bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rat-Bite Fever: Developing and testing a modified time-kill protocol based on Edberg and Edberg 1983 experiemnt in order to test S. moniliformis growth in 0.05% SPS and proposed growth curve
Authors: Szewc A M , Bell M , Kelly A , Humrighouse B , McQuiston J 
Published: October 2021

Abstract

Introduction/Objective
Streptobacillus moniliformis is the primary causative agent of rat-bite fever (RBF) and Haverhill fever (HF). Rat-bite fever and Haverhill fever are difficult to diagnose in a clinical setting and are likely severely under-represented and under-reported worldwide. Clinical presentation often includes fever, chills, myalgia, headache, and vomiting. Patients may also develop a maculopapular rash covering their extremities approximately 2-4 days after onset of fever followed by polyarthritis in roughly 50% of patients with a mortality rate of 10-13% if left untreated. This is further complicated by the fact that submission and processing guidelines of clinical samples for the recovery of the organism are based on ‘outdated’ techniques and clinical laboratory methods that are over 50 years removed from current procedures, instrumentation and guidance.

Methods/Case Report
DNA from collected frozen time-point samples, were collected (n=84) and extracted using an in-house custom protocol utilizing 180 µl of bacterial lysis buffer with 20 µl of PCR grade proteinase K, for a total of 200 µl. The blood culture time-point samples were then thawed on ice, and 200 µl of blood culture sample was then added to the lysis mix, vortexed and incubated at 65°C for 10 minutes (an additional 95°C inactivation step was omitted to avoid whole blood clotting). After incubation, each sample was vortexed briefly again and extracted using the Roche automated MagNA Pure Compact instrument with an initial input volume of 400 µl and stored in a final elution buffer volume of 100 µl. All quantatitive time kill data was colleced via a CDC in-house designed PCR assay developed for S. moniliformis.

Results (if a Case Study enter NA)
Experimenting with varying amounts of blood inoculum, 10 ml of blood was determined to provide the best results for detection and growth/viability as well as propose a theoretical growth curve for the organism.

Conclusion
We found that in 100% of the isolates tested (and all the variations of testing within), SPS (up to a concentration of 0.05 % w/v) in commercially available blood culture bottles appeared to be inactivated, allowing for the growth detection and culturing of S. moniliformis using an automated continuous blood culture system when 10 ml of blood was inoculated.
Sequencing for COVID-19 in the Pandemic Era: What Does it Mean?
Authors: Petersen J M , Jhala D 
Published: October 2021

Abstract

Introduction/Objective
SARS-CoV-2 has been developing mutations over the course of the pandemic, leading to the rise of variants. The sequencing of these variants, however, has an unclear role for the medical center providing patient treatment.

Methods/Case Report
Patient specimens that were positive for the presence of SARS-CoV-2 with a cycle threshold &lt;30 by reverse transcriptase polymerase chain reaction (RT-PCR) were sent for sequencing at the Veterans Health Administration Public Health Reference Laboratory (PHRL). Testing for SARS-CoV-2 was by RT-PCR was initially done by either the Abbott Alinity m SARS-CoV-2 assay (Chicago IL) or the Cepheid Xpert Xpress SARS-CoV- 2/Flu/RSV assay (Sunnyvale CA). All sent patient specimens had been selected by the clinical team for concern of the presence of a SARS-CoV-2 variant.

Results (if a Case Study enter NA)
There were a total of 8 patients (4 males and 4 females) that were sent for sequencing. The patient ages ranged from 38 to 80 years (average 58.8). The racial proportion of the 8 patients was 2 African Americans, 2 Caucasian Americans, and 4 unanswered. All were positive for SARS-CoV-2 by RT-PCR (4 Abbott assay and 4 Cepheid assay). Six of the sequenced samples showed the NextClade 20I/501Y.V1, Pango Lineage B.1.1.7, a variant first identified in the United Kingdom; four of these six patients had documentation of vaccination prior to the infection. One sequence was a NextClade 20C Pango Lineage B.1.526.1, a variant first identified in New York. The last sequence identified was a NextClade 20G, Pango Lineage B.1, a variant predominantly seen in the United States.

