bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of several routine methods for fosfomycin and mecillinam susceptibility testing of Enterobacterales urine isolates
Authors: Massip C , Feletti L , Chagneau C V , Dumont Y , Maurin E , Muggeo A , Pichon M , Pompilio M , Buchler F , Halimi D , Dubois D 
Published: August 2024

Abstract

Objectives
Performance evaluation of routine laboratory methods to determine the susceptibility of Enterobacterales urinary isolates to fosfomycin (oral administration) and mecillinam.

Methods
We collected 347 Enterobacterales isolates from monomicrobial midstream urine samples from women with significant bacteriuria and leukocyturia. Mostly non-Escherichia coli isolates (i.e. Klebsiella spp., Citrobacter koseri, Enterobacter cloacae complex and Proteus mirabilis) were included (n = 298). Performance of VITEK®2, ETEST®, and disc diffusion to determine fosfomycin and mecillinam susceptibility was evaluated following International Organization for Standardization (ISO) 20776-2:2021 (or 20776-2:2007 for disc diffusion) in comparison with the agar dilution reference method.

Results
For fosfomycin testing, VITEK®2 and ETEST® were close to reaching ISO requirements (essential agreement  ≥ 90%; bias  ±30%) for C. koseri, E. coli and P. mirabilis. Categorical agreement (CA) and major error rates were acceptable for disc diffusion. Fosfomycin displayed lower activity against E. cloacae complex and Klebsiella spp., with MIC50 (minimum inhibitory concentration required to inhibit the growth of 50% of tested isolates) equal to the E. coli EUCAST breakpoint (8 mg/L). For these species, the three alternative techniques overestimated MICs and resistance, and did not meet performance criteria. For mecillinam testing of Enterobacterales isolates, apart from P. mirabilis, ETEST® nearly fulfilled ISO requirements, and CA rates were acceptable for disc diffusion. ISO criteria were reached for C. koseri and E. coli testing with VITEK®2, apart from too high rates of very major errors. For P. mirabilis, performances were unacceptable, whatever the routine method used.

Conclusions
Commercially available tests may serve as alternatives to agar dilution to assess fosfomycin (oral) and mecillinam susceptibility of Enterobacterales urinary isolates, with important interspecies variabilities. Additional studies comprising more fosfomycin- and mecillinam-resistant isolates are needed to strengthen our conclusions.
Use of teicoplanin monotherapy for the treatment of enterococcal infective endocarditis: a retrospective and comparative study at a referral centre
Authors: Villamarín Miguel , Fernández-Hidalgo Nuria , Viñado Belén , González-López Juan José , Rello Pau , Escolà-Vergé Laura 
Published: August 2024

Abstract

Objectives
Clinical experience in the use of teicoplanin for treating enterococcal infective endocarditis (EIE) is scarce. The aim of this study was to describe the characteristics and outcomes of patients with EIE treated with teicoplanin monotherapy compared to standard therapy with ampicillin plus ceftriaxone.

Methods
All consecutive adult patients diagnosed with EIE between January 2018 and September 2022 at a referral centre were reviewed. Characteristics of individuals treated with teicoplanin for ≥14 days [the treated with teicoplanin (TT) group] were compared with those who received ampicillin plus ceftriaxone (AC group).

Results
Sixty-six patients were included [61 (92%) E. faecalis infective endocarditis (IE) and 5 (8%) E. faecium IE]. Twenty-seven (41%) received teicoplanin: eight as first-line treatment and 19 as continuation therapy.
The median duration of teicoplanin treatment was 30 (25–43) days. Surgery was indicated in 14/27 (52%) in the TT group and in 21/39 (54%) in the AC group, but was finally performed in 11/14 (79%) and 13/21 (62%) (P = 0.46), respectively. In-hospital mortality rate was 3/27 (11%) in the TT group and 12/39 (31%) in the AC group (P = 0.06). Patients treated with teicoplanin were more often discharged on outpatient parenteral antibiotic therapy [18/27 (67%) versus 6/39 (15%), P &lt; 0.001] and median hospital stay was shorter [29 days (IQR 20–61) versus 50 days (IQR 43–68), P = 0.006]. One-year cumulative mortality was 8/27 (30%) in the TT group and 13/39 (33%) in the AC group (P = 0.46). There was one relapse in each group.

