bluuebunny/crossref_metadata_2025_split huggingface dataset:
A prospective longitudinal study of chronic pulmonary aspergillosis in pulmonary tuberculosis in Indonesia (APICAL)
Authors: Setianingrum Findra , Rozaliyani Anna , Adawiyah Robiatul , Syam Ridhawati , Tugiran Mulyati , Sari Cut Yulia Indah , Nandipinto Finny , Ramnath Johannes , Arifin Arief Riadi , Handayani Diah , Burhan Erlina , Rumende Martin , Wahyuningsih Retno , Rautemaa-Richardson Riina , Denning David W 
Published: November 2021

ObjectivesChronic pulmonary aspergillosis (CPA) can complicate recovery from pulmonary TB. CPA may also be misdiagnosed as bacteriologically negative TB. This study aimed to determine the incidence of CPA in patients treated for TB in Indonesia, a country with a high incidence of TB.MethodsIn this prospective, longitudinal cohort study in patients treated for pulmonary TB, clinical, radiological and laboratory findings were analysed. Sputum was collected for fungal culture and TB PCR. Patients were assessed at baseline (0–8 weeks) and at the end (5–6 months) of TB therapy. CPA diagnosis was based on symptoms (≥3 months), characteristic radiological features and positiveAspergillusserology, and categorised as proven, probable and possible.ResultsOf the 216 patients recruited, 128 (59%) were followed up until end of TB therapy. At baseline, 91 (42%) had microbiological evidence for TB.Aspergillus-specific IgG was positive in 64 (30%) patients and went from negative to positive in 16 (13%) patients during TB therapy. The incidence rates of proven and probable CPA at baseline were 6% (n=12) and 2% (n=5) and end of TB therapy 8% (n=10) and 5% (n=7), respectively. Six patients (two with confirmed TB) developed an aspergilloma. Diabetes mellitus was a significant risk factor for CPA (p=0.040). Persistent cough (n=5, 50%; p=0.005) and fatigue (n=6, 60%; p=0.001) were the most common symptoms in CPA.ConclusionCPA should be considered a relatively frequent differential diagnosis in patients with possible or proven TB in Indonesia. Lack of awareness and limited access toAspergillus-specific IgG tests and CT imaging are obstacles in establishing a CPA diagnosis.
Exploring requirements and detector solutions for FCC-ee
Authors: Azzi Patrizia , Perez Emmanuel 
Published: November 2021

AbstractCircular colliders have the advantage of delivering collisions to multiple interaction points, which allow different detector designs to be studied and optimised—up to four for FCC-ee. On the one hand, the detectors must satisfy the constraints imposed by the invasive interaction region layout. On the other hand, the performance of heavy-flavour tagging, of particle identification, of tracking and particle-flow reconstruction, and of lepton, jet, missing energy and angular resolution, need to match the physics programme and the exquisite statistical precision offered by FCC-ee. During the FCC feasibility study (2021–2025), benchmark physics processes will be used to determine, via appropriate simulations, the requirements on the detector performance or design that must be satisfied to ensure that the systematic uncertainties of the measurements are commensurate with their statistical precision. The usage of the data themselves, in order to reach the challenging goals on the stability and on the alignment of the detector, in particular for the programme at and around the Z peak, will also be studied. In addition, the potential for discovering very weakly coupled new particles, in decays of Z or Higgs bosons, could motivate dedicated detector designs that would increase the efficiency for reconstructing the unusual signatures of such processes. These studies are crucial input to the further optimisation of the two concepts described in the FCC-ee conceptual design report, CLD and IDEA, and to the development of new concepts which might actually prove to be better adapted to the FCC-ee physics programme, or parts thereof.
Estimates of late Albian atmospheric CO
2
based on stomata of
Pseudofrenelopsis
from Jilin Province, NE China
Authors: Li Ting , Yang Xiao-Ju , Zhu Yan-Bin 
Published: November 2021

