bluuebunny/crossref_metadata_2025_split huggingface dataset:
HIV Type-1 Genotyping in the Context of the COVID-19 Pandemic: A Critical Tool for Identifying Antiretroviral Drug Resistance and Optimizing Treatment Strategies
Authors: Simonyan H , Dabash A , Yee R 
Published: November 2023

Abstract

Introduction/Objective
The COVID-19 pandemic strained the healthcare system and the WHO recently reported increased rates of antibiotic resistance. Meanwhile, antiretroviral resistance can also lead to treatment failure and disease progression, especially in HIV patients. Here, we investigated the rates of HIV drug resistance (HIVDR) in our HIV population between pre and post-COVID-19 eras.

Methods/Case Report
The post-COVID-19 era began on 03/11/2020. Patients positive for HIV-1 between 01/2019- 08/2021 were included (total: 94 patients, 46 pre-COVID-19; 48 post-COVID-19). Patients’ charts were reviewed for demographics, laboratory results (including HIV-1 sequencing/genotyping (e.g., Genosure)), clinical presentation and management. Student t-test and Fisher exact test were calculated.

Results (if a Case Study enter NA)
Most patients were male (70%) and had a mean age of 49 years. 70% of patients had sufficient viral loads in samples reflexed to HIV genotyping. Post-COVID-19 patients harbored lower viral loads (1.8x105 vs. 3.4x105 copies/mL, p=0.05), CD4 counts (174 vs. 196 cells/mcL, p=0.7), CD8 counts (555 vs. 800 cells/mcL, p=0.04), and higher CD4/CD8 ratio (0.312 vs. 0.266, p=0.57). Overall, 20% of patients had HIVDR. Following COVID-19 pandemic, there was a 9% increase in HIVDR, predominantly seen in non-nucleotide reverse transcriptase inhibitors (NNRTI), although insignificant. Specifically, high resistance was documented for drugs Efavirenz (16%), Nevirapine (16%), and Rilpivirine (13%). We observed an increased prevalence of G190A, K101, K103, and E138 mutations conferring resistance to NNRTIs. Changes to therapy were observed in 47.8% (42/88) of total cases, with an increase of 12.5% in patients from post-COVID-19 era. Additionally, changes to therapy were observed more in patients with infectious diseases consultation (16% increase).

Conclusion
Increasing HIVDR was seen in our patient population post-COVID-19. Continued surveillance is critical to managing HIVDR and improving patient outcomes. The clinical utility of sequencing tests can outweigh the cost if results are appropriately acted upon which may involve the participation of other clinical teams and the antimicrobial stewardship committee.
Liquid Biopsy as a Powerful Therapeutic Tool in Veteran Patients with Prostate Carcinoma
Authors: Dalal S , Petersen J M , Jhala D , Allbee A 
Published: November 2023

Abstract

Introduction/Objective
The National Comprehensive Cancer Network (NCCN) guidelines currently recommend somatic tumor molecular testing for alterations in homologous recombination (HR) DNA repair genes in patients with metastatic prostate cancer, which can be performed on either the sampled tumor tissue itself or by liquid biopsy.
Particularly when the sampled tumor tissue may be limited, liquid biopsy with next generation sequencing is a recently available attractive alternative that is minimally invasive (requiring just phlebotomy). Based on the information gathered from circulating tumor cells (CTC), a tumor molecular profile can be obtained that can impact treatment, particularly if a HR DNA repair mutation is found as that may predict response to a poly (ADP-ribose) polymerase (PARP) enzyme inhibitor such as Olaparib. However, the literature of metastatic prostate cancers targeted by liquid biopsies and the mutations found is sparse, particularly for the veteran population.

Methods/Case Report
A retrospective review was performed of all patients with a submitted liquid biopsy specimen at a Veteran Affairs Medical Center (VAMC) October 23rd, 2019, to March 3rd, 2023 to examine those patients with
metastatic prostate cancer. Information on mutations detected was collected.

Results (if a Case Study enter NA)
There were a total of 64 patient specimens with a history of metastatic prostate cancer, from which 56 had an available liquid biopsy report with the first liquid biopsy collection occurring on October 23rd, 2019. HR DNA repair mutations found included CHEK2 (6/56), ATM (4/56), and BRCA1 (1/56). Outside of HR DNA repair genes, relatively common detected mutations were found in TP53 (25/56), PTEN (6/56), BRAF (4/56), and an AR amplification (4/56). 7 of the 56 reports had no reportable genomic alterations detected.

