bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Rare Case of Acute Interstitial Pneumonia Diagnosed at Autopsy
Authors: Conner E , Troxclair D , Khokhar H , Beversdorf W 
Published: October 2020

Abstract

Introduction/Objective
Acute interstitial pneumonia (AIP) is a rare disease clinically characterized by rapidly progressing respiratory failure in individuals with no history of respiratory illness or other inciting factors. While most often diagnosed in middle-aged adults, it may present in any age group. Initial presentation is described as influenza- like, and respiratory failure requiring ventilatory support often progresses within weeks to months. Prognosis is poor, with an estimated mortality rate approaching 80% without treatment.

Methods
We present the case of a 44-year-old male nonsmoker with no significant medical history, who presented in 2018 with 1.5 months of dyspnea and headache initially diagnosed as atypical pneumonia. Chest imaging revealed bilateral opacities; however, microbial workup revealed no evidence of infectious etiology. Autoimmune serology studies were likewise unrevealing. Despite aggressive supportive and medical management, he deteriorated to respiratory failure and succumbed.

Results
At autopsy, the lungs were symmetrically congested and edematous (combined weight 2,340 g) but free of evident consolidation or discrete lesions. Microscopic examination revealed diffuse alveolar damage with extensive hyaline membrane formation, interstitial edema, and fibroblastic proliferation. The vasculature was severely congested, and the alveoli contained hemorrhage and scattered macrophages. No fungal or mycobacterial elements were identified by staining. Based on the histologic features and clinical context, the diagnosis of AIP was made.

Conclusion
AIP is a rare, aggressive, and diagnostically challenging disease that includes a broad range of both clinical and histologic differentials. Timely recognition and intervention with aggressive respiratory support and high- dose glucocorticoids are the mainstays of clinical management. The diagnostic role of histology is significant, but hinges on early clinical consideration of AIP as disease progression may later preclude the biopsy procedure. We share this case to raise awareness of this rapidly progressive and diagnostically troubling interstitial lung disease while emphasizing the importance of clinicopathologic correlation.
Heterogeneity and Geographical Patterns of PD-L1 Positive Tumor Infiltrating Immune Cells in Colonic Adenocarcinoma
Authors: Messersmith L , Williams G , Broadwater` D R , Brady R 
Published: October 2020

Abstract

Introduction/Objective
Programmed death-ligand 1 (PD-L1) status is an important prognostic and predictive biomarker. PD-L1 status is difficult to accurately assess in tumor cells (TCs) due to tumor heterogeneity and lack of standardized histologic evaluation. PD-L1 expression by tumor infiltrating immune cells (TIICs) is an independent prognostic marker and may provide fewer diagnostic challenges, as TIICs appear less heterogeneous. We examined the geographical patterns of PD-L1 expression in TCs and TIICs in order to evaluate heterogeneity and ease of histological evaluation.

Methods
197 blocks of colonic adenocarcinoma from 33 patients were retrospectively reviewed and stained for PD- L1. PD-L1 was interpreted as positive or negative in the TCs and TIICs. Geographical patterns of expression were recorded for the TCs and the TIICs at the surface, center of tumor, and invasive margin. Geographical patterns were compared using a chi-square test.

Results
56% of blocks had PD-L1 positive TCs. 42.7% showed positive TCs at the invasive margin. 38.2% had positive TCs at the invasive margin and surface. No blocks had positive TCs at the center of the tumor. 79% of blocks had PD-L1 positive TIICs. 20% showed positive TIICs at the invasive margin. 37.4% had positive TIICs at the surface and invasive margin. 15.5% of TIICs expressed PD-L1 throughout the tumor. There was a statistically significant difference in PD-L1 expression on TCs versus TIICs in 4 of the 7 geographic patterns.

