bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transient acute kidney injury after chimeric antigen receptor T-cell therapy in patients with hematological malignancies
Authors: León-Román Juan , Iacoboni Gloria , Bermejo Sheila , Carpio Cecilia , Bolufer Mónica , García-Carro Clara , Sánchez-Salinas Mario , Alonso-Martínez Carla , Bestard Oriol , Barba Pere , Soler María José 
Published: February 2024

ABSTRACT

Background
Acute kidney injury (AKI) occurs in 30% of patients infused with chimeric antigen receptor (CAR) T-cells. The purpose of this study was to identify risk factors and long-term outcomes after AKI in patients who received CAR T-cell therapy.

Methods
Medical records of 115 adult patients with R/R hematological malignancies treated with CD19-targeted CAR T-cells at Vall d'Hebron University Hospital between July 2018 and May 2021. Baseline demographic data including age, gender, ethnicity, body mass index (BMI), and co-morbidities, as well as the type of hematological neoplasia and prior lines of therapy were collected. Laboratory parameters including serum creatinine and whole blood hemoglobin were retrospectively reviewed and values were gathered for days +1, +7, +14, +21, and +28 post-infusion.

Results
A total of 24/115 (21%) patients developed AKI related to CAR T-cell therapy; 6/24 with AKI over chronic kidney disease (CKD). Two patients had AKI in the context of lymphodepleting (LD) chemotherapy and the other 22 after CAR T-cell infusion, starting at day+1 in 3 patients, day+7 in 13 patients, day +14 in 1 patient, day+21 in 2 patients, and day+28 in 3 patients. Renal function was recovered in 19/24 (79%) patients within the first month after infusion. Male gender, CKD, cytokine release syndrome (CRS), and immune effector cell-associated neurotoxicity syndrome (ICANS) were associated with AKI. Male gender, CKD, ICANS grade ≥3 and CRS grade ≥2 were identified as independent risk factors for AKI on multivariable analysis. In terms of the most frequent CAR T-cell related complications, CRS was observed in 95 (82%) patients and ICANS in 33 (29%) patients. Steroids were required in 34 (30%) patients and tocilizumab in 37 (32%) patients. Six (5%) patients were admitted to the intensive care unit (1 for septic shock, 4 for CRS grade ≥2 associated to ICANS grade ≥2, and 1 for CRS grade ≥3). A total of 5 (4.4%) patients died in the first 30 days after CAR T-cell infusion for reasons other than disease progression, including 4 cases of infectious complications and 1 of heart failure.

Conclusion
Our results suggest that AKI is a frequent but mild adverse event, with fast recovery in most patients.
Normal values of myocardial blood flow measured with dynamic myocardial computed tomography perfusion
Authors: Møller Mathias B , Linde Jesper J , Fuchs Andreas , Køber Lars V , Nordestgaard Børge G , Kofoed Klaus F 
Published: February 2024

Abstract

Aims
Dynamic myocardial computed tomography (CT) perfusion (DM-CTP) can, in combination with coronary CT angiography (CCTA), provide anatomical and functional evaluation of coronary artery disease (CAD). However, normal values of myocardial blood flow (MBF) are needed to identify impaired myocardial blood supply in patients with suspected CAD. We aimed to establish normal values for MBF measured using DM-CTP, to assess the effects of age and sex, and to assess regional distribution of MBF.

Methods and results
A total of 82 healthy individuals (46 women) aged 45–78 years with normal coronary arteries by CCTA underwent either rest and adenosine stress DM-CTP (n = 30) or adenosine-induced stress DM-CTP only (n = 52). Global and segmental MBF were assessed. Global MBF at rest and during stress were 0.93 ± 0.42 and 3.58 ± 1.14 mL/min/g, respectively. MBF was not different between the sexes (P = 0.88 at rest and P = 0.61 during stress), and no correlation was observed between MBF and age (P = 0.08 at rest and P = 0.82 during stress). Among the 16 myocardial segments, significant intersegmental differences were found (P &lt; 0.01), which was not related to age, sex, or coronary dominance.