Conclusion
Teicoplanin seems an effective treatment for selected patients with enterococcal IE, mainly to facilitate discharge.
Development of electronic health record based algorithms to identify individuals with diabetic retinopathy
Authors: Breeyear Joseph H , Mitchell Sabrina L , Nealon Cari L , Hellwege Jacklyn N , Charest Brian , Khakharia Anjali , Halladay Christopher W , Yang Janine , Garriga Gustavo A , Wilson Otis D , Basnet Til B , Hung Adriana M , Reaven Peter D , Meigs James B , Rhee Mary K , Sun Yang , Lynch Mary G , Sobrin Lucia , Brantley Milam A , Sun Yan V , Wilson Peter W , Iyengar Sudha K , Peachey Neal S , Phillips Lawrence S , Edwards Todd L , Giri Ayush 
Published: August 2024

Abstract

Objectives
To develop, validate, and implement algorithms to identify diabetic retinopathy (DR) cases and controls from electronic health care records (EHRs).

Materials and Methods
We developed and validated electronic health record (EHR)-based algorithms to identify DR cases and individuals with type I or II diabetes without DR (controls) in 3 independent EHR systems: Vanderbilt University Medical Center Synthetic Derivative (VUMC), the VA Northeast Ohio Healthcare System (VANEOHS), and Massachusetts General Brigham (MGB). Cases were required to meet 1 of the following 3 criteria: (1) 2 or more dates with any DR ICD-9/10 code documented in the EHR, (2) at least one affirmative health-factor or EPIC code for DR along with an ICD9/10 code for DR on a different day, or (3) at least one ICD-9/10 code for any DR occurring within 24 hours of an ophthalmology examination. Criteria for controls included affirmative evidence for diabetes as well as an ophthalmology examination.

Results
The algorithms, developed and evaluated in VUMC through manual chart review, resulted in a positive predictive value (PPV) of 0.93 for cases and negative predictive value (NPV) of 0.91 for controls. Implementation of algorithms yielded similar metrics in VANEOHS (PPV = 0.94; NPV = 0.86) and lower in MGB (PPV = 0.84; NPV = 0.76). In comparison, the algorithm for DR implemented in Phenome-wide association study (PheWAS) in VUMC yielded similar PPV (0.92) but substantially reduced NPV (0.48). Implementation of the algorithms to the Million Veteran Program identified over 62 000 DR cases with genetic data including 14 549 African Americans and 6209 Hispanics with DR.

Conclusions/Discussion
We demonstrate the robustness of the algorithms at 3 separate healthcare centers, with a minimum PPV of 0.84 and substantially improved NPV than existing automated methods. We strongly encourage independent validation and incorporation of features unique to each EHR to enhance algorithm performance for DR cases and controls.
Rousseau, American Laicite, and the Future of Religious Liberty in America
Authors: Gibson M Troy 
Published: August 2024

Abstract
There is a growing cultural tension between religious orthodoxy and the prevailing form of progressivism which centers the modern self in such a way that would please the eighteenth-century Romantic Jean-Jacques Rousseau. But Rousseau’s priority of the self led him to embrace a particular view of church and state as well as religious liberty, which, if implemented, would be a new experiment in the American context. What are the implications of this ascendant version of progressivism for religious liberty as it has been understood in the American context, vacillating as it has in the past between strict separation or accommodation? What would the emerging progressivism do with religious liberty given its philosophical commitments to a this-worldly immanent frame and rise of the psychologized self (expressive individualism)? I argue that religious liberty, in its robust paradigmatic American form, cannot survive any of these outcomes without undergoing radical redefinition, and instead a new paradigm of religious liberty, which I call American Laïcité, must replace the older version. With American Laïcité, as Rousseau would have it, though religion is a rather fixed aspect of human nature, only religion that sacralizes the immanent, one centered on self-expression and never practices or teaches any form of exclusivism or inequality can expect to be either accommodated or tolerated within society.
Relative contribution of biotic and abiotic factors to population fluctuations of Auchenorrhyncha community that could play a role in the Cape Saint Paul Wilt Disease (CSPWD) (lethal yellowing) pathosystem in Ghana
Authors: Tettey Elizabeth , Aidoo Owusu F , Ativor Isaac N , Yankey Egya N 
Published: August 2024

