bluuebunny/crossref_metadata_2025_split huggingface dataset:
The correlation calibration of PAPER-64 data
Authors: Gogo Tamirat G , Ma Yin-Zhe , Kittiwisit Piyanat , Sievers Jonathan L , Parsons Aaron R , Pober Jonathan C , Jacobs Daniel C , Cheng Carina , Kolopanis Matthew , Liu Adrian , Kohn Saul A , Aguirre James E , Ali Zaki S , Bernardi Gianni , Bradley Richard F , DeBoer David R , Dexter Matthew R , Dillon Joshua S , Klima Pat , MacMahon David H E , Moore David F , Nunhokee Chuneeta D , Walbrugh William P , Walker Andre 
Published: December 2021

ABSTRACT
Observation of redshifted 21-cm signal from the Epoch of Reionization (EoR) is challenging due to contamination from the bright foreground sources that exceed the signal by several orders of magnitude. Removal of this very high foreground relies on accurate calibration to keep the intrinsic property of the foreground with frequency. Commonly employed calibration techniques for these experiments are the sky model-based and the redundant baseline-based calibration approaches, which can suffer from sky-modelling error and array redundancy imperfection respectively. In this work, we introduce the hybrid correlation calibration (CorrCal) scheme, which aims to bridge the gap between redundant and sky-based calibration by relaxing redundancy of the array and including sky information into the calibration formalisms. We apply the CorrCal to the data of Precision Array for Probing the Epoch of Reionization (PAPER) experiment, which was pre-calibrated using redundant baseline calibration. We show about $6\%$ suppression at the bin right on the horizon limit of the foreground wedge-like structure, relative to the pre-calibrated power spectra. This small improvement of the foreground power spectra around the wedge limit could be suggestive of reduced spectral structure in the data after CorrCal calibration, which lays the foundation for future improvement of the calibration algorithm and implementation method.
Joint Inference of Migration and Reassortment Patterns for Viruses with Segmented Genomes
Authors: Stolz Ugnė , Stadler Tanja , Müller Nicola F , Vaughan Timothy G 
Published: December 2021

AbstractThe structured coalescent allows inferring migration patterns between viral subpopulations from genetic sequence data. However, these analyses typically assume that no genetic recombination process impacted the sequence evolution of pathogens. For segmented viruses, such as influenza, that can undergo reassortment this assumption is broken. Reassortment reshuffles the segments of different parent lineages upon a coinfection event, which means that the shared history of viruses has to be represented by a network instead of a tree. Therefore, full genome analyses of such viruses are complex or even impossible. Although this problem has been addressed for unstructured populations, it is still impossible to account for population structure, such as induced by different host populations, whereas also accounting for reassortment. We address this by extending the structured coalescent to account for reassortment and present a framework for investigating possible ties between reassortment and migration (host jump) events. This method can accurately estimate subpopulation dependent effective populations sizes, reassortment, and migration rates from simulated data. Additionally, we apply the new model to avian influenza A/H5N1 sequences, sampled from two avian host types, Anseriformes and Galliformes. We contrast our results with a structured coalescent without reassortment inference, which assumes independently evolving segments. This reveals that taking into account segment reassortment and using sequencing data from several viral segments for joint phylodynamic inference leads to different estimates for effective population sizes, migration, and clock rates. This new model is implemented as the Structured Coalescent with Reassortment package for BEAST 2.5 and is available at https://github.com/jugne/SCORE.
Rituximab administration during the second trimester of pregnancy for systemic lupus erythematosus: Case report and review of the literature on rheumatic disease
Authors: Colquhoun Matthew , Thanopoulou Vasiliki , Quick Vanessa , Mouyis Maria 
Published: December 2021

ABSTRACT
Rituximab (RTX) is an anti-CD20 monoclonal antibody that is used in the treatment of many rheumatic diseases, for both licensed and unlicensed indications. Due to concerns regarding foetal B cell depletion and possible infection, there is conflicting advice about whether the drug should be administered during pregnancy, with some organisations advising administration if the potential benefit to the mother outweighs the risk to the foetus and some advising stopping RTX 6 months prior to conception. Caution in particular is advised about administering RTX in later trimesters when maternal immunoglobulin G (IgG) is transported across the placenta. There have been few literatures thus far examining the safety of administering RTX from the second trimester onwards in rheumatic diseases. We present a case where RTX was used during the second trimester for the treatment of refractory systemic lupus erythematosus, without adverse effect on the neonate.
Measuring metacognitive performance: type 1 performance dependence and test-retest reliability
Authors: Guggenmos Matthias 
Published: December 2021