Conclusion
PD-L1 expression on TCs of colonic adenocarcinoma is more heterogeneous than PD-L1 expression by TIICs. TIICs express PD-L1 more consistently throughout the tumor and are easier to identify and report. PD-L1 expression by TIICs is an independent prognostic indicator and may be more useful than TCs when evaluating the tumor microenvironment and determining PD-L1 status.
Diagnostic Challenges And Clinical Implications For Systemic EBV-Associated T-Cell Lymphoproliferative Disorders Of Childhood
Authors: Yasa Benkli C , Marcogliese A , Elghetany M , Punia J , Fisher K , Curry C , El-Mallawany N , Allen C , McClain K , John T , Gaikwad A 
Published: October 2020

Abstract

Introduction/Objective
Systemic EBV-associated T-cell lymphoproliferative disorders of childhood (S-EBV-T-LPD) comprise three major forms: EBV-positive hemophagocytic lymphohistiocytosis (EBV-HLH), systemic EBV-positive T- cell lymphoma (S-EBV-TCL), and systemic T-cell chronic active EBV infection (S-T-CAEBV). These disorders are rare in children and young adults in Western countries and are associated with poor outcomes. Frequently patients were treated initially for EBV-HLH and subsequently found to have relapsed/refractory EBV-HLH vs S-EBV-TCL or overt EBV+ TCL, the latter of which requires different therapy than EBV-HLH. We report the clinicopathologic findings of 13 cases, including 8 previously reported. (PMID: 31099136)

Methods
Thirteen cases of S-EBV-T-LPD were identified at Texas Children’s Hospital from 1990 to 2020. Clinicopathologic and relevant laboratory parameters were recorded.

Results
Patients included six females and seven males of Hispanic (n=6), Asian (4), and Caucasian origins (3) ages 1-22 years (median 2). All had fever, hepatosplenomegaly, cytopenias, abnormal EBV serologies, and significantly elevated peripheral blood EBV- DNA load by quantitative PCR. Histologic features were variable ranging from EBV+ T-cell infiltrates with subtle architectural distortion and mild atypia to overt morphologic appearance of lymphoma.
Consistent findings were aberrant T-cell populations identified by immunohistochemistry (n=4) or bone marrow flow cytometry (n=9, 1-50%, mean 16%). Five patients were classified as overt EBV+ TCL with abnormal karyotyping identified in 3. Seven patients had pathology findings indistinguishable between EBV-HLH and S-EBV-TCL and were classified as EBV-HLH/S-EBV-TCL. One patient had S-T-CAEBV. Outcomes were dismal after HLH-directed immuno/chemotherapy protocols with/without bone marrow transplant as only three EBV-HLH/S-EBV-TCL patients were alive at 1.5, 2.5 months, and 9 years follow-up.

Conclusion
This series from North America demonstrate challenges in the diagnosis and management of S-EBV-T- LPD cases. Particularly, EBV-HLH and S-EBV-TCL, which require vastly different treatment strategies, may initially present with overlapping clinicopathological features. Further studies are needed to address clear diagnostic criteria to guide appropriate management.
Blood Provision for Cardiac Ablation (CA) Procedures in the Catheterization Laboratory; a Veteran Affairs Medical Center (VAMC) Experience in a Non-Trauma Center Setting
Authors: Petersen J M , Patel V , Jhala D 
Published: October 2020

Abstract

Introduction/Objective
Cardiac perforation is a life-threatening complication (~1% risk, with reported rates between 0.2% to 5%) of CA procedures. As cardiac perforation may lead to extensive bleeding, it would be reasonable for a medical center carrying out CA to be capable of arranging for a massive transfusion protocol and for surgical repair as required. However, there is sparse literature to guide a non-trauma medical center implementing a CA program on what the number of red blood cell (RBC) units for crossmatch should be for each case.

Methods
In interdisciplinary collaborative meetings, the CA program logistics were agreed to between the multiple clinical services. Given the case series on the amount of drained blood in complicated cases, there was agreement that three units of RBCs would be crossmatched for each case. Education was provided on the massive transfusion protocol and on blood bank procedures. As part of quality assurance/quality improvement, records were reviewed from the beginning of the CA program (10/1/2019) to 1/31/2019 to determine number of patient cases, crossmatched units, and transfused units for quality assurance purposes.

Results
A total of fifteen patients underwent CA procedures, for which three units were crossmatched for each patient. As there were no cardiac perforations with the cardiac ablation procedures so far, no units were transfused. The organized approach for ensuring adequate blood bank support and education led to the reassurance, alleviation of clinical anxiety, and building of a successful CA program. Education sessions completed with thorough understanding of blood bank procedures including the massive transfusion protocol, labeling of blood bank specimens, and on ordering of blood for crossmatch.

