bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysing the informal economy: Data challenges, research design, and research transparency
Authors: Ackrill Rob , Igudia Eghosa 
Published: November 2023

AbstractAnalyses of the informal economy are vital to understanding economic activity in developing countries, but challenges abound when analysing something that is so difficult to measure. In this article, we explore these challenges and what they mean for research and research design in studies of the informal economy. We review key economic theories developed to study the informal economy, before critically discussing the range of methods of data collection available for researchers. All approaches to data collection have limitations, yet many studies fail to reflect adequately on these in their design and presentation. In reviewing data sources for economic analyses of informality, we give particular attention to surveys designed and led by academic researchers, the consideration of which is omitted from leading official organisations' own reports on data collection in the informal economy. In the absence of a unifying theory and data sources that deliver the ‘comprehensive and accurate’ data called for by some authors we argue, first, that no one source of data is intrinsically superior; and second, that research on the informal economy must embrace transparency—around the data used, their alignment with the underlying theory adopted, and the detailed arrangements for data collection and analysis.
Systemic corticosteroids for outpatient respiratory viral infections in lung transplant recipients
Authors: Ghandi Vardhil , Li David , Weinkauf Justin , Lien Dale , Hirji Alim , Varughese Rhea , Weatherald Jason , Sligl Wendy , Kabbani Dima , Schwartz Ilan , Doucette Karen , Cervera Carlos , Halloran Kieran 
Published: November 2023

AbstractIntroductionRespiratory viral infections (RVI) in lung transplant recipients (LTR) have variably been associated with rejection and chronic lung allograft dysfunction. Our center has used systemic corticosteroids to treat outpatient RVI in some cases, but evidence is limited. We reviewed all adult LTR diagnosed with outpatient RVI January 2017 to December 2019. The primary outcome was recovery of lung function (forced expiratory volume in 1 s [FEV1]) at next stable visit between 1 and 12 months postinfection, expressed as a ratio over stable preinfection FEV1 (FEV1 recovery ratio).MethodsWe identified 100 adult LTR with outpatient RVI diagnoses eligible for study, 36% of whom received corticosteroids. We modelled the adjusted association between corticosteroid use and FEV1 recovery ratio using linear regression.ResultsSteroid‐treated patients had a lower FEV1 presentation ratio (0.92 vs. 1.04, p = .0070) and were more likely to have chronic lung allograft dysfunction at time of infection (25% vs. 5%, p = .0077). Mean FEV1 recovery ratio was 1.02 (SD 0.19) with no association with corticosteroid therapy via multivariable linear regression (p = .5888).ConclusionsSteroid treatment was not associated with FEV1 recovery. This suggests corticosteroids may not have a role in the management of RVI in this population.
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A gene network-driven approach to infer novel pathogenicity-associated genes: application to
Pseudomonas aeruginosa
PAO1
Authors: De Ronika , Whiteley Marvin , Azad Rajeev K. 
Published: November 2023

ABSTRACT

Hard-wired within the genome of a pathogen is the information regarding factors responsible for its pathogenicity. Advances in functional genomics, particularly gene expression analysis, have made possible genome-wide interrogation of a pathogen to decipher pathogenicity-associated genes. Standard protocols assess differential expression of genes during pathogenesis; however, often a conservative approach is taken, which requires expression fold change above an arbitrarily defined threshold and a statistical significance test to infer a gene as differentially expressing. This renders a high-confidence set of differentially expressed genes in pathogenesis, however, at the cost of numerous false negatives. To circumvent this problem and comprehensively catalog pathogenicity-associated genes, we have developed a novel pipeline that uses standard protocol in combination with gene co-expression network of a pathogen constructed using publicly available RNA-Seq data sets. We assessed the efficacy of this pipeline on
Pseudomonas aeruginosa
PAO1, a model bacterial pathogen, highlighting the power of our network-based approach in discovering novel genes or pathways associated with the pathogenesis, or antibiotic resistance of this strain. Complementing standard protocol with a gene network-based method thus elevated the ability to identify pathogenicity-associated genes in
P
.
aeruginosa
PAO1.

