bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multilocus Sequence Typing of Emerging Azole-Resistant Candida auris Isolates from Critically Ill Patients in a New York City Medical Center
Authors: Weidmann Maxwell , Srivastava-Malick Mahavrat , Shi Jun , Wu Fann 
Published: November 2023

Abstract
Candida auris has developed into a slow-moving global pandemic since its emergence in 2009, particularly as a source of nosocomial infection amongst immunocompromised and critically-ill patients. According to CDC data, C. auris emergence has accelerated in the US during the COVID-19 pandemic and has garnered particular attention for its high level of resistance to multiple classes of antifungals. C. auris has been categorized into five genetically diverse clades, each with unique antifungal drug resistance patterns. We have observed a sharp increase in cases identified at our tertiary medical center in New York City over the past three years. In this study, we designed a set of C. auris-specific oligonucleotides to determine the clonality of isolates through Multilocus Sequence Typing (MLST) of four genetic loci known to have a high level of divergence amongst Candida species. From 2020 through 2022 we identified 22 patients with C. auris bloodstream infection at our institution by Matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) and performed MLST on isolates that were available from 19 patients. We assessed four genetic loci: ITS1/ITS2, D1/D2, RPB1 and RPB2; ERG11 was included to assess for mutations associated with fluconazole resistance. We found that the number of blood stream infections increased from 2 cases in 2020 to 12 in 2022. Our MLST results showed that all C. auris isolates from blood and body fluids belong to CDC-defined Clade 1c, which carries the ERG11 gene mutation resulting the amino acid substitution K143R in 14-α-Demethylase associated with fluconazole resistance. These isolates also demonstrated fluconazole resistance by in vitro testing (19/19), amphotericin resistance was present in 44% of isolates with available data (7/16), and all isolates were susceptible to micafungin (19/19). Of 19 patients with blood cultures positive for C. auris, 13 (68%) were in a critical care setting at time of collection, 17 (89%) had been in an ICU during the same admission, and 8 (42%) expired within 3 months of C. auris positivity. MLST is considered a relatively fast and inexpensive method of sequence-based strain typing and has recently been applied to assessing the clonality of C. auris isolates. We show that the use of C. auris-specific oligonucleotides for sequencing, rather than those derived from other Candida species, produces high quality data for MLST, as well as the detection of specific mutations involved in antifungal resistance, such as ERG11. Further assessment is needed by the gold standard in sequence typing, Whole Genome Sequencing (WGS), to confirm our analysis of clonality here. MLST may therefore represent a useful tool in understanding the interrelatedness of invasive C. auris infections in hospitalized patients as well as inform clinical decision-making around infection control and empiric antifungal therapy.
Detection of Prostate Cancer Screening Disparities Using Geospatial Analysis of Laboratory Results
Authors: Azimi Vahid , Zaydman Mark 
Published: November 2023

