bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Quantile-Conserving Ensemble Filter Framework. Part II: Regression of Observation Increments in a Probit and Probability Integral Transformed Space
Authors: Anderson Jeffrey L. 
Published: July 2023

Abstract
Traditional ensemble Kalman filter data assimilation methods make implicit assumptions of Gaussianity and linearity that are strongly violated by many important Earth system applications. For instance, bounded quantities like the amount of a tracer and sea ice fractional coverage cannot be accurately represented by a Gaussian that is unbounded by definition. Nonlinear relations between observations and model state variables abound. Examples include the relation between a remotely sensed radiance and the column of atmospheric temperatures, or the relation between cloud amount and water vapor quantity. Part I of this paper described a very general data assimilation framework for computing observation increments for non-Gaussian prior distributions and likelihoods. These methods can respect bounds and other non-Gaussian aspects of observed variables. However, these benefits can be lost when observation increments are used to update state variables using the linear regression that is part of standard ensemble Kalman filter algorithms. Here, regression of observation increments is performed in a space where variables are transformed by the probit and probability integral transforms, a specific type of Gaussian anamorphosis. This method can enforce appropriate bounds for all quantities and deal much more effectively with nonlinear relations between observations and state variables. Important enhancements like localization and inflation can be performed in the transformed space. Results are provided for idealized bivariate distributions and for cycling assimilation in a low-order dynamical system. Implications for improved data assimilation across Earth system applications are discussed.
Uprising on the Dance Floor: New Chilean Pop and Protest in Postdictatorship Chile
Authors: Simonetto Patricio , Shalloe Thomas 
Published: July 2023

New Chilean Pop catalyzed and reinforced a queer exploration of social exclusion, an alternative and sometimes a counter culture. An analysis of Javiera Mena and Álex Anwandter’s music and filmography reveals a musical scene that has been led by queer and feminist artists whose work has evolved alongside national social movements and a counter-telling of the political, social, cultural, and economic legacy of Augusto Pinochet’s bloody regime (1973–1990). El Nuevo Pop Chileno catalizó y reforzó una exploración queer de la exclusión social, así como una cultura alternativa y, a veces, contracultural. Un análisis de la música y filmografía de Javiera Mena y Álex Anwandter revela una escena musical que ha sido liderada por artistas queer y feministas cuyo trabajo ha evolucionado junto con los movimientos sociales nacionales y una contranarrativa del legado político, social, cultural y económico del sangriento régimen de Augusto Pinochet (1973–1990).
Left atrium volume and ventricular volume ratio algorithm as indication of pulmonary hypertension etiology
Authors: Granot Yoav , Ziv-Baran Tomer , Berliner Shlomo , Topilsky Yan , Aviram Galit 
Published: July 2023

Background Pressure overload of the right heart (pulmonary hypertension [PH]) can be an acute or a chronic process with various pathophysiologic changes affecting the dimensions of the heart chambers. The automatic four-chamber volumetric analysis tool is now available to measure the volume of the cardiac chambers in patients undergoing a computed tomography pulmonary angiogram (CTPA). Purpose To characterize the volumetric changes that occurred in response to increased systolic pulmonary arterial pressures (sPAP) in acute events, such as acute pulmonary embolism (APE), compared with other etiologies. Material and Methods Consecutive patients who underwent CTPA and echocardiography within 24 h between 2011 and 2015 were included. Differences in cardiac chamber volumes were investigated in correlation to the patients’ sPAP. Results The final cohort of 961 patients included 221 (23%) patients diagnosed with APE. The right (RV) to left (LV) ventricular volume ratio (VVR) was higher, while the left atrial (LA) volume index was smaller ( P < 0.001) in the patients with APE. A decision tree for the prediction of APE showed that an RV to left VVR >2.8 was characteristic of APE, whereas an LA volume index >37.5 mL/m² was more compatible with PH due to other etiologies ( P < 0.001). Conclusion The combination of VVR and LA volume index may help in differentiating between APE and chronic PH. CTPA-based volumetric information may be used to help clarify the underlying etiology of the dyspnea.
Bringing therapy home: Exploring parents’ experiences of telehealth for children with developmental coordination disorder
Authors: Bourke Aisling , O’Connor Una , Boyle Bryan , Kennedy Jessica , Lynch Helen 
Published: July 2023

