bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conservation, uncertainty and intellectual humility
Authors: Michaels Sarah , Auld Graeme , Cooke Steven J , Young Nathan , Bennett Joseph R , Vermaire Jesse C 
Published: November 2023

SummaryInterventions in environmental conservation are intended to make things better, not worse. Yet unintended and unanticipated consequences plague environmental conservation; key is how uncertainty plays out. Insights from the intellectual humility literature offer constructive strategies for coming to terms with uncertainty. Strategies such as self-distancing and self-assessment of causal complexity can be incorporated into conservation decision-making processes. Including reflection on what we know and do not know in the decision-making process potentially reduces unintended and unanticipated consequences of environmental conservation and management decisions. An important caution is not to have intellectual humility legitimate failing to act in the face of uncertainty.
Automated VR therapy for improving positive self-beliefs and psychological well-being in young patients with psychosis: a proof of concept evaluation of Phoenix VR self-confidence therapy
Authors: Freeman Daniel , Freeman Jason , Ahmed Memoona , Haynes Phoebe , Beckwith Helen , Rovira Aitor , Lages Miguel Andre , Ward Rupert , Bousfield Matthew , Riffiod Ludovic , Kabir Thomas , Waite Felicity , Rosebrock Laina 
Published: November 2023

AbstractBackground:Low self-confidence in patients with psychosis is common. This can lead to higher symptom severity, withdrawal from activities, and low psychological well-being. There are effective psychological techniques to improve positive self-beliefs but these are seldom provided in psychosis services. With young people with lived experience of psychosis we developed a scalable automated VR therapy to enhance positive-self beliefs.Aims:The aim was to conduct a proof of concept clinical test of whether the new VR self-confidence therapy (Phoenix) may increase positive self-beliefs and psychological well-being.Method:Twelve young patients with non-affective psychosis and with low levels of positive self-beliefs participated. Over 6 weeks, patients were provided with a stand-alone VR headset so that they could use Phoenix at home and were offered weekly psychologist meetings. The outcome measures were the Oxford Positive Self Scale (OxPos), Brief Core Schema Scale, and Warwick-Edinburgh Well-being Scale (WEMWBS). Satisfaction, adverse events and side-effects were assessed.Results:Eleven patients provided outcome data. There were very large end-of-treatment improvements in positive self-beliefs (OxPos mean difference = 32.3; 95% CI: 17.3, 47.3; Cohen’s d=3.0) and psychological well-being (WEMWBS mean difference = 11.2; 95% CI: 8.0, 14.3; Cohen’s d=1.5). Patients rated the quality of the VR therapy as: excellent (n=9), good (n=2), fair (n=0), poor (n=0). An average of 5.3 (SD=1.4) appointments were attended.Conclusions:Uptake of the VR intervention was high, satisfaction was high, and side-effects extremely few. There were promising indications of large improvements in positive self-beliefs and psychological well-being. A randomized controlled clinical evaluation is warranted.
Three visions of the global: global international relations, global history, global historical sociology
Authors: Barnett Michael , Lawson George 
Published: November 2023

AbstractGlobal international relations (IR) generates space for theoretical expressions drawn from outside the experiences of the modern West. Alongside these demands for theoretical pluralism can be found a concern for widening IR's historical frames of reference. Yet, to date, the relationship between global IR and history is the least developed part of the project's agenda. This article suggests two ways in which this relationship can be strengthened. One draws from global history, shows how transboundary connections and relational dynamics forge the units used by advocates of global IR in their analysis: West and non-West, core and periphery, metropole and colony. The other draws from global historical sociology as it advances the role of power asymmetries for understanding the patterns and entanglements in transboundary connections. Connecting global IR to global history and global historical sociology can help produce a fuller understanding of the interactive connections and asymmetrical entanglements between peoples, places, ideas, and institutions that drive historical development. We illustrate this potential through a brief analysis of the rise of the West. This, in turn, demonstrates the ways in which three visions of the global – global IR, global history, and global historical sociology – can be mutually beneficial.
Characterizing Performance of Freshwater Wetland Methane Models Across Time Scales at FLUXNET‐CH4 Sites Using Wavelet Analyses
Authors: Zhang Zhen , Bansal Sheel , Chang Kuang‐Yu , Fluet‐Chouinard Etienne , Delwiche Kyle , Goeckede Mathias , Gustafson Adrian , Knox Sara , Leppänen Antti , Liu Licheng , Liu Jinxun , Malhotra Avni , Markkanen Tiina , McNicol Gavin , Melton Joe R. , Miller Paul A. , Peng Changhui , Raivonen Maarit , Riley William J. , Sonnentag Oliver , Aalto Tuula , Vargas Rodrigo , Zhang Wenxin , Zhu Qing , Zhu Qiuan , Zhuang Qianlai , Windham‐Myers Lisamarie , Jackson Robert B. , Poulter Benjamin 
Published: November 2023