Abstract
Black men experience higher prevalence and mortality from prostate cancer (PCa) but are less likely to undergo PCa screening with prostate-specific antigen (PSA). The reasons for this disparity are multifactorial and include lack of access, PCa education, and mistrust in the healthcare system. Identifying geographic regions with low PSA screening and high positivity rates could potentially help inform targeted interventions. This study aimed to examine racial, socioeconomic, and geospatial disparities in PSA screening and positivity rates in the Siteman Cancer Center (St. Louis, MO) catchment region. The results of all PSA screening tests ordered in the Barnes-Jewish Healthcare Corporation (St. Louis, MO) and performed from 9/2019-12/2022 were retrieved from the laboratory information system with patient demographics. Patient addresses were geocoded using ArcGIS Pro (ESRI, Redlands, CA) and assigned to a census tract of residence. The PSA screening-eligible population was defined as the number of persons ≥50 years of age based on U.S. Census data. Social Vulnerability Index (SVI) values were retrieved from the Centers for Disease Control. The PSA screening rate was calculated by census tract as the total number of PSA tests performed/PSA screening-eligible population. The PSA positivity rate was calculated by census tract as the number of PSA positive tests/total PSA tests. All census tracts with fewer than 10 PSA tests performed were omitted from PSA positivity analysis. Hotspot analysis was performed by calculating Local Moran’s I statistic per census tract and comparing with 999 randomly-generated maps. A total of 90,994 screening tests for 60,005 patients (48,024 White [80%], 10,425 Black [17%], and 1,556 Other [3%]) were performed for patients in the catchment region. Black patients were 78% more likely to receive a positive PSA screen than White patients (p&lt;0.001). Of those screening positive, Black patients had a significantly higher median[IQR] (7.94[6.2-13.7 ng/mL]) PSA result compared to White patients (7.4[6.2-10.1 ng/mL]) (p&lt;0.001) and a median[IQR] age of 67[61-74 years] vs. 69[63-76 years] (p&lt;0.001). In a multivariate logistic regression using age, race, and census tract of residence SVI to predict PSA positivity, only census tract SVI was not statistically significant. A model using only age and race demonstrated that every 10 years of age and Black race were associated with 11% and 7% increased odds of receiving a PSA positive test, respectively (p&lt;0.001). 75 and 191 of 789 census tracts in the catchment region were identified as PSA positivity hotspots and PSA screening cold spots, respectively. In conclusion, this study confirms previous reports of higher PSA values among Black patients and suggests that geospatial analysis of PSA testing can identify geographic regions with low testing and high positivity rates.
Simplifying molecular testing through electronic order entry
Authors: Kwon Regina , Krumm Niklas , Hoffman Noah , Mathias Patrick , Konnick Eric 
Published: November 2023

Abstract
Our solid-tumor molecular laboratory receives more than 3,000 orders each year, with about two-thirds coming from internal providers. Before this project, molecular tests were ordered using one of two different paper forms, which the care team then faxed or e-mailed to the Genetics Preanalytical Service (GPS). These requests led to frequent modifications and cancellations due to the complexity of molecular testing. A small fraction of requisitions were lost due to transmission errors. We undertook a project to design, develop, and implement computerized physician order entry (CPOE) in Epic (Epic Systems Corp., Verona, WI) and Sunquest (Clinisys, Tucson, AZ). We conducted extensive interviews with the directors of the molecular lab, laboratory medicine IT, GPS, anatomic pathology staff, laboratory scientists, laboratory genetic counselors, oncologists, clinicians, and nurse coordinators. The order itself and other technical changes underwent iterative review and testing by a subset of interviewees. Five oncologists participated in formal beta-testing. The user interviews allowed us to produce a detailed process diagram that drew attention to specific areas of repetition or risk. We proposed a new workflow that would eliminate repetition, provide redundant order-tracking, and automate some lab processes. Once approved, we built the electronic order in Epic and modified existing laboratory programs and interfaces as needed. The process of placing an order, which previously typically involved both nurses and doctors over several calendar days, was now being completed in fewer than 5 minutes by a single practitioner. Requisition status events were no longer created manually in Sunquest by GPS. Certain data-entry tasks were eliminated through the incorporation of label printers. Within one month of launch, more than 50% of somatic molecular orders arrived via CPOE, increasing to 90% within six months. At a rate of 125 CPOE orders per month, time savings range from 20 hours per month for GPS staff, 50 hours per month for nursing, and 20 hours per month for physicians. The success of this project demonstrates the feasibility of replacing a paper-based process for a complex test menu with CPOE. Due to the intricacies of molecular testing, such a change will undoubtedly involve multiple divisions. We attribute the success of this project to early involvement by key stakeholder groups, including developers; an extended testing phase to ensure reliability at roll-out; creation of straightforward reference documents; and rapid response to user questions, especially during the first weeks post-launch.
Anticoagulation management in patients tested for heparin-induced thrombocytopenia in the cardiothoracic intensive care unit diverges from expert guidelines
Authors: Spies Nicholas , Jackups Ronald , Zaydman Mark 
Published: November 2023

