bluuebunny/crossref_metadata_2025_split huggingface dataset:
Data Release 2 of S-PLUS: Accurate template-fitting based photometry covering ∼1000 deg2 in 12 optical filters
Authors: Almeida-Fernandes F , SamPedro L , Herpich F R , Molino A , Barbosa C E , Buzzo M L , Overzier R A , de Lima E V R , Nakazono L M I , Oliveira Schwarz G B , Perottoni H D , Bolutavicius G F , Gutiérrez-Soto L A , Santos-Silva T , Vitorelli A Z , Werle A , Whitten D D , Costa Duarte M V , Bom C R , Coelho P , Sodré L , Placco V M , Teixeira G S M , Alonso-García J , Barbosa C L , Beers T C , Bonatto C J , Chies-Santos A L , Hartmann E A , Lopes de Oliveira R , Navarete F , Kanaan A , Ribeiro T , Schoenell W , Mendes de Oliveira C 
Published: January 2022

ABSTRACT
The Southern Photometric Local Universe Survey (S-PLUS) is an ongoing survey of ∼9300 deg2 in the southern sky in a 12-band photometric system. This paper presents the second data release (DR2) of S-PLUS, consisting of 514 tiles covering an area of 950 deg2. The data has been fully calibrated using a new photometric calibration technique suitable for the new generation of wide-field multifilter surveys. This technique consists of a χ2 minimization to fit synthetic stellar templates to already calibrated data from other surveys, eliminating the need for standard stars and reducing the survey duration by ∼15 per cent. We compare the template-predicted and S-PLUS instrumental magnitudes to derive the photometric zero-points (ZPs). We show that these ZPs can be further refined by fitting the stellar templates to the 12 S-PLUS magnitudes, which better constrain the models by adding the narrow-band information. We use the STRIPE82 region to estimate ZP errors, which are ≲ 10 mmags for filters J0410, J0430, g, J0515, r, J0660, i, J0861 and z; ≲ 15 mmags for filter J0378; and ≲ 25 mmags for filters u and J0395. We describe the complete data flow of the S-PLUS/DR2 from observations to the final catalogues and present a brief characterization of the data. We show that, for a minimum signal-to-noise threshold of 5, the photometric depths of the DR2 range from 19.1 to 20.5 mag (measured in Petrosian apertures), depending on the filter. The S-PLUS DR2 can be accessed from the website: https://splus.cloud.
Young Exoplanet Transit Initiative follow-up observations of the T Tauri star CVSO 30 with transit-like dips
Authors: Bischoff R , Raetz St , Fernández M , Mugrauer M , Neuhäuser R , Huang P C , Chen W P , Sota A , Jiménez Ortega J , Hambaryan V V , Zieliński P , Dróżdż M , Ogłoza W , Stenglein W , Hohmann E , Michel K-U 
Published: January 2022

ABSTRACT
The T Tauri star CVSO 30, also known as PTFO 8-8695, was studied intensively with ground-based telescopes as well as with satellites over the last decade. It showed a variable light curve with additional repeating planetary transit-like dips every ∼10.8 h. However, these dimming events changed in depth and duration since their discovery and from autumn 2018 on, they were not even present or near the predicted observing times. As reason for the detected dips and their changes within the complex light curve, e.g. a disintegrating planet, a circumstellar dust clump, stellar spots, possible multiplicity, and orbiting clouds at a Keplerian co-rotating radius were discussed and are still under debate. In this paper, we present additional optical monitoring of CVSO 30 with the meter class telescopes of the Young Exoplanet Transit Initiative in Asia and Europe over the last 7 yr and characterize CVSO 30 with the new Early Data Release 3 of the European Space Agency-Gaia mission. As a result, we describe the evolution of the dimming events in the optical wavelength range since 2014 and present explanatory approaches for the observed variabilities. We conclude that orbiting clouds of gas at a Keplerian co-rotating radius are the most promising scenario to explain most changes in CVSO 30’s light curve.
SIBELIUS-DARK: a galaxy catalogue of the local volume from a constrained realization simulation
Authors: McAlpine Stuart , Helly John C , Schaller Matthieu , Sawala Till , Lavaux Guilhem , Jasche Jens , Frenk Carlos S , Jenkins Adrian , Lucey John R , Johansson Peter H 
Published: January 2022

