bluuebunny/crossref_metadata_2025 huggingface dataset:
Vascular Pattern and Density in Clear Cell vs Clear Cell Papillary Renal Cell Carcinoma
Authors: Canete-Portillo S , Rodriguez Pena M , Wang D , Netto G J , Magi-Galluzzi C , Sanchez D F
Published: October 2020

Introduction/Objective

Renal cell carcinomas (RCCs) are well-vascularized tumors. Although clear cell RCC (ccRCC) shows a characteristic vascular network, in some cases may show overlapping features with other RCCs. Microvessel density (MVD) and architectural vascular arrangement in RCC have been characterized using CD31 and CD34 immunohistochemical (IHC) stains. To date, no studies have evaluated the vascular distribution in ccRCC compared to clear cell papillary RCC (ccpRCC). We aimed to identify potential differences in MVD, vascular pattern architecture and extent in ccRCC and ccpRCC.

Methods

Fifteen cases of ccRCC and 15 cases of ccpRCC were included in the study. ERG IHC stain and Bioquant Osteo 2019 Imaging Analysis Software were used to evaluate MVD in 12 cases (6 ccRCC, 6 ccpRCC). CD34 was used to evaluate architectural vascular pattern and its extent (% of tumor) in all cases. Mann–Whitney U test in STATA version 16.0 was used for statistical analysis.

Results

MVD means were 30.64 (CI: 17.9-43.29) in ccRCC and 29.2 (CI: 17.82-40.57) in ccpRCC. CD34 highlighted 4 distinct vascular patterns: lacunae, pseudoacinar, Golgi-like and scattered. The extent of patterns ranged from 0% to 90%. Heterogeneous distribution of different vascular patterns was found in both RCC groups. Although lacunae pattern was present in all RCC cases, pseudoacinar (100.0% vs 31.0%), Golgi-like (53.8% vs 100%) and scattered (53.8% vs 38.0%) patterns showed different distribution in ccRCC vs ccpRCC, respectively. Lacunae+pseudoacinar was the most frequent combination in all ccRCCs; lacunae+Golgi-like was identified in 77% of ccpRCCs. Pseudoacinar was the most extensive pattern in ccRCCs, meanwhile Golgi-like was the predominant pattern in ccpRCCs (p value<0.05).

Conclusion

There was no difference in MVD between ccRCC and ccpRCC. However, the extent of vascular patterns pseudoacinar and Golgi-like was significantly different between ccRCC and ccpRCC. Distinct architectural vascular arrangement could help discriminate these entities.
Peripheral T-cell Lymphoma, NOS With Epstein-Barr Virus Positivity in an Elderly Patient With Myelodysplastic Syndrome: An Autopsy Case Report
Authors: Lanceta J , Xue W , Hurford M , Wu H
Published: October 2020

Casestudy

Epstein-Barr virus (EBV)-associated peripheral T-cell lymphomas are a group of aggressive neoplasms with a geographic predilection for South America and Asia, but are very rare in Western populations.

Results

We report a case of a 74-year-old Caucasian female who presented with pancytopenia and B symptoms with EBV-IgG detected on admission. Past medical history included: ITP, chronic urticaria, and recently diagnosed myelodysplastic syndrome (MDS) on bone marrow biopsy one month prior to admission. Excisional biopsies of an enlarged right neck lymph node (repeated within 6 months) and right axillary lymph node five years ago were negative for a lymphoproliferative disorder at the time. Repeated bone marrow biopsy, performed during the current admission, confirmed the diagnosis of MDS, with scattered T-cells without aberrant immunophenotype. Despite aggressive treatment from multiple specialties, the patient deteriorated and expired four weeks later from complications of MDS. At autopsy, there was diffuse lymphadenopathy involving the mediastinum, axilla, pelvis and peripancreatic fat. Lymph node sections demonstrated nodal architecture effacement by diffuse, vaguely nodular lymphoid infiltrates.

Histologically, the infiltrates were composed of medium to large lymphocytes with round to slight irregular nuclei, rare Reed-Sternberg-like multinucleated cells, clumped chromatin, and indistinct nucleoli. Individual cell necrosis was abundant with mitotic figures readily identifiable. Immunohistochemistry revealed CD2+ CD3+ neoplastic T-cells that co-express MUM1 and a subset of CD30, while negative for CD4, CD5, CD8, CD56, ALK1, and TDT. EBV-encoded RNA in-situ hybridization was focally positive. The final postmortem diagnosis was peripheral T-cell lymphoma, not otherwise specified (NOS), with focal EBV positivity.

Conclusion

Co-existence of a de-novo MDS and non-Hodgkin lymphoma without any prior chemotherapeutic exposure is a highly unusual finding, although MDS-like presentations can occur with EBV-associated lymphomas. Peripheral T-cell lymphoma, NOS is an aggressive lymphoma and EBV positivity has been found correlated with a poor prognosis. This case demonstrates how postmortem examination remains an important tool in clinical- pathological correlation and highlights the potential pathogenetic role EBV plays in MDS and T-cell lymphoma.
Brush Licking Toxicity: Toxin & Microorganism Growth On Paint Brushes
Authors: Hoang C , Flaws M , Moore N , Lerret N
Published: October 2020

Introduction/Objective

A common practice utilized by painters is licking their paint brush bristles to form a sharp point for fine lines and details. Literature details artists careless around their mediums have a higher incidence of becoming ill, yet if their brushes harbor any toxic substances or pathogenic bacteria it is currently unknown. Therefore, this study aims to determine if there is risk associated with brush licking, by determining if pathogenic bacteria and/or heavy metals are present on the brushes of volunteer artists.

