bluuebunny/crossref_metadata_2025_split huggingface dataset:
Left atrial function assessed by speckle tracking echocardiography in anthracycline-induced cardiotoxicity: a case report
Authors: Sueta Daisuke , Usuku Hiroki , Kinoshita Yui , Tsujita Kenichi 
Published: November 2020

Abstract

Background
The onset prevention and early diagnosis in cardiotoxicity due to cancer chemotherapy are important, and it is important to detect cardiac dysfunction at an early stage and start treatment to enhance the therapeutic effect.

Case summary
A 31-year-old female with breast cancer received chemotherapy with epirubicin (400 mg/m2) and cyclophosphamide followed by docetaxel. Two months after the initiation of her chemotherapy, the left ventricular (LV) ejection fraction (LVEF) determined by echocardiography fell to 41.2%, and she was diagnosed with cancer therapy-related cardiac dysfunction (CTRCD). Three months after the initiation of cancer treatment, the peak velocity of late diastolic transmitral Doppler flow (A wave) became undetectable. Peak longitudinal strain (LS) and peak LS rate, which reflect left atrium (LA) reservoir function, gradually declined like the LVEF and LV-global LS (GLS). Seven months after the initiation of cancer treatment, she was diagnosed with acute decompensated heart failure. The changes in peak LS and peak LS at the onset were greater than those in LVEF and LV-GLS.

Discussion
This is a case report suggesting that LA reservoir function might be a more sensitive indicator than LVEF or LV-GLS in detecting CTRCD and that LA booster function might be the earliest. Left atrium reservoir function might be a more sensitive than conventional LV pump function and optimal indicator in CTRCD.
Successful transcatheter aortic valve implantation in a patient after an apico-aortic conduit for severe aortic stenosis complicated by haemolytic anaemia: a case report
Authors: Kim Kitae , Ehara Natsuhiko , Koyama Tadaaki , Furukawa Yutaka 
Published: November 2020

Abstract

Background
Apico-aortic conduit (AAC) which connects the left ventricular (LV) apex directly to the descending aorta through a valved conduit, is an alternative to surgical aortic valve replacement (AVR) for patients with aortic stenosis (AS) who are inoperable or high risk for surgical AVR and are not suitable candidates for transcatheter aortic valve implantation (TAVI).

Case summary
An 84-year-old man with severe AS underwent an AAC combined with coronary artery bypass grafting 8 years earlier. A saphenous vein graft was anastomosed from the conduit to the left anterior descending artery. He had developed haemolytic anaemia requiring frequent blood transfusions. The stenosis at the anastomosis of the left ventricle and the conduit might be the cause of a turbulent flow and a shear stress which led to mechanical haemolysis. We expected that dilatation of native aortic valve would reduce the blood flow at the anastomosis site and thereby improve haemolytic anaemia. Since balloon aortic valvuloplasty improved haemolytic anaemia without exacerbation of myocardial ischaemia, transsubclavian TAVI was performed. After the TAVI, significant reductions in the pressure gradient between the left ventricle and the ascending aorta and that between the left ventricle and the conduit were achieved, and the patient remained clinically stable without the recurrence of haemolytic anaemia.

Discussion
This is the first report regarding mechanical haemolytic anaemia after AAC which might result from a turbulence and a shear stress by the stenosis of the anastomosis of the LV apex and the conduit. A careful monitoring for conduit dysfunction should be made after AAC.
Relationship Between Serum IGF-1 and BMI Differs by Age
Authors: Sherlala Rehab A , Kammerer Candace M , Kuipers Allison L , Wojczynski Mary K , Ukraintseva Svetlana V , Feitosa Mary F , Mengel-From Jonas , Zmuda Joseph M , Minster Ryan L 
Published: November 2020

Abstract

Background
Serum levels of insulin-like growth factor 1 (IGF-1) and body mass index (BMI) are both associated with susceptibility to age-related diseases. Reports on the correlation between them have been conflicting, with both positive to negative correlations reported. However, the age ranges of the participants varied widely among these studies.

Methods
Using data on 4241 participants (aged 24–110) from the Long Life Family Study, we investigated the relationship between IGF-1 and BMI by age groups using regression analysis.

Results
When stratified by age quartile, the relationship between IGF-1 and BMI varied: in the first quartile (Q1, 20–58 years) the relationship was negative (β = −0.2, p = .002); in Q2 (58–66 years) and Q3 (67–86 years) the relationship was negative (β = −0.07, β = −0.01, respectively) but nonsignificant; and in Q4 (87–110 years) the relationship was positive (β = 0.31, p = .0002). This pattern did not differ by sex. We observed a similar age-related pattern between IGF-1 and BMI among participants in the third National Health and Nutritional Examination Survey.

