bluuebunny/crossref_metadata_2025_split huggingface dataset:
Klebsiella pneumoniae Isolated from Critically Ill Patient with Nosocomial Pneumonia Elicits a Proteinopathy
Authors: Hanna S , Pankratz K , Pham A , Dickey Z , Morrow A , Voth S , Morrow R , Wagener B , Pittet J , Choi C , Lin M , Stevens T 
Published: October 2024

Abstract

Introduction/Objective
Gram-negative opportunist Klebsiella pneumoniae has been identified by the World Health Organization as a critical threat partially due to its prevalence in nosocomial pneumonia. Survivors often suffer increased long-term morbidity and mortality secondary to end-organ damage, including impaired cognition.
Pseudomonas aeruginosa lung infection generates an endothelial-derived tauopathy, yet whether K. pneumoniae infection elicits this phenomenon is unknown. We hypothesize K. pneumoniae infection triggers pathogenic tau release from endothelial cells, contributing to an infection-induced proteinopathy.

Methods/Case Report
We utilized wildtype, control, and tau-/- pulmonary microvascular endothelial cells (PMVECs). Tau was monitored via immunoblotting. K. pneumoniae (Kp 1-008) was isolated from the bronchoalveolar lavage of a critically ill patient diagnosed with a monomicrobial nosocomial pneumonia. Supernatants were filter-sterilized and boiled prior to transfer to naïve cells to determine transmissibility. Barrier permeability was assessed via transwell assays, cell viability through resazurin, and amyloid burden was monitored with Congo Red and Thioflavin T.

Results (if a Case Study enter NA)
Kp 1-008 infection induced permeability and tau release from control cells in a dose-dependent manner. Tau and amyloid burden increased over time in supernatants from control PMVECs. Sterile infection supernatants from control cells increased permeability and impaired oxidative metabolism in naïve cells whereas supernatants from tau-/- cells were markedly less pathogenic. Kp 1-008 induced proteinopathic cytotoxicity persisted strongly through two passages when derived from control cells but one passage when produced from tau-/- PMVECs.

Conclusion
Our results suggest that 1) K. pneumoniae infection of PMVECs generates a lung endothelial-derived proteinopathy and 2) endothelial tau is a significant contributor to its virulence.
A Retrospective Analysis of Broad-Range Microbial PCR-Sequencing Findings and Culture Results in 101 Bronchoalveolar Lavage Specimens
Authors: Hamid A , Qin X 
Published: October 2024

Abstract

Introduction/Objective
Pneumonia is a significant cause of illness and death, identifying its cause is challenging and critical for effective antibiotic treatment and for reducing the length of stay. Bronchoalveolar lavage is commonly performed to obtain high-quality lower respiratory tract samples. While traditional culture methods have been the standard for pathogen detection, microbial rRNA broad-range polymerase chain reaction (BR-PCR) has emerged as an alternative method.

Methods/Case Report
A retrospective analysis was conducted on 101 patients suspected of severe pulmonary infections at Oregon Health and Science University (OHSU).

Results (if a Case Study enter NA)
When important microbial etiology is considered, culture detected 26%, while BR- PCR detected 20%. Both methods proved effective in detecting common pathogens; however, culture demonstrated superiority in detecting fungal pathogens due to potential sampling biases associated with PCR. Furthermore, culture holds the advantages of being faster and more cost-effective, although it may fail to detect difficult to non-cultivable organisms, like Legionella spp. Culture is indispensable for susceptibility testing and strain typing purposes. More often than not, BR-PCR captures airway microbiota indiscriminately with minimal clinical significance, potentially confusing clinical interpretation.

Conclusion
Novel technologies like Biofire Pneumonia Panel (BPP), a multiplex PCR, have shown promise in the rapid detection of pneumonia pathogens including bacteria, viruses, and resistance genes (&lt; 2 hours), complementing the traditional culture methods for microbiological diagnosis. Based on this analysis we recommend introducing BPP at OHSU.
Targeted microscopic rare cell retrieval yields sufficient deoxyribonucleic acid for molecular testing in fixed tissue with low tumor fraction
Authors: Fakhari M , Mullane P , Gu W , Dong F , Lowe A C 
Published: October 2024

Abstract

Introduction/Objective
DNA extracted from formalin-fixed paraffin-embedded tissue (FFPE) blocks is often utilized for molecular oncologic testing. Cases with low tumor fraction often fail to obtain adequate tumor for molecular testing.
We hypothesized that targeted retrieval of visualized tumor cells from FFPE sections, including those with low tumor fraction, could yield sufficient DNA for molecular testing.

