bluuebunny/crossref_metadata_2025 huggingface dataset:
Alcohol-related cognitive impairments in patients with and without cirrhosis
Authors: Angerville Bernard , Jurdana Marie-Alix , Martinetti Margaret P , Sarba Ruxandra , Nguyen-Khac Éric , Naassila Mickael , Dervaux Alain
Published: February 2024

Aims

up to 80% of patients with alcohol use disorder display cognitive impairments. Some studies have suggested that alcohol-related cognitive impairments could be worsened by hepatic damage. The primary objective of this study was to compare mean scores on the Brief Evaluation of Alcohol-Related Neurocognitive Impairments measure between alcohol use disorder patients with (CIR+) or without cirrhosis (CIR−).

Methods

we conducted a prospective case–control study in a hepatology department of a university hospital. All patients were assessed using the Evaluation of Alcohol-Related Neuropsychological Impairments test.

Results

a total of 82 patients (50 CIR+, 32 CIR−) were included in this study. CIR− patients were significantly younger than CIR+ patients (respectively, 45.5 ± 6.8 vs 60.1 ± 9.0; P < .0001). After adjusting for age and educational level, the mean Evaluation of Alcohol-Related Neuropsychological Impairments total scores in the CIR+ group were significantly lower than in the group of CIR− patients (14.1 ± 0.7 vs 7.8 ± 0.4, respectively, P < .0001). The mean subscores on delayed verbal memory, alphabetical ordination, alternating verbal fluency, visuospatial abilities, and ataxia subtests were also significantly lower in the CIR+ than in the CIR− group (respectively, 1.9 ± 0.2 vs 2.8 ± 0.2; 1.8 ± 0.2 vs 2.7 ± 0.2; 2.2 ± 0.2 vs 3.6 ± 0.2; 0.7 ± 0.2 vs 1.6 ± 0.2; 0.7 ± 0.2 vs 3.1 ± 0.2; P < .0001 for all comparisons).

Conclusions

in the present study, alcohol use disorder patients with cirrhosis presented more severe cognitive impairments than those without cirrhosis. Longitudinal studies are needed to investigate how cirrhosis can influence cognitive impairments.
Unpublishing as Form: Hart Crane, Jack Spicer, and the Thresholds of Periodical Publication
Authors: Bratton Francesca
Published: February 2024

Rejections are a given in any poet’s career. This essay considers how rejections and the idea of the unpublished fragment might shape poetic form, how practical decisions might turn into aesthetic ones. Both Hart Crane and Jack Spicer had careers among magazines, the experiments of their writing entwined with ephemeral publishing cultures and communities. This essay explores how, through their own distinct experiments with splintered forms of the long poem, magazine rejections also created opportunities in Crane’s and Spicer’s poetry. Both poets turned practical processes into aesthetic experiments, exploring the states between writing, submission, publication, and acceptance or rejection.Yet practical decisions can turn into aesthetic ones. Indeed, the playful tension between practicality and aesthetics sits at the heart of poetic form. Crane and Spicer both incorporated rejections—unpublished poems or poems waiting on publication through various submissions—into the form of their work.
Isohydric stomatal behaviour alters fruit vascular flows and minimizes fruit size reductions in drought-stressed ‘Hass’ avocado (Persea americana Mill.)
Authors: Kaneko Teruko , Gould Nick , Campbell David , Clearwater Michael J
Published: February 2024

Background and Aims

Plant water status is important for fruit development, because many fleshy fruits contain large amounts of water. However, there is no information on vascular flows of Persea americana ‘Hass’ avocado. The aims of this research were to explore the impact of drought stress on the water relationships of the ‘Hass’ avocado plant and its fruit growth.

Methods

Well-watered and water-stressed ‘Hass’ avocado plants were compared. Over 4 weeks, water flows through the shoot and fruit pedicel were monitored using external sap flow gauges. Fruit diameter was monitored using linear transducers, and stomatal conductance (gs), photosynthesis (A) and leaf and stem water potentials (Ѱleaf and Ѱstem) were measured to assess the response of the plants to water supply.

Key Results

In well-watered conditions, the average water inflow to the shoot was 72 g day−1. Fruit water inflow was 2.72 g day−1, but there was water loss of 0.37 g day−1 caused by the outflow (loss back into the tree) through the vascular tissues and 1.06 g day−1 from the fruit skin. Overall, fruit volume increased by 1.4 cm3 day−1. In contrast, water flow into fruit of water-stressed plants decreased to 1.88 g day−1, with the outflow increasing to 0.61 g day−1. As a result, increases in fruit volume were reduced to 0.4 cm3 day−1. The values of A, gs and sap flow to shoots were also reduced during drought conditions. Changes in the hourly time-courses of pedicel sap flow, fruit volume and stem water potential during drought suggest that the stomatal response prevented larger increases in outflow from the fruit. Following re-watering, a substantial recovery in growth rate was observed.