Abstract

Stomata characteristics of two extinct conifer Cheirolepidiaceae species,
Pseudofrenelopsis gansuensis
and
Pseudofrenelopsis dalatzensis
, were used to reconstruct the atmospheric carbon dioxide concentration levels during the late Albian of the Cretaceous. A sequence of fossil samples was collected from five beds in the Dalazi Formation in the Zhixin and Luozigou basins of Jilin Province, northeastern China. The stomatal index was used to estimate the palaeo-
p
CO
2.
The average stomatal index value of the two species was 4.1 and the atmospheric CO
2
content was
c.
1200 ppmv by the average of Recent standardization and Carboniferous standardization. During the short interval from 104.8 ± 0.5 Ma to 104.0 ± 0.4 Ma in the late Albian, the atmospheric CO
2
content presents a decreasing tendency, with the highest value being
c.
1300 ppmv in the Luozigou Basin. In addition, the higher atmospheric CO
2
values of the late Albian are likely linked to a ‘greenhouse climate’ during the time of Oceanic Anoxic Event 1c (OAE1c).
In Silico Epitope Prediction Analyses Highlight the Potential for Distracting Antigen Immunodominance with Allogeneic Cancer Vaccines
Authors: James C. Alston , Ronning Peter , Cullinan Darren , Cotto Kelsy C. , Barnell Erica K. , Campbell Katie M. , Skidmore Zachary L. , Sanford Dominic E. , Goedegebuure S. Peter , Gillanders William E. , Griffith Obi L. , Hawkins William G. , Griffith Malachi 
Published: November 2021

Allogeneic cancer vaccines are designed to induce antitumor immune responses with the goal of impacting tumor growth. Typical allogeneic cancer vaccines are produced by expansion of established cancer cell lines, transfection with vectors encoding immunostimulatory cytokines, and lethal irradiation. More than 100 clinical trials have investigated the clinical benefit of allogeneic cancer vaccines in various cancer types. Results show limited therapeutic benefit in clinical trials and currently there are no FDA-approved allogeneic cancer vaccines. We used recently developed bioinformatics tools including the pVACseq suite of software tools to analyze DNA/RNA-sequencing data from the The Cancer Genome Atlas to examine the repertoire of antigens presented by a typical allogeneic cancer vaccine, and to simulate allogeneic cancer vaccine clinical trials. Specifically, for each simulated clinical trial, we modeled the repertoire of antigens presented by allogeneic cancer vaccines consisting of three hypothetical cancer cell lines to 30 patients with the same cancer type. Simulations were repeated ten times for each cancer type. Each tumor sample in the vaccine and the vaccine recipient was subjected to human leukocyte antigen (HLA) typing, differential expression analyses for tumor-associated antigens (TAA), germline variant calling, and neoantigen prediction. These analyses provided a robust, quantitative comparison between potentially beneficial TAAs and neoantigens versus distracting antigens present in the allogeneic cancer vaccines. We observe that distracting antigens greatly outnumber shared TAAs and neoantigens, providing one potential explanation for the lack of observed responses to allogeneic cancer vaccines. This analysis provides additional rationale for the redirection of efforts toward a personalized cancer vaccine approach.

Significance:
A comprehensive examination of allogeneic cancer vaccine antigen repertoire using large-scale genomics datasets highlights the large number of distracting antigens and argues for more personalized approaches to immunotherapy that leverage recent strategies in tumor antigen identification.
Aneurysm and Artery Dissection Following the Use of Vascular Endothelial Growth Factor Inhibitor: A Real‐World Analysis Using a Spontaneous Reporting System
Authors: Wang Shuyue , Chen Mingzhu , Zhang Xinghui , Zhang Lingjian , Jia Min , Shen Zhiwen , Wang Junyan , Zhao Bin , Gong Yang , Gong Jian 
Published: November 2021

Background
Pharmacological inhibition of angiogenesis via the vascular endothelial growth factor pathway is an important therapeutic target that prevents tumor growth and the formation of metastases. Although vascular endothelial growth factor inhibitor (VPI) is well understood as a well‐defined safety profile, few real‐world studies are comparing the incidence, clinical features, and prognosis of the aneurysm and artery dissection.

Methods and Results

To evaluate and compare the links between different VPIs and aneurysm and artery dissection, we identified 634 reports with VPIs in the US Food and Drug Administration Adverse Event Reporting System database ranging between January 2004 to March 2020. We used the reporting odds ratio for the association between the use of VPIs and aneurysm and artery dissection. The reporting odds ratio (3.68, 95%, 2.18‒6.23) shows that ramucirumab has a stronger correlation than other VPIs. The results show a significant difference in onset time (
P
<0.001). The median time to aneurysm and artery dissection was 79.5 (interquartile interval, 19.0–273.5) days after VPI administration. The results also show that VPI‐associated aneurysm and artery dissection was reported more often in men (n=336, 59.68% versus n=227, 40.32%), and there were more cases in patients aged between 45 to 74 years than those <45 years (n=312, 68.12% versus n=18, 3.93%); patients aged ≥75 years accounted for 27.95% (n=128). Finally, the suspected drugs generally led to 19.98% deaths and 29.81% hospitalizations.

