bluuebunny/crossref_metadata_2025_split huggingface dataset:
Maximizing Reflexive Hepatitis C Virus (HCV) RNA Testing of HCV Antibody-Reactive Samples Within United States Public Health Laboratories
Authors: Johnson Lauren N , Gaynor Anne M , Wroblewski Kelly , Buss Sarah N 
Published: September 2023

Abstract
Hepatitis C virus (HCV) infection can have serious consequences when untreated and diagnosis is the first step in any treatment regimen. In the Unites States a 2-step algorithm consisting of HCV antibody screening and HCV RNA testing of HCV antibody-reactive specimens is recommended for detection of current HCV infection. We conducted a survey of HCV diagnostic practices in US public health laboratories and convened a meeting of HCV subject matter experts to identify opportunities for improvement in HCV diagnosis. Automatic reflexive HCV RNA testing of HCV antibody-reactive specimens was identified as a gap in laboratory practice. Only 54% of respondent laboratories always automatically reflexed or referred an anti-HCV-reactive specimen to an HCV RNA test. To facilitate diagnosis and ensure patients are not lost to follow-up, laboratories should ensure that the entire HCV testing algorithm can be completed with a sample(s) collected during a single patient visit.
What Hepatitis C Virus (HCV) Diagnostic Tools Are Needed to Advance Diagnosis of Current HCV Infection in Outreach Settings and in a Nonclinical Setting?
Authors: Page Kimberly , Feinberg Judith 
Published: September 2023

Abstract
Given the growing hepatitis C virus (HCV) epidemic in the United States, it is imperative to implement a coordinated, equitable public health approach to HCV testing that will facilitate immediate access to treatment, especially for individuals with limited healthcare access and those who inject drugs. Point-of-care RNA diagnostic tests have the greatest potential to address this need. Future regulatory approval has been facilitated by a recent change in the US Food and Drug Administration's approach to evaluating point-of-care diagnostic tests that have been developed and validated.
Down-Classification of Hepatitis C Virus Diagnostics: Implications for Screening and Diagnosis
Authors: Terrault Norah 
Published: September 2023

Abstract
In November 2021, the United States Food and Drug Administration reclassified 2 types of hepatitis C virus (HCV) diagnostic tests (HCV antibody and HCV nucleic acid) from class III to class II, providing a less burdensome pathway to market for diagnostic companies. This down-classification is anticipated to facilitate innovation in HCV diagnostics, particularly for new point-of-care viral detection assays, and ultimately support HCV elimination efforts by increasing the ease of screening as well as test-and-treat models of HCV care.
Development and Validation of Three Automated High-Throughput Molecular Tests to Detect Monkeypox Virus Infections
Authors: Anderson Mark , Hodges Austin , Luk Ka-Cheung , Olivo Ana , Forberg Kenn , Meyer Todd V , Strobel Carolyn , Kim Mark , Toolsie Dan , Moore Nicholas M , Goldstein Yitzchak , Rodgers Mary , Lucic Danijela , Cloherty Gavin 
Published: September 2023

Abstract

Background
The 2022 outbreak of the clade IIb monkeypox virus and subsequent global spread lead to an urgent need for the development of high-throughput, sensitive, and reproducible diagnostic tests.

Methods
We developed 3 assays to detect monkeypox virus, 2 (MPXV+ and MPXV) for m2000 RealTime and 1 (MPXV) for Alinity m platforms. Dual targets in E9L and B6R (MPXV+) and J2L and B7R (MPXV) increased mutation resistance. In silico prediction indicates MPXV+ cross-reactivity with orthopox viruses and specific monkeypox virus detection with MPXV.

Results
m2000 RealTime MPXV+ and MPXV assay sensitivity was determined to be 3.2 plaque-forming units/mL using a reference virus culture diluted into universal transport medium (UTM). Alinity m MPXV lower limit of detection was 200 copies/mL using monkeypox virus plasmids in pooled UTM matrix. m2000 RealTime MPXV+ and MPXV assays were validated with lesion swabs in UTM and 1:1 saliva to UTM mixtures. Commercially available and remnant clinical lesion specimens in UTM were tested with RealTime MPXV+, RealTime MPXV and Alinity m MPXV assays and demonstrated high agreement to known mpox (MPX)-positive specimens.