Conclusion
At the present time, sequencing of SARS-CoV-2 does not have a clear clinical role. However, from a public health and epidemiological point of view, sequencing has a role in SARS-CoV-2 variant tracing and detection. Vaccine protection against variant SARS-CoV-2 may not be complete as some infected patients had been vaccinated.
Using Deep Learning for Whole Slide Image Prostate Cancer Diagnosis and Grading in South Florida Veteran Population
Authors: Jayaratne N , Sasikumar A , Subasinghe S , Borkowski A , Mastorides S , Thomas L , Mastorides E , DeLand L 
Published: October 2021

Abstract

Introduction/Objective
Prostate cancer is the most common non-cutaneous malignancy in veterans, with approximately 11,000 new prostate cancer cases diagnosed in the Veteran’s Affairs system each year. Prostate cancer diagnosis and grading can be challenging even for experienced pathologists. Although large VA medical centers have pathologists that specialize in urologic pathology, the vast majority have not. We hypothesized that the AI-augmented diagnosis and grading may provide the solution for such situations.

Methods/Case Report
Dataset consisted of 10,000 prostate biopsy whole slide images (WSI) from the Kaggle PANDA challenge, and 6,000 WSI from the James A. Haley Veterans’ Hospital. Two Classification models were trained on the combined Kaggle and VA datasets using whole slide labels, and not annotated slides that resemble semi-supervised training.
Two-Class Classification to predict Benign: ISUP [0] / Cancerous: ISUP [1,2,3,4,5] Three-Class Classification to predict Benign: ISUP [0] / Low-grade: ISUP [1,2] / High-grade: ISUP [3,4,5] WSI split into “tiles” were used for training the models to reduce whitespace around samples, manage large images, and normalize dimensions/orientations.

Results (if a Case Study enter NA)
Models trained purely as binary and 3-class classifiers performed very well. Two-Class Model:
Accuracy = 0.937
Precision = 0.965
F1 = 0.94
AUC = 0.979
Three-Class Model:
Accuracy 0.89
o Benign:
Precision=0.897
f1=0.928
o Low-grade:
Precision=0.866
f1=0.841
o High-grade:
Precision=0.91
f1=0.878
We plan to develop multi-stage prediction models using these 2-Class and 3-Class classifiers as the first stage and a cancer grade predictor in the second stage.

Conclusion
We successfully showed that AI can augment pathologist’s diagnosis and grading of prostate cancer.
Applying Best Practice to Converting Blood Collection Tube Suppliers: Overcoming Laboratory Supply Shortages
Authors: Tsang P C , Absar S F , Gingrich D 
Published: October 2021

Abstract

Introduction/Objective
Changing blood tube suppliers is a complex process that requires systematic validation. It can serve to expand a laboratory’s options during a supply shortage, and can lead to cost savings. Just prior to the pandemic, our laboratory underwent a large-scale conversion of blood tube suppliers after successful validation of serum, plasma, and whole blood tubes for blood bank, chemistry, immunology, hematology, coagulation, molecular diagnostics, and flow cytometry.

Methods/Case Report
First, we designed a patient consent form for collecting extra blood samples. Per CLSI standards, validation of blood tubes is needed for each testing methodology but not for each analyte. Hence, we selected high-impact assays to represent each testing methodology used by our instrument platforms. We designed comparison studies to test the new blood tubes for result accuracy, precision and specimen stability that covered an assay’s reportable range. Allowable error limits were set based on Westgard and CAP guidelines. Spiked specimens were used when positive patient samples were not feasible. We also took the opportunity to optimize the blood tube sizes, e.g., converting the lavender-top tubes from 2 ml (vendor A) to 3 ml (vendor B). We then confirmed with our reference labs the acceptability of the new vendor’s products, and administered an electronic survey to solicit staff feedback. Finally, we coordinated supply chain, formulary changes and test catalog updates.

Results (if a Case Study enter NA)
Data analyses showed 100% acceptable performance of the new supplier’s blood tubes. The survey showed that our phlebotomists supported the new products, citing their ease of use and good vacuum. Our hematology technologists provided favorable feedback on the larger lavender-top tubes that reduced the number of insufficient samples. On the economic front, this supplier conversion has yielded a 26% cost savings.

