bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improving Patient Value Through Cross-Country Collaboration
Authors: Yip Tameson , Ford Jennifer , Ramsower Colleen , Glinsmann-Gibson Betty , Robetorye Ryan , Rimsza Lisa 
Published: September 2019

Abstract

Introduction
Lymph2Cx lymphoma cell-of-origin assay (LM2CX) was developed by the Lymphoma/Leukemia Molecular Profiling Project (LLMPP) to better categorize diffuse large B-cell lymphoma (DLBCL). NanoString has licensed the assay and is currently pursuing FDA approval. In the meantime, the test is offered exclusively as a lab-developed test (LDT) by the Mayo Clinic Molecular Diagnostics–Arizona Lab (MDAZL) to Mayo Clinic Enterprise patients. In order to comply with these restrictions, the normal workflow for Mayo Clinic Rochester has been modified as cases are sent to Arizona. Rochester consultants order LM2CX using their local laboratory information system (LIS). Slides are prepared by Rochester histology and then shipped to Arizona, where they are entered into the Arizona LIS and processed. In July 2018, we discovered numerous cases that were ordered but not shipped. Because this step took place at the LIS transition between Arizona and Rochester, it was not detected immediately.

Methods
Allied Health Staff (AHS) colleagues in Rochester and Arizona had the unique opportunity to collaborate. After Arizona AHS identified the problem, they reached out to the Rochester pathology reporting specialists (PRSs) and began a joint improvement project. Together, we were able to measure the impact of the problem, with Arizona auditing digitally, while Rochester audited physical cases. We found 29% of the cases were handled improperly over a 6-month time period. In order to eliminate the gap, Rochester implemented several improvements, including training, tagging all LM2CX cases, and huddle discussions, while Arizona AHS monitored the process digitally.

Results
Since implementation of improvements, we have had zero defects. Modifications to AHS/consultant training in Rochester will ensure continued success.

Conclusions
This intervention illustrates the importance of strong collaborations in order to quickly respond to testing issues and provide the greatest value to patients.
Prevalence of Urinary Tract Infections (UTIs) Among Pregnant Women Attending Antenatal Clinic at Ile-Ife, Southwestern Nigeria
Authors: Onifade Jaiyeola , Oladipo Adegboyega 
Published: September 2019

Abstract

Objectives
This is a prospective study that reports the prevalence of urinary tract infections (UTIs) and the bacteriological causative agents among pregnant women attending antenatal clinics at a secondary care hospital in Ile-Ife, southwestern Nigeria. In total, 335 midstream clean-catch urine samples were collected from pregnant women between April and July 2017.

Methods
These were cultured for the presence of bacterial pathogens. All the isolates were subjected to antibiotic sensitivity testing on Mueller Hinton agar by a modified Kirby-Bauer disk diffusion technique using CLSI guidelines. Data were analyzed using SPSS for Windows version 16 and WHONET 5.

Results
A total of 190 showed significant bacterial growth while 145 showed no significant bacterial growth. Bacterial agents isolated included Klebsiella spp. showing the highest occurrence of 60 (31.5%), followed by Escherichia coli and Staphylococcus aureus with prevalences of 49 (25.7%) and 32 (16.8%), respectively. Other organisms implicated are Proteus mirabilis (20 [10.5%]), coagulase-negative staphylococci (24 [12.3%]), and Pseudomonas aeruginosa with the least prevalence (5 [2.6%]). They have a resistance to antibiotics such as amoxycillin (64%), gentamicin (52.6%), erythromycin (62.5%), ceftazidime (69%), cefotaxime (74%), and ceftriaxone (79.6%) but a high sensitivity to tetracycline (88.5%), nitrofurantoin (96.3%), and imipenem (100%), respectively.

Conclusion
This study indicated a high prevalence of UTIs (56.7%) in pregnant women, though most of them showed no clinical manifestation.
Histologic Characterization of Histoplasmomas
Authors: Demkowicz Ryan , Procop Gary 
Published: September 2019

Abstract

Introduction
Histoplasmomas are often found incidentally in surgical specimens, but there are no clear reporting guidelines to describe the subtle differences in the stages of organization of the granuloma. This study establishes grading criteria to more clearly communicate the stage of organization and resolution of these lesions, with the hope that this information could inform clinical decisions.