Conclusions
RealTime MPXV+, RealTime MPXV, and Alinity MPXV are high throughput and sensitive assays used for the detection of monkeypox virus. These assays maybe useful during MPX outbreaks.
Oral Favipiravir Exposure and Pharmacodynamic Effects in Adult Outpatients With Acute Influenza
Authors: Hayden Frederick G , Lenk Robert P , Epstein Carol , Kang Lih Lisa 
Published: September 2023

Abstract

Background
The pharmacokinetics of oral favipiravir and the relationships of plasma concentrations to antiviral effects are incompletely studied in influenza.

Methods
Serial plasma samples were collected from adults with uncomplicated influenza who were randomized to favipiravir (1800 mg twice a day on day 1, 800 mg twice a day on days 2 to 5; n = 827) or placebo (n = 419) in 2 phase 3 trials. Post hoc analyses assessed the frequency of reaching an average minimum concentration (Cmin) ≥20 µg/mL, its association with antiviral efficacy, and factors associated with reduced favipiravir exposure.

Results
Wide interindividual variability existed in favipiravir concentrations, and this regimen failed to reach an average Cmin&gt;20 µg/mL in 41%–43% of participants. Those attaining this threshold showed greater reductions in nasopharyngeal infectious virus titers on treatment days 2 and 3 and lower viral titer area under the curve compared to those who did not. Those with average Cmin &lt;20 µg/mL had over 2-fold higher mean ratios of the metabolite T-705M1 to favipiravir, consistent with greater metabolism, and were more likely to weigh &gt;80 kg (61.5%–64%).

Conclusions
Higher favipiravir levels with average Cmin&gt;20 µg/mL were associated with larger antiviral effects and more rapid illness alleviation compared to placebo and to favipiravir recipients with lower average Cmin values in uncomplicated influenza.
Clinical Trials Registration . NCT1068912 and NCT01728753.
Linezolid Population Pharmacokinetic Model in Plasma and Cerebrospinal Fluid Among Patients With Tuberculosis Meningitis
Authors: Abdelgawad Noha , Wasserman Sean , Abdelwahab Mahmoud Tareq , Davis Angharad , Stek Cari , Wiesner Lubbe , Black John , Meintjes Graeme , Wilkinson Robert J , Denti Paolo 
Published: September 2023

Abstract

Background
Linezolid is evaluated in novel treatment regimens for tuberculous meningitis (TBM). Linezolid pharmacokinetics have not been characterized in this population, particularly in cerebrospinal fluid (CSF), as well as, following its co-administration with high-dose rifampicin. We aimed to characterize linezolid plasma and CSF pharmacokinetics in adults with TBM.

Methods
In the LASER-TBM pharmacokinetic substudy, the intervention groups received high-dose rifampicin (35 mg/kg) plus 1200 mg/day of linezolid for 28 days, which was then reduced to 600 mg/day. Plasma sampling was done on day 3 (intensive) and day 28 (sparse). A lumbar CSF sample was obtained on both visits.

Results
Thirty participants contributed 247 plasma and 28 CSF observations. Their median age and weight were 40 years (range, 27–56) and 58 kg (range, 30–96). Plasma pharmacokinetics was described by a 1-compartment model with first-order absorption and saturable elimination. Maximal clearance was 7.25 L/h, and the Michaelis-Menten constant was 27.2 mg/L. Rifampicin cotreatment duration did not affect linezolid pharmacokinetics. CSF-plasma partitioning correlated with CSF total protein up to 1.2 g/L, where the partition coefficient reached a maximal value of 37%. The plasma-CSF equilibration half-life was ∼3.5 hours.

Conclusions
Linezolid was readily detected in CSF despite high-dose rifampicin coadministration. These findings support continued clinical evaluation of linezolid plus high-dose rifampicin for the treatment of TBM in adults.
Clinical Trials Registration.  ClinicalTrials.gov (NCT03927313).
Fair-Weather Abusers? Civil War Dynamics and the Onset of State-Sponsored Violence
Authors: Keels Eric , Greig J Michael 
Published: September 2023

