bluuebunny/crossref_metadata_2025_split huggingface dataset:
Realization of controllable open system with NMR
Authors: Ho Le Bin , Matsuzaki Yuichiro , Matsuzaki Masayuki , Kondo Yasushi 
Published: September 2019

Abstract
An open quantum system is now attracting much attention because a quantum device such as quantum computers and quantum sensors is an emerging technology. Here, we present a model of the open system that shows either time-homogeneous Markovian relaxations or non-Markovian relaxations depending on its parameters that we can control. This model is fully described with the master equation that is analytically solvable. More importantly, this model can be easily realized with molecules in isotropic liquids and measured with NMR techniques.
Models and Modelling for Teacher Courses?
Authors: Borg Marks Joan 
Published: September 2019

Abstract
Mental modelling has been given importance in educational research by a number of prominent researchers who have claimed that models and modelling are central to understanding key concepts in science. Asking, however, by how far the several research studies conducted on mental modelling and the consequent recommendations presented thereof are being applied by teachers in the classrooms to help in the teaching and learning process, remains a relevant question that needs to be addressed. Students at all levels studying science/physics are expected to learn the basic concepts of physics and teachers are expected to teach these to students in the most effective of ways. This is a primary objective especially with students in primary schools who need to have a good basis of scientific ideas and concepts, on which to build further ideas for the understanding of physics. Teaching that looks at the mental models held by students, trying to help in the evolution of students’ ideas and visualizations of a concept, offers one way of making teaching more effective and learning more meaningful. This paper describes a short study about how the author probed students’ mental models of concepts related to simple electric circuits. The reactions from colleagues when the study was presented at a staff development course helped the author to reflect on the importance of having modules on mental models and modelling in teachers’ pre-service and in-service courses. It will be argued that including mental modelling in teacher preparation programs offers a better chance for teachers to be better informed about how scientific reasoning and understanding develop. Thus, teachers can be better prepared to probe students’ ideas and to better address problems with students’ learning, whilst improving the quality of their teaching.
Twelve-Hour Urine Collection Can Be Utilized to Estimate 24-Hour Total Urinary Nitrogen in Critically Trauma Patients
Authors: Liao Hsuan-Chieh , O’Keefe Grant , Woo Fred , Lawrence Lisa , Baird Geoffrey 
Published: September 2019

Abstract
Patients suffering from trauma, burns, and sepsis are frequently in a hypermetabolic state, and as the majority of urinary nitrogen comes from amino acid metabolism, the determination of total urinary nitrogen (TUN) provides an accurate measurement of all nitrogen excreted in urine and can be used as an indicator of catabolic stress. To evaluate whether time of collection influences the performance of TUN test, 12-hour urine specimens were collected from ICU trauma patients and the 12-hour results were correlated with results from 24-hour collections.
Two consecutive 12-hour urine samples were collected (06:00-18:00 hours and 18:00-06:00 hours) from surgical ICU patients. Total urinary nitrogen levels were measured in each 12-hour sample, as well as in a pooled sample (24 hours). Pyrochemiluminescence was used to determine TUN level on an Antek 9000N elemental analyzer. In this approach, the urine sample is completely oxidized at high temperature in a quartz pyrotube. Nitrogen is converted to nitric oxide (·NO), then mixed with O3 (ozone) to form nitrogen dioxide (NO2). Light is emitted and specific wavelengths between 650 and 900 nm were measured in a photomultiplier tube. The measured chemiluminescent emission is specific and proportional to the amount of nitrogen in the sample.
Fifty 12-hour urine samples from 16 patients were collected. One patient was excluded from the study due to acute renal injury during the collection period. There was no significant observed circadian effect on measured TUN. The 12-hour TUN (g/total volume) was multiplied by 2 to compare to 24-hour TUN for statistical analysis. There was strong correlation between either day or night 12-hour TUN and corresponding pooled 24-hour TUN, with correlation coefficients ranging from 0.93 to 0.98 and regression slopes ranging from 0.98 to 1.01. No statistically significant difference was found between the 12-hour TUN and 24-hour TUN approaches.
A 12-hour TUN collection was overall highly predictive of 24-hour TUN collection and has the advantage of convenience of sample collection and improved clinical efficiency. Serial 12-hour urine collection is therefore preferred for monitoring nitrogen balance and adjusting protein intake for critically ill ICU patients.
An Updated “Call Database” to Support Lab Consultation and Quality Improvement Projects
Authors: Krumm Niklas , Hoffman Noah 
Published: September 2019