Methods/Case Report
Unstained sections of various thicknesses were cut from low tumor fraction blocks and visualized by light microscopy and the RareCyte CyteFinder II (Seattle, WA). Microscopic cell retrieval was performed on the RareCyte using 40 µm diameter needles from identified regions of interest. Samples were deparaffinized using Zymo Research (Tustin, CA) solution, and digested and purified using Zymo-Spin Column technology. Sample DNA was quantified with NanoDrop Spectrophotometer (Chino, CA).

Results (if a Case Study enter NA)
Regions of interest were morphologically identifiable on 4-10 µm thick sections and harder to visualize on 12 µm thick sections. Targeted microscopic cell retrieval was performed with 40 µm diameter needles. Retrieval was performed from 26 to 34 regions of interest per sample and pooled for molecular testing. Samples (n=4) yielded a mean of 81.0 ng of DNA ± 18.4 ng (1.8 ng/µL ± 0.4 ng/µL) and a median of 87.75 ng (1.95 ng/µL).

Conclusion
Targeted microscopic cell retrieval from low tumor fraction FFPE slides using the RareCyte CyteFinder II can provide sufficient DNA material for molecular testing. Application of this technology has the possibility of recovering sufficient tumor DNA for molecular testing from specimens that may be deemed unsuitable for molecular testing according to current standards. We aim to focus on increasing sample size and completing comprehensive molecular analysis as we continue to expand this work.
Transforming growth factor-beta and Epithelial-mesenchymal transition is considered an attractive pivotal Genetic-Biomarker for Hepatocellular carcinoma with hepatitis C virus-infection patients
Authors: Fyala A S , Sultan A 
Published: October 2024

Abstract

Introduction/Objective
Hepatocellular carcinoma (HCC) is the most common cause of cancer worldwide. HCC is induced by hepatitis C-virus (HCV) which represents a major health problem in Egypt. The transforming growth factor- beta (TGF-β) is a potent cytokine that has a multifunctional pro-fibrotic activity, for enhancing liver-inflammation, fibrosis, tumor-progression, and metastasis. TGF-β has a vital role in the regulation of tumorigenesis, by controlling epithelial-mesenchymal-transition (EMT), apoptosis, proliferation, and differentiation process. The dysregulation of TGF-β, Wnt/β-catenin signaling pathways, by HCV-core protein is implicated in the development of HCC.

Methods/Case Report
The study aims to determine the effect of the HCV-infection in HCC patients with a set of growth-factors, EMT, and anti-apoptotic protein expression levels by using western blotting and immunohistochemistry staining analysis.

Results (if a Case Study enter NA)
These results observed an insignificant increase in the expression of TGF-β protein for HCC/HCV-infected cells compared to the HCV-uninfected cells, and the expression of the β-catenin protein level is elevated in the nucleus. Also, it showed that Bcl-2 protein is a significant increase in HCV-infected when compared to HCV-free groups. Positive staining for p53 protein was detected in the HCC/HCV-infected, more than in HCC/HCV-uninfected cells.
This data indicated that the core-protein of HCV can switch TGF-β from a tumor suppressor to a tumor promoter by suppressing apoptosis of hepatocytes and increasing EMT expression by activation of Wnt/β-catenin signaling pathway. Therefore, HCV-core protein enhances the nuclear accumulation of β-catenin expression protein to activate downstream target genes, which regulate cell-growth and cell-cycle progression.

Conclusion
It is speculated that HCV may exert an anti-apoptotic effect, and thus enhance tumorigenesis. Also, the accumulation of nuclear Wnt/β-catenin and p53 correlates with TGF-β expression, typically a late event in hepato- carcinogenesis. Taken together, the expression level of TGF-β, Wnt/β-catenin, Bcl-2, and p53 genotype in HCV is considered an indicator of shortened survival in patients, and may be an attractive clinically pivotal genetic biomarker to mediate liver pathogenesis.
Beamion LUNG-1, a Phase Ia/Ib trial of the HER2-specific tyrosine kinase inhibitor, zongertinib (BI 1810631), in patients with HER2-driven tumors: outcomes according to HER2 aberration type
Authors: Berz D , Heymach J , Opdam F , Barve M , Tu H , Wu Y , Mueller A M , Schroeter L , Sadrolhefazi B , Yoh K , Yamamoto N 
Published: October 2024

Abstract

Introduction/Objective
Beamion LUNG-1 (NCT04886804) is an ongoing, Phase Ia/Ib trial evaluating the novel HER2- specific tyrosine kinase inhibitor, zongertinib, in patients with HER2 aberration-positive solid tumors (Phase Ia) and HER2 mutation-positive NSCLC (Phase Ib). Here, we report data from Phase Ia according to HER2 aberration type.