Introduction: Developmental coordination disorder (DCD) significantly impacts a child’s motor skills and ability to learn and perform self-care and academic tasks. Telehealth is a rapidly emerging service delivery model, ensuring expanded access to services and continuity of care. Many benefits to the use of telehealth have been identified; yet, there is a dearth of published evidence available on the experiences of parents of children with DCD. Aim: The aim of this study was to explore parents’ experiences of implementing a telehealth motor skills programme for their child with DCD. Method: This study utilised a qualitative descriptive approach to best capture parents’ experiences of a telehealth programme. Data were collected through in-depth, semi-structured interviews with eight participants and analysed using thematic analysis. Measures to ensure the trustworthiness of the study were observed within the naturalistic paradigm comprising criteria of credibility, transferability, dependability and confirmability. Findings: This study uncovered three major themes: (1) Parents in the dark, (2) telehealth in the family and (3) telehealth: what success looks like. Ten further subthemes highlighted the factors for success and parents’ considerations for future service delivery. Conclusion: Challenges for parents in accessing traditional occupational therapy services present an opportunity to explore alternative means of delivery such as telehealth. Parents, however, are clear in their preference for a blended approach for future services.
Vascular Endothelial Growth Factor as Potential Biomarker for COVID-19 Severity
Authors: Josuttis David , Schwedler Christian , Heymann Guido , Gümbel Denis , Schmittner Marc Dominik , Kruse Marianne , Hoppe Berthold 
Published: July 2023

Introduction COVID-19 is characterized by immunological responses to viral replication and coherent with endothelitis, microvascular disturbance of lung vasculature and coagulopathy. Vascular Endothelial Growth Factor (VEGF) is a proangiogenic mediator regulating endothelial changes. It is induced by proinflammatory signaling and hypoxia. We sought to determine whether VEGF levels differ between SARS-CoV-2-positive patients of different disease severity and whether VEGF might be useful in risk stratification. Methods After retrospective screening of all SARS-CoV-2-positive patients treated in Unfallkrankenhaus Berlin in 2020, we included those with documented VEGF measurement. We extracted laboratory values and clinical parameters. An exploratory data analysis was performed to detect possible relations between VEGF level and clinical disease features. Results We included 167 SARS-CoV-2-positive patients of which 139 suffered from COVID-19. Seventy-one of the COVID-19 patients had to be treated in the intensive care unit (ICU), those patients exhibited higher VEGF levels than those being admitted to normal wards (535 vs 279 pg/L, P < .001). APACHE-2 (Acute Physiology And Chronic Health Evaluation Score) correlated with mortality and patients with high values showed higher VEGF concentrations on admission (456 vs 875 pg/L, p = 0.006). Receiver operating characteristic analytic revealed that the occurrence of organ dysfunctions like acute respiratory distress syndrome (ARDS), shock, or acute kidney injury could be predicted by VEGF. It was significantly higher in patients who later died compared to survivors (637 vs 389 pg/mL, P = 0.041) and predicted mortality with same accuracy as established markers. In our cohort, association of VEGF above 277 pg/L on admission with risk of ARDS could be confirmed in logistic regression adjusting for possible confounding factors (odds ratio 3.1, 95% confidence interval: 1.34-7.7). Discussion Even though there are several limitations to this retrospective study it revealed that in COVID-19 patients VEGF can contribute to the prediction of necessity of ICU, mortality and the prediction of ARDS, kidney injury or shock. Its use in risk stratification and potential pathogenetic involvement should be further investigated.
Maxillary Arch Dimensions in Children with Unilateral Cleft Lip and Palate Receiving Alveolar Bone Grafting
Authors: van Stein Callenfels Dewi M.E. , Bos Annemieke , Jonkman Ronald E.G. 
Published: July 2023