Abstract
Clinical laboratories may have “on-call” residents and fellows, a practice that assists the laboratory in providing quality support to clinicians and provides valuable clinical experience to trainees. A Call Database may be used as a tool to facilitate call handoffs, as an educational resource and knowledge base for trainees, and as a call logging and review tool as required by the Accreditation Council for Graduate Medical Education (ACGME). The Call Database at our institution currently contains over 51,000 entries and is used by all clinical pathology residents and fellows while “on call.”
Prior versions of our Call Database (first developed in 2004 and updated in 2014) were self-hosted applications with limited feature sets that were difficult to support; moreover, they provided few guarantees around electronic protected health information (ePHI), a topic of increasing concern as HIPAA compliance among clinical laboratories is increasingly audited. A review of the current application also identified that it has limited usefulness in supporting faculty review of calls, does not easily allow structured data entry for quality improvement projects, and lacks features commonly seen in modern web applications (eg, rich text editing and file attachments). Here we describe the latest update to our existing Call Database addressing these feature limitations. In addition, we discuss our approach to using a modern cloud-based infrastructure design that address prior shortcomings in data security, user management, and ease of development.
The updated Call Database is a single-page web application, compatible with a wide range of local and cloud environments. We updated the user interface with features such as auto-saving of entries, rich text entry, file attachments, and topic tagging. Several new features facilitate the faculty review process: (1) a dedicated “review mode” for rapid viewing and commenting of relevant calls, (2) automated weekly emails by topic sent to faculty, and (3) a user “mention” feature so that trainees can solicit the opinion of faculty in the text of a call or comment itself. Finally, we provide support for customizing the structured data fields of call entries, which enables support of quality improvement and monitoring projects via the call database (eg, a customized entry for monitoring use of specific send-out tests, massive transfusion reactions, etc.).
Our application delivers a modern, performant, and easy to use call database for use by trainees and faculty alike. We utilize the Amazon Cloud (AWS) to host the application and have developed a specific set of compliance and risk review documents to address HIPAA compliance. Future work will incorporate user feedback and will focus on supporting the implementation of our application at other sites or clinical pathology residency programs.
Sample Dilution Is Not an Effective Mitigation for Hemolysis Interference in Anti-Xa Heparin Activity Assays
Authors: Khan Jenna , Chandler Wayne 
Published: September 2019

Abstract
The presence of hemolysis or icterus can interfere with chromogenic anti-Xa assays for unfractionated heparin monitoring (heparin activity), resulting in falsely lower estimates of heparin activity. Dilution is a common method for mitigating interference in spectroscopic assays that measure a single analyte by endpoint analysis and has been proposed as a solution for hemolysis interference in heparin activity assays. Heparin activity assays measure heparin/antithrombin complex activity using a chromogenic rate of absorbance change method. Heparin activity is a complex equilibrium of heparin binding to multiple proteins, including antithrombin, heparin cofactor II, platelet factor 4, histidine-rich glycoprotein, vitronectin, fibronectin, and others; some enhance while others neutralize heparin activity. The objective of this study was to determine how dilution affects heparin activity with different starting levels of antithrombin. First samples were diluted without interference (no hemolysis). Samples with 1 U/mL heparin in pooled normal plasma (PNP) and 50% PNP (to simulate 50% antithrombin levels) were diluted 1:1 with PNP versus OK buffer. Dilution resulted in nonlinear changes. Samples with 100% antithrombin recovered 88% of expected activity with PNP versus 74% with OK buffer; samples with 50% antithrombin recovered 111% with PNP versus 77% with OK buffer. Samples were then spiked with varying concentrations of hemolysate and 1:1 dilutions with PNP demonstrated nonlinear recoveries ranging from 41% to 84%. We were unable to recover the original heparin activity with or without hemolysis due to the complex interaction of initial heparin, antithrombin, and other binding protein concentrations with diluent antithrombin and other diluent heparin binding protein levels. When PNP is used as the diluent, the recovery will be lower when the initial antithrombin level is normal due to the addition of other heparin binding proteins; when the initial antithrombin level is low, the recovery is higher due to the addition of antithrombin from the diluent plasma. The recovery is always lower when buffer is used due to dilution of sample antithrombin. Careful consideration should be taken in evaluating the utility of sample dilution to mitigate interference from hemolysis and icterus in heparin activity assays, particularly in patients with fluctuating levels of antithrombin, such as those on extracorporeal life support or with liver failure.
Medium- and Short-Chain L-3-Hydroxyl-Acetyl-Coenzyme A Deficiency: A New Identified Mutation in Four Cases
Authors: Feng Sheng , Cooper Deborah , Tan Lu , Meyers Gail , Bennett Michael 
Published: September 2019