ABSTRACT
We present sibelius-dark, a constrained realization simulation of the local volume to a distance of 200 Mpc from the Milky Way. sibelius-dark is the first study of the ‘Simulations Beyond The Local Universe’ (sibelius) project, which has the goal of embedding a model Local Group-like system within the correct cosmic environment. The simulation is dark-matter-only, with the galaxy population calculated using the semi-analytic model of galaxy formation, galform. We demonstrate that the large-scale structure that emerges from the sibelius constrained initial conditions matches well the observational data. The inferred galaxy population of sibelius-dark also match well the observational data, both statistically for the whole volume and on an object-by-object basis for the most massive clusters. For example, the K-band number counts across the whole sky, and when divided between the northern and southern Galactic hemispheres, are well reproduced by sibelius-dark. We find that the local volume is somewhat unusual in the wider context of ΛCDM: it contains an abnormally high number of supermassive clusters, as well as an overall large-scale underdensity at the level of ≈5 per cent relative to the cosmic mean. However, whilst rare, the extent of these peculiarities does not significantly challenge the ΛCDM model. sibelius-dark is the most comprehensive constrained realization simulation of the local volume to date, and with this paper we publicly release the halo and galaxy catalogues at z = 0, which we hope will be useful to the wider astronomy community.
Marking the shells of juvenile and adult eastern oysters, Crassostrea virginica, with the fluorochrome dye calcein and measuring growth and mortality after marking
Authors: Spires Jason E , North Elizabeth W 
Published: January 2022

ABSTRACT
Techniques for positive re-identification of finfish are well developed and are used to estimate vital rates, migration patterns and stock structure. Fluorochrome dyes, like nontoxic calcein, have been used with success to mark hard parts of fish and the shells of some molluscs. Yet, despite the commercial and ecological importance of the eastern oyster Crassostrea virginica, a systematic evaluation of the effectiveness of calcein for marking this species does not exist. In this study, methods that have been used for marking freshwater mussels with calcein were tested on 2-week- and 2-month-old juvenile C. virginica and on 3-year-old adult C. virginica. Individuals were immersed in 250 mg l−1 of calcein for 24 h either once (single treatment) or three times (triple treatment), and then observed to determine whether marks were visible, how long they remained visible and whether calcein influenced growth and mortality of the different age classes. Results indicated that all marked individuals were recognizable under blue light, that multiple distinct marks were possible on juveniles and that marks on juveniles could remain visible for 3.75 years. Growth of juveniles and adults treated with calcein was not significantly different from controls after 11 months. Survivorship did not differ between treated and control individuals for all treatments and ages, except the 2-month-old juvenile oysters that were immersed three times. Results indicate that calcein is an effective and safe marking technique for juvenile oysters from robust cohorts, and could be used to enhance studies of growth, mortality, larval transport and settlement in situ.
How do megaprojects influence institutional change?
Authors: Msulwa Rehema 
Published: January 2022

Abstract
A growing body of research emphasizes the importance of institutions for megaproject performance. Extant studies focus on understanding the characteristics of favourable institutional environments and the governance structures that projects can adopt to navigate both favourable and unfavourable environments. This paper contributes to this research by foregrounding the link between megaprojects and changes in the institutional environments within which they are embedded. Building on a case study of the Thames Tideway Tunnel—the UK’s largest water and sewerage infrastructure project since the privatization of the industry in 1989—the paper presents two distinct ways that projects can interact with formal institutions: institutional compliance and institutional change. A more holistic understanding of the latter is essential because megaprojects can reconfigure production and consumption patterns to the benefit of some and the detriment of others. By contributing to changes in the institutional environment, megaprojects can further entrench these reconfigured patterns into long-enduring formal rules and practices.
Investigating the performance of PPP in major healthcare infrastructure projects: the role of policy, institutions, and contracts
Authors: Vecchi Veronica , Cusumano Niccolò , Casalini Francesca 
Published: January 2022