Abstract
Heparin-induced thrombocytopenia (HIT) is a rare, life-threatening complication in patients receiving heparin products. Clinical scoring tools, such as the ‘4T’ score, aim to help identify patients at risk for HIT and are recommended by expert guidelines. For example, the American Society of Hematology (ASH) recommends that patients with an intermediate or high-risk 4T score are presumptively treated for HIT by withdrawing heparin and starting an alternative anticoagulant. At our institution, laboratory HIT testing involves an in-house latex immunoassay (LIA) that, if positive, reflexes to a send-out serotonin release assay (SRA) at the Blood Center of Wisconsin. This confirmation may take several days to result, underscoring the importance of presumptive treatment. Anecdotally, we have observed that clinicians have expressed reservations about the use of the 4T score in the cardiothoracic intensive care unit (CTICU). These reservations may lead to increased HIT testing in patients with low 4T scores and delays in the initiation of alternative anticoagulants. We set out to objectively determine if clinical practice in the CTICU is aligned with ASH guidelines. To do so, we used anticoagulant usage as a proxy for medical decisions made at the time of order for HIT laboratory testing. Data was extracted from the electronic medical records of all patients who were admitted to the CTICU between 5/2018 and 7/2022 and administered a heparin product (n = 1,602). Patients that were not tested for HIT (n = 1,449) were excluded. The remaining patients’ (n = 153) medication record timings were normalized such that the time of their first LIA was set to zero to allow for relative comparisons. 25 (16%) of the LIAs were positive, of which 5 (20%) were confirmed by SRA. Of the 153 patients, 136 (89%) received heparin within 24 hours prior to LIA order, while 6 (4%) were already on alternative anticoagulation (bivalirudin). Of the patients on heparin prior to LIA, 18 (13%) were switched to bivalirudin upon LIA order, 66 (49%) had heparin discontinued without an alternative, and 52 (39%) were continued on heparin. Our results suggest that the prevalence of HIT in this cohort is 3.3% by SRA, much lower than the expected pretest probability estimated for intermediate- and high-risk 4T scores in published meta-analyses. In addition, the observed anticoagulation practices varied widely and diverged from ASH guidelines, where only 17% of patients were on alternative anticoagulation when the testing was ordered. Future work will investigate these patterns across LIA positivity and 4T scores while attempting to address the clinical outcomes of these treatment decisions.
Delayed Hemolytic Transfusion Reactions Could be Prevented by a National Alloimmunization Registry
Authors: Stanek Caroline , Miller Brianna , Marques Marisa 
Published: November 2023

Abstract
Evanescence of alloantibodies to RBC antigens places patients at risk of delayed hemolytic transfusion reactions (DHTRs) unless the transfusion service is aware of their alloantibody history. In the past year, three patients with sickle cell disease (SCD) developed a DHTR at our institution because their pre-transfusion testing did not reflect their full alloimmunezation. We sought to determine how often the pre-transfusion antibody screen is negative or fails to show the full alloimmunization profile. We reviewed the electronic records of all current adult patients with SCD receiving chronic outpatient RBC transfusions (including red cell exchange) to collect demographic and laboratory results to answer this question. Our analysis included 162 patients of African-American descent: 80 (49%) males and 82 (51%) females, with an average age of 34 years. The majority, 92 or 56%, had a history of alloimmunization with a mean number of 3 antibodies (range: 1-10). The most common were to the C, E, and K antigens. The next two most common alloantibodies were nonspecific, representing alloimmunization to an antigen that could not be further determined, followed by the D antigen. In 81 patients, the most recent antibody screen did not reflect their history, with most being completely negative (n=69), and the rest (n=12) unable to detect all alloantibodies of which they had a history. The antibodies most often undetectable were: Anti-E, Anti-C, and Anti-D. These are simultaneously the second, first, and fifth most common antibodies in this population, all of which are considered clinically significant and capable of causing a hemolytic transfusion reaction. Of note, the alloantibodies implicated in the recent DHTRs we observed, were to the JKa, Jkb, Fya and the S antigens. In addition, 28 individuals (17% of the total) had at least one antibody to a low incidence antigen (LIA) such as Goa, V, Vs, Jsa, Kpa and Lua. Five (3%) patients were exclusively sensitized to one or more low incidence antigens. Considering that commercially available reagent red cells utilized to perform pre-transfusion testing may lack LIAs, knowing the history of alloimmunization is the only way to prevent hemolytic reactions. In conclusion, evanescence and limitations of the commercially available reagents to test patients with SCD prior to a transfusion place them at increased risk of transfusion reactions. One potential way to minimize risk from the latter is to perform serologic crossmatching of all units intended for patients with SCD, independent of the result of the antibody screen. This is the practice we have instituted several years ago in our transfusion service. However, the solution to both problems is a national repository of alloimmunization histories accessible to all transfusion services. Such informatics tools would help avoid DHTRs in patients with and without SCD.
Monitoring Infected Reticulocytes During Murine Malaria Infection
Authors: Gordy Dominique , Hudson Krystalyn , Thomas Tiffany , Shah Shivang , Stone Elizabeth 
Published: November 2023

