bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Rare Case of Amyloid Light Chain Amyloidosis with Extensive Hepatic Involvement
Authors: Prakash V , Ajmal I , Daley W , Varshney N , Petrasek J 
Published: November 2022

Abstract

Introduction/Objective
Amyloid light chain (AL) amyloidosis is a life-threatening disease entity, with an incidence of 10–15 per million per year in the USA. Amyloidosis is caused by the extracellular deposition of insoluble fibrillary amyloid protein resulting in multiorgan damage. Though amyloidosis is primarily a systemic disease, 10%-20% of cases can be localized.

Methods/Case Report
We present a case of a 37-year-old male admitted with predominant hepatic manifestations, whose liver biopsy led to the diagnosis of amyloidosis. The patient presented with intermittent abdominal pain, weight loss, persistent hypoglycemia, hepatomegaly, and raised liver enzymes. Imaging studies showed hepatomegaly with a heterogeneous lace like appearance of the liver parenchyma. Liver biopsy revealed an extensive deposition of amyloid protein in peri-sinusoidal spaces. The amyloid protein is highlighted by crystal violet stain and revealed apple- green birefringence on polarized microscopy after Congo red staining. On further evaluation, elevated kappa and lambda free light chains with increased kappa-lambda ratio were identified by serum protein electrophoresis. Subsequent bone marrow aspirate and biopsy identified a monoclonal kappa positive plasma cell neoplasm with an amorphous eosinophilic infiltrate. Liquid chromatography-tandem mass spectrometry on bone marrow biopsy detected a peptide profile consistent with AL (kappa) type amyloid deposition.

Results (if a Case Study enter NA)
NA.

Conclusion
AL amyloidosis patients with predominant hepatic involvement have a worse prognosis. Rapid diagnosis and prompt clinical intervention prevents further organ damage. This case study aims to promote awareness of the unusual presentations of amyloidosis.
60-Year-Old Patient with Invasive Mold Infection Consequent to an Encounter with a Barnyard Animal
Authors: Puello Yocum B , Lavik J 
Published: November 2022

Abstract

Introduction/Objective
Lichtheimia and Scedosporium species are ubiquitous fungi associated with a range of clinical presentations. We report a complex soft tissue coinfection caused by Lichtheimia spp. and Scedosporium spp. following a puncture wound by a rooster spur.

Methods/Case Report
A 60-year-old immunosuppressed man with a history of heart transplant presented with a non-healing wound 2-months after sustaining a lower leg puncture secondary to a rooster spur. The patient was previously treated with Augmentin for presumed cellulitis without improvement. To characterize the ongoing disease process, the wound was sampled with tissue portions routed for both histopathologic review and culture. In short order, the biopsy demonstrated invasive hyaline pauciseptate fungal hyphae consistent with organisms of the Mucorales order. In congruence, culture rapidly revealed a mucoraceous mold, subsequently identified as a Lichtheimia spp. Thus, the patient was treated with liposomal amphotericin B. However, days later, a second fungus - a Scedosporium spp. - was isolated from the original specimen. Consequently, isavuconazonium sulfate therapy was added. Re-review of the initial biopsy enabled distinction of two populations of fungal hyphae plausibly representing both molds. Despite numerous debridements and optimal medical management, the patient was ultimately referred for amputation.

Results (if a Case Study enter NA)
NA.

Conclusion
When encountered in an immunocompromised host, providers understandably respond to an invasive mucoraceous mold with alarm followed by quick, decisive action. However, septate molds, such as the Scedosporium spp., can also be aggressive. Further, the presence of more than one invasive mold presents a treatment challenge as the mucormycetes may require surgery coupled with amphotericin B therapy; whereas, the a Scedosporium spp. may be wholly resistant to amphotericin B. This case illustrates the critical role that an alert pathologist plays in guiding management through integration of data from different diagnostic modalities. It also constitutes an emphatic reminder that an illness may be caused by more than one actionable, invasive fungus.
Investigation of Drug ResistantAcinetobacter baumannii Virulence Factors Implicated in Intracellular Survival Within Differentiated THP-1 Cells
Authors: Wheibe E , Connolly K , Grier J , Fiester S 
Published: November 2022