Abstract
Despite decades of rigorous research on the use of government-sponsored violence in armed conflicts, there remains significant uncertainty as to when and where leaders choose to target civilians in war. We argue that the variation in the use of state repression is explained in part by how soldiers perceive battlefield gains by rebel forces. Specifically, while strong opposition forces are often a necessary condition for elites convincing agents to engage in state-sponsored brutality, this is modified by the soldiers’ beliefs surrounding the outcome of the war. If government soldiers believe that rebels are likely to win the war, we posit that they will likely shirk orders to target civilians, fearing post-war accountability. We test this argument by examining subnational variation in battlefield dynamics and the use of government one-sided violence from 1992 to 2010.
Investigation of genomic mutations and their association with phenotypic resistance to new and repurposed drugs in Mycobacterium tuberculosis complex clinical isolates
Authors: Mok Simone , Roycroft Emma , Flanagan Peter R , Wagener Johannes , Fitzgibbon Margaret M 
Published: September 2023

Abstract

Background
WGS has the potential to detect resistance-associated mutations and guide treatment of MDR TB. However, the knowledge base to confidently interpret mutations associated with the new and repurposed drugs is sparse, and phenotypic drug susceptibility testing is required to detect resistance.

Methods
We screened 900 Mycobacterium tuberculosis complex genomes from Ireland, a low TB incidence country, for mutations in 13 candidate genes and assessed their association with phenotypic resistance to bedaquiline, clofazimine, linezolid, delamanid and pretomanid.

Results
We identified a large diversity of mutations in the candidate genes of 195 clinical isolates, with very few isolates associated with phenotypic resistance to bedaquiline (n = 4), delamanid (n = 4) and pretomanid (n = 2). We identified bedaquiline resistance among two drug-susceptible TB isolates that harboured mutations in Rv0678. Bedaquiline resistance was also identified in two MDR-TB isolates harbouring Met146Thr in Rv0678, which dated back to 2007, prior to the introduction of bedaquiline. High-level delamanid resistance was observed in two isolates with deletions in ddn, which were also resistant to pretomanid. Delamanid resistance was detected in two further isolates that harboured mutations in fbiA, but did not show cross-resistance to pretomanid. All isolates were susceptible to linezolid and clofazimine, and no mutations found were associated with resistance.

Conclusions
More studies that correlate genotypic and phenotypic drug susceptibility data are needed to increase the knowledge base of mutations associated with resistance, in particular for pretomanid. Overall, this study contributes to the development of future mutation catalogues for M. tuberculosis complex isolates
Siderophore-producingBacillus amyloliquefaciensBM3 mitigate arsenic contamination and suppressFusariumwilt in brinjal plants
Authors: Pradhan Smriti , Choudhury Abhinandan , Dey Sovan , Hossain Md Firoj , Saha Aniruddha , Saha Dipanwita 
Published: September 2023

AbstractAimArsenic contamination in agricultural soils poses a serious health risk for humans. Bacteria that produce siderophores, primarily for iron acquisition, can be relevant in combating arsenic toxicity in agricultural soils and simultaneously act as biocontrol agents against plant diseases. We evaluated the arsenic bioremediation and biocontrol potential of the rhizosphere isolate Bacillus amyloliquefaciens BM3 and studied the interaction between the purified siderophore bacillibactin and arsenic.Methods and resultsBM3 showed high arsenic resistance [MIC value 475 and 24 mM against As(V) and As(III), respectively] and broad spectrum in-vitro antagonism against several phytopathogenic fungi. BM3 was identified by biochemical characterization and 16S rRNA gene sequencing. Scanning electron microscopy (SEM) analysis revealed increased cell size of BM3 when grown in presence of sub-lethal arsenic concentrations. Bioremediation assays showed a 74% and 88.1% reduction in As(V) and As(III) concentrations, respectively. Genetic determinants for arsenic resistance (arsC and aoxB) and antifungal traits (bacAB and chiA) were detected by PCR. Arsenic chelating ability of bacillibactin, the siderophore purified from culture filtrate of BM3 and identified through spectroscopic data analysis, was observed in CAS assay and fluorescence spectrometry. In-vivo application of talc-based formulation of BM3 in brinjal seedlings showed significant reduction in Fusarium wilt disease.ConclusionStrain B. amyloliquefaciens BM3 may be useful in arsenic bioremediation and may be considered for large field trials as an alternative to chemical fungicides by inhibiting soil borne pathogens.
The relationship between electronic health records user interface features and data quality of patient clinical information: an integrative review
Authors: Madandola Olatunde O , Bjarnadottir Ragnhildur I , Yao Yingwei , Ansell Margaret , Dos Santos Fabiana , Cho Hwayoung , Dunn Lopez Karen , Macieira Tamara G R , Keenan Gail M 
Published: September 2023

Abstract

Objectives
Electronic health records (EHRs) user interfaces (UI) designed for data entry can potentially impact the quality of patient information captured in the EHRs. This review identified and synthesized the literature evidence about the relationship of UI features in EHRs on data quality (DQ).