Abstract
Medium- and short-chain L-3-hydroxyacyl-coenzyme A dehydrogenase (M/SCHAD, SCHAD) deficiency is a mitochondrial fatty acid oxidation disorder (FAOD). This enzyme catalyzes the penultimate step in fatty acid oxidation, the NAD+ dependent conversion of L-3-hydroxyacyl-CoA to 3-ketoacyl-CoA for medium- and short-chain acyl-CoA intermediates (C4-C12). The clinical presentations of most patients are recurrent hypoglycemia associated with hyperinsulinism. We presented four infants with C4 acyl-carnitine elevation identified by newborn screening that also showed an unusual phenotype of congenital hypotonia and gross developmental delay. Enzymatic studies confirmed the disease. Sequencing analysis of all the HADH coding exons on the four patients revealed a homozygous variant of a novel change (c.908G>T, p.Gly303Val). Western blot analysis subsequently confirmed the lack of the SCHAD protein. In addition, there is another previously reported benign variant (c.257T>C) identified in three infants. Therefore, we postulate that the HADH variant (c.908G>T) is indeed pathogenic and associated with a severe phenotype as evidenced by the cases described herein. Population screening for the c.908G>T mutation suggests this mutation to be common among Puerto Ricans. We recommend that SCHAD deficiency is included as part of the differential diagnosis of all infants with congenital hypotonia.
Updates to a Lab-Developed Bioinformatics Pipeline and Application for Interpretation of Clinical Next-Generation Sequencing Panels
Authors: Christensen Paul , Subedi Sishir , Hendrickson Heather , Thomas Jessica , Li Zejuan , Long S Wesley , Olsen Randall 
Published: September 2019

Abstract

Objectives
Our goal was to enhance our next-generation sequencing (NGS) molecular oncology workflow from sequencing to analysis through improvements to our custom-built and previously described NGS application.

Methods
Over 1 year, we collected feedback regarding workflow pain-points and feature requests from all end users of our NGS application. The application consists of a series of scripted pipelines, a MySQL database, and a Java Graphic User Interface (GUI); the end users include molecular pathologists (MPs), medical technologist/medical laboratory technologists (MTs/MLTs), and the molecular laboratory manager. These feedback data were used to engineer significant changes to the pipelines and software architecture. These architecture changes provided the backbone to a suite of feature enhancements aimed to improve turnaround time, decrease manual processes, and increase efficiency for the molecular laboratory staff and directors.

Summary
The key software architecture changes include implementing support for multiple environments, refactoring common code in the different pipelines, migrating from a per-run pipeline model to a per-sample pipeline model, and key updates to the MySQL database. These changes enabled development of many technical and user experience improvements. We eliminated the need for the pipelines to be launched manually from the Linux command line. Multiple pipelines can be executed concurrently. We created a per-sample pipeline status monitor. Sample entry is integrated with our Laboratory Information System (LIS) barcodes, thus reducing the possibility of transcription errors. We developed quality assurance reports. Socket-based integration with Integrated Genomics Viewer (IGV) was enhanced. We enabled rapid loading of key alignment data into IGV over a wireless network. Features to support resident and fellow driven variant and gene annotation reporting were developed. Support for additional clinical databases was implemented.