Abstract
As a major setback to the global coconut industry, lethal yellowing disease (LYD), caused by phytoplasmas, continues to threaten coconut palms in the Americas, the Caribbean, Africa, and Oceania. Despite its economic impacts, limited information exists on LYD vectors, which impedes the prevention and management of the disease. Using double-sided yellow sticky traps, we investigate the factors that influence the seasonal abundance and population dynamics of three sap-sucking insects of LYD, i.e., Diostrombus (Hemiptera: Derbidae) sp. and Patara sp. (Hemiptera: Derbidae), and Nedoptepa curta Dmitriev (Hemiptera: Cicadellidae), on five coconut genotypes (Sri Lanka Green Dwarf (SGD), Vanuatu Tall (VTT), SGD × VTT, Malayan Yellow Dwarf (MYD) × VTT, and West African Tall (WAT)) in the Western Region, and one (SGD) in the Central Region of Ghana from April 2019 to May 2021. The results showed that N. curta and Patara sp. were the most abundant species in the Western and Central Regions, respectively. There was a significant difference between the coconut cultivars and sap-sucking insects. The peak population development of the sap-sucking insects was recorded during the dry season on all the coconut genotypes at all sampling locations. A significant positive correlation was detected between temperature and the population of N. curta and Patara sp. In the Agona Nkwanta, VTT had the highest population of N. curta, whereas WAT had the highest population of Patara sp. and Diostrombus sp. These findings provide useful information for assessing the role of factors that could affect the Cape Saint Paul Wilt disease pathosystem.
High-cost treatments for advanced lung cancer in Japan (Lung Cancer Study Group of the Japan Clinical Oncology Group)
Authors: Watanabe Kageaki , Sasaki Keita , Machida Ryunosuke , Shimizu Junichi , Yamane Yuki , Tamiya Motohiro , Saito Shin , Takada Yuji , Yoh Kiyotaka , Yoshioka Hiroshige , Murakami Haruyasu , Kitazono Satoru , Goto Yasuhiro , Horinouchi Hidehito , Ohe Yuichiro 
Published: August 2024

Abstract

Background
The treatment of lung cancer has made dramatic progress in the past decade, but due to the high cost of drugs, the total pharmaceutical cost has been rising explosively. There are currently no data available in Japan on which regimens are used, to what extent they are used, and what their total cost is.

Methods
Sixty Japanese centers belonging to the Lung Cancer Study Group of the Japan Clinical Oncology Group were surveyed for information about the first-line treatment for advanced lung cancer in practice from July 2021 to June 2022. Three types of cancer were included: driver gene mutation-negative NSCLC, EGFR mutation-positive NSCLC, and extensive-stage small cell lung cancer (ES-SCLC).

Results
Recent treatment costs for ICIs or ICI plus chemotherapy were about 20–55 times higher than those for conventional chemotherapy. Of the 3738 patients with driver gene aberration-negative NSCLC, 2573 (68.8%) received treatments with monthly cost of 500 000 Japanese yen (JPY) or more; 2555 (68.4%) received ICI therapy. Of the 1486 patients with EGFR mutation-positive NSCLC, 1290 (86.8%) received treatments with a monthly cost of 500 000 JPY or more; 1207 (81.2%) received osimertinib. ICI treatments with a monthly cost of 500 000 JPY or more were administered to 607 (56.3%) of 1079 patients with ES-SCLC. Elderly NSCLC patients received slightly more high-cost treatment than younger patients.

Conclusion
Recent treatments cost many times more than conventional chemotherapy. This study revealed that high-cost treatments were widely used in advanced lung cancer and some of high-cost treatments were used despite the lack of clear evidence. Physicians should pay attention to the cost of treatments they use.
A Bayesian spatial–temporal varying coefficients model for estimating excess deaths associated with respiratory infections
Authors: Zhang Yuzi , Chang Howard H , Iuliano Angela D , Reed Carrie 
Published: August 2024

