bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Vital Role of Special Stains in Immunocompromised Cases: A Focus on Histoplasmosis Screenings for Enhanced Kaposi`s Sarcoma Diagnosis Beyond H&E Morphology
Authors: Robinson B , Habecker J , Lukande R , Cherepow L 
Published: October 2024

Abstract

Introduction/Objective
This case report emphasizes the critical importance of thorough pathology-based investigation before making a definitive diagnosis of Kaposi’s Sarcoma (KS). In particular, we demonstrate the importance of using special stains in addition to H&E staining to determine if the lesion is KS or a fungal infection, specifically cutaneous Histoplasmosis. This highlights the necessity of comprehensive diagnostics to ensure accurate and timely identification of underlying conditions, guiding appropriate treatment strategies.

Methods/Case Report
In Kampala Uganda, a 56-year-old male with a history of HIV/AIDS presented with skin lesions on the lower extremities. The lesions were initially suspected to be Kaposi’s Sarcoma due to their appearance and the patient’s immunocompromised status. Skin biopsy results supported the initial suspicion, showing spindle cell proliferation in the dermis, a common feature of KS. Given his compromised immune system, it was imperative to conduct a thorough investigation to rule out potential etiologies, including opportunistic infections. Additional tests, including a Grocott Methenamine-Silver Nitrate stain, revealed the presence of Histoplasmosis. The patient did not exhibit typical symptoms of Disseminated Histoplasmosis, such as respiratory distress or fever. Resource constraints hindered comprehensive follow-up, impacting long-term outcome assessment.

Results (if a Case Study enter NA)
NA

Conclusion
Histoplasmosis is widespread in Africa, accounting for 61% of global cases, with 87% concentrated in Western and Central Africa. The coexistence of KS and Histoplasmosis poses diagnostic challenges due to overlapping clinical manifestations. KS primarily affects the skin, while Histoplasmosis causes invasive vascular and pulmonary infections. However, in Africa, notably in immunocompromised individuals, histoplasmosis can cause cutaneous infections. Failure to recognize and address fungal infections may result in delayed or inappropriate treatment, exacerbating the patient’s condition. This case report underscores the importance of maintaining a high index of suspicion for opportunistic infections in this population for timely intervention.
Road to automated urinalysis analyzer: Validation of Sysmex UN-3000 to supplant manual urinalysis
Authors: Walczak M , Boisvert D , Maharjan A S 
Published: October 2024

Abstract

Introduction/Objective
Traditionally, urinalysis encompasses the chemical analysis of urine by dipstick and manual microscopy for formed elements. High specimen volume and varying subjectivity among individuals performing microscopic analysis make the practice both imprecise and inefficient. Implementation of Sysmex UN- Series™Automated Urinalysis (Sysmex Corporation, Kobe, Japan) fulfilled our need for automation, addressing both issues at hand. Automated urinalysis offers a solution for laboratories to meet the growing demand for faster result turn around times(TAT) with ever increasing specimen volumes. We expect greater sensitivity and reproducibility in terms of comparison to manual microscopy, as well as quicker TAT with the change in methodology.

Methods/Case Report
Using both unpreserved and preserved urine tubes, a macroscopic comparative study between Clinitek Advantus(manual) and Clinitek Novus (automated) methods was carried out on 141 urines with greater than 60 abnormal patients. Similarly, a microscopic study between the laboratory’s manual microscopy procedure and the Sysmex UF-5000 was carried out on 112 urines with greater than 60 abnormal patients. RBCs, WBCs, Epithelial cells were evaluated under high power field(40X); casts and crystals were evaluated under lower power field(10X). The Reference Range Interval for both chemical and microscopic was verified using 44 normal patient specimens. The quantified values are converted to high and low power field (hpf/lpf), analogous to the current system in the laboratory.

Results (if a Case Study enter NA)
Most parameters had &gt;90% agreement between manual and automated method. Parameters falling below 90% were checked to see if discrepancies fell within 1 degree. Automated system is more sensitive than manual and our average TAT for urinalysis dropped 50%.

