bluuebunny/crossref_metadata_2025_split huggingface dataset:
RNASeq Analysis for Accurate Identification of Fusion Partners in Tumor Specific Translocations Detected by Standard FISH Probes in Hematologic Malignancies
Authors: Koduru Prasad , Chen Weina , Fuda Franklin , Kaur Gurbakhash , Awan Farrukh , John Samuel , Garcia Rolando , Gagan Jeffrey 
Published: February 2024

Background: Fluorescence labeled DNA probes and in situ hybridization methods had shorter turn round time for results revolutionized their clinical application. Signals obtained from these probes are highly specific, yet they can produce fusion signals not necessarily representing fusion of actual genes due to other genes included in the probe design. In this study we evaluated discordance between cytogenetic, FISH and RNAseq results in 3 different patients with hematologic malignancies and illustrated the need to perform next generation sequencing (NGS) or RNASeq to accurately interpret FISH results. Methods: Bone marrow or peripheral blood karyotypes and FISH were performed to detect recurring translocations associated with hematologic malignancies in clinical samples routinely referred to our clinical cytogenetics laboratory. When required, NGS was performed on DNA and RNA libraries to detect somatic alterations and gene fusions in some of these specimens. Discordance in results between these methods is further evaluated. Results: For a patient with plasma cell leukemia standard FGFR3 / IGH dual fusion FISH assay detected fusion that was interpreted as FGFR3-positive leukemia, whereas NGS/RNASeq detected NSD2::IGH. For a pediatric acute lymphoblastic leukemia patient, a genetic diagnosis of PDGFRB-positive ALL was rendered because the PDGFRB break-apart probe detected clonal rearrangement, whereas NGS detected MEF2D::CSF1R. A MYC-positive B-prolymphocytic leukemia was rendered for another patient with a cytogenetically identified t(8;14) and MYC::IGH by FISH, whereas NGS detected a novel PVT1::RCOR1 not previously reported. Conclusions: These are 3 cases in a series of several other concordant results, nevertheless, elucidate limitations when interpreting FISH results in clinical applications, particularly when other genes are included in probe design. In addition, when the observed FISH signals are atypical, this study illustrates the necessity to perform complementary laboratory assays, such as NGS and/or RNASeq, to accurately identify fusion genes in tumorigenic translocations.
How I treat the co-occurrence of venous and arterial thromboembolism: anticoagulation, antiplatelet therapy, or both?
Authors: May Jori E. , Moll Stephan 
Published: February 2024

Abstract
Arterial and venous thromboses are classically considered distinct disease states, with arterial thrombosis mediated predominantly by platelets and therefore, treated with antiplatelet therapy, and venous thrombosis mediated by the plasmatic coagulation system and treated with anticoagulation. However, co-occurrence of arterial and venous events is common, and there is increasing evidence of shared risk factors and pathophysiologic overlap. This presents a management challenge: does the patient with venous and arterial thrombosis, require anticoagulation, antiplatelet therapy, or both? Herein, we present a structured approach to the evaluation and management of patients with venous thrombosis who are also at risk for or have a history of an arterial thromboembolic event. We emphasize the importance of defining the indications for antithrombotic therapy, as well as the evaluation of factors that influence both thrombotic and bleeding risk, including disorder-specific and patient-specific factors, as well as the inherent risk balance of antithrombotic therapy regimens. We illustrate this approach in 4 cases, discussing the unique considerations and recent updates in the management of venous thrombosis, acute noncardioembolic ischemic stroke, coronary artery disease and acute myocardial infarction, and peripheral artery disease after revascularization.
The influence of voxelotor on cerebral blood flow and oxygen extraction in pediatric sickle cell disease
Authors: Brothers Rowan O. , Turrentine Katherine B. , Akbar Mariam , Triplett Sydney , Zhao Hongting , Urner Tara M. , Goldman-Yassen Adam , Jones Richard A. , Knight-Scott Jack , Milla Sarah S. , Bai Shasha , Tang Amy , Brown R. Clark , Buckley Erin M. 
Published: February 2024