Methods
For an 11-year period, all surgical pathology cases with histoplasmomas in the final diagnosis with slides available were included in the study. After confirmation that Histoplasma yeasts were present, the granulomas were graded as

follows
grade 1, active granulomas with or without necrosis with minimal to no fibrous rim formation; grade 2, minimal to moderate granulomatous inflammation remained associated with a well-developed fibrous rim; and grade 3, no granulomatous inflammation remained, and a well-developed fibrous rim was present. Calcification and necrosis were also noted. Histoplasma yeasts was semiquantified. One to five yeasts were characterized as rare, 6 to 10 as few, 11 to 50 as moderate, and >50 yeasts as many.

Results
Forty-two cases were included in the study. The lesions were graded as

follows
3 grade 1, 19 grade 2, and 20 grade 3 lesions. Calcifications increased with grade (grade 1: 0 [0%], grade 2: 10 [52.6%], grade 3: 18 [95%]). All histoplasmomas had necrosis. The number of yeasts detected, stratified by grade, was as

follows
grade 1, rare (1) and many (2); grade 2, rare (6), few (1), moderate (1), and many (11); and grade 3, rare (2), moderate (4), and many (14). None of the patients developed active histoplasmosis for the duration of their follow-up at our institution.

Conclusion
The proposed grading of histoplasmomas provides an indication to clinicians of the stage of activity or resolution of an excised histoplasmoma. These data do not support the use of antifungal therapy in patients with grade 2 or 3 histoplasmomas.
Incidence of Enteropathogenic Escherichia coli among Infants at Eleyele Comprehensive Health Centre, Ile-Ife, Osun State
Authors: Faseyi Kayode , Onifade Jaiyeola 
Published: September 2019

Abstract

Objectives
This work was carried out to find the incidence of enteropathogenic Escherichia coli in children below 5 years of age who complained of having diarrhea at Eleyele Comprehensive Health Centre, Obafemi Awolowo University Teaching Hospital Complex, Ile-Ife. The work was also done to determine the incidence in different age groups of both sexes.

Methods
All specimens were cultured as routinely done at the bacteriology laboratory in Obafemi Awolowo University Teaching Hospital for stool samples. Colonies of lactose fermenters were processed after overnight incubation at 37°C. Nonlactose fermenter colonies were discarded. Out of 200 colonies isolates on MacConkey agar, there were 150 lactose fermenters and these were all processed. The other 70, which were Gram-positive cocci, were discarded. These were subjected to biochemical examination such as treating them with sugars, for the production of acid and gas, indole production, motility with sugars, citrate utilization, Voges-Proskauer, and methyl red tests.

Results
Out of 150 strains examined, only 80 strains obeyed IMVic ++ -- reactions. These were serotyped to know the enteropathogenic strains. From the result obtained, 23 strains reacted positively with polyvalent antisera (polyvalent 2, 3, 4 antisera), of which 13 strains gave a positive reaction with corresponding monovalent antisera. There were five strains from polyvalent 2 antisera, five strains from polyvalent 3 antisera, and three strains from polyvalent 4 antisera. In close study of this work, total percentage of females with diarrhea was 44.5% while total percentage of males with diarrhea was 55.5%. Out of these 80, E coli was isolated, and from these, 13 enteropathogenic E strains were isolated (16.25%). Patient aged below 2 years gave nine strains (69.2%), aged 2 to 3 years gave two strains (15.4%), aged 3 to 4 years gave one strain (7.7%), and aged 4 to 5 years gave one strain (7.7%). Also, close examination of result revealed that male children had the greater percentage of enteropathogenic infection, with 8 strains out of the 13 strains serotyped (61.5%) and female children with 5 strains (38.5%).

Conclusion
E coli remains an important cause of infant diarrhea. Although epidemics of infant diarrhea caused by enteropathogenic E coli have almost disappeared from the developed countries, it is still very common in developing countries. The relative importance of enteropathogenic E coli as a cause of infant diarrhea needs to be reassessed and new diagnostic techniques will also help to simplify this task.
Gene Mutation of Sulfonamide (SulI) and Tetracycline (TetA/B) Is Responsible for Multidrug Resistance (MDR) of Escherichia coli Isolated From Urinary Tract Infections (UTIs) of Egyptian Patients
Authors: Abdelmonem Mohamed , Husseiny Mohamed Amira , Shafik Hesham , Shehata Mohamed , EL-Sherbiny Gamal , Fyala Amira 
Published: September 2019