Conclusion
The automated urinalysis technology enabled us to focus only on samples requiring intervention based on pathological criteria, resulting in reduced overall TAT and workload burden, and improved consistency in reporting across specimens.
Detecting and Reporting Extended Spectrum Beta-Lactamases Producers: Evaluation of Three Approaches and the Clinical Impact
Authors: Swanson K J , Nault D , Demessie G , Mendoza S , Yee R , Nagao P 
Published: October 2024

Abstract

Introduction/Objective
Since the COVID-19 pandemic, bacteria producing extended spectrum beta-lactamases (ESBLs) have increased &gt;30%. Laboratories can perform phenotypic microbroth dilution or molecular approaches to identify ESBL producers. However, the gold standard is a laborious double disc synergy test. We evaluated the concordance among the three approaches, the clinical impact, and justification of reporting ESBL producers.

Methods/Case Report
Seventy-eight ESBL producers identified by microbroth dilution (MicroScan WalkAway, Beckman Coulter, Brea, California, USA) or detection of blaCTX-M gene from blood cultures (BCID2 Panel, BioFire, Biomerieux, Salt Lake City, Utah, USA) were tested using double disc synergy test retrospectively. Concordance among the methods evaluated. Discordant cases were reviewed with subsequent patient chart review.

Results (if a Case Study enter NA)
Tested isolates included E. coli (n=44, 57%), K. pneumoniae (n=19, 24%), K. oxytoca (n=7, 9%), and P. mirabilis (n=8, 10%). Concordance between microbroth dilution and disk diffusion was 86% (67/78). For isolates with genotypic testing (n=16), concordance with microbroth dilution and disk diffusion was 93% and 88%, respectively. Overall concordance was 88%. There were 12 isolates (E. coli:8, P. mirabilis: 2, and K. pneumoniae:2) with discordant results from one method. The susceptibility profile of discordant isolates revealed resistance to ceftriaxone or ceftazidime (11/12), penicillin (11/12), and aztreonam (6/12); 10/12 isolates were resistant to at least 2 groups of these antibiotics, a phenotype of ESBL producers. Clinical teams acknowledged presence of ESBLs in 83% (10/12) of cases and 58% (7/12) warranted treatment with meropenem or combinational therapy.
Infection prevention implemented contact isolate procedures in all cases.

Conclusion
Our current in-house methods (e.g., microbroth dilution and genotypic testing) are still justified for ESBL testing to optimize patient care in a timely fashion. In the minor cases with discordant results, clinical care was unaffected. Laboratory workflow changes need to take laboratory efficiency, patient outcomes, and actionable clinical changes into consideration.
Pathogenesis of Klebsiella Pneumoniae Induced Proteinopathy is Amyloid Strain Dependent
Authors: Hanna S , Morrow A , Voth S , Morrow R , Choi C , Lin M , Stevens T , Pittet J , Wagener B 
Published: October 2024

Abstract

Introduction/Objective
The World Health Organization has labeled Klebsiella pneumoniae (KP), a Gram-negative bacterium, as a ‘Critical Priority’ pathogen due to its increasing prevalence in serious conditions like pneumonia and sepsis, along with its growing resistance to multiple drugs. Infections with KP have been linked to the collapse of microtubules and the release of harmful proteins called amyloid-beta (Aβ) and tau from lung endothelial cells. These infection-induced lung endothelial amyloids can spread like prions and are stable under heat.

Methods/Case Report
However, the mechanisms behind these effects and whether the infection-generated proteinopathy depends on tau and/or Aβ were not well understood. This study hypothesized that KP infection triggers tau dysfunction, breakdown of microtubules, increased lung barrier permeability, and the production and release of toxic amyloids. To test this, researchers used CRISPR/Cas9 technology to create lung endothelial cells without tau and/or amyloid precursor protein (APP). They confirmed gene deletion through various methods and exposed these cells, along with regular cells, to a highly virulent KP strain.

Results (if a Case Study enter NA)
The results showed that the KP strain (Kp 1-008) caused disruption of cellular structures, increased permeability, and bacterial spread within hours of infection. Supernatants containing proteins from infected cells, when applied to healthy cells, led to barrier disruption, permeability, and cell death. Interestingly, different pathologies were induced by supernatants from cells lacking tau or APP, indicating that either tau or Aβ alone could propagate damage in a strain- specific manner. The most severe damage required both tau and Aβ together.