Abstract

Introduction/Objective
Acinetobacter baumannii is a nosocomial opportunistic pathogen that is usually associated with mucosal infections such as pneumonia, urinary tract infections or sepsis and less commonly with more severe illnesses such as meningitis, wound infection, or necrotizing fasciitis. Of late, A. baumanniihas been flagged by the CDC as an urgent threat due to multidrug-resistant properties it has acquired, making it a major concern to public health. Due to a sparsity of information on the virulence factors of immune evasion, it has been difficult to understand how this bacterium is able to gain a foothold and cause severe infections. We sought to study how necrotizing fasciitis-associated strains of A. baumannii interact with human macrophages to assess their capabilities in evasion of the host immune response.

Methods/Case Report
To this end, extensively drug resistant A. baumannii was isolated at two timepoints (strains NFAb-1 and NFAb-2) from a patient over the course of a lethal necrotizing fasciitis infection that led to sepsis. The intracellular survival of these two strains was compared with each other, as well as to the type strains, ATCC 19606 and ATCC 17978, within a human macrophage-differentiated monocyte cell line, THP-1. Survival studies were complemented with quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) to investigate expression of potential bacterial virulence factors, Catalase E (KatE), Phospholipase C (PLC), Outer membrane protein A (ompA), and Pilus A (PilA), that could contribute to immune evasion.

Results (if a Case Study enter NA)
The intracellular survival assay demonstrated enhanced survival and bacterial growth of NFAb-1 and NFAb-2 within macrophages compared to ATCC 19606 and 17978. Examining gene expression, KatE, PLC, and OmpA didn’t show any significant differences between the bacterial strains, while the PilA gene had much higher expression in NFAb-1 and NFAb-2 compared to ATCC 19606 and 17978.

Conclusion
This data establishes these nectrotizing fasciitis-causing A. baumannii strains are more likely to sruvivie a macrophage-mediatied immune response and expression of pilus-assocated genes may play a role in these interactions. our studies demonstrate a need to further investigate A. baumannii mechanisms of virulence to understand its ability to evade the immune response in hopes of understanding and combating infections.
Trending the Variants of SARS-CoV-2 in the Veteran Population: How Things Have Changed from Before to the Interesting Present
Authors: Petersen J M , Jhala D 
Published: November 2022

Abstract

Introduction/Objective
In both the past and for the foreseeable future, SARS-CoV-2 (the coronavirus that causes COVID-19 disease) will continue to evolve. This evolution has already and will lead to new variants that will then cause surges of infection. These outbreaks in the past with the variant responsible have previously been reported individually. However, a timeline perspective on the changing SARS-CoV-2 variant landscape is sparse in the literature, particularly for testing performed at a Veteran Affairs Medical Center (VAMC). The Veteran population has increased comorbidities compared to the general population leading to susceptibility to infection including SARS-CoV-2. Hence, it is of utmost importance to explore the trending variants of SARS-CoV-2 in the veteran population as this epidemiological information may help in preventing transmission, which remains key in the management of COVID-19.

Methods/Case Report
Samples from selected patients from March 2021 to June 2022 who tested positive for SARS- CoV-2 by reverse transcriptase polymerase chain reaction with a cycle threshold or number &lt;30 (required for sequencing) were sent for SARS-CoV-2 sequencing analysis.

Results (if a Case Study enter NA)
There were a total of 19 VAMC patients who were sequenced during the entire study period (March 2021 to June 2022). From March to May 2021, there were 8 patients, from which 6 demonstrated Pango Lineage B.1.1.7, 1 demonstrated Pango Lineage B.1.526.1, and 1 demonstrated Pango Lineage B.1. Later in 2021 (August to October 2021), there were 4 patients all of which demonstrates the Delta variant; 2 of these 4 demonstrated the Delta subvariant Pango Lineage AY.25 and the other 2 demonstrated Pango Lineage AY.44. By May to June 2022, there were 7 patients, all of whom demonstrated infection by the Omicron variant. Interestingly, 6 of these 7 patients demonstrated the newly emerging subvariant BA.2.12.1 and the remaining 1 demonstrated BA.2.9.

