bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimating causal effects under non-individualistic treatments due to network entanglement
Authors: Toulis P , Volfovsky A , Airoldi E M 
Published: August 2024

Summary
In many observational studies, the treatment assignment mechanism is not individualistic, as it allows the probability of treatment of a unit to depend on quantities beyond the unit’s covariates. In such settings, unit treatments may be entangled in complex ways. In this article, we consider a particular instance of this problem where the treatments are entangled by a social network among units. For instance, when studying the effects of peer interaction on a social media platform, the treatment on a unit depends on the change of the interactions network over time. A similar situation is encountered in many economic studies, such as those examining the effects of bilateral trade partnerships on countries’ economic growth. The challenge in these settings is that individual treatments depend on a global network that may change in a way that is endogenous and cannot be manipulated experimentally. In this paper, we show that classical propensity score methods that ignore entanglement may lead to large bias and wrong inference of causal effects. We then propose a solution that involves calculating propensity scores by marginalizing over the network change. Under an appropriate ignorability assumption, this leads to unbiased estimates of the treatment effect of interest. We also develop a randomization-based inference procedure that takes entanglement into account. Under general conditions on network change, this procedure can deliver valid inference without explicitly modelling the network. We establish theoretical results for the proposed methods and illustrate their behaviour via simulation studies based on real-world network data. We also revisit a large-scale observational dataset on contagion of online user behaviour, showing that ignoring entanglement may inflate estimates of peer influence.
Minimum spanning tree analysis of unimpaired individuals at risk of Alzheimer’s disease
Authors: García-Colomo Alejandra , López-Sanz David , Stam Cornelis J , Hillebrand Arjan , Carrasco-Gómez Martín , Spuch Carlos , Comis-Tuche María , Maestú Fernando 
Published: August 2024

Abstract
Identifying early and non-invasive biomarkers to detect individuals in the earliest stages of the Alzheimer’s disease continuum is crucial. As a result, electrophysiology and plasma biomarkers are emerging as great candidates in this pursuit due to their low invasiveness. This is the first magnetoencephalography study to assess the relationship between minimum spanning tree parameters, an alternative to overcome the comparability and thresholding problem issues characteristic of conventional brain network analyses, and plasma phosphorylated tau231 levels in unimpaired individuals, with different risk levels of Alzheimer’s disease. Seventy-six individuals with available magnetoencephalography recordings and phosphorylated tau231 plasma determination were included. The minimum spanning tree for the theta, alpha and beta bands for each subject was obtained, and the leaf fraction, tree hierarchy and diameter were calculated. To study the relationship between these topological parameters and phosphorylated tau231, we performed correlation analyses, for the whole sample and considering the two risk sub-groups separately. Increasing concentrations of phosphorylated tau231 were associated with greater leaf fraction and tree hierarchy values, along with lower diameter values, for the alpha and theta frequency bands. These results emerged for the whole sample and the higher risk group, but not for the lower risk group. Our results indicate that the network topology of cognitively unimpaired individuals with elevated plasma phosphorylated tau231 levels, a marker of Alzheimer’s disease pathology and amyloid-β accumulation, is already altered, shifting towards a more integrated network increasing its vulnerability and hub-dependency, mostly in the alpha band. This is indicated by increases in leaf fraction and tree hierarchy, along with reductions in diameter. These results match the initial trajectory proposed by theoretical models of disease progression and network disruption and suggest that changes in brain function and organization begin early on.
ETS1 deficiency in macrophages suppresses colorectal cancer progression by reducing the F4/80+TIM4+ macrophage population
Authors: Cao Yuanyuan , Guo Anning , Li Muxin , Ma Xinghua , Bian Xiaofeng , Chen YiRong , Zhang Caixia , Huang Shijia , Zhao Wei , Zhao Shuli 
Published: August 2024