Conclusion
MBF assessed by DM-CTP in healthy individuals with normal coronary arteries displays significant intersegmental heterogeneity which does not seem to be affected by age, sex, or coronary dominance. Normal values of MBF may be helpful in the clinical evaluation of suspected myocardial ischaemia using DM-CTP.
The quality of care and long-term mortality of out of hospital cardiac arrest survivors after acute myocardial infarction: a nationwide cohort study
Authors: Weight Nicholas , Moledina Saadiq , Hennessy Tommy , Jia Haibo , Banach Maciej , Rashid Muhammad , Siller-Matula Jolanta M , Thiele Holger , Mamas Mamas A 
Published: February 2024

Abstract

Aims
The long-term outcomes of out of hospital cardiac arrest (OHCA) survivors are not well known.

Methods and results
Using the Myocardial Ischaemia National Audit Project (MINAP) registry, linked to Office for National Statistics mortality data, we analysed 661 326 England, Wales, and Northern Ireland acute myocardial infarction (AMI) patients; 14 127 (2%) suffered OHCA and survived beyond 30 days of hospitalization. Patients dying within 30 days of admission were excluded. Mean follow-up for the patients included was 1500 days. Cox regression models were fitted, adjusting for demographics and management strategy. OHCA survivors were younger (in years) {64 [interquartile range (IQR) 54–72] vs. 70 (IQR 59–80), P &lt; 0.001}, more often underwent invasive coronary angiography (88% vs. 71%, P &lt; 0.001) and percutaneous coronary intervention (72% vs. 45%, P &lt; 0.001). Overall, the risk of mortality for OHCA patients that survived past 30 days was lower than patients that did not suffer cardiac arrest [adjusted hazard ratio (HR) 0.91; 95% CI; 0.87–0.95, P &lt; 0.001]. ‘Excellent care’ according to the mean opportunity-based quality indicator (OBQI) score compared to ‘Poor care’, predicted a reduced risk of long-term mortality post-OHCA for all patients (HR: 0.77, CI; 0.76–0.78, P &lt; 0.001), more for STEMI patients (HR: 0.73, CI; 0.71–0.75, P &lt; 0.001), but less significantly in NSTEMI patients (HR: 0.79, CI; 0.78–0.81, P &lt; 0.001).

Conclusion
OHCA patients remain at significant risk of mortality in-hospital. However, if surviving over 30 days post-arrest, OHCA survivors have good longer-term survival up to 10 years compared to the general AMI population. Higher-quality inpatient care appears to improve long-term survival in all OHCA patients, more so in STEMI.
Relating soil moisture and Sentinel-2 vegetation index patterns to spruce bark beetle infestations prior to outbreak
Authors: Xu Chunyan , Förster Michael , Gränzig Tobias , May Johannes , Kleinschmit Birgit 
Published: February 2024

Abstract
Central Europe experienced severe droughts from 2018 to 2020, which led to bark beetle infestations in Norway spruce (Picea abies L.). While recent studies have identified these droughts as a major factor in the dieback of spruces, the exact mechanism through which drought stress influences spruce vitality and increases vulnerability to infestations is not well understood. To gain insights into the spatial and temporal relations between infestations and drought stress, this study compared soil moisture index (SMI) data for the entire soil layer from the German Drought Monitor and Sentinel-2 satellite time series for healthy and bark beetle infested spruce stands preceding the infestation. The study used t-tests to compare pre-infestation monthly sums of SMI and vegetation indices (VIs) for healthy and infested stands. Yearly trajectories of six VIs were used to compare the separability between infested and healthy plots. The results showed that the monthly sum values of SMI for healthy spruce plots were statistically significantly higher than the infested plots from May 2017 to January 2018, while the monthly sum values of Inverted Red Edge Chlorophyll Index of healthy spruce plots were significantly higher than infested plots during growing seasons. With these findings, the study provides useful information for the understanding of the relation of soil moisture and remote sensing VIs patterns in relation to bark beetle infestations.
Application of Infrared Spectroscopy in the Identification of Fallen Trees from the Amazon Rainforest (Myristicaceae)
Authors: Eugenio da Silva Claudia , Nascimento Cristiano Souza do , de Freitas Jorge Alves , de Araújo Roberto Daniel , Nascimento Claudete Catanhede do , Higuchi Niro 
Published: February 2024

