bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of an Automated Hemoglobin A1c Reflex on Socioeconomic Disparities in Testing Frequency and Glycemic Control
Authors: Azimi Vahid , Farnsworth Christopher 
Published: November 2022

Abstract
The American Diabetes Association recommends semiannual hemoglobin A1c (A1c) testing for diabetic patients with stable glycemic control and quarterly testing for patients with a change in therapy or who do not meet A1c goals. To aid in achieving this goal our laboratory performs an automated, add-on A1c test for any diabetic and hospitalized patient with no A1c ordered in the previous 60 days. The primary aim of this study was to determine the impact of an automated reflex on A1c testing frequency and glycemic control. Our second aim was to determine socioeconomic differences of reflexed A1c testing. All A1c results performed by the BJH laboratory from 5/1/2016-1/22/22 and associated patient demographics were retrieved from the laboratory information system. Patient addresses were geocoded, and a CDC-validated social vulnerability index (SVI) was assigned to each patient based on their census tract of residence. Patients were then stratified in the bottom SVI half (most vulnerable) and the upper SVI half (least vulnerable). A total of 32,861 A1c’s were performed on 17,699 patients, 6,341 of whom had &gt;1 test. 2,952 (46.6%) patients had at least one reflexed A1c (add-on group). The median average time between A1c tests was 144.4 days in the add-on group and 209.0 days in the no add-on group (p&lt;0.001). The average time between A1c tests for patients in the add-on group in the bottom SVI half was 143.8 days vs. 145.3 days in the top SVI half (p=0.84). In contrast, the median average time between A1c tests for patients in the no add-on group in the bottom SVI half was 215.5 days and was 199.5 days in the top SVI half (p&lt;0.05). The number of patients with A1c in the uncontrolled range (A1c =9%) decreased by 11.5% in the add-on group compared to 1.7% in the no add-on group (p&lt;0.001). In those with add-on testing, the proportion of patients in the bottom SVI with initial A1c =9% and a longitudinal decrease in A1c was 11.3% compared to 11.9% in the top SVI half (p=0.39). In the no add-ons group, the proportion of patients with A1c =9% increased by 3.3% in the bottom SVI and decreased by 12.1% in the top SVI (p=0.01). A socioeconomic disparity is observed in A1c testing frequency and rates of uncontrolled diabetes over time for patients without add-on testing, but not for patients with add-on testing. Automatic add-on testing for hospitalized diabetic patients may reduce socioeconomic disparities in A1c testing frequency and glycemic control.
Rapid Analysis and Integration of Patient Clinical Data with SARS-CoV-2 Genome Sequence Data
Authors: Kinskey Jacob , Hsu Jim , Davis Jim , Olsen Randy , Long Scott , Christensen Paul 
Published: November 2022

Abstract

Objectives
The COVID-19 pandemic has evolved the importance of monitoring viral evolution and correlated clinical outcomes in directing patient care and health policy. Our institution sequences the viral genome from essentially all SARS-CoV-2 infected patients in our hospital system’s diverse patient population, allowing for continuous monitoring of the virus composition in a major US metroplex. Our objective was to support the vision of near real-time assessment using bioinformatics and data management methods designed to enable rapid and accurate analyses.

Methods
Our bioinformatics pipeline is designed to analyze genomic data with paired patient data as rapidly as possible. To always have the most up-to-date patient information available, all co-morbidity, therapeutic and outcomes data are extracted from the Electronic Medical Record (EMR) system every night. Essentially all positive SARS-CoV-2 samples in our healthcare system are sequenced with an Illumina NovaSeq 6000 instrument in batches of 768 genomes. Immediately after the batched sequencing data is complete, the pipeline assembles the genomes using a Singularity container provided by the Bacterial and Viral Bioinformatics Resource Center (BV-BRC). Lineage calls are made using the latest available version of Pangolin. The genomic data is merged with the patient data, and 36 different statistical analyses (such as age, ethnicity, co-morbidity, admission rate, and mortality rate comparisons) are performed in 11 different patient cohorts (such as all Omicron vs Delta, vaccinated vs non-vaccinated, and monoclonal antibody recipients only). 30 interactive Tableau figures are automatically refreshed with the latest data, and summary reports are emailed to key stakeholders. The pipeline is orchestrated using the Snakemake workflow management system on an on-premise high-performance compute cluster (HPC).

