bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reconsidering Transitional Justice
Authors: Carpenter Christine 
Published: April 2022

Abstract
The transitional justice literature has, for decades, sought to understand and advocate for mechanisms through which a society may transition from a period of autocracy and mass atrocity into one of democracy, peace and stability. However, this field has left certain geographic regions under-examined — including, for example, events taking place in 20th-century China. Seeking to augment the literature’s consideration of transitional justice, this article employs the case study method to examine two pivotal events in China’s recent history: the 1949 Communist Revolution and the Gang of Four Trials in 1979. It is argued that incorporating these examples into the literature could supplement our understanding of transitional justice and that, by broadening the lens on this concept, events that have long existed on the margins could be internalized to enrich the field’s discussion. In order to accomplish this, the article puts forward a new framework through which transitional justice examples may be analysed — employing a graphical aid to visually designate both the type of justice sought and the degree of transition achieved.
Biological and Molecular Factors Predicting Response to Adoptive Cell Therapies in Cancer
Authors: Ferrer Gerardo , Álvarez-Errico Damiana , Esteller Manel 
Published: April 2022

AbstractAdoptive cell therapy (ACT) constitutes a major breakthrough in cancer management that has expanded in the past years due to impressive results showing durable and even curative responses for some patients with hematological malignancies. ACT leverages antigen specificity and cytotoxic mechanisms of the immune system, particularly relying on the patient’s T lymphocytes to target and eliminate malignant cells. This personalized therapeutic approach exemplifies the success of the joint effort of basic, translational, and clinical researchers that has turned the patient’s immune system into a great ally in the search for a cancer cure. ACTs are constantly improving to reach a maximum beneficial clinical response. Despite being very promising therapeutic options for certain types of cancers, mainly melanoma and hematological malignancies, these individualized treatments still present several shortcomings, including elevated costs, technical challenges, management of adverse side effects, and a limited population of responder patients. Thus, it is crucial to discover and develop reliable and robust biomarkers to specifically and sensitively pinpoint the patients that will benefit the most from ACT as well as those at higher risk of developing potentially serious toxicities. Although unique readouts of infused cell therapy success have not yet been identified, certain characteristics from the adoptive cells, the tumor, and/or the tumor microenvironment have been recognized to predict patients’ outcome on ACT. Here, we comment on the importance of biomarkers to predict ACT chances of success to maximize efficacy of treatments and increase patients’ survival.
A confounding bronchopulmonary situs abnormality after bilateral lung transplantation
Authors: Ghosh Subha , Fox Steven , Mehta Atul C 
Published: April 2022

Abstract
A 36-year-old female with a past medical history of primary ciliary dyskinesia and bilateral lung transplantation was noted to have a rare and confounding postsurgical anatomy acquired as a result of transplantation. Bronchoscopy and computed tomography showed isomeric main bronchi with a tri-lobed right lung, a bi-lobed left lung and dextrocardia. This rare phenomenon can be observed in lung transplant recipients with situs ambiguous morphology of their native lungs, who receive donor lungs with normal situs solitus morphology. To the best of our knowledge, ours is the first reported case of such a composite bronchopulmonary situs abnormality. Careful review of bronchial anatomy should be done with the help of CT imaging prior to undertaking any bronchial interventions in these subset of patients with bronchial isomerism and bilateral lung transplantation.
Prospective Validation of a Machine Learning Model for Low-Density Lipoprotein Cholesterol Estimation
Authors: Ghayad Jean Pierre , Barakett-Hamadé Vanda , Sleilaty Ghassan 
Published: April 2022

Abstract

Objective
We aim to prospectively validate a previously developed machine learning algorithm for low-density lipoprotein cholesterol (LDL-C) estimation.

Methods
We retrospectively and prospectively evaluated a machine learning algorithm based on k-nearest neighbors (KNN) according to age, sex, health care setting, and triglyceridemia against a direct LDL-C assay. The agreement of low-density lipoprotein-k-nearest neighbors (LDL-KNN) with the direct measurement was assessed using intraclass correlation coefficient (ICC).