Abstract
Malaria infection is a major cause of mortality worldwide. According to the 2022 World Health Organization Malaria Report, malaria caused approximately 247 million infections and 619,000 deaths in 2021, with more than 470,000 children dying of malaria. The gold-standard for measuring parasitemia is counting infected red blood cells (RBCs) by eye using Giemsa staining whole blood smears. This method is time consuming and is subject to error by both who is counting, the number of cells counted, and which frames are selected for counting. Automating the process of measuring malaria infection by flow cytometry decreases both the time required to obtain accurate parasitemia counts and the possible error on behalf of the researcher. Hundreds of thousands of cells can be counted by flow cytometry in a shorter period of time. Animal models of malaria infection are widespread and well-characterized. The rodent malaria strain P. berghei has shown preferential infection of reticulocytes over mature RBCs. Here we outline a method of measuring P. berghei blood stage infection in reticulocytes and mature RBCs and comparing the results to Giemsa stained whole blood smears. Using commercially available P. berghei ANKA expressing green-fluorescent protein (GFP), we infected wild type mice with 1x106 parasitized RBCs by intraperitoneal injection. Whole blood samples were collected daily starting day 3 post infection through day 7 by tail vein collection. Random and representative fields of Giemsa stained peripheral smears were selected to measure the percentage of parasitemia in mature RBCs and reticulocytes for a total cell count of approximately 1000. For flow cytometry, whole blood was incubated in 500uL of 1X SYBR Green I Nucleic Acid Gel Stain in PBS at 37°C for 20 minutes in the dark, washed with PBS, and stained with anti-CD71 to label reticulocytes. During the early stages of infection, the reticulocyte percentage of infected animals is not significant from uninfected animals, approximately 1.86%. As parasitemia increases over time, although the percentage of total reticulocytes decreases, the percentage of infected reticulocytes increases. On day 3 through 7 for one experimental replicate, day 3 demonstrated 1.86% total reticulocytes, and of these 2.56% reticulocytes were infected; day 4 had 0.66% total reticulocytes, and of these 32.92% were infected; day 5 showed 0.18% reticulocytes with 71.81% infected reticulocytes; on day 6 there were 0.04% reticulocytes with 75.44% infected reticulocytes; and day 7 had 0.01% reticulocytes with 69.56% infected reticulocytes. There was a strong correlation (R2 = 0.9147) when comparing flow cytometry to measure parasitemia with counting parasitemia by peripheral smear. This flow cytometry panel is an excellent tool to assess malarial infection of reticulocytes compared to mature RBCs and can be applied to other malarial species while decreasing bias, error and time needed to conduct the experiment.
‘Reputation, reputation, reputation! Oh, I have lost my reputation!’; A literature review on alcohol addiction in the British Sikh and/or Punjabi community and the barriers to accessing support
Authors: Kaur Karamdeep 
Published: November 2023

Abstract

Aims
The literature review aimed to identify the barriers the Punjabi and/or Sikh community have in accessing support for alcohol addiction.