Abstract
Voxelotor is an inhibitor of sickle hemoglobin polymerization that is used to treat sickle cell disease. Although voxelotor has been shown to improve anemia, the clinical benefit on the brain remains to be determined. This study quantified the cerebral hemodynamic effects of voxelotor in children with sickle cell anemia (SCA) using noninvasive diffuse optical spectroscopies. Specifically, frequency-domain near-infrared spectroscopy combined with diffuse correlation spectroscopy were used to noninvasively assess regional oxygen extraction fraction (OEF), cerebral blood volume, and an index of cerebral blood flow (CBFi). Estimates of CBFi were first validated against arterial spin–labeled magnetic resonance imaging (ASL-MRI) in 8 children with SCA aged 8 to 18 years. CBFi was significantly positively correlated with ASL-MRI–measured blood flow (R2 = 0.651; P = .015). Next, a single-center, open-label pilot study was completed in 8 children with SCA aged 4 to 17 years on voxelotor, monitored before treatment initiation and at 4, 8, and 12 weeks (NCT05018728). By 4 weeks, both OEF and CBFi significantly decreased, and these decreases persisted to 12 weeks (both P &lt; .05). Decreases in CBFi were significantly correlated with increases in blood hemoglobin (Hb) concentration (P = .025), whereas the correlation between decreases in OEF and increases in Hb trended toward significance (P = .12). Given that previous work has shown that oxygen extraction and blood flow are elevated in pediatric SCA compared with controls, these results suggest that voxelotor may reduce cerebral hemodynamic impairments. This trial was registered at www.ClinicalTrials.gov as #NCT05018728.
How I treat ETP-ALL in children
Authors: Summers Ryan J. , Teachey David T. , Hunger Stephen P. 
Published: February 2024

Abstract
Early T-cell precursor acute lymphoblastic leukemia (ETP-ALL) is a unique subtype of immature T-cell ALL that was initially associated with a dramatically inferior prognosis compared with non-ETP T-cell ALL (Not-ETP) when it was first described in 2009. Analyses of larger patient cohorts treated with more contemporary regimens, however, have shown minimal survival differences between ETP and Not-ETP. In this manuscript, we use representative cases to explore therapeutic advances and address common clinical questions regarding the management of children, adolescents, and young adults with ETP-ALL. We describe our recommended treatment approach for a child or adolescent with newly diagnosed ETP-ALL, with an emphasis on the prognostic significance of induction failure and detectable minimal residual disease and the role of hematopoietic stem cell transplant in first remission. We discuss the interplay between the ETP immunophenotype and genomic markers of immaturity in T-cell ALL. Finally, we review novel therapeutic approaches that should be considered when managing relapsed or refractory ETP-ALL.
Distinct regulatory networks control toxin gene expression in elapid and viperid snakes
Authors: Modahl Cassandra M. , Han Summer Xia , van Thiel Jory , Vaz Candida , Dunstan Nathan L. , Frietze Seth , Jackson Timothy N. W. , Mackessy Stephen P. , Kini R. Manjunatha 
Published: February 2024

Abstract
Background
Venom systems are ideal models to study genetic regulatory mechanisms that underpin evolutionary novelty. Snake venom glands are thought to share a common origin, but there are major distinctions between venom toxins from the medically significant snake families Elapidae and Viperidae, and toxin gene regulatory investigations in elapid snakes have been limited. Here, we used high-throughput RNA-sequencing to profile gene expression and microRNAs between active (milked) and resting (unmilked) venom glands in an elapid (Eastern Brown Snake, Pseudonaja textilis), in addition to comparative genomics, to identify cis- and trans-acting regulation of venom production in an elapid in comparison to viperids (Crotalus viridis and C. tigris).

Results
Although there is conservation in high-level mechanistic pathways regulating venom production (unfolded protein response, Notch signaling and cholesterol homeostasis), there are differences in the regulation of histone methylation enzymes, transcription factors, and microRNAs in venom glands from these two snake families. Histone methyltransferases and transcription factor (TF) specificity protein 1 (Sp1) were highly upregulated in the milked elapid venom gland in comparison to the viperids, whereas nuclear factor I (NFI) TFs were upregulated after viperid venom milking. Sp1 and NFI cis-regulatory elements were common to toxin gene promoter regions, but many unique elements were also present between elapid and viperid toxins. The presence of Sp1 binding sites across multiple elapid toxin gene promoter regions that have been experimentally determined to regulate expression, in addition to upregulation of Sp1 after venom milking, suggests this transcription factor is involved in elapid toxin expression. microRNA profiles were distinctive between milked and unmilked venom glands for both snake families, and microRNAs were predicted to target a diversity of toxin transcripts in the elapid P. textilis venom gland, but only snake venom metalloproteinase transcripts in the viperid C. viridis venom gland. These results suggest differences in toxin gene posttranscriptional regulation between the elapid P. textilis and viperid C. viridis.