AbstractIn the wake of the Covid-19 pandemic, public private partnerships (PPP) can prove useful to close the healthcare investment gap and accelerate long-term recovery, by matching public and private money. Despite their extensive application in the delivery of major infrastructure projects globally, their performance remains contested. Drawing on a unique set of data of PPP contracts for healthcare investments in Italy, the paper explores the antecedents (namely, policies, institutions, and contracts), that have influenced the capacity of PPP contracts to deliver performance, measured in terms of value for money (VfM), and contract stability. Results show that although explicit policy goals have a clear contribution, VfM can benefit from competent central PPP institutions, which should play a hands-on role in the planning, design, and project management activities. At the same time, centralised PPP units, if not combined with local competent authorities and strong governance mechanisms, may increase the risk of contract renegotiation.
Between a Rock and a Hard Polytomy: Phylogenomics of the Rock-Dwelling Mbuna Cichlids of Lake Malaŵi
Authors: Scherz Mark D , Masonick Paul , Meyer Axel , Hulsey C Darrin 
Published: January 2022

AbstractWhole genome sequences are beginning to revolutionize our understanding of phylogenetic relationships. Yet, even whole genome sequences can fail to resolve the evolutionary history of the most rapidly radiating lineages, where incomplete lineage sorting, standing genetic variation, introgression, and other factors obscure the phylogenetic history of the group. To overcome such challenges, one emerging strategy is to integrate results across different methods. Most such approaches have been implemented on reduced representation genomic data sets, but whole genomes should provide the maximum possible evidence approach. Here, we test the ability of single nucleotide polymorphisms extracted from whole genome resequencing data, implemented in an integrative genomic approach, to resolve key nodes in the phylogeny of the mbuna, rock-dwelling cichlid fishes of Lake Malaŵi, which epitomize the phylogenetic intractability that often accompanies explosive lineage diversification. This monophyletic radiation has diversified at an unparalleled rate into several hundred species in less than 2 million years. Using an array of phylogenomic methods, we consistently recovered four major clades of mbuna, but a large basal polytomy among them. Although introgression between clades apparently contributed to the challenge of phylogenetic reconstruction, reduction of the data set to nonintrogressed sites still did not help to resolve the basal polytomy. On the other hand, relationships among six congeneric species pairs were resolved without ambiguity, even in one case where existing data led us to predict that resolution would be difficult. We conclude that the bursts of diversification at the earliest stages of the mbuna radiation may be phylogenetically unresolvable, but other regions of the tree are phylogenetically clearly supported. Integration of multiple phylogenomic approaches will continue to increase confidence in relationships inferred from these and other whole-genome data sets. [Incomplete lineage sorting; introgression; linkage disequilibrium; multispecies coalescence; rapid radiation; soft polytomy.]
A Conserved Hypothetical Gene Is Required but Not Sufficient for Ptr ToxC Production inPyrenophora tritici-repentis
Authors: Shi Gongjun , Kariyawasam Gayan , Liu Sanzhen , Leng Yueqiang , Zhong Shaobin , Ali Shaukat , Moolhuijzen Paula , Moffat Caroline S. , Rasmussen Jack B. , Friesen Timothy L. , Faris Justin D. , Liu Zhaohui 
Published: January 2022

The fungus Pyrenophora tritici-repentis causes tan spot, an important foliar disease of wheat worldwide. The fungal pathogen produces three necrotrophic effectors, namely Ptr ToxA, Ptr ToxB, and Ptr ToxC to induce necrosis or chlorosis in wheat. Both Ptr ToxA and Ptr ToxB are proteins, and their encoding genes have been cloned. Ptr ToxC was characterized as a low–molecular weight molecule 20 years ago but the one or more genes controlling its production in P. tritici-repentis are unknown. Here, we report the genetic mapping, molecular cloning, and functional analysis of a fungal gene that is required for Ptr ToxC production. The genetic locus controlling the production of Ptr ToxC, termed ToxC, was mapped to a subtelomeric region using segregating biparental populations, genome sequencing, and association analysis. Additional marker analysis further delimited ToxC to a 173-kb region. The predicted genes in the region were examined for presence/absence polymorphism in different races and isolates leading to the identification of a single candidate gene. Functional validation showed that this gene was required but not sufficient for Ptr ToxC production, thus it is designated as ToxC1. ToxC1 encoded a conserved hypothetical protein likely located on the vacuole membrane. The gene was highly expressed during infection, and only one haplotype was identified among 120 isolates sequenced. Our work suggests that Ptr ToxC is not a protein and is likely produced through a cascade of biosynthetic pathway. The identification of ToxC1 is a major step toward revealing the Ptr ToxC biosynthetic pathway and studying its molecular interactions with host factors.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Transfusion-Associated Delirium in Children: No Difference Between Short Storage Versus Standard Issue RBCs
Authors: Traube Chani , Tucci Marisa , Nellis Marianne E. , Avery K. Leslie , McQuillen Patrick S. , Fitzgerald Julie C. , Muszynski Jennifer A. , Cholette Jill M. , Schwarz Adam J. , Stalets Erika L. , Quaid Maureen A. , Hanson Sheila J. , Lacroix Jacques , Reeder Ron W. , Spinella Philip C. ,   for the Transfusion-Associated Delirium ABC-PICU Study Group
Published: January 2022