Abstract
Research on metacognition—thinking about thinking—has grown rapidly and fostered our understanding of human cognition in healthy individuals and clinical populations. Of central importance is the concept of metacognitive performance, which characterizes the capacity of an individual to estimate and report the accuracy of primary (type 1) cognitive processes or actions ensuing from these processes. Arguably one of the biggest challenges for measures of metacognitive performance is their dependency on objective type 1 performance, although more recent methods aim to address this issue. The present work scrutinizes the most popular metacognitive performance measures in terms of two critical characteristics: independence of type 1 performance and test-retest reliability. Analyses of data from the Confidence Database (total N = 6912) indicate that no current metacognitive performance measure is independent of type 1 performance. The shape of this dependency is largely reproduced by extending current models of metacognition with a source of metacognitive noise. Moreover, the reliability of metacognitive performance measures is highly sensitive to the combination of type 1 performance and trial number. Importantly, trial numbers frequently employed in metacognition research are too low to achieve an acceptable level of test-retest reliability. Among common task characteristics, simultaneous choice and confidence reports most strongly improved reliability. Finally, general recommendations about design choices and analytical remedies for studies investigating metacognitive performance are provided.
Precision medicine biomarkers in brain metastases: applications, discordances, and obstacles
Authors: Steindl Ariane , Brastianos Priscilla K , Preusser Matthias , Berghoff Anna S 
Published: December 2021

Abstract
Brain metastases (BM) present a common cause of mortality and morbidity in several metastatic cancer entities. New therapeutic developments during the last decades, including targeted and immune-related therapies, have shown considerable extra- and intracranial response rates in specific subgroups of BM patients. However, differences in the molecular alteration in the BM tumor tissue compared to extracranial tumors leads to heterogeneous therapeutic responses. Therefore, an accurate molecular analyzation of BM tissue, if possible, has become an essential part in therapeutic decision making in BM patients. The concordance of predictive molecular biomarkers between multiple sites including extracranial and intracranial tumor tissue have been analyzed for some but not all biomarkers routinely applied in modern precision medicine approaches. In the present review, we summarize the current evidence of predictive biomarkers for personalized therapy approaches in the treatment of parenchymal BM.
Management of brain metastases in lung cancer: evolving roles for radiation and systemic treatment in the era of targeted and immune therapies
Authors: Myall Nathaniel J , Yu Helena , Soltys Scott G , Wakelee Heather A , Pollom Erqi 
Published: December 2021

Abstract
Brain metastases are a common occurrence in both non-small cell and small cell lung cancer with the potential to affect quality of life and prognosis. Due to concerns about the accessibility of the central nervous system by systemic chemotherapy agents, the management of brain metastases has historically relied on local therapies including surgery and radiation. However, novel targeted and immune therapies that improve overall outcomes in lung cancer have demonstrated effective intracranial activity. As a result, the management of brain metastases in lung cancer has evolved, with both local and systemic therapies now playing an important role. Factors such as tumor histology (non-small versus small cell), oncogenic driver mutations, and symptom burden from intracranial disease impact treatment decisions. Here, we review the current management of brain metastases in lung cancer, highlighting the roles of stereotactic radiosurgery and novel systemic therapies as well as the ongoing questions that remain under investigation.
Laser interstitial thermal therapy for brain metastases
Authors: Srinivasan Ethan S , Grabowski Matthew M , Nahed Brian V , Barnett Gene H , Fecci Peter E 
Published: December 2021

AbstractLaser interstitial thermal therapy (LITT) is a minimally invasive treatment for intracranial lesions entailing thermal ablation via a stereotactically placed laser probe. In metastatic disease, it has shown the most promise in the treatment of radiographically progressive lesions after initial stereotactic radiosurgery, whether due to recurrent metastatic disease or radiation necrosis. LITT has been demonstrated to provide clinical benefit in both cases, as discussed in the review below. With its minimal surgical footprint and short recovery period, LITT is further advantaged for patients who are otherwise high-risk surgical candidates or with lesions in difficult to access locations. Exploration of the current data on its use in metastatic disease will allow for a better understanding of the indications, benefits, and future directions of LITT for these patients.
Motor neuron disease risk and magnetic field exposures
Authors: Sorahan Tom , Nichols Linda 
Published: December 2021

Abstract

Background
Many studies have investigated magnetic field exposure and the risks of motor neuron disease (MND). Meta-analyses have found positive associations but a causal relationship has not been established.