Objective To analyse the maxillary arch dimensions of children aged 9 and 12 with unilateral cleft lip and palate (UCLP) who received orthodontic treatment and secondary alveolar bone grafting. Design This retrospective cohort study was performed on 30 patients with UCLP. Setting All patients were treated at the Cleft Lip and Palate Centre, which is part of the University Medical Centre Amsterdam and Academic Centre for Dentistry Amsterdam, the Netherlands. Patients/Participants Children with non-syndromic UCLP who received pre- and postsurgical orthodontics combined with secondary alveolar bone grafting between the ages of 9 and 12 years were included. Main Outcome Measures Maxillary arch dimensions were assessed on 60 digitised dental casts with measurements of the intermolar widths, interpremolar widths, arch perimeters, arch lengths, arch widths, and palatal depths. Results The results of a paired-samples t-test revealed a statistically significant increase ( P < .05) in intermolar width 1, intermolar width 3, interpremolar width 1, arch perimeter, and arch width between the ages of 9 (T0) and 12 (T1). Intermolar width 2 and the palatal depth decreased statistically significantly between T0 and T1. Conclusions Analysis of maxillary arch dimensions of children with UCLP indicates significant changes between 9 and 12 years of age. This suggests that orthodontic treatment and secondary alveolar bone grafting can be effective in improving maxillary arch dimensions. However, there is a need for collaborative research and data collection in order to provide sensible and evidence-based care to patients with cleft lip and palate.
Germ line variants in patients with acute myeloid leukemia without a suspicion of hereditary hematologic malignancy syndrome
Authors: Guijarro Francesca , López-Guerra Monica , Morata Jordi , Bataller Alex , Paz Sara , Cornet-Masana Josep Maria , Banús-Mulet Antònia , Cuesta-Casanovas Laia , Carbó Josep Maria , Castaño-Díez Sandra , Jiménez-Vicente Carlos , Cortés-Bullich Albert , Triguero Ana , Martínez-Roca Alexandra , Esteban Daniel , Gómez-Hernando Marta , Álamo Moreno José Ramón , López-Oreja Irene , Garrote Marta , Risueño Ruth M. , Tonda Raúl , Gut Ivo , Colomer Dolors , Díaz-Beya Marina , Esteve Jordi 
Published: July 2023

Abstract
Germ line predisposition in acute myeloid leukemia (AML) has gained attention in recent years because of a nonnegligible frequency and an impact on management of patients and their relatives. Risk alleles for AML development may be present in patients without a clinical suspicion of hereditary hematologic malignancy syndrome. In this study we investigated the presence of germ line variants (GVs) in 288 genes related to cancer predisposition in 47 patients with available paired, tumor-normal material, namely bone marrow stroma cells (n = 29), postremission bone marrow (n = 17), and saliva (n = 1). These patients correspond to 2 broad AML categories with heterogeneous genetic background (AML myelodysplasia related and AML defined by differentiation) and none of them had phenotypic abnormalities, previous history of cytopenia, or strong cancer aggregation. We found 11 pathogenic or likely pathogenic variants, 6 affecting genes related to autosomal dominant cancer predisposition syndromes (ATM, DDX41, and CHEK2) and 5 related to autosomal recessive bone marrow failure syndromes (FANCA, FANCM, SBDS, DNAJC21, and CSF3R). We did not find differences in clinical characteristics nor outcome between carriers of GVs vs noncarriers. Further studies in unselected AML cohorts are needed to determine GV incidence and penetrance and, in particular, to clarify the role of ATM nonsense mutations in AML predisposition.
Nonrestrictive diet does not increase infections during post-HSCT neutropenia: data from a multicenter randomized trial
Authors: Stella Federico , Marasco Vincenzo , Levati Giorgia Virginia , Guidetti Anna , De Filippo Annamaria , Pennisi Martina , Vismara Cecilia , Miceli Rosalba , Ljevar Silva , Tecchio Cristina , Mordini Nicola , Gobbi Giorgia , Saracino Lucia , Corradini Paolo 
Published: July 2023