Conclusion
This study provides a reference that may provide helpful guidance to other blood banks on what the number of RBCs to be crossmatched prior to each CA procedure. Multidisciplinary collaborative meetings in advance are an essential component for ensuring adequate support for CA procedures or any new service that requires blood product support. Thorough education of clinical staff on blood bank procedures particularly the massive transfusion protocol is also recommended. This procedure for massive transfusion should be available to be referred to in real time.
Blood Requests and Utilization in Elective Surgical Patients in a Nigerian Teaching Hospital
Authors: Olatinwo A T , Bolarinwa A , Adeyemo T 
Published: October 2020

Abstract

Introduction/Objective
Although requesting for blood is a very common practice for patients for surgical interventions, the average requirement for a particular procedure is usually based on subjective anticipation of blood loss rather than on evidence based estimates. Over-ordering of blood components results in wasting of technical time, reagents and imposes extra cost on patients.
The objective of this study is to assess blood ordering and utilization in a Nigerian Tertiary Hospital.

Methods
A review of one year data collected from the records of all discharged surgical patients and blood bank registers was done. Blood utilization was calculated using crossmatch to transfusion ratio (C/T), transfusion probability (%T), and transfusion index (TI).

Results
A crossmatch request for 1,228 units for 569 patients was made. Requests was higher for gynaecological cases (24.8 %) followed by orthopaedic procedures and least for cardiothoracic and urological surgeries (1.4 % each). Out of the crossmatched units, 880 units was transfused for 373 patients. The overall of C/T, %T, and TI were 1.4, 65.6%, and 1.55 respectively. The highest C/T was observed in elective caesarean sections (2.25) and
neurosurgeries (2.2) while the lowest C/T was observed in oral maxillofacial surgeries (1.09)

Conclusion
Unnecessary crossmatching with minimal transfusion practice was observed in many elective surgical cases. Blood request pattern for elective surgeries needs to be revised and unnecessary requests minimized. There is a need for a Hospital blood transfusion committee which should come up with blood request policies and transfusion guidelines for elective surgical procedures and also conduct regular blood transfusion service audits.
FR-Match: robust matching of cell type clusters from single cell RNA sequencing data using the Friedman–Rafsky non-parametric test
Authors: Zhang Yun , Aevermann Brian D , Bakken Trygve E , Miller Jeremy A , Hodge Rebecca D , Lein Ed S , Scheuermann Richard H 
Published: October 2020

AbstractSingle cell/nucleus RNA sequencing (scRNAseq) is emerging as an essential tool to unravel the phenotypic heterogeneity of cells in complex biological systems. While computational methods for scRNAseq cell type clustering have advanced, the ability to integrate datasets to identify common and novel cell types across experiments remains a challenge. Here, we introduce a cluster-to-cluster cell type matching method—FR-Match—that utilizes supervised feature selection for dimensionality reduction and incorporates shared information among cells to determine whether two cell type clusters share the same underlying multivariate gene expression distribution. FR-Match is benchmarked with existing cell-to-cell and cell-to-cluster cell type matching methods using both simulated and real scRNAseq data. FR-Match proved to be a stringent method that produced fewer erroneous matches of distinct cell subtypes and had the unique ability to identify novel cell phenotypes in new datasets. In silico validation demonstrated that the proposed workflow is the only self-contained algorithm that was robust to increasing numbers of true negatives (i.e. non-represented cell types). FR-Match was applied to two human brain scRNAseq datasets sampled from cortical layer 1 and full thickness middle temporal gyrus. When mapping cell types identified in specimens isolated from these overlapping human brain regions, FR-Match precisely recapitulated the laminar characteristics of matched cell type clusters, reflecting their distinct neuroanatomical distributions. An R package and Shiny application are provided at https://github.com/JCVenterInstitute/FRmatch for users to interactively explore and match scRNAseq cell type clusters with complementary visualization tools.
Psoriasis-like skin disorder in transgenic mice expressing a RIG-I Singleton–Merten syndrome variant
Authors: Abu Tayeh Ahmed , Funabiki Masahide , Shimizu Shota , Satoh Saya , Sumin Lee , Iwakura Yoichiro , Kato Hiroki , Fujita Takashi 
Published: October 2020