Abstract
Escherichia coli (E coli) is one of the most commonly found pathogens in hospitals. Infections such as gastroenteritis, cystitis, urinary tract infections (UTI), meningitis, septicemia, and peritonitis were previously treated with broad-spectrum antibiotics. However, the emergence of infectious diseases involving multidrug-resistant (MDR) bacterial pathogens is still a major threat to human health.
This study aimed to investigate the SulI (sulfonamide), TetA (tetracycline), and TetB resistance genes in E coli isolated from urine specimens from hospitalized patients. In the present cross-sectional study, a total of 55 strains of E coli were isolated from urine cultures of patients who had UTIs in ElKasr ElEiny and ELShorta hospitals. Samples were analyzed for bacteriological, biochemical examination, and agar disc-diffusion to evaluate their antibiotic susceptibility patterns. Polymerase chain reaction (PCR) method also was used to detect SulI, TetA/B genes by specific primers.
The results suggested that E coli isolates were resistant to all multiple drugs used. Ampicillin showed the highest resistance of all the isolates followed by sulfonamide and tetracycline at 70%, 62%, and 53%, respectively. The lowest resistance detected with levofloxacin was 12%; however, there is no difference in the resistance pattern of gentamycin and aztreonam. The genotypes’ amplification revealed a positive correlation between SulI (sulfonamide) and TetA/B (tetracycline) resistance encoding genes and was shown in all the tested isolates as 100%.
In our study, we found a mutation for sulfonamide and tetracycline genes in E coli that was isolated from UTI patients. The mutation is responsible for a multidrug-resistant strain due to the overuse of antibiotics. However, the World Health Organization recommends the use of trimethoprim-sulfamethoxazole and ampicillin as the first choice for UTI treatment. Our study recommends regulating and limiting the use of those antibiotics in order to minimize the dissemination of multidrug resistance for E coli.
Choosing the Right Test (Influenza) Versus Respiratory Viral Panel With Faster Turnaround Time and Cost Savings
Authors: Lin Bo , Christian Manan , Kogan Margarita , Zuretti Alejandro 
Published: September 2019

Abstract

Introduction
Respiratory infections are very common in hospital patients. Viral pathogens including influenza (Flu) and respiratory syncytial virus (RSV) are frequent causes. Respiratory viral panels (RVPs) have been routinely ordered in our institution with a turnaround time (TAT) of 48 hours at a cost of approximately $170/test. Meanwhile, Flu and RSV PCR are offered in house with a TAT of only 40 minutes and much lower cost ($40/test) than RVP. Here, we examined the optimization of use of these tests in our medical center.

Methods
Results of the specimens sent for RVP testing as well as their results from Flu/RSV PCR and the negative result rate were reviewed. The TAT and costs were compared between RVP and Flu/RSV PCR.

Results
We reviewed 69 specimens from MICU sent for RVP during 10/1/2018 to 1/31/2019. Total negative specimen rate was 74%. The specimens identified positive for Flu or RSV by RVP were also positive for in-house Flu/RSV PCR. Therefore, we have recommended clinicians to order in-house highly sensitive and specific Flu/RSV PCR first for faster TAT and cost saving. Since the recommendation, the number of RVP orders has dropped from 660 (January 2018) to 131 (January 2019), with savings of more than $80,000 in 1 month.

Conclusion
In-house Flu/RSV PCR test is highly sensitive and specific for identifying the common viral pathogens in patients with respiratory infection. It is fast and relatively low cost compared to RVP and should be considered as an effective first-line test.
An Unusual Case of Fetal/Neonatal Alloimmune Thrombocytopenia
Authors: Vazmitsel Maryna , Chen Dong , Gruner Barbara , Coberly Emily 
Published: September 2019

Abstract

Objectives
Fetal/neonatal alloimmune thrombocytopenia (FNAIT) occurs when maternal IgG alloantibodies against paternal human platelet antigens (HPA) cross the placenta and cause the destruction of fetal platelets. The vast majority (up to 95%) of FNAIT cases are caused by antibodies against HPA-1a or HPA-5b antigens, while the remaining cases are usually due to antibodies against a variety of other HPA antigens. Cases of FNAIT due to anti-HLA antibodies are extremely uncommon and have only rarely been reported. We present a case of FNAIT suspected to be caused by anti-HLA class I alloantibodies.