Abstract
Tumor-associated macrophages (TAMs) take on pivotal and complex roles in the tumor microenvironment (TME); however, their heterogeneity in the TME remains incompletely understood. ETS proto-oncogene 1 (ETS1) is a transcription factor that is mainly expressed in lymphocytes. However, its expression and immunoregulatory role in colorectal cancer (CRC)-associated macrophages remain unclear. In the study, the expression levels of ETS1 in CD68+ macrophages in the CRC microenvironment were significantly higher than those in matched paracarcinoma tissues. Importantly, ETS1 increased the levels of chemokines C-C motif chemokine ligand 2 (CCL2) and C-X-C motif chemokine ligand 10 (CXCL10) in lipopolysaccharide-stimulated THP-1 cells. It also boosted the migration and invasion of CRC cells during the in vitro co-culture. In the ETS1 conditional knockout mouse model, ETS1 deficiency in macrophages ameliorated the histological changes in DSS-induced ulcerative colitis mouse models and prolonged the survival in an azomethane/dextran sodium sulfate (AOM/DSS)-induced CRC model. ETS1 deficiency in macrophages substantially inhibited tumor formation, reduced F4/80+TIM4+ macrophages in the mesenteric lymph nodes, and decreased CCL2 and CXCL10 protein levels in tumor tissues. Moreover, ETS1 deficiency in macrophages effectively prevented liver metastasis of CRC and reduced the infiltration of TAMs into the metastasis sites. Subsequent studies have indicated that ETS1 upregulated the expression of T-cell immunoglobulin mucin receptor 4 in macrophages through the signal transducer and activator of the transcription 1 signaling pathway activated by the autocrine action of CCL2/CXCL10. Collectively, ETS1 deficiency in macrophages potentiates antitumor immune responses by repressing CCL2 and CXCL10 expression, shedding light on potential therapeutic strategies for CRC.
Application of Diagnostic Stewardship to Fungal Polymerase Chain Reaction: Low Yield of Follow-up Testing on Plasma and Bronchoalveolar Lavage After a Negative Result
Authors: Wang Tong , Park Bosung , Anderson Gavin , Shaller Brian , Budvytiene Indre , Banaei Niaz 
Published: August 2024

Abstract

Background
Early diagnosis of invasive fungal disease is essential for optimizing management. Although the clinical utility of fungal polymerase chain reaction (PCR) testing on plasma and bronchoalveolar lavage (BAL) has been established, the role of follow-up testing remains unclear.

Methods
This was a retrospective single-center study. The yield of follow-up PCR for Aspergillus species, Mucorales agents, Fusarium species, Scedosporium species, dimorphic fungi, Pneumocystis jirovecii, and Candida species on plasma and/or BAL was measured at intervals of 1, 2, 3, and 4 weeks following a negative result.

Results
A total of 1389 follow-up tests on 406 plasma specimens from 264 patients and 983 BAL specimens from 431 patients were evaluated. Overall, the positivity rate at 1, 2, 3, and 4 weeks was 2.7% (4/148), 3.3% (4/123), 5.1% (4/78), and 3.5% (2/57), respectively, on plasma, and 0% (0/333), 0.3% (1/288), 0.4% (1/228), and 0.7% (1/134), respectively, on BAL. Conversions occurred with Aspergillus species, Mucorales agents, and Fusarium species PCR on plasma and Aspergillus species and P jirovecii PCR on BAL. All patients who converted were immunocompromised. Within 1 week of a prior negative test, 2 Aspergillus and 2 Mucorales PCRs were positive on plasma, and zero tests were positive on BAL. In week 1, only 1 Aspergillus species that was positive on day 7 was classified as probable fungal disease.

Conclusions
Fungal PCR follow-up testing on plasma and BAL within 4 weeks of a prior negative result was of low yield and rarely generated a positive result considered clinically significant in the first week.
HLA-DQA1*05 Associates With Anti-Tumor Necrosis Factor Immunogenicity and Low Adalimumab Trough Concentrations in Inflammatory Bowel Disease Patients From the SERENE Ulcerative Colitis and Crohn’s Disease Studies
Authors: Reppell Mark , Zheng Xiuwen , Dreher Ingeborg , Blaes Jonas , Regan Elina , Haslberger Tobias , Guay Heath , Pivorunas Valerie , Smaoui Nizar 
Published: August 2024

Abstract

Background and Aims
Anti-tumor necrosis factor (anti-TNF) therapies are commonly prescribed treatments for Crohn’s disease (CD) and ulcerative colitis (UC). Many patients treated with anti-TNF therapy eventually develop anti-drug antibodies (ADAs). Understanding the factors associated with immunogenicity in anti-TNF-treated patients can help guide treatment. The Humira SERENE studies were Phase 3 trials investigating adalimumab induction regimens in CD and UC patients.