Conclusions

In summary, a reduction in growth of avocado fruit was observed with induced water deficit, but the isohydric stomatal behaviour of the leaves helped to minimize negative changes in water balance. Also, there was substantial recovery after re-watering, hence the short-term water stress did not decrease avocado fruit size. Negative impacts might appear if the drought treatment were prolonged.
Post-Digital Connectivities: Framing Offline Encounters in a Digital Prospection Space
Authors: Lyons Agnieszka , Tagg Caroline
Published: February 2024

This paper explores the use of mobile technologies in facilitating offline encounters, through a post-digital lens which posits the digital not as new or disruptive but as a ubiquitous and accepted part of everyday social connectivities. In the paper, we explore ways in which migrants draw on jointly assembled semiotic repertoires, affordances, and constraints of the digital space, as well as cultural knowledge and spatial relating, to establish common ground and an interpretative framework for engaging in ensuing offline encounters. Drawing on an interactional analysis of data from a large linguistic ethnographic project, we focus on how a group of Polish immigrants who live in different parts of London bring their offline contexts and socially or culturally motivated expectations into their interactions to facilitate alignment in interactional frames in the context of limited familiarity with each other. Overall, our analysis points to the role of group messaging in creating a digital prospection space in which a joint frame of reference can be interactively constructed in anticipation of an offline encounter.
The collision between human rights and arbitration: the game of inconsistencies at the Court of Arbitration for Sport
Authors: Shahlaei Faraz
Published: February 2024

This article depicts a clash between arbitration and international human rights law (IHRL) norms. It discusses the IHRL aspects of cases arbitrated by the Court of Arbitration for Sport (CAS). Procedural and substantive IHRL claims are being increasingly raised before CAS. However, CAS panels seem to be inconsistent in dealing with the issue. This article analyses the jurisprudence of CAS to identify inconsistencies, chaos, and contradictions in its approach to human rights claims. It also offers several factors that may contribute to this contradictory treatment of IHRL claims by CAS panels including the flexible nature of arbitral proceedings, inadequate expertise in IHRL among counsel and arbitrators, and the possibility of favouritism towards sport governing bodies. It concludes that the inconsistencies and contradictions in CAS jurisprudence make it difficult to regard it as a truly effective remedy for violations of human rights and that reforms are needed if human rights claims are to be given due consideration and the mechanism can be viewed as an effective remedy.
Localization of the Submandibular Glands Using High-Frequency Ultrasound
Authors: Jiang Liya , Hu Jintian , Jia Ying , Zhou Hongru , Su Xueshang , Zhuang Jun , Yuan Li , Zheng Qiaoyuan , Chai Hongli
Published: February 2024

Background

Injecting botulinum toxin (BTX) into the submandibular glands (SMGs) can treat drooling symptoms in neurological diseases and improve the aesthetics of SMG hypertrophy and ptotic SMGs.

Objectives

This study aimed to define the size and position of the SMGs by high-frequency ultrasound, and to perform statistical analysis to improve the safety and accuracy of BTX injection therapy.

Methods

Neck ultrasonography with high-frequency ultrasound was performed on 214 volunteers. The length, height, and thickness of the SMGs, and the distance between the SMGs and the midline, the anterior border of the sternocleidomastoid, the mandible, and the surface were measured.

Results

The SMGs were almond-shaped with a mean [standard deviation] length of 33.7 [4.7] mm, a thickness of 13.3 [2.9] mm, and a height of 27.6 [6.0] mm. The length and height were significantly different between underage and youth groups. The size of the SMGs did not show any notable differences with increasing BMI; however, their depth, and the distance from the mandible, midline, and anterior border of the sternocleidomastoid increased. No significant differences were observed between the affected and healthy sides in patients with microtia, hemifacial microsomia, or cleft lip and palate.

Conclusions

Ultrasound provides more comprehensive information regarding the size and position of the SMGs, which can serve as a reference in BTX therapy and in the diagnosis of SMG diseases involving size alterations.