Conclusion
To our knowledge, our study is the most comprehensive of all blood collection device comparison analyses published. Our validation strategies that were designed to comply with best practice standards have led to our confidence in the interchangeability of the new and old blood tube products. This initiative serves to elucidate a protocol to add vendor options that can be replicated by other laboratories to mitigate blood tube supply shortages and backorders. It has helped us control supply costs without compromising quality.
The first case of BRG (SMARCA4)/INI Deficient Tracheal Carcinoma: A Case Report and Review of the Literature
Authors: Omo-Ogboi A C , Wang W , Zhao B 
Published: October 2021

Abstract

Introduction/Objective
Primary tumors of the trachea are rare, they account for less than 0.1% of tumors in humans. In adults, 90% of primary tracheal tumors are malignant, with squamous cell carcinoma and adenoid cystic carcinoma accounting for two-thirds, with other forms occurring less frequently. The BRG (SMARCA4)/INI deficient tumor is a relatively new defined entity which is recently introduced in the WHO Classification of Tumors, 5th edition, 2021. The gene SMARCA4 is located at 19p13. Loss of SMARCA4 has been reported in several aggressive tumors with high- grade undifferentiated rhabdoid morphology but has not been reported in the trachea. Hence, we report the first case of BRG (SMARCA4)/ INI deficient tracheal carcinoma.

Methods/Case Report
We present a 60-year-old male with a history of tobacco abuse, shortness of breath, and a tracheal mass on chest imaging. Bronchoscopy was performed and showed a fleshy friable lesion at the anterior trachea with evidence of blood dripping into the distal airways.

Results (if a Case Study enter NA)
Microscopic examination showed a high grade, poorly differentiated carcinoma with tumor necrosis, high mitotic counts, and marked nuclear pleomorphism. Immunohistochemical stains were performed. The tumor cells were strongly and diffusely positive for CK-7 and weakly positive for synaptophysin, negative for pan-cytokeratin, TTF-1, CK-20, p40, CK5/6, and chromogranin. Then BRG (SMARCA4) and INI 1 (BAR47) were performed and showed negative staining on BRG expression, while INI 1 is intact (nuclear expression). These features are consistent with BRG (SMARCA4)/ INI deficient carcinoma.

Conclusion
BRG (SMARCA4)/ INI deficient carcinoma is a new entity in the trachea, which is very aggressive with a poor prognosis. Targeted therapy or clinical trials may be available as additional cases are diagnosed in the future.
Rare presentation of kappa light chain proximal tubulopathy with fibrillar aggregates
Authors: Alkashash A M , Phillips C L 
Published: October 2021

Abstract

Introduction/Objective
Patients with dysproteinemias may show a spectrum of renal alterations due to organized deposits of excess immunoglobulins, including primary amyloidosis, myeloma cast nephropathy, monoclonal immunoglobulin deposition disease, and light chain proximal tubulopathy (LCPT). Among the least common is LCPT, which shows ultrastructural cytoplasmic light chain inclusions with crystalline morphology or rarely fibrillar aggregates. We present the case of a patient with LCPT with fibrillar aggregates that is the only such case registered in our large academic surgical pathology electronic database. Our aim is to increase understanding and recognition of this rare variant.

Methods/Case Report
A 73-year-old man presented with 540 mg/day proteinuria, serum creatinine 5.73 mg/dL, platelets 178,000/cc, and 20% plasma cells in his bone marrow biopsy specimen. Kidney needle biopsy cores examined by light, fluorescent and transmission electron microscopy (EM) showed kappa light chain cast nephropathy and kappa LCPT with fibrillary aggregates, the latter requiring unmasking of kappa epitopes using pronase-treated paraffin sections. Congo red stain was negative. By EM, proximal tubules contained intracellular bundles of tightly aggregated fibrils with mean fibril diameter of 7.7 +/- 1.6 nm. Individual bundles were variably shaped as round, oval, spicular or irregular blobs. Fibrils were not seen in glomeruli.

Results (if a Case Study enter NA)
NA

Conclusion
This rare presentation of LCPT with fibrillar aggregates reinforces the utility of renal biopsy diagnosis that includes careful ultrastructural examination of renal tubules. In the absence of EM, the unique fibrillar organization of these cytoplasmic light chain aggregates would otherwise go unrecognized.
Relapse of Myelodysplastic Syndrome after Allogeneic Hematopoietic Stem Cell Transplantation as Blood Bank Sees It: a Case Report
Authors: Kanakis C E , Gvozdjan K 
Published: October 2021

Abstract

Introduction/Objective
Allogeneic hematopoietic stem cell transplantation (allo-HSCT) is a curative treatment option for patients with myelodysplastic syndrome (MDS). Nonetheless, a large proportion of patients with MDS experience disease relapse. Declining donor chimerism and detection of recurrent gene mutations have been used as indicators of graft failure and recurrent disease. Blood Bank serologic findings have rarely been described as first indicators of disease relapse in this setting and could potentialy add to engraftment and relapse surveillance testing.