Conclusions
Our results that the relationship between IGF-1 and BMI differs by age may explain some of the inconsistency in reports about their relationship and encourage additional studies to understand the mechanisms underlying it.
A Practical Guide to MeasuringEx vivoJoint Mobility Using XROMM
Authors: Manafzadeh Armita R 
Published: November 2020

SynopsisX-Ray Reconstruction of Moving Morphology (XROMM), though traditionally used for studies of in vivo skeletal kinematics, can also be used to precisely and accurately measure ex vivo range of motion from cadaveric manipulations. The workflow for these studies is holistically similar to the in vivo XROMM workflow but presents several unique challenges. This paper aims to serve as a practical guide by walking through each step of the ex vivo XROMM process: how to acquire and prepare cadaveric specimens, how to manipulate specimens to collect X-ray data, and how to use these data to compute joint rotational mobility. Along the way, it offers recommendations for best practices and for avoiding common pitfalls to ensure a successful study.
Facilitating reproducible research through direct connection of data analysis with manuscript preparation: StatTag for connecting statistical software to Microsoft Word
Authors: Welty Leah J , Rasmussen Luke V , Baldridge Abigail S , Whitley Eric W 
Published: November 2020

Abstract

Objectives
To enhance reproducible research by creating a broadly accessible, free, open-source software tool for connecting Microsoft Word to statistical programs (R/R Markdown, Python, SAS, Stata) so that results may be automatically updated in a manuscript.

Materials and Methods
We developed StatTag for Windows as a Microsoft Word plug-in using C# and for macOS as a native application using Objective-C. Source code is available under the MIT license at https://github.com/stattag.

Results
StatTag links analysis file(s) (R/R Markdown, SAS, Stata, or Python) and a Word document, invokes the statistical program(s) to obtain results, and embeds selected output in the document. StatTag can accommodate multiple statistical programs with a single document and features an interface to view, edit, and rerun statistical code directly from Word.

Discussion and Conclusion
StatTag may facilitate reproducibility within increasingly multidisciplinary research teams, improve research transparency through review and publication, and complement data-sharing initiatives.
An integrated disease-specific graded prognostic assessment scale for melanoma: contributions of KPS, CITV, number of metastases, and BRAF mutation status
Authors: Ahluwalia Manmeet , Ali Mir A , Joshi Rushikesh S , Park Eun Suk , Taha Birra , McCutcheon Ian , Chiang Veronica , Hong Angela , Sinclair Georges , Bartek Jiri , Chen Clark C 
Published: November 2020

AbstractBackgroundStereotactic radiosurgery (SRS) remains a mainstay therapy in the treatment of melanoma brain metastases (BM). While prognostic scales have been developed for melanoma patients who underwent SRS treatment for BM, the pertinence of these scales in the context of molecularly targeted therapies remains unclear.MethodsThrough a multi-institutional collaboration, we collated the survival patterns of 331 melanoma BM patients with known BRAF mutation status treated with SRS. We established a prognostic scale that was validated in an independent cohort of 174 patients. All patients with BRAF mutations in this series were treated with BRAF inhibitors. Prognostic utility was assessed using Net Reclassification Index (NRI &gt; 0) and integrated discrimination improvement (IDI) metrics.ResultsIn a multivariate Cox proportional hazards model, BRAF mutation status, KPS, number of metastases, and cumulative intracranial tumor volume (CITV) independently contributed to survival prognostication for melanoma patients with SRS-treated BM (P &lt; .05 for all variables). These variables were incorporated into a prognostic scale using the disease-specific graded prognostic assessment (ds-GPA) framework. This integrated melanoma ds-GPA scale was validated in 2 independent cohorts collated through a multi-institutional collaboration. In terms of order of prognostic importance, BRAF mutation status exerted the greatest influence on survival, while KPS, the number of metastases, and CITV exhibited comparable, lesser impacts.ConclusionsOptimal survival prognostication for SRS-treated patients with melanoma BM requires an integrated assessment of patient characteristics (KPS), tumor characteristics (CITV and number of metastases), and the mutational profile of the melanoma (BRAF mutation status).
Mebendazole and temozolomide in patients with newly diagnosed high-grade gliomas: results of a phase 1 clinical trial
Authors: Gallia Gary L , Holdhoff Matthias , Brem Henry , Joshi Avadhut D , Hann Christine L , Bai Ren-Yuan , Staedtke Verena , Blakeley Jaishri O , Sengupta Soma , Jarrell T Che , Wollett Jessica , Szajna Kelly , Helie Nicole , Mattox Austin K , Ye Xiaobu , Rudek Michelle A , Riggins Gregory J 
Published: November 2020

Abstract

Background
Mebendazole is an anthelmintic drug introduced for human use in 1971 that extends survival in preclinical models of glioblastoma and other brain cancers.