Methods
We imputed alleles for 7 HLA genes in 1100 patients from the SERENE CD and SERENE UC trials. We then tested these alleles for association with time to immunogenicity. Subsequently, we tested loci significantly associated with immunogenicity for their association with patients who had consistently low drug serum concentrations.

Results
This study replicated the association of HLA-DQA1*05 with time to immunogenicity (hazard ratio [HR] 1.42, p = 2.22E-06). Specifically, HLA-DQA1*05:05 was strongly associated (HR 1.76, p = 2.02E-10) and we detected a novel association represented by HLA-DRB1*01:02 (HR 3.16, p = 2.92E-07). Carriage of HLA-DQA1*05:05 and HLA-DRB1*01:02 was associated with patients who experienced consistently low adalimumab trough concentrations (HLA-DQA1*05:05: odds ratio [OR] 1.98, p = 0.0049; HLA DRB1*01:02: OR 7.06, p = 7.44E-05).

Conclusions
We found a significant association between alleles at genes in the human HLA locus and the formation of adalimumab immunogenicity and low adalimumab drug serum concentrations in large clinical studies of CD and UC patients. This work extends previous findings in CD to UC and directly shows a genetic association in patients with low drug concentrations. This work builds on existing literature to suggest that genetic screening could be a useful tool for clinicians concerned with patient anti-TNF immunogenicity.

Clinical Trial Registration Numbers
SERENE CD (NCT02065570), SERENE UC (NCT02065622).
Offence, Shakespeare, and Performance
Authors: Smialkowska Monika 
Published: August 2024

Abstract
Offence is a highly topical and much debated issue in contemporary Western societies. Fierce arguments rage between those who advocate mechanisms such as safe spaces, no platforming, and sensitivity readers to protect people from encountering offence, and those who maintain that curtailing the expression of offensive ideas stifles dialogue and impoverishes intellectual exchanges. This article sheds new light on the phenomenon of offence by examining it in the context of literary production, dissemination, and consumption. It focuses on drama as a performative genre, uniquely suited to embodying and interrogating emotions underpinning offensive exchanges. Through analysing representations of offence in several Shakespeare plays and discussing three actual or planned Shakespearean productions which caused offence to twenty-first-century audiences, it illuminates the ambiguities and contradictions inherent in defining offence. In particular, it demonstrates how difficult it is to determine agency in offensive exchanges: to establish who ‘owns’ offence, whether it originates with the offender or the offended party, and who has the right to decide what its consequences should be. Simultaneously, it argues that offence includes an element of social performance, as we do not only feel but also act offended. Because of the performative nature of offence, theatre and drama theory offer us a perfect laboratory and vocabulary for engaging with this vital issue.
Commercial fishery no-take zones for African penguins minimize fisheries losses at the expense of conservation gains
Authors: McInnes Alistair M , Weideman Eleanor A , Carpenter-Kling Tegan , Barham Peter , Christian Murray , Day Kirsten , Glencross Jacqueline S , Hagen Christina , Kock Alison , Lawrence Cloverley , Ludynia Katrin , Makhado Azwianewi , Pichegru Lorien , Shannon Lynne , Sherley Richard B , Smith Craig , Steinfurth Antje , Stander Nicky , Upfold Leshia , Waller Lauren 
Published: August 2024

Abstract
The African penguin population has declined precipitously in recent decades, and if current rates of decline persist, this species could become extinct in the wild by 2035. Resource extraction of small pelagic fish prey by the purse-seine fishery around African penguin breeding colonies has been identified as a demographically meaningful threat to African penguins. Consequently, long-term, effective no-take zones around breeding colonies have been endorsed by an expert panel of scientists constituted by the South African government. Here, we consider the six largest South African penguin colonies that currently hold 76% of the global population. We evaluate the adequacy of different no-take zone options using a trade-off mechanism recommended by the expert panel. For all six colonies except Bird Island, Algoa Bay, which is subject to the least fishing pressure, the current no-take zone delineations are assessed as having little benefit to the African penguin and little to no cost to the purse-seine fishery. Four of the six current no-take zones include ≤50% of the African penguins’ core foraging areas. Alternative no-take zones that approximate a more balanced trade-off offer more impactful alternatives to the current fisheries restrictions. Given the urgent need to implement evidence-based conservation interventions for the endangered African penguin, we recommend the substitution of the current no-take zones with those proposed herein.
Generic reasoning: A programmatic sketch
Authors: Faroldi Federico L G 
Published: August 2024