Method
A systematic review of the literature was undertaken of four scholarly databases, Google Scholar and grey literature on UK-based research conducted after 1980 into alcohol addiction in the Punjabi and/or Sikh community. Fourteen papers met the inclusion criteria outlined in the paper and were included in the review.

Results
Ten main barriers to accessing support were found; stigma, religion, lack of understanding of addiction, over reliance on a medical model of treatment and disregard of therapy, cultural implications of being a member of the Punjabi and/or Sikh community and the addiction community, gender and generational differences and a lack of government commitment to alcohol support for BME communities with a lack of culturally specific services.

Conclusion
Despite the many barriers explored, the role of stigma remained a powerful theme throughout often underpinning other barriers. A key recommendation across many papers was the need for culturally sensitive support services. Several areas for future research were identified.
Assessing protein model quality based on deep graph coupled networks using protein language model
Authors: Liu Dong , Zhang Biao , Liu Jun , Li Hui , Song Le , Zhang Guijun 
Published: November 2023

Abstract
Model quality evaluation is a crucial part of protein structural biology. How to distinguish high-quality models from low-quality models, and to assess which high-quality models have relatively incorrect regions for improvement, are remain a challenge. More importantly, the quality assessment of multimer models is a hot topic for structure prediction. In this study, we propose GraphCPLMQA, a novel approach for evaluating residue-level model quality that combines graph coupled networks and embeddings from protein language models. The GraphCPLMQA consists of a graph encoding module and a transform-based convolutional decoding module. In encoding module, the underlying relational representations of sequence and high-dimensional geometry structure are extracted by protein language models with Evolutionary Scale Modeling. In decoding module, the mapping connection between structure and quality is inferred by the representations and low-dimensional features. Specifically, the triangular location and residue level contact order features are designed to enhance the association between the local structure and the overall topology. Experimental results demonstrate that GraphCPLMQA using single-sequence embedding achieves the best performance compared with the CASP15 residue-level interface evaluation methods among 9108 models in the local residue interface test set of CASP15 multimers. In CAMEO blind test (20 May 2022 to 13 August 2022), GraphCPLMQA ranked first compared with other servers (https://www.cameo3d.org/quality-estimation). GraphCPLMQA also outperforms state-of-the-art methods on 19, 035 models in CASP13 and CASP14 monomer test set.
FireProt 2.0: web-based platform for the fully automated design of thermostable proteins
Authors: Musil Milos , Jezik Andrej , Horackova Jana , Borko Simeon , Kabourek Petr , Damborsky Jiri , Bednar David 
Published: November 2023

Abstract
Thermostable proteins find their use in numerous biomedical and biotechnological applications. However, the computational design of stable proteins often results in single-point mutations with a limited effect on protein stability. However, the construction of stable multiple-point mutants can prove difficult due to the possibility of antagonistic effects between individual mutations. FireProt protocol enables the automated computational design of highly stable multiple-point mutants. FireProt 2.0 builds on top of the previously published FireProt web, retaining the original functionality and expanding it with several new stabilization strategies. FireProt 2.0 integrates the AlphaFold database and the homology modeling for structure prediction, enabling calculations starting from a sequence. Multiple-point designs are constructed using the Bron–Kerbosch algorithm minimizing the antagonistic effect between the individual mutations. Users can newly limit the FireProt calculation to a set of user-defined mutations, run a saturation mutagenesis of the whole protein or select rigidifying mutations based on B-factors. Evolution-based back-to-consensus strategy is complemented by ancestral sequence reconstruction. FireProt 2.0 is significantly faster and a reworked graphical user interface broadens the tool’s availability even to users with older hardware. FireProt 2.0 is freely available at http://loschmidt.chemi.muni.cz/fireprotweb.