bluuebunny/crossref_metadata_2025_split huggingface dataset:
Incidence of Invasive Fungal Infections in Patients Initiating Ibrutinib and Other Small Molecule Kinase Inhibitors—United States, July 2016–June 2019
Authors: Gold Jeremy A W , Tolu Seda S , Chiller Tom , Benedict Kaitlin , Jackson Brendan R 
Published: December 2021

Abstract
We analyzed administrative data to determine the 1-year incidence of invasive fungal infections (IFIs) in patients beginning small molecule kinase inhibitor (SMKI) therapy. The incidence of IFIs by small molecule kinase inhibitor ranged from 0.0% to 10.6%, with patients taking midostaurin having the highest incidence. An IFI developed in 38 of 1286 patients taking ibrutinib (3.0%).
Selective Targeting of Tumour Necrosis Factor Receptor 1 Induces Stable Protection from Crohn’s-Like Ileitis in TNFΔARE Mice
Authors: Chakraborty Rajrupa , Maltz Mia R , Del Castillo Diana , Tandel Purvi N , Messih Nathalie , Anguiano Martha , Lo David D 
Published: December 2021

Abstract

Background and Aims
Crohn’s disease is a debilitating chronic inflammatory disorder of the mammalian gastrointestinal tract. Current interventions using anti-tumour necrosis factor [anti-TNF] biologics show long-term benefit in only half of patients. This study focused on the role of the TNF receptor 1 [TNFR1] in pathogenesis in a TNF-driven model of ileitis.

Methods
We studied TNFΔAU-rich element [ARE]/+ [TNFdARE] mice, which develop progressive ileitis similar to Crohn’s ileitis. Histopathological analysis and gene expression profiling were used to characterize disease progression from 5 to 16 weeks. Mice with TNFR1 hemizygosity [TNFdARE/R1het] allowed us to assess gene dosage effects. Transcriptional profiling established inflection points in disease progression; inflammatory gene expression increased at 8 weeks with a plateau by 10 weeks, so these were selected as endpoints of treatment using the TNF biologic infliximab and the TNFR1-specific XPro1595. Differences in recruitment of cells in the lamina propria were assessed using flow cytometry.

Results
TNFdARE/R1het mice displayed stable long-term protection from disease, associated with decreased recruitment of CD11bhiF4/80lo monocytes and CD11bhiLy6Ghi neutrophils, suggesting an important role of TNFR1 signalling in pathogenesis, and indicating potential benefit from TNFR1-specific intervention. Treatment with infliximab and XPro1595 both showed a similar impact on disease in TNFdARE mice. Importantly, these beneficial effects were greatly surpassed by hemizygosity at the TNFR1 locus.

Conclusions
Treatment with either infliximab or XPro1595 produced moderate protection from ileitis in TNFdARE mice. However, hemizygosity at the TNFR1 locus in TNFdARE mice showed far better protection, implicating TNFR1 signalling as a key mediator of TNF-driven disease.
Long-term outcomes in a randomized controlled trial of multimodality imaging-guided left ventricular lead placement in cardiac resynchronization therapy
Authors: Fyenbo Daniel Benjamin , Sommer Anders , Nørgaard Bjarne Linde , Kronborg Mads Brix , Kristensen Jens , Gerdes Christian , Jensen Henrik Kjærulf , Jensen Jesper Møller , Nielsen Jens Cosedis 
Published: December 2021

Abstract

Aims
This study aims to investigate the long-term occurrence of the composite endpoint of heart failure (HF) hospitalization or all-cause death (primary endpoint) in patients randomized to cardiac resynchronization therapy (CRT) using individualized multimodality imaging-guided left ventricular (LV) lead placement compared with a routine fluoroscopic approach. Furthermore, this study aims to evaluate whether inter-lead electrical delay (IED) is associated with improved response rate of this endpoint.