Methods

We obtained 17 volunteer paint brushes and inoculated specialized collection and transport media (E- Swab, BD Biosciences, San Jose, CA) while the volunteer completed a qualitative de-identified survey indicating brush licking status. Brushes were swirled in the E-swab collection tube, then subbed to sheep blood agar plates and chocolate agar plates for bacteria growth analysis. Matrix-assisted laser desorption/ionization time-of-flight (MALDI- TOF) technology was used for identification. With the remaining E-Swab media, lead (3M, St. Paul, MN) and arsenic (HACH, Loveland, CO) testing using commercial kits was done. MALDI-TOF identification and heavy metal testing results were then compared to survey results.

Results

One of 17 specimens (6%) had pathogenic bacteria identified (Pseudomonas aeruginosa). This specimen’s survey also indicated routine brush licking. The sensitivity and specificity of MALDI-TOF for Pseudomonas aeruginosa is 96.67% and 97.87%, respectively. The remaining 16/17 (94%) had normal flora present. Importantly, the specimen containing Pseudomonas aeruginosa also had high levels of arsenic at 50 ppb. None of the specimen tested contained lead.

Conclusion

Our results indicated there is indeed some risk associated with brush licking. However, due to the small sample size, statistical significance could not be determined. Nonetheless, with the lack of knowledge surrounding this subject, it is beneficial to further explore and educate painters on the toxicities of brush licking.
Afirma Testing in Thyroid Nodules with Indeterminate Cytology: A single Medical Institute Experience
Authors: Yang Z , Zhang T , Layfield L , Esebua M
Published: October 2020

Introduction/Objective

About 10 to 30% of thyroid fine needle aspiration (FNA) nodules have indeterminate cytology, including Bethesda III, IV, and V. Afirma Gene Expression Classifier (GEC) measuring the expression of 167 mRNA was designed to classify the indeterminate thyroid nodules into benign and suspicious categories. This study aimed to evaluate the clinical performance of the Afirma GEC testing in these indeterminate thyroid lesions.

Methods

Medical records of patients with indeterminate thyroid FNA results and corresponding Afirma GEC results from November 2012 to December 2019 were retrieved. Subsequent surgical follow-up results were obtained. GEC results were compared to the histologic diagnoses.

Results

1. There were 77 cases with indeterminate thyroid FNA results. Cytology diagnosis included 67 Bethesda III and 10 Bethesda IV. Afirma GEC results were benign for 41 cases (53%), suspicious for 32 cases (42%), and non- diagnostic for 4 cases (5%). Twenty seven of 32 cases (84%) with suspicious GEC results had surgical follow-up which revealed 12 malignant and 15 benign histologic diagnoses. Only 11 of 41 cases (27%) with benign GEC results had surgery which showed 8 benign and 3 malignant diagnoses. Based on the data, the sensitivity of this test is 80% and specificity is 65%. Positive predictive value (PPV) is 44% and negative predictive value (NPV) is 73%.

The false positive cases include 5 Hurthle cell adenoma, 4 nodular hyperplasia, 3 follicular adenoma, 2 Noninvasive follicular thyroid neoplasm with papillary-like nuclear features (NIFPT), and 1 lymphocytic thyroiditis. The false negative cases include 2 minimally invasive follicular carcinoma (from same patient) and 1 papillary thyroid carcinoma.

Conclusion

1. We demonstrated in this study that a little more than half of the cases with indeterminate thyroid cytology had negative Afirma GEC results.

2.Afirma test has relatively low specificity (65%) and PPV (44%). The sensitivity (80%) and NPV (73%) is relatively higher but is lower than the values in most literature. This could be due to the fact that majority of the Afirma GEC negative cases in this study did not have surgical follow-up and the sample size is small.

3.Afirma GEC test is a relatively good “rule-out” molecular test for indeterminate thyroid nodules but is not a reliable “rule-in” test due to the low specificity and PPV.
Monomorphic Epitheliotropic Intestinal T-Cell Lymphoma (MEITL) Presenting As An Obstructive Pancreaticoduodenal Mass: A Case Report
Authors: Ritter J P , Flores R , Nazarullah A
Published: October 2020

Casestudy: A 74-year-old woman of Scottish descent presented with obstructive jaundice and weight loss. Imaging revealed a head of pancreas mass with extrahepatic bile duct dilation. Fine needle aspiration cytology of the mass was non-diagnostic, therefore the patient underwent a pancreaticoduodenectomy. Gross examination revealed a circumferential, necrotic lesion involving the periampullary duodenum with invasion into the pancreas and peri-pancreatic soft tissue. Microscopically, the lesion was composed of diffuse sheets of monomorphic medium-sized cells with fine chromatin, inconspicuous nucleoli, and scant pale cytoplasm. The duodenal mucosa overlying the lesion was ulcerated. Epitheliotropism was noted in the duodenal villi, crypt epithelium and pancreatic duct epithelium. The tumor showed extensive areas of necrosis and conspicuous perineural invasion. The duodenal mucosa uninvolved by the tumor showed no evidence of an underlying enteropathy, such as Celiac disease. By immunohistochemistry, the neoplastic cells were positive for CD45, CD3, CD8, CD56, TIA-1, granzyme B, TCR-BF1, and TCR-gamma, and were negative pan B-cell markers, CD4, CD5, CD25, CD30, EBER, HHV-8, and TCL-1. Molecular studies for T cell clonality revealed clonal TCR-alpha-beta and gamma-delta gene rearrangements. Given the morphologic and immunophenotypic findings, the diagnosis of monomorphic epitheliotropic intestinal T-cell lymphoma (MEITL) was rendered. This case is unique with features not typical of MEITL, namely mass-like pancreaticoduodenal presentation resulting in a Whipple resection, extensive necrosis, and perineural invasion.
Indeterminate Dendritic Cell Tumor (IDCT) of GI Tract, Lymph Node and Spleen Masquerading as Refractory Inflammatory Bowel Disease
Authors: Huang W , Bayerl M G
Published: October 2020