Abstract
Mutations in DDX58 (DExD/H-box helicase 58), which encodes the cytoplasmic RNA sensor retinoic acid-inducible gene I (RIG-I), were recently identified in the rare autoimmune disease Singleton–Merten syndrome (SMS). We report the spontaneous development of psoriasis-like skin lesions as an SMS-like symptom in transgenic mice harboring one of the RIG-I SMS variants, E373A. Histological analysis revealed typical characteristics of psoriasis, including the abnormal proliferation and differentiation of keratinocytes leading to epidermal hyperplasia, and infiltrates consisting of neutrophils, dendritic cells and T cells. Levels of the IL-23/IL-17 immune axis cytokines were high in the skin lesions. Rag2−/− transgenic mice showed partial amelioration of the phenotype, with down-regulation of inflammatory cytokines, including IL-17A, suggesting the importance of lymphocytes for the pathogenesis similar to that of human psoriasis. Of note, IL-17A deficiency abolished the skin phenotype, and treatment using the JAK inhibitor tofacitinib not only prevented onset, but also improved the skin manifestations even after onset. Our study provides further evidence for the involvement of RIG-I activation in the onset and progression of psoriasis via type I interferon signaling and the IL-23/IL-17 axis.
An observational cohort study of bacterial co-infection and implications for empirical antibiotic therapy in patients presenting with COVID-19 to hospitals in North West London
Authors: Wang Liyang , Amin Amit K , Khanna Priya , Aali Adnan , McGregor Alastair , Bassett Paul , Gopal Rao Guduru 
Published: October 2020

Abstract

Objectives
To describe the prevalence and nature of bacterial co-infections in COVID-19 patients within 48 hours of hospital admission and assess the appropriateness of empirical antibiotic treatment they received.

Methods
In this retrospective observational cohort study, we included all adult non-pregnant patients who were admitted to two acute hospitals in North West London in March and April 2020 and confirmed to have COVID-19 infection within 2 days of admission. Results of microbiological specimens taken within 48 hours of admission were reviewed and their clinical significance was assessed. Empirical antibiotic treatment of representative patients was reviewed. Patient age, gender, co-morbidities, inflammatory markers at admission, admission to ICU and 30 day all-cause in-hospital mortality were collected and compared between patients with and without bacterial co-infections.

Results
Of the 1396 COVID-19 patients included, 37 patients (2.7%) had clinically important bacterial co-infection within 48 hours of admission. The majority of patients (36/37 in those with co-infection and 98/100 in selected patients without co-infection) received empirical antibiotic treatment. There was no significant difference in age, gender, pre-existing illnesses, ICU admission or 30 day all-cause mortality in those with and without bacterial co-infection. However, white cell count, neutrophil count and CRP on admission were significantly higher in patients with bacterial co-infections.

Conclusions
We found that bacterial co-infection was infrequent in hospitalized COVID-19 patients within 48 hours of admission. These results suggest that empirical antimicrobial treatment may not be necessary in all patients presenting with COVID-19 infection, although the decision could be guided by high inflammatory markers.
Bioavailability of the calcium salt of dl-methionine hydroxy analog compared with dl-methionine for nitrogen retention and the preference of nursery pigs for diets based on the 2 forms of methionine
Authors: Wang Minqi Q , Huyen La T T , Lee Jung W , Ramos Sheila H , Htoo John K , Kinh La V , Lindemann Merlin D 
Published: October 2020