Methods
A single-center dose-escalation and safety study of mebendazole in 24 patients with newly diagnosed high-grade gliomas in combination with temozolomide was conducted. Patients received mebendazole in combination with adjuvant temozolomide after completing concurrent radiation plus temozolomide. Dose-escalation levels were 25, 50, 100, and 200 mg/kg/day of oral mebendazole. A total of 15 patients were enrolled at the highest dose studied of 200 mg/kg/day. Trough plasma levels of mebendazole were measured at 4, 8, and 16 weeks.

Results
Twenty-four patients (18 glioblastoma and 6 anaplastic glioma) were enrolled with a median age of 49.8 years. Four patients (at 200 mg/kg) developed elevated grade 3 alanine aminotransferase (ALT) and/or aspartate transaminase (AST) after 1 month, which reversed with lower dosing or discontinuation. Plasma levels of mebendazole were variable but generally increased with dose. Kaplan–Meier analysis showed a 21-month median overall survival with 41.7% of patients alive at 2 years and 25% at 3 and 4 years. Median progression-free survival (PFS) from the date of diagnosis for 17 patients taking more than 1 month of mebendazole was 13.1 months (95% confidence interval [CI]: 8.8–14.6 months) but for 7 patients who received less than 1 month of mebendazole PFS was 9.2 months (95% CI: 5.8–13.0 months).

Conclusion
Mebendazole at doses up to 200 mg/kg demonstrated long-term safety and acceptable toxicity. Further studies are needed to determine mebendazole’s efficacy in patients with malignant glioma.
Near haploidization is a genomic hallmark which defines a molecular subgroup of giant cell glioblastoma
Authors: Baker Tiffany G , Alden Jay , Dubuc Adrian M , Welsh Cynthia T , Znoyko Iya , Cooley Linda D , Farooqi Midhat S , Schwartz Stuart , Li Yvonne Y , Cherniack Andrew D , Lindhorst Scott M , Gener Melissa , Wolff Daynna J , Meredith David M 
Published: November 2020

Abstract

Background
Giant cell glioblastoma (gcGBM) is a rare histologic subtype of glioblastoma characterized by numerous bizarre multinucleate giant cells and increased reticulin deposition. Compared with conventional isocitrate dehydrogenase (IDH)-wildtype glioblastomas, gcGBMs typically occur in younger patients and are generally associated with an improved prognosis. Although prior studies of gcGBMs have shown enrichment of genetic events, such as TP53 alterations, no defining aberrations have been identified. The aim of this study was to evaluate the genomic profile of gcGBMs to facilitate more accurate diagnosis and prognostication for this entity.

Methods
Through a multi-institutional collaborative effort, we characterized 10 gcGBMs by chromosome studies, single nucleotide polymorphism microarray analysis, and targeted next-generation sequencing. These tumors were subsequently compared to the genomic and epigenomic profile of glioblastomas described in The Cancer Genome Atlas (TCGA) dataset.

Results
Our analysis identified a specific pattern of genome-wide massive loss of heterozygosity (LOH) driven by near haploidization in a subset of glioblastomas with giant cell histology. We compared the genomic signature of these tumors against that of all glioblastomas in the TCGA dataset (n = 367) and confirmed that our cohort of gcGBMs demonstrated a significantly different genomic profile. Integrated genomic and histologic review of the TCGA cohort identified 3 additional gcGBMs with a near haploid genomic profile.

Conclusions
Massive LOH driven by haploidization represents a defining molecular hallmark of a subtype of gcGBM. This unusual mechanism of tumorigenesis provides a diagnostic genomic hallmark to evaluate in future cases, may explain reported differences in survival, and suggests new therapeutic vulnerabilities.
Staphylococcus aureus Bacteremia in Patients Infected With COVID-19: A Case Series
Authors: Cusumano Jaclyn A , Dupper Amy C , Malik Yesha , Gavioli Elizabeth M , Banga Jaspreet , Berbel Caban Ana , Nadkarni Devika , Obla Ajay , Vasa Chirag V , Mazo Dana , Altman Deena R 
Published: November 2020

Abstract

Background
Previous viral pandemics have shown that secondary bacterial infections result in higher morbidity and mortality, with Staphylococcus aureus being the primary causative pathogen. The impact of secondary S. aureus bacteremia on mortality in patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains unknown.