Methods/Case Report
Phase Ia enrolled patients with HER2 aberration-positive (by local assessment: gene mutations, rearrangements, amplification, or overexpression) advanced/metastatic solid tumors. Patients received escalating doses of zongertinib BID (≥15 mg) or QD (≥60 mg), guided by a Bayesian model with overdose control.
The primary endpoint of Phase Ia was maximum tolerated dose (MTD) based on dose-limiting toxicities (DLTs).

Results (if a Case Study enter NA)
At data cut-off (January 29, 2024), 83 patients received zongertinib (BID n=17; QD n=66). Three patients had DLTs during the MTD evaluation period (G3 decreased platelets, G3 diarrhea, G4 neutropenia); the MTD was not reached. Treatment-related adverse events (TRAEs; all/G3/G4/G5) were reported in 76%/8%/1%/0% of patients. Confirmed investigator-assessed ORR/DCR rates in evaluable patients/patients with NSCLC (n=74/n=41) were 35%/85% and 44%/93%; median duration of response was 12.7/15.8 months, respectively. Based on preliminary data, 43 patients were HER2 mutation-positive (TKD/non-TKD/unknown n=36/n=6/n=1; A775_G776insYVMA n=16; G778dupGSP insertions n=3; S310F n=2); 23 patients overexpressed HER2 (2+/3+); 17 had HER2 amplification; 3 patients had NRG1 fusions. ORR/DCR rates (regardless of confirmation) in patients with TKD mutation-positive, A775_G776insYVMA-positive, non-TKD mutation-positive, G778dupGSP-positive and S310F- positive tumors were 64%/97%, 69%/94%, 20%/100%, 33%/100% and 50%/100%, respectively. ORR/DCR rates (regardless of confirmation) in patients with HER2 overexpressing tumors (+/- amplification) were 39%/83%. Of the 3 patients with NRG1 fusions, one had a partial response and two had stable disease.

Conclusion
In this preliminary analysis, zongertinib showed promising activity across a broad range of tumor types with different HER2 aberrations, including aberrations that have historically been difficult to treat. Updated data will be presented.
Comprehensive Approach to TB Diagnosis Powered by Machine Learning in Endemic Countries
Authors: Khan T , Khan I H , Ravindran R 
Published: October 2024

Abstract

Introduction/Objective
Tuberculosis (TB), a leading cause of mortality worldwide, is primarily diagnosed through methods that face numerous challenges, including lengthy result times and diagnostic inaccuracy, particularly in the context of drug-resistant strains and latent infections. This study proposes a novel approach that integrates multiple diagnostic modalities with machine learning to enhance TB diagnosis accuracy.

Methods/Case Report
The Machine learning model was tailored for the classification of radiological images, specifically CT scans, using original DICOM images to preserve valuable voxel information. The study involved a curated dataset of CT scans from Pakistan, TB-positive (smear+/Culture+ n=72; smear+/culture- n= 3; smear-/Culture+ n=16; smear-/Culture- n=14; clinical and radiological diagnosis only n= 12) and healthy (n=103) scans from COVID-CTSet were included in the training to assess the specificity of the model. Data preprocessing included noise reduction, histogram matching, and data augmentation techniques to ensure a robust training dataset. The methodology also incorporated using k-fold cross validation and a custom learning rate scheduling strategy to optimize the model’s training process. To further test its robustness, the model was evaluated by swapping random patches and analyzing 60 mm patches from the entire CT scan for local feature categorization.

Results (if a Case Study enter NA)
The model has demonstrated outstanding performance, with sensitivity and specificity exceeding 95% on our internal dataset (n=117) and aligning well with clinical, smear, culture, and anti-TB antibody findings. It also showed promising results on the external NIH TB Portal’s dataset (n= 1,460). The model is robust to variations in CT scanner image quality and noise profiles, maintaining strong generalization across datasets. Even when analyzing random 60mm patches, effectively classifying all local features

Conclusion
Our study enhances tuberculosis diagnostic methods in endemic regions by blending machine learning with conventional diagnostic techniques. This approach improves TB detection, particularly the early and accurate identification in areas impacted by drug-resistant strains and asymptomatic latent infections. By integrating radiological and clinico-pathological data, we aim to develop a comprehensive diagnostic score. Moving forward, we plan to further integrate this method into clinical decision support systems and adapt the approach to other infectious diseases.
Efficiently Improving Laboratory Workflow with Continuous Sample Loading by Validating the COBAS 5800 for HIV and HCV Viral Loads
Authors: Petersen J M , Jhala D 
Published: October 2024