Methods and results
We reviewed follow-up data until November 2020 for all 182 patients included in the ImagingCRT trial for the occurrence of HF hospitalization and all-cause death. During median (inter-quartile range) time to primary endpoint/censuring of 6.7 (3.3–7.9) years, the rate of the primary endpoint was 60% (n = 53) in the imaging group compared with 52% (n = 48) in the control group [hazard ratio (HR) 1.22, 95% confidence interval (CI) 0.83–1.81, P = 0.31]. Neither the risk of HF hospitalization (HR 1.11, 95% CI 0.62–1.99, P = 0.72) nor of all-cause death differed between treatment groups (HR 1.23, 95% CI 0.82–1.85, P = 0.32). The risk of the primary endpoint was significantly reduced among those with IED ≥100 ms when compared with those with IED &lt;100 ms (HR 0.62, 95% CI 0.39–0.98, P = 0.04).

Conclusions
In this study, an individualized multimodality imaging-guided strategy targeting LV lead placement towards the latest mechanically activated non-scarred myocardial segment during CRT implantation did not reduce HF hospitalization or all-cause death when compared with routine LV lead placement during long-term follow-up. Targeting the latest electrical activation should be studied as an alternative individualized strategy for optimizing LV lead placement in CRT recipients.
Doctors and patients’ perspectives on obesity. A Q-methodology study
Authors: Shahed Qays , Baranowska Karolina , Galavazi Marije C , Cao Yang , van Nieuwenhoven Michiel A 
Published: December 2021

Abstract

Background
Obesity is associated with stigma and discrimination. Health care providers should approach these patients professionally and without stigma, since treatment of obesity requires a relationship with mutual understanding between the doctor and patient.

Objective
To explore how patients and general practitioners (GPs) perceive obesity, using Q-methodology, which allows quantitative analysis of qualitative data.

Methods
A Q-methodology study, comprising 24 patients with obesity and 24 GPs. We created 48 statements with viewpoints on obesity. All participants sorted these statements in a forced grid with a quasi-normal distribution ranking from −5 (most disagree) to +5 (most agree). Subsequently, factor analysis was performed. Six patients were interviewed to explain their viewpoints.

Results
Analysis yielded 3 dominant groups (factors) of patients: (i) They acknowledge the importance of healthy lifestyle and feel mistreated by health care. (ii) They have a decreased quality of life, but do not blame health care, and (iii) They don’t need treatment and don’t have an impaired quality of life. For the GPs, the 3 dominant factors were: (i) They have understanding for the patients and feel that health care is insufficient, (ii) They believe that obesity may be hereditary but mainly is a lifestyle problem, and (iii) They believe obesity can be treated but is very difficult.

Conclusions
Viewpoints on obesity were different, both within and between the groups. Some GPs consider obesity mainly as a lifestyle problem, rather than a chronic disease. If patients and doctors can find mutual viewpoints on obesity, both patient satisfaction and a treatment strategy will be more effective.
The H2A N-terminal tail is required to alleviate copper-induced stress in Saccharomyces cerevisiae
Authors: Singh Sakshi , Sahu Rakesh Kumar , Sugathan Anaswara , Tomar Raghuvir Singh 
Published: December 2021

ABSTRACT
Histone tail residues drive many biological processes by regulating genome-wide transcription. Functions of histone H3 and H4 tail residues in stress-responsive gene transcriptional programs have been extensively studied. The H2A tail residues have been shown to regulate DNA damage repair and oxidative stress response, but the involvement of N-terminal tail of H2A (H2ANtT) in proteostasis regulation is unknown. The unfolded protein response pathway (UPR) is an essential mechanism adopted by cells to prevent protein toxicity in response to ER stress. The disturbance in ER can occur by various factors such as heat stress, redox imbalance, exposure to xenobiotics and metals. Copper is utilized as a cofactor by cellular enzymes, but excessive copper affects ER homeostasis. We found that cells lacking 1–20 residues of H2ANtT are intolerant to copper stress, owing to the accumulation of misfolded proteins in the mutant cells. H2A 1–20 truncation also reduces the physiological UPR, and copper exposure further aggravates this effect. Furthermore, the expression of a spliced version of HAC1 mRNA in H2A∆(1–20) cells, encoding the downstream transcription factor of UPR signalling, rescues their growth under copper stress. Altogether these results provide evidence that H2ANtT reduces copper-induced ER stress by regulating UPR signalling.
The De Novo Genome Sequencing of Silver Pheasant (Lophura nycthemera)
Authors: Li Xue-Juan , Wang Xiao-Yang , Yang Chao , Lin Li-Liang , Zhao Le , Yu Xiao-Ping , Lei Fu-Min , Huang Yuan 
Published: December 2021