Results
The analysis comprised 31,853 retrospective and 6599 prospective observations, with a mean age of 54.2 ± 17.2 years. LDL-KNN exhibited an ICC greater than 0.9 independently of age, sex, and disease status. LDL-KNN was in satisfactory agreement with direct LDL-C in observations with normal triglyceridemia and mild hypertriglyceridemia but displayed an ICC slightly below 0.9 in severely hypertriglyceridemic patients and lower in very low LDL-C observations.

Conclusion
LDL-KNN performs robustly across ages, genders, health care settings, and triglyceridemia. Further algorithm development is needed for very low LDL-C observations.
BusyBee Web: towards comprehensive and differential composition-based metagenomic binning
Authors: Schmartz Georges P , Hirsch Pascal , Amand Jérémy , Dastbaz Jan , Fehlmann Tobias , Kern Fabian , Müller Rolf , Keller Andreas 
Published: April 2022

Abstract
Despite recent methodology and reference database improvements for taxonomic profiling tools, metagenomic assembly and genomic binning remain important pillars of metagenomic analysis workflows. In case reference information is lacking, genomic binning is considered to be a state-of-the-art method in mixed culture metagenomic data analysis. In this light, our previously published tool BusyBee Web implements a composition-based binning method efficient enough to function as a rapid online utility. Handling assembled contigs and long nanopore generated reads alike, the webserver provides a wide range of supplementary annotations and visualizations. Half a decade after the initial publication, we revisited existing functionality, added comprehensive visualizations, and increased the number of data analysis customization options for further experimentation. The webserver now allows for visualization-supported differential analysis of samples, which is computationally expensive and typically only performed in coverage-based binning methods. Further, users may now optionally check their uploaded samples for plasmid sequences using PLSDB as a reference database. Lastly, a new application programming interface with a supporting python package was implemented, to allow power users fully automated access to the resource and integration into existing workflows. The webserver is freely available under: https://www.ccb.uni-saarland.de/busybee.
Multi-CSAR: a web server for scaffolding contigs using multiple reference genomes
Authors: Liu Shu-Cheng , Ju Yan-Ru , Lu Chin Lung 
Published: April 2022

Abstract
Multi-CSAR is a web server that can efficiently and more accurately order and orient the contigs in the assembly of a target genome into larger scaffolds based on multiple reference genomes. Given a target genome and multiple reference genomes, Multi-CSAR first identifies sequence markers shared between the target genome and each reference genome, then utilizes these sequence markers to compute a scaffold for the target genome based on each single reference genome, and finally combines all the single reference-derived scaffolds into a multiple reference-derived scaffold. To run Multi-CSAR, the users need to upload a target genome to be scaffolded and one or more reference genomes in multi-FASTA format. The users can also choose to use the ‘weighting scheme of reference genomes’ for Multi-CSAR to automatically calculate different weights for the reference genomes and choose either ‘NUCmer on nucleotides’ or ‘PROmer on translated amino acids’ for Multi-CSAR to identify sequence markers. In the output page, Multi-CSAR displays its multiple reference-derived scaffold in two graphical representations (i.e. Circos plot and dotplot) for the users to visually validate the correctness of scaffolded contigs and in a tabular representation to further validate the scaffold in detail. Multi-CSAR is available online at http://genome.cs.nthu.edu.tw/Multi-CSAR/.
Impact of kidney transplantation in obese candidates: a time-dependent propensity score matching study
Authors: Castelli Christel , Foucher Yohann , Boucquemont Julie , Prezelin-Reydit Mathilde , Giral Magali , Savoye Emilie , Hazzan Marc , Lenain Rémi 
Published: April 2022

ABSTRACT

Background
Although kidney transplantation (KT) is considered the best treatment for end-stage renal disease (ESRD), there are concerns about its benefit in the obese population because of the increased incidence of post-transplant adverse events. We compared patients who underwent KT versus patients awaiting KT on dialysis.

Methods
We estimated the life expectancy [restricted mean survival time (RMST)] for a 10-year follow-up by matching on time-dependent propensity scores. The primary outcome was time to death.