Conclusions
Our comparative transcriptomic and genomic analyses between toxin genes and isoforms in elapid and viperid snakes suggests independent toxin regulation between these two snake families, demonstrating multiple different regulatory mechanisms underpin a venomous phenotype.
Unique properties of titanium dioxide quantum dots assisted regulation of growth and biochemical parameters of Hibiscus sabdariffa plants
Authors: Abdelhameed Reda E. , Abdalla Hanan , Ibrahim Manar A. 
Published: February 2024

AbstractOwing to the uniqueness of quantum dots (QDs) as a potential nanomaterial for agricultural application, hence in the present study, titanium dioxide quantum dots (TiO2 QDs) were successfully synthesized via sol-gel technique and the physico-chemical properties of the prepared TiO2 QDs were analyzed. Based on the results, the TiO2 QDs showed the presence of anatase phase of TiO2. TEM examination revealed spherical QDs morphology with an average size of 7.69 ± 1.22 nm. The large zeta potential value (-20.9 ± 2.3 mV) indicate greater stability of the prepared TiO2 QDs in aqueous solutions. Moreover, in this work, the application of TiO2 QDs on Hibiscus sabdariffa plants was conducted, where H. sabdariffa plants were foliar sprayed twice a week in the early morning with different concentrations of TiO2 QDs (0, 2, 5, 10, 15 and 30 ppm) to evaluate their influence on these plants in terms of morphological indexes and biochemical parameters. The results exhibited an increasing impact of the different used concentrations of TiO2 QDs on morphological indexes, such as fresh weight, dry weight, shoot length, root length, and leaf number, and physio-biochemical parameters like chlorophyll a, chlorophyll b, carotenoid contents, total pigments and total phenolic contents. Remarkably, the most prominent result was recorded at 15 ppm TiO2 QDs where plant height, total protein and enzymatic antioxidants like catalase and peroxidase were noted to increase by 47.6, 20.5, 29.5 and 38.3%, respectively compared to control. Therefore, foliar spraying with TiO2 QDs positively serves as an effective strategy for inducing optimistic effects in H. sabdariffa plants.
Impact of body mass index on long-term outcomes in patients undergoing percutaneous coronary intervention stratified by diabetes mellitus: a retrospective cohort study
Authors: Rao Chongyou , Zhong Qin , Wu Rilige , Li Zongren , Duan Yongjie , Zhou You , Wang Chi , Chen Xu , Wang Ruiqing , He Kunlun 
Published: February 2024

Abstract
Background
Patients with diabetes mellitus (DM) caused by obesity have increased in recent years. The impact of obesity on long-term outcomes in patients undergoing percutaneous coronary intervention (PCI) with or without DM remains unclear.

Methods
We retrospectively analysed data from 1918 patients who underwent PCI. Patients were categorized into four groups based on body mass index (BMI, normal weight: BMI < 25 kg/m2; overweight and obese: BMI ≥ 25 kg/m2) and DM status (presence or absence). The primary endpoint was the occurrence of major adverse cardiac and cerebrovascular events (MACCE; defined as all-cause death, myocardial infarction, stroke, and unplanned repeat revascularization).

Results
During a median follow-up of 7.0 years, no significant differences in MACCE, myocardial infarction, or stroke were observed among the four groups. Overweight and obese individuals exhibited lower all-cause mortality rates compared with normal-weight patients (without DM: hazard ratio [HR]: 0.54, 95% confidence interval [CI]: 0.37 to 0.78; with DM: HR: 0.57, 95% CI: 0.38 to 0.86). In non-diabetic patients, the overweight and obese group demonstrated a higher risk of unplanned repeat revascularization than the normal-weight group (HR:1.23, 95% CI:1.03 to 1.46). After multivariable adjustment, overweight and obesity were not significantly associated with MACCE, all-cause death, myocardial infarction, stroke, or unplanned repeat revascularization in patients with and without diabetes undergoing PCI.

Conclusion
Overweight and obesity did not demonstrate a significant protective effect on long-term outcomes in patients with and without diabetes undergoing PCI.
How do quantitative studies involving people with dementia report experiences of standardised data collection? A narrative synthesis of NIHR published studies
Authors: Gridley Kate , Baxter Kate , Birks Yvonne 
Published: February 2024

Abstract
Background
People with dementia are routinely included as research participants in trials and other quantitative studies in which they are invited to respond to standardised measures. This paper reviews the reporting of standardised data collection from people with dementia in reports published in the National Institute for Health and Care Research (NIHR) Journals Library. The aim was to understand how the administration of standardised, self-report measures with people with dementia is reported in NIHR monographs and what could be learnt from this about the feasibility and acceptability of data collection approaches for future studies.

Methods
This was a systematic review with narrative synthesis. Broad search terms (Dementia OR Alzheimer*) were used to search the NIHR Journals Library website in December 2021. All studies that used (or intended to use) standardised measures to collect research data directly from people with dementia were eligible for inclusion. Information was extracted (where reported) on the process of data collection, dementia severity, levels of missing data and the experiences and reflections of those involved.

Results
Searches returned 42 records, from which 17 reports were assessed as eligible for inclusion, containing 22 studies. Response rates from participants with dementia in these studies varied considerably and appeared to be related to dementia severity and place of residence. Little information was reported on the process of data collection or the reasons for missing data, and most studies did not report the experiences of participants or those administering the measures. However, there was an indication from two studies that standardised data collection could provoke emotional distress in some participants with dementia.

