bluuebunny/crossref_metadata_2025_split huggingface dataset:
Wild-type MIC distributions and epidemiological cutoff values for 5-flucytosine and Candida species as determined by EUCAST broth microdilution
Authors: Delma Fatima Zohra , Melchers Willem J G , Verweij Paul E , Buil Jochem B 
Published: October 2024

Abstract

Objectives
EUCAST has established clinical breakpoints and epidemiological cutoff values (ECOFFs) for Candida spp. However, limited data are available for 5-flucytosine (5-FC). We assessed the in vitro susceptibility of 5-FC against a large collection of clinical Candida species using EUCAST methodology and determined the associated ECOFFs.

Methods
A total of 5622 Candida isolates were collected from patients across the Netherlands between 2008 and 2024. 5-FC MICs were determined using the EUCAST microbroth dilution reference method. Furthermore, MICs were extracted from the EUCAST website. The MICs from this study and those extracted were used to determine ECOFFs and local ECOFFs (L-ECOFFs).

Results
5-FC exhibited potent in vitro activity against C. albicans, N. glabratus and C. parapsilosis, while decreased susceptibility was observed for C. tropicalis, Pichia species, K. marxianus, Y. lipolytica, and C. auris. The ECOFFs (mg/L) and the percentages of WT isolates for 5-FC were: C. albicans: 0.5 (97.2%), N. glabratus: 0.5 (96.6%), C. parapsilosis: 0.5 (99.5%) and P. kudriavzevii: 8 (99.4%). The L-ECOFF (mg/L) and the percentages of WT isolates for 5-FC were: C. dubliniensis: 0.25 (96.8%), C. tropicalis: 0.25 (67.2%), K. marxianus: 0.25 (48.0%), C. lusitaniae: 0.25 (86.5%), M. guillermondii: 0.125 (95.9%) and P. norvegiensis: 8 (94.2%).

Conclusions
5-FC remains a valuable drug to manage difficult-to-treat invasive Candida infections. In vitro susceptibility cannot be predicted based on species identification for most Candida species, but requires MIC-testing. ECOFFs will help to interpret the MICs to support treatment decisions.
Better Prediction of Clinical Outcome with Estimated Glomerular Filtration Rate by CKD-EPI 2021
Authors: Lee Kwang Seob , Jang Jaehyeok , Jang Hanmil , Kang Hyein , Rim John Hoon , Lim Jong-Baeck 
Published: October 2024

Abstract

Background
While the real-world impact of estimated glomerular filtration rate (eGFR) equation change on clinical outcome in a longitudinal cohort setting is limited, external valuation of equation performance should be performed in different population cohorts. This study aimed to compare differential impacts of eGFR values, calculated by 5 equations in a Korean patient population, on clinical outcomes.

Methods
This retrospective longitudinal follow-up cohort study analyzed 23 246 participants with standardized creatinine/cystatin C assay-based laboratory results. The primary exposure was baseline eGFR calculated by 5 different equations including the recently developed 2021 race-free Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI) equations. Clinical outcomes including all-cause mortality, renal replacement therapy, and albuminuria were analyzed to estimate the hazard ratio of the eGFR on clinical outcomes.

Results
Among the 5 equations, CKD-EPI 2021 with creatinine and cystatin C (CKD-EPI 2021-CrCys) showed an earlier increase in hazard ratios for all clinical outcomes, while CKD-EPI 2012 with cystatin C showed a higher hazard ratio for all-cause mortality at low eGFR. Replacing CKD-EPI 2012 with CKD-EPI 2021-CrCys, 5.4% of patients with mortality and 3.3% of patients who received renal replacement therapy were reclassified to a lower risk stage.

Conclusions
The 2021 CKD-EPI equations were acceptable in a Korean population, with better predictive power for clinical outcomes when compared to previous equations. The updated race-free factors for eGFR calculation improved identification of patients at risk for clinical outcomes.
Genome analysis of Streptomyces recifensis SN1E1 to investigate mechanisms for inhibiting fire blight disease
Authors: Lee Su In , Kim Da-Ran , Kwak Youn-Sig 
Published: October 2024

Abstract

Aim
Fire blight, attributed to the bacterium Erwinia amylovora, significantly damages economically important crops, such as apples and pears. Conventional methods for managing fire blight involve the application of chemical pesticides, such as streptomycin and oxytetracycline. Nevertheless, apprehensions are increasing regarding developing antibiotic and pesticide-resistant strains, compounded by documented instances of plant toxicity. Here, we present that Streptomyces recifensis SN1E1 has exhibited remarkable efficacy in suppressing apple fire blight disease. This study aims to unravel the molecular-level antimicrobial mechanisms employed by the SN1E1 strain.