IMPORTANCE

We present here a new systems-level approach to decipher genetic factors and biological pathways associated with virulence and/or antibiotic treatment of bacterial pathogens. The power of this approach was demonstrated by application to a well-studied pathogen
Pseudomonas aeruginosa
PAO1. Our gene co-expression network-based approach unraveled known and unknown genes and their networks associated with pathogenicity in
P. aeruginosa
PAO1. The systems-level investigation of
P. aeruginosa
PAO1 helped identify putative pathogenicity and resistance-associated genetic factors that could not otherwise be detected by conventional approaches of differential gene expression analysis. The network-based analysis uncovered modules that harbor genes not previously reported by several original studies on
P. aeruginosa
virulence and resistance. These could potentially act as molecular determinants of
P. aeruginosa
PAO1 pathogenicity and responses to antibiotics.
Putative novel hydrogen- and iron-oxidizing sheath-producing Zetaproteobacteria thrive at the Fåvne deep-sea hydrothermal vent field
Authors: Hribovšek Petra , Olesin Denny Emily , Dahle Håkon , Mall Achim , Øfstegaard Viflot Thomas , Boonnawa Chanakan , Reeves Eoghan P. , Steen Ida Helene , Stokke Runar 
Published: November 2023

ABSTRACT

Iron-oxidizing Zetaproteobacteria are well known to colonize deep-sea hydrothermal vent fields around the world where iron-rich fluids are discharged into oxic seawater. How inter-field and intra-field differences in geochemistry influence the diversity of Zetaproteobacteria, however, remains largely unknown. Here, we characterize Zetaproteobacteria phylogenomic diversity, metabolic potential, and morphologies of the iron oxides they form, with a focus on the recently discovered Fåvne vent field. Located along the Mohns ridge in the Arctic, this vent field is a unique study site with vent fluids containing both iron and hydrogen with thick iron microbial mats (Fe mats) covering porously venting high-temperature (227–267°C) black smoker chimneys. Through genome-resolved metagenomics, we demonstrate that Zetaproteobacteria,
Ghiorsea
spp., likely produce tubular iron oxide sheaths dominating the Fe mats at Fåvne, as observed via microscopy. With these structures,
Ghiorsea
may provide a surface area for members of other abundant taxa such as Campylobacterota, Gammaproteobacteria, and Alphaproteobacteria. Furthermore,
Ghiorsea
likely oxidizes both iron and hydrogen present in the fluids, with several
Ghiorsea
populations co-existing in the same niche. Homologs of Zetaproteobacteria Ni,Fe hydrogenases and iron oxidation gene
cyc2
were found in genomes of other community members, suggesting exchange of these genes could have happened in similar environments. Our study provides new insights into Zetaproteobacteria in hydrothermal vents, their diversity, energy metabolism and niche formation.

IMPORTANCE

Knowledge on microbial iron oxidation is important for understanding the cycling of iron, carbon, nitrogen, nutrients, and metals. The current study yields important insights into the niche sharing, diversification, and Fe(III) oxyhydroxide morphology of
Ghiorsea
, an iron- and hydrogen-oxidizing Zetaproteobacteria representative belonging to Zetaproteobacteria operational taxonomic unit 9. The study proposes that
Ghiorsea
exhibits a more extensive morphology of Fe(III) oxyhydroxide than previously observed. Overall, the results increase our knowledge on potential drivers of Zetaproteobacteria diversity in iron microbial mats and can eventually be used to develop strategies for the cultivation of sheath-forming Zetaproteobacteria.
A follow-up study: 6-year cART-free virologic control of rhesus macaques after PD-1-based DNA vaccination against pathogenic SHIV
SF162P3CN
challenge
Authors: He Xiaoen , Wong Yik Chun , Zhong Menglong , Mo Yufei , Li Bo , Yim Lok Yan , Li Xin , Liu Wan , Du Yanhua , Wang Hui , Zhang Haoji , Chen Zhiwei 
Published: November 2023