Results
In patients with a body mass index (BMI) ≥30 kg/m2 (n = 2155 patients per arm), the RMST was 8.23 years [95% confidence interval (CI) 8.05–8.40] in the KT group versus 8.00 years (95% CI 7.82–8.18) in the awaiting KT group, a difference of 2.71 months (95% CI −0.19–5.63). In patients with a BMI ≥35 kg/m2 (n = 212 patients per arm), we reported no significant difference [8.56 years (95% CI 7.96–9.08) versus 8.66 (95% CI 8.10–9.17)]. Hence we deduced that KT in patients with a BMI between 30 and 35 kg/m2 was beneficial in terms of life expectancy.

Conclusion
Regarding the organ shortage, KT may be questionable for those with a BMI ≥35 kg/m2. These results do not mean that a BMI ≥35 kg/m2 should be a barrier to KT, but it should be accounted for in allocation systems to better assign grafts and maximize the overall life expectancy of ESRD patients.
Electronic alerts and a care bundle for acute kidney injury—an Australian cohort study
Authors: Kotwal Sradha , Herath Sanjeeva , Erlich Jonathan , Boardman Sally , Qian Jennifer , Lawton Paul , Campbell Craig , Whatnall Andrew , Teo Su , Horvath A Rita , Endre Zoltán H 
Published: April 2022

ABSTRACTBackgroundEarly recognition of hospital-acquired acute kidney injury (AKI) may improve patient management and outcomes.MethodsThis multicentre study was conducted at three hospitals (H1—intervention; H2 and H3—controls) served by a single laboratory. The intervention bundle [an interruptive automated alerts (aAlerts) showing AKI stage and baseline creatinine in the eMR, a management guide and junior medical staff education] was implemented only at H1. Outcome variables included length-of-stay (LOS), all-cause in-hospital mortality and management quality.ResultsOver 6 months, 639 patients developed AKI (265 at H1 and 374 at controls), with 94.7% in general wards; 537 (84%) patients developed Stage 1, 58 (9%) Stage 2 and 43 (7%) Stage 3 AKI. Median LOS was 9 days (IQR 4–17) and was not different between intervention and controls. However, patients with AKI stage 1 had shorter LOS at H1 [median 8 versus 10 days (P = 0.021)]. Serum creatinine had risen prior to admission in most patients. Documentation of AKI was better in H1 (94.8% versus 83.4%; P = 0.001), with higher rates of nephrology consultation (25% versus 19%; P = 0.04) and cessation of nephrotoxins (25.3 versus 18.8%; P = 0.045). There was no difference in mortality between H1 versus controls (11.7% versus 13.0%; P = 0.71).ConclusionsMost hospitalized patients developed Stage 1 AKI and developed AKI in the community and remained outside the intensive care unit (ICU). The AKI eAlert bundle reduced LOS in most patients with AKI and increased AKI documentation, nephrology consultation rate and cessation of nephrotoxic medications.
Improving Management Through Worker Evaluations: Evidence from Auto Manufacturing
Authors: Cai Jing , Wang Shing-Yi 
Published: April 2022

Abstract
Using a randomized experiment with an automobile manufacturing firm in China, we measure the effects of letting workers evaluate their managers on worker and firm outcomes. In the treatment teams, workers evaluate their managers monthly. We find that providing feedback leads to significant reductions in worker turnover and increases in team-level productivity. In addition, workers report higher levels of happiness and well-being. The evidence suggests that these results are driven by learning by managers, leading to changes in their behavior and an overall better relationship between managers and workers.
Enriching research quality: A proposition for stakeholder heterogeneity
Authors: Franssen Thomas 
Published: April 2022