Conclusion
In conclusion, KP infection disturbs cellular structures, promoting barrier breakdown and bacterial dissemination. It also generates toxic tau and Aβ proteins. Either of these proteins can spread harm from cell to cell, but together, they enhance the severity and potency of the resulting lung endothelial protein damage caused by the infection. The study sheds light on the complex mechanisms of KP-related infections and their impact on cellular structures and protein pathways.
Rare Case of Subcutaneous Phaeohyphomycosis Caused by Exophiala jeanselmei
Authors: Aravind A , Sharma P , Jhaveri T , Pridmore C , Sontakke S , Smith D 
Published: October 2024

Abstract

Introduction/Objective
Phaeohyphomycosis is a neglected tropical infection caused by dematiaceous fungi containing melanin in their cell wall. Currently, the prevalence of phaeohyphomycosis is very low in the United States compared to other mycotic agents. Trauma often precedes phaeohyphomycosis, and there are a limited number of cases associated with healthcare settings. This case report describes a nosocomial phaeohyphomycosis caused by Exophiala jeanselmei.

Methods/Case Report
A 60-year-old male with multiple myeloma, on immunosuppressive therapy, presented with a large fluctuant mass on the dorsum of his right hand. The mass had developed 6 months ago as a hematoma following a blown vein during a blood draw. Despite treatment with antibiotics, the mass continued to grow. The patient underwent surgical excision of the lesion, and the purulent aspirate was sent to the microbiology lab. Aerobic, anaerobic, mycobacterial, and fungal cultures, along with Gram and AFB stains, were performed. Direct microscopy of the aspirate revealed numerous leukocytes and few yeast cells. No sclerotic bodies were observed. Fungal growth with black pigmentation was observed during the second week of incubation. Colonies initially appeared smooth black and mucoid, later transforming into raised dome-shaped structures with a suede-like texture. Microscopic analysis revealed budding yeast cells and subglobose to broadly ellipsoidal germinating cells, which developed into short torulose hyphae before gradually transforming into unswollen hyphae. The isolate was further identified through D2 rDNA sequencing, revealing a 100% match for Exophiala jeanselmei. The patient was prescribed a one-month course of itraconazole treatment. The patient is progressing well during follow-up.

Results (if a Case Study enter NA)
NA

Conclusion
This case emphasizes the need for heightened clinical awareness in diagnosing phaeohyphomycosis, particularly in healthcare environments. Unique traumatic events like venepuncture should raise suspicion of phaeohyphomycosis. Culture and molecular diagnostics play a crucial role in confirming fungal causes and guiding treatment, leading to better patient outcomes.
Assessing the Feasibility of a Cancer Biomarker Testing Navigator in the Laboratory
Authors: Pineault L , Valencia K , Buhay J , Brown A , Spiczka A , Ziemnik S , Kelly M , Morgante J , Datta Mitra A , Yanamura L P , Gilliland M , Ferea A , Kim J 
Published: October 2024

Abstract

Introduction/Objective
Cancer biomarker testing is a crucial component of precision oncology, as it can guide medical treatment decisions with targeted therapies and immune checkpoint inhibitors. However, complex, fragmented, and inefficient operational processes involved in biomarker testing lead to delays, errors, and variability in testing. One potential solution is to introduce a novel role in the pathology laboratory: the cancer biomarker testing navigator (BTN).

Methods/Case Report
The American Society for Clinical Pathology (ASCP) conducted a mixed-methods project to assess the current state of biomarker testing operations and explore how a BTN may improve biomarker testing processes. ASCP conducted an online survey, focus groups, and worked with two hospital-based cancer centers on a feasibility pilot.

Results (if a Case Study enter NA)
Survey and focus group insights reveal several operational challenges around the biomarker testing process. 47 completed the survey and 16 participated in the focus groups. Participants report that biomarker test orders may be incorrect or incomplete. 37% of survey respondents experience delays preparing tissue samples for send-out cancer biomarker testing. 42% of survey respondents are unable to track the processing status of send-out tests. Excessive time is required to coordinate and facilitate send-out tests, especially when multiple reference laboratories are used since each has its own portal, requisition form, specimen requirements, etc. 87% agree they would benefit significantly from having a dedicated person to coordinate and manage cancer biomarker tests.
The cancer centers that piloted this role found that they could catch and correct defects such as incorrect test ordered, incorrect specimen types marked on the test order, outdated requisition used, etc. The BTN also found instances where the test report was incomplete or had not been uploaded into the EHR.
The BTN role could be justified by evaluating metrics such as task efficiency, workplace satisfaction in the lab, and levels of service satisfaction from oncologists. Patient care can be improved by reducing delays in testing and by reviewing other metrics of quality care delivery.