Introduction/Objective

Indeterminate dendritic cell tumor (IDCT) is an extremely rare neoplasm, most frequently presenting in skin with cells resembling precursors to Langerhans cells. We report an exceptional case of IDCT occurring in GI tract, spleen, and lymph nodes of a 66-year-old lady, mimicking inflammatory bowel disease (IBD).

Methods

Four years prior to the diagnosis of IDCT, she was diagnosed with ulcerative colitis (UC) based on bloody diarrhea and pan-colitis. Her colitis became refractory to medical treatments and she developed pancytopenia, splenomegaly and abdominal lymphadenopathy. A FNA of abdominal lymph node and a colonoscopic biopsy both showed non-necrotizing granulomas, which along with her multiple oral ulcers suggested Crohn’s disease. Due to failure to medical treatments, she underwent proctocolectomy and ileostomy, followed later by subtotal colectomy with excision of a splenule and lymph nodes.

Results

All specimens from the final operation showed involvement by IDCT characterized by polygonal cells with abundant eosinophilic cytoplasm, oval nuclei with occasional nuclear grooves, open chromatin and eosinophilic nucleoli. By immunohistochemistry, the tumor cells expressed S100, CD1a, cyclin D1, BRAFV600E. Langerin staining was observed in <5% of cells, suggesting partial differentiation of tumor cells (frequently seen in IDCT) vs. reactive Langerhans cells. No overt cytological atypia and no necrosis were observed. Eosinophils, neutrophils, lymphocytes and plasma cells were sparse. There was no emperioloperesis. The colon showed multifocal active and chronic inflammation and ulcerations associated with the IDCT infiltrate. These specimens were diagnostic of IDCT.

Conclusion

Absence Langerin in the majority of cells excluded the possibility of Langerhans cell histiocytosis. The presence of CD1a and absence of bone involvement excluded the possibility of Erdheim-Chester disease.

Retrospectively, it appears that the patient’s symptoms were due to IDCT rather than IBD. The clinical course of IDCT is highly variable, but the BRAF mutation offers a promising new therapeutic target for this patient.
An Interesting Case Report of A Concurrent Classic Hodgkin Lymphoma and Gray Zone Lymphoma in the Mediastinum
Authors: Mai B , Huddin J , Hu Z
Published: October 2020

Casestudy

A 52-year-old female presented with night sweats, chills, anorexia, and weight loss. Computed tomography and positron emission tomography showed a soft tissue infiltration in the anterior mediastinum and hypermetabolic bilateral supraclavicular, mediastinal, right hilar, and left internal mammary lymph nodes. An anterior mediastinal mass resection and thymectomy was subsequently performed.

Results

Sections of the mediastinal mass showed Hodgkin/Reed-Sternberg cells (HRS) admixed with small lymphocytes, histiocytes, plasma cells, and eosinophils. The HRS cells are positive for CD30, CD15, and MUM1, faintly positive for PAX5, and negative for CD20, CD45, CD79a, and BCL6. The morphology and immunophenotype is diagnostic of nodular sclerosis classic Hodgkin lymphoma (CHL). Sections of the thymectomy specimen showed similar morphology, however, in an area that represents 10-20% of the specimen, there are nodular and diffuse lymphoid infiltrates consisting of small lymphocytes, histiocytes, and large atypical cells. The large atypical cells are positive for CD20, CD23, CD30, CD45, CD79a, BCL2, BCL6, MUM-1, and PAX5, and negative for CD1a, CD3, CD57, and Cyclin D1. The background small CD3-positive lymphocytes form a rosette around most of the large atypical cells. CD21 and CD23 stains highlight residual follicular structures. In situ hybridization for EBV-encoded RNA (EBER) is negative. The presence of residual follicular meshwork with an immunophenotype of large B cell lymphoma supports a diagnosis of a gray zone lymphoma (GZL). Overall, CHL is involving 80-90% and GZL is involving 10-20% of the thymic tissue. The patient was subsequently placed on ABVD chemotherapy and achieved remission.

Conclusion

An accurate diagnosis of GZL is challenging. GZL is a rare type of lymphoma with morphological features between CHL and diffuse large B-cell lymphoma (DLBCL). It is even rarer to encounter a CHL concurrently present with a GZL. The optimal therapeutic approach for cases with concurrent lymphoma diagnosed with CHL and GZL needs further investigation.
Leveraging Existing Institutional Resources to Maintain Quality Assurance Practices in Anatomic Pathology in the Era of Social Distancing
Authors: Arriola A , Aneja A , Rong Y , Taraif S , jhala N
Published: October 2020

Introduction/Objective

Due to the COVID-19 pandemic, hospitals had to adapt practices to incorporate social distancing while maintaining quality assurance (QA) in anatomic pathology (AP). Prior to this, our general surgical pathology (SP) and cytopathology (CP) services held daily consensus conferences (CC) at a multi-headed microscope. Implementing social distancing meant only a few faculty were present onsite and avoidance of interactions at the multi-headed scope. In an effort to preserve QA through CC, faculty exploited the use of web conferencing through our HIPAA-compliant Zoom. We describe the utility of this new practice.