Abstract
Infections are a major cause of morbidity and mortality during neutropenia after hematopoietic stem cell transplantation (HSCT). The use of a low-microbial protective diet (PD) in the peritransplantation period is a standard of care, although its efficacy has never been tested prospectively. We conducted a multicenter, randomized, noninferiority trial, enrolling all consecutive adult patients undergoing high-dose induction chemotherapy or HSCT with the objective to compare nonrestrictive diet (NRD) vs PD. Overall, 222 patients were enrolled, randomly assigned, and analyzed. One hundred seventy-five subjects (79%) received autologous HSCT (auto-HSCT), 41 (18%) received allogeneic HSCT (allo-HSCT), and 6 (3%) patients received high-dose induction chemotherapy. There was no significant difference in terms of incidence of grade ≥2 infections and death during neutropenia in the 2 arms. In multivariable analysis, only multiple myeloma diagnosis, fluoroquinolone prophylaxis, and the absence of mucositis were associated with a lower incidence of grade ≥2 infections. We did not report any significant variation in terms of hospitalization length, incidence of mucositis and gastrointestinal infections, body weight, and serum albumin variations in the 2 arms. In allo-HSCT recipients, the incidence of acute graft-versus-host disease grade ≥3 was similar. NRD was associated with higher patient-reported satisfaction. In conclusion, NRD is not inferior to a traditional PD during neutropenia after HSCT, and our results demonstrated that implementing a restrictive diet unnecessary burdens patients' quality of life. The clinical trial was registered prospectively in the clinical trial registry of the Istituto Nazionale dei Tumori of Milan as INT54/16.
MTG-Link: leveraging barcode information from linked-reads to assemble specific loci
Authors: Guichard Anne , Legeai Fabrice , Tagu Denis , Lemaitre Claire 
Published: July 2023

Abstract
Background
Local assembly with short and long reads has proven to be very useful in many applications: reconstruction of the sequence of a locus of interest, gap-filling in draft assemblies, as well as alternative allele reconstruction of large Structural Variants. Whereas linked-read technologies have a great potential to assemble specific loci as they provide long-range information while maintaining the power and accuracy of short-read sequencing, there is a lack of local assembly tools for linked-read data.

Results
We present MTG-Link, a novel local assembly tool dedicated to linked-reads. The originality of the method lies in its read subsampling step which takes advantage of the barcode information contained in linked-reads mapped in flanking regions. We validated our approach on several datasets from different linked-read technologies. We show that MTG-Link is able to assemble successfully large sequences, up to dozens of Kb. We also demonstrate that the read subsampling step of MTG-Link considerably improves the local assembly of specific loci compared to other existing short-read local assembly tools. Furthermore, MTG-Link was able to fully characterize large insertion variants and deletion breakpoints in a human genome and to reconstruct dark regions in clinically-relevant human genes. It also improved the contiguity of a 1.3 Mb locus of biological interest in several individual genomes of the mimetic butterfly Heliconius numata.

Conclusions
MTG-Link is an efficient local assembly tool designed for different linked-read sequencing technologies. MTG-Link source code is available at https://github.com/anne-gcd/MTG-Link and as a Bioconda package.
Chimeras in Merlot grapevine revealed by phased assembly
Authors: Sichel V. , Sarah G. , Girollet N. , Laucou V. , Roux C. , Roques M. , Mournet P. , Cunff L. Le , Bert P.F. , This P. , Lacombe T. 
Published: July 2023