Materials and methods
We performed an integrative review of research studies by conducting a structured search in 5 databases completed on October 10, 2022. We applied Whittemore & Knafl’s methodology to identify literature, extract, and synthesize information, iteratively. We adapted Kmet et al appraisal tool for the quality assessment of the evidence. The research protocol was registered with PROSPERO (CRD42020203998).

Results
Eleven studies met the inclusion criteria. The relationship between 1 or more UI features and 1 or more DQ indicators was examined. UI features were classified into 4 categories: 3 types of data capture aids, and other methods of DQ assessment at the UI. The Weiskopf et al measures were used to assess DQ: completeness (n = 10), correctness (n = 10), and currency (n = 3). UI features such as mandatory fields, templates, and contextual autocomplete improved completeness or correctness or both. Measures of currency were scarce.

Discussion
The paucity of studies on UI features and DQ underscored the limited knowledge in this important area. The UI features examined had both positive and negative effects on DQ. Standardization of data entry and further development of automated algorithmic aids, including adaptive UIs, have great promise for improving DQ. Further research is essential to ensure data captured in our electronic systems are high quality and valid for use in clinical decision-making and other secondary analyses.
Using natural language processing to identify the status of homelessness and housing instability among serious illness patients from clinical notes in an integrated healthcare system
Authors: Xie Fagen , Wang Susan , Viveros Lori , Rich Allegra , Nguyen Huong Q , Padilla Ariadna , Lyons Lindsey , Nau Claudia L 
Published: September 2023

Abstract

Background
Efficiently identifying the social risks of patients with serious illnesses (SIs) is the critical first step in providing patient-centered and value-driven care for this medically vulnerable population.

Objective
To apply and further hone an existing natural language process (NLP) algorithm that identifies patients who are homeless/at risk of homeless to a SI population.

Methods
Patients diagnosed with SI between 2019 and 2020 were identified using an adapted list of diagnosis codes from the Center for Advance Palliative Care from the Kaiser Permanente Southern California electronic health record. Clinical notes associated with medical encounters within 6 months before and after the diagnosis date were processed by a previously developed NLP algorithm to identify patients who were homeless/at risk of homelessness. To improve the generalizability to the SI population, the algorithm was refined by multiple iterations of chart review and adjudication. The updated algorithm was then applied to the SI population.

Results
Among 206 993 patients with a SI diagnosis, 1737 (0.84%) were identified as homeless/at risk of homelessness. These patients were more likely to be male (51.1%), age among 45-64 years (44.7%), and have one or more emergency visit (65.8%) within a year of their diagnosis date. Validation of the updated algorithm yielded a sensitivity of 100.0% and a positive predictive value of 93.8%.

Conclusions
The improved NLP algorithm effectively identified patients with SI who were homeless/at risk of homelessness and can be used to target interventions for this vulnerable group.
Validation of PVT VIABLE® for Detection of Legionella in Potable and Non-Potable Water: AOAC Performance Tested MethodSM 082303
Authors: Wickenberg Leah , Gabrie Katherine , McCarthy Patrick , Cain Melissa 
Published: September 2023

Abstract

Background
Phigenics Validation Test (PVT) VIABLE® (Viability Identification Assay by Legionella Enrichment) is a method to detect viable Legionella bacteria in building water systems.

Objective
To evaluate PVT VIABLE against the ISO 11731:2017 Water Quality—Enumeration of Legionella reference method for the detection of viable Legionella species in potable and non-potable water.

Methods
PVT VIABLE was tested for inclusivity (n = 50 strains of Legionella) and exclusivity (n = 30 non-target strains), robustness, and stability. A multi-laboratory instrument variation study was performed to evaluate the PCR data. The matrix study was performed on potable and non-potable water samples inoculated with Legionella pneumophila at a low (n = 20) and high fractional level (n = 5). Samples were analyzed using the PVT VIABLE and confirmed using ISO 11731:2017.

Results
Statistical analysis showed no difference between PVT VIABLE and ISO 11731:2017 for 100 mL test portions of potable and non-potable water. PVT VIABLE demonstrated high levels of specificity and sensitivity in the inclusivity and exclusivity study. Results of the robustness and stability studies demonstrated the method was sufficiently robust to handle small method changes and met the method claims of stability.