Conclusions
The designed feature enhancements to our previously reported NGS application have added significant sophistication and safety to our clinical NGS workflow. For example, our NGS consensus conference can be held in a conference room over a wireless network, and a trainee can prepare and present each case without ever leaving the application. To date, we have analyzed 2,540 samples using three different assays (TruSight Myeloid Sequencing Panel, AmpliSeq Cancer Hotspot Panel, GlioSeq) and four sequencing instruments (NextSeq, MiSeq, Proton, PGM) in this application. The code is freely available on GitHub.
Procalcitonin as a Biomarker in Early Sepsis in Cancer Patients Presenting to the Emergency Department
Authors: Li Jieli , Meng Qing 
Published: September 2019

Abstract

Background
In the United States, sepsis is responsible for 9% of all cancer-related deaths. Patients with cancer presenting with sepsis have worse outcomes, which is probably because of immunosuppression, due to the disease burden itself or the effects of chemotherapy. Biomarkers are noninvasive rapid diagnostic tools, assisting in the early diagnosis of patients with suspected sepsis. The identification of a biomarker with reasonable sensitivity and specificity for early sepsis could potentially result in a beneficial effect on clinical outcomes in these patient populations. Procalcitonin (PCT) is a promising marker for identification of bacterial infections, but its role in oncology populations has less been studied. We investigated the performance characteristics of sepsis biomarkers for diagnosis of verified bacterial sepsis.

Methods
This was a retrospective study of patients admitted between June 1, 2018, and January 31, 2019, from the Emergency Department, MD Anderson Cancer Center. Approximately 51% adult patients were diagnosed with sepsis. Sepsis was defined by Surviving Sepsis Campaign (SSC) definitions. Three biomarkers were evaluated based on hospital records: (1) PCT ≥0.08 ng/mL, (2) C-reactive protein (CRP) ≥13 mg/L, (iii) white blood cells (WBCs) ≥11 K/µL. The diagnostic performances of the individual biomarkers were compared using the area under the receiver operating characteristic (ROC) curve (AUC).

Results
In total, 635 adult sepsis patients were included and investigated during the study period. For diagnosis of bacterial sepsis based on SSC criteria, the analysis yielded a CRP with sensitivity of 71% (95% CI, 56%-86%) and specificity of 22% (95% CI, 15%-29%), respectively. The area under the ROC curve was 52% (95% CI, 41%-68%). The sensitivity of WBCs was 18% (95% CI, 12%-24%), specificity was 84% (95% CI, 71%-97%), and the area under the ROC curve was 51% (95% CI, 43%-68%). However, the PCT reached the sensitivity of 77% (95% CI, 60%-93%) and specificity of 65% (95% CI, 48%-82%), respectively. The area under the ROC curve was 79% (95% CI, 67%-91%), significantly increased.

Conclusion
In this study, the diagnosis accuracy and specificity of PCT are much higher than those of CRP or WBC in cancer patients. PCT is a useful marker for early detection of sepsis in emergency department patients with suspected infection, especially in cancer patients with neutropenia. Further studies on the role of PCT in this population are warranted.
Anemia in Hidradenitis Suppurativa, Hepcidin as a Diagnostic Tool
Authors: Ghias Mondana , Cameron Sophie , Shaw Fiona , Soliman Yssra , Kutner Allison , Chaitowitz Mark , Cohen Steven , Gil Morayma Reyes 
Published: September 2019