Abstract
The infrared spectrum carries the so-called fingerprint of a plant, a characteristic that can help the identification of wood from an integrative perspective. Fourier-transform near-infrared spectroscopy (FT-NIRS) was evaluated for its potential use in the taxonomic identification of natural fallen trees from the Amazon rainforest (Myristicaceae). Trees found on the forest floor (Amazonas, Brazil) were surveyed, and eight individuals were selected for the study. The material was removed from the trunk for anatomical identification based on xylem structure and obtaining NIR spectra (10,000 to 4,000 cm-1). A total of 1,080 spectra were collected and used in the multivariate analysis. Absorption bands in the NIR region and chemometrics (calibration models) were used to interpret the spectra, which indicated similarity trends at the genus and species levels. Linear discriminant analysis (LDA) was able to differentiate Iryanthera ulei and Virola (five species), which were misclassified in the field as a single species (Virola sp.). The accuracy of the results obtained by chemometric models (LDA 7 and 14) indicates the robustness of NIR spectroscopy, which can be used as a new tool in the integrative taxonomy of plant material from tropical forests that are difficult to identify and can analyzing many tests quickly and securely.
Study Implications: The taxonomic identification of natural fallen trees found on the floor of tropical forests is quite complex given the lack of flowers, fruits, and leaves in field collection. Fourier-transform near-infrared spectroscopy demonstrated its capability to distinguish between wood samples from fallen trees belonging to the Myristicaceae family. The chemometric model successfully discriminated the samples, which had been erroneously lumped together in the field under the single species designation of Virola sp. This technique has been previously overlooked for providing differentiation. Our study highlights its efficacy to address misclassifications and allow taxonomic identification.
High-density genetic linkage mapping in Sitka spruce advances the integration of genomic resources in conifers
Authors: Tumas Hayley , Ilska Joana J , Gérardi Sebastien , Laroche Jerome , A’Hara Stuart , Boyle Brian , Janes Mateja , McLean Paul , Lopez Gustavo , Lee Steve J , Cottrell Joan , Gorjanc Gregor , Bousquet Jean , Woolliams John A , MacKay John J 
Published: February 2024

Abstract
In species with large and complex genomes such as conifers, dense linkage maps are a useful resource for supporting genome assembly and laying the genomic groundwork at the structural, populational, and functional levels. However, most of the 600+ extant conifer species still lack extensive genotyping resources, which hampers the development of high-density linkage maps. In this study, we developed a linkage map relying on 21,570 single nucleotide polymorphism (SNP) markers in Sitka spruce (Picea sitchensis [Bong.] Carr.), a long-lived conifer from western North America that is widely planted for productive forestry in the British Isles. We used a single-step mapping approach to efficiently combine RAD-seq and genotyping array SNP data for 528 individuals from 2 full-sib families. As expected for spruce taxa, the saturated map contained 12 linkages groups with a total length of 2,142 cM. The positioning of 5,414 unique gene coding sequences allowed us to compare our map with that of other Pinaceae species, which provided evidence for high levels of synteny and gene order conservation in this family. We then developed an integrated map for P. sitchensis and Picea glauca based on 27,052 markers and 11,609 gene sequences. Altogether, these 2 linkage maps, the accompanying catalog of 286,159 SNPs and the genotyping chip developed, herein, open new perspectives for a variety of fundamental and more applied research objectives, such as for the improvement of spruce genome assemblies, or for marker-assisted sustainable management of genetic resources in Sitka spruce and related species.
A k-mer-based bulked segregant analysis approach to map seed traits in unphased heterozygous potato genomes
Authors: Sonsungsan Pajaree , Nganga Mwaura Livingstone , Lieberman Meric C , Amundson Kirk R , Stewart Victoria , Plaimas Kitiporn , Comai Luca , Henry Isabelle M 
Published: February 2024