Methods

From 3/25-4/30/20, all SP and CP cases selected for CC were presented by respective pathologists (n=8) in their own offices by using individual microscopes with cameras, image acquisition software, and screen-sharing through Zoom. One pathologist was responsible for sending out a new CC Zoom link daily and recording the consensus diagnosis. All onsite pathologists and those at home participated.

Results

We presented 95 SP and 31 CP cases through Zoom compared to 300 SP and 60 CP cases presented at a similar timeframe prior to social distancing. This 68% and 48% decline could be attributed to elective procedure cancellation. We assigned a consensus diagnosis to all cases, with 77% overall being malignant diagnoses, and breast being the most common SP specimen type (22%). Additionally, all participating pathologists felt comfortable with the new format irrespective of being onsite or at home. Apart from minor audio issues, we did not notice significant lag time or visual disturbances that interfered with diagnostic abilities. Importantly, the transition did not involve investing in new technology.

Conclusion

The new virtual CC allowed our department to maintain QA practices in AP without sacrificing quality and serves as a starting point to investigating the use of this technology to other applications in AP, such as overnight frozen sections.
Optimizing the Handling of Invasive Fungal Sinusitis Surgical Specimens
Authors: Ababneh E , Dermawan J , Thomas M , Wang X , Blank A , Bakhshwin A , Terzioglu M , Miller B , Shah A , Griffith C , Chute D
Published: October 2020

Introduction/Objective

Invasive fungal sinusitis (IFS) is an aggressive disease characterized by invasion of fungal hyphae into tissue/neurovascular bundles. This project assessed the handling of IFS specimens and implemented protocols to improve turnaround time (TAT).

Methods

A retrospective review of cases accessioned with a clinical concern for IFS from 2014-2019 was performed. TAT for each step in the specimen processing was recorded. A flowchart was created using stakeholder interviews and a revised protocol was developed after assessing critical needs. Assessment of interventions was performed following implementation of the new protocol. The protocol will be evaluated by prospective direct case-by-case feedback and after a 6-month interval (projected August/2020). At 6-months, goals are a 24 hours median time between frozen section and sign-out and elimination of outliers (greater than 2 working days).

Results

We identified 53 specimens from 32 patients in the pre-intervention period (36 cases positive for IFS). Median time from frozen section to final sign-out was 28 (5-312) hours. Four areas for improvements were identified:

(1) triaging specimens to different protocols according to arrival time, (2) optimized triaging for available histology processors, (3) standardized GMS ordering, and (4) standardized case delivery/communication with sign-out staff. Interventions include: protocol for processing specimens based on time of day, new histology protocols to expedite GMS performance, an email group for rapid communication with staff pathologists and histology, and a worksheet/checklist to track each case. After implementation of the protocol, 8 cases from 7 patients were received. Median time from frozen section to final sign-out was reduced to 20 (2 – 50) hours.

Conclusion

The protocol for handling IFS specimens became live on 2/1/2020. It has reduced TAT of suspected IFS cases, from a median of 28 hours to 20 hours. The longest interval to sign-out went from312 hours to 50 hours.
A High-Resolution Liquid Chromatography-Mass Spectrometry Method for Identification of Toxic Natural Products in Clinical Cases
Authors: Luo Y R , Yun C , Lynch K L , Comstock K
Published: October 2020

Introduction/Objective

Many natural products have biological effects on humans and animals. Poisoning caused by natural products is often found in clinical toxicology cases. Liquid chromatography-high-resolution-mass spectrometry (LC-HRMS) has recently emerged as a powerful analytical tool for large-scale target screening, and the application of LC-HRMS can be expanded to solve the clinical cases of natural product poisoning.

Methods

The LC-HRMS method is based on a spectral library of 121 natural products. The spectral library was constructed by analyzing standards either in a Q-TOF mass spectrometer (only MS2 spectra acquired) or in an Orbitrap Tribrid mass spectrometer (MS2 and MS3 spectra acquired).

Results

The LC-HRMS method was verified for the limit of detection (LOD) and matrix effects in both serum and urine matrices. For each compound, the LOD was evaluated from 1.0 ng/ml to 1000 ng/ml for urine samples and from 0.50 ng/ml to 500 ng/ml for serum samples. The matrix effects were determined at three concentration levels andranged from 30.4% to 123.5% for urine samples and from 23.4% to 132.9% for serum samples. The LC-HRMS method was successfully applied to identify the culprits in three clinical cases. In addition, the combined use of MS2 and MS3 spectra enhanced the accuracy of compound identification, in library search reducing the importance of retention time that varies among instruments and consumable lots. In Case 1, the patient presented with paresthesias, arrhythmias, and stiffened arms and legs. The toxic alkaloid aconitine was identified in the serum sample and the extract of herbs that the patient ingested. In Case 2, the patients presented with weakness, dizziness, and vomiting.

The symptoms were caused by mistakenly taking Nicotiana glauca leaves and the alkaloid anabasine was identified as the culprit. In Case 3, the patients were suspected of intoxicated by taking too much extract of lupini beans. The culprit alkaloids from lupini beans lupanine and sparteine were found in the serum samples.