Conclusion
The BTN role in the laboratory is a novel solution for ensuring the proper collection and triage of pathology samples for biomarker testing. This role could serve as a liaison between the laboratory and ordering clinicians, provide collection and testing guidance, and help with benchmarking and quality measurement initiatives.
The Importance of Pathogenesis: A Molecular Investigation on A Solitary Choriocarcinoma Lung Lesion with No Primary Lesion
Authors: luu L , LUU L 
Published: October 2024

Abstract

Introduction/Objective
We present an exceedingly rare case of metastatic choriocarcinoma to the lung with no primary lesion. Notably, this is the only case where STR molecular studies have been conducted.

Methods/Case Report
A 43-year-old G1P1001 female with no past medical history presents with severe shortness of breath, left-sided back, and chest pain for severe shortness of breath, left sided back and chest pain. Patients pregnancy test was positive with a B-hCG of 17944 u/L. Transvaginal ultrasound was negative for IUP. CTAP showed no masses in the uterine cavity or ovaries. D-dimer was elevated at 623 ng/ml. However, CTA chest was negative for pulmonary emboli but revealed a RLL mass measuring 2.6 x 2.5 cm x 2.9 cm with lobulated areas suspicious for vascular structures and connection to the right pulmonary vein.
Patient was treated with a complete right lower lobectomy. An endometrial biopsy was performed and was negative for malignancy with no significant findings.
Grossly, the mass was well-circumscribe, hemorrhagic, and necrotic, measuring 3.5 cm. Microscopically, the malignant cells had highly pleomorphic and hyperchromatic nuclei. There were also multiple multinucleated cells and mitotic figures present. Some of the cells had nested architecture leading to us to suspect a pleomorphic lung adenocarcinoma with choriocarcinomatous differentiation. We performed IHC staining that demonstrated strong positivity of AE1/AE3, CK7, hCG and a high Ki-67 index. The neoplastic cells also had focal p63 and p40 positivity. Furthermore, TTF1 and SALL4 were both negative. This staining pattern as well as patient’s clinical history of no gynecological lesion, lead us to favor lung adenocarcinoma with choriocarcinomatous differentiation. However, due to the abundance of syncytiotrophoblastic and trophoblastic cells, metastatic choriocarcinoma could not be ruled out.
Therefore, the case was sent out for external consultation and Short Tandem Repeat (STR) molecular testing. Surprisingly, the STR testing results showed some STR of paternal origin indicating a metastatic gestational choriocarcinoma.
The patient’s surgery was highly successful and lead to a down trending of b-hCG from 17944 to 1768 after removal.

Results (if a Case Study enter NA)
NA

Conclusion
Performing STR testing was pivotal in this case as it revealed the presence of DNA of paternal origin, providing crucial evidence that the tumor was of gestational origin, guiding the diagnosis towards metastatic gestational choriocarcinoma.
Identification and Validation of a novel Circulating miRNA Predictive Biomarkers for acquired Bortezomib Resistance in Multiple Myeloma patients at Southeast Medical Center
Authors: Bamfield-Cummings S , Silva J 
Published: October 2024

Abstract

Introduction/Objective
Bortezomib is used to treat multiple myeloma but some patients become resistant to it. MiRNAs, small non-coding RNAs that regulate gene expression, may serve as biomarkers for drug resistance in cancer. Dysregulation of miRNA expression is common in cancer development. We investigated whether plasma miRNAs can serve as clinical indicators for bortezomib resistance in multiple myeloma. We hypothesize that there is a significant difference in miRNA signature between sensitive and resistant Bortezomib multiple myeloma samples derived from African American male patients.