Results
The bioinformatics analysis for a batched run containing 768 genomes, including genome assembly, all patient cohort comparisons and dashboard updates, completes in four hours.

Conclusion
Throughout the COVID-19 pandemic, but especially during the early weeks of each surge, our hospital leaders have been extremely interested in the analysis for each sequencing run. The use of a modular, container-based architecture orchestrated using a workflow manager on an on-premise HPC enables us to deliver results very quickly. The performance of this design allowed for dynamic decision making of our organization as new strains emerged in the Houston area.
A case report of type 2M Von Willebrand disease with unique mutations
Authors: Qi Xiaohua , Fang Yanan 
Published: November 2022

Abstract
Von Willebrand disease (vWD) is the most common inherited bleeding disorder. It results from quantitative or qualitative defects of the von Willebrand factor (vWF) protein, and is divided into three types, namely type 1, type 2(2A, 2B, 2M, and 2N), and type 3 vWD. Here we report a case of 55-year-old female who presented with recurrent gastrointestinal bleeding due to angiodysplasia. Her past medical history is significant for vWD (type unknown) with hemoptysis, epistaxis and menorrhagia requiring Humate-P replacement multiple times. She has one sister with mild vWD of unknown type and 4 other siblings with no bleeding history. Coagulation testing shows normal PT and aPTT. Von Willebrand panel shows vWF antigen of 33%, VWF ristocetin cofactor activity of 15%, and Factor VIII of 87%. The ratio (VWF: RCo/VWF: Ag) is low (0.45) and the multimer pattern is normal. This is consistent with type 2M vWD. VWD gene sequencing shows heterozygous variants of c.4241T&gt;G (p.Val1414Gly) and c.5227G&gt;A (p.Val1743Met). Of note, one variant (c.4241T&gt;G/p.Val1414Gly) has been reported in two individuals with type 2A but not in type 2M vWD. This may truly represent different types of vWD caused by same mutation or could be due to variation in testing and/or result interpretation among laboratories. The other variant c.5227G&gt;A(p.Val1743Met) in A3 domain has never been reported with uncertain significance. Further investigation including vWF panel testing and genetic analysis in family members would help characterize those mutations.
Measuring clinical lead testing coverage to support a population health initiative
Authors: Ko Kyungmin , Dowlin Michael , Mroue Youssef , Chong Thomas , Oezguen Numan , Singh Ila 
Published: November 2022

Abstract
Despite national efforts to reduce lead exposure, some children are still exposed to lead, leading to damage to the nervous system, delayed development, and learning and behavioral problems. CDC has recommended targeting high-risk groups for screening. In addition, Texas Department of State Health Services reported a concerning 17% lead testing coverage of 0-to-5-year-olds in in Harris County (where Houston is located). With the eventual goal of improving lead-related clinical care in a large pediatric hospital network, we asked the following questions: 1) What are the high-risk groups specific to our patient population? 2) For patients who are screened positive, are we adequately confirming the results? 3) For those with confirmed lead exposure, are we providing adequate follow-up care? To answer these questions, we analyzed lead testing and hemoglobin testing data on all children less than 6 years of age from the Texas Children’s Hospital’s electronic health record between 2017 and 2021. Lead screening could be performed on capillary or venous blood, but for elevations on capillary blood we analyzed if the results were confirmed with a venous blood test, as recommended by CDC. We used hemoglobin testing as an indicator of follow-up care of lead-exposed children, because an anemia work-up is recommended for such children. We repeated analysis using two different lead level thresholds, because of recent change to the CDC blood lead reference value from 5 mcg/dL to 3.5 mcg/dL in May 2021. We found 273 children (0.33% of children with capillary blood test) to have cBLL = 3.5mcg/dL. There was a significant racial disparity in the rate of lead screening. For example, the screening rate of Black children was 14%, whereas that of White children were 23%. There was a geographic discrepancy between the areas with most elevated cBLL and testing volume. For example, the area where cBLL was most frequently elevated (3.7%) received less than a fifth of tests compared to the most well-tested area. Only 75% of children with a cBLL = 5mcg/dL received a timely venous blood lead test for confirmation, and this dropped to 43% for children with a cBLL = 3.5mcg/dL. Similarly, only 75% of children with a confirmed venous lead level = 5 mcg/dL received a follow-up repeat vBLL test, and 55% received a follow-up hemoglobin measurement. There is room for improvement in population lead health, in terms of both equity and resource distribution. Improvement of lead-related clinical practice could benefit hundreds of children in the Houston metropolitan area.
Patient Outcomes in CMV and SARS-CoV-2 Coinfection
Authors: Walley Debbie 
Published: November 2022