Conclusion

The involvement of a toxicology laboratory with the capability to perform the LC-HRMS method and with experience in the investigation of undifferentiated cases provides a unique diagnostic advantage in cases where exposure to toxic substances is possible.
A Rare Case of Babesia microti in San Francisco East Bay
Authors: Abdelmonem M , Yu T , Scot J , Bandak R , Davis V , Javaherchian V , Hatten G , Gines M
Published: October 2020

Introduction/Objective

Babesia microti, a zoonotic intraerythrocytic parasite, is the primary etiological agent of human Babesiosis in the United States. Human infections range from subclinical illness to severe disease resulting in death, with symptoms being related to host immune status. Despite advances in our understanding and management of B. microti, the incidence of infection in the United States has increased. Therefore, research focused on eradicating disease and optimizing clinical management is essential. Here we review this remarkable organism, with emphasis on the clinical, diagnostic, and therapeutic aspects of human disease.

Methods

A 71-year-old Asian man presented to the emergency department in our San Francisco East Bay community hospital in July 2019 with complaints of high fever and chills for the last five days. The patient is a resident of Taiwan. He was visiting his daughter in New Jersey where he worked in her garden. He came to California to visit his son when he noted feelings of excessive tiredness, muscle aches, and headache. He also described a decrease in appetite and nausea with vomiting and diarrhea.

Results

His chest x-ray showed increased diffuse bilateral pulmonary infiltrate. He has a history of coronary artery disease post stent placement in 2011 and history of benign prostatic hypertrophy post transurethral resection of the prostate (TURP) On physical exam, He was febrile (103.1°F) and scleral icterus was identified. Laboratory workup revealed findings suggestive of hemolysis including increased LDH (401 U/L) and increased unconjugated bilirubin (1.7 mg/dL), critically low platelets and white blood cells of (32 and 2.9), while hemoglobin & hematocrit values in the normal range (13. g/dL & 36.8%, respectively). Elevated liver enzymes were also noted; AST 72 U/L and ALT 59 U/L. Upon examination of the blood smear, Malaria -like organisms were detected, and Maltese cross forms were also visible in the red blood cells. Those findings were also seen using Giemsa stain and were confirmed at the Alameda county lab. PCR was also positive for Babesia microti. Investigation for concurrent infection with Ehrlichia chaffeensis, Anaplasma phagocytophilum and Borrelia burgdorferi was negative.

Conclusion

This case highlights the importance of timely and effective collaboration between the laboratory staff and clinicians.
Transmission Of ESBL Producing Klebsiella Ozaenae Between Wildlife And Domesticated Animals
Authors: Leu-Burke G M , Hernandez B
Published: October 2020

Introduction/Objective

Animal and human interaction can result in zoonotic transmission, colonization and risk for infectious disease. However wildlife exposure to humans through domesticated animals is not fully understood.

Alaska’s largest urban city, Anchorage, is home to approximately one thousand moose migrating into city parks and suburban backyards with an environmental impact from fecal contamination. As domesticated canines inhabit the same environment there is a potential public health for microbial transfer from wildlife to humans.

Methods

In order to determine potential risk of zoonosis from wildlife to domesticated animals, we ground collected fecal samples from three related canines (Chico, Kali, Chubs), moose habituating the canine’s backyard and from an unrelated canine (Odin) who lived nearby, but did not inhabit the same backyard environment. Observation of canine outdoor activity, including rolling and digging in the soil, was also evaluated. Using standard microbial techniques, all fecal samples were cultured for enterobacteriaceae and further identified by biochemical testing, along with antimicrobial resistance using conventional minimum inhibition concentration antibiotic panels. Phenotypic evaluation for extended spectrum beta-lactamase enzyme was performed using antibiotic disc diffusion.

Results

Fecal samples from the moose contained identical biotype and antimicrobial resistance of ESBL producing Klebsiella ozaenae with related canines Chico and Chubs. Chico and Chubs consistently exposed themselves to moose fecal matter by digging in contaminated soil, indicating aerosol transmission. Although Kali and Odin interacted with Chico and Chubs, they were not colonized suggesting a lack of microbial transmission between domesticated animals.

Conclusion

Close proximity to moose in urban Anchorage draws our attention to their commensal microbiome and potential for infectious transfer. Domesticated animals inhabit shared environment and are at risk for colonization during exposure to wildlife fecal contaminated soil and water. In a limited study, we found transfer of ESBL Klebsiella ozaenae from moose to domesticated animals in a shared urban residence. Human contact with infected domesticated animals, along with aerosol soil exposure during gardening or landscaping activities, presents opportunity for zoonosis from urban wildlife and a risk for colonization of multi-drug resistant bacteria.
A Retrospective Analysis of Joint Cultures: Only Time Will Tell (Or Will It?)
Authors: Altenburger D , Strayer S , Carroll S
Published: October 2020

Introduction/Objective

Multiple textbooks and guidelines, including CLSI, recommend holding joint cultures for 14 days. This prevents false negative results from “slower growers” which include Actinomyces species and Propionibacterium acnes. Holding of these cultures can be a burden for small microbiology labs.

Methods

A retrospective analysis of three years of joint cultures held for 14 days was reviewed. The length of time for the culture to turn positive and the organism that grew was noted.

Results

A total of 67 positive joint cultures were evaluated, which covered a period of 3 years at our institution. Of these, only 1 culture turned positive following day 5 (Propionibacterium acnes grew on day 6). The average time to positive for Propionibacterium acnes was 4 days. In comparison, the average growth time for Staphylococcus aureus and Proteus was 1 day, Pseudomonas aeruginosa was 1.2 days, all Streptococcus species was 2.4 days and Staphylococcus epidermidis was 2.7 days. No cultures grew Actinomyces during our study.