Conclusion
Liquid biopsies continues to be a minimally invasive, highly useful powerful therapeutic tool in veteran patients with metastatic prostate carcinoma for molecular profiling. Not uncommonly in the Veteran population, these molecular findings include mutations in HR DNA repair genes that as noted by the NCCN may predict response to PARP inhibitor chemotherapy.
Genome Sequencing-Based Prognosis, Mutational Analysis, and Survival Rate of Pediatric Acute Myeloid Leukemia
Authors: Memon M D , Kazacheuskaya L , Ong M , Cotelingam J , Patil A , Centeno L 
Published: November 2023

Abstract

Introduction/Objective
Pediatric Acute Myeloid Leukemia (AML) is a rare diagnosis that once carried a poor prognosis, but with recent improvement, the survival rate now reaches 80%. Although studies of most genetic mechanisms of AML involved adult studies, but dissimilar mutational profiles and treatment responses in pediatric patients have become evident. Information regarding pediatric AML-specific whole genome sequencing, a prognostic prediction system, and overall survival is limited. Hence, we aimed to analyze the genomic profile, epidemiological characteristics, and overall survival of pediatric AML.

Methods/Case Report
We utilized cBioPortal cancer genomics [The Cancer Genome Atlas (TCGA) PanCancer Atlas, TCGA Firehose Legacy, and TCGA Nature 2013] to study genetic mutations associated with pediatric AML. Epidemiological characteristics and genetic profiles available on cBioportal were evaluated. Gene mutations with the most statistically significant shortest overall survival and survival in days from the samples were used for gene query, and survival rate with the most common mutations was calculated. Log-rank test and Kaplan–Meier estimators were used in analyzing the survival function. Patients with two or more overlapping mutations were excluded.

Results (if a Case Study enter NA)
We identified 899 patients with Pediatric AML, out of 886 had all demographic data available, 50.8% were males, 71.6% were Caucasian, and 11.3% were African American. 568 (63.2%) were alive, and 318 (35.4%) were deceased. 159 patients were diagnosed at less than or equal to 2 years of age, and 150 patients had 80-90% blasts in their samples. 440 (42.9%) had relapse of disease at the bone marrow, whereas 72 (7.0%) had relapse at other sites. The common mutations associated with reduced survival were C4ORF36, HERC5, GPRIN3, NFKB1, NUP88, QRFPR, SPRY1, and UNC5C. Median survival data of patients was available for GPRIN3, NFKB1, NUP88, SPRY1, UNC5C, and was 25.00, 11.00, 15.00, 59.00, and 14.00 months respectively. Comparison with the unaltered group was not available (p &lt; 0.0001). Survival was lowest amongst NFKB1 (11.00 months), NUP88 (15.00 months), and UNC5C (14.00 months). In survival analysis, the same genes were associated with lowest survival after initial diagnosis (p = 7.301e-4).

Conclusion
Our study found that NFKB1, NUP88, and UNC5C genes were associated with the worst prognosis in pediatric AML with median survival of 11.00, 15.00, and 14.00 months. Furthermore it may result in improve the prognosis of these patients.
Invasive Pancreatic Adenocarcinoma with Squamous Differentiation Arising in an IOPN with Novel MDM2 Amplification
Authors: Wilkins R , Zee S 
Published: November 2023

Abstract

Introduction/Objective
Intraductal oncocytic papillary neoplasms (IOPNs) are rare pancreatic tumors that are genetically distinct from intraductal papillary mucinous neoplasms (IPMNs). Morphologic and molecular characterization of invasive adenocarcinomas associated with IOPNs remains limited due to the rarity of this entity.