Conclusions
Through this review we identified both variation in levels of missing data and gaps in reporting which make it difficult to ascertain the reasons for this variation. We also identified potential risks to the well-being of participants with dementia which may be associated with the content of standardised measures and the context of data collection. Open reporting of and reflection upon data collection processes and the experiences of people involved is essential to ensure both the success of future data collection and the wellbeing of study participants.

Trial registration
Registered with Research on Research https://ror-hub.org/study/2905/.
Comparing Bayesian hierarchical meta-regression methods and evaluating the influence of priors for evaluations of surrogate endpoints on heterogeneous collections of clinical trials
Authors: Collier Willem , Haaland Benjamin , Inker Lesley A. , Heerspink Hiddo J.L. , Greene Tom 
Published: February 2024

Abstract
Background
Surrogate endpoints, such as those of interest in chronic kidney disease (CKD), are often evaluated using Bayesian meta-regression. Trials used for the analysis can evaluate a variety of interventions for different sub-classifications of disease, which can introduce two additional goals in the analysis. The first is to infer the quality of the surrogate within specific trial subgroups defined by disease or intervention classes. The second is to generate more targeted subgroup-specific predictions of treatment effects on the clinical endpoint.

Methods
Using real data from a collection of CKD trials and a simulation study, we contrasted surrogate endpoint evaluations under different hierarchical Bayesian approaches. Each approach we considered induces different assumptions regarding the relatedness (exchangeability) of trials within and between subgroups. These include partial-pooling approaches, which allow subgroup-specific meta-regressions and, yet, facilitate data adaptive information sharing across subgroups to potentially improve inferential precision. Because partial-pooling models come with additional parameters relative to a standard approach assuming one meta-regression for the entire set of studies, we performed analyses to understand the impact of the parameterization and priors with the overall goals of comparing precision in estimates of subgroup-specific meta-regression parameters and predictive performance.

Results
In the analyses considered, partial-pooling approaches to surrogate endpoint evaluation improved accuracy of estimation of subgroup-specific meta-regression parameters relative to fitting separate models within subgroups. A random rather than fixed effects approach led to reduced bias in estimation of meta-regression parameters and in prediction in subgroups where the surrogate was strong. Finally, we found that subgroup-specific meta-regression posteriors were robust to use of constrained priors under the partial-pooling approach, and that use of constrained priors could facilitate more precise prediction for clinical effects in trials of a subgroup not available for the initial surrogacy evaluation.

Conclusion
Partial-pooling modeling strategies should be considered for surrogate endpoint evaluation on collections of heterogeneous studies. Fitting these models comes with additional complexity related to choosing priors. Constrained priors should be considered when using partial-pooling models when the goal is to predict the treatment effect on the clinical endpoint.
Group sequential designs for pragmatic clinical trials with early outcomes: methods and guidance for planning and implementation
Authors: Parsons Nick R. , Basu Joydeep , Stallard Nigel 
Published: February 2024

Abstract
Background
Group sequential designs are one of the most widely used methodologies for adaptive design in randomized clinical trials. In settings where early outcomes are available, they offer large gains in efficiency compared to a fixed design. However, such designs are underused and used predominantly in therapeutic areas where there is expertise and experience in implementation. One barrier to their greater use is the requirement to undertake simulation studies at the planning stage that require considerable knowledge, coding experience and additional costs. Based on some modest assumptions about the likely patterns of recruitment and the covariance structure of the outcomes, some simple analytic expressions are presented that negate the need to undertake simulations.

Methods
A model for longitudinal outcomes with an assumed approximate multivariate normal distribution and three contrasting simple recruitment models are described, based on fixed, increasing and decreasing rates. For assumed uniform and exponential correlation models, analytic expressions for the variance of the treatment effect and the effects of the early outcomes on reducing this variance at the primary outcome time-point are presented. Expressions for the minimum and maximum values show how the correlations and timing of the early outcomes affect design efficiency.

Results
Simulations showed how patterns of information accrual varied between correlation and recruitment models, and consequentially to some general guidance for planning a trial. Using a previously reported group sequential trial as an exemplar, it is shown how the analytic expressions given here could have been used as a quick and flexible planning tool, avoiding the need for extensive simulation studies based on individual participant data.

Conclusions
The analytic expressions described can be routinely used at the planning stage of a putative trial, based on some modest assumptions about the likely number of outcomes and when they might occur and the expected recruitment patterns. Numerical simulations showed that these models behaved sensibly and allowed a range of design options to be explored in a way that would have been difficult and time-consuming if the previously described method of simulating individual trial participant data had been used.