OBJECTIVES:
Primary objective is to determine if transfusion of short storage RBCs compared with standard issue RBCs reduced risk of delirium/coma in critically ill children. Secondary objective is to assess if RBC transfusion was independently associated with delirium/coma.

DESIGN:
This study was performed in two stages. First, we compared patients receiving either short storage or standard RBCs in a multi-institutional prospective randomized controlled trial. Then, we compared all transfused patients in the randomized controlled trial with a single-center cohort of nontransfused patients matched for confounders of delirium/coma.

SETTING:
Twenty academic PICUs who participated in the Age of Transfused Blood in Critically Ill Children trial.

PATIENTS:
Children 3 days to 16 years old who were transfused RBCs within the first 7 days of admission.

INTERVENTIONS:
Subjects were randomized to either short storage RBC study arm (defined as RBCs stored for up to seven days) or standard issue RBC study arm. In addition, subjects were screened for delirium prior to transfusion and every 12 hours after transfusion for up to 3 days.

MEASUREMENTS AND MAIN RESULTS:
Primary outcome measure was development of delirium/coma within 3 days of initial transfusion. Additional outcome measures were dose-response relationship between volume of RBCs transfused and delirium/coma, and comparison of delirium/coma rates between transfused patients and individually matched nontransfused patients. We included 146 subjects in the stage I analysis; 69 were randomized to short storage RBCs and 77 to standard issue. There was no significant difference in delirium/coma development between study arms (79.5% vs 70.1%; p = 0.184). In the stage II analysis, adjusted odds for delirium in the transfused cohort was more than eight-fold higher than in the nontransfused matched cohort, even after controlling for hemoglobin (adjusted odds ratio, 8.9; CI, 2.8–28.4; p < 0.001).

CONCLUSIONS:
RBC transfusions (and not anemia) are independently associated with increased odds of subsequent delirium/coma. However, storage age of RBCs does not affect delirium risk.
Lung- and Diaphragm-Protective Ventilation by Titrating Inspiratory Support to Diaphragm Effort: A Randomized Clinical Trial
Authors: de Vries Heder J. , Jonkman Annemijn H. , de Grooth Harm J. , Duitman Jan Willem. , Girbes Armand R. J. , Ottenheijm Coen A. C. , Schultz Marcus J. , van de Ven Peter M. , Zhang Yingrui , de Man Angelique M. E. , Tuinman Pieter R. , Heunks Leo M. A. 
Published: January 2022

OBJECTIVES:
Lung- and diaphragm-protective ventilation is a novel concept that aims to limit the detrimental effects of mechanical ventilation on the diaphragm while remaining within limits of lung-protective ventilation. The premise is that low breathing effort under mechanical ventilation causes diaphragm atrophy, whereas excessive breathing effort induces diaphragm and lung injury. In a proof-of-concept study, we aimed to assess whether titration of inspiratory support based on diaphragm effort increases the time that patients have effort in a predefined “diaphragm-protective” range, without compromising lung-protective ventilation.

DESIGN:
Randomized clinical trial.

SETTING:
Mixed medical-surgical ICU in a tertiary academic hospital in the Netherlands.

PATIENTS:
Patients (n = 40) with respiratory failure ventilated in a partially-supported mode.

INTERVENTIONS:
In the intervention group, inspiratory support was titrated hourly to obtain transdiaphragmatic pressure swings in the predefined “diaphragm-protective” range (3–12 cm H2O). The control group received standard-of-care.