Methods
The patient is a term infant boy born to a 32-year-old G2T2L2 mother. The mother had a previous diagnosis of Still disease (an adult form of systemic juvenile rheumatoid arthritis) but experienced complete resolution of symptoms and was off all treatment during the pregnancy. At birth, laboratory testing revealed isolated severe thrombocytopenia (platelet count 38,000/mcL) in an otherwise healthy-appearing infant.

Results
The infant had no evidence of bleeding, and testing for TORCH infection, sepsis, and DIC was negative. The maternal blood type was O positive. The maternal platelet count was normal. FNAIT was suspected and the infant was given two platelet transfusions from the same HPA 1a and 5b antigen-negative donor with no significant or sustained improvement in platelet count. Maternal platelet antibody testing subsequently revealed an absence of HPA antibodies, but anti-HLA class I alloantibodies were present. The infant was treated with three subsequent doses of IVIg with improvement in platelet count. No significant hemorrhage occurred.

Conclusion
HLA class I antibodies are commonly found in multiparous women but are not generally thought to cause significant fetal complications during subsequent pregnancies. This case suggests that, although rarely reported, HLA class I alloantibodies may be capable of causing FNAIT.
A Cost-Effectiveness Model for Different Treatments of Bleeding in Patients With Acquired Hemophilia
Authors: Najafzadeh Parisa , Kim Chong , Wang Dandan , Simmons Sierra , Pham Huy 
Published: September 2019

Abstract

Objectives
Acquired hemophilia A (AHA) is an autoimmune disorder with significant morbidity and mortality. Currently, bleeding AHA patients with high titer inhibitors can be treated with activated prothrombin complex concentrate (aPCC), recombinant factor VIIa (rFVIIa), or recombinant porcine-sequence factor VIII (rpFVIII). Given that these replacement therapies have inherent benefits and limitations, a cost-effectiveness analysis (CEA) was performed.

Methods
In high-titered AHA patients with bleeding treated with aPCC, rFVIIa, or rpFVIII, a Markov model was developed such that these patients were transitioned into four different health states: (1) continuous bleeding, (2) thrombosis, (3) stop bleeding, and (4) death, with states (2), (3), and (4) modeled as absorbing states during a 6-day period. Since the assessment for transition between stages (1) and (3) occurred at the beginning of the next day in the model, we assumed that the patient only required half of the medication dose on the day prior to the day the bleeding stopped. Model parameters, including probabilities, health utility index, and costs, were from the medical literature, except for the costs of aPCC, rFVIIa, and factor VIII assay, which were institutional data.

Results
During the 6-day period, aPCC is the least expensive option ($1,778) while rFVIIa is the most expensive ($13,925). The average quality-adjusted life days (QALDs) gained for aPCC is also slightly higher. Overall, aPCC prevailed over both rpFVIIIa and rFVIIa in deterministic and probabilistic analyses. When compared to aPCC, the incremental cost-effectiveness ratios (ICERs) for rpFVIII and rFVIIa are –$308,121/QALD and –$1,442,461/QALD, respectively. Sensitivity analyses confirmed the rmodel robustness across tested ranges of all input variables.

Conclusion
In high-titered AHA patients with bleeding, aPCC is the most cost-effective treatment option when compared to rpFVIII and rFVIIa. Thus, aPCC may be considered in these patients, if available, and provided there is no clinical contraindication.
Highly Effective Model for Implementation of In-House Platelets in a Tertiary Hospital Setting Without a Trauma Center: Corporal Michael J. Crescenz Veterans Affairs Medical Center (CMCVAMC) Experience
Authors: Patel Vijal , Petersen Jeffrey , Jhala Darshana 
Published: September 2019

Abstract

Introduction
Platelet products have a limited shelf life and are costly. Hence, it remains crucial to balance clinical usage and wastage in a tertiary hospital setting without a trauma center. Considering this, an innovative system model was established to reduce wastage: the CMCVAMC—starting October 2017—arranged to transfer the platelet unit to a nearby facility with a trauma center when product has a short expiration date and there is no anticipated need for the product. This is a cost-effective measure to reduce platelet wastage and ensure the appropriate blood product availability.

Method
QA/QI data were reviewed to determine the degree of platelet wastage both a year prior to the implementation of this platelet transfer to another facility and after the past implementation of this transfer to February 2019. The cost of each platelet product was determined from the blood supplier (American Red Cross). From these comparisons prior to and after implementation, a determination of reduction of product wastage and cost savings was made.