Abstract
Experiments were conducted to determine the relative bioavailability (RBV) of the calcium salt of the hydroxy analog of dl-methionine (MHA-Ca, 84%) to dl-methionine (dl-Met, 99%) as Met sources fed to pigs. In experiment 1, 42 crossbred barrows (initial BW of 15.0 ± 0.7 kg) were allotted to 7 treatments in an N-balance study. The basal diet (BD) was formulated to contain 15.4% CP and 0.22% Met (70% of requirement). Diets included (1) BD, (2) BD + 0.025% dl-Met, (3) BD + 0.050% dl-Met, (4) BD + 0.075% dl-Met, (5) BD + 0.038% MHA-Ca, (6) BD + 0.077% MHA-Ca, and (7) BD + 0.115% MHA-Ca. An increase in dietary inclusion rates of both Met sources linearly increased (P &lt; 0.01) N retained (g/d) and N retention (% of intake). Using linear slope-ratio regression, the RBV value of MHA-Ca to dl-Met for N retained (g/d) was 63.0% on a product-to-product basis (75.0% on an equimolar basis). In experiment 2, 40 crossbred barrows (initial BW of 15.5 ± 1.5 kg) were allotted to 5 treatments in another N-balance study. The BD was formulated to contain 17.0% CP and 0.22% Met (70% of requirement). Diets included (1) BD, (2) BD + 0.030% dl-Met, (3) BD + 0.060% dl-Met, (4) BD + 0.046% MHA-Ca, and (5) BD + 0.092% MHA-Ca. Increasing levels of dl-Met or MHA-Ca increased N retained (g/d) and N retention (% of intake) linearly (P &lt; 0.001) and quadratically (P &lt; 0.05). Using linear slope-ratio regression, a product-to-product RBV value of MHA-Ca to dl-Met was 68.4% (81.4% on an equimolar basis) for N retained (g/d). In experiment 3, 276 pigs (12 barrow and 11 gilt replicates; initial BW of 7.09 ± 1.1 kg) were used in 3 diet preference studies. Pigs were randomly allotted to 1 of 3 treatment comparisons of feed choice: (1) BD (0.23% Met) or BD + 0.07% dl-Met; (2) BD or BD + 0.0825% MHA-Ca, and (3) BD + 0.07% dl-Met or BD + 0.0825% MHA-Ca. Pigs consumed a higher percentage (55 vs. 45%; P = 0.008) of their total feed intake from the diet supplemented with 0.07% dl-Met in Comparison 1, but a lower percentage (45 vs. 55%; P = 0.003) of their total feed intake from the diet supplemented with 0.0825% MHA-Ca in Comparison 2. There was no diet preference for dl-Met or MHA-Ca in Comparison 3. The observed Met source preference differences occurred in the barrow replicates but not in the gilt replicates. These results demonstrated the mean RBV of MHA-Ca to dl-Met of 65.7% on a product-to-product (wt/wt) basis or 78.2% on an equimolar basis and that a preference for Met sources was observed in barrows but not in gilts.
The COVID-19 Pandemic and Ecological Connectivity
Authors: Clark Janine Natalya 
Published: October 2020

Abstract
The ongoing COVID-19 pandemic has affected multiple aspects of our lives. This interdisciplinary article reflects on the significance of the pandemic from a largely unexplored angle, through a focus on the key concept of ecological connectivity, which broadly refers to the inter-connections between diffe-Srent elements of an ecosystem. Examining the pandemic through the lens of ecological connectivity, the article also theorizes it (and zoonotic diseases more generally) as a violation of this connectivity. It uses this idea as a core thread for linking COVID-19, international criminal law and transitional justice. Its key argument in this regard is that war crimes and human rights violations can themselves be viewed, in part, as violations of ecological connectivity. This theorization, in turn, provides a novel basis for thinking about the wider ecological dimensions and legacies of war crimes and gross violations of human rights, and, by extension, the potential role of international criminal law and transitional justice in helping to restore damaged connectivities through a relational approach to justice.
Orbital eccentricity–multiplicity correlation for planetary systems and comparison to the Solar system
Authors: Bach-Møller Nanna , Jørgensen Uffe G 
Published: October 2020

ABSTRACT
The orbit eccentricities of the Solar system planets are unusually low compared to the average of known exoplanetary systems. A power-law correlation has previously been found between the multiplicity of a planetary system and the orbital eccentricities of its components, for systems with multiplicities above two. In this study we investigate the correlation for an expanded data sample by focusing on planetary systems as units (unlike previous studies that have focused on individual planets). Our full data sample contains 1171 exoplanets, in 895 systems, and the correlation between eccentricity and multiplicity is found to follow a clear power law for all multiplicities above one. We discuss the correlation for several individual subsamples and find that all samples consistently follow the same basic trend regardless of e.g. planet types and detection methods. We find that the eccentricities of the Solar system fit the general trend and suggest that the Solar system might not show uncommonly low eccentricities (as often speculated) but rather uncommonly many planets compared to a ‘standard’ planetary system. The only outlier from the power-law correlation is, consistently in all the samples, the one-planet systems. It has previously been suggested that this may be due to additional unseen exoplanets in the observed one-planet systems. Based on this assumption and the power-law correlation, we estimate that the probability of a system having eight planets or more is of the order of 1 per cent, in good agreement with recent predictions from analyses based on independent arguments.