Conclusions
We identified signals for aneurysm and artery dissection following various VPIs in real‐world practice via the Food and Drug Administration Adverse Event Reporting System, which represents the first step for continued pharmacovigilance investigation.
Relationship Between the Ratio of Acceleration Time/Ejection Time and Mortality in Patients With High‐Gradient Severe Aortic Stenosis
Authors: Altes Alexandre , Thellier Nicolas , Bohbot Yohann , Ringle Griguer Anne , Verdun Stéphane , Levy Franck , Castel Anne Laure , Delelis François , Mailliet Amandine , Tribouilloy Christophe , Maréchaux Sylvestre 
Published: November 2021

Background
The ratio of acceleration time/ejection time (AT/ET) is a simple and reproducible echocardiographic parameter that integrates aortic stenosis severity and its consequences on the left ventricle. No study has specifically assessed the prognostic impact of AT/ET on outcome in patients with high‐gradient severe aortic stenosis (SAS) and no or mild symptoms. We sought to evaluate the relationship between AT/ET and mortality and determine the best predictive AT/ET cutoff value in these patients.

Methods and Results

A total of 353 patients (median age, 79 years; 46% women) with high‐gradient (mean pressure gradient ≥40 mm Hg and/or aortic peak jet velocity ≥4 m/s) SAS, left ventricular ejection fraction ≥50%, and no or mild symptoms were studied. The impact of AT/ET ≤0.35 or >0.35 on all‐cause mortality was retrospectively studied. During a median follow‐up of 39 (25th–75th percentile, 23–62) months, 70 patients died. AT/ET >0.35 was associated with a considerable increased mortality risk after adjustment for established prognostic factors in SAS under medical and/or surgical management (adjusted hazard ratio [HR], 2.54; 95% CI, 1.47–4.37;
P
<0.001) or conservative management (adjusted HR, 3.29; 95% CI, 1.70–6.39;
P
<0.001). Moreover, AT/ET >0.35 improved the predictive performance of models including established risk factors in SAS with better global model fit, reclassification, and discrimination. After propensity matching, increased mortality risk persisted when AT/ET >0.35 (adjusted HR, 2.10; 95% CI, 1.12–3.90;
P
<0.001).

Conclusions
AT/ET >0.35 is a strong predictor of outcome in patients with SAS and no or only mild symptoms and identifies a subgroup of patients at higher risk of death who may derive benefit from earlier aortic valve replacement.
Effects of Renin‐Angiotensin–Aldosterone System Inhibitors on Long‐Term Major Adverse Cardiovascular Events in Sepsis Survivors
Authors: Ou Shu‐Yu , Lee Yi‐Jung , Lo Yuan , Chen Chen‐Hsiu , Huang Yu‐Chi , Kuo Yu‐Ting , Chia Yuan‐Yi 
Published: November 2021

Background
Sepsis is known to increase morbidity and duration of hospital stay and is a common cause of mortality worldwide. Renin‐angiotensin‐aldosterone system inhibitors (RAASis) are commonly used to treat hypertension but are usually discontinued during hospitalization for sepsis because of concerns about renal hypoperfusion. The aim of our study was to investigate whether RAASis should be continued after discharge in sepsis survivors and to identify the effects on the clinical outcomes.

Methods and Results
A total of 9188 sepsis survivors aged 20 years and older who were discharged from January 1, 2012 to December 31, 2019 were included in our analyses. We further divided sepsis survivors into RAASi users and nonusers. These groups were matched by propensity scores before the outcomes of interest, including all‐cause mortality and major adverse cardiac events (MACE), were examined. After propensity score matching, 3106 RAASi users and 3106 RAASi nonusers were included in our analyses. Compared with RAASi nonusers, RAASi users had lower risks of all‐cause mortality (hazard ratio [HR], 0.68; 95% CI, 0.62–0.75), MACEs (HR, 0.87; 95% CI, 0.81–0.94), ischemic stroke (HR, 0.85; 95% CI, 0.76–0.96), myocardial infarction (HR, 0.74; 95% CI, 0.61–0.90), and hospitalization for heart failure (HR, 0.84; 95% CI, 0.77–0.92). Subgroup analyses stratified by admission to the ICU and the use of inotropes showed similar results.