AbstractProcess‐based land surface models are important tools for estimating global wetland methane (CH4) emissions and projecting their behavior across space and time. So far there are no performance assessments of model responses to drivers at multiple time scales. In this study, we apply wavelet analysis to identify the dominant time scales contributing to model uncertainty in the frequency domain. We evaluate seven wetland models at 23 eddy covariance tower sites. Our study first characterizes site‐level patterns of freshwater wetland CH4 fluxes (FCH4) at different time scales. A Monte Carlo approach was developed to incorporate flux observation error to avoid misidentification of the time scales that dominate model error. Our results suggest that (a) significant model‐observation disagreements are mainly at multi‐day time scales (<15 days); (b) most of the models can capture the CH4 variability at monthly and seasonal time scales (>32 days) for the boreal and Arctic tundra wetland sites but have significant bias in variability at seasonal time scales for temperate and tropical/subtropical sites; (c) model errors exhibit increasing power spectrum as time scale increases, indicating that biases at time scales <5 days could contribute to persistent systematic biases on longer time scales; and (d) differences in error pattern are related to model structure (e.g., proxy of CH4 production). Our evaluation suggests the need to accurately replicate FCH4 variability, especially at short time scales, in future wetland CH4 model developments.
An Ensemble Machine Learning Approach for Tropical Cyclone Localization and Tracking From ERA5 Reanalysis Data
Authors: Accarino Gabriele , Donno Davide , Immorlano Francesco , Elia Donatello , Aloisio Giovanni 
Published: November 2023

AbstractTropical Cyclones (TCs) are counted among the most destructive phenomena that can be found in nature. Every year, globally an average of 90 TCs occur over tropical waters, and global warming is making them stronger and more destructive. The accurate localization and tracking of such phenomena have become a relevant and interesting area of research in weather and climate science. Traditionally, TCs have been identified in large climate data sets through the use of deterministic tracking schemes that rely on subjective thresholds. This study presents a Machine Learning (ML) ensemble approach for locating TCs center coordinates. The ensemble combines TCs center estimates of different ML models that agree about the presence of a TC in input data. ERA5 reanalysis data was used for model training and testing jointly with the International Best Track Archive for Climate Stewardship (IBTrACS) records. Compared to single models estimates, the ML ensemble approach was able to improve TCs localization in terms of Euclidean Distance with respect to the observed TCs locations from IBTrACS. Moreover, a hybrid tracking scheme was defined: starting from the individual TC center locations detected by the ML ensemble approach, a deterministic tracking algorithm was used for reconstructing TC trajectories. The hybrid tracking scheme was then compared with four deterministic trackers reported in literature, achieving a Probability of Detection and a False Alarm Rate of 71.49% and 23%, respectively, over 40 years of reanalysis data.
Silica‐Bearing Mounds and Strata in the Southwest Melas Basin, Valles Marineris, Mars: Evidence for a Hydrothermal Origin
Authors: Rogers Emma R. , Qualizza Briar R. , Heidenreich Joseph R. , Dawson Henry G. , Horgan Briony H. N. 
Published: November 2023

AbstractA small basin on the Southwest (SW) margin of Melas Chasma in Valles Marineris, Mars, hosts a variety of previously identified sedimentary fans and layered strata hypothesized to have been formed by one or more paleolakes. This basin also contains light‐toned layered mounds that have distinct spectral absorption bands consistent with amorphous hydrated silica (e.g., opal). While the general morphology and mineralogy of these features and the basin itself have been previously characterized, the formation mechanism of the hydrated silica features and their temporal relationships with the proposed paleolake remain to be determined. We use Compact Reconnaissance Imaging Spectrometer for Mars visible through short‐wave infrared reