bluuebunny/crossref_metadata_2025_split huggingface dataset:
Radiomic signatures of posterior fossa ependymoma: Molecular subgroups and risk profiles
Authors: Zhang Michael , Wang Edward , Yecies Derek , Tam Lydia T , Han Michelle , Toescu Sebastian , Wright Jason N , Altinmakas Emre , Chen Eric , Radmanesh Alireza , Nemelka Jordan , Oztekin Ozgur , Wagner Matthias W , Lober Robert M , Ertl-Wagner Birgit , Ho Chang Y , Mankad Kshitij , Vitanza Nicholas A , Cheshier Samuel H , Jacques Tom S , Fisher Paul G , Aquilina Kristian , Said Mourad , Jaju Alok , Pfister Stefan , Taylor Michael D , Grant Gerald A , Mattonen Sarah , Ramaswamy Vijay , Yeom Kristen W 
Published: November 2021

Abstract

Background
The risk profile for posterior fossa ependymoma (EP) depends on surgical and molecular status [Group A (PFA) versus Group B (PFB)]. While subtotal tumor resection is known to confer worse prognosis, MRI-based EP risk-profiling is unexplored. We aimed to apply machine learning strategies to link MRI-based biomarkers of high-risk EP and also to distinguish PFA from PFB.

Methods
We extracted 1800 quantitative features from presurgical T2-weighted (T2-MRI) and gadolinium-enhanced T1-weighted (T1-MRI) imaging of 157 EP patients. We implemented nested cross-validation to identify features for risk score calculations and apply a Cox model for survival analysis. We conducted additional feature selection for PFA versus PFB and examined performance across three candidate classifiers.

Results
For all EP patients with GTR, we identified four T2-MRI-based features and stratified patients into high- and low-risk groups, with 5-year overall survival rates of 62% and 100%, respectively (P &lt; .0001). Among presumed PFA patients with GTR, four T1-MRI and five T2-MRI features predicted divergence of high- and low-risk groups, with 5-year overall survival rates of 62.7% and 96.7%, respectively (P = .002). T1-MRI-based features showed the best performance distinguishing PFA from PFB with an AUC of 0.86.

Conclusions
We present machine learning strategies to identify MRI phenotypes that distinguish PFA from PFB, as well as high- and low-risk PFA. We also describe quantitative image predictors of aggressive EP tumors that might assist risk-profiling after surgery. Future studies could examine translating radiomics as an adjunct to EP risk assessment when considering therapy strategies or trial candidacy.
Diffusion MRI is an early biomarker of overall survival benefit in IDH wild-type recurrent glioblastoma treated with immune checkpoint inhibitors
Authors: Hagiwara Akifumi , Oughourlian Talia C , Cho Nicholas S , Schlossman Jacob , Wang Chencai , Yao Jingwen , Raymond Catalina , Everson Richard , Patel Kunal , Mareninov Sergey , Rodriguez Fausto J , Salamon Noriko , Pope Whitney B , Nghiemphu Phioanh L , Liau Linda M , Prins Robert M , Cloughesy Timothy F , Ellingson Benjamin M 
Published: November 2021

Abstract

Background
Diffusion MRI estimates of the apparent diffusion coefficient (ADC) have been shown to be useful in predicting treatment response in patients with glioblastoma (GBM), with ADC elevations indicating tumor cell death. We aimed to investigate whether the ADC values measured before and after treatment with immune checkpoint inhibitors (ICIs) and the changes in these ADC values could predict overall survival (OS) in patients with recurrent IDH wild-type GBM.

Methods
Forty-four patients who met the following inclusion criteria were included in this retrospective study: (i) diagnosed with recurrent IDH wild-type GBM and treated with either pembrolizumab or nivolumab and (ii) availability of diffusion data on pre- and post-ICI MRI. Tumor volume and the median relative ADC (rADC) with respect to the normal-appearing white matter within the enhancing tumor were calculated.

Results
Median OS among all patients was 8.1 months (range, 1.0–22.5 months). Log-rank test revealed that higher post-treatment rADC was associated with a significantly longer OS (median, 10.3 months for rADC ≥ 1.63 versus 6.1 months for rADC &lt; 1.63; P = .02), whereas tumor volume, pretreatment rADC, and changes in rADC after treatment were not significantly associated with OS. Cox regression analysis revealed that post-treatment rADC significantly influenced OS (P = .02, univariate analysis), even after controlling for age and sex (P =.01, multivariate analysis), and additionally controlling for surgery after ICI treatment (P = .045, multivariate analysis).

Conclusions
Elevated post-treatment rADC may be an early imaging biomarker for OS benefits in GBM patients receiving ICI treatment.
Singlet Oxygen Leads to Structural Changes to Chloroplasts during their Degradation in the Arabidopsis thaliana plastid ferrochelatase two Mutant
Authors: Fisher Karen E , Krishnamoorthy Praveen , Joens Matthew S , Chory Joanne , Fitzpatrick James A J , Woodson Jesse D 
Published: November 2021

Abstract
During stress, chloroplasts produce large amounts of reactive oxygen species (ROS). Chloroplasts also contain many nutrients, including 80% of a leaf’s nitrogen supply. Therefore, to protect cells from photo-oxidative damage and to redistribute nutrients to sink tissues, chloroplasts are prime targets for degradation. Multiple chloroplast degradation pathways are induced by photo-oxidative stress or nutrient starvation, but the mechanisms by which damaged or senescing chloroplasts are identified, transported to the central vacuole and degraded are poorly defined. Here, we investigated the structures involved with degrading chloroplasts induced by the ROS singlet oxygen (1O2) in the Arabidopsis thaliana plastid ferrochelatase two (fc2) mutant. Under mild 1O2 stress, most fc2 chloroplasts appeared normal, but had reduced starch content. A subset of chloroplasts was degrading, and some protruded into the central vacuole via ‘blebbing’ structures. A 3D electron microscopy analysis demonstrated that up to 35% of degrading chloroplasts contained such structures. While the location of a chloroplast within a cell did not affect the likelihood of its degradation, chloroplasts in spongy mesophyll cells were degraded at a higher rate than those in palisade mesophyll cells. To determine if degrading chloroplasts have unique structural characteristics, allowing them to be distinguished from healthy chloroplasts, we analyzed fc2 seedlings grown under different levels of photo-oxidative stress. A correlation was observed among chloroplast swelling, 1O2 signaling and the state of degradation. Finally, plastoglobule (PG) enzymes involved in chloroplast disassembly were upregulated while PGs increased their association with the thylakoid grana, implicating an interaction between 1O2-induced chloroplast degradation and senescence pathways.
‘Passing’, but Far from Perfect: Assessing Public Confidence in Police and Desire for Reform in Pennsylvania
Authors: Kruis Nathan E , Donohue Richard H , Perry Payton , Rowland Nicholas J 
Published: November 2021

Abstract
With data collected from a representative sample of 522 Pennsylvania residents, this study measures public confidence in police and analyses public support for policing practices. Adopting a mixed-method approach, this study also analyses public desire for police reform and correlates of support for police reform. Findings reveal that participants expressed moderate levels of confidence in their local police, although confidence varied across racial groups. Despite this avowed confidence, participants also expressed desire for police reforms. The most supported reforms were those intended to increase officers’ training on mental illness, substance use dependency, and de-escalation techniques; enhance officers’ capabilities of handling critical incidents involving vulnerable populations; implement policing models that incorporate community input and oversight; and increase officer transparency and accountability. A key finding on police reform suggests that the racial divide in support for police reform is usefully informed by including, and not ignoring, significant generational, regional, and political divides. Policy implications based on these findings are discussed within.
Substitution of distal and active site residues reduces product inhibition of E1 from Acidothermus Cellulolyticus
Authors: Summers Samantha R , Alamdari Sarah , Kraft Casey J , Brunecky Roman , Pfaendtner Jim , Kaar Joel L 
Published: November 2021

Abstract
Cellulases are largely afflicted by inhibition from their reaction products, especially at high-substrate loading, which represents a major challenge for biomass processing. This challenge was overcome for endoglucanase 1 (E1) from Acidothermus cellulolyticus by identifying a large conformational change involving distal residues upon binding cellobiose. Having introduced alanine substitutions at each of these residues, we identified several mutations that reduced cellobiose inhibition of E1, including W212A, W213A, Q247A, W249A and F250A. One of the mutations (W212A) resulted in a 47-fold decrease in binding affinity of cellobiose as well as a 5-fold increase in the kcat. The mutation further increased E1 activity on Avicel and dilute-acid treated corn stover and enhanced its productivity at high-substrate loadings. These findings were corroborated by funnel metadynamics, which showed that the W212A substitution led to reduced affinity for cellobiose in the +1 and +2 binding sites due to rearrangement of key cellobiose-binding residues.
Analysis of Factors Influencing Anxiety and Depression among Hospitalized Patients with Chronic Wounds
Authors: Yan Ruihong , Strandlund Kara , Ci Hai , Huang Yinyan , Zhang Yixuan , Zhang Yujuan 
Published: November 2021

ABSTRACT

OBJECTIVE
To investigate the prevalence of anxiety and depression among hospitalized patients with a chronic wound and explore the influence of demographic factors, disease characteristics, social support, and coping styles on their mental status.

METHODS
Investigators recruited 216 patients with a chronic wound. The Self-rating Anxiety Scale and Self-rating Depression Scale were used to measure anxiety and depression. Patients’ coping style and their social support were assessed through face-to-face interviews.

RESULTS
Overall, 36.6% of participants presented with symptoms of anxiety, and 37% showed depressive symptoms. Participants who typically had less than 5 hours of sleep; experienced more severe pain; or had an odorous wound, negative coping style, or lower level of social support had a higher prevalence of anxiety and depression (P < .05). Men with higher monthly incomes who lived in the city were more likely to develop anxiety than women with lower monthly incomes who lived outside the city (P < .05). Participants with fewer years of education and without spouses were more likely to experience depression than married participants with more education (P < .05).

CONCLUSIONS
The prevalence of anxiety and depression among hospitalized patients with a chronic wound is high. Support from loved ones including a spouse and a positive coping style are key protective factors for mental health and well-being.
Early pregnancy loss
Authors: Chichester Melanie , Harding Kimberly M. 
Published: November 2021

Abstract:
One of every five pregnancies ends in miscarriage, disputing the common misconception that miscarriage is rare. Early pregnancy loss has a complex impact on women's mental health, requiring compassionate, trauma-informed care. This article explores the emotional and psychological impacts of miscarriage, and strategies for nurses to support the needs of patients after a miscarriage.
The voice of adolescents
Authors: Lapp Valerie , Fowler Susan B. , Miller Harriet D. 
Published: November 2021

Abstract:
There is a lack of understanding of the pediatric patient experience in isolation. This qualitative, descriptive study interviewed adolescent patients during their hospital stay about their perception of isolation. This article analyzes the themes gleaned from the interviews as well as nursing practice implications and strategies in caring for young patients in isolation.
Current and Upcoming Treatment Modalities in Myasthenia Gravis
Authors: Beladakere Ramaswamy Swathi , Singh Shivangi , Hooshmand Sara , Junsang Cho , Sweeney Megan , Govindarajan Raghav 
Published: November 2021

Abstract
Myasthenia gravis (MG) is one of the extensively studied autoimmune disorder. There has been a dramatic increase in research to further understand molecular pathogenesis of MG and clinical trials for new drugs in MG treatment in the past decade. This review article is to consolidate the available information in simple terms with students, residents, and fellows as target audience for easy learning and help application of this knowledge to clinical practice.
Anti-TIF-1α/γ Antibody-Positive Dermatomyositis Associated With Metastatic Prostatic Adenocarcinoma
Authors: Psomadakis Corinna E. , Maron Samuel Z. , Ng Melissa J. , Kessler Alaina J. , Bryce Clare H. , Shanker Vicki L. , Scelsa Stephen N. 
Published: November 2021

Abstract
Dermatomyositis (DM) is an autoimmune myopathy characterized by proximal muscle weakness and distinct skin findings. DM is associated with an increased risk of malignancy in adults. We describe a case of dermatomyositis with unusually severe oropharyngeal dysphagia and respiratory muscle weakness on presentation, who was found to have underlying metastatic prostate cancer. Prostate cancer is uncommonly associated with DM. The patient tested positive for antitranscription intermediate family-1 (anti-TIF-1, also known as anti-p155/410) antibodies, which are linked to malignancy-associated DM in adults and are associated with dysphagia and more severe cutaneous findings.
What Is in the Myopathy Literature?
Authors: Lacomis David 
Published: November 2021

Abstract
This edition concentrates on inflammatory myopathies with reports of reclassification of polymyositis, cancer associations, evaluation of subclinical cardiac involvement, myositis-specific and -associated antibodies, and immune checkpoint inhibitor myositis. A number of reports address sporadic late-onset nemaline myopathy and point out its diagnostic difficulty and the importance of identifying an associated monoclonal gammopathy that is likely of clinical significance and may warrant aggressive immunotherapy. Finally, treatment of nondystrophic channelopathies is addressed.
An Advanced Surgical Dressing for High-risk Patients Undergoing Breast Cancer Surgery: A Case-control Study
Authors: Nicotera A. , Ferrando P.M. , Ala A. , Brunetti M. , D’Anna M.R. , Passera R. , Malan F. 
Published: November 2021

Background:
Oncological breast surgeries, classified as breast conserving surgery, oncoplastic surgery, and mastectomies (standard or with tissue sparing and reconstruction), are burdened with an overall complication rate up to 33%. Aquacel Ag Surgical is a combined hydrofiber-hydrocolloids dressing. The aim of this study is to evaluate the incidence of surgical site complications in patients presenting with three or more risk factors (or two, of which at least one classified as “high risk”), undergoing breast cancer surgery with/without reconstruction, comparing advanced (Aquacel Ag Surgical) with traditional dressing.

Methods:
This is a retrospective, monocentric, case-control study based at the breast unit of the Città della Salute e della Scienza Hospital of Turin, Italy. Forty-two patients who underwent breast surgeries and met the inclusion criteria were enrolled, from February 1 to July 31, 2018. The primary endpoint was comparing the incidence of surgical site complications (skin alterations, infection, and wound dehiscence) in the two groups. The secondary endpoints were evaluating patient’s quality of life, aesthetic outcomes, and compliance to the dressings.

Results:
The distribution of risk factors at the baseline between the two groups was balanced, without statistically significant differences. Wound complications’ incidence at 1 week was lower in the advanced dressing group (P = 0.015). On the bivariate descriptive analysis, advanced dressing proved to be easier to remove for the operator (P = 0.026). The aesthetic outcomes vouched for better scores in the advanced dressing group.

Conclusion:
In the presented study Aquacel Ag Surgical dressing reduces surgical site complications in the first week after surgery in patients affected by three or more risk factors (or two with at least one classified as “high risk”).
NEW BIOMARKER QUANTIFYING THE EFFECT OF ANTI-VEGF THERAPY IN EYES WITH PROLIFERATIVE DIABETIC RETINOPATHY ON ULTRAWIDE FIELD FLUORESCEIN ANGIOGRAPHY
Authors: Fan Wenying , Nittala Muneeswar Gupta , Wykoff Charles C. , Brown David M. , Uji Akihito , Hemert Jano Van , Fleming Alan , Robertson Gavin , Sadda Srinivas R. , IP Michael 
Published: November 2021

Purpose:
To quantify changes of the retinal vascular bed area (RVBA) in mm2 on stereographically projected ultrawide field fluorescein angiography images in eyes with proliferative diabetic retinopathy after antivascular endothelial growth factor injection.

Methods:
This is a prospective, observational study. The early-phase ultrawide field fluorescein angiography images (Optos 200Tx) of 40 eyes with proliferative diabetic retinopathy and significant nonperfusion obtained at baseline and after six months (NCT02863354) were stereographically projected by correcting peripheral distortion. The global retinal vasculature on ultrawide field fluorescein angiography was extracted for calculating RVBA by summing the real size (mm2) of all the pixels automatically.

Results:
For the entire cohort, the global RVBA for the entire retina decreased from 67.1 ± 15.5 to 43.6 ± 18.8 mm2 after anti-VEGF treatment at six months (P < 0.001). In the subgroup receiving monthly anti-VEGF injections, the global RVBA decreased from 68.7 ± 16.2 to 33.9 ± 13.3 mm2 (P < 0.001). In the subgroup receiving anti-VEGF every three months, the global RVBA decreased from 65.6 ± 15.1 to 50.8 ± 19.3 mm2 (P = 0.004).

Conclusion:
RVBA seems to be a new biomarker to indicate efficiency of retinal vascular changes after anti-VEGF injection. Eyes with proliferative diabetic retinopathy and significant nonperfusion demonstrate reduced RVBA after anti-VEGF treatment.
MELD-Na Accurately Predicts 6-Month Mortality in Patients With Decompensated Cirrhosis
Authors: Brown Cristal , Aksan Nazan , Muir Andrew J. 
Published: November 2021

Goal:
The goal of this study was to determine the accuracy of Model of End-stage Liver Disease—Sodium (MELD-Na) in predicting 6-month mortality for patients listed for liver transplantation on the United Network of Organ Sharing (UNOS) waitlist.

Background:
End-stage liver disease patients underutilize hospice services despite significant morbidity and mortality associated with advanced liver disease. A well-known barrier to hospice referral is clinician uncertainty in identifying patients with an expected survival of <6 months, a requirement for a referral.