Methods/Case Report
A 72-year-old, ABO group O, RhD positive male with history of anti-Fyb alloimmunization underwent allo-HSCT from an ABO group B, RhD negative, Fyb positive donor as part of the treatment for MDS. Successful engraftment was achieved, and the patient’s red blood cell phenotype transitioned to ABO group B, RhD negative, Fyb positive. Two years following allo-HSCT, the patient received chemotherapy for recurrent cholangiocarcinoma. Supportive blood component transfusions were provided, all of which typed as RhD negative. However, new antibody with anti-D specificity was detected in serum while the patient still typed as ABO group B, RhD negative, preceding anti-D and later recurrent anti-Fyb detection in eluate, and prompting further chimerism testing. Declining donor chimerism was noted (72% donor, compared to &gt;98% donor on prior chimerism testing). Chemotherapy and donor-lymphocyte infusion were initiated.

Results (if a Case Study enter NA)
NA

Conclusion
The early detection of de novowlvw anti-D was most consistent with resurgence of patient’s erythroids within the bone marrow in the presence of donor’s immune system. This was followed by sufficient peripheralization of patient’s red blood cells and detection of anti-D in the eluate. Lastly, the switch to recipient’s immune system is evidenced by recurrent detection of anti-Fyb in the eluate. This case, therefore, emphasizes the utility of Blood Bank serology in raising suspicion for disease relapse and guiding further allo-HSCT patient management. More systematic use of Blood Bank serology may serve as a time- and cost-effective adjunct to the current strategies employed for detection of disease recurrence in allo-HSCT recipients.
Renal allograft rejection with thrombotic microangiopathy associated with a Kidd blood group system alloantibody
Authors: Lee E S , McHenry A , Siddon A , Tormey C 
Published: October 2021

Abstract

Introduction/Objective
The Kidd blood group antigens are urea transporters found on the surface of red blood cells, renal tubular epithelial cells, and endothelial cells in the renal medulla and vasa recta. While controversial, some reports have described an association between Kidd antigen donor/recipient mismatches and kidney transplant rejection when recipients possess or form anti-Kidd alloantibodies. To date, none of these reports have described development of a thrombotic microangiopathy (TMA) in the renal graft associated with these antibodies. We describe a case of fulminant renal transplant rejection associated with TMA in a patient with anti-Jk(a) alloantibodies who received a deceased-donor kidney transplant (DDKT).

Methods/Case Report
A 64-year-old woman with end-stage renal disease secondary to AL amyloidosis caused by plasma cell neoplasm received a DDKT associated with delayed graft function. No pre- or post-transplant donor specific antibodies (DSA) were detected, the flow crossmatch testing was negative, and a pre-operative type and screen identified anti-Jk(a) alloantibodies. On post-transplant day 5, her creatinine remained elevated at 6 mg/dL (ref range: 0.4–1.3 mg/dL) with an acute drop in platelets and undetectable haptoglobin. Allograft biopsy showed a combination of TMA with some additional evidence of acute cellular rejection. Tacrolimus was stopped to rule out drug-induced TMA, and the workup showed negative Shiga toxin, normal ADAMTS13 activity, negative atypical HUS genetic testing, and negative antiphospholipid syndrome testing. Genotyping of the donor kidney was positive for the Jk(a) antigen. Eculizumab, IVIG, and a trial of 8 sessions of therapeutic plasma exchange (TPE) were administered. Her creatinine improved (1.93–2.05 mg/dL), indicating a significant antibody-mediated etiology to her delayed graft function. About one month later, her creatinine worsened, and she received another trial of TPE with IVIG and eculizumab. Despite a mild decrease in her creatinine, repeat biopsies showed acute cellular rejection, persistent TMA, and chronic allograft injury. No DSAs were ever detected. Her creatinine never recovered, and she is now dialysis-dependent.