Conclusion
SARS-CoV-2 has continued to evolve throughout the course of the pandemic, which has led to variants and subvariants that have predominated for a time to cause an outbreak only to be replaced later by a different strain. This timeline epidemiological perspective demonstrates that the Veteran population has also been affected by the variants that have led to outbreaks in the past within the general population.
SARS-CoV-2 Detection by Extraction-free qRT-PCR for Massive and Rapid COVID-19 Diagnosis During a Pandemic
Authors: Martirosyan G , Avetyan D , Zakaryan R , Hayrapetyan V , Khachatryan G , Sirunyan T , Ghukasyan L , Arakelyan A 
Published: November 2022

Abstract

Introduction/Objective
COVID-19 pandemic severely impacted the healthcare and economy on a global scale. It is widely recognized that mass testing is an efficient way to contain the spread of SARS-CoV-2 infection as well as aid in the development of informed policies for disease management. Here we optimized two different protocols for qRT- PCR with direct samples and systematically compared them with the laboratory standard qRT-PCR detection assay.

Methods/Case Report
RNA samples from 270 subjects collected in two phases at 2020-2021. The groups consisted from positive (n = 240) and negative (n = 30) samples. We compared the performance of qRT-PCR in direct heat- inactivated (95 °C for 5 min, H), heat-inactivated and pelleted (95 °C for 5 min and centrifuged for 10 min at 12,000 g, HC) against standard laboratory protocol for SARS-CoV-2 qRT-PCR (targeting ORF1ab and N genes). Accuracy, sensitivity, and specificity for PCR assays were calculated using caret and epiR packages available in the R software environment for statistical computing. The Wilcoxon matched rank test was used to compare differences in Ct values.

Results (if a Case Study enter NA)
Our study suggests that HC samples show higher accuracy for SARS-CoV-2 detection PCR assay compared to direct H (89 % (95 % CI: 80–95 %) vs 83 % (95 % CI: 74–91 %) of the detection in RNA). The median ΔCt was lower by 1.55 and 2.29 cycles (Wilcoxon signed-rank test p = 0.0018 and &lt; 0.0001 for ORF1ab and N genes, accordingly) in HC samples compared to H samples.

Conclusion
Our results suggest that purified RNA provides more accurate results; heat-inactivated and pelleted sample testing with qRT-PCR showed a slight drop in accuracy. However, the latter could also help to significantly increase testing capacity. Switching to the direct sample testing is justified if the number of tests is doubled at least.
Filamentous Bacteria Resembling Fungal Hyphae: A Diagnostic Pitfall
Authors: Sham S , Bendari A , Hosseini H , Otero Espinal D , Vele O , Duong S 
Published: November 2022

Abstract

Introduction/Objective
When exposed to antibiotics or a host immune response, Gram-negative bacilli grow with inhibited septation producing long continuous cells; a phenomenon known as filamentation.

Methods/Case Report
We present a case of a 68-year-old man with quadriplegia, which was caused by the right vertebral artery dissection and subarachnoid hemorrhage requiring an emergent posterior inferior cerebellar artery direct bypass surgery. Lung lower lobe infiltrates were noted 3 days after the surgery. A bronchial wash culture was negative for growth, and a sputum specimen grew Serratia marcescens. The patient was treated with piperacillin/tazobactam, vancomycin, cefepime, cefazolin. After the surgery, he suddenly developed severe cerebral vasospasm of the posterior circulation with cerebellar strokes requiring emergent posterior fossa decompression. He remained on ventricular drainage by external ventricular drainage. After two days, the patient's cerebrospinal fluid (CSF) was sent for evaluation, on which a high segmented neutrophil count of 35% and Gram-negative filamentous organisms with occasional swellings were noted. Multi-drug resistant Serratia marcescens was isolated from the CSF specimen four days later. Neurosurgical procedures were reported to be highly associated with S. marcescens meningitis. The filamentous organisms noted on Gram-stained direct smear most likely represented Gram-negative S. marcescens with filamentation due to administration of sub-inhibitory concentrations of antibiotics.

Results (if a Case Study enter NA)
NA.