Abstract
This study examines clinical outcomes in patients with cytomegalovirus (CMV) and SARS-CoV-2 coinfection. Between June and November 2020, previously immunocompetent patients with SARS-CoV-2 and CMV coinfection were identified at Houston Methodist Hospital as part of routine clinical correlation by a molecular pathologist. SARS-CoV-2 nasopharyngeal specimens were analyzed by real time reverse-transcriptase polymerase chain reaction (RT-PCR). All CMV tests were performed on plasma or bronchoalveolar lavage (BAL) specimens and analyzed by competitive polymerase chain reaction. 65 previously immunocompetent patients with CMV and SARS-CoV-2 coinfection were identified. Patient demographics include 41 male patients (63%) and 24 female patients (37%) ranging in age from 34 to 86 years (mean: 66.04, median 68). Documented pre-existing conditions include 27 patients with hypertension 41.5%), 19 patients with diabetes mellitus (29.2%), 9 patients with coronary artery disease (13.8%), and 3 patients with asthma (4.6%). Eight patients (12.3%) had no documented pre-existing conditions. The plasma CMV viral load ranged from &lt;300 to 21,566 IU/mL. The CMV PCR results from bronchoalveolar lavage and bronchial wash specimens ranged from &lt;300 to 59,127 IU/mL. CMV PCR was initially negative in 10 patients then positive on serial testing. 60 patients were critically ill requiring ventilator support (92.3%). 47 patients (72.3%) expired, 7 patients (10.8%) were transferred to a long term acute care facility, 3 patients (4.6%) were discharged to a rehabilitation facility, 3 patients (4.6%) were discharged home, and 1 patient (1.5%) remained in-patient at the time of analysis. The prevalence of CMV seropositivity and medical comorbidities increases with age. Reactivation of latent CMV is a known occurrence in critically ill patients that is associated with poor outcomes. The majority of the patients in our cohort were 50 years old, and all were severely to critically ill with a mortality rate of 72.3% These findings suggest CMV portends a worse prognosis in patients with COVID-19. These findings also demonstrate the importance of clinical correlation in molecular testing.
MECOM copy number alterations identify a new group of myeloid neoplasms with a poor prognosis
Authors: Yang David , Karlin Kirill , Bryke Christine , Michaels Phillip 
Published: November 2022

Abstract

Objective
Myeloid neoplasms (MNs) harboring inv(3)(q21q26)/t(3;3)(q21;q26) or MECOM gene rearrangements as identified by fluorescence in situ hybridization (FISH) are known to carry a poor prognosis. The objective of this study is to assess prognostic impact of MNs with copy number alterations (CNA) in MECOM as compared to MNs with inv(3)/t(3;3) or MECOM rearrangements. We present those initial comparative results and secondarily assess whether genetic mutations that confer a worse clinical outcome are also associated with MNs with MECOM CNA.

Methods
A retrospective review of electronic pathology records was performed at Beth Israel Deaconess Medical Center. All MNs from 2016 – current with MECOM FISH (Abbott Molecular, Abbott Park, IL) confirmed analyses were extracted. Other additional items extracted included karyotype and next-generation sequencing (NGS) results of a 65 gene myeloid panel (SmartGenomics Myeloid Profile, PathGroup, Nashville, TN). Kaplan-Meier and ANOVA were performed using GraphPad Prism (San Diego, CA).

Results
A total of 307 cases were identified in which MECOM FISH was performed. Exclusion of cases lacking inv(3)/t(3;3), MECOM rearrangement, or MECOM CNA provided an initial study cohort of 20 cases. 5 cases had MECOM rearrangement with inv(3)/t(3;3), 7 had MECOM rearrangement without inv(3)/t(3;3), and 8 had MECOM CNA. 13 of 20 cases had a complex karyotype, 13 of 20 cases had a monosomal karyotype, 10 of 20 cases had both a complex and monosomal karyotype. Of the 20 cases in which MECOM FISH demonstrated inv(3)/t(3;3), MECOM rearrangement, or CNA, NGS was performed on 16 cases. Genes known to be associated with a significant negative overall survival (OS) include ASXL1, EZH2, IDH2, KRAS, NRAS, RAD21, RUNX1, SRSF2, STAG2, TP53 with single and multiple mutations found in 9 of 20 cases. Kaplan-Meier analysis revealed no significant difference in OS among the three MECOM aberration groupings (Log-rank test; p=0.77). Single factor ANOVA analysis revealed enrichment for high risk gene mutations in MECOM CNA (p=0.04) and TP53 mutations (p=0.04) when compared to MNs with MECOM rearrangements.