Conclusion

The consequences of missing a positive culture can be grave. In general, culture media has improved and provided increased growth rates. With resources becoming more limited, it may be time to revisit guidelines. This study is too small to be conclusive; a larger study may provide confirmation of the findings.
Use of the BioFire Film Array Blood Culture Identification(BCID) Panel(BioFire Diagnostics, Salt Lake City, Utah) on Pleural Fluid Samples in Pediatric Patients Hospitalized for Community Acquired Pneumonia(CAP)
Authors: Drehner D M , Nazario A , Franco G , Riggins S , Cadilla A , Alexander K
Published: October 2020

Introduction/Objective

CAP accounts for approximately 124,000 pediatric hospitalizations annually. Those patients often have received antibiotics prior to admission. Many have concurrent viral infections. Bacterial infections accompanying viral respiratory infections are known to increase morbidity and mortality. Traditional bacterial culture methods are often negative because of previous antibiotic therapy. The BCID, a multiplex polymerase chain reaction(PCR) assay, can identify 19 bacterial pathogens in approximately 90 minutes. It is FDA approved for blood culture isolates. We hypothesized it would detect bacterial pathogens in pleural effusions.

Methods

BCID panels were done on residual pleural fluid samples from 10 patients with severe community acquired pneumonia during the period 5/2018 – 12/2019. The patients had positive radiographic findings of pneumonia, were inpatients, had intact immune systems by clinical history and had received antibiotic therapy for more than 8 hours before specimen collection. Treatment required 133 inpatient days. 6 of 10 were diagnosed with viral respiratory pathogens. 1 of 9 had a positive blood culture. 1 of 10 had a positive pleural fluid culture.

Results

10 of 10 pleural fluid specimens were positive for a pathogen on the BCID panel – 8, Streptococcus pneumoniae, 1, Staphylococcus aureus and I, Streptococcus pyogens. Two of ten had confirmatory positive cultures. Also, one pleural fluid gram stain showed gram positive cocci in chains and clusters. The BCID detected Streptococcus pyogens. Anti Streptolysin O was strongly positive, 964(0 – 70) IU/mL.

Conclusion

The yield of bacterial culture plummets with previous antibiotic treatment. FDA approved multiplex PCR panels have narrowly defined specimen requirements. That increases the cost and decreases test applicability.

Despite a history of appropriate immunizations in the sample population Streptococcus pneumoniae may be prevalent in the complex pediatric pneumonia population. The BCID may be effective at pathogen detection in cases of complex pneumonia where patients have received prior antibiotic treatment.
Incidence of Androgen Receptor and DNA Repair Gene Mutations in Advanced Solid Malignancies: Clinical Impact of Liquid Biopsy at Veteran Affairs Medical Center
Authors: Dalal S , Jhala D
Published: October 2020

Introduction/Objective

The advent of Liquid biopsy targeting genetic mutations in solid tumors is a major milestone in field of precision oncology. This minimally invasive, novel revolutionary technique analyses circulating tumor cells (CTC) in peripheral blood and detects signature genomic alterations. DNA repair gene (DDR) mutations have been reported in 25-40% of prostatic cancers and >50% of non-small cell lung cancers (NSCLC), being more common in late-stage and hormone refractory prostate cancers. One of the DDR, especially Tp53 has been found to be associated with poor prognosis and increased germline mutations. We herein present a quality assurance study to determine feasibility of liquid biopsy for personalized management in veterans for advanced solid malignancies and its clinical impact.

Methods

Quality assurance documentation from Foundation One (Cambridge MA, NGS) on liquid biopsies performed for the Corporal Michael J. Crescenz Veteran Affairs Medical Center (CMCVAMC) from May 2019 to April 15, 2020 were reviewed. Statistical data for adequacy, cases with notable mutations, frequency and type of mutations of AR, DNA damage repair (DDR) gene and Tp53 were noted.

Results

A total of 31 liquid biopsies were performed over this time period, of which 29/31 (93.50%) were adequate for evaluation. 23/29 (79.30%) showed notable mutations, in 4/23 (17.39%) guided treatment decisions based on androgen receptor (AR) amplification, and 7/29 (24.1%) of all cases showed DDR gene mutations indicating poor outcome and resistance to the current therapy. Greater than 50% (16/29 (55.7%)) of the veterans with advanced cancers harbored Tp53 mutation, which instills hope and future insight for patient tailored oncologic therapy.

Conclusion

The minimally invasive liquid biopsy shows a great promise as a diagnostic and prognostic tool in the personalized clinical management of advanced prostate and NSCLC in veteran patient population with unique demographic characteristics. Difference in frequency of the genetic mutations (DDR, TP53, AR) in this cohort provides valuable information for disease progression, lack of response, mechanism of resistance to the implemented therapy and clinical decision making. Precision oncology can be further tailored for this cohort by focusing on DNA repair genes and Tp53 in future for personalized targeted therapy.
Does the Two-Tier System Accurately Predict Progression of Endometrial Hyperplasia to Endometrial Carcinoma in High-Risk Populations? A Retrospective Study in a Safety-Net Hospital
Authors: Zhao X , Wang C , Taraif S
Published: October 2020

Introduction/Objective

In 2014, the WHO simplified the classification of endometrial hyperplasia (EH) into a two-tier system: endometrial hyperplasia without atypia/benign endometrial hyperplasia (BEH) and atypical endometrial hyperplasia (AEH)/endometrioid intraepithelial neoplasia (EIN), as opposed to the 1994 WHO 4-tier scheme. We conducted this study to assess the diagnostic validity of the two-tier scheme in predicting upgrade to endometrioid adenocarcinoma (EA) in our high-risk patient population.