Aims
To investigate the risks of MND and occupational exposure to magnetic fields in a large UK cohort.

Methods
Mortality of 37 986 employees of the former Central Electricity Generating Board of England and Wales was investigated for the period 1987–2018. Employees were first employed in the period 1942–82 and were still in employment on the 1 November, 1987. Detailed calculations enabled estimates to be made of magnetic field exposures. Observed deaths were compared with expected numbers based on mortality rates for the general population of England and Wales and Poisson regression was used to calculate rate ratios (relative risks) for categories of lifetime, lagged (distant) and lugged (recent) magnetic field exposure.

Results
Mortality from MND in the total cohort was similar to national rates (observed 69, expected 71.3, SMR 97, 95% CI 76–122). There were no statistically significant trends of risks increasing with lifetime, recent or distant magnetic field exposure, although positive associations were observed for some categories of recent exposure.

Conclusions
The study did not find that the cohort had elevated risks of MND as a consequence of occupational lifetime exposure to magnetic fields, although a possible role for recent exposures could usefully be investigated in other datasets.
Darunavir/Cobicistat/Emtricitabine/Tenofovir Alafenamide Versus Dolutegravir/Abacavir/Lamivudine in Antiretroviral-Naive Adults (SYMTRI): A Multicenter Randomized Open-Label Study (PReEC/RIS-57)
Authors: Podzamczer D , Micán R , Tiraboschi J , Portilla J , Domingo P , Llibre J M , Ribera E , Vivancos M J , Morano L , Masiá M , Gómez C , Fanjul F , Payeras A , Inciarte A , Estrada V , Rivero A , Castro Á , Bernal E , Vinuesa D , Knobel H , Troya J , Macías J , Montero M , Sanz J , Navarro-Alcaraz A , Caicedo A , Fernández G , Martínez E , Moreno S 
Published: December 2021

Abstract

Background
Darunavir/cobicistat/emtricitabine/tenofovir alafenamide (D/C/F/TAF) is the reference for combination therapy based on protease inhibitors due to its efficacy, tolerability, and convenience. Head-to-head randomized comparisons between D/C/F/TAF and combination therapy based on integrase inhibitors in antiretroviral-naive patients are lacking.

Methods
Adult (&gt;18 years old) human immunodeficiency virus-infected antiretroviral-naive patients (HLA-B∗5701 negative and hepatitis B virus negative), with viral load (VL) ≥500 c/mL, were centrally randomized to initiate D/C/F/TAF or dolutegravir/abacavir/lamivudine (DTG/3TC/ABC) after stratifying by VL and CD4 count. Clinical and analytical assessments were performed at weeks 0, 4, 12, 24, and 48. The primary endpoint was VL &lt;50 c/mL at week 48 in the intention-to-treat (ITT)-exposed population (US Food and Drug Administration snapshot analysis, 10% noninferiority margin).

Results
Between September 2018 and 2019, 316 patients were randomized and 306 patients were included in the ITT-exposed analysis (151 D/C/F/TAF and 155 DTG/3TC/ABC). Almost all (94%) participants were male and their median age was 35 years. Forty percent had a baseline VL &gt;100 000 copies/mL, and 13% had &lt;200 CD4 cells/μL. Median weight was 73 kg and median body mass index was 24 kg/m2. At 48 weeks, 79% (D/C/F/TAF) versus 82% (DTG/3TC/ABC) had VL &lt;50 c/mL (difference, −2.4%; 95% confidence interval [CI], −11.3 to 6.6). Eight percent versus four percent experienced virologic failure but no resistance-associated mutations emerged. Four percent versus six percent had drug discontinuation due to adverse events. In the per-protocol analysis, 94% versus 96% of patients had VL &lt;50 c/mL (difference, −2%; 95% CI, −8.1 to 3.5). There were no differences in CD4 cell count or weight changes.