Summary
Our analysis of MNs with MECOM aberrations by FISH reveal that MECOM with CNA display similarly poor overall survival as MNs with inv(3)/t(3;3) and MECOM rearrangements. Additionally, the MECOM CNA group was enriched for high risk gene mutations and TP53 as compared to inv(3)/t(3;3) and MECOM rearrangement groups. Overall, the initial results of this study reveal a new group of MNs harboring MECOM CNA that confer a poor prognosis and high risk mutational profile.
Barotrauma in a Previously Healthy and Young COVID-19 Patient: an Autopsy Case Report
Authors: Kadow Z , Wilken N , Gallardo J , Xu Y 
Published: November 2022

Abstract

Introduction/Objective
Since the emergence of a novel SARS-CoV-2 virus caused coronavirus disease 2019 (COVID-19), a great number of autopsy studies have been published. However, histopathologic studies focused on pulmonary barotrauma are very rare. Here we report an autopsy confined to the lungs on a young COVID-19 patient.

Methods/Case Report
The patient was a 37-year-old male, non-smoker, with no significant past medical history, and a body mass index of 24.1, who presented with shortness of breath and cough. A computerized tomography (CT) showed features of atypical pneumonia. The main abnormal laboratory data included elevated partial thromboplastin time, fibrinogen, and D-Dimer. The patient had been on mechanical ventilation for 35 days, and was complicated by recurrent pneumothoraces, hypotension, and worsening hypoxia. An autopsy limited to the lungs was performed after the patient expired. Grossly, the lungs showed increased weight, adhesions on visceral pleural surface, patchy consolidation and dilated subpleural cysts. Histological examination revealed cystically dilated/remodeled airspaces with extensive coagulative necrosis, focal alveolar hemorrhage and edema, focal confluent fibrosis, and subpleural blebs. Fresh fibrinous thrombi were seen in small- and medium-sized vessels. Viral cytopathic changes or significant inflammation were not observed. The findings in the lungs were consistent with barotrauma in COVID-19.

Results (if a Case Study enter NA)
NA.

Conclusion
This case demonstrates various histopathologic changes of the lungs in a previously healthy and young COVID-19 patient with prolonged hospital course of mechanical ventilation. The features of diffuse alveolar damage with inflammation usually seen in the early stage of barotrauma are not identified. Our findings in the lungs may represent the histopathologic characteristics of the later stage of barotrauma in COVID-19.
Pseudogout Causing Thoracic Outlet Syndrome
Authors: Abraham A , Duke W 
Published: November 2022

Abstract

Introduction/Objective
Calcium pyrophosphate dihydrate (CPPD) crystal deposition or pseudogout is a common entity encountered in routine practice. However, when a common entity presents in uncommon locations with unusual clinical manifestations, it creates a diagnostic conundrum. Pseudogout commonly occurs in the joint extremities including knee, wrist, shoulder, hip, and ankle joints. The sternoclavicular joint is a rare site for pseudogout with very low incidence. To the best of our knowledge, there are only two other cases of pseudogout mimicking a tumor causing vascular obstruction in the literature.

Methods/Case Report
A 63 year old male presented with an enlarging supraclavicular mass. A computed tomography angiography scan of the chest revealed an irregular soft tissue mass located behind the medial clavicle measuring up to 4 cm and was noted to compress and partially occlude the right subclavian vein. Partial occlusion of right axillary vein, right internal jugular vein, and right brachiocephalic vein were also noted on imaging. The venous compression led to outflow obstruction and resultant recurrent deep vein thrombosis of the right upper extremity. Due to compression by the mass, he required stenting of the right subclavian vein which unfortunately reoccluded. Subsequently, the patient underwent excision of the mass and partial resection of the first rib with decompression of the thoracic outlet. The excisional biopsy revealed dense rhomboid-shaped CPPD crystal depositions in irregular nodules within a background of fibrinoid material and fragments of unremarkable cartilaginous tissue. The patients compressive symptoms were relieved following the excision. While clinically and radiologically the mass was concerning for a malignant tumor, histological examination provided a definitive diagnosis of a benign process.