Abstract
Disease surveillance data are used for monitoring and understanding disease burden, which provides valuable information in allocating health programme resources. Statistical methods play an important role in estimating disease burden since disease surveillance systems are prone to undercounting. This paper is motivated by the challenge of estimating mortality associated with respiratory infections (e.g. influenza and COVID-19) that are not ascertained from death certificates. We propose a Bayesian spatial–temporal model incorporating measures of infection activity to estimate excess deaths. Particularly, the inclusion of time-varying coefficients allows us to better characterize associations between infection activity and mortality counts time series. Software to implement this method is available in the R package NBRegAD. Applying our modelling framework to weekly state-wide COVID-19 data in the US from 8 March 2020 to 3 July 2022, we identified temporal and spatial differences in excess deaths between different age groups. We estimated the total number of COVID-19 deaths in the US to be 1,168,481 (95% CI: 1,148,953 1,187,187) compared to the 1,022,147 from using only death certificate information. The analysis also suggests that the most severe undercounting was in the 18–49 years age group with an estimated underascertainment rate of 0.21 (95% CI: 0.16, 0.25).
Health disparities among incarcerated populations: a crucial laboratory and pathology review
Authors: Price Banks Diane , McGuire Morgane , Samedi Von , Whitehead Stephanie , Upton Melissa P , Jackson Nicole R 
Published: August 2024

Abstract

Background
The United States notoriously has one of the highest rates of incarceration in the world, yet scant attention to the health care needs of those incarcerated exists within laboratory medicine and pathology training and education. This article explores health disparities among incarcerated and released individuals regarding diagnostic laboratory testing and pathology services.

Methods
A literature search was conducted for articles published between 2002 and 2023 using keywords including “healthcare,” “incarcerated,” “laboratory services,” “pathology services,” and “health insurance for prisoners.” Central themes were extracted and discussed to reveal the realities of health care during and after release from incarceration. Excluded from the analysis were articles about the immediate or extended family of incarcerated persons.

Results
Incarcerated individuals have an increased risk for the development and exacerbation of communicable and noncommunicable diseases and mental health disorders, which results in exceedingly high morbidity and mortality rates.

Conclusion
Policy changes are needed to mitigate disparities and improve health outcomes for incarcerated and released persons. Central to these disparities is decreased access to laboratory and pathology services, impeded by inadequate health care funding for these carceral institutions. Providing additional funding to the carceral system’s health care budget is necessary to improve access to pathology and laboratory services.
Introduction
Authors: Risvas Michail 
Published: August 2024

Abstract
This introductory chapter provides an overview of the importance and complexity of non-discrimination clauses in international economic law. It starts with the Permanent Court of International Justice (PCIJ) handling cases involved with discrimination. Discrimination cases are difficult cases, partly because legal clauses prohibiting discrimination are conceptually linked with the idea of equality. The chapter explains that certain aspects of the principle of non-discrimination in international economic law may reflect obligations under customary law or form part of international public policy. It then looks into the argument that non-discrimination obligations in investment treaty arbitration fall within the ‘disparate treatment’ discrimination paradigm.
Conclusions
Authors: Risvas Michail 
Published: August 2024

Abstract
This chapter covers the importance of the work on non-discrimination in international investment treaty arbitration. It explains that case law of investment treaty arbitral tribunals on non-discrimination obligations contained in investment treaties demonstrated that there is no jurisprudence constante about key legal questions. Moreover, non-discrimination obligations in international investment treaty arbitration fall within the ‘disparate treatment’ paradigm. Thus, disparate treatment and disparate impact are considered as main paradigms of discrimination demonstrated by non-discrimination legislation and case law in the US, EU, and international human rights law. The chapter looks into a comprehensive and systematic analytical and normative framework of the most complex areas of international investment law.
Generalization of filter theory of EQ-algebras based on lattices
Authors: Nazifi Mohadese , Asghari Larimi Mohsen , Bakhshi Mahmood 
Published: August 2024