Methods and results
We identified four antimicrobial-associated biosynthetic gene clusters within the genomics of S. recifensis SN1E1. To validate antimicrobial activity against E. amylovora, knock-out mutants of biosynthetic genes linked to antimicrobial activity were generated using the CRISPR/Cas9 mutagenesis system. Notably, the whiE4 and phzB deficient mutants displayed statistically reduced antibacterial activity against E. amylovora

Conclusion
This research establishes a foundation for environmental and biological control studies. The potential utilization of environmentally friendly microbial agents derived from the SN1E1 strain holds promise for the biological control of fire blight disease.
Sign language delays in deaf 3- to 5-year-olds with hearing parents
Authors: Morere Donna A , Allen Thomas E 
Published: October 2024

Abstract
Deaf children of hearing parents (DOH) are at risk for early language delays (ELD) due to environmental and etiological factors, compounding the previously reported higher incidence of ELD in deaf children of deaf parents (DOD) compared to the general population. Archival data from the online database of the Visual Communication and Sign Language Checklist yielded 147 ratings of DOH 3- to 5-year-old children whose parents reported American sign language (ASL) being used in the home at least equally to spoken language. Research goals included (1) examining the incidence of ELD in this cohort, (2) investigating differences in outcomes based on the scaling method used, (3) exploring patterns among the ratings of DOH children identified with ELD, (4) comparing the DOH outcomes to published DOD data, and (5) investigating differences between ratings and individual children. The DOH outcomes suggested an incidence of ELD twice that of the previous DOD sample, with a higher percentage of more severe delays. Even DOH children not identified with ELD demonstrated less well-developed ASL skills than their DOD peers. This emphasizes the need for ongoing monitoring of early ASL skills to allow for early identification of needs and adjustment of interventions to address ASL development.
Surgical challenges of simultaneous laparoscopic management of gastrointestinal stromal tumor and adrenocortical nodular hyperplasia in a 39-year-old female patient: a case report
Authors: Gavrankapetanovic Ali , Bektesevic Admir , Brzika Sanela , Hasic Nedim , Letic Emina , Rasic Ismar 
Published: October 2024

Abstract
Adrenocortical nodular hyperplasia and gastrointestinal stromal tumors are rare conditions, and their simultaneous occurrence in a single patient poses diagnostic and therapeutic challenges. Here, we present the case of a 39-year-old female patient who underwent surgical resection for concurrent adrenocortical nodular hyperplasia and GIST on the posterior part of the gastric fundus. The patient presented with symptoms of hyperaldosteronism and malignant hypertension, leading to the discovery of these two distinct tumors. Preoperative evaluation revealed normal laboratory findings and hormone levels, except for hyperaldosteronism and hypertension. The surgical intervention included left suprarenal gland removal and wedge resection of the gastric tumor. The patient experienced a successful outcome without intraoperative complications and remained normotensive during follow-up visits, with sustaining hormonal balance. This case underscores the importance of multidisciplinary collaboration and tailored surgical planning in managing complex neoplastic conditions.
Cholecystocutaneous fistula after cholecystectomy
Authors: Sah Raju , Rawal Sushil Bahadur , Malla Srijan , Rayamajhi Jyoti , Bhat Pawan Singh 
Published: October 2024

Abstract
Cholecystocutaneous fistula is an exceedingly rare type of external biliary fistula, where an abnormal connection forms between the gallbladder and the skin. Cholecystocutaneous fistula commonly develops in the setting of chronic calculus cholecystitis or following a previous surgical intervention involving the biliary tract. Patients with cholecystocutaneous fistula often present with systemic symptoms, such as fever, nausea, and vomiting, as well as localized symptoms in the right upper quadrant of the abdomen, where the external opening of the fistula is typically found. Ultrasonography, computed tomography, magnetic resonance imaging, magnetic resonance cholangiopancreatography (MRCP), and fistulograms (computed tomography or X-ray) are commonly used. Computed tomography has proven to be more effective than ultrasonography in delineating the fistulous tract and the associated fluid collections. Open cholecystectomy with excision of the fistulous tract is considered the gold standard and is curative in the majority of cases. However, a laparoscopic approach has become a viable alternative, especially in the hands of experienced surgeons.
Machine learning-enabled computer vision for plant phenotyping: a primer on AI/ML and a case study on stomatal patterning
Authors: Tan Grace D , Chaudhuri Ushasi , Varela Sebastian , Ahuja Narendra , Leakey Andrew D B 
Published: October 2024

AbstractArtificial intelligence and machine learning (AI/ML) can be used to automatically analyze large image datasets. One valuable application of this approach is estimation of plant trait data contained within images. Here we review 39 papers that describe the development and/or application of such models for estimation of stomatal traits from epidermal micrographs. In doing so, we hope to provide plant biologists with a foundational understanding of AI/ML and summarize the current capabilities and limitations of published tools. While most models show human-level performance for stomatal density (SD) quantification at superhuman speed, they are often likely to be limited in how broadly they can be applied across phenotypic diversity associated with genetic, environmental, or developmental variation. Other models can make predictions across greater phenotypic diversity and/or additional stomatal/epidermal traits, but require significantly greater time investment to generate ground-truth data. We discuss the challenges and opportunities presented by AI/ML-enabled computer vision analysis, and make recommendations for future work to advance accelerated stomatal phenotyping.
Non-conventional approach for deriving the radial sizes of coronal mass ejections at different instances: discrepancies in the estimates between remote and in situ observations
Authors: Agarwal Anjali , Mishra Wageesh 
Published: October 2024

ABSTRACT
Understanding the evolution of radial sizes and instantaneous expansion speeds of coronal mass ejections (CMEs) is crucial for assessing their impact duration on Earth’s environment. We introduce a non-conventional approach to derive the CME’s radial sizes and expansion speeds at different instances during its passage over a single-point in situ spacecraft. We also estimate the CME’s radial sizes and expansion speeds during its journey from the Sun to 1 au using the 3D kinematics of different CME features, including the leading edge, centre, and trailing edge. The continuous 3D kinematics of the CME is estimated by employing the graduated cylindrical shell and stereoscopic self-similar expansion reconstruction methods on multipoint observations from coronagraphs and heliospheric imagers combined with the drag-based model. We choose the 2010 April 3 CME as a suitable case for our study, promising a more accurate comparison of its remote and in situ observations. We show that the introduced non-conventional approach can provide better accuracy in estimating radial sizes and instantaneous expansion speeds of CMEs at different instances. We examine the aspect ratio of the CME, which influences its expansion behaviour and shows the discrepancy between its value in the corona and interplanetary medium. Our study highlights significant inconsistencies in the arrival time, radial size, and expansion speed estimates obtained from remote and in situ observations. We advocate for future studies leveraging multispacecraft in situ observations and our non-conventional approach to analyse them to improve the comprehension of CME dynamics in the solar wind.
Extracting key information from spectroscopic galaxy surveys
Authors: Wang Yuting , Zhao Gong-Bo , Peacock John A 
Published: October 2024

ABSTRACT
We develop a novel method to extract key cosmological information, which is primarily carried by the baryon acoustic oscillations (BAO) and redshift space distortions (RSD), from spectroscopic galaxy surveys based on a joint principal component analysis (PCA) and massive optimized parameter estimation and data compression (MOPED) algorithm. We apply this method to galaxy samples from BOSS DR12, and find that a PCA manipulation is effective at extracting the informative modes in the 2D correlation function $\xi (s, \mu)$, giving a tighter constraint on BAO and RSD parameters compared to that using the lowest three multipole moments by the traditional method; i.e. the figure of merit of BAO and RSD parameters is improved by 17 per cent. We then perform a compression of the informative PC modes for BAO and RSD parameters using the MOPED scheme, reducing the dimension of the data vector to the number of interesting parameters, manifesting the joint PCA and MOPED as a powerful tool for clustering analysis with almost no loss of constraining power.
Comprehensive investigations on spectral and temporal features of GX 5−1 using AstroSat observations
Authors: Thomas Neal Titus , Giridharan L , Gudennavar S B , Bubbly S G 
Published: October 2024