Abstract
High-throughput sequencing-based methods for bulked segregant analysis (BSA) allow for the rapid identification of genetic markers associated with traits of interest. BSA studies have successfully identified qualitative (binary) and quantitative trait loci (QTLs) using QTL mapping. However, most require population structures that fit the models available and a reference genome. Instead, high-throughput short-read sequencing can be combined with BSA of k-mers (BSA-k-mer) to map traits that appear refractory to standard approaches. This method can be applied to any organism and is particularly useful for species with genomes diverged from the closest sequenced genome. It is also instrumental when dealing with highly heterozygous and potentially polyploid genomes without phased haplotype assemblies and for which a single haplotype can control a trait. Finally, it is flexible in terms of population structure. Here, we apply the BSA-k-mer method for the rapid identification of candidate regions related to seed spot and seed size in diploid potato. Using a mixture of F1 and F2 individuals from a cross between 2 highly heterozygous parents, candidate sequences were identified for each trait using the BSA-k-mer approach. Using parental reads, we were able to determine the parental origin of the loci. Finally, we mapped the identified k-mers to a closely related potato genome to validate the method and determine the genomic loci underlying these sequences. The location identified for the seed spot matches with previously identified loci associated with pigmentation in potato. The loci associated with seed size are novel. Both loci are relevant in future breeding toward true seeds in potato.
A simple, robust, broadly applicable insertion mutagenesis method to create random fluorescent protein: target protein fusions
Authors: Pike Andrew , Pietryski Cassandra , Deighan Padraig , Kuehner Jason , Lau Derek , Seshan Anupama , March Paul E 
Published: February 2024

Abstract
A simple, broadly applicable method was developed using an in vitro transposition reaction followed by transformation into Escherichia coli and screening plates for fluorescent colonies. The transposition reaction catalyzes the random insertion of a fluorescent protein open reading frame into a target gene on a plasmid. The transposition reaction is employed directly in an E. coli transformation with no further procedures. Plating at high colony density yields fluorescent colonies. Plasmids purified from fluorescent colonies contain random, in-frame fusion proteins into the target gene. The plate screen also results in expressed, stable proteins. A large library of chimeric proteins was produced, which was useful for downstream research. The effect of using different fluorescent proteins was investigated as well as the dependence of the linker sequence between the target and fluorescent protein open reading frames. The utility and simplicity of the method were demonstrated by the fact that it has been employed in an undergraduate biology laboratory class without failure over dozens of class sections. This suggests that the method will be useful in high-impact research at small liberal arts colleges with limited resources. However, in-frame fusion proteins were obtained from 8 different targets suggesting that the method is broadly applicable in any research setting.
Nucleosomes at the Dawn of Eukaryotes
Authors: Hocher Antoine , Warnecke Tobias 
Published: February 2024

Abstract
Genome regulation in eukaryotes revolves around the nucleosome, the fundamental building block of eukaryotic chromatin. Its constituent parts, the four core histones (H3, H4, H2A, H2B), are universal to eukaryotes. Yet despite its exceptional conservation and central role in orchestrating transcription, repair, and other DNA-templated processes, the origins and early evolution of the nucleosome remain opaque. Histone-fold proteins are also found in archaea, but the nucleosome we know—a hetero-octameric complex composed of histones with long, disordered tails—is a hallmark of eukaryotes. What were the properties of the earliest nucleosomes? Did ancestral histones inevitably assemble into nucleosomes? When and why did the four core histones evolve? This review will look at the evolution of the eukaryotic nucleosome from the vantage point of archaea, focusing on the key evolutionary transitions required to build a modern nucleosome. We will highlight recent work on the closest archaeal relatives of eukaryotes, the Asgardarchaea, and discuss what their histones can and cannot tell us about the early evolution of eukaryotic chromatin. We will also discuss how viruses have become an unexpected source of information about the evolutionary path toward the nucleosome. Finally, we highlight the properties of early nucleosomes as an area where new tools and data promise tangible progress in the not-too-distant future.
Allocating health care resources in jails and prisons during COVID-19: a qualitative study of carceral decision-makers
Authors: Doan Brandon , Kramer Camille , Saloner Brendan , Song Minna , Sufrin Carolyn B , Rubenstein Leonard S , Eber Gabriel B 
Published: February 2024

Abstract
COVID-19 created acute demands on health resources in jails and prisons, burdening health care providers and straining capacity. However, little is known about how carceral decision-makers balanced the allocation of scarce resources to optimize access to and quality of care for incarcerated individuals. This study analyzes a national sample of semi-structured interviews with health care and custody officials (n = 32) with decision-making authority in 1 or more carceral facilities during the COVID-19 pandemic. Interviews took place between May and October 2021. We coded transcripts using a directed content analysis approach and analyzed data for emergent themes. Participants reported that facilities distributed personal protective equipment to staff before incarcerated populations due to staff's unique role as potential vectors of COVID-19. The use of testing reflected not only an initial imperative to preserve limited supplies but also more complex decision-making about the value of test results to facility operations. Participants also emphasized the difficulties caused by limited physical space, insufficient staff, and stress from modifying job roles. The rapid onset of COVID-19 confronted decision-makers with unprecedented resource allocation decisions, often with life-or-death consequences. Planning for future resource allocation decisions now may promote more equitable decisions when confronted with a future pandemic event.
Caregiving for dementia: trends pre-post onset and predictive factors of family caregiving (2002–2018)
Authors: Ingraham Bailey C , Barthold Douglas , Fishman Paul , Coe Norma B 
Published: February 2024