ABSTRACT

An effective vaccine for combination antiretroviral therapy (cART)-free virologic control of HIV-1 by enhancing antigen-specific effector-memory CD8
+
T lymphocytes could be useful in controlling the AIDS pandemic. Previously, we demonstrated that a programmed death-1 (PD-1)-based DNA vaccine, pRhPD1-p27, was effective in inducing Gag-p27-specific effector-memory CD8
+
T cells for viremia suppression in rhesus macaques infected with pathogenic SHIV
SF162P3CN
for 2 years. In this follow-up study, we report on two pRhPD1-p27-vaccinated and SHIV
SF162P3CN
-infected macaques that have remained alive to date with undetectable viremia levels and low proviral loads over 6 years in the absence of cART, achieving a state of sustained virologic control. Polyfunctional effector-memory Gag-p27-specific T cells were maintained in these macaques. Moreover, several T cell epitopes found at 6 years post-viral challenge were identical to those induced during the vaccination phase, indicating sustained vaccine-induced memory T cell responses. The viral challenge resulted in
de novo
Nef-specific T cell responses, which were also maintained. These Gag-p27- and Nef-specific T cell responses were stronger than those in some SHIV
SF162P3CN
-infected macaques that showed viremia control after experimental therapy using a tandem bispecific neutralizing antibody. Our findings indicate that the PD-1-based DNA vaccine strategy holds promise as a clinical immunotherapy for long-term HIV-1 suppression.

IMPORTANCE

Efficient strategies for HIV-1 cART-free virologic control are critical for ending the AIDS pandemic. The essential role of effector-memory CD8
+
T cells in controlling viremia and eliminating virus-infected cells has made them a promising target for vaccine development. It has been previously reported that PD-1-based DNA vaccination was effective in inducing polyfunctional effector-memory CD8
+
T cells for AIDS virus control for 2 years in rhesus monkeys. This follow-up study extends the findings and shows that a viremia-free period of over 6 years was detected in two monkeys immunized with PD-1-based DNA vaccine against pathogenic SHIV
SF162P3CN
infection in the absence of antiretroviral therapy. Long-term vaccine-induced memory T cell responses were detected. Our results warrant the clinical trials of PD-1-based DNA vaccines for achieving HIV-1 cART-free virologic control used either alone or in combination with other biomedical interventions.
United States regulatory approval of medical devices used for endovascular neurosurgery: A two-decade review of FDA regulatory files
Authors: Bhenderu Lokeshwar S , Hardigan Trevor , Roa Jorge , Philbrick Brandon D , Hoang Alex , Faraji Amir H , Britz Gavin W , Yaeger Kurt A 
Published: November 2023

Background
The evolution of neuroendovascular technologies has progressed substantially. Over the last two decades, the introduction of new endovascular devices has facilitated treatment for more patients, and as a result, the regulatory environment concerning neuroendovascular devices has evolved rapidly in response.

Objective
To examine trends in the approval of neuroendovascular devices by the United States Food and Drug Administration (FDA) over the last 20 years.

Methods
Open-access US FDA databases were queried between January 2000 and December 2022 for all devices approved by the Neurological Devices Advisory Committee. Neuroendovascular devices were manually classified and grouped by category. Device approval data, including approval times, approval pathway, and presence of predicate devices, were examined.

Results
A total of 3186 neurological devices were approved via various US FDA pathways during the study period. 320 (10.0%) corresponded to neuroendovascular devices, of which 301 (94.1%) were approved via the 510(k) pathway. The percentage of 510(k) pathway neuroendovascular devices increased from 6.9% to 14.3% of all neuro devices before and after 2015, respectively. There was an increase in approval times for neuroendovascular devices cleared after 2015.

Conclusion
Over the last two decades, the neuroendovascular device armamentarium has rapidly expanded, especially after positive stroke trials in 2015. Regulatory approval times are significantly affected by device category, generation, company size, and company location, and a vast majority are approved by the 510(k) pathway. These results can guide further innovation in the endovascular device space and may act as a roadmap for future regulatory planning.
Impact of NNLO QED corrections on lepton-proton scattering at MUSE
Authors: Engel T. , Hagelstein F. , Rocco M. , Sharkovska V. , Signer A. , Ulrich Y. 
Published: November 2023