Conclusion
PVT VIABLE allows the end user to obtain presumptive results for viable Legionella spp. contamination of potable and non-potable water in 2–3 days.

Highlights
PVT VIABLE provides viable Legionella results in 2–3 days versus 10–14 days for traditional spread plating. This novel diagnostic tool also differentiates between Legionella pneumophila sg1, Legionella pneumophila sg2–15, and Legionella spp. without the need for additional confirmation steps as outlined in ISO 11731:2017.
Optical Breast Imaging: A Review of Physical Principles, Technologies, and Clinical Applications
Authors: Poplack Steven P , Park Eun-Yeong , Ferrara Katherine W 
Published: September 2023

Abstract
Optical imaging involves the propagation of light through tissue. Current optical breast imaging technologies, including diffuse optical spectroscopy, diffuse optical tomography, and photoacoustic imaging, capitalize on the selective absorption of light in the near-infrared spectrum by deoxygenated and oxygenated hemoglobin. They provide information on the morphological and functional characteristics of different tissues based on their varied interactions with light, including physiologic information on lesion vascular content and anatomic information on tissue vascularity. Fluorescent contrast agents, such as indocyanine green, are used to visualize specific tissues, molecules, or proteins depending on how and where the agent accumulates. In this review, we describe the physical principles, spectrum of technologies, and clinical applications of the most common optical systems currently being used or developed for breast imaging. Most notably, US co-registered photoacoustic imaging and US-guided diffuse optical tomography have demonstrated efficacy in differentiating benign from malignant breast masses, thereby improving the specificity of diagnostic imaging. Diffuse optical tomography and diffuse optical spectroscopy have shown promise in assessing treatment response to preoperative systemic therapy, and photoacoustic imaging and diffuse optical tomography may help predict tumor phenotype. Lastly, fluorescent imaging using indocyanine green dye performs comparably to radioisotope mapping of sentinel lymph nodes and appears to improve the outcomes of autologous tissue flap breast reconstruction.
It Looks Like “Theirs”: When and Why Human Presence in the Photo Lowers Viewers’ Liking and Preference for an Experience Venue
Authors: Lu Zoe Y , Jung Suyeon , Peck Joann 
Published: September 2023

Abstract
Consumers and marketers often post photos of experiential consumption online. While prior research has studied how human presence in social media images impacts viewers’ responses, the findings are mixed. The present research advances the current understanding by incorporating viewers’ need for self-identity into their response model. Six studies, including an analysis of field data (14,725 Instagram photos by a top travel influencer) and five controlled experiments, find that the presence (vs. absence) of another human in the photo of an identity-relevant experience (e.g., a vacation, a wedding) can lower viewers' liking and preference for the venue (i.e., the vacation destination, the wedding venue) in the photo. This effect is mediated by viewers' feelings of others' ownership of the venue and moderated by the relevance of the experience to the viewer’s self-identity as well as the distinctiveness of the human in the photo. This research is the first to investigate the impact of human presence in shared photos through the lens of psychological ownership and the identity-signaling function of ownership. The findings offer practical insights into when marketers should avoid human presence in advertisements and how to mitigate the negative impact of human presence in online photos.
Post-Colonial Consumer Respect and the Framing of Neocolonial Consumption in Advertising
Authors: Varman Rohit , Belk Russell W , Sreekumar Hari 
Published: September 2023

Abstract
This study of the production, representation, and reception of post-colonial advertising in India reveals a politics of consumer respectability. The post-colonial politics of consumer respectability is located at the intersection of center–periphery relations, class divisions, and colorism in a way that it frames neocolonial consumption. Advertisers depict middle-class consumer respectability by asserting Indian nationalism and by degrading the West as a symbol of colonialism. Such depictions are class- and color-based and show under-class and dark-skinned consumers in subordinate positions. Furthering such neocolonial frames of consumption, Indian advertising advances the middle-class desire for Eurocentric modernity by reinforcing the colonial trope of India as temporally lagging behind the West. Finally, middle-class consumer respectability involves a neocolonial whitening of self with epidermalized shaping of inter-corporeality and agency. In uncovering the theoretical implications of advertising as a site of avenging degradation, desiring modernity, and whitening of self, this study contributes by offering insights into how the politics of post-colonial consumer respectability furthers neocolonial frames of consumption.