bluuebunny/crossref_metadata_2025 huggingface dataset:
Impact of cancer diagnosis on distribution and trends of cardiovascular hospitalizations in the USA between 2004 and 2017
Authors: Kobo Ofer , Raisi-Estabragh Zahra , Gevaert Sofie , Rana Jamal S , Van Spall Harriette G C , Roguin Ariel , Petersen Steffen E , Ky Bonnie , Mamas Mamas A
Published: August 2022

Background and aims

There is limited data on temporal trends of cardiovascular hospitalizations and outcomes amongst cancer patients. We describe the distribution, trends of admissions, and in-hospital mortality associated with key cardiovascular diseases among cancer patients in the USA between 2004 and 2017.

Methods

Using the Nationwide Inpatient Sample we, identified admissions with five cardiovascular diseases of interest: acute myocardial infarction (AMI), pulmonary embolism (PE), ischaemic stroke, heart failure, atrial fibrillation (AF) or atrial flutter, and intracranial haemorrhage. Patients were stratified by cancer status and type. We estimated crude annual rates of hospitalizations and annual in-hospital all-cause mortality rates.

Results

From >42.5 million hospitalizations with a primary cardiovascular diagnosis, 1.9 million (4.5%) had a concurrent record of cancer. Between 2004 and 2017, cardiovascular admission rates increased by 23.2% in patients with cancer, whilst decreasing by 10.9% in patients without cancer. The admission rate increased among cancer patients across all admission causes and cancer types except prostate cancer. Patients with haematological (9.7–13.5), lung (7.4–8.9), and GI cancer (4.6–6.3) had the highest crude rates of cardiovascular hospitalizations per 100 000 US population. Heart failure was the most common reason for cardiovascular admission in patients across all cancer types, except GI cancer (crude admission rates of 13.6–16.6 per 100 000 US population for patients with cancer).

Conclusions

In contrast to declining trends in patients without cancer, primary cardiovascular admissions in patients with cancer is increasing. The highest admission rates are in patients with haematological cancer, and the most common cause of admission is heart failure.
Thinking with Spirits, or Dwelling and Knowing in the Work of Aimé Césaire
Authors: Allen-Paisant Jason
Published: August 2022

This article discusses Aimé Césaire’s ethical commitment to more-than-human existence. The intention is not to read Césaire as an ‘eco-poet’, or through the lens of contemporary ‘eco-poetics’, terms which might not have meant much to him in the period from the 1930s to the 1950s, when his poetic project took shape. Even if we may today read Césaire’s poetry in the light of contemporary eco-poetic and eco-philosophical thought, this article is more concerned with examining in his work a set of epistemological viewpoints that take shape around poetry and which reveal the essence of an ethical position concerning the human’s relationship to the natural world. These ethical questions are central to Césaire’s understanding of what Négritude was to be, and, more broadly, to his critique of imperialism and colonialism. The article therefore shows how Césaire’s poetics of creativity and ethics in relation to non-human life develops in interaction with history. If the idea of poetry as possession is the glue that connects all of these ideas, it is because it shows the way they are animated by an African ‘animist’ sensibility that unites the sacred and the secular and intertwines mind and thought with nature.
Cancer as a death sentence: developing an initial program theory for an IVR intervention
Authors: Ilozumba Onaedo , Kabukye Johnblack , de Keizer Nicolet , Cornet Ronald , Broerse Jacqueline E W
Published: August 2022

To address current trends in poor health-seeking behaviour and late cancer diagnosis in many low- and middle-income countries, like Uganda, it is important to explore innovative awareness building interventions. One possible intervention is a common digital format, an interactive voice response (IVR) system, which is suitable for individuals with low technological and reading literacy. It is increasingly acknowledged that developing digital interventions requires co-creation with relevant stakeholders and explication of program developers’ assumptions, to make them effective, sustainable, and scalable. To this end, we sought to develop an initial program theory for a co-created IVR system for cancer awareness in Uganda. Utilising principles of the realist approach, a qualitative exploratory study was conducted through seven focus group discussions (FGDs) with people living with cancer (PLWC), health workers, and policy makers. Thematic analysis of the transcripts resulted in the emergence of four major themes. Through all themes the most consistent finding was that myths, misconceptions, and misinformation about cancer were related to every aspect of the cancer journey and influenced the experiences and lives of PLWC and their caregivers. Participants were positive about the potential of an IVR system but also had reservations about the design and reach of the system. The resulting initial program theory proposes that a context-specific IVR system has the potential to improve awareness on cancer, provided attention is given to aspects such as language, message framing, and accuracy.
Identifying transcription factor–DNA interactions using machine learning
Authors: Bang Sohyun , Galli Mary , Crisp Peter A , Gallavotti Andrea , Schmitz Robert J
Published: August 2022

Machine learning approaches have been applied to identify transcription factor (TF)–DNA interaction important for gene regulation and expression. However, due to the enormous search space of the genome, it is challenging to build models capable of surveying entire reference genomes, especially in species where models were not trained. In this study, we surveyed a variety of methods for classification of epigenomics data in an attempt to improve the detection for 12 members of the auxin response factor (ARF)-binding DNAs from maize and soybean as assessed by DNA Affinity Purification and sequencing (DAP-seq). We used the classification for prediction by minimizing the genome search space by only surveying unmethylated regions (UMRs). For identification of DAP-seq-binding events within the UMRs, we achieved 78.72 % accuracy rate across 12 members of ARFs of maize on average by encoding DNA with count vectorization for k-mer with a logistic regression classifier with up-sampling and feature selection. Importantly, feature selection helps to uncover known and potentially novel ARF-binding motifs. This demonstrates an independent method for identification of TF-binding sites. Finally, we tested the model built with maize DAP-seq data and applied it directly to the soybean genome and found high false-negative rates, which accounted for more than 40 % across the ARF TFs tested. The findings in this study suggest the potential use of various methods to predict TF–DNA interactions within and between species with varying degrees of success.
Violent Interference: Structural Violence, Quantum International Relations, and the Ethics of Entanglement
Authors: Murphy Michael P A
Published: August 2022

Despite frequent reference in both academic and activist contexts, the concept of structural violence still poses a challenge for many ontological, epistemological, and political perspectives. While the ethical stakes of physical violence are generally accessible, conceptual barriers limit the ability to explore the important ethical dimensions of structural violence. Inspired by recent interventions into “quantum international relations,” I argue that the difficulty of understanding structural violence is because conventional social science abides a Newtonian physical imaginary. Drawing on Karen Barad's philosophical methodology of “diffractive reading,” I re-read Johan Galtung's landmark article Violence, Peace, and Peace Research through a critical quantum social–theoretic lens. Identifying key quantum-like elements of Galtung's theory of structural violence allows for a process of “quantizing by translation,” where quantum-like concepts are freed from the constraints of Newtonian social science. By approaching structural violence as a quantum-like social phenomenon, homologous to the concept of destructive interference, we gain an important conceptual model. In instances of structural violence, entangled social wavefunctions of social structures interfere destructively with constituent individuals and groups by limiting the spectrum of future potentialities. Conversely, structural privilege describes the constructive interference of those same social structures extending the spectrum of future potentialities for other constituent individuals and groups. To account for multiple and intersecting elements of identity and social standing, intersectional accounts of structural violence recognize the complex interaction of constructive and destructive interferences at play in delimiting spectra of future potentialities.
Effect of combined maternal and post-hatch dietary 25-hydroxycholecalciferol supplementation on broiler chicken Pectoralis major muscle growth characteristics and satellite cell mitotic activity
Authors: Avila Luis P , Leiva Samuel F , Abascal-Ponciano Gerardo A , Flees Joshua J , Sweeney Kelly M , Wilson Jeanna L , Meloche Kathryn J , Turner Bradley J , Litta Gilberto , Waguespack-Levy April M , Pokoo-Aikins Anthony , Starkey Charles W , Starkey Jessica D
Published: August 2022

Skeletal muscle growth is largely dependent on the proliferation and differentiation of muscle-specific stem cells known as satellite cells (SC). Previous work has shown that dietary inclusion of the vitamin D3 metabolite, 25-hydroxycholecalciferol (25OHD3), also called calcidiol, can promote skeletal muscle growth in post-hatch broiler chickens. Improving vitamin D status of broiler breeder hens by feeding 25OHD3 in addition to vitamin D3 has also been shown to positively impact progeny. Yet, whether combined pre- and post-hatch supplementation with 25OHD3 produces an additive or synergistic SC-mediated, skeletal muscle growth response remains unanswered. To evaluate the effect of combined maternal and post-hatch dietary 25OHD3 supplementation on the growth and SC mitotic activity of the Pectoralis major (PM) muscles in broiler chickens, a randomized complete block design experiment with the main effects of maternal diet (MDIET) and post-hatch diet (PDIET) arranged in a 2 × 2 factorial treatment structure was conducted. From 25 to 36 wk of age, broiler breeder hens were fed 1 of 2 MDIET formulated to provide 5,000 IU D3 (MCTL) or 2,240 IU of D3 + 2,760 IU of 25OHD3 per kg of feed (M25OHD3). Their male broiler chick offspring (n = 400) hatched from eggs collected from 35 to 36 wk of age were reared in raised floor pens. Broilers were fed 1 of 2 PDIET formulated to provide 5,000 IU of D3 per kg of feed (PCTL) or 2,240 IU of D3 + 2,760 IU of 25OHD3 per kg of feed (P25OHD3). Muscle was collected at days 4, 8, 15, 22, and 29 and stored until immunofluorescence analysis. Data were analyzed as a 2-way ANOVA with SAS GLIMMIX. Dietary 25OHD3 was effectively transferred from hen plasma to egg yolks (P = 0.002) and to broiler progeny plasma (days 4 to 22; P ≤ 0.044). Including 25OHD3 in either MDIET or PDIET altered PM hypertrophic growth prior to day 29 (P ≥ 0.001) and tended to reduce Wooden Breast severity (P ≤ 0.089). Mitotic SC populations were increased in PM of MCTL:P25OHD3 and M25OHD:PCTL-fed broilers at d 4 (P = 0.037). At d 8, the PM mitotic SC populations were increased 33% by P25OHD3 (P = 0.054). The results of this study reveal that combined maternal and post-hatch 25OHD3 supplementation does not produce additive or synergistic effects on SC-mediated broiler muscle growth. However, vitamin D status improvement through dietary 25OHD3 inclusion in either the maternal or post-hatch diet stimulated broiler breast muscle growth by increasing proliferating SC populations.
Association of Pre-procedural Anxiety With Procedure-Related Pain During Outpatient Pediatric Burn Care: A Pilot Study
Authors: Vest Eurella , Armstrong Megan , Olbrecht Vanessa A , Thakkar Rajan K , Fabia Renata B , Groner Jonathan I , Noffsinger Dana , Tram Nguyen K , Xiang Henry
Published: August 2022

The relationship between preprocedural anxiety and pain is not clear but has the potential to change the way pediatric patients need to be cared for prior to burn procedures. Using results from our recent randomized clinical trial among outpatient burn patients (n = 90) aged 6–17 years, the objective of this subsequent analysis was to assess whether preprocedural anxiety was associated with self-reported and researcher-observed pain scores. Anxiety before the dressing change was assessed using an abbreviated State-Trait Anxiety Inventory for Children (range 6–21) and reported with 95% confidence intervals (CI). Self-reported pain was reported using a Visual Analog Scale (range 0–100) and observed pain was assessed using the Face, Legs, Activity, Cry, and Consolability-revised scale. Over half of patients (58.9%) reported mild anxiety (score < 12) and about 5% of patients reported severe anxiety (score > 16). Younger children (6–8 years) reported higher anxiety scores than older children (15–17 years), but the difference did not achieve statistical significance (mean = 12.7, 95% CI: 11.5 to 13.9, P = .09). Nonparametric spearman correlation indicated that anxiety score was significantly correlated with observed pain (P = .01) and self-reported overall pain neared statistical significance (P = .06). In the final logistic regression of reporting moderate-to-severe pain (pain score > 30), the association between anxiety scores and self-reported overall moderate-to-severe pain was statistically significant (P = .03) when adjusting for race, healing degree, and pain medication use within 6 hr prior to burn dressing care. This pilot study provides preliminary data showing that anxiety before outpatient pediatric burn dressing changes is significantly associated with self-reported overall moderate-to-severe pain.
Long-term wellbeing and neurocognitive functioning of diffuse low-grade glioma patients and their caregivers: A longitudinal study spanning two decades
Authors: Boele Florien W , den Otter Patricia W M , Reijneveld Jaap C , de Witt Hamer Philip C , van Thuijl Hinke F , Lorenz Linda M C , Wesseling Pieter , Lagerwaard Frank J , Taphoorn Martin J B , Kouwenhoven Mathilde C M , Snijders Tom J , Douw Linda , Klein Martin
Published: August 2022

Background

While patients with diffuse low-grade glioma (LGG) often survive for years, there is a risk of tumor progression which may impact patients’ long-term health-related quality of life (HRQOL) and neurocognitive functioning (NCF). We present a follow-up of LGG patients and their informal caregivers (T3) who took part in our previous HRQOL investigations (T1, M = 7 and T2 M = 13 years after diagnosis).

Methods

Participants completed HRQOL (short form-36 health survey [SF-36]; EORTC-BN20), fatigue (Checklist Individual Strength [CIS]), and depression (Center for Epidemiological Studies-Depression [CES-D]) questionnaires and underwent NCF assessments. T3 scores were compared with matched controls. Changes over time (T1–T2–T3) on group and participant level were assessed. Where available, histology of the initial tumor was revised and immunohistochemical staining for IDH1 R132H mutant protein was performed.

Results

Thirty patients and nineteen caregivers participated. Of N = 11 with tissue available, 3 patients had confirmed diffuse LGG. At T3, patients (M = 26 years after diagnosis) had HRQOL and NCF similar to, or better than controls, yet 23.3% and 53.3% scored above the cut-off for depression (≥16 CES-D) and fatigue (≥35 CIS), respectively. Caregivers’ HRQOL was similar to controls but reported high rates of fatigue (63.2%). Over time, patients’ mental health improved (P < .05). Minimal detectable change in HRQOL over time was observed in individual patients (30% improvement; 23.3% decline; 20% both improvement and decline) with 23.3% remaining stable. NCF remained stable or improved in 82.8% of patients.

Conclusions

While HRQOL and NCF do not appear greatly impacted during long-term survivorship in LGG, depressive symptoms and fatigue are persistent.
EANO - EURACAN - SNO Guidelines on circumscribed astrocytic gliomas, glioneuronal, and neuronal tumors
Authors: Rudà Roberta , Capper David , Waldman Adam D , Pallud Johan , Minniti Giuseppe , Kaley Thomas J , Bouffet Eric , Tabatabai Ghazaleh , Aronica Eleonora , Jakola Asgeir S , Pfister Stefan M , Schiff David , Lassman Andrew B , Solomon David A , Soffietti Riccardo , Weller Michael , Preusser Matthias , Idbaih Ahmed , Wen Patrick Y , van den Bent Martin J
Published: August 2022

In the new WHO 2021 Classification of CNS Tumors the chapter “Circumscribed astrocytic gliomas, glioneuronal and neuronal tumors” encompasses several different rare tumor entities, which occur more frequently in children, adolescents, and young adults. The Task Force has reviewed the evidence of diagnostic and therapeutic interventions, which is low particularly for adult patients, and draw recommendations accordingly. Tumor diagnosis, based on WHO 2021, is primarily performed using conventional histological techniques; however, a molecular workup is important for differential diagnosis, in particular, DNA methylation profiling for the definitive classification of histologically unresolved cases. Molecular factors are increasing of prognostic and predictive importance. MRI finding are non-specific, but for some tumors are characteristic and suggestive. Gross total resection, when feasible, is the most important treatment in terms of prolonging survival and achieving long-term seizure control. Conformal radiotherapy should be considered in grade 3 and incompletely resected grade 2 tumors. In recurrent tumors reoperation and radiotherapy, including stereotactic radiotherapy, can be useful. Targeted therapies may be used in selected patients: BRAF and MEK inhibitors in pilocytic astrocytomas, pleomorphic xanthoastrocytomas, and gangliogliomas when BRAF altered, and mTOR inhibitor everolimus in subependymal giant cells astrocytomas. Sequencing to identify molecular targets is advocated for diagnostic clarification and to direct potential targeted therapies.
Cancer as a Disease of the Cell
Authors: Neugut Alfred I
Published: August 2022

This commentary highlights cases in which human-to-human transfers of cancers have occurred and what this could mean for a cure for cancer.
Sleep characterization with smart wearable devices: a call for standardization and consensus recommendations
Authors: Baumert Mathias , Cowie Martin R , Redline Susan , Mehra Reena , Arzt Michael , Pépin Jean-Louis , Linz Dominik
Published: August 2022

The general public increasingly adopts smart wearable devices to quantify sleep characteristics and dedicated devices for sleep assessment. The rapid evolution of technology has outpaced the ability to implement validation approaches and demonstrate relevant clinical applicability. There are untapped opportunities to validate and refine consumer devices in partnership with scientists in academic institutions, patients, and the private sector to allow effective integration into clinical management pathways and facilitate trust in adoption once reliability and validity have been demonstrated. We call for the formation of a working group involving stakeholders from academia, clinical care and industry to develop clear professional recommendations to facilitate appropriate and optimized clinical utilization of such technologies.
Fusarium oxysporum f. sp. vasinfectum Identified on Okra in South Carolina, United States
Authors: Keinath Anthony P. , Rennberger Gabriel , DuBose Virginia B. , Zardus Sierra H. , Rollins P. Andrew
Published: August 2022

Fusarium oxysporum f. sp. vasinfectum, the causal agent of Fusarium wilt on okra, was recovered in August 2020 on a commercial farm in South Carolina from cultivar Clemson Spineless, an heirloom cultivar still widely grown throughout the southeastern United States. An isolate recovered from discolored vascular tissue in the stem of a diseased plant was identified as F. oxysporum f. sp. vasinfectum based on sequences of the translation elongation factor 1-alpha and beta-tubulin genes. Two inoculation techniques were compared, injecting microconidia into stems and drenching microconidia around the base of plants. Drenching was a significantly more effective inoculation technique than stem injection ( P < 0.05), with 77% and 40% of inoculated plants showing vascular discoloration and 73% and 45% of inoculated plants yielding colonies of F. oxysporum when pieces of vascular tissue were cultured on Komada's medium, respectively. This study provides the first confirmation of the presence of F. oxysporum f. sp. vasinfectum on okra in South Carolina.
Defining Opioid-related Problems Using a Health Care Safety Net Institution’s Inpatient Electronic Health Records: Limitations of Diagnosis-based Definitions
Authors: Arifkhanova Aziza , Prieto José Tomás , Davidson Arthur J. , Al-Tayyib Alia , Hawkins Ethan , Kraus Emily , McEwen Dean , Podewils Laura Jean , Foldy Seth , Gillespie Elizabeth , Taub Julie , Shlay Judith C.
Published: August 2022

Background

Measuring clinically relevant opioid-related problems in health care systems is challenging due to the lack of standard definitions and coding practices. Well-defined, opioid-related health problems (ORHPs) would improve prevalence estimates and evaluation of clinical interventions, crisis response, and prevention activities. We sought to estimate prevalence of opioid use disorder (OUD), opioid misuse, and opioid poisoning among inpatients at a large, safety net, health care institution.

Methods

Our study included events documented in the electronic health records (EHRs) among hospitalized patients at Denver Health Medical Center during January 1, 2017 to December 31, 2018. Multiple EHR markers (ie, opioid-related diagnostic codes, clinical assessment, laboratory results, and free-text documentation) were used to develop diagnosis-based and extended definitions for OUD, opioid misuse, and opioid poisoning. We used these definitions to estimate number of hospitalized patients with these conditions.

Results

During a 2-year study period, 715 unique patients were identified solely using opioid-related diagnostic codes; OUD codes accounted for the largest proportion (499/715, 69.8%). Extended definitions identified an additional 973 unique patients (~136% increase), which includes 155/973 (15.9%) who were identified by a clinical assessment marker, 1/973 (0.1%) by a laboratory test marker, and 817/973 (84.0%) by a clinical documentation marker.

Conclusions

Solely using diagnostic codes to estimate prevalence of clinically relevant ORHPs missed most patients with ORHPs. More inclusive estimates were generated using additional EHR markers. Improved methods to estimate ORHPs among a health care system’s patients would more fully estimate organizational and economic burden to more efficiently allocate resources and ensure capacity to provide clinical services.
The Effects of Body Mass Index & Spine Flexibility on Surgical Outcomes for Patients with Adolescent Idiopathic Scoliosis
Authors: Linden Gabriel S. , Hresko M. Timothy , Cook Danielle , Birch Craig M. , Hedequist Daniel J. , Hogue Grant D.
Published: August 2022

Study Design.

Retrospective cohort study.

Objective.

To investigate the relationship between body mass index (BMI), spine flexibility index (FI), and their combined effects on adolescent idiopathic scoliosis (AIS) surgical outcomes.

Background.

BMI and FI are two factors considered during pre-surgical planning for AIS correction, but there is sparse research about their relationship. We hypothesize that AIS patients with increased BMI may be associated with decreased FI - a combination which could lead to worsened surgical outcomes.

Methods.

AIS patients ages 11-19 at surgery, who underwent posterior fusion at a single-center from 2011-2017, were reviewed. Patients without proper radiographs to assess FI, or a previous spine surgical history, were excluded. FI was categorized as stiff (FI<50) or flexible (FI≥50), and patients were separated by major curve region. BMI was categorized as underweight (<5th percentile), healthy-weight (5th-85th percentile), overweight (85th-95th percentile), or obese (>95th percentile). Regression analysis was conducted to test BMI and FI’s effects on intraoperative, immediate postoperative, and two-year postoperative outcomes.

Results.

543 patients (82% female), with an average age of 14.9 years, were included. 346 patients had available two-year data. A 10% increase in BMI was associated with a 1.3% decrease in FI for patients with major thoracolumbar/lumbar curves (P=0.01). Obese patients were most likely to have a postoperative complication (P=0.003) or two-year complication (P=0.04). Revision surgery occurred after 58% of postoperative complications (15/26) and 80% of two-year complications (4/5). FI was negatively associated with initial curve magnitude (P<0.001), operative time (P=0.02), and blood loss (P=0.02). Overweight patients with flexible curves were 10.0 times more likely to sustain a postoperative complication than healthy-weight patients with stiff curves (P=0.001).

Conclusion.

Elevated BMI was associated with decreased FI in patients with major thoracolumbar/lumbar curves. Patients with a high BMI and high FI were associated with the greatest risk of postoperative complication.
Centrosome Defects in Hematological Malignancies: Molecular Mechanisms and Therapeutic Insights
Authors: Hu Mingzheng , Wang Yijie , Zhou Jun
Published: August 2022

Defects in centrosomes are associated with a broad spectrum of hematological malignancies, such as leukemia and lymphoma. Centrosomes in these malignancies display both numerical and structural aberrations, including alterations in the number and size of centrioles, inappropriate post-translational modification of centrosomal proteins, and extra centrosome clustering. There is accumulating evidence that centrosome defects observed in hematological malignancies result from multiple factors, including dysregulation of the centrosome cycle and impairment of centriole biogenesis. In this review, we discuss the plausible mechanisms of centrosome defects and highlight their consequences in hematological malignancies. We also illustrate the latest therapeutic strategies against hematological malignancies by targeting centrosome anomalies.
Bullous systemic lupus erythematosus in females
Authors: Sprow Grant , Afarideh Mohsen , Dan Joshua , Hedberg Matthew L. , Werth Victoria P.
Published: August 2022

Bullous systemic lupus erythematosus (BSLE) is a rare blistering presentation of systemic lupus erythematosus, typically affecting women with the highest incidence in those of African descent. The key pathogenic insult includes the formation of autoantibodies against type VII collagen, which weaken the basement membrane zone and lead to the formation of subepidermal blisters. The acute vesiculobullous eruptions in BSLE generally tend to affect photo-distributed areas, although they can arise unrelated to sun exposure (eg, mucous membranes, axillae). The bullae can arise from erythematous macules, inflammatory plaques, or previously normal skin. Their appearance can range from small, grouped vesicles reminiscent of lesions in dermatitis herpetiformis to large, tense blisters, similar to bullous pemphigoid. Internal organ involvement occurs in up to 90% of those affected. This mostly includes lupus nephritis (classes III–V, lifetime prevalence of up to 90%), arthralgias/arthritis, and cytopenias, while serositis and neuropsychiatric involvement are rare. First-line management with dapsone should be considered in mild disease with stable underlying systemic lupus erythematosus. As discussed in this review, the off-label use of rituximab (an anti-CD20 B-cell depleting agent) has been shown to be safe and effective in several refractory cases of BSLE unresponsive to dapsone, glucocorticoids, or steroid-sparing immunosuppressants.
Efficacy of pharmacologic treatment for treating gastrointestinal angiodysplasias-related bleeding: a systematic review and meta-analysis
Authors: Gkolfakis Paraskevas , Fostier Romane , Tziatzios Georgios , Lazaridis Nikolaos , Fernandez Y Viesca Michael , Facciorusso Antonio , Despott Edward , Triantafyllou Konstantinos , Devière Jacques , Arvanitakis Marianna
Published: August 2022

Introduction

We evaluated the efficacy of pharmacologic treatments for patients with overt or occult bleeding due to gastrointestinal angiodysplasias (GIADs).

Methods

A systematic computer-aided literature search across Medline, Cochrane, Scopus and Embase databases was performed. Studies evaluating pharmacologic treatments for patients presenting with GIADs-related overt or occult bleeding were included. Post-treatment rebleeding was the primary outcome. Need for red blood cells (RBC) transfusion, post-treatment hemoglobin levels and adverse events rate comprised secondary outcomes. Results are presented as odds ratio (OR), mean difference (MD) or pooled rates (%) with 95% confidence intervals (95%CI).

Results

Four types of pharmacologic treatment were identified (25 studies): somatostatin analogs, hormonal therapy, thalidomide and angiogenesis inhibitors. Pharmacologic treatment of any kind led to significantly reduced bleeding episodes [OR (95% CI), 0.08 (0.04–0.18)]. No pharmacologic treatment was superior to others (P = 0.46). Overall, pooled rebleeding rate post-treatment was 34% (26–43%). Similarly, significantly fewer patients required RBC transfusion during the post-treatment period [0.03 (0.03–0.07)], with no differences among various treatments (P = 0.83), yielding an overall pooled transfusion rate of 33% (19–46%). Administration of pharmacological treatment led to significant improvement in terms of hemoglobin levels [MD (95% CI), 3.21 g/dL (2.42–3.99)]. The pooled rate of adverse events was 32% (22–42%).

Conclusion

In patients with GIADs administration of any pharmacologic treatment significantly decreases rebleeding episodes and transfusions leading to higher hemoglobin values. One-third of them experience at least one adverse event related to the treatment.
Lateral force removal of fungal spores to demonstrate how surface properties affect fungal spore retention
Authors: Whitehead Kathryn A. , Deisenroth Ted , Preuss Andrea , Liauw Christopher M. , Verran Joanna
Published: August 2022

Microbial biofouling on polymer surfaces can lead to their biodeterioration. This may result in deterioration of the surface, leading to cracking and fracturing. Fungal spores from
Aspergillus niger
1957,
Aspergillus niger
1988 and
Aureobasidium pullulans
were tested to determine their strength of attachment on three surfaces, p(γ-MPS-co-MMA), p(γ-MPS-co-LMA) and spin-coated poly(methyl methacrylate) (PMMAsc), using lateral force measurements. The results demonstrate that
A. niger
1957 and
A. niger
1988 spores were most easily removed from the p(γ-MPS-co-MMA) surface, which was the surface with the highest
R
a
value. The
A. niger
1957 and
A. pullulans
spores were most difficult to remove from the PMMAsc surface, which was the hardest surface.
A. niger
1988 spores were the most difficult to remove from p(γ-MPS-co-LMA), the most hydrophobic surface. The results with
A. pullulans
were difficult to elucidate since the spores bound to all three surfaces and were removed with similar rates of force. The lateral force results demonstrate that spore attachment to a surface is a multi-factorial process, and independent surface and microbial factors influence spore binding. Thus, each environmental scenario needs to be considered on an individual basis, since a solution to one biofouling issue will probably not translate across to other systems.

This article is part of the theme issue 'Nanocracks in nature and industry'.
Genomic ascertainment for UBA1 variants and VEXAS syndrome: a population-based study
Authors: Beck David B. , Bodian Dale L. , Shah Vandan , Mirshahi Uyenlinh L. , Kim Jung , Ding Yi , Strande Natasha T. , Cantor Anna , Haley Jeremy S. , Cook Adam , Hill Wesley , Grayson Peter C. , Ferrada Marcela A. , Kastner Daniel L. , Carey David J. , Stewart Douglas R.
Published: August 2022

Importance

VEXAS (vacuoles, E1-ubiquitin-activating enzyme, X-linked, autoinflammatory, somatic) syndrome is a disease with rheumatologic and hematologic features caused by somatic variants in UBA1. Pathogenic variants are associated with a broad spectrum of clinical manifestations. Knowledge of prevalence, penetrance, and clinical characteristics of this disease have been limited by ascertainment biases based on known phenotypes. This study used a genomic ascertainment approach to overcome these limitations and better define UBA1-related disease.

Objective

Determine the prevalence of pathogenic variants in UBA1 and associated clinical manifestations in an unselected population using a genomic ascertainment approach.

Design, Setting and Participants

This cohort study evaluated UBA1 variants in exome data from 163,096 participants within the Geisinger MyCode Community Health Initiative. Clinical phenotypes were determined from Geisinger electronic health record (EHR) data up to January 1st, 2022.

Main outcomes and measures

Prevalence of somatic UBA1 variation; presence of rheumatologic, hematologic, pulmonary, dermatologic, and other symptoms in individuals with somatic UBA1 variation; structured and manual review of EHR; review of bone marrow biopsies; survival in carriers of somatic UBA1 variation.