Abstract
A single significant instance may support general conclusions, with possible exceptions being tolerated. This is the case in practical human reasoning (e.g. moral and legal normativity: general rules tolerating exceptions), in theoretical human reasoning engaging with external reality (e.g. empirical and social sciences: the use of case studies and model organisms) and in abstract domains (possibly mind-unrelated, e.g. pure mathematics: the use of arbitrary objects). While this has been recognized in modern times, such a process is not captured by current models of supporting general conclusions. This paper articulates the thesis that there is a kind of reasoning, generic reasoning, previously unrecognized as an independent type of reasoning. A theory of generic reasoning explains how a single significant instance may support general conclusions, with possible exceptions being tolerated. This paper will adopt, as a working hypothesis, that generic reasoning is irreducible to currently recognized kinds of ‘pure’ reasoning. The aim is to understand generic reasoning, both theoretically and in its applications.
Biesta’s world-centred education: subjectification revisited?
Authors: Guillemin Elodie 
Published: August 2024

Abstract
This article explores Biesta’s recent revisiting of his iconic and at times contested notion of education as subjectification. First, I look at how Biesta presents his notion by attending to his answers to the criticisms it has faced concerning elusiveness, oversimplification, and self-centredness. Then, going beyond the declarative level, I explore a concrete example of education as subjectification from Biesta’s 2022 book, World-Centred Education. Analysing the example of Homer Lane and Jason, I examine the ambivalence between Biesta’s explicit statements on subjectification as a form of spontaneous and noncoercive teaching aimed at cultivating freedom and the more complex picture that emerges from a close reading of the original story. From this analysis, I find important conceptual limitations to education as subjectification: it could conceal part of the institutional context of education and the teacher’s active role, and also reduce freedom to an individualistic concept. I thus conclude by suggesting that the language of subjectification should always be engaged with critically—but never in isolation—and with a stereoscopic optic in mind.
Multi-institutional prospective observational study of radiotherapy for metastatic bone tumor
Authors: Harada Hideyuki , Shikama Naoto , Notsu Akifumi , Shirato Hiroki , Yamada Kazunari , Uezono Haruka , Koide Yutaro , Kubota Hikaru , Yamazaki Takuya , Ito Kei , Heianna Joichi , Okada Yukinori , Tonari Ayako , Katoh Norio , Wada Hitoshi , Ejima Yasuo , Yoshida Kayo , Kosugi Takashi , Takahashi Shigeo , Komiyama Takafumi , Uchida Nobue , Miwa Misako , Watanabe Miho , Nagakura Hisayasu , Ikeda Hiroko , Saito Tetsuo , Asakawa Isao , Takahashi Takeo , Shigematsu Naoyuki 
Published: August 2024

Abstract
Purpose of this study is to evaluate patient characteristics, treatments and outcomes in bone metastasis radiotherapy practice. Patients for whom radiotherapy for bone metastasis was planned at 26 institutions in Japan between December 2020 and March 2021 were consecutively registered in this prospective, observational study. Study measures included patient characteristics, pain relief, skeletal-related events (SREs), overall survival and incidence of radiation-related adverse events. Pain was evaluated using a numerical rating scale (NRS) from 0 to 10. Irradiated dose was analyzed by the biologically effective dose (BED) assuming α/β = 10. Overall, 232 patients were registered; 224 patients and 302 lesions were fully analyzed. Eastern Cooperative Oncology Group Performance Status was 0/1/2/3/4 in 23%/38%/22%/13%/4%; 59% of patients had spinal metastases and 84% had painful lesions (NRS ≥ 2). BED was &lt;20 Gy (in 27%), 20–30 Gy (24%), 30–40 Gy (36%) and ≥ 40 Gy (13%); 9% of patients were treated by stereotactic body radiotherapy. Grade 3 adverse events occurred in 4% and no grade 4–5 toxicity was reported. Pain relief was achieved in 52% at 2 months. BED is not related to pain relief. The cumulative incidence of SREs was 6.5% (95% confidence interval (CI) 3.1–9.9) at 6 months; no factors were significantly associated with SREs. With spinal lesions, 18% of patients were not ambulatory at baseline and 50% of evaluable patients in this group could walk at 2 months. The 6-month overall survival rate was 70.2% (95% CI 64.2–76.9%). In conclusion, we report real-world details of radiotherapy in bone metastasis.
Mapping socio-economic status using mixed data: a hierarchical Bayesian approach
Authors: Virgili-Gervais Gabrielle , Schmidt Alexandra M , Bixby Honor , Cavanaugh Alicia , Owusu George , Agyei-Mensah Samuel , Robinson Brian , Baumgartner Jill 
Published: August 2024