ABSTRACT
Comprehensive spectrotemporal analyses of the Z-type neutron star low-mass X-ray binary GX 5−1 were performed using 10 broad-band observations from AstroSat/Soft X-ray Telescope and Large Area X-ray Proportional Counter (LAXPC) instruments. The LAXPC-20 hardness–intensity diagram showed horizontal and normal branches (HBs and NBs) of the Z track which exhibited secular motion. The time-averaged spectra in the energy range 0.7–25.0 keV could be fitted with the model combination – $\tt {constant}\, \times \, \tt {tbabs}\, \times \, \tt {edge}\, \times \, \tt {edge}\, \times \, \tt {thcomp}\, \times \, \tt {diskbb}$. This yielded $\Gamma \, \sim$ 2, $kT_{\mathrm{ e}}\, \sim$ 3.3 keV, and $F_{\mathrm{ disc}}$/$F_{\mathrm{ total}}\, \sim$ 0.8 indicating the soft/intermediate spectral state of the source during the observations. Flux-resolved spectral analysis revealed a positive correlation between $kT_{\mathrm{ in}}$ and $F_{\mathrm{ bol}}$. However, a negative correlation was observed between them in one of the NBs. Time-averaged temporal analysis revealed multiple HB oscillations (HBOs) and NB oscillations (NBOs), and peaked noise components in the $\sim$5–50 Hz range. Furthermore, flux-resolved temporal analysis showed that the frequency of the HBOs correlates positively whereas the strength of HBOs correlates negatively with $F_{\mathrm{ bol}}$, indicating their probable origin from the accretion disc. In contrast, the frequency and strength of NBOs remain fairly constant with $F_{\mathrm{ bol}}$, suggesting that they originate from a different region in the system. Using the relativistic precession model along with highest frequency of the HBO, the upper limits of the magnetic dipole moment ($\mu$) and field strength (B) at the poles of the neutron star in the system were found to be 25.60$\times \, 10^{25}$ G cm3 and 3.64$\times \, 10^{8}$ G, respectively, for $k_{\mathrm{ A}}$ = 1.
Biological and prognostic relevance of epigenetic regulatory genes in high-grade gliomas
Authors: Aulakh Sonikpreet , Xiu Joanne , Hinton Andrew , Darabi Sourat , Demeure Michael J , Sengupta Soma , Kesari Santosh , Ashley David M , Sumrall Ashley Love , Glantz Michael J , Spetzler David 
Published: October 2024

Abstract

Background
High-grade gliomas (HGGs) are the most aggressive type of gliomas and have the poorest outcomes. Chromatin remodeling (CR) genes have been implicated in multiple oncogenic pathways in numerous cancer types. In gliomagenesis, CR genes have been implicated in regulating the stemness of glioma cells, the tumor microenvironment (TME), and resistance to therapies.

Methods
We performed molecular profiling of 4244 HGGs and evaluated associations of CR mutations with other cancer-related biomarkers, infiltration by immune cells, and immune gene expression. We also evaluated the association between CR mutations and survival in wild-type IDH HGG patients.

Results
Nearly 10% of HGGs carry mutations in CR genes, with a higher prevalence (15%) in HGGs with IDH mutations. Analysis of cooccurrence with other biomarkers revealed that CR-mutated HGGs possess favorable genetic alterations which may have prognostic value. CR-mutated HGGs with wild-type IDH demonstrated colder TME and worse OS overall compared to the CR-wild-type HGGs.

Conclusions
Our study reveals the prognostic effects of CR mutations in HGG and points to several biomarker candidates that could suggest sensitivity to emerging therapeutic strategies.
The Longitudinal Evidence on Social Ties and Fruit and Vegetable Intake among Aging Adults: A Systematic Review
Authors: Mehranfar Sanaz , Madani Civi Rana , Plunkett Riley , Murphy Rachel A , Cohen Tamara R , Conklin Annalijn I 
Published: October 2024

Abstract

Context
Social ties are associated with the mortality and morbidity of aging populations; however, the role of social ties in healthy eating practices or gender differences in this link is less understood.

Objective
The objective of this study was to examine the longitudinal evidence for the impact of changes in social ties on fruit and vegetable (FV) intakes among aging adults, with attention to gender differences.

Data Sources
Medline, Embase, Scopus, CINAHL, and ProQuest databases were searched until December 2022.