MEASUREMENTS AND MAIN RESULTS:
Transdiaphragmatic pressure, transpulmonary pressure, and tidal volume were monitored continuously for 24 hours in both groups. In the intervention group, more breaths were within “diaphragm-protective” range compared with the control group (median 81%; interquartile range [64–86%] vs 35% [16–60%], respectively; p < 0.001). Dynamic transpulmonary pressures (20.5 ± 7.1 vs 18.5 ± 7.0 cm H2O; p = 0.321) and tidal volumes (7.56 ± 1.47 vs 7.54 ± 1.22 mL/kg; p = 0.961) were not different in the intervention and control group, respectively.

CONCLUSIONS:
Titration of inspiratory support based on patient breathing effort greatly increased the time that patients had diaphragm effort in the predefined “diaphragm-protective” range without compromising tidal volumes and transpulmonary pressures. This study provides a strong rationale for further studies powered on patient-centered outcomes.
Surgically Treated Neuroma in Upper Extremity: Patient Characteristics and Factors Influencing Outcome of Surgery
Authors: Nyman Erika , Dahlin Emma , Gudinge Hanna , Dahlin Lars B. 
Published: January 2022

Background:
Neuroma formation occurs after inappropriately or untreated nerve injuries. Patients surgically treated for neuroma were characterized and factors influencing outcome evaluated.

Methods:
In a retrospective observational study, data from medical records of patients surgically treated for neuroma in two Swedish regions were analyzed.

Results:
In 115 included patients (median age at surgery 45 years [IQR 29–55]), 55% (62/115) were men and 49% (56/115) were manual laborers. Most affected nerves were in hand or lower forearm (76/115, 66%). Smoking habits, affected nerves, and cause/mechanism(s) of injury differentiated the sexes. More motor nerve injuries were observed among women and more mixed nerve injuries among men. Iatrogenic injuries, such as injury to superficial sensory radial nerve or thenar branch of median nerve, more frequently affected women (27/52, 52%). Pain, the dominant preoperative symptom, improved after surgery. Overall, surgery cured/improved 79 of 115 (69%) patients. Patients treated with repair or reconstruction (n = 62) were younger than patients given neuroma transpositions (n = 43) and sensory nerve injuries were more often treated by transposition. No difference in outcome was observed concerning patient characteristics or surgical methods. Most patients had one surgery (102/115, 89%). No specific risk factors for a re-operation could be identified, but need for re-operation(s) was associated with poor outcome, even after repeated surgery.

Conclusions:
Patients with a neuroma benefit from surgery with significantly reduced pain, but symptoms may remain. Surgical method does not affect outcome. Preventing neuroma formation is crucial, presently highlighted in a high frequency of iatrogenic injuries, especially among women.
Organ Donation Decision in Families With Brain-Dead Patients
Authors: Rafii Forough , Rahimi Sara 
Published: January 2022

Background and Aim:
Organ donation decision is a complicated process for bereaved families; however, its attributes and associated factors are not clear. Accordingly, the purpose of this study was to analyze the concept of organ donation decision in families with brain-dead patients.

Methods:
Concept analysis was performed using Rodgers' evolutionary method. For this purpose, PubMed, OVID, Scopus, and ProQuest databases were searched in English from 1985 to 2019. In total, 54 articles were analyzed using the thematic analysis to identify the attributes, antecedents, and consequences of the concept. The validity of the data was provided by examining the analysis process by 2 independent researchers.

Findings/Conclusions:
Organ donation decision in these families is a complicated and conflicting process of vicarious decision-making that begins with an organ donation request: a difficult, painful, and critical experience that requires extensive interpersonal interactions and is ultimately influenced by various factors, leading to the acceptance or refusal. The antecedents include deceased-related factors, family-related factors, the quality of organ donation request, and the quality of health care professionals' interactions. The consequences include the positive outcomes (grief solace, gift of life, and promoting human values) and negative outcomes (ambiguity, doubt and regret, and psychological inconsistency). The results of this concept analysis led to a better understanding of the complexity of an organ donation decision in these families. In this way, in addition to knowledge development, it assists the health care staff to support families in making the organ donation decision.

Implications for Case Management Practice:
Although case managers rarely participate in organ donation, they definitely need to understand the concepts related to organ donation decision while advocating for the patients or families. The results of this concept analysis can broaden the case managers' and other health care professionals' knowledge about families' organ donation decision and help them take more effective interventions for management of this process. Case managers and the health care team can use the information of this article for informing families about brain death, negotiating with families for organ donation, preparing information, and caring and facilitating the families in making the clear and unconflicted decision.