Methods

Retrospective review from Aug 2009 to August 2019 revealed 144 cases of EH diagnosed on biopsy. The cases were reclassified using the 2014 two-tier scheme to 81 BEH and 63 AEH. The excisional diagnoses, if available, were compared with the initial biopsy results.

Results

At hysterectomy, 22 AEH (50%) were diagnosed as benign, with no residual AEH, 15 cases were upgraded to EA (34.1%), and 7 had residual AEH (15.9%). Endometrial polyp was identified in 29 cases out of 63 AEH, 24 of which had a follow-up excision. Among those, 6 were upgrade to EA (25%), significantly lower than the upgrade rate of AEH without polyp (45%) (p=0.0344).

Conclusion

In our high-risk patient population, the likelihood of upgrade to EA at excision of a biopsy-diagnosed AEH is significantly higher than BEH and is in line with what was reported in the literature for other populations. Patients with endometrial polyps were less likely to progress to EA. Our study demonstrated the diagnostic validity of the two- tiered classification in high-risk population and supports the emphasis on cytological atypia.
Host-dependent dispersal demonstrates both-sex host specificity in cuckoos
Authors: Lee Jin-Won , Moon Hye-Kyoung , Noh Hee-Jin , Kim Myun-Sik , Yoo Jeong-Chil
Published: October 2020

In a parasite species, the dispersal of individuals should be dependent on the host species to which they are specialized; thus, any sexual/individual difference in host specificity may influence their dispersal patterns and, hence, population genetic structures. However, such predictions remain poorly verified in generalist avian brood parasites that are composed of multiple lineages of host-specific races. Here, we show the dispersal consequences inferred from spatial genetic structures and their association with host specificity in brood parasitic common cuckoos Cuculus canorus in which female-specific host race formation has been widely accepted. Genetic sampling from adult cuckoos confirmed restricted dispersal in both sexes and resultant genetic structures between populations where different host species breed allopatrically, whereas it was not the case between distant areas inhabited by the same host species. Contrary to the female host race hypothesis, our results demonstrate that male cuckoos may also have host specificity and disperse accordingly, conclusively allowing us to hypothesize the formation of a host race including both sexes.
Dppa2/4 as a trigger of signaling pathways to promote zygote genome activation by binding to CG-rich region
Authors: Li Hanshuang , Long Chunshen , Xiang Jinzhu , Liang Pengfei , Li Xueling , Zuo Yongchun
Published: October 2020

Developmental pluripotency-associated 2 (Dppa2) and developmental pluripotency-associated 4 (Dppa4) as positive drivers were helpful for transcriptional regulation of zygotic genome activation (ZGA). Here, we systematically assessed the cooperative interplay of Dppa2 and Dppa4 in regulating cell pluripotency and found that simultaneous overexpression of Dppa2/4 can make induced pluripotent stem cells closer to embryonic stem cells (ESCs). Compared with other pluripotency transcription factors, Dppa2/4 can regulate majorities of signaling pathways by binding on CG-rich region of proximal promoter (0–500 bp), of which 85% and 77% signaling pathways were significantly activated by Dppa2 and Dppa4, respectively. Notably, Dppa2/4 also can dramatically trigger the decisive signaling pathways for facilitating ZGA, including Hippo, MAPK and TGF-beta signaling pathways and so on. At last, we found alkaline phosphatase, placental-like 2 (Alppl2) was completely silenced when Dppa2 and 4 single- or double-knockout in ESC, which is consistent with Dux. Moreover, Alppl2 was significantly activated in mouse 2-cell embryos and 4–8 cells stage of human embryos, further predicted that Alppl2 was directly regulated by Dppa2/4 as a ZGA candidate driver to facilitate pre-embryonic development.
Chapter Four Didymus and comedy
Authors: Benuzzi Federica
Published: October 2020

Didymus’ commentaries on the comic playwrights and his Comic Vocabulary responded to the interests of the readership of Attic comedy primarily in two ways: by summarizing the opinions of previous scholars and by offering a wide range of explanations, useful also to less specialized readers. Although his exegesis of comedy is now preserved only through quotations (mainly in the scholia to Aristophanes), it is still possible to identify the main features and interests of Didymus’ interpretative work and highlight its relevance for both ancient and contemporary readers of Greek comedy.
Chapter SixThe compiler compiled: Didymus in Imperial scholarly and miscellanistic literature
Authors: DiGiulio Scott J
Published: October 2020