AbstractChimerism is the phenomenon when several genotypes coexist in a single individual. Used to understand plant ontogenesis they also have been valorised through new cultivar breeding. Viticulture has been taking economic advantage out of chimeras when the variant induced an important modification of wine type such as berry skin colour. Crucial agronomic characters may also be impacted by chimeras that aren’t identified yet. Periclinal chimera where the variant has entirely colonised a cell layer is the most stable and can be propagated through cuttings. In grapevine, leaves are derived from both meristem layers, L1 and L2. However, lateral roots are formed from the L2 cell layer only. Thus, comparing DNA sequences of roots and leaves allows chimera detection. In this study we used new generation Hifi long reads sequencing, recent bioinformatics tools and trio-binning with parental sequences to detect periclinal chimeras on ‘Merlot’ grapevine cultivar. Sequencing of cv. ‘Magdeleine Noire des Charentes’ and ‘Cabernet Franc’, the parents of cv. ‘Merlot’, allowed haplotype resolved assembly. Pseudomolecules were built with a total of 33 to 47 contigs and in few occasions a unique contig for one chromosome. This high resolution allowed haplotype comparison. Annotation was transferred from PN40024 VCost.v3 to all pseudomolecules. After strong selection of variants, 51 and 53 ‘Merlot’ specific periclinal chimeras were found on the Merlot-haplotype-CF and Merlot-haplotype-MG respectively, 9 and 7 been located in a coding region. A subset of positions was analysed using Molecular Inversion Probes (MIPseq) and 69% were unambiguously validated, 25% are doubtful because of technological noise or weak depth and 6% invalidated. These results open new perspectives on chimera detection as an important resource to improve cultivars through clonal selection or breeding.
Shocked to death: a case report of cardiogenic shock and death following electrocardioversion for atrial fibrillation
Authors: Hashem Anas Mohamad , Al Ali Omar , Khalouf Amani , Shehadah Ahmed , Mohammed Moghniuddin , Mahmoud Amir , Laguio-Vila Maryrose , Rao Mohan 
Published: July 2023

Abstract
Background
Atrial fibrillation (AF) is prevalent, especially in patients with heart failure. Their prevalence increases with age and both conditions are interrelated. Electrocardioversion (ECV) is considered a safe and effective procedure and is among one of the recommended therapies to terminate AF back to normal sinus rhythm. Our study highlights one of the rare complications following ECV.

Case summary
A 71-year-old female with a history of atrial fibrillation underwent electrocardioversion and developed sudden onset of ventricular stunning resulting in refractory cardiogenic shock. She was treated with mechanical cardiac support including IABP and Impella. Both provided minimal support then rapid clinical deterioration happened leading to imminent death.

Conclusion
Patients with atrial fibrillation and heart failure treated with electrocardioversion might develop refractory cardiogenic shock and death as a complication of this procedure.
Frequency and impact of medication reviews for people aged 65 years or above in UK primary care: an observational study using electronic health records
Authors: Joseph Rebecca M. , Knaggs Roger D. , Coupland Carol A. C. , Taylor Amelia , Vinogradova Yana , Butler Debbie , Gerrard Louisa , Waldram David , Iyen Barbara , Akyea Ralph K. , Ashcroft Darren M. , Avery Anthony J. , Jack Ruth H. 
Published: July 2023

Abstract
Background
Medication reviews in primary care provide an opportunity to review and discuss the safety and appropriateness of a person’s medicines. However, there is limited evidence about access to and the impact of routine medication reviews for older adults in the general population, particularly in the UK. We aimed to quantify the proportion of people aged 65 years and over with a medication review recorded in 2019 and describe changes in the numbers and types of medicines prescribed following a review.

Methods
We used anonymised primary care electronic health records from the UK’s Clinical Practice Research Datalink (CPRD GOLD) to define a population of people aged 65 years or over in 2019. We counted people with a medication review record in 2019 and used Cox regression to estimate associations between demographic characteristics, diagnoses, and prescribed medicines and having a medication review. We used linear regression to compare the number of medicines prescribed as repeat prescriptions in the three months before and after a medication review. Specifically, we compared the ‘prescription count’ - the maximum number of different medicines with overlapping prescriptions people had in each period.

Results
Of 591,726 people prescribed one or more medicines at baseline, 305,526 (51.6%) had a recorded medication review in 2019. Living in a care home (hazard ratio 1.51, 95% confidence interval 1.40-1.62), medication review in the previous year (1.83, 1.69-1.98), and baseline prescription count (e.g. 5-9 vs 1 medicine 1.41, 1.37-1.46) were strongly associated with having a medication review in 2019. Overall, the prescription count tended to increase after a review (mean change 0.13 medicines, 95% CI 0.12-0.14).

Conclusions
Although medication reviews were commonly recorded for people aged 65 years or over, there was little change overall in the numbers and types of medicines prescribed following a review. This study did not examine whether the prescriptions were appropriate or other metrics, such as dose or medicine changes within the same class. However, by examining the impact of medication reviews before the introduction of structured medication review requirements in England in 2020, it provides a useful benchmark which these new reviews can be compared with.