Conclusions
We could not demonstrate the noninferiority of D/C/F/TAF relative to DTG/ABC/3TC as initial antiretroviral therapy, although both regimens were similarly well tolerated.
Can lightning strike twice? Wild-type transthyretin cardiac amyloidosis associated with rare liver disease
Authors: Bhattacharya Priyanka T , Fox Alyson N , Marboe Charles C , Lagana Stephen M , Remotti Helen E , D’Armiento Jeanine M , Goldklang Monica P , Eisenberger Andrew B , Griffin Jan M , Maurer Mathew S 
Published: December 2021

ABSTRACT
Wild-type ATTR cardiac amyloidosis (ATTRwt-CA) is not as rare as previously thought to be. Patients with infiltrative cardiac amyloidosis often present with right-sided heart failure (HF) symptomatology. Clinically significant liver disease and cirrhosis has not been reported in ATTRwt-CA. We present two cases of ATTRwt-CA with right-sided HF and abnormal liver function tests initially thought to be secondary to congestive hepatopathy but found to have rare and unrelated liver disease. These cases highlight the importance of developing a broad differential diagnosis and leveraging a multidisciplinary team approach in evaluating patients for unusual causes of cirrhosis/other chronic liver diseases when ATTR cardiac amyloidosis patients present with congestive hepatopathy.
Assessing nephrology competence in general paediatrics—A survey of general paediatricians, paediatric nephrologists, residents, and program directors
Authors: Kirpalani Amrit , Prasad Charushree , Jawa Natasha A , Atkinson Adelle R , Feldman Mark , Jeffers Justin M , Noone Damien G 
Published: December 2021

Abstract

Objective
The objective of this study was to identify nephrology topics of lowest perceived competency and importance for general paediatricians.

Methods
Surveys were distributed to general paediatricians, paediatric residents, paediatric residency program directors, and paediatric nephrologists. Perceived importance and competence were rated on a 5-point Likert scale. Means and 95% confidence intervals were calculated.

Results
Mean perceived competency from general paediatricians across all nephrology domains was 3.0, 95%CI (2.9 to 3.1) and mean importance was 3.2, 95%CI (3.1 to 3.3). Domains scoring below the means for competence and importance, respectively were kidney stones (2.5, 95%CI [2.2 to 2.7]) and 2.6, 95%CI [2.3 to 2.8]), acute kidney injury (2.5, 95%CI [2.2 to 2.8] and 2.4, 95%CI [2.1 to 2.8]), chronic kidney disease (1.9, 95%CI [1.7 to 2.2] and 2.1, 95%CI [1.8 to 2.4]), tubular disorders (1.8, 95%CI [1.6 to 2.0] and 2.0, 95%CI [1.8 to 2.3]), and kidney transplant (1.6, 95%CI [1.4 to 1.8] and 1.7, 95%CI [1.4 to 1.9]). Residents, program directors, and paediatric nephrologists agreed that stones, chronic kidney disease, tubular disorders, and transplant were of lower importance. However, acute kidney injury was the domain with the largest discrepancy in perceived importance between residents (4.4, 95%CI [4.2 to 4.6]), nephrologists (4.2, 95%CI [3.8 to 4.6]), and program directors (4.2, 95%CI [3.7 to 4.7]) compared to general paediatricians ([2.4, 95%CI [2.1 to 2.8]; P&lt;0.05).

Conclusion
Paediatricians did not believe acute kidney injury was important to their practice, despite expert opinion and evidence of long-term consequences. Educational interventions must address deficits in crucial domains of renal health in paediatrics.
Long-term follow-up after lymphodepleting autologous haematopoietic cell transplantation for treatment-resistant systemic lupus erythematosus
Authors: Goklemez Sencer , Hasni Sarfaraz , Hakim Frances T , Muraro Paolo A , Pirsl Filip , Rose Jeremy , Memon Sarfraz , Fowler Daniel F , Steinberg Seth M , Baker Eva H , Panch Sandya R , Gress Ronald , Illei Gabor G , Lipsky Peter E , Pavletic Steven Z 
Published: December 2021

Abstract

Objective
Autologous haematopoietic cell transplantation (AHSCT) improves immunologic dysfunction in patients with SLE. However, the curative potential of this therapy remains uncertain. This study reports outcomes in SLE patients receiving a lymphodepleting, reduced intensity regimen for AHSCT in SLE.

Methods
Eight patients with SLE refractory to treatment, including i.v. cyclophosphamide (CYC), were enrolled. Five had LN and three CNS involvement as primary indications for transplant. Haematopoietic cell mobilization with CYC, G-CSF and rituximab was followed by collection of CD34+ positively selected cells. The conditioning regimen consisted of concurrent administration of CYC, fludarabine and rituximab. All immunosuppressive medications were discontinued at the start of mobilization and CS were rapidly tapered after the transplant.