Few ancient scholars were as prolific as Didymus of Alexandria, who was hailed by some in antiquity as the greatest of the grammarians. Yet, despite his polymathic output and seemingly positive ancient reputation, Didymus was much maligned for his carelessness and the compilatory nature of his work, attitudes which have continued in modern scholarship. This chapter aims to reassess the earliest period of Didymus’ reception by looking closely at the scholarly and miscellaneous texts of the Roman Empire that cite and discuss the Alexandrian. By examining four particular points of reception—Roman educationalists, Harpocration, Athenaeus, and Macrobius—this chapter illustrates that while Roman authors were particularly interested in using a caricature of Didymus as a straw man for their own arguments, Greek figures more readily engaged with Didymus and his work per se. These two traditions evolve in parallel and use Didymus to represent both the positive and negative facets of polymathy; each freely cites, and transforms, him to suit their literary purposes. As a result, Didymus’ reception throughout antiquity is considerably more complex than has been previously acknowledged: he is a figure of both authority and consternation, even among the authors most similar to himself.
Indigenous Systems of Management for Culturally and Ecologically Resilient Pacific Salmon (Oncorhynchusspp.) Fisheries
Authors: Atlas William I , Ban Natalie C , Moore Jonathan W , Tuohy Adrian M , Greening Spencer , Reid Andrea J , Morven Nicole , White Elroy , Housty William G , Housty Jess A , Service Christina N , Greba Larry , Harrison Sam , Sharpe Ciara , Butts Katherine I R , Shepert William M , Sweeney-Bergen Elissa , Macintyre Donna , Sloat Matthew R , Connors Katrina
Published: October 2020

Pacific salmon (Oncorhynchus spp.) are at the center of social–ecological systems that have supported Indigenous peoples around the North Pacific Rim since time immemorial. Through generations of interdependence with salmon, Indigenous Peoples developed sophisticated systems of management involving cultural and spiritual beliefs, and stewardship practices. Colonization radically altered these social–ecological systems, disrupting Indigenous management, consolidating authority within colonial governments, and moving most harvest into mixed-stock fisheries. We review Indigenous management of salmon, including selective fishing technologies, harvest practices, and governance grounded in multigenerational place-based knowledge. These systems and practices showcase pathways for sustained productivity and resilience in contemporary salmon fisheries. Contrasting Indigenous systems with contemporary management, we document vulnerabilities of colonial governance and harvest management that have contributed to declining salmon fisheries in many locations. We suggest that revitalizing traditional systems of salmon management can improve prospects for sustainable fisheries and healthy fishing communities and identify opportunities for their resurgence.
QbD-Based UPLC Method for Quantification of Brexpiprazole in Presence of Impurities and Application to In Vitro Dissolution
Authors: Nadella Prasad Nukendra , Nadh Ratnakaram Venkata , Navuluri Srinivasu
Published: October 2020

Quality-by-design-based UPLC method was developed for chromatographic separation to quantify the antischizophrenic drug brexpiprazole in the presence of impurities. Research findings from pH-scouting studies were used as control variables which influence the chromatographic separation. The peak tailing and resolution are the response variables and established the design-space by DoE-study for selection of suitable chromatographic conditions. Separation was achieved with lower particle size stationary phase and buffer pH 2.0 in the mobile phase. The present method developed through C18 50 × 2.1 mm, Ethylene-Bridged-Hybrid technology column with 1.7 μm particles, mobile phase consists of pH 2.0 buffer and acetonitrile (67:33 v/v), flow rate of 0.5 mL min−1 and detection wavelength at 215 nm. The retention time of brexpiprazole is 0.6 min and all impurities were eluted within 2 min. The method linearity ranges were 20.4–61.3 μg mL−1 for assay and 0.88–6.59 μg mL−1 for dissolution with correlation-coefficients of 0.9999 and 0.9998 for assay and dissolution, respectively. The recovery values were found in between 99.3 and 100.9%. The method shows stability-indicating on the basis of noninterference of placebo, and impurities from forced-degradation studies. Method validation was carried out according to ICH guideline Q2 (R1).
Genetic Risk Scores Identify Genetic Aetiology of Inflammatory Bowel Disease Phenotypes
Authors: Voskuil M D , Spekhorst L M , van der Sloot K W J , Jansen B H , Dijkstra G , van der Woude C J , Hoentjen F , Pierik M J , van der Meulen A E , de Boer N K H , Löwenberg M , Oldenburg B , Festen E A M , Weersma R K
Published: October 2020

Background and Aims

Inflammatory bowel disease [IBD] phenotypes are very heterogeneous between patients, and current clinical and molecular classifications do not accurately predict the course that IBD will take over time. Genetic determinants of disease phenotypes remain largely unknown but could aid drug development and allow for personalised management. We used genetic risk scores [GRS] to disentangle the genetic contributions to IBD phenotypes.

Methods

Clinical characteristics and imputed genome-wide genetic array data of patients with IBD were obtained from two independent cohorts [cohort A, n = 1097; cohort B, n = 2156]. Genetic risk scoring [GRS] was used to assess genetic aetiology shared across traits and IBD phenotypes. Significant GRS–phenotype (false-discovery rate [FDR] corrected p <0.05) associations identified in cohort A were put forward for replication in cohort B.

Results

Crohn’s disease [CD] GRS were associated with fibrostenotic CD [R2 = 7.4%, FDR = 0.02] and ileocaecal resection [R2 = 4.1%, FDR = 1.6E-03], and this remained significant after correcting for previously identified clinical and genetic risk factors. Ulcerative colitis [UC] GRS [R2 = 7.1%, FDR = 0.02] and primary sclerosing cholangitis [PSC] GRS [R2 = 3.6%, FDR = 0.03] were associated with colonic CD, and these two associations were largely driven by genetic variation in MHC. We also observed pleiotropy between PSC genetic risk and smoking behaviour [R2 = 1.7%, FDR = 0.04].

Conclusions

Patients with a higher genetic burden of CD are more likely to develop fibrostenotic disease and undergo ileocaecal resection, whereas colonic CD shares genetic aetiology with PSC and UC that is largely driven by variation in MHC. These results further our understanding of specific IBD phenotypes.