Conclusions
In our study, we found that RAASi users had reduced risks of all‐cause mortality and MACEs. These findings suggested a beneficial effect of RAASi use by sepsis survivors after discharge.
Phenomenology, Scientific Method and the Transformation Problem
Authors: Lopes Jesse , Byron Chris 
Published: November 2021

Abstract
We argue in this article that Marx’s scientific method coupled with his analysis of the phenomenological consciousness of agents trapped within the capitalist mode of production provides a sufficient solution to the transformation problem. That is, Marx needs no amending – mathematical, philosophical, or otherwise – and the tools he uses to demonstrate and resolve the problem – science and phenomenology – were already clearly spelled out in his texts. Critics of Marx either fail to understand his scientific method, or are themselves trapped within a non-scientific capitalist phenomenology. Similarly, Marxists that mathematically resolve the transformation problem fail to realise that Marx’s scientific analysis alone demonstrates that a mathematical solution to the transformation problem is a misapprehension of the relation between Marx’s abstract theory and concrete phenomena. Consequently, we also criticise the monetary theorists who try to dismiss the problem as pointless by claiming that Marx was not a pre-monetary theorist.
Pushing Social Philosophy to Its Democratic Limits
Authors: Hogan Brendan 
Published: November 2021

Abstract
Roberto Frega’s Pragmatism and the Wide View of Democracy reformulates the question of democracy posed by our current historic conjuncture using the resources of a variety of pragmatic thinkers. He brings into the contemporary conversation regarding democracy’s fortunes both classical and somewhat neglected figures in the pragmatic tradition to deal with questions of power, ontology, and politics. In particular, Frega takes a social philosophical starting point and draws out the consequences of this fundamental shift in approach to questions of democratic and political theory. This turn to social philosophy as a theoretically more sufficient conceptual vocabulary, extended in detail by Frega, raises questions regarding the work that a social ontology does in clarifying the role of economic and political approaches to democracy that are worth further exploration. Likewise, the practical proposals for moving beyond methodological nationalism with respect to forming publics for the sake of problem-solving, while providing a clarifying and fresh starting point, are still too beholden to models of agency and expressions of coordinated action that themselves are the very fruit of those systems which undermine democratic power in the first instance.
Compensation for Wrongful Conviction/Miscarriage of Justice in Hong Kong in Light of A v Secretary for Justice and Another [2020] hkcfi 427; hcal 176/2018 (11 March 2020)
Authors: Mujuzi Jamil Ddamulira 
Published: November 2021

Abstract
Article 14(6) of the International Covenant on Civil and Political Rights (iccpr) provides for the right to compensation for wrongful conviction or miscarriage of justice. In Hong Kong, there are two compensation schemes for people who have been wrongfully convicted – the statutory scheme under Article 11(5) of the Bill of Rights Ordinance and the ex gratia scheme (also applicable to wrongful imprisonment). Although there are cases in which Hong Kong courts have dealt with the right to compensation under the ex gratia scheme, it was only in March 2020, in A v Secretary for Justice and Another, that the High Court, for the first time, dealt with a case on the right to compensation under Article 11(5). In this article, the author discusses the right to compensation for wrongful conviction in Hong Kong generally and in particular under Article 11(5) of the Bill of Rights Ordinance. The author deals with the case of A v Secretary for Justice and Another and illustrates how the High Court’s interpretation of Article 11(5) of the Bill of Rights Ordinance is likely to impact on the right to compensation for wrongful conviction in Hong Kong in the future.
The clinical and functional outcomes of a large naturalistic cohort of young people accessing national early psychosis services
Authors: Brown Ellie , Gao Caroline X. , Staveley Heather , Williams Georgia , Farrelly Simone , Rickwood Debra , Telford Nic , Papanastasiou Cerissa , McGorry Pat , Thompson Andrew 
Published: November 2021