Level of Evidence: 4
Molecular basis and functional development of membrane-based microbial metabolism
Authors: Yamada Mamoru
Published: February 2024

My research interest has so far been focused on metabolisms related to the “membrane” of microorganisms, such as the respiratory chain, membrane proteins, sugar uptake, membrane stress and cell lysis, and fermentation. These basic metabolisms are important for the growth and survival of cell, and their knowledge can be used for efficient production of useful materials. Notable achievements in research on metabolisms are elucidation of the structure and function of membrane-bound glucose dehydrogenase as a primary enzyme in the respiratory chain, elucidation of ingenious expression regulation of several operons or by divergent promoters, elucidation of stress-induced programed-cell lysis and its requirement for survival during a long-term stationary phase, elucidation of molecular mechanism of survival at a critical high temperature, elucidation of thermal adaptation and its limit, isolation of thermotolerant fermenting yeast strains, and development of high-temperature fermentation and green energy production technologies. These achievements are described together in this review.
A comprehensive review of deep learning-based variant calling methods
Authors: Junjun Ren , Zhengqian Zhang , Ying Wu , Jialiang Wang , Yongzhuang Liu
Published: February 2024

Genome sequencing data have become increasingly important in the field of personalized medicine and diagnosis. However, accurately detecting genomic variations remains a challenging task. Traditional variation detection methods rely on manual inspection or predefined rules, which can be time-consuming and prone to errors. Consequently, deep learning–based approaches for variation detection have gained attention due to their ability to automatically learn genomic features that distinguish between variants. In our review, we discuss the recent advancements in deep learning–based algorithms for detecting small variations and structural variations in genomic data, as well as their advantages and limitations.
SpatialDDLS: an R package to deconvolute spatial transcriptomics data using neural networks
Authors: Mañanes Diego , Rivero-García Inés , Relaño Carlos , Torres Miguel , Sancho David , Jimenez-Carretero Daniel , Torroja Carlos , Sánchez-Cabo Fátima
Published: February 2024

Spatial transcriptomics has changed our way to study tissue structure and cellular organization. However, there are still limitations in its resolution, and most available platforms do not reach a single cell resolution. To address this issue, we introduce SpatialDDLS, a fast neural network-based algorithm for cell type deconvolution of spatial transcriptomics data. SpatialDDLS leverages single-cell RNA sequencing data to simulate mixed transcriptional profiles with predefined cellular composition, which are subsequently used to train a fully connected neural network to uncover cell type diversity within each spot. By comparing it with two state-of-the-art spatial deconvolution methods, we demonstrate that SpatialDDLS is an accurate and fast alternative to the available state-of-the art tools.

Availability and implementation

The R package SpatialDDLS is available via CRAN-The Comprehensive R Archive Network: https://CRAN.R-project.org/package=SpatialDDLS. A detailed manual of the main functionalities implemented in the package can be found at https://diegommcc.github.io/SpatialDDLS.
Tick-tock, racing the clock: parasitism is associated with decreased sprint performance in the Eastern fence lizard
Authors: Wild Kristoffer H , Gienger C M
Published: February 2024

Host–parasite relationships are important components of ecological systems that influence the evolution of both hosts and parasites. High levels of ectoparasitic infections can disrupt host homeostasis, causing adverse effects on health and performance. However, the effects of natural ectoparasite levels on host physiology are less understood, with most research designs implementing experimental or hormonal manipulations of hosts. In this study, we examined the interplay between tick parasitism and host characteristics on body condition and locomotor performance in Eastern fence lizards in natural settings. We found a higher frequency of tick infections in male lizards relative to females, with larger males being more likely to experience tick infection. Infected lizards had reduced locomotor performance, max sprint speed and 2-m run speed. Together this suggests an energetic trade-off between increased immune function and reduced locomotor performance, which is consistent with the immunocompetence–handicap hypothesis. Higher numbers of ticks on adult male lizards may be explained by age as well as the immunosuppressive effects of testosterone. Tick infection did not appear to reduce overall body condition of lizard hosts. Our findings shed light on the interplay between ectoparasitic infection, host characteristics, and locomotor performance under natural conditions. Such insights are crucial for understanding host–parasite dynamics and determining the trade-offs for hosts within ecological contexts.
Individualized treatment rule characterization via a value function surrogate
Authors: Freeman Nikki L B , Browder Sydney E , McGinigle Katharine L , Kosorok Michael R
Published: February 2024

Precision medicine is a promising framework for generating evidence to improve health and health care. Yet, a gap persists between the ever-growing number of statistical precision medicine strategies for evidence generation and implementation in real-world clinical settings, and the strategies for closing this gap will likely be context-dependent. In this paper, we consider the specific context of partial compliance to wound management among patients with peripheral artery disease. Using a Gaussian process surrogate for the value function, we show the feasibility of using Bayesian optimization to learn optimal individualized treatment rules. Further, we expand beyond the common precision medicine task of learning an optimal individualized treatment rule to the characterization of classes of individualized treatment rules and show how those findings can be translated into clinical contexts.
Clustering blood donors via mixtures of product partition models with covariates
Authors: Argiento Raffaele , Corradin Riccardo , Guglielmi Alessandra , Lanzarone Ettore
Published: February 2024