Methods/Case Report
We present a 68-year-old female who initially presented with abdominal pain and jaundice. MRI revealed a 2.6 cm mass in the pancreatic head with abutment of the superior mesenteric vein and dilation of the biliary and pancreatic duct. Biopsy revealed adenocarcinoma with mucinous features. The patient was started on gemcitabine and abraxane. Her treatment course was complicated by biliary and duodenal obstruction requiring common bile duct and duodenal stenting. Surgical management with pancreaticoduodenectomy was performed six months following initial diagnosis. Gross examination revealed a 2.5 cm ill-defined tumor surrounding the main pancreatic duct adjacent to the common bile duct. Microscopy revealed an IOPN arising within the pancreatic duct exhibiting a complex papillary growth pattern. There was an associated moderately to poorly differentiated invasive carcinoma with mucinous and squamous differentiation with lymph node metastasis. Molecular testing (FoundationOne®CDx) revealed ARID1A mutation and amplification of MDM2, CDK4, and ERBB3. Patient is alive and without radiologic evidence of disease recurrence at 6 months follow-up.

Results (if a Case Study enter NA)
NA

Conclusion
To our knowledge, our case is the first report of an invasive pancreatic adenocarcinoma with squamous differentiation arising in association with an IOPN. In addition, our case showed MDM2 amplification which has not been previously identified in pancreatic adenocarcinoma arising in IOPNs. Although recent literature demonstrated that less than 30% of IOPN showed invasive disease and even fewer cases with lymph node metastasis, our case showed extensive invasion with metastases to 2 lymph nodes. This may suggest that MDM2 amplification may play a role in more aggressive disease since it is implicated with poorer outcome in conventional pancreatic adenocarcinoma. Further molecular studies of IOPN may help to identify prognostic features of this entity.
Congenital Pulmonary Airway Malformation Type 1 with Pulmonary Neuroendocrine Cell Hyperplasia in an Adult Male: a Rare Case Report
Authors: Huffman G , Xu Y 
Published: November 2023

Abstract

Introduction/Objective
Congenital pulmonary airway malformations (CPAM) is rare, usually diagnosed in the pediatric population, and may occur in adults. Pulmonary neuroendocrine cell hyperplasia (PNECH) mimicking diffuse idiopathic pulmonary neuroendocrine cell hyperplasia (DIPNECH) associated with CPAM has not been described previously. We report a case of CPAM Type 1 with PNECH.

Methods/Case Report
A 33-year-old male, with past medical history of latent tuberculosis (TB) by Quantiferon blood testing, recurrent pneumonia, recurrent lung abscesses, and lung cavitary lesion for three years, presented with fever, cough with hemoptysis, shortness of breath, and left-sided chest pain. Computerized tomography of chest displayed a 10.8 cm cavitary lesion in the left lower lobe of the lung. The patient underwent left lower lobectomy of the lung. Grossly, the lobectomy specimen revealed a 10.5 cm irregular cavity communicating to the superior segmental bronchus of the left lower lobe. Microscopically, the dominant large cyst was surrounded by lung parenchyma and small cystically dilated spaces resembling bronchioles under the fibrotic pleura. The large cyst was lined by respiratory epithelium with rare pathognomonic mucous cells in clusters. Cyst walls contained smooth muscle, small islands of cartilage, and focal intense acute and chronic inflammatory cell infiltrates with hemorrhage. There were multiple foci of proliferation of pulmonary neuroendocrine cells centered around bronchioles surrounding the large cyst. The neuroendocrine cells were arranged from individual cells and cellular aggregates to larger tumorlets, highlighted by Synaptophysin and Chromogranin immunostains. No granuloma or necrosis was present. No acid-fast bacilli or fungal microorganisms were identified by special stains. The findings are consistent with CPAM type 1, with PNECH.

Results (if a Case Study enter NA)
NA

Conclusion
Our study demonstrates a histologically diagnosed adult congenital pulmonary airway malformations type 1 with an incidental pulmonary neuroendocrine cell hyperplasia, which mimics diffuse idiopathic pulmonary neuroendocrine cell hyperplasia. To the best of our knowledge, this is the first report of such an association.
COVID-19 Infection Can be Associated with Pauci-Immune Type of Crescentic Glomerulonephritis: A Case Report
Authors: Pokharel A , Metcalf B D , Li W , Kanaan H D , Zhang P L 
Published: November 2023

Abstract

Introduction/Objective
COVID-19 infection is known to cause various podocytopathies, but the pauci-immune type of crescentic glomerulonephritis (C-GN) following COVID-19 infection has only rarely been reported.
We report a case in which a positive proteinase-3 was correlated with a pauci-immune type of C-GN in a patient who contracted COVID-19 infection.