Abstract

Introduction/Objective
A regional veteran affairs medical center (VAMC) was using the COBAS AmpliPrep/COBAS Taqman (Roche, Basel Switzerland) with a throughput of 72 tests/8 hours without continuous loading capability.
However, a newer cobas 5800 System (Roche, Basel Switzerland) was validated to allow for continuous loading with better parameters for workflow including 144 tests/per 8 hours with a capacity for continuous loading of samples without batching. As validation experiences between the two instruments is sparse in the literature, the validation is described.

Methods/Case Report
The validation process included a linearity study using 24 samples with levels (100, 600, 6,000, 60,000, 600,000, 2,000,000, and 6,000,000 copies/mL for HIV and 100, 300, 3,000, 30,000, 300,000, 3,000,000, and 30,000,000 copies/mL for HCV) across the analytical range, a precision study at a low (1,000 copies/mL) and high (100,000 copies/mL for HIV, 1,000,000 copies/ML for HCV) values of a triplicate run over 5 days, an accuracy study based on the precision study, a limit of detection study using 20 control samples at the limit of detection, control monitoring (high and low positive controls) over 9 runs, and a method correlation between the Cobas 5800 and the Cobas AmpliPrep/COBAS Taqman.

Results (if a Case Study enter NA)
The validation study resulted as expected. For the method correlation, the results were plotted and evaluated with an R2 of 0.937 (HIV from 91 samples) and 0.9646 (HCV from 74 samples). Linearity across the analytical range had an R2 of 0.9967 (HIV) and 0.9950 (HCV). All samples were detected at the limit of detection study. Both the accuracy and precision yielded expected results. The values from running the controls (high and low positive) over 9 runs remained within the expected range and within two standard deviations for all runs.

Conclusion
The COBAS 5800, which has improved capabilities compared to the COBAS AmpliPrep/COBAS Taqman, was validated for clinical use successfully.
Solitary Loss of PMS2 in a patient with Colon carcinoma
Authors: Umah C , Singh N 
Published: October 2024

Abstract

Introduction/Objective
In the United States, there are about 150,000 new cases of Colorectal cancer (CRC) and about 50,000 CRC related deaths each year. Hereditary nonpolyposis colorectal cancer (Lynch Syndrome) accounts for 2% - 4% of CRC. It is characterized by germline mutations in mismatch repair (MMR) genes - MLH1, MSH2, MSH6 and PMS2. Patients with Lynch syndrome have up to an 80% lifetime risk (LTR) of CRC and up to 60% LTR of endometrial cancer. Lynch syndrome patients also have an associated LTR of ovarian cancer (38%), upper urologic tract cancer (18%), gastric cancer (13%), small bowel cancer (6%), hepatobiliary tract cancer (4%), and brain tumors (3% - usually glioblastoma).

Methods/Case Report
A 76-year-old man with history of moderately differentiated colorectal adenosarcoma involving the transverse colon and a recently diagnosed grade group 5 (Gleason 4 + 5) prostate adenocarcinoma, currently being managed at an outside hospital. The case was sent to UAB for DNA MMR/microsatellite instability (MSI) status evaluation testing. Immunostaining showed loss of PMS2 and intact expression of MLH1, MSH2 and MSH6. These results were confirmed by the IdyIIa MSI assay which detected microsatellite instability in 5 of 7 markers and negative for BRAF V600E variant confirming microsatellite instable tumor.

Results (if a Case Study enter NA)
NA

Conclusion
Solitary loss of PMS2 in colonic adenocarcinoma is uncommon and may be caused by an underlying germline mutation of MLH-1 or PMS2, thus could represent Lynch Syndrome. Our patient’s age doesn’t favor Lynch syndrome. Next step would be to perform MLH-1 promoter methylation to confirm sporadic nature of carcinoma.
Somatic methylation of the MLH1 promoter occurs in approximately 80% of CRC with defective MMR. Prostate cancer is not currently considered a part of Lynch syndrome.
DNA Methylation Profiling Confirms a Challenging Glioblastoma, Atypical Mesenchymal Type Which Mimics Intracranial Mesenchymal Tumor
Authors: Aljumaili Z , Ibrahim N , Gao Y , Rivera D , Bhattacharjee M , TAKEI H , Zhang X 
Published: October 2024

Abstract

Introduction/Objective
Brain tumors exhibit distinct DNA methylation patterns that reflect their cellular origin, molecular subtype, and clinical behavior. DNA methylation signatures provide valuable insights into tumor heterogeneity, evolution, and treatment response, guiding personalized therapeutic strategies. Our case, glioblastoma, atypical mesenchymal type confirmed by DNA methylation profile and it reflects the clonal evolution of the glioblastoma metaplasia with minimal glial component which was histologically challenging.