Methods/Case Report
Specific Aim 1: Discovery: To identify miRNAs using five BTZ-resistant and five sensitive African American male bone marrow samples using RNA sequencing technology. Using log2fold change ≥ 1.3, p ≤ 0.05, and known function as screening criteria of statistically significant upregulated miRNAs.
Specific Aim 2: Analytical validation: Quantitative reverse-transcription PCR (qRT-PCR) technology using bone African American Male Bone Marrow samples to confirm the differential expression of candidate miRNAs identified in Aim 1. Using log2fold change ≥ 1.3, p ≤ 0.05, and Two-tailed student T-Test known function as screening criteria of statistically significant upregulated miRNAs.
Specific Aim 3: Clinical Validation: To be performed using patients’ serum and qRT-PCR technology. Using log2fold change ≥ 1.3, p ≤ 0.05, known function, and Two-tailed student T-Test as the screening criteria of statistically significant upregulated miRNAs.

Results (if a Case Study enter NA)
We identified upregulated and downregulated miRNAs from African American males with MM in 5-BTZ-resistant and 5-BTZ-sensitive bone marrow samples using RNA sequencing. Four statistically significant upregulated miRNAs were identified and validated using RT-qPCR and bioinformatic target prediction (has-miR-18a-3p, has-miR-18a-5p, has-miR-20a-5p, has-mir-664a-5p). Using log2fold change ≥ 1.3, p ≤ 0.05, and Two-tailed student T-Test, and known function as screening criteria, has-miR-18a-5p and has-miR-20a-5p were validated as statistically significant upregulated miRNAs among the BTZ-resistant bone marrow samples. These miRNAs will now undergo clinical validation.

Conclusion
According to the qRT-PCR analysis, significant differential expression was observed between the Bortezomib-sensitive and Bortezomib-resistant groups was has-miR-18a-5p (p ≤ 0.02) and has-miR-20a-5p (p ≤ 0.04) as statistically significant differential expressed miRNAs and are associated with promoting carcinogenesis.
Novel human PDX1 Asn196Thr variant causes pancreas agenesis and reduces the generation of duodenal enteroendocrine cells
Authors: Yang X , Ishibashi J , Haemmerle M W , Stoffers D A , Schiaffini R , Rapini N , Miraglia del Giudice E , Cristina Digilio M , Mucciolo M , Cianfarani S , Barbetti F , Zanfardino A , Piscopo A , Iafusco D , Iorio R 
Published: October 2024

Abstract

Introduction/Objective
Pancreatic and duodenal homeobox 1 (PDX1) is a well-studied transcription factor required for pancreas organogenesis. PDX1 mutations are associated with the development of diabetes. An 8-month-old female patient with previously uncharacterized compound heterogeneous PDX1 missense mutations (Thr151Met and Asn196Thr) was identified in this study. The patient has permanent neonatal diabetes, pancreas hypoplasia, and a malformed gallbladder.

Methods/Case Report
PDX1 Thr151Met and Asn196Thr variants in the patient were identified by next-generation sequencing gene panel and confirmed by Sanger sequencing. To examine how the mutations affect PDX1 functions in vitro, we expressed mouse Pdx1 Thr152Met and Asn197Thr, homologous to human PDX1 Thr151Met and Asn196Thr, respectively, in mouse insulinoma MIN6 cells and human embryonic kidney 293T cells and examined protein localization, protein stability, DNA binding, and protein-protein interaction. We also generated embryonic day 18 mouse embryos carrying Pdx1 Asn197Thr missense mutation using CRISPR/Cas9 to examine its roles in the development of the pancreas and other digestive organs in vivo.

Results (if a Case Study enter NA)
We found that the Pdx1 Asn197Thr variant, but not Thr152Met, altered its nuclear localization and disrupted PDX1-Onecut 1 interaction. Neither variant significantly affected PDX1 protein stability, but both reduced PDX1 binding to the Pdx1 gene promoter. Importantly, we found that the Pdx1 Asn197Thr variant caused pancreas agenesis and a reduction in the generation of enteroendocrine cells in the proximal duodenum in mouse models.

Conclusion
Our data indicated that the PDX1 Asn196Thr variant impairs its DNA binding and protein-protein interaction, causing pancreas agenesis and a reduction in the generation of duodenal enteroendocrine cells.