Motivated by the problem of accurately predicting gap times between successive blood donations, we present here a general class of Bayesian nonparametric models for clustering. These models allow for the prediction of new recurrences, accommodating covariate information that describes the personal characteristics of the sample individuals. We introduce a prior for the random partition of the sample individuals, which encourages two individuals to be co-clustered if they have similar covariate values. Our prior generalizes product partition models with covariates (PPMx) models in the literature, which are defined in terms of cohesion and similarity functions. We assume cohesion functions that yield mixtures of PPMx models, while our similarity functions represent the denseness of a cluster. We show that including covariate information in the prior specification improves the posterior predictive performance and helps interpret the estimated clusters in terms of covariates in the blood donation application.
Nonparametric predictive model for sparse and irregular longitudinal data
Authors: Wang Shixuan , Kim Seonjin , Ryan Cho Hyunkeun , Chang Won
Published: February 2024

We propose a kernel-based estimator to predict the mean response trajectory for sparse and irregularly measured longitudinal data. The kernel estimator is constructed by imposing weights based on the subject-wise similarity on L2 metric space between predictor trajectories, where we assume that an analogous fashion in predictor trajectories over time would result in a similar trend in the response trajectory among subjects. In order to deal with the curse of dimensionality caused by the multiple predictors, we propose an appealing multiplicative model with multivariate Gaussian kernels. This model is capable of achieving dimension reduction as well as selecting functional covariates with predictive significance. The asymptotic properties of the proposed nonparametric estimator are investigated under mild regularity conditions. We illustrate the robustness and flexibility of our proposed method via extensive simulation studies and an application to the Framingham Heart Study.
Intravenous gentamicin therapy induces functional type VII collagen in patients with recessive dystrophic epidermolysis bullosa: an open-label clinical trial
Authors: Woodley David T , Hao Michelle , Kwong Andrew , Levian Brandon , Cogan Jon , Hou Yingping , Mosallaei Daniel , Kleinman Elana , Zheng Kate , Chung Claire , Kim Gene , Peng David , Chen Mei
Published: February 2024

Background

Recessive dystrophic epidermolysis bullosa (RDEB) is an incurable widespread blistering skin disorder caused by mutations in the gene encoding for type VII collagen (C7), the major component of anchoring fibrils.

Objectives

To evaluate the efficacy and safety of intravenous (IV) gentamicin readthrough therapy in patients with RDEB harbouring nonsense mutations. The primary outcomes were increased expression of C7 in patients’ skin and safety assessments (ototoxicity, nephrotoxicity, autoimmune response); secondary outcomes included measuring wound healing in target wounds and assessment by a validated Epidermolysis Bullosa Disease Activity and Scarring Index (EBDASI) scoring system.

Methods

An open-label pilot trial to assess two different IV gentamicin regimens between August 2018 and March 2020 with follow-up through to 180 days post-treatment was carried out. Three patients with RDEB with confirmed nonsense mutations in COL7A1 in either one or two alleles and decreased baseline expression of C7 at the dermal–epidermal junction (DEJ) of their skin participated in the study. Three patients received gentamicin 7.5 mg kg–1 daily for 14 days and two of the three patients further received 7.5 mg kg–1 IV gentamicin twice weekly for 12 weeks. Patients who had pre-existing auditory or renal impairment, were currently using ototoxic or nephrotoxic medications, or had allergies to aminoglycosides or sulfate compounds were excluded.

Results

After gentamicin treatment, skin biopsies from all three patients (age range 18–28 years) exhibited increased C7 in their DEJ. With both regimens, the new C7 persisted for at least 6 months post-treatment. At 1 and 3 months post-treatment, 100% of the monitored wounds exhibited > 85% closure. Both IV gentamicin infusion regimens decreased EBDASI total activity scores. Of the patients assessed with the EBDASI, all exhibited decreased total activity scores 3 months post-treatment. All three patients completed the study; no adverse effects or anti-C7 antibodies were detected.