Abstract
Silver pheasant (Lophura nycthemera) belongs to Phasianidae, Galliformes, which exhibits high subspecific differentiation. In this study, we assembled a novel genome based on 98.42 Gb of Illumina sequencing data and 30.20 Gb of PacBio sequencing data. The size of the final assembled genome was 1.01 Gb, with a contig N50 of 6.96 Mb. Illumina paired-end reads (94.96%) were remapped to the contigs. The assemble genome shows high completeness, with a complete BUSCO score of 92.35% using the avian data set. A total of 16,747 genes were predicted from the generated assembly, and 16,486 (98.44%) of the genes were annotated. The average length of genes, exons, and introns were 19,827.53, 233.69, and 1841.19 bp, respectively. Noncoding RNAs included 208 miRNAs, 40 rRNAs, and 264 tRNAs, and a total of 189 pseudogenes were identified; 116.31 Mb (11.47%) of the genome consisted of repeat sequences, with the greatest proportion of LINEs. This assembled genome provides a valuable reference genome for further studies on the evolutionary history and conversion genetics of L. nycthemera and the phylogenomics of the Galliformes lineage.
Orthotropic anisotropy analysis and parameter estimation from 3-D vertical seismic profile data
Authors: Asgharzadeh Mehdi , Ahmadi Pouya , Bóna Andrej , Urosevic Milovan 
Published: December 2021

SUMMARY
Orthotropic velocity models are commonly considered as to have the lowest complexity (or highest symmetry) that can realistically describe the combined effect of Earth’s velocity heterogeneity in the vertical and in the horizontal (radial) directions. Velocity heterogeneity in the vertical direction is commonly caused by horizontal stratification of subsurface rock layers with different elastic properties or caused intrinsically by microlayered rocks such as shales. In the horizontal direction, azimuthal variation of the Earth’s stress field can initially lead to preferential deformation of pore space in the rocks and eventual development of aligned (vertical) fractures that are commonly regarded as the main cause for seismic azimuthal anisotropy. Building an appropriate orthotropic velocity model that can explain seismic velocity variations in vertical planes and along any azimuthal direction can therefore enhance the quality of seismic data processing and imaging. This, however, requires knowledge of several anisotropy parameters defined in the three symmetry planes of the orthotropic model and also the orientation of these planes. A combination of P- and S-wave slowness and polarization data derived from vertical seismic profile (VSP) measurements has been routinely used to estimate parameters of less complex anisotropic media such as transverse isotropy with vertical axes of symmetry (VTI). The accuracy of anisotropy parameter estimation by these methods depends primarily on the availability of data that are used in the inversion and the size of anisotropy parameters. In this study, we develop a benchmark for the accuracy of orthotropic parameters that are estimated from 3-D VSP measurements using P-wave slowness only method. Through numerical analysis, we model a wide range of fracture-induced orthotropic symmetries by adding vertical fractures to a background VTI media and show that the accuracy of our orthotropic parameter estimation method is dependent on anisotropy in the host media, intensity of fracturing, noise level in slowness data and slowness data coverage in both the dip and azimuthal planes. We then expand our accuracy analysis work to multilayer media by examining the accuracy of P-wave slowness method for orthotropic anisotropy parameter estimation by inverting finite-difference data generated in a pseudo 3-D VSP experiment. We show that, for a typical 3-D VSP experiment, reasonable estimates of orthotropic parameters in the model can only be obtained with slowness data taken from Xmax/Z ≥ 1 and line azimuth interval ϕ ≤ 10° where Xmax is the maximum source to receiver offset and Z is the receiver depth. We finally describe how field VSP measurements can be inverted for orthotropic anisotropy parameters.
Zooming in and out: a holistic framework for research on maternal, late foetal and newborn survival and health
Authors: Singh Neha S , Blanchard Andrea K , Blencowe Hannah , Koon Adam D , Boerma Ties , Sharma Sudha , Campbell Oona M R 
Published: December 2021