Methods
This was a retrospective observational case series of patients with coronavirus disease 2019 (COVID-19) who developed secondary S. aureus bacteremia across 2 New York City hospitals. The primary end point was to describe 14-day and 30-day hospital mortality rates of patients with COVID-19 and S. aureus bacteremia. Secondary end points included predictors of 14-day and 30-day hospital mortality in patients with COVID-19 and S. aureus bacteremia.

Results
A total of 42 patients hospitalized for COVID-19 with secondary S. aureus bacteremia were identified. Of these patients, 23 (54.8%) and 28 (66.7%) died at 14 days and 30 days, respectively, from their first positive blood culture. Multivariate analysis identified hospital-onset bacteremia (≥4 days from date of admission) and age as significant predictors of 14-day hospital mortality and Pitt bacteremia score as a significant predictor of 30-day hospital mortality (odds ratio [OR], 11.9; 95% CI, 2.03–114.7; P = .01; OR, 1.10; 95% CI, 1.03–1.20; P = .02; and OR, 1.56; 95% CI, 1.19–2.18; P = .003, respectively).

Conclusions
Bacteremia with S. aureus is associated with high mortality rates in patients hospitalized with COVID-19. Further investigation is warranted to understand the impact of COVID-19 and secondary S. aureus bacteremia.
Plasma and Cerebrospinal Fluid Therapeutic Drug Monitoring of Ceftolozane and Tazobactam During Treatment of Multidrug-Resistant Pseudomonas aeruginosa Meningitis
Authors: McCreary Erin K , Byers Karin E , Fernandes Carolyn , Kline Ellen G , Nicolau David P , Shields Ryan K 
Published: November 2020

Abstract
We report a case of multidrug-resistant Pseudomonas aeruginosa meningitis treated with ceftolozane-tazobactam with concomitant therapeutic drug monitoring of plasma and cerebral spinal fluid. The data suggest that ceftolozane-tazobactam may be an option for select central nervous system infections; however, treatment decisions should be interpreted on a case-by-case basis.
Severe Acute Respiratory Syndrome Coronavirus 2 Seroprevalence Among Adults in a Tropical City of the Caribbean Area, Colombia: Are We Much Closer to Herd Immunity Than Developed Countries?
Authors: Mattar Salim , Alvis-Guzman Nelson , Garay Evelin , Rivero Ricardo , García Alejandra , Botero Yesica , Miranda Jorge , Galeano Ketty , de La Hoz Fernando , Martínez Caty , Arrieta Germán , Faccini-Martínez Álvaro A , Guzmán Camilo , Kerguelen Hugo , Moscote Maria , Contreras Hector , Contreras Veronica 
Published: November 2020

Abstract
A serological survey was carried out in Monteria (500 000 population), a mid-size city in Colombia. An overall prevalence of 55.3% (95% confidence interval, 52.5%–57.8%) was found among a sample of 1.368 people randomly selected from the population. Test positivity was related to economic characteristics with the highest prevalence found in the most impoverished areas, representing 83.8% of the city’s population. We found a prevalence that might be associated with some important level of population immunity.
Severe Acute Respiratory Syndrome Coronavirus 2 Lethality Did not Change Over Time in Two Italian Provinces
Authors: Flacco Maria Elena , Acuti Martellucci Cecilia , Bravi Francesca , Parruti Giustino , Mascitelli Alfonso , Mantovani Lorenzo , Boccia Stefania , Manzoli Lamberto 
Published: November 2020

Abstract
This retrospective cohort study included all the subjects diagnosed with severe acute respiratory syndrome coronavirus 2 infection (n = 2493) in 2 Italian provinces. Two hundred fifty-eight persons died, after a median of 14.0 ± 11.0 days. Adjusting for age, gender, and main comorbidities, the ≥28-day case-fatality rate did not decrease from March to April 2020 (adjusted hazard ratio, 0.93; P = .6).
Simulating within host human immunodeficiency virus 1 genome evolution in the persistent reservoir
Authors: Jones Bradley R , Joy Jeffrey B 
Published: November 2020