Data Extraction
Longitudinal studies evaluating changes in living arrangement, marital status, social network, or social participation and changes in FV intake among middle- and older-age adults were included. Data from the included studies were extracted using a standardized template and analyzed using a narrative approach.

Data Analysis
A total of 4956 titles were eligible after deduplication, and 75 full texts were screened. Seven studies met the inclusion criteria, and all examined marital transitions only. Five marital transitions were assessed: staying married, becoming widowed, becoming divorced, remaining unmarried, and becoming married. Both the quantity and variety of fruit and/or vegetables eaten were studied. Three of the included studies had only male or only female populations. The studies found that marital dissolution (divorce or widowhood), and remaining unmarried, were associated with reduced FV intakes in older women or men, compared with staying married. The associations were stronger in men than in women. Two studies showed that becoming married was associated with increased vegetable intakes, but 3 reported null results. The included studies were of medium quality.

Conclusions
There is a paucity of longitudinal research on whether changes in social ties are associated with changes in FV intakes among aging adults. This review showed that specific marital transitions may influence healthy eating habits, especially in older men. No evidence exists on whether changes in other social ties might alter healthy eating.

Systematic Review Registration
PROSPERO registration No. CRD42022365795.
Climatic shifts and vegetation response in Western India: a four-decade retrospective through GIS and multi-variable analysis
Authors: Vishvendra Raj Singh Bhanwar , Agarwal Vivek , Sanwal Varun 
Published: October 2024

Abstract
Climate change is having a profound impact on Western India, manifesting in altered weather patterns and ecological shifts. This research paper delves into an extensive analysis of meteorological data spanning the years 1981 to 2018, covering nearly four decades of climatic variations. Utilizing data from 40 meteorological stations across the region, examined changes in key climate variables including precipitation, humidity, wind speed, pressure, and temperature. We used Geographic Information Systems (GIS) to analyze spatial patterns of climate and forest cover changes. This approach visualized and quantified the climate changes over the studied period effectively. The results showed an average temperature increase of 0.66°C and a decrease in precipitation by 25.36 mm, indicating a trend towards warmer and drier conditions. The spatial analysis provided a clearer understanding of how these changes are distributed across Western India, linking them directly to shifts in forest ecosystems as evidenced by changes in the Normalized Difference Vegetation Index (NDVI) for the corresponding months and years. The findings from this research are critical for policymakers, as they offer valuable insights that can inform strategies for environmental conservation and restoration, ensuring sustainable management of the region's natural resources in the face of ongoing global warming.
Evolution and functional divergence of glycosyltransferase genes shaped the quality and cold tolerance of tea plants
Authors: Wang Jingming , Hu Yutong , Guo Danyang , Gao Ting , Liu Tianqi , Jin Jieyang , Zhao Mingyue , Yu Keke , Tong Wei , Ge Honghua , Pan Yuting , Zhang Mengting , Lu Mengqian , Jing Tingting , Du Wenkai , Tang Xiaoyan , Zhao Chenjie , Zhao Wei , Bao Zhijie , Schwab Wilfried , Xia Enhua , Song Chuankui 
Published: October 2024

Abstract
Plant uridine diphosphate–dependent glycosyltransferases (UGTs) play a key role in plant growth and metabolism. Here, we examined the evolutionary landscape among UGTs in 28 fully sequenced species from early algae to angiosperms. Our findings revealed a distinctive expansion and contraction of UGTs in the G and H groups in tea (Camellia sinensis), respectively. Whole-genome duplication and tandem duplication events jointly drove the massive expansion of UGTs, and the interplay of natural and artificial selection has resulted in marked functional divergence within the G group of the sinensis-type tea population. In Cluster II of group G, differences in substrate selection (e.g. abscisic acid) of the enzymes encoded by UGT genes led to their functional diversification, and these genes influence tolerance to abiotic stresses such as low temperature and drought via different modes of positive and negative regulation, respectively. UGTs in Cluster III of the G group have diverse aroma substrate preferences, which contribute a diverse aroma spectrum of the sinensis-type tea population. All Cluster III genes respond to low-temperature stress, whereas UGTs within Cluster III-1, shaped by artificial selection, are unresponsive to drought. This suggests that artificial selection of tea plants focused on improving quality and cold tolerance as primary targets.