Methods/Case Report
The patient was a 56-year-old woman who had a normal baseline serum creatinine (sCr) two years ago before she developed acute respiratory failure and acute kidney injury (sCr at 1.57 mg/dl) with significant proteinuria (urine protein/creatinine ratio [UPCR] at 1.02) and 2-3+ hematuria following a COVID-19 infection. The ANCA screening tests, including a recent one, were negative several times, but her protein-3 was low positive (14) and myeloperoxidase-3 was negative recently. Her current sCr increased to 2.93 mg/dl with UPCR at 3.1 and 2+ hematuria. A renal biopsy was performed, which showed one glomerulus for light microscopy and one glomerulus for immunofluorescent studies in the absence of proliferation, crescentic formation, or necrosis. Immunofluorescent stains were all negative in the glomerulus, but the methylene-blue stained sections for electron microscopy revealed three glomeruli with cellular crescents without necrosis. The ultrastructural examination did not show additional findings. The biopsy was consistent with proteinase-3 associated C-GN, pauci-immune type. She started cyclophosphamide treatment.

Results (if a Case Study enter NA)
N/A

Conclusion
COVID-19 can be associated with the pauci-immune type of C-GN. Under this condition, the ANCA screening test can be deceiving (false negative) in ruling out C-GN, so more specific tests such as myeloperoxidase and proteinase-3 should be ordered to enhance the chances of detecting renal vasculitis.
Red Blood Cell Aliquoting: Improving O Negative Red Blood Cell Utilization in Neonate and Pediatric Inpatients at UC Davis Medical Center
Authors: Sharma N , Thomas B , Olario A , Kicin A , Padda R , McGill M , Barnhard S 
Published: November 2023

Abstract

Introduction/Objective
UC Davis Medical Center (UCDMC) is the Sacramento region’s only level 1 adult and pediatric trauma center. It serves a 65,000 square mile area that includes 6 million residents from 33 counties across Northern and Central California. Nearly 7000 patients are transfused annually at UCDMC. Blood supply restrictions, especially on group O negative red blood cells (RBCs), escalated by the COVID-19 pandemic, posed significant patient safety risk. We sought to mitigate this risk by employing restrictive O negative RBC transfusions as recommended by AABB Choosing Wisely, through ABO matched small volume transfusions in neonate and pediatric patients.

Methods/Case Report
We conducted monthly audits starting in January 2021 to identify trends in O negative RBC use at UCDMC. We partnered with our blood supplier, American Red Cross (ARC), to modify hospital blood inventory. In 2022, we implemented the RBC aliquoting procedure using AS-3 RBCs to facilitate ABO matched small volume transfusions in neonates and children to conserve O negative blood supply. We reviewed regulatory standards, developed standard operating procedures, performed extensive technical validations, and worked with IT to enhance laboratory information system for product manufacturing, labeling, and traceability. We developed education documents for physicians, other providers, nurses, and transfusion services staff including sustainable competency and training. We conducted audits post implementation to measure goal performance in Q4 of FY22, compared to pre- implementation baseline data from Q1 of FY22.

Results (if a Case Study enter NA)
N/A

Conclusion
We achieved 57% reduction in O negative RBC utilization post implementation of the RBC aliquoting procedure in Q4 of FY22. Overall O negative RBC use trend at UCDMC improved with a 58% reduction between January 2021 to December 2022. Subsequent reduction of orders was achieved.We conclude that ABO matched RBC aliquot transfusion in neonates and pediatrics is an effective laboratory practice to reduce O negative RBC usage.
A rare cause of Acquired Hemolytic Anemia in a child; Donath-Landsteiner antibody
Authors: Abdelmonem M , Shan H , Cai W , Roque A , Chang S , Cabungan M , Papakonstantino K , Virk M S , Yunce M 
Published: November 2023

Abstract

Introduction/Objective
INTRODUCTION: The Donath-Landsteiner (DL) antibody is known to cause paroxysmal cold hemoglobinuria (PCH), a rare form of intravascular hemolytic anemia which is precipitated by an IgG biphasic hemolysin with specificity to the P blood group antigen and most commonly reported in children. The DL test is a serologic test specifically examines, the biphasic nature of the antibody activity.