Abstract
Dominant approaches to research quality rest on the assumption that academic peers are the only relevant stakeholders in its assessment. In contrast, impact assessment frameworks recognize a large and heterogeneous set of actors as stakeholders. In transdisciplinary research non-academic stakeholders are actively involved in all phases of the research process and actor-network theorists recognize a broad and heterogeneous set of actors as stakeholders in all types of research as they are assigned roles in the socio-material networks, also termed ‘problematizations’, that researchers reconfigure. Actor-network theorists consider research as a performative act that changes the reality of the stakeholders it, knowingly or unknowingly, involves. Established approaches to, and notions of, research quality do not recognize the heterogeneity of relevant stakeholders nor allow for reflection on the performative effects of research. To enrich the assessment of research quality this article explores the problematization as a potential new object of evaluation. Problematizations are proposals for how the future might look. Hence, their acceptance does not only concern fellow academics but also all other human and other-than-human actors that figure in them. To enrich evaluative approaches, this article argues for the inclusion of stakeholder involvement and stakeholder representation as dimensions of research quality. It considers a number of challenges to doing so including the identification of stakeholders, developing quality criteria for stakeholder involvement and stakeholder representation, and the possibility of participatory research evaluation. It can alternatively be summarized as raising the question: for whose benefit do we conduct evaluations of research quality?
Letters of wishes and their ongoing importance in a trustee’s decision-making
Authors: Sanders Nigel , Yates Charlotte 
Published: April 2022

Abstract
With the rise in judicial commentary on the significance of letters of wishes—in part led by beneficiaries disputing the construction, validity or weight that a trustee has given to them—their status as important relevant considerations for a trustee to take into account when engaging in a decision-making process has been established. However, the Courts are continuing to have to grapple with myriad circumstances and different scenarios in which expressions of wishes are made and fall to be considered. This article considers the importance of a settlor's letters of wishes, a trustee's duty to take a settlor's wishes into consideration, the position where there are multiple letters of wishes, which letter of wishes applies where a trust to trust appointment is concerned and the approach the courts are likely to follow when considering letters of wishes.
Heavy metals in road-deposited sediment and runoff in urban and intercity expressways
Authors: Gao Shuohan , Wang Xinjun , Li Hua , Kong Yaping , Chen Jiding , Chen Zheng 
Published: April 2022

Abstract
Road-deposited sediments (RDS) accumulated on road surfaces are an important environmental medium that often provides transport for heavy metals. In order to understand the characteristics of heavy metals in RDS, we investigated the size distribution and heavy metal (i.e. Cd, Cr, Cu, Ni, Pb and Zn) concentrations in RDS and road runoff in typical expressways of suburban and rural area in China. The results demonstrated that RDS particles from all impervious expressway surfaces were predominantly coarse particles (&gt;250 $\mu$m, 58.4% ± 3.8%) and the RDS on all expressways contained more heavy metals than background soils. Furthermore, the concentrations of Cd, Cr, Cu, Ni, Pb and Zn increased with traffic volume, suggesting that these heavy metals are mainly derived from traffic activities. Moreover, it is found that although heavy metals were concentrated in fine grain fractions, the total loading is highest for the coarsest particles due to their large mass percentage. Additionally, it reveals that the heavy metal concentrations in road runoff of suburban expressway are higher than that in urban expressway. Our findings enhance the understanding of expressway pollution, and imply that for controlling runoff pollution from RDS, transportation agencies should be concerned with both fine and coarse particles and take cleaning methods into account.
The Rapid Screening for Somatosensory Tinnitus Tool: a Data-Driven Decision Tree Based on Specific Diagnostic Criteria
Authors: Michiels Sarah , Cardon Emilie , Gilles Annick , Goedhart Hazel , Vesala Markku , Van Rompaey Vincent , Van de Heyning Paul , Schlee Winfried 
Published: April 2022

Background:
Somatosensory or somatic tinnitus (ST) is a type of tinnitus where changes in somatosensory afference from the cervical spine or temporomandibular area alter the tinnitus perception. Very recently, the diagnostic value of a set of 16 diagnostic criteria for ST was determined. The next step in the development of easily applicable diagnostic criteria is to provide an uncomplicated model, based on the existing criteria, which can easily be used in clinical practice.

Objectives:
This study aims to construct an accurate decision tree, combining several diagnostic criteria, to optimize both sensitivity and specificity of ST diagnosis.

Design:
An online survey was launched on the online forum Tinnitus Talk, managed by Tinnitus Hub in a convenience sample of participants with tinnitus. The survey included 42 questions, both on the presence of diagnostic criteria for ST and on other potentially influencing factors. A decision tree was constructed to classify participants with and without ST using the rpart package in R. Tree depth was optimized during a five-fold cross-validation. Finally, model performance was evaluated on a subset containing 20% of the original dataset.