Methods/Case Report
A 56-year-old gentleman presented with headaches. MRI brain demonstrated a heterogeneous enhancing mass with areas of central necrosis in the left temporal lobe, measuring approximately 49 x 34 mm, with surrounding T2 FLAIR hyperintensity extending into the left basal ganglia, causing compression of the left lateral ventricle and uncal herniation. He underwent left-sided craniotomy for tumor resection. Microscopic examination revealed hypercellular spindle cell neoplasm, forming fascicles. Brisk mitotic activity and geographic necrosis were evident. GFAP highlighted narrow margins of the tumor which could represent the entrapped glial tissue. CD99 stained the tumor cells, Other immunohistochemical stains for spindle cell work up, like S100, EMA, PR STAT6 and desmin were all negative. A diagnosis of intracranial mesenchymal tumor /sarcoma was considered.
Methylation profiling results showed class calibrated scores of 0.9741, compatible with Glioblastoma, IDH-wildtype, atypical mesenchymal type with a cytogenetic profile including gain of chromosome 7 (including EGFR) and loss of chromosome 10 (including PTEN), and loss of CDKN2A/B.

Results (if a Case Study enter NA)
NA

Conclusion
Although histopathological examination and immunohistochemical study are fundamental in diagnosing brain tumors, the rapid development of cytogenetic and molecular diagnostic modalities has significantly contributed to diagnostic accuracy and the potential for targeted treatment. Particularly, DNA methylation profiling has proven valuable in diagnosing morphologically challenging cases with prognostic value. Eventually, DNA methylation profiling will be adopted as a major cancer diagnostic criterion and will become a standard procedure performed at major academic centers.
Bihemispheric IDH-Wildtype Glioblastoma with Unilateral FGFR3-TACC3 Fusion in Patient with Breast Cancer History: A Case Report and Literature Review
Authors: Farooq S , Zeches B A , Boyer P , Lee S , Jo J 
Published: October 2024

Abstract

Introduction/Objective
Adult IDH-wild type glioblastomas comprise a heterogeneous spectrum of neoplasms, characterized by poor prognosis and resistance to the chemoradiotherapy. For WHO integrated diagnosis classification and to establish treatment options, molecular analysis is necessary. Herein, we present a case of a glioblastoma, IDH-wildtype with involvement of both cerebral hemispheres and an uncharacteristic in-frame fusion limited to one hemisphere.

Methods/Case Report
The patient is a 52-year-old woman with past medical history of metastatic breast cancer who presented with headache and worsening facial pain. Brain magnetic resonance imaging brain demonstrated a right frontal lobe lesion with vasogenic edema. The patient was treated with Gamma Knife radiosurgery. Scans revealed enlargement and a new left frontal lobe lesion. Bihemispheric tumor resection and GammaTile placement was undertaken.

Results (if a Case Study enter NA)
Histologically, the tumor was composed of hypercellular astrocytes, microvascular proliferation, and necrosis with no evidence of metastatic disease. Immunohistochemistically, neoplastic cells showed glial fibrillary acidic protein expression and elevated Ki-67 proliferation index. Molecular examination revealed in the right hemisphere lesion post-radiation (1) FGFR3::TACC3 (exon 17::exon 11) fusion and (2) TERT promoter, while the left hemisphere lesion which did not receive radiation showed clinically relevant variants in (1) TERT promoter, (2) TP53, (3) NF1, and (3) PIK3CA without identification of a fusion. An integrated diagnosis of glioblastoma, IDH- wildtype, CNS WHO grade 4 was established bilaterally.

Conclusion
The fibroblast growth factor receptor 3 (FGFR3)-transforming acidic coiled-coil 3 (TACC3) fusion is identified as a rare molecular feature in glioblastomas with an estimated prevalence of 4%. Clinical trials suggest that F3T3-positive tumors have a better prognosis than those without the translocation. The identification of the oncogenic FGFR3-TACC3 fusion highlights the possibility of identifying patients potentially responsive to targeted therapy with FGFR kinase inhibitors. The significance of the molecular differences in the right and left hemisphere lesions is uncertain; glioblastomas are heterogeneous tumors with intra-and intertumoral heterogeneity but it may suggest independent origins.