AbstractWe present the complete next-to-next-to-leading order (NNLO) pure pointlike QED corrections to lepton-proton scattering, including three-photon-exchange contributions, and investigate their impact in the case of the MUSE experiment. These corrections are computed with no approximation regarding the energy of the emitted photons and taking into account lepton-mass effects. We contrast the NNLO QED corrections to known next-to-leading order corrections, where we include the elastic two-photon exchange (TPE) through a simple hadronic model calculation with a dipole ansatz for the proton electromagnetic form factors. We show that, in the low-momentum-transfer region accessed by the MUSE experiment, the improvement due to more sophisticated treatments of the TPE, including inelastic TPE, is of similar if not smaller size than some of the NNLO QED corrections. Hence, the latter have to be included in a precision determination of the low-energy proton structure from scattering data, in particular for electron-proton scattering. For muon-proton scattering, the NNLO QED corrections are considerably smaller.
The effects of thermal radiation and heat source/sink on the flow and heat transfer characteristics of a hybrid nanofluid over a vertical stretching cylinder: Regression analysis
Authors: Shaheen Abida , Waqas Hassan , Imran Muhammad , Raza Mohsan , Rashid Saima 
Published: November 2023

Originality: A novel category of working fluids, consisting of two substantial components diffused in a conventional fluid, has been identified and investigated widely in recent years. These types of fluids are called hybrid nanofluids. Problem statement: A wide range of engineering and industrial structures, including heat-transferring components, energy production, extrusion procedures, engine cooling purposes, thermal structures, thermal exchangers, chemical procedures, manufacturing processes and hybrid power plants, have been proposed for use with nanomaterials with improved thermal properties. These nanomaterial-based applications hold the promise of improved performance and efficiency in a variety of technological and industrial processes. The heat transmission and magnetohydrodynamic stagnation significance flow of hybrid nanofluids Fe3O4–ZrO2 and Fe3O4/water, the form factor of a stretched cylinder under the influence of heat production, nonlinear thermal radiation and nanoparticle volume fractions have been investigated in this study. Methodology: Utilizing proper similarity transformations, the processes of partial differential equations are further transformed into nondimensional solutions of ordinary differential equations. The bvp4c approach is employed to achieve a numerical solution. The flow and temperature profiles are displayed as a function of the contained factors. Graphs show the effects of changing the physical characteristics involved. Tables emphasize the skin friction factor and Nusselt numbers. Results: The temperature profile of fluids diminished due to an increment in the values of the temperature relaxation parameter and Eckert number. When the porosity factor is increased the temperature of fluids is improved. The effects of streamlines for various components are discussed. The 3D surface, contour plots and residual plots for various factors have also been investigated. Applications: Hybrid nanofluids have the potential to improve heat transfer efficiency in a variety of technical applications, including cooling structures, heat exchangers and thermal energy storage systems.
Combined Vorinostat and Chloroquine Inhibit Sodium–Iodide Symporter Endocytosis and Enhance Radionuclide Uptake In Vivo
Authors: Read Martin L. , Brookes Katie , Zha Ling , Manivannan Selvambigai , Kim Jana , Kocbiyik Merve , Fletcher Alice , Gorvin Caroline M. , Firth George , Fruhwirth Gilbert O. , Nicola Juan P. , Jhiang Sissy , Ringel Matthew D. , Campbell Moray J. , Sunassee Kavitha , Blower Philip J. , Boelaert Kristien , Nieto Hannah R. , Smith Vicki E. , McCabe Christopher J. 
Published: November 2023

Abstract

Purpose:
Patients with aggressive thyroid cancer are frequently failed by the central therapy of ablative radioiodide (RAI) uptake, due to reduced plasma membrane (PM) localization of the sodium/iodide symporter (NIS). We aimed to understand how NIS is endocytosed away from the PM of human thyroid cancer cells, and whether this was druggable in vivo.

Experimental Design:
Informed by analysis of endocytic gene expression in patients with aggressive thyroid cancer, we used mutagenesis, NanoBiT interaction assays, cell surface biotinylation assays, RAI uptake, and NanoBRET to understand the mechanisms of NIS endocytosis in transformed cell lines and patient-derived human primary thyroid cells. Systemic drug responses were monitored via 99mTc pertechnetate gamma counting and gene expression in BALB/c mice.