Methods:
Retrospective cross-sectional analysis was performed from UNOS data spanning February 27, 2002, to September 30, 2019. Inclusion criteria of patients aged 18 years and above, diagnosis of cirrhosis, liver transplant eligible, and listed in the UNOS database. Exclusion criteria included fulminant hepatic failure, prior history of liver transplantation, diagnosis of hepatocellular carcinoma, receipt of liver transplant in <180 days, or removal from waiting list <180 days for a reason other than death.

Measurement:
Mortality by 180 days.

Results:
Of the 93,157 patients that met inclusion criteria, MELD-Na was calculated for all patients with sodium, total bilirubin, international normalized ratio, and creatinine available (N=79,611). The c-statistic with 95% confidence interval for MELD-Na for the predicted 6-month mortality was 0.83 (0.827-0.835). Mean MELD-Na of 28.2 was associated with ≤50% 6-month survival.

Conclusion:
MELD-Na is an objective, quick measure that can aid providers in identifying patients with increased 6-month mortality in time-constrained settings, and a score of 28 can trigger the discussion for hospice as a means of improving value-based health care.
Understanding components of mobility during the COVID-19 pandemic
Authors: Edsberg Møllgaard Peter , Lehmann Sune , Alessandretti Laura 
Published: November 2021

Travel restrictions have proven to be an effective strategy to control the spread of the COVID-19 epidemics, in part because they help delay disease propagation across territories. The question, however, as to how different types of travel behaviour, from commuting to holiday-related travel, contribute to the spread of infectious diseases remains open. Here, we address this issue by using factorization techniques to decompose the temporal network describing mobility flows throughout 2020 into interpretable components. Our results are based on two mobility datasets: the first is gathered from Danish mobile network operators; the second originates from the Facebook Data-For-Good project. We find that mobility patterns can be described as the aggregation of three mobility network components roughly corresponding to travel during workdays, weekends and holidays, respectively. We show that, across datasets, in periods of strict travel restrictions the component corresponding to workday travel decreases dramatically. Instead, the weekend component, increases. Finally, we study how each type of mobility (workday, weekend and holiday) contributes to epidemics spreading, by measuring how the effective distance, which quantifies how quickly a disease can travel between any two municipalities, changes across network components.
This article is part of the theme issue ‘Data science approaches to infectious disease surveillance’.
pISA-tree - a data management framework for life science research projects using a standardised directory tree
Authors: Petek Marko , Zagorščak Maja , Blejec Andrej , Ramšak Živa , Coll Anna , Baebler Špela , Gruden Kristina 
Published: November 2021

AbstractWe developed pISA-tree, a straightforward and flexible data management solution for organisation of life science project-associated research data and metadata. pISA-tree was initiated by end-user requirements thus its strong points are practicality and low maintenance cost. It enables on-the-fly creation of enriched directory tree structure (project/Investigation/Study/Assay) based on the ISA model, in a standardised manner via consecutive batch files. Templates-based metadata is generated in parallel at each level enabling guided submission of experiment metadata. pISA-tree is complemented by two R packages, pisar and seekr. pisar facilitates integration of pISA-tree datasets into bioinformatic pipelines and generation of ISA-Tab exports. seekr enables synchronisation with the FAIRDOMHub repository. Applicability of pISA-tree was demonstrated in several national and international multi-partner projects. The system thus supports findable, accessible, interoperable and reusable (FAIR) research and is in accordance with the Open Science initiative. Source code and documentation of pISA-tree are available at https://github.com/NIB-SI/pISA-tree.
Modern microbial mats from the Chihuahuan Desert provide insights into ecological stability throughout Earth’s history
Authors: Madrigal-Trejo David , Sánchez-Pérez Jazmín , Espinosa-Asuar Laura , Souza Valeria 
Published: November 2021

AbstractMicrobial mats are complex ecological assemblages that are found in the Precambrian fossil record and in extant extreme environments. Hence, these structures are regarded as highly stable ecosystems. In this work, we assess the ecological stability in a modern, fluctuating, hypersaline pond from the Cuatro Ciénegas Basin. From the 2016 to 2019 metagenomic sampling of this site, we found that this microbial site is sensitive to disturbances, which leads to high taxonomic replacement. Additionally, the mats have shown to be functionally stable throughout time, and could be differentiated between dry and rainy seasonal states. We speculate that this microbial system could represent modern analogs of ancient microbial mats where functions were preserved over time, whereas composition was subject to diversification in the face of local and planetary perturbations.