Results (if a Case Study enter NA)
NA

Conclusion
We speculate that anti-Jk(a) antibodies interacting with a Jk(a)-positive donor kidney account for graft TMA. This case underscores the potential importance of matching Kidd antigens in kidney transplantation.
Associations of Stay-at-Home Order Enforcement With COVID-19 Population Outcomes: An Interstate Statistical Analysis
Authors: Huntley Kyle S , Wahood Waseem , Mintz Joel , Raine Samuel , Hardigan Patrick , Haffizulla Farzanna 
Published: October 2021

Abstract
In the United States, state governors initially enacted coronavirus diseases 2019 (COVID-19)-mitigation policies with limited epidemiologic data. One prevailing legislative approach, from March to May 2020, was the implementation of “stay-at-home” (SAH) executive orders. Although social distancing was encouraged, SAH orders varied between states, and the associations between potential legal prosecution and COVID-19 outcomes are currently unknown. Here, we provide empirical evidence on how executive enforcement of movement restrictions may influence population health during an infectious disease outbreak. A generalized linear model with negative binomial regression family compared COVID-19 outcomes in states with law-enforceable stay-at-home (eSAH) orders versus those with unenforceable or no SAH orders (uSAH), controlling for demographic factors, socioeconomic influences, health comorbidities, and social distancing. COVID-19 incidence was less by 1.22 cases per day per capita in eSAH states compared with uSAH states (coefficient = −1.22, 95% confidence interval (CI): −1.83, −0.61; P &lt; 0.001), and each subsequent day without an eSAH order was associated with a 0.03 incidence increase (coefficient = 0.03, 95% CI: 0.03, 0.04; P &lt; 0.001). Daily mortality was 1.96 less for eSAH states per capita (coefficient = −1.96, 95% CI: −3.25, −0.68; P = 0.004). Our findings suggest allowing the enforcement of public health violations, compared with community education alone, is predictive of improved COVID-19 outcomes.
The Influence of Sagittal Head Tilt on Periorbital Appearance: Implications for Clinical Photography and the Evaluation of Postoperative Results
Authors: Vaca Elbert E , Bricker Jonathan T , Mioton Lauren M , Fagien Steven , Alghoul Mohammed S 
Published: October 2021

Abstract

Background
Consistency in standardized periorbital photography—specifically, controlling for sagittal head tilt—is challenging yet critical for accurate assessment of preoperative and postoperative images.

Objectives
To systematically assess differences in topographic measurements and perceived periorbital attractiveness at varying degrees of sagittal head tilt.

Methods
Standardized frontal photographs were obtained from 12 female volunteers (mean age 27.5 years) with the Frankfort plane between −15° and +15°. Unilateral periorbital areas were cropped, and topographic measurements were obtained. The images of each individual eye, at varying head tilt, were ranked in order of attractiveness by 11 blinded evaluators.

Results
Inter-rater and intra-rater reliability was excellent (intraclass correlation &gt; 0.9). Downward sagittal head tilt was linearly associated with an improved aesthetic rating (Spearman’s correlation; ρ = 0.901, P &lt; 0.001). However, on subgroup analysis, eyes with lower lid bags received the highest aesthetic score at neutral head tilt. Pretarsal show and upper lid fold heights progressively decreased (P &lt; 0.001), positive intercanthal tilt became more pronounced (P &lt; 0.001), and the apex of the brow (P &lt; 0.001) and lid crease (P = 0.036) arcs lateralized with downward sagittal head tilt, contributing to a more angular appearance of the eye. Marginal reflex distance (MRD) 1 was maintained, while MRD2 progressively increased (P &lt; 0.001) with downward head tilt.

Conclusions
Negative sagittal head tilt significantly improves periorbital aesthetics; however, in the presence of lower eyelid bags, this also increases demarcation of the eyelid cheek junction which may be aesthetically detrimental. Controlling for sagittal head tilt is critical to reliably compare preoperative and postoperative clinical photographs.
Neither glutamate nor alanine but arginine sensitizes BY-2 cells to arsenate
Authors: Nahar Nur-E-Nazmun , Prodhan Md Yeasin , Mimata Yoshiharu , Yonezawa Anna , Nakamura Toshiyuki , Nakamura Yoshimasa , Munemasa Shintaro , Murata Yoshiyuki 
Published: October 2021

ABSTRACT
Arsenic is toxic for plants. Our previous results showed that the application of proline enhanced the sensitivity of tobacco BY-2 cells to arsenate. In order to clarify the enhancement mechanism, we investigated the effects of other amino acids on the arsenate-stressed BY-2 cells. Glutamate at up to 10 m m did not affect the cell growth in the absence or presence of arsenate. Arginine at up to 10 m m did not affect the growth in the absence of arsenate but arginine at 10 m m enhanced the inhibition of the cell growth by arsenate. Alanine at up to 10 m m did not affect the cell growth under nonstressed condition but alanine at 10 m m significantly improved the cell growth under arsenate stress. These results suggest that alanine mitigates arsenate stress in BY-2 cells and that arginine like proline enhances the sensitivity of BY-2 cells to arsenate.