Results

In a retrospective study of 163,096 participants (mean age 52.8 years; 94% of European ancestry, 61% female), 11 individuals harbored somatic, known pathogenic UBA1 variants, with 100% having clinical manifestations consistent with VEXAS syndrome. We found a previously unreported UBA1 variant (c.1861A>T; p.Ser621Cys) in a symptomatic patient. Disease-causing UBA1 variants were found in ∼1 in 14,000 unrelated individuals, and ∼1 in 4,000 men >50 years old. A disease-causing UBA1 variant confers a ∼ 6.6 higher probability of mortality vs. age-, sex-, and BMI-matched non-carriers. The majority (7, 58%) of individuals did not meet criteria for rheumatologic and hematologic diagnoses previously associated with VEXAS syndrome, however all individuals had anemia (mean 7.8 g/dL, median 7.5g/dL), mostly macrocytic (91%) with concomitant thrombocytopenia (91%). Finally, we identified a pathogenic variant in one male prior to onset of VEXAS-related signs or symptoms and two females had disease with heterozygous variants.

Conclusions and relevance

This cohort study showed that the prevalence, penetrance, and expressivity of pathogenic UBA1 variants were higher than expected. More expansive UBA1 testing will lead to molecular diagnoses and improved treatment for patients.
Evidence to inform effective alcohol pricing policies in the European Union
Authors: Angus Colin
Published: August 2022

Aim

To map current alcohol pricing policies across the European Union and United Kingdom and review the latest evidence on their effectiveness

Design

Current policies were mapped using publicly available data. Evidence was systematically reviewed using a three-stage approach: a) a systematic search for published studies in PubMed and Google Scholar, b) a snowball search of grey literature and hand-searching the references of existing reviews and c) consultation with topic experts.

Setting

Any appraisal or evaluation on the impact of an alcohol pricing policy in an EU or UK nation that reported alcohol consumption or health outcomes.

Participants

The general population

Measurements

Any reported measures of alcohol consumption or alcohol-related health outcomes.

Findings

The mapping exercise found that there is substantial variation in both the levels and structures of alcohol taxation across Europe. The review found 83 studies, consisting of 34 prospective modelling studies and 49 retrospective evaluations. These came primarily from the UK and Scandinavia. The majority of studies looked at the impact of changes to alcohol taxation, although a substantial minority looked at the impacts of Minimum Unit Pricing for alcohol. Studies consistently fond that increases in taxation, or the introduction of Minimum Unit Pricing, have led to reductions in alcohol consumption and improvements in public health and, in spite of concerns about cross-border sales moderating these benefits, there is little evidence to support these concerns in practice.

Conclusion

There is ample evidence to show that alcohol pricing policies can and have worked across Europe and are likely to form a key part of any effective policy approach to reduce alcohol-related harm.
Identify Non-Mutational p53 Functional Deficiency in Human Cancers
Authors: Li Qianpeng , Zhang Yang , Luo Sicheng , Zhang Zhang , Oberg Ann L. , Kozono David E. , Lu Hua , Sarkaria Jann N. , Ma Lina , Wang Liguo
Published: August 2022

An accurate assessment ofTP53’s functional status is critical for cancer genomic medicine. However, there is a significant challenge in identifying tumors with non-mutational p53 inactivations that are not detectable through DNA sequencing. These undetected cases are often misclassified as p53-normal, leading to inaccurate prognosis and downstream association analyses. To address this issue, we build the support vector machine (SVM) models to systematically reassess p53’s functional status inTP53wild-type (TP53WT) tumors from multiple TCGA cohorts. Cross-validation demonstrates the excellent performance of the SVM models with a mean AUC of 0.9822, precision of 0.9747, and recall of 0.9784. Our study reveals that a significant proportion (87-99%) ofTP53WTtumors actually have compromised p53 function. Additional analyses uncovered that these genetically intact but functionally impaired (termed as predictively reduced function of p53 orTP53WT-pRF) tumors exhibit genomic and pathophysiologic features akin to p53 mutant tumors: heightened genomic instability and elevated levels of hypoxia. Clinically, patients withTP53WT-pRF tumors experience significantly shortened overall survival or progression-free survival compared to those withTP53WT-pN (predictive normal function of p53) tumors, and these patients also display increased sensitivity to platinum-based chemotherapy and radiation therapy.
Inferring Single-Molecule Chromatin Interactions via Online Convex Network Dictionary Learning
Authors: Peng Jianhao , Pan Chao , Lyu Hanbaek , Kim Minji , Cheng Albert , Milenkovic Olgica
Published: August 2022

Motivation

Genomes of multicellular systems are compartmentalized and dynamically folded within the three-dimensional (3D) confines of the nucleus in order to facilitate gene regulation. Among the 3D-genome mapping technologies currently in use, droplet-based, barcode-linked sequencing (ChIA-Drop) has the unique capability to capture complex multi-way chromatin interactions at the single-molecule level. ChIA-Drop data gives rise to higher-order interaction networks in which nodes represent genomic fragments while (hyper)edges capture observed physical contacts. The problem of interest is to use this data to create a “dictionary” of interaction patterns (subnetworks) that accurately describe all global chromatin structures and associate dictionary elements with cellular functions.