Abstract
Hidradenitis suppurativa (HS) is a chronic inflammatory skin disease characterized by recurrent nodules, abscesses, and dermal tracts. We recently reported a high prevalence of anemia in HS patients. These data led to the hypothesis that chronic inflammation in HS predominantly causes anemia of chronic disease (ACD) through upregulation of IL-6 and hepcidin, a key regulator of iron homeostasis. Hepcidin is widely accepted as a marker distinguishing ACD from iron deficiency anemia (IDA) in inflammatory conditions. The purpose of this study was to measure serum hepcidin in HS patients to classify the type of anemia observed in this cohort. We measured hematologic data, inflammatory markers, and serum hepcidin using an enzyme-linked immunosorbent assay (ELISA; R&D Systems) in 55 patients with varying degrees of HS severity. Independent Student t tests and one-way ANOVA were used to compare hepcidin levels in HS patients with anemic and nonanemic states. Of 55 HS patients evaluated in this study, 42 (76%) were female and the average age was 37.6 ± 13.2 years. The mean hemoglobin (Hb) was 12.2 ± 2.0 g/dL and mean hepcidin was 19.5 ± 12.9 ng/mL. Anemic patients (n = 26) with reduced iron stores (ferritin ≤30 ng/mL) had significantly lower hepcidin than anemic patients with adequate iron stores (9.7 ± 15.8 ng/mL vs 23.8 ± 11.1, P = .03). Elevated hepcidin in this subset suggests that ACD is the predominant cause of anemia. Analysis by ANOVA also found that hepcidin levels were significantly greater in patients with more severe HS, as measured by HS-Physician Global Assessment scores (P = .005). Hepcidin may serve as a surrogate biomarker for active disease and inflammation in HS. These findings affirm the utility of hepcidin as a promising tool for distinguishing IDA from ACD and, in turn, help identify HS patients in whom dietary iron supplementation is unlikely to be beneficial.
Can We Predict the Number of Circulating CD34+ Cells From the Complete Blood Cell Count Before and After Plerixafor in Patients With Lymphoproliferative Disorders?
Authors: Fakhari Mahtab , Costa Luciano J , Williams Lawrence A , Marques Marisa B 
Published: September 2019

Abstract
Stem cell transplant is a common treatment for hematopoietic neoplasms. We use a standardized stem cell mobilization regimen consisting of the following: day 1, 6 mg of pegfilgrastim (pegylated formulation of granulocyte-colony stimulating factor); day 3, 24 mg of plerixafor (reversible CXCR4 antagonist) followed by peripheral blood stem cell collection (PBSC) on day 4 after collecting a sample to measure the circulating CD34+ cells by flow cytometry. Since the latter results are not available as quickly as a STAT complete blood count (CBC), we hypothesized that the difference in CBC parameters from DAY 3 TO DAY 4 could be useful to predict the final collection yield. To test our theory, we carried out the following process from September 2018 to February 2019: day 3, CBC with differential before plerixafor; day 4, CBC with differential and sample for CD34+ cells before starting PBSC. We collected the following data from the electronic medical records: gender, age, and CBC parameters preplerixafor (evening of day 3) and morning of day 4 (preapheresis) plus circulating CD34+ count. We used a paired Student t test to compare the results of each patient. Fifty-seven adults (35 males, 22 females) with a median age of 64 ± 13 years were included; 76% had the diagnosis of multiple myeloma. On day 3 (preplerixafor), the median hematocrit was 36 ± 8%, the WBC count was 29 ± 13 × 103/µL, and the platelet count was 189 ± 64 × 103/µL. On the next morning (day 4), the hematocrit and platelet counts were not significantly different at 36 ± 4% and 182 ± 60 × 103/µL, respectively (P > .05). However, the median WBC count was significantly higher with a median of 43 ± 16 × 103/µL (P = 2.5 × 10–20). In both CBCs with differential, neutrophils comprised the majority at 82% and 74% pre- and postplerixafor, respectively (P = .01), lymphocytes went from 7% to 8% (P > .05), and monocytes increased from 6% to 6.5% (P = .02). The median CD34+ count preapheresis was 40 ± 47 cells/µL. We did not find any strong correlation between day 3 and day 4 CBC parameters and the CD34+ count, with only a very weak trend for higher CD34+ cells with increasing day 4 WBC count (R2 = 0.225). We conclude that the precollection CD34+ cell count is the best way to predict the PBSC yield and must be performed in order to ensure the target number of CD34+ cells is met for a successful engraftment.