Conclusion
Gram-negative bacilli can develop abnormal morphology including elongation, swelling, and filamentation due to stress or sub-inhibitory antibiotic exposure, and it is important for microbiologists and pathologists to be aware of this phenomenon to avoid misinterpretation that may lead to inappropriate treatment.
Molecular Solid Tumor Algorithm – Simplified Patient-Centric/Cost-Effective Approach by Pathologists
Authors: Poonam F , Loos C , Wells A , Ehsan A 
Published: November 2022

Abstract

Introduction/Objective
The process from the time the patient is diagnosed with cancer and receives their first treatment is complex and time-consuming. It requires adherence to national comprehensive cancer network (NCCN) guidelines; is challenged with limited tissue, how and when to order tests, and reimbursement timelines with pre- authorizations. We evaluated the role of the pathologists, who are an integral part of patient care, along with oncologists and surgeons.

Methods/Case Report
254 cases from various types of solid tumors (paraffin-embedded blocks) were collected from several pathology departments. Tests (two panels NGS-DNA/RNA expression, FISH, PD-L1, and IHC) were ordered as early as on the day of diagnosis to as late as 18 months following the diagnosis. Cancer cases reviewed were Colo-Rectal (72), Lung (48), Breast (24), Gastric (10), CNS (8), Melanoma (4), Head/Neck (20), GU (16), Sarcomas (8), Thyroid (6), Hepatic (8), Female Genital Tract (7) and Unknown Primary (23).

Results (if a Case Study enter NA)
We evaluated pathology reports, identified blocks, reviewed H&E slides, utilized NCCN guidelines in collaboration with oncologists. Tests were ordered using established billing criteria. Following tests were performed: PD-L1 (190 - 75%), FISH (50 - 20%), and NGS – two simple panel approach (215 - 85%). Using the aforesaid methods, our NGS results were successful in &gt;95%. We were able to identify actionable and prognostic mutations in &gt;80% of tumors.

Conclusion
Our algorithm has been designed considering NCCN guidelines and are updated frequently with new therapeutic targets and actionable mutations. The emphasis is to conserve diagnostic tissue and ensure timely ordering of tests as medically necessary. This can be adopted by pathologists in conjunction with clinical information, pathology reports, and be used as a part of diagnostic workups to reduce delays in treatment, avoid tissue loss, utilize current billing (inpatient/outpatient) practices, pre-authorization and eventually improving patient care as well as reduce overall healthcare costs.
Clinico-Demographic Characteristics of Patients with SARS-CoV-2 Antibodies: A Single Tertiary Center Retrospective Study in Bohol, Philippines
Authors: Salillas A L , Clapis A B , Almocera E G , San Juan A T 
Published: November 2022

Abstract

Introduction/Objective
Coronavirus Disease 2019 (COVID-19) caused by SARS-CoV-2 continues to be a global threat until the present. Most of the infected patients are asymptomatic which can be a challenge in controlling the spread of disease. Antibody detection by chemiluminescence immunoassay (CLIA) is a good complementary test to Real-Time Reverse Transcription – Polymerase Chain Reaction (rRT-PCR) as an indirect marker for disease.

Methods/Case Report
This retrospective study assessed the clinico-demographic characteristics of 184 SARS-CoV-2 IgM and IgG antibody-reactive patients at Gov. Celestino Gallares Memorial Hospital from July 1, 2020 – May 31, 2021.

Results (if a Case Study enter NA)
A total of 184 cases were included in the study out of 4,138 patients tested for anti-SARS-CoV-2 IgM and IgG antibodies by CLIA. Within this population, 97 were outpatients and 87 were inpatients. Majority of patients needing hospitalization were aged ≥60-year-old males (33.33%) and that the probability of being admitted decreases with younger age. Most of the outpatients who were reactive to antibodies against SARS-CoV-2 were frontline workers compared to non-frontline workers and non-workers (27.84% versus 1.03% and 19.59%). Most common comorbidities were hypertension (24.46%), cardiovascular disease (15.76%), diabetes mellitus (11.41%), and chronic kidney disease (11.41%). All five mortalities were diagnosed hypertensive who later developed critical disease.