Abstract
In this article, considering the notion of a lattice-valued set (${\mathcal{L}}$-set, for short) we introduce the notions of ${\mathcal{L}}$-prefilter and ${\mathcal{L}}$-filter in EQ-algebras. We provide several characterizations and equivalent conditions for these concepts and also characterize the ${\mathcal{L}}$-prefilter and ${\mathcal{L}}$-filter generated by an ${\mathcal{L}}$-set. Subsequently, we study the lattice structure of these filters and prove that in an $\ell $EQ-algebra, the lattice of ${\mathcal{L}}$-prefilters is a complete Brouwerian lattice, and hence it forms a Heyting lattice. In a residuated $\ell $EQ-algebra, we show that the lattice of ${\mathcal{L}}$-filters is also a Heyting lattice. They also form a semi-De Morgan algebra. Moreover, we demonstrate that the skeleton of an $\ell $EQ-algebra under appropriate operations forms a Boolean algebra. Furthermore, we introduce (relative) ${\mathcal{L}}$-congruences in EQ-algebras and investigate their properties. We also explore the relationships between ${\mathcal{L}}$-prefilters/${\mathcal{L}}$-filters and ${\mathcal{L}}$-congruences. We prove that ${\mathcal{L}}$-prefilters induce a relative ${\mathcal{L}}$-equivalence relation and ${\mathcal{L}}$-filters correspond to relative ${\mathcal{L}}$-congruences, and state and prove some isomorphism theorems.
Altered interactions between cis-regulatory elements partially resolve BLADE-ON-PETIOLE genetic redundancy in Capsella rubella
Authors: Tran Thi Chi , Mähl Karoline , Kappel Christian , Dakhiya Yuri , Sampathkumar Arun , Sicard Adrien , Lenhard Michael 
Published: August 2024

Abstract
Duplicated genes are thought to follow one of three evolutionary trajectories that resolve their redundancy: neofunctionalization, subfunctionalization, or pseudogenization. Differences in expression patterns have been documented for many duplicated gene pairs and interpreted as evidence of subfunctionalization and a loss of redundancy. However, little is known about the functional impact of such differences and about their molecular basis. Here, we investigate the genetic and molecular basis for the partial loss of redundancy between the two BLADE-ON-PETIOLE genes BOP1 and BOP2 in red shepherd's purse (Capsella rubella) compared to Arabidopsis (Arabidopsis thaliana). While both genes remain almost fully redundant in A. thaliana, BOP1 in C. rubella can no longer ensure wild-type floral organ numbers and suppress bract formation, due to an altered expression pattern in the region of the cryptic bract primordium. We use two complementary approaches, transgenic rescue of A. thaliana atbop1 atbop2 double mutants and deletions in the endogenous AtBOP1 promoter, to demonstrate that several BOP1 promoter regions containing conserved noncoding sequences interact in a nonadditive manner to control BOP1 expression in the bract primordium and that changes in these interactions underlie the evolutionary divergence between C. rubella and A. thaliana BOP1 expression and activity. Similarly, altered interactions between cis-regulatory regions underlie the divergence in functional promoter architecture related to the control of floral organ abscission by BOP1. These findings highlight the complexity of promoter architecture in plants and suggest that changes in the interactions between cis-regulatory elements are key drivers for evolutionary divergence in gene expression and the loss of redundancy.
Upregulation of PECTATE LYASE5 by a NAC transcription factor promotes fruit softening in apple
Authors: Su Qiufang , Yang Huijuan , Li Xianglu , Zhong Yuanwen , Feng Yifeng , Li Hongfei , Tahir Muhammad Mobeen , Zhao Zhengyang 
Published: August 2024

Abstract
Flesh firmness is a critical breeding trait that determines consumer selection, shelf life, and transportation. The genetic basis controlling firmness in apple (Malus × domestica Borkh.) remains to be fully elucidated. We aimed to decipher genetic variance for firmness at harvest and develop potential molecular markers for marker-assisted breeding. Maturity firmness for 439 F1 hybrids from a cross of “Cripps Pink” and “Fuji” was determined in 2016 and 2017. The phenotype segregated extensively, with a Gaussian distribution. In a combined bulked segregant analysis (BSA) and RNA-sequencing analysis, 84 differentially expressed genes were screened from the 10 quantitative trait loci regions. Interestingly, next-generation re-sequencing analysis revealed a Harbinger-like transposon element insertion upstream of the candidate gene PECTATE LYASE5 (MdPL5); the genotype was associated with flesh firmness at harvest. The presence of this transposon repressed MdPL5 expression and was closely linked to the extra-hard phenotype. MdPL5 was demonstrated to promote softening in apples and tomatoes. Subsequently, using the MdPL5 promoter as bait, MdNAC1-L was identified as a transcription activator that positively regulates ripening and softening in the developing fruit. We also demonstrated that MdNAC1-L could induce the up-regulation of MdPL5, MdPG1, and the ethylene-related genes MdACS1 and MdACO1. Our findings provide insight into TE-related genetic variation and the PL-mediated regulatory network for the firmness of apple fruit.