Aims: Services for individuals with a first episode of psychosis or at ultra-high risk of psychosis have become a treatment model of choice in mental health care. The longitudinal changes in clinical and functional outcomes as a result of real-world treatment remain under-reported. Methods: We analysed data from first episode of psychosis and ultra-high risk services delivered across Australian primary youth mental health care services known as headspace between 19 June 2017 and 30 September 2019. Outcome measures were completed and entered into a minimum dataset every 90 days a participant was receiving treatment and included psychiatric symptomatology (Brief Psychiatric Rating Scale and psychological distress, K10) and psychosocial functioning (Social and Occupational Functioning Assessment Scale and My Life Tracker). Linear mixed-effects models were used to evaluate changes in outcome over time. Results: Outcome data from a total of 1252 young people were evaluated (643 first episode of psychosis, 609 ultra-high risk). Of those who entered ultra-high risk services, 11.8% transitioned to first episode of psychosis services. Overall, substantial improvement in clinical (Brief Psychiatric Rating Scale, K10) and functional (Social and Occupational Functioning Assessment Scale, My Life Tracker) outcomes were seen across groups and outcomes. Ultra-high risk patients showed a greater reduction in distress symptoms, while first episode of psychosis patients experienced a greater reduction in positive psychosis symptoms. Although clinical outcomes showed a plateau effect after approximately 3 months of care, improvement in functional outcomes (Social and Occupational Functioning Assessment Scale, My Life Tracker) continued later in treatment. Conclusion: These findings support the use of real-time, real-world and low-cost administrative data to rigorously evaluate symptomatic and functional outcomes in early psychosis treatment settings. Findings that functional outcomes improve past the remittance of clinical outcomes also support the functional recovery focus of early psychosis services and remaining high levels of distress suggest the need for ultra-high risk services to extend beyond 6 months of care.
Family History of Psychiatric Disorders and Clinical Factors Associated With a Schizophrenia Diagnosis
Authors: Díaz-Castro Lina , Hoffman Kurt , Cabello-Rangel Héctor , Arredondo Armando , Herrera-Estrella Miguel Ángel 
Published: November 2021

Background Schizophrenia (SCH) and bipolar disorder (BD) have both shared and unique genetic risk factors and clinical characteristics. The aim of the present study was to identify potential risk factors significantly associated with SCH, relative to a BD reference group. Methods Data were obtained from medical records of patients that entered a major Mexico City hospital during 2009–2010 presenting psychotic symptoms (n = 1132; 830 cases of SCH, 302 cases of BD; 714 men and 418 women). SCH and BD diagnoses were compared with respect to a number of family and clinical characteristics. Logistic and linear regression analyses were used to respectively identify factors selectively associated with the SCH diagnosis relative to the BD diagnosis and explore the relationship between PANSS scores and parental age at time of birth to the age of SCH onset. Results Patients with SCH showed greater functional impairment than those with BD. Family history of mental illness, premorbid schizoid-like personality, and obstetric trauma were significantly associated with the SCH diagnosis. The association of obstetric trauma with SCH was greatest in male patients with a family history of mental illness. In women, increased paternal and decreased maternal age at time of the patient’s birth were associated with an earlier age of SCH onset. Conclusion Male gender, showing premorbid schizoid-like personality, familial SCH, and obstetric trauma are risk factors that distinguish SCH from BD. Additionally, our results suggest that risk for SCH relative to BD may be importantly influenced by interactions between familial risk, gender, and obstetric trauma.
Revision Stapes Surgery: Hearing Symptoms and Associations With Intraoperative Findings and Outcomes
Authors: Luryi Alexander L. , Schettino Amy , Michaelides Elias M. , Babu Seilesh , Bojrab Dennis I. , Schutt Christopher A. 
Published: November 2021

ObjectiveStapes surgery for otosclerosis occasionally requires revision due to recurrent or persistent conductive hearing loss (CHL). This study examines outcomes after revision stapes surgery.Study DesignRetrospective review.SettingSingle tertiary neurotology center.MethodsPatients undergoing revision stapes surgery for otosclerosis from 2008 to 2017 were reviewed. Postoperative air‐bone gaps (ABGs) were the primary outcome measure.ResultsDuring the study period, 150 patients underwent revision stapes surgery. One hundred patients (67%) had gradually progressive recurrent CHL; 16 (11%), sudden recurrent CHL; 13 (9%), persistent CHL; and 21 (14%), no CHL. For 129 patients with CHL, the mean ABG improved from 23.7 to 9.3 dB (P <. 0005). The most common intraoperative findings for these patients were prosthesis displacement with incus necrosis (38%) or without it (43%), normal anatomy with seemingly good prosthesis placement (6%), and abundant scar tissue (6%). Patients with recurrent hearing loss achieved lower mean ABGs than patients with persistent hearing loss (8.8 vs 13.2 dB, P =. 02). There were no associations between onset pattern of CHL or intraoperative findings and hearing outcomes (P >. 05). Four patients (2.7%) developed sensorineural hearing loss after revision, defined as an increase in bone conduction pure tone average ≥15 dB, all of whom had previous replacement of a malpositioned prosthesis.ConclusionsRevision stapes surgery confers significant improvement in hearing for patients with persistent and recurrent CHL, although patients with persistent CHL after initial surgery see less improvement with revision.