Results
Since the implementation of this platelet transfer, there have been no platelets expiring on the shelf. In contrast, from October 2016 to October 2017 prior to implementation of platelet transfer, platelet products were often wasted or expired. In contrast, from October 2017 to February 2019, there has been no wastage of platelets.

Conclusion
This is a highly effective model for a tertiary hospital without a trauma center to bring in house platelets without wastage of a costly product while maintaining appropriate availability of the product. This quality improvement system study demonstrates that the measure resulted in significant savings and this serves as a model for other similar facilities. This is an innovative, easy to implement, and cost-effective system model that can be used in other tertiary facilities without a trauma center.
DeepMSPeptide: peptide detectability prediction using deep learning
Authors: Serrano Guillermo , Guruceaga Elizabeth , Segura Victor 
Published: September 2019

Abstract

Summary
The protein detection and quantification using high-throughput proteomic technologies is still challenging due to the stochastic nature of the peptide selection in the mass spectrometer, the difficulties in the statistical analysis of the results and the presence of degenerated peptides. However, considering in the analysis only those peptides that could be detected by mass spectrometry, also called proteotypic peptides, increases the accuracy of the results. Several approaches have been applied to predict peptide detectability based on the physicochemical properties of the peptides. In this manuscript, we present DeepMSPeptide, a bioinformatic tool that uses a deep learning method to predict proteotypic peptides exclusively based on the peptide amino acid sequences.

Availability and implementation
DeepMSPeptide is available at https://github.com/vsegurar/DeepMSPeptide.

Supplementary information
Supplementary data are available at Bioinformatics online.
Adaptive Viral Load Monitoring Frequency to Facilitate Differentiated Care: A Modeling Study From Rakai, Uganda
Authors: Ssempijja Victor , Nason Martha , Nakigozi Gertrude , Ndyanabo Anthony , Gray Ron , Wawer Maria , Chang Larry W , Gabriel Erin , Quinn Thomas C , Serwadda David , Reynolds Steven J 
Published: September 2019

Abstract

Background
After scale-up of antiretroviral therapy (ART), routine annual viral load monitoring has been adopted by most countries, but reduced frequency of viral load monitoring may offer cost savings in resource-limited settings. We investigated if viral load monitoring frequency could be reduced while maintaining detection of treatment failure.

Methods
The Rakai Health Sciences Program performed routine, biannual viral load monitoring on 2489 people living with human immunodeficiency virus (age ≥15 years). On the basis of these data, we built a 2-stage simulation model to compare different viral load monitoring schemes. We fit Weibull regression models for time to viral load &gt;1000 copies/mL (treatment failure), and simulated data for 10 000 individuals over 5 years to compare 5 monitoring schemes to the current viral load testing every 6 months and every 12 months.

Results
Among 7 monitoring schemes tested, monitoring every 6 months for all subjects had the fewest months of undetected failure but also had the highest number of viral load tests. Adaptive schemes using previous viral load measurements to inform future monitoring significantly decreased the number of viral load tests without markedly increasing the number of months of undetected failure. The best adaptive monitoring scheme resulted in a 67% reduction in viral load measurements, while increasing the months of undetected failure by &lt;20%.

Conclusions
Adaptive viral load monitoring based on previous viral load measurements may be optimal for maintaining patient care while reducing costs, allowing more patients to be treated and monitored. Future empirical studies to evaluate differentiated monitoring are warranted.
Oseltamivir Resistance in Severe Influenza A(H1N1)pdm09 Pneumonia and Acute Respiratory Distress Syndrome: A French Multicenter Observational Cohort Study
Authors: Behillil Sylvie , May Faten , Fourati Slim , Luyt Charles-Edouard , Chicheportiche Thomas , Sonneville Romain , Tandjaoui-Lambiotte Yacine , Roux Damien , Guérin Laurent , Mayaux Julien , Maury Eric , Ferré Alexis , Georger Jean-François , Voiriot Guillaume , Enouf Vincent , van der Werf Sylvie , Dessap Armand Mekontso , de Prost Nicolas 
Published: September 2019

AbstractIn a multicenter cohort study including 22 oseltamivir-treated patients with influenza A(H1N1)pdm09 acute respiratory distress syndrome, prevalence of the H275Y substitution in the neuraminidase, responsible for highly reduced sensitivity to oseltamivir, was 23%. Patients infected with the H275Y mutant virus had higher day 28 mortality than others (80% vs 12%; P = .011).