Results:
We identified an acidic dipeptide within the NIS C-terminus that mediates binding to the σ2 subunit of the Adaptor Protein 2 (AP2) heterotetramer. We discovered that the FDA-approved drug chloroquine (CQ) modulates NIS accumulation at the PM in a functional manner that is AP2 dependent. In vivo, CQ treatment of BALB/c mice significantly enhanced thyroidal uptake of 99mTc pertechnetate in combination with the histone deacetylase (HDAC) inhibitor vorinostat/SAHA, accompanied by increased thyroidal NIS mRNA. Bioinformatic analyses validated the clinical relevance of AP2 genes with disease-free survival in RAI-treated DTC, enabling construction of an AP2 gene–related risk score classifier for predicting recurrence.

Conclusions:
NIS internalization is specifically druggable in vivo. Our data, therefore, provide new translatable potential for improving RAI therapy using FDA-approved drugs in patients with aggressive thyroid cancer.
See related commentary by Lechner and Brent, p. 1220
The Academic and Behavioral Impacts of an Autism Health Insurance Mandate: Evidence from Massachusetts
Authors: Coffey Stephanie 
Published: November 2023

Abstract
Today, all 50 states have enacted mandates requiring some level of insurance coverage for the treatment of autism spectrum disorders (ASD). In this paper, I examine the impact of Massachusetts’ mandate, ARICA (An Act Relative to Insurance Coverage for Autism) on the academic and behavioral outcomes of students with ASD in the state. Using administrative data on Massachusetts public school students, I use a triple difference strategy to estimate impacts on special education setting, attendance, suspensions, and achievement. I find that ARICA increased inclusion for students with ASD; they were 4 percentage points more likely to be fully included after the reform. Further, days suspended decreased by about 26 percent, and the likelihood of receiving a suspension decreased by about 2 percentage points. I find that improvements in student outcomes were larger for students in grades 6–8 (versus elementary students). While I find no statistically significant improvement in test scores for students with ASD overall, math (English language arts) achievement increased by 0.09 (0.13) standard deviation for students in middle grades.
Comparative Analysis of Mortality and Amputation Rates in Patients Undergoing Atherectomy for Infra-Popliteal Peripheral Arterial Disease: Insight From the VQI
Authors: Jamil Yasser , Nanna Michael G. , Chaar Cassius Iyad Ochoa , Mena-Hurtado Carlos , Attaran Robert Ramak 
Published: November 2023

Introduction: Infra-popliteal peripheral arterial disease (IPPAD) poses challenges due to high restenosis and occlusion rates. The BASIL-2 trial demonstrated the superiority of endovascular treatment compared with surgical bypass in patients with IPPAD. However, the association between different endovascular modalities and clinical outcomes has not been conclusive. Hypothesis: Combining plain old balloon angioplasty (POBA) with atherectomy is associated with improved clinical outcomes compared with POBA alone. Methods: Patients who underwent POBA vs POBA+atherectomy for IPPAD from the Vascular Quality Initiative database were identified. To mitigate potential selection bias, we employed propensity score matching (PSM) to balance the distribution of confounding variables for mortality identified on multivariable logistic regression. Subsequently, we compared patient characteristics and long-term outcomes between the 2 treatment groups. Results: Among patients who underwent endovascular intervention for IPPAD, 19 979 individuals (80.8%) were treated with POBA alone, while 4747 (19.2%) were treated with both POBA+atherectomy after PSM. Propensity score matching ensured minimal differences in baseline characteristics, such as indication for lower extremity revascularization (LER) and history of LER. After PSM, patients receiving POBA+atherectomy experienced higher rates of technical success and lower perioperative complications, such as renal complications and hematoma, compared with POBA alone. During long-term follow-up, patients who underwent atherectomy had lower rates of major amputation and major adverse limb events (MALE) but slightly lower freedom from reintervention. Nonetheless, there were no differences in mortality. Conclusion: Combining POBA with atherectomy appears to be a safe approach in patients with IPPAD, with lower rates of long-term amputation and MALE at the cost of a higher risk of reintervention. Clinical Impact The use of adjunctive atherectomy is associated with improved long-term outcomes in patients with infra-popliteal disease.