Abstract
We propose a Bayesian hierarchical model to estimate a socio-economic status (SES) index based on mixed dichotomous and continuous variables. In particular, we extend Quinn’s ([2004]. Bayesian factor analysis for mixed ordinal and continuous responses. Political Analysis, 12(4), 338–353. https://doi.org/10.1093/pan/mph022) and Schliep and Hoeting’s ([2013]. Multilevel latent Gaussian process model for mixed discrete and continuous multivariate response data. Journal of Agricultural, Biological, and Environmental Statistics, 18(4), 492–513. https://doi.org/10.1007/s13253-013-0136-z) factor analysis models for mixed dichotomous and continuous variables by allowing a spatial hierarchical structure of key parameters of the model. Unlike most SES assessment models proposed in the literature, the hierarchical nature of this model enables the use of census observations at the household level without needing to aggregate any information a priori. Therefore, it better accommodates the variability of the SES between census tracts and the number of households per area. The proposed model is used in the estimation of a socio-economic index using 10% of the 2010 Ghana census in the Greater Accra Metropolitan area. Out of the 20 observed variables, the number of people per room, access to water piping and flushable toilets differentiated high and low SES areas the best.
Joint Venture Disputes
Authors: Timothy A 
Published: August 2024

Abstract
This chapter examines how joint venture disputes typically arise between the parties to the joint venture. The use of industry custom and practice (to the extent that it can be proved to exist) in resolving joint venture disputes is considered in this chapter, as is the role which case law takes in shaping joint venture disputes in the energy and natural resource sectors. This chapter goes on to consider, by reference to certain arbitration awards, the factors which tribunals have taken into consideration in reaching their decisions on international joint venture disputes. This chapter concludes with a review of the fora which are most commonly utilized for the resolution of joint venture disputes, and the kinds of issues which are the most recurring in relation to joint venture disputes.
Accounting Procedure
Authors: Timothy A 
Published: August 2024

Abstract
This chapter considers where the accounting provisions have caused disputes to arise. This relates principally, but not exclusively, to disputes in joint ventures governed by a joint operating agreement (JOA), where there are controversies over the level of costs incurred. The cases reviewed demonstrate that a number of issues can give rise to disputes. This includes the nature of costs that can be charged to the joint account, how they should be shared and the ability of the non-operators to review and audit the costs charged. In many cases, the rights to charge costs and to audit those costs are subject to express time limits and the precise application of these time limits is addressed in the cases condisdered in this chapter.
Scope of Operator’s Duties/Authority
Authors: Timothy A 
Published: August 2024

Abstract
This chapter considers the scope of the authority of the person which is appointed to act as the operator in the performance of the joint venture agreement. This definition will be important to the operator and to the parties (so that the operator and the parties have a clear understanding of the boundaries of the operator’s mandate to act), and also to any third parties who contract with the operator (given particularly the ability of the operator to bind the parties to a contract with a third party if the operator is acting as the agent of the parties). Issues of whether the operator has the necessary authority to act, and whether the operator might have acted ultra vires, will be of concern to third parties dealing with the operator. This chapter considers the scope of the operator’s authority to act in the performance of the joint venture agreement. The associated issue of how operations under the joint venture agreement are properly authorized in the first place is considered in Chapter 6. The wider issue of scope, which relates to the intended business purposes of the joint venture agreement, is considered in Chapter 4.