Results

To construct interpretable chromatin dictionaries, we introduce a new algorithm termed online convex network dictionary learning (online cvxNDL). Unlike classical dictionary learning for image or text processing, online cvxNDL uses special subgraph sampling methods and produces interpretable subnetwork representatives corresponding to “convex mixtures” of patterns observed in real data. To demonstrate the utility of the method, we perform an in-depth study of RNAPII-enriched ChIA-Drop data from Drosophila Melanogaster S2 cell lines. Our results are two-fold: First, we show that online cvxNDL allows for accurate reconstruction of the original interaction network data using only a collection of roughly 25 dictionary elements and their “representatives” directly observed in the data. Second, we identify collections of interaction patterns of chromatin elements shared by related processes on different chromosomes and those unique to certain chromosomes. This is accomplished through Gene Ontology (GO) enrichment analysis that allows us to associate dictionary element representatives with functional properties of their corresponding chromatin region and in the process, determine what we call the “span” and “density” of chromatin interaction patterns.

Availability and Implementation

The code and dataset are available at: https://github.com/jianhao2016/online_cvxNDL/

Contact

milenkov@illinois.edu
Reference BioImaging to assess the phenotypic trait diversity of bryophytes within the family Scapaniaceae
Authors: Peters Kristian , König-Ries Birgitta
Published: August 2022

Macro- and microscopic images of organisms are pivotal in biodiversity research. Despite that bioimages have manifold applications such as for assessing the diversity of form and function, FAIR bioimaging data in the context of biodiversity are still very scarce, especially for difficult taxonomic groups such as bryophytes. Here, we present a high-quality reference dataset containing macroscopic and bright-field microscopic images documenting various phenotypic attributes of the species belonging to the family of Scapaniaceae occurring in Europe. To encourage data reuse in biodiversity and adjacent research areas, we annotated the imaging data with machine-actionable meta-data using community-accepted semantics. Furthermore, raw imaging data are retained and any contextual image processing like multi-focus image fusion and stitching were documented to foster good scientific practices through source tracking and provenance. The information contained in the raw images are also of particular interest for machine learning and image segmentation used in bioinformatics and computational ecology. We expect that this richly annotated reference dataset will encourage future studies to follow our principles.
Efficient sampling designs to assess biodiversity spatial autocorrelation : should we go fractal ?
Authors: Laroche F.
Published: August 2022

Quantifying the autocorrelation range of species distribution in space is necessary for applied ecological questions, like implementing protected area networks or monitoring programs. However, the power of spatial sampling designs to estimate this range is negatively related with other objectives such as estimating environmental effects acting upon species distribution. Mixing random sampling points and systematic grid (‘hy-brid’ designs) is a classic solution to make a trade-off. However, fractal designs (i.e. self-similar designs with well-identified scales) could make an even better compromise, because they cover a wide array of possible autocorrelation range values across scales. Using maximum likelihood estimation in an optimal design of experiments approach, we compared errors of hybrid and fractal designs when simultaneously estimating an effect acting upon a response variable and the residual autocorrelation range. We found that Pareto-optimal sampling strategies depended on the feasible grid mesh size (FGMS) over the study area, given the sampling budget. When the FMGS was shorter than expected autocorrelation range values, grid design was the best option on all criteria. When the FMGS was around or larger than expected autocorrelation range values, the choice of designs depended on the effect under study. Fractal designs outperformed hybrid designs when studying the effect of a monotonic environmental gradient across space, while grid design was more efficient for other types of question. Beyond the niche identified in our analysis, fractal designs may also appear interesting when studying response variables with more heterogeneous spatial structure across scales, and when considering more practical criteria of performance such as the distance needed to cover the design.
Candidate proteins associated with popping expansion capacity of popcorn
Authors: Gemelli Talita Mayara de Campos Jumes , Romani Isaac , Dos Santos Natália Ferreira , Machado Maria de Fátima P.S. , Scapim Carlos Alberto , Domont Gilberto Barbosa , Nogueira Fábio César Sousa , Gonela Adriana
Published: August 2022

The mechanical resistance of the popcorn pericarp has a positive and direct relationship to its expansion volume. It allows enough time for the endosperm to gelatinize completely before its extravasation. Expansion is a polygenic trait that has been extensively studied. However, no records in the literature indicate proteins that directly affect pericarp thickness and integrity. Therefore, the present work aimed to identify candidate pericarp proteins associated with the expansion capacity of popcorn kernels using the shotgun proteomic approach. The analyses were carried out in the pericarp of two popcorn inbred lines, P11 (expansion volume of 30 mL g-1) and P16 (expansion volume of 14 mL g-1), in two developmental stages (15 and 25 DAP). A total of 803 non-redundant proteins were identified. Most of them were involved in key processes associated with pericarp development and thickening. Two candidate proteins stood out among the differentially abundant proteins. Peroxidase was up-accumulated in P11/25 DAP (high popping expansion) and was 1.498 times more abundant in this inbred line, while xyloglucan endotransglucosylase/hydrolase was more abundant in P16 (low popping expansion) in both developmental stages. Thus, the peroxidase protein increases expandability, whereas xyloglucan endotransglucosylase/hydrolase decreases it, even though its specific role has not been elucidated. These proteins should be further investigated, as they may be used to improve expansion capacity in popcorn breeding programs.