Abstract
The complexities of viral evolution can be difficult to elucidate. Software simulating viral evolution provides powerful tools for exploring hypotheses of viral systems, especially in situations where thorough empirical data are difficult to obtain or parameters of interest are difficult to measure. Human immunodeficiency virus 1 (HIV-1) infection has no durable cure; this is primarily due to the virus’ ability to integrate into the genome of host cells, where it can remain in a transcriptionally latent state. An effective cure strategy must eliminate every copy of HIV-1 in this ‘persistent reservoir’ because proviruses can reactivate, even decades later, to resume an active infection. However, many features of the persistent reservoir remain unclear, including the temporal dynamics of HIV-1 integration frequency and the longevity of the resulting reservoir. Thus, sophisticated analyses are required to measure these features and determine their temporal dynamics. Here, we present software that is an extension of SANTA-SIM to include multiple compartments of viral populations. We used the resulting software to create a model of HIV-1 within host evolution that incorporates the persistent HIV-1 reservoir. This model is composed of two compartments, an active compartment and a latent compartment. With this model, we compared five different date estimation methods (Closest Sequence, Clade, Linear Regression, Least Squares, and Maximum Likelihood) to recover the integration dates of genomes in our model’s HIV-1 reservoir. We found that the Least Squares method performed the best with the highest concordance (0.80) between real and estimated dates and the lowest absolute error (all pairwise t tests: P &lt; 0.01). Our software is a useful tool for validating bioinformatics software and understanding the dynamics of the persistent HIV-1 reservoir.
Species boundaries and phylogeographic patterns in new species ofNannoniscus(Janiroidea: Nannoniscidae) from the equatorial Pacific nodule province inferred from mtDNA and morphology
Authors: Kaiser Stefanie , Kihara Terue Cristina , Brix Saskia , Mohrbeck Inga , Janssen Annika , Jennings Robert M 
Published: November 2020

AbstractSpatial patterns of genetic variation (based on COI and 16S mtDNA) for morphologically similar species in the isopod genus Nannoniscus G.O. Sars. 1870 were examined that occur broadly across the Clarion Clipperton Fracture Zone (CCZ). Samples were obtained from five different licence areas as well as an Area of Particular Environmental Interest (APEI-6) with sites located at various distances (a few to several hundred kilometres) from one another. Applying three different species delimitation (SD) methods (sGMYC, mPTP and ABGD) of the molecular data, we could distinguish between four and 12 different molecular taxonomic operational units (MOTUs). Morphological analyses could confirm five distinct phenotypic clades that represent species new to science and are described here: Nannoniscus brenkei sp. nov., Nannoniscus hilario sp. nov., Nannoniscus magdae sp. nov., Nannoniscus menoti sp. nov. and Nannoniscus pedro sp. nov. Despite the assumed limited dispersal capacity of Nannoniscus species, we found haplotypes of two species to be geographically widespread (up to &gt; 1400 km apart), as opposed to several divergent clades occurring in close vicinity or even sympatry. Geographic distance appeared to explain the phylogeographic structure of Nannoniscus species to some extent, although oceanographic features and level of environmental heterogeneity were probably equally important.
Pediatric Trauma Arrival Times and the Swing Shift
Authors: Berg Patrick , Chestovich Paul J. , Jones Stephanie , Allenback Gayle , McNickle Allison G. , Saquib Syed F. , Fraser Douglas R. , Kuhls Deborah A. 
Published: November 2020

Background
Trauma center staff and trainees are often assigned to a day and night shift. However, for adult trauma, the swing shift has been found to offer superior clinical exposure compared with a standard day or night shift for trainees. We characterized patterns in pediatric trauma arrival times based on the hour, weekday, and month and studied whether or not the swing shift also maximizes exposure to hands-on experiences in managing pediatric trauma.

Methods
We performed a retrospective review of the trauma database at our urban, level 2 pediatric trauma center. We identified all the pediatric trauma activations in the last 13 years (2006–2018). A retrospective shift log was created, which included day (7:00 am to 7:00 pm), night (7:00 pm to 7:00 am), and swing (noon to midnight) shifts. The shifts were compared using the Wilcoxon match-pairs signed rank test. Weekends data were also compared with weekdays, and comparisons were also made for pediatric patients with Injury Severity Scores (ISS) >15.

Results
There were 3532 pediatric patients identified for our study. The swing shift had 1.98 times more activations than the night shift, and 1.33 more than the day shift (P < 0.001). The swing shift was also superior to both the day and night shifts for exposure to patients with Injury Severity Score greater than 15 (P < 0.001). Weekend days had 1.28 times more trauma than the weekdays (P < 0.001). Peak arrival time was between the hours of 3:00 pm and 9:00 pm, and patient age did not have an effect on this trend.

Conclusions
Experience in managing pediatric trauma patients will improve for trainees who utilize the swing shift. In addition, the hours between 3:00 pm and 9:00 pm on weekends may represent a time of particularly high likelihood of pediatric trauma arrivals, which may require extra staff and hospital resources.

Level of Evidence: Therapeutic Study, Level IV