Methods/Case Report
CASE PRESENTATION: A 4-year-old previously healthy boy presented at an academic medical center with rhinorrhea and nasal congestion. His family reported that his urine became darker almost coke colored after his symptoms started. His initial vitals; temperature of 37.1 C, heart rate of 140, blood pressure of 122/87 and O2 saturation of 96% on room air.
Laboratory investigations showed a hemoglobin level of 4.2 g/dL, hematocrit level of 12.5%, platelets count of 229 K/uL, indirect bilirubin of 6.2mg/dL, haptoglobin &lt;30 mg/dL, LDH &gt;1800 U/L. Direct antiglobulin test was positive with complement only. Thermal Amplitude and indirect Donath-Landsteiner tests were both positive. Respiratory viral panel was positive for Rhinovirus.
The antibody screen was negative, and the patient was provided supportive care including as needed RBC transfusion, warming of fluids and body. By day day 9 patient Hgb stabilized, LDH, bilirubin and haptoglobin normalized and his urine turned yellow color and was discharged in stable condition.

Results (if a Case Study enter NA)
NA

Conclusion
CONCLUSIONS PCH is classified as a cold autoimmune hemolytic anemia caused by an IgG antibody that sensitizes RBCs at cold temperatures by attaching complement to the RBCs, causing intravascular hemolysis upon rewarming. The DL test for PCH involves in vitro testing for hemolysis with the patient's serum, washed group-O cells expressing the P antigen, and fresh normal serum. To prevent autoadsorption of the antibody and hemolysis, blood should be collected in prewarmed tubes that do not contain anticoagulants and kept at 37°C during the collection procedure. A high index of suspicion especially in pediatric population should be maintained after a viral infection. The treatment is usually supportive.
Hemapheresis Clinic Scheduling Quality Improvement Project
Authors: Zaidi A , Allison D , Campbell-Lee S , Janiszewski S 
Published: November 2023

Abstract

Introduction/Objective
Outpatient (OP) Red blood cell exchange (RCE) therapy is used to treat patients with severe manifestations of sickle cell disease. Like any blood transfusion, a patient must have an active type and screen, drawn 24 to 72 hours prior to scheduled RCE procedure. UIH Hemapheresis clinic performs several types of apheresis procedures treating sickle cell disease, kidney transplant rejection and autoimmune disorders. Outpatient clinic staff perceived that most RCE procedures are scheduled disproportionately between Wednesday through Friday, which creates an unbalanced schedule that is lighter on Monday and Tuesday, and heavier Wednesday through Friday. The study's objective was to determine if there is a significant difference between the number of outpatient procedures scheduled on the different days of the week. If significant differences are identified, processes may be improved to schedule a more balanced OP clinic week. Potential benefits may include a more balanced patient to nursing staff ratios which can improve patient care and more efficient RBC utilization which can ease workload across multiple cross-functional departments such as nursing staff, reference labs and in-house blood bank staff.

Methods/Case Report
The UIH Epic Hemapheresis Clinic schedule was searched to identify how many total OP procedures, including RCE, were scheduled each day of the week between 01AUG2021 – 31JUL2022. Only OP procedures occurring in complete five-day weeks were included. Weekends and weeks having clinic closures for holidays were excluded

Results (if a Case Study enter NA)
Our study show that the lowest number of OP RCE (mean 1.4) and total number of OP procedures (mean 2.6) were on Monday. Wednesday is the busiest day with overall averaging 3.5 total procedures (Standard Deviation: 1.56). However, Friday is the most variable, with the largest SD for both RBCX (SD 1.4) and Total number of procedures (SD 1.7).

Conclusion
Contributing factors to low procedure volume on Monday are likely multifactorial. Some patients may prefer not to come to the hospital on Saturday for type and screen, while some may forget they need labs.
Transportation issues are another factor. One intervention the clinic has implemented is automatic appointment call reminders. Staff encourage patients or caregivers to sign up for the EPIC MyChart app which also notifies patients of upcoming appointments. Future studies need to be conducted to address other bottlenecks within the scheduling workflow and to determine ways to optimize patient appointment adherence.