Conclusions

IV gentamicin induced the readthrough of nonsense mutations in patients with RDEB and restored functional C7 in their skin, enhanced wound healing and improved clinical parameters. IV gentamicin may be a safe, efficacious, low-cost and readily available treatment for this population of patients with RDEB.
Can diffusion tensor imaging unlock the secrets of the growth plate?
Authors: Kvist Ola , Santos Laura A , De Luca Francesca , Jaramillo Diego
Published: February 2024

“How tall will I be?” Every paediatrician has been asked this during their career. The growth plate is the main site of longitudinal growth of the long bones. The chondrocytes in the growth plate have a columnar pattern detectable by diffusion tensor imaging (DTI). DTI shows the diffusion of water in a tissue and whether it is iso- or anisotropic. By detecting direction and magnitude of diffusion, DTI gives information about the microstructure of the tissue. DTI metrics include tract volume, length, and number, fractional anisotropy (FA), and mean diffusivity. DTI metrics, particularly tract volume, provide quantitative data regarding skeletal growth and, in conjunction with the fractional anisotropy, be used to determine whether a growth plate is normal. Tractography is a visual display of the diffusion, depicting its direction and amplitude. Tractography gives a more qualitative visualization of cellular orientation in a tissue and reflects the activity in the growth plate. These two components of DTI can be used to assess the growth plate without ionizing radiation or pain. Further refinements in DTI will improve prediction of post-imaging growth and growth plate closure, and assessment of the positive and negative effect of treatments like cis-retinoic acid and growth hormone administration.
Unravelling the evolutionary history and promoting conservation genetics of Anadenanthera colubrina var. cebil (Leguminosae), a paradigmatic species in Seasonally Dry Tropical Forests
Authors: Zerda Moreira Andrea , García María Victoria , Barrandeguy María Eugenia
Published: February 2024

Seasonally Dry Tropical Forests (SDTFs) exhibit a patchy distribution throughout the Neotropics and are considered one of the most threatened tropical forests in the world. Nonetheless, their conservation has often been neglected in comparison to efforts directed towards other biomes. The distribution pattern of Anadenanthera colubrina (Vell.) Brenan var. cebil (Griseb) Altschul allows an adequate mapping of this biome. The main objectives of this work are to study the historical processes that determined the current distribution of A. colubrina var. cebil under the hypothesis that the demographic history of the remaining fragments of SDTFs in Argentina leads back to a single event of ancestral divergence, and identify Argentinean localities with priority for conservation. Plastid genetic diversity of A. colubrina var. cebil from northern Argentina is characterised using three plastid microsatellite loci. From this, genetic characterization, population genetics, and Bayesian inference were carried out. The results from approximate Bayesian computations show that the Misiones and Piedmont Subandean nuclei diverged from an ancestral population in the early Neogene while the Formosa population derived from the Misiones nucleus in the late Neogene. Two out of five locations from the Misiones nucleus and three of nine locations from the Subandean Piedmont nucleus are proposed as priority conservation areas.
Trends of fruit morphogenesis in Pandanaceae: comparative carpology of Freycinetia Gaudich
Authors: Bobrov Alexey V F Ch , Zdravchev Nikita S , Romanov Mikhail S , Iovlev Petr S , Mikhaylova Anna A , Kuptsov Kirill V , Timchenko Anton S , Vasekha Natalia D , Sorokin Alexey N
Published: February 2024

With the current reassessment of the phylogeny of Pandanales, revealing the peculiarities of fruit structure of representatives of the order, as well as determination of apomorphies and plesiomorphies of the families included in the order are of importance. With the aim to fill in gaps in the data on fruit structure and to determine principal trends of fruit morphogenesis in Pandanaceae, the present study focused on pericarp anatomy in the genus Freycinetia, fruits of which are traditionally referred to as berries. The present investigation confirmed the lack of a continuous sclerenchymatous zone in the pericarp of Freycinetia species, and the fruit is treated as a superior paracarpous berry of Nuphar type. Fusiform groups of longitudinally elongated sclereids are revealed in the mesocarp of Freycinetia palawanensis (incertae sedis) and F. graminifolia (section Solmsiella). Since this character is treated as specific for the subgenus Gaudichaudiella, the inclusion of these two studied species in this subgenus is proposed. The principal carpological plesiomorphies and apomorphies of the family are outlined, and two scenarios for fruit morphogenesis, from berries to ‘drupaceous’ fruits and vice versa, are proposed.
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

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

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 < 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

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 < 0.001}, more often underwent invasive coronary angiography (88% vs. 71%, P < 0.001) and percutaneous coronary intervention (72% vs. 45%, P < 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 < 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 < 0.001), more for STEMI patients (HR: 0.73, CI; 0.71–0.75, P < 0.001), but less significantly in NSTEMI patients (HR: 0.79, CI; 0.78–0.81, P < 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

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

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

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

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

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

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

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

Persons 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.