Results:
Data of 7981 participants were used to construct a decision tree for ST diagnosis. Four criteria were included in the final decision tree: ‘Tinnitus and neck/jaw pain increase/decrease simultaneously’, ‘Tension in suboccipital muscles’, ‘Somatic modulation’, and ‘Bruxism’. The presented model has an accuracy of 82.2%, a sensitivity of 82.5%, and a specificity of 79%. Receiver operator characteristic curves demonstrated an area under the curve of 0.88.

Conclusions:
Based on a 42-item survey, a decision tree was created that was able to detect ST patients with high accuracy (82.2%) using only 4 questions. The RaSST is therefore expected to be easily implementable in clinical practice.
Identifying exposure pathways mediating adverse birth outcomes near active surface mines in Central Appalachia
Authors: Ruktanonchai Corrine W. , McKnight Molly X. , Buttling Lauren , Kolivras Korine , Krometis Leigh-Anne , Gohlke Julia 
Published: April 2022

Background:
Previous work has determined an association between proximity to active surface mining within Central Appalachia and an increased risk of preterm birth (PTB) and low birthweight (LBW). Multiple potential exposure pathways may exist; however, including inhalation of particulate matter (airshed exposure), or exposure to impacted surface waters (watershed exposure). We hypothesize that this relationship is mediated by exposure to contaminants along one or both of these pathways.

Methods:
We geolocated 194,084 birth records through health departments in WV, KY, VA, and TN between 1990 and 2015. We performed a mediation analysis, iteratively including within our models: (a) the percent of active surface mining within 5 km of maternal residence during gestation; (b) the cumulative surface mining airshed trajectories experienced during gestation; and (c) the percent of active surface mining occurring within the watershed of residency during gestation.

Results:
Our baseline models found that active surface mining was associated with an increased odds of PTB (1.09, 1.05–1.13) and LBW (1.06, 1.02–1.11), controlling for individual-level predictors. When mediators were added to the baseline model, the association between active mining and birth outcomes became nonsignificant (PTB: 0.48, 0.14–1.58; LBW 0.78, 0.19–3.00), whereas the association between PTB and LBW remained significant by airshed exposure (PTB: 1.14, 1.11–1.18; LBW: 1.06, 1.03–1.10).

Conclusions:
Our results found that surface mining airsheds at least partially explained the association between active mining and adverse birth outcomes, consistent with a hypothesis of mediation, while mediation via the watershed pathway was less evident.
Publish or Perish: A Cross-Sectional, Bibliometric Analysis of Physician Assistant Faculty Publications
Authors: Garino Alexandria , Wang Lei , Min Elana A. 
Published: April 2022

Purpose:
Little is known about physician assistant (PA) educators' publishing practices and the collective impact of their published works. The goal of this study was to describe the scholarly output of the PA professoriate in a way that is useful to both promotion committees and individual educators who are planning careers.

Methods:
A cross-sectional study was performed to demonstrate publishing patterns. The name of each PA-credentialed educator in academic health centers was searched in Scopus. Citations of peer-reviewed articles published through 2019 were retrieved and de-duplicated. The number of publications, h-indices, journal names, and keywords were collected between May 2019 and January 2020. Differences among academic ranks were explored, and keywords were analyzed. Frequently used journals were determined and their impact factors retrieved.

Results:
A total of 364 faculty met inclusion criteria. Between 1972 and 2019, 895 peer-reviewed articles were published; 603 were published in the last 10 years. Approximately half the study cohort (n = 172) published at least one peer-reviewed article that met inclusion criteria (range 1-89; median = 2). Overall, productivity remained steady over the last 10 years (range 0-59; median = 2). Faculty at the professor and associate level had a median h-index of 2.00 and assistants had a median h-index of 1.00. PhD-prepared faculty published more articles and had higher h-indices than faculty with other types of degrees.

Conclusions:
The results provide benchmarking data that can be used for promotion and professional development. More faculty must publish and increase the citation rate of their publications if we are to improve the reputation of the PA educator literature.