Results
Five of eight patients achieved a complete response, including a decline in the SLEDAI to zero, which was sustained in four patients for a median of 165 months (range 138–191). One patient achieved a partial response, which was followed by relapse at month 18. Two patients with nephritis and underlying comorbidities in most organs had early deaths from infection and multiorgan failure. AHSCT resulted in profound lymphodepletion, followed by expansion of Treg cells and repopulation of naive T and B cells. Patients with a complete response showed a sustained suppression of the SLE-associated IFN-induced gene signature, marked depletion of memory and plasmablast B cells and resultant sustained elimination of anti-dsDNA antibody.

Conclusion
Durable clinical and serologic remissions with suppression in the IFN gene signature can be achieved in refractory SLE following lymphodepleting AHSCT.

Trial registration
ClinicalTrials.gov, https://clinicaltrials.gov, NCT00076752.
Screening for preclinical parenchymal lung disease in rheumatoid arthritis
Authors: Esposito Anthony J , Sparks Jeffrey A , Gill Ritu R , Hatabu Hiroto , Schmidlin Eric J , Hota Partha V , Poli Sergio , Fletcher Elaine A , Xiong Wesley , Frits Michelle L , Iannaccone Christine K , Prado Maria , Zaccardelli Alessandra , Marshall Allison , Dellaripa Paul F , Weinblatt Michael E , Shadick Nancy A , Rosas Ivan O , Doyle Tracy J 
Published: December 2021

Abstract

Objectives
Pulmonary disease is a common extraarticular manifestation of RA associated with increased morbidity and mortality. No current strategies exist for screening this at-risk population for parenchymal lung disease, including emphysema and interstitial lung disease (ILD).

Methods
RA patients without a diagnosis of ILD or chronic obstructive pulmonary disease underwent prospective and comprehensive clinical, laboratory, functional and radiological evaluations. High resolution CT (HRCT) scans were scored for preclinical emphysema and preclinical ILD and evaluated for other abnormalities.

Results
Pulmonary imaging and/or functional abnormalities were identified in 78 (74%) of 106 subjects; 45% had preclinical parenchymal lung disease. These individuals were older with lower diffusion capacity but had similar smoking histories compared with no disease. Preclinical emphysema (36%), the most commonly detected abnormality, was associated with older age, higher anti-cyclic citrullinated peptide antibody titres and diffusion abnormalities. A significant proportion of preclinical emphysema occurred among never smokers (47%) with a predominantly panlobular pattern. Preclinical ILD (15%) was not associated with clinical, laboratory or functional measures.

Conclusion
We identified a high prevalence of undiagnosed preclinical parenchymal lung disease in RA driven primarily by isolated emphysema, suggesting that it may be a prevalent and previously unrecognized pulmonary manifestation of RA, even among never smokers. As clinical, laboratory and functional evaluations did not adequately identify preclinical parenchymal abnormalities, HRCT may be the most effective screening modality currently available for patients with RA.
Paternal inflammatory arthritis is associated with a higher risk of miscarriage: results of a large multicentre study (iFAME-Fertility)
Authors: Perez-Garcia Luis F , Röder Esther , Smeele Hieronymus T W , Goekoop Robbert , Hazes Johanna M W , Kok Marc R , Tchetverikov Ilja , van der Helm-van Mil Annette , van der Kaap Jos , Kok Petra , Krijthe Bouwe P , Dolhain Radboud J E M 
Published: December 2021

Abstract

Objectives
Paternal preconception health is recognized as an important contributor to pregnancy outcomes. Nonetheless, pregnancy outcomes of partners of men with inflammatory arthritis (IA) have never been studied. Our objective was to describe the pregnancy outcomes of partners of men diagnosed with IA.

Methods
We performed a multicentre cross-sectional retrospective study conducted in the Netherlands. Men with IA who were over 40 years old that reported at least one positive pregnancy test were included. To analyse the impact of IA on pregnancy outcomes, pregnancies were classified into two groups: pregnancies conceived after the diagnosis of IA and before the diagnosis of IA.

Results
In total, 408 male participants diagnosed with IA reported 897 singleton pregnancies that resulted in 794 live births. Pregnancies conceived after the diagnosis of IA had higher rate of miscarriage (12.27 vs 7.53%, P = &lt;0.05). This increased risk was still present after adjusting for confounders [OR 2.03 (95% CI 1.12, 3.69) P = 0.015].

Conclusions
This is the largest study to describe the pregnancy outcomes of partners of men diagnosed with IA and the first to demonstrate that paternal IA is associated with a higher risk of miscarriage. Notwithstanding, the overall rate of miscarriage reported in our study could be comparable to previously reported population estimates.