Results (if a Case Study enter NA)
NA.

Conclusion
Pseudogout is a rare mimicker of bone and soft tissue tumors and differentiation from an enchondroma, or grade 1 chondrosarcoma becomes a challenge especially on small tissue biopsies and is a possible diagnostic pitfall.
Systemic and Local Disease Manifestations Following COVID-19 Vaccination
Authors: Mahalingam V D , Huang J Z , Bernacki K D , Amin M B , Zhang P 
Published: November 2022

Abstract

Introduction/Objective
COVID-19 vaccine-related lymphadenopathy, particularly in the ipsilateral axilla, is a relatively well-known side effect of mRNA vaccines with many reports in radiology, but less is known regarding histopathology and additional sites of lymphadenopathy, as well as other localized potential vaccine-related mass manifestations. In addition to a case of minimal change disease, we report two cases here with associated systemic and local pathologic changes related to COVID-19 vaccination.

Methods/Case Report
In case #1, a 17-year-old male presented with a 2.4 cm left postauricular mass. He had originally noticed the mass six months prior and thought that it had recently been growing. The mass was soft, nonfluctuant, and nontender to palpation. Given the risk of malignancy, a resection was performed. Histology showed an enlarged lymph node composed of mixed inflammatory cell components consistent with lymphoid hyperplasia and no evidence of malignancy. On further chart review, the patient had received his second COVID-19 vaccination just prior to noticing the mass enlarging. A SARS-CoV-2 Anti-Spike IgG assay was as high as 24,396 AU/ml, suggesting that this benign lymphadenopathy was most likely related to his vaccination. For case #2, a 47-year-old male developed a painless right deltoid mass shortly after receiving his vaccination at the same area that subsequently increased in size over seven months to 6.5 cm. Imaging showed a heterogeneous mass within the deltoid muscle concerning for malignancy and a biopsy was performed. Sections showed wavy, bland spindle cells with nuclei staining diffusely positive for beta-catenin, consistent with fibromatosis at his vaccination site.

Results (if a Case Study enter NA)
NA.

Conclusion
In summary, these case reports show potential systemic and local reactive effects in response to COVID-19 vaccination.
A Rare Case of Primary Cardiac Undifferentiated Pleomorphic Sarcoma with Brain Metastases
Authors: Monika F , Groh D 
Published: November 2022

Abstract

Introduction/Objective
Undifferentiated pleomorphic sarcomas are highly malignant undifferentiated fibroblastic tumors with an aggressive clinical course. Primary cardiac undifferentiated pleomorphic sarcomas are extremely rare (incidence &lt; 0.1%) and most commonly occur in the left atrium. We report a case of a left atrial undifferentiated pleomorphic sarcoma that was thought to be a cardiac myxoma on imaging studies.

Methods/Case Report
A 22-year-old female without past medical or family history presented to the emergency department for a cerebrovascular accident. During clinical work up, transesophageal echocardiogram revealed a 3 cm mass attached to left atrial septum and a 1.8 cm mass attached to the interatrial septum with associated thrombus formation. The patient underwent surgical excision of the mass. Histological analysis revealed a tumor comprised of spindle and epithelioid cells with abundant nuclear atypia, mitotic figures, and necrosis. Extensive immunohistochemical analysis did not show specific lineage and the tumor was classified as an undifferentiated pleomorphic sarcoma. Two months after initial surgery, the patient presented with additional neurologic deficits and brain lesions. The pathologic findings in the brain biopsy specimen were identical to those in the cardiac specimen and consistent with metastatic undifferentiated pleomorphic sarcoma. This case provides insight into the metastatic behavior of high-grade cardiac sarcomas and their unusual clinical and radiographic presentations, including neurologic manifestations that are unique to the primary cardiac location of the tumor.

Results (if a Case Study enter NA)
NA

Conclusion
In conclusion, because the majority of cardiac undifferentiated pleomorphic sarcomas occur in the left atrium, these growths can be mistakenly diagnosed as benign myxoma preoperatively. This case provides insight into the metastatic behavior of high-grade cardiac sarcomas and their unusual clinical and radiographic presentations, including neurologic manifestations that are unique to the primary cardiac location of the tumor.