a GapmeR and found that Ntrk2 was also suppressed, leading to an improved alveolar phenotype in BPD male pups. From the results of our study, we can propose circNfix and Ntrk2 as novel key regulators in the pathogenesis and sexual dimorphism of BPD, while simultaneously proposing the use of circNfix GapmeR towards a potential therapeutic application.
Older people predialysis care pathways and early morbidity–mortality upon start of dialysis
Authors: Hamroun Aghiles , Aymes Estelle , Couchoud Cécile , Béchade Clémence , Moranne Olivier , Beuscart Jean-Baptiste , Gauthier Victoria , Dauchet Luc , Amouyel Philippe , Stengel Bénédicte , Glowacki François 
Published: October 2024

ABSTRACT

Background
The ageing of the population with advanced chronic kidney disease (CKD) increases the complexity of care pathways. Our aim was to identify subgroups of older people according to predialysis care pathways and describe their association with early morbidity–mortality after transition to dialysis.

Methods
This study included 22 128 incident dialysis patients aged ≥75 years during 2009–2017 from the French nationwide registry linked to the National Health Data System. Predialysis care pathways were identified by ascending hierarchical classification based on preselected healthcare use indicators in the previous year. Their association with a composite outcome of death or hospitalization ≥50% of the time off dialysis within the first year of dialysis was studied by multivariable logistic regression accounting for demographics, comorbidities, functional status, conditions of dialysis initiation, socioeconomic deprivation index and home-to-dialysis center travel time.

Results
Five care pathway profiles were identified, characterized by limited healthcare use (Cluster 1, 28%), non-nephrology ambulatory care (Cluster 2, 17%), nephrology ambulatory care (Cluster 3, 37%) and a high level of non-nephrology or nephrology hospitalizations (Clusters 4 and 5, both 9%). Profile subgroups did not differ according to patient age and comorbidities, but Clusters 1, 2 and 4 displayed higher levels of social deprivation. Compared with Cluster 3, the odds ratios of primary composite outcome were significantly increased for Clusters 1, 4 and 5 [odds ratio (95% confidence interval) of 1.16 (1.08–1.25), 1.17 (1.05–1.32) and 1.12 (1.01–1.25), respectively]. Moreover, prolonged hospitalizations were also more common in all groups, compared with Cluster 3.

Conclusion
Despite a similar comorbidity profile, older people with advanced CKD experience very heterogeneous predialysis care pathways, some of which associated with higher burden of hospitalization after the transition to dialysis.
Symptom management in isocitrate dehydrogenase mutant glioma
Authors: Walbert Tobias , Avila Edward K , Boele Florien W , Hertler Caroline , Lu-Emerson Christine , van der Meer Pim B , Peters Katherine B , Rooney Alasdair G , Templer Jessica W , Koekkoek Johan A F 
Published: October 2024

Abstract
According to the 2021 World Health Organization classification of CNS tumors, gliomas harboring a mutation in isocitrate dehydrogenase (mIDH) are considered a distinct disease entity, typically presenting in adult patients before the age of 50 years. Given their multiyear survival, patients with mIDH glioma are affected by tumor and treatment-related symptoms that can have a large impact on the daily life of both patients and their caregivers for an extended period of time. Selective oral inhibitors of mIDH enzymes have recently joined existing anticancer treatments, including resection, radiotherapy, and chemotherapy, as an additional targeted treatment modality. With new treatments that improve progression-free and possibly overall survival, preventing and addressing daily symptoms becomes even more clinically relevant. In this review we discuss the management of the most prevalent symptoms, including tumor-related epilepsy, cognitive dysfunction, mood disorders, and fatigue, in patients with mIDH glioma, and issues regarding patient’s health-related quality of life and caregiver needs in the era of mIDH inhibitors. We provide recommendations for practicing healthcare professionals caring for patients who are eligible for treatment with mIDH inhibitors.
A novel approach to peer support for academic researchers
Authors: Khodabakhsh S , Hoffmann C , Sauchelli S , Shi G , Mitchell A 
Published: October 2024

Abstract

Background
Academic researchers experience high levels of stress, isolation and loneliness, which compromise their well-being. There is a particular need to address these issues amongst early career and postgraduate research staff. ‘Spaces for Listening’ is an initiative to increase active listening and provide peer support.

Aims
To assess the feasibility, acceptability and potential impacts of Spaces for Listening in an academic setting.

Methods
Early career and postgraduate researchers from a large university in the UK were invited to attend ‘Academic Spaces for Listening’ (ASfL). Five ASfL sessions (including in-person and Chinese language) were held. A mixed-methods study using online survey and in-depth interviews was conducted. Quantitative data were analysed using descriptive statistics, and qualitative data were analysed using principles of thematic analysis. The qualitative and quantitative findings were integrated at the interpretation phase.

Results
A total of 25 participants attended an ASfL session, 22 of them completed the survey and 6 participants participated in semi-structured interviews. Participants were very satisfied with the session content (68%, n = 15), organization (68%, n = 15) and delivery (68%, n = 15). Four themes were identified from qualitative analysis: (i) the ‘Academic Spaces for Listening’ (ASfL) experience; (2) impact of ASfL; (3) potential challenges of ASfL and (4) ASfL in the future. Interpersonal connectedness was an important outcome for participants during the session. Participants showed interest in the future of ASfL.

Conclusions
Implementing Spaces for Listening in an academic setting is feasible and was well received by participants. The initiative may fill a gap in the social interactions amongst academic researchers.
Correlating Climate Conditions With Pseudomonas aeruginosa Prevalence in Diabetic Foot Infections Within the United States
Authors: Winski Rebecca , Xu Jiachen , Townsend Jonathan , Chan Arthur , Wattengel Bethany A , Davis Matthew , Puckett Andrew , Huntsman Kyle , O’Leary Ashley L , Mergenhagen Kari A 
Published: October 2024

Abstract

Background
The 2023 “International Working Group on the Diabetic Foot/Infectious Disease Society of America Guidelines on the Diagnosis and Treatment of Diabetes-Related Foot Infections” (DFIs) provides recommendations for Pseudomonas coverage based on the climate region.

Methods
This was a retrospective national study of veterans between 1/1/2010 and 3/23/2024 with diabetes mellitus and a culture below the malleolus wound. Prevalence of Pseudomonas was categorized based on climate zones according to the International Energy Conservation Code. Multivariable logistic regression was used to determine odds ratios and 97.5% CIs.

Results
The prevalence of Pseudomonas significantly varied between US climates. Pseudomonas was most prevalent within the Hot Humid climate, where it was isolated in 11.6% of DFI cultures. Pseudomonas was least prevalent within the Very Cold climate, where it was isolated in 6.2% of cultures. In the multivariable logistic regression model, hot and humid climates were associated with an odds of P. aeruginosa of 1.92 (97.5% CI, 1.69–2.20), a hot, dry climate was associated with an odds of 1.65 (97.5% CI, 1.44–1.90), and a humid climate was associated with an odds of 1.65 (97.5% CI, 1.45–1.89). A lower Charlson Comorbidity Index, inpatient admission, recent antipseudomonal antibiotic use, and swabs were less likely to have Pseudomonas. Recent admission increased the odds of P. aeruginosa (odds ratio [OR], 1.34; 97.5% CI, 1.27–1.41). History of P. aeruginosa was associated with an increase in P. aeruginosa (OR, 8.90; 97.5% CI, 8.29–9.56).

Conclusions
The prevalence of DFI organisms varies within different US climates. Utilization of local climate information may allow for more accurate and targeted empiric antibiotic selection when treating DFIs.