Abstract
Research is needed to understand why some countries succeed in greater improvements in maternal, late foetal and newborn health (MNH) and reducing mortality than others. Pathways towards these health outcomes operate at many levels, making it difficult to understand which factors contribute most to these health improvements. Conceptual frameworks provide a cognitive means of rendering order to these factors and how they interrelate to positively influence MNH. We developed a conceptual framework by integrating theories and frameworks from different disciplines to encapsulate the range of factors that explain reductions in maternal, late foetal and neonatal mortality and improvements in health. We developed our framework iteratively, combining our interdisciplinary research team’s knowledge, experience and review of the literature. We present a framework that includes health policy and system levers (or intentional actions that policy-makers can implement) to improve MNH; service delivery and coverage of interventions across the continuum of care; and epidemiological and behavioural risk factors. The framework also considers the role of context in influencing for whom and where health and non-health efforts have the most impact, to recognize ‘the causes of the causes’ at play at the individual/household, community, national and transnational levels. Our framework holistically reflects the range of interrelated factors influencing improved MNH and survival. The framework lends itself to studying how different factors work together to influence these outcomes using an array of methods. Such research should inform future efforts to improve MNH and survival in different contexts. By re-orienting research in this way, we hope to equip policy-makers and practitioners alike with the insight necessary to make the world a safer and fairer place for mothers and their babies.
Politicians’ views on societal responsibility and possibility to promote newly arrived migrants’ health in Sweden
Authors: Svanholm Sara , Carlerby Heidi , Viitasara Eija 
Published: December 2021

Summary
Newly arrived migrants in Sweden risk facing ill health. Politicians at the local and regional levels are involved in many decisions regarding the social determinants of health. The aim of this study was to explore politicians’ views on different societal actors’ responsibility and possibility to promote newly arrived migrants’ health. Data were collected through online questionnaires completed by 667 politicians from municipality and regional councils in northern Sweden. Bivariate analysis was performed using the Wilcoxon signed-rank test. Multivariate analyses were performed using cluster analysis and binary logistic regression analysis. The results show that politicians generally rate societal actors’ responsibility and possibility to promote the general population’s health higher than newly arrived migrants’ health. Moreover, they consider societal actors’ responsibility to be greater than their possibility to promote health. Factors significantly contributing to politicians’ high ratings of societal responsibility and possibility are attitude (odds ratio [OR] = 2.156, 95% confidence interval [CI]: 1.306–3.558), specific knowledge of newly arrived migrants’ health status (OR = 1.528, 95% CI: 1.005–2.323), personal interest in public health (OR = 2.452, 95% CI: 1.460–4.119), being a municipality politician (OR = 1.659, 95% CI: 1.031–2.670) and being female (OR = 1.934, 95% CI: 1.333–2.806). This study shows that politicians generally rate societal responsibility and possibility to promote newly arrived migrants’ health rather high. Personal characteristics are important for politicians’ high or low ratings of responsibility and possibility, suggesting insufficient structural support for politicians in health promotion.
Filing the world: Archives as cultural heritage and the power of remembering
Authors: Ghezzi Agnese 
Published: December 2021

Abstract
This article analyzes the relationship of archives to law and history, taking a critical look at the complex interplay between preservation, memory, and forgetting. Going beyond the idea of the archive as fixed and immovable, the article considers the archive in its dynamism, its chronological evolution, and its changing relations to both the state and the private individual. The article draws on examples from both national legislation and international bodies to highlight different problems arising from crucial dichotomies. The case of Italy shows how the significance of archives oscillates between historical and administrative; the French case underlines the clash between state secrecy and public access; and English-speaking countries bring about a discussion on the contrasts between private and public property. Cases of national as well as international bodies provide examples of archives’ relationship to memory and oblivion, as well as of global and local management. The article considers how the establishment of dedicated institutions, guidelines, and constraints shapes the process of document preservation and access, enabling or frustrating the dissemination of historical awareness, administrative transparency, and human rights recognition.
The Human Rights Approach to the Refugee Definition: Rising Sun or Falling Star?
Authors: Storey Hugo 
Published: December 2021