AbstractPersons living with Alzheimer's and other related forms of dementia rely heavily on care from family and friends for assistance with daily activities (“family care”), but little is known about care transitions over time. We analyzed data from the Health and Retirement Study to describe caregiving patterns, from 2 years before dementia onset and up to 6 years after. Using sociodemographic data from the interview prior to dementia onset, we determined if there are significant factors that predict receipt of family care at dementia onset. We found that one-third (33%) of people living with dementia were receiving help with daily activities 2 years prior to their first positive dementia screen and this increased to 60% during the first positive screen. Nearly all of those receiving assistance received family care. We found multiple significant predictors of receiving family care at onset, including race, education, access to private health insurance, number of activities of daily living that were difficult, number of chronic conditions, and already receiving help. This demonstrates potential gaps in dementia care, and which subpopulations may benefit most from targeted interventions for household members who do not have adequate caregiving resources or programs that provide additional formal care.
Sustained Increase in Pediatric Inflammatory Bowel Disease Incidence Across the South West United Kingdom Over the Last 10 Years
Authors: Green Zachary , Ashton James J , Rodrigues Astor , Spray Christine , Howarth Lucy , Mallikarjuna Akshatha , Chanchlani Neil , Hart James , Bakewell Christopher , Lee Kwang Yang , Wahid Amar , Beattie R Mark 
Published: February 2024

Abstract

Background
Pediatric inflammatory bowel disease (pIBD) incidence has increased over the last 25 years. We aim to report contemporaneous trends across the South West United Kingdom.

Methods
Data were provided from centers covering the South West United Kingdom (Bristol, Oxford, Cardiff, Exeter, and Southampton), with a total area at-risk population (&lt;18 years of age) of 2 947 534. Cases were retrieved from 2013 to 2022. Incident rates were reported per 100 000 at-risk population, with temporal trends analyzed through correlation. Subgroup analysis was undertaken for age groups (0-6, 6-11, and 12-17 years of age), sex, and disease subtype. Choropleth maps were created for local districts.

Results
In total, 2497 pIBD cases were diagnosed between 2013 and 2022, with a mean age of 12.6 years (38.7% female). Diagnosis numbers increased from 187 to 376, with corresponding incidence rates of 6.0 per 100 000 population per year (2013) to 12.4 per 100 000 population per year (2022) (b = 0.918, P &lt; .01). Female rates increased from 5.1 per 100 000 population per year in 2013 to 11.0 per 100 000 population per year in 2022 (b = 0.865, P = .01). Male rates increased from 5.7 per 100 000 population per year to 14.4 per 100 000 population per year (b = 0.832, P = .03). Crohn’s disease incidence increased from 3.1 per 100 000 population per year to 6.3 per 100 000 population per year (b = 0.897, P &lt; .01). Ulcerative colitis increased from 2.3 per 100 000 population per year to 4.3 per 100 000 population per year (b = 0.813, P = .04). Inflammatory bowel disease unclassified also increased, from 0.6 per 100 000 population per year to 1.8 per 100 000 population per year (b = 0.851, P = .02). Statistically significant increases were seen in those ≥12 to 17 years of age, from 11.2 per 100 000 population per year to 24.6 per 100 000 population per year (b = 0.912, P &lt; .01), and the 7- to 11-year-old age group, with incidence rising from 4.4 per 100 000 population per year to 7.6 per 100 000 population per year (b = 0.878, P = .01). There was no statistically significant increase in very early onset inflammatory bowel disease (≤6 years of age) (b = 0.417, P = .231).

Conclusions
We demonstrate significant increases in pIBD incidence across a large geographical area including multiple referral centers. Increasing incidence has implications for service provision for services managing pIBD.