Conclusion
The continued use of antibody detection by CLIA as a complementary test with rRT-PCR is still recommended not only for better detection of COVID-19 especially in asymptomatic patients but also to observe changes in antibody titer especially in the advent of COVID-19 vaccines.
Leadership Insights From a Pathology Peer-to-Peer Learning Collaborative in Immuno-oncology
Authors: Kim J , Kelly M , Beumer K 
Published: November 2022

Abstract

Introduction/Objective
As the use of immuno-oncology (IO) expands into more cancers, there is a growing need for pathologists and laboratory professionals to demonstrate leadership and guide biomarker testing processes and procedures at their own institutions. To educate and empower its members, the American Society for Clinical Pathology worked in collaboration with Q Synthesis to develop a peer-to-peer learning collaborative. This project was supported by an educational grant from Bristol Myers Squibb.

Methods/Case Report
18 pathologists and laboratory professionals participated in a 10-month program: IO ChangeMakers. Learners completed online modules covering scientific updates on IO biomarker testing. Through small-group, case-based discussions, learners reviewed operational challenges and opportunities to refine biomarker testing. They applied this knowledge to lead IO improvement projects at their own institutions.

Results (if a Case Study enter NA)
The learners identified the following leadership insights around IO biomarker testing: Reflex testing: Develop or refine reflex biomarker testing processes to ensure that tissue is sent for PD-L1 testing at the time of cancer diagnosis. Establish testing criteria with oncologists and implement steps to reduce delays in testing. Interobserver concordance: Evaluate interobserver concordance among pathologists scoring PD-L1, especially in upper GI cancers where the combined positive score (CPS) is used. Scoring upper GI cancers is challenging because of the spatial distribution of PD-L1 within a tumor. Tissue handling: Identify ways to improve tissue processing and handling to preserve small amounts of tissue for biomarker testing. If quantity is not sufficient, prioritize PD-L1 testing and contact the oncologist to order a liquid biopsy. Confusion around different PD-L1 antibody clones: Pathologists and clinicians are often confused about the use of different PD-L1 antibody clones (eg, 22C3, SP142, etc.) and scoring criteria (eg, TPS ≥ 1%, CPS ≥ 10, TC ≥ 25%, etc.). Develop education and reference guides to ensure the right PD-L1 test is ordered based on the type of tumor and intended treatment. Test ordering to reporting: In many cancer centers, biopsy samples are being sent out for PD-L1 testing. Refine electronic test ordering, tracking status, and reporting results.

Conclusion
Pathologists have numerous opportunities to lead improvement efforts in IO biomarker testing. As the use of IO expands into more cancers, there will be a growing need for pathologists to demonstrate leadership in this area.
An Exceedingly Rare Case of Nodular Fasciitis of Tongue in an Infant
Authors: Ansari S , Blessing M 
Published: November 2022

Abstract

Introduction/Objective
Nodular fasciitis is a rapidly growing but benign self-limited myofibroblastic/fibroblastic tumor of unknown etiology. It was first described in the literature by Konwaler in 1955 and can occur in any location. Nodular fasciitis of the tongue is a rare entity in infancy with only one case reported so far. Accurate diagnosis of this entity is crucial to avoid a possible misdiagnosis of malignancy leading to radical resections.

Methods/Case Report
A 6-month old, previously heathy full term male presented to pediatric otolaryngology clinic with a rapidly growing painless mass on the right tongue. The mass was associated with feeding difficulty. There was no history of trauma to the area, no personal and family history of cancer was noted. Computed tomography scan demonstrated a 1.5 x 1.4 x 1.5 cm mass confined to the right anterior undersurface of tongue. Biopsy of the mass showed ulcerated mucosa with an underlying spindle cell lesion composed of reactive-appearing myofibroblasts arranged in a variably fascicular to "tissue-culture" pattern, intermixed with inflammatory cells and scattered extravasated erythrocytes. These morphologic features in conjunction with immunohistochemistry and demonstration of fusion of SRSF3 [serine and arginine rich splicing factor 3] and USP6 [ubiquitin specific peptidase 6] by Targeted next-generation RNA sequencing confirmed the diagnosis of nodular fasciitis. On follow up, spontaneous regression of the mass occurred in 3 months.

Results (if a Case Study enter NA)
NA.

Conclusion
Nodular fasciitis of tongue in infancy is an exceedingly rare entity and this case demonstrates the importance of including this unique entity in the differential diagnosis of a rapidly-growing tongue lesion. Because it can simulate malignancy both clinically and histologically, awareness and familiarity with this benign proliferative lesion is crucial in effective management.