Abstract
Until recently, the human rights approach to the refugee definition appeared destined to become a permanent feature of international refugee law. Now, however, doubts have set in. The object of this article is to address the main criticisms that have been levelled and to seek to put them in a wider perspective, reflecting briefly on where the law on refugee status is heading now that the 1951 Refugee Convention has entered its eighth decade. To this end, this article commences with a description of the human rights approach and a brief summary of how and why it came to become the ‘dominant’ approach and its underlying justifications. It then turns to consider the major criticisms raised, breaking these down into three clusters. The first cluster seeks to argue that such an approach is not warranted by proper application of the rules of treaty interpretation enjoined by the 1969 Vienna Convention on the Law of Treaties. The second cluster identifies a number of other conceptual concerns: that such an approach depends on extraneous standards that lack refugee specificity; that it substitutes one set of indeterminate terms for another (for example, torture as one form of persecution); that it is unduly complex and unwieldy; that it wrongly assumes an equivalency between international refugee law and international human rights norms; and that it promotes a ‘principle of surrogacy’ that lacks any clear foundation. A third cluster dwells on the deficiencies of the human rights approach as a paradigm when examined from an empirical and comparative perspective: its failure to have become entrenched at a global level; its ‘sheer variety’ and lack of any clear contents; and its failure to help with difficult questions of refugee law. The article seeks to rebut these criticisms one by one and, in the course of doing so, to highlight the ways in which, far from being in decline, the human rights approach is a rising sun rather than a falling star.
Sequential Delivery of Live Attenuated Influenza Vaccine and Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in the Ferret Model Can Reduce SARS-CoV-2 Shedding and Does Not Result in Enhanced Lung Pathology
Authors: Ryan Kathryn A , Schewe Katarzyna E , Crowe Jonathan , Fotheringham Susan A , Hall Yper , Humphreys Richard , Marriott Anthony C , Paterson Jemma , Rayner Emma , Salguero Francisco J , Watson Robert J , Whittaker Catherine J , Carroll Miles W , Dibben Oliver 
Published: December 2021

Abstract
Cocirculation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza viruses could pose unpredictable risks to health systems globally, with recent studies suggesting more severe disease outcomes in coinfected patients. The initial lack of a readily available coronavirus disease 2019 (COVID-19) vaccine has reinforced the importance of influenza vaccine programs during the COVID-19 pandemic. Live attenuated influenza vaccine (LAIV) is an important tool in protecting against influenza, particularly in children. However, it is unknown whether LAIV administration influences the outcomes of acute SARS-CoV-2 infection or disease. To investigate this, quadrivalent LAIV was administered to ferrets 3 days before or after SARS-CoV-2 infection. LAIV administration did not exacerbate the SARS-CoV-2 disease course or lung pathology with either regimen. In addition, LAIV administered before SARS-CoV-2 infection significantly reduced SARS-CoV-2 replication and shedding in the upper respiratory tract. This study demonstrated that LAIV administration in close proximity to SARS-CoV-2 infection does not exacerbate mild disease and can reduce SARS-CoV-2 shedding.
COVID-19 Cluster Linked to Aerosol Transmission of SARS-CoV-2 via Floor Drains
Authors: Han Taewon , Park Heedo , Jeong Yungje , Lee Jungmin , Shon Eungyeong , Park Man-Seong , Sung Minki 
Published: December 2021

Abstract

Background
Recently, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission through exposure to aerosols has been suggested. Therefore, we investigated the possibility of aerosol SARS-CoV-2 transmission within an apartment complex where residents reported testing positive for SARS-CoV-2 despite having no direct contact with other SARS-CoV-2–infected people.

Methods
Information on symptom onset and exposure history of the patients was collected by global positioning system (GPS) tracking to investigate possible points of contact or spread. Samples collected from patients and from various areas of the complex were analyzed using RNA sequencing. Phylogenetic analysis was also performed.

Results
Of 19 people with confirmed SARS-CoV-2 infection, 5 reported no direct contact with other residents and were from apartments in the same vertical line. Eight environmental samples tested positive for the virus. Phylogenetic analyses revealed that 3 of the positive cases and 1 environmental sample belonged to the B.1.497 lineage. Additionally, 3 clinical specimens and 1 environmental sample from each floor of the complex had the same amino acid substitution in the ORF1ab region.

Conclusions
SARS-CoV-2 transmission possibly occurs between different floors of an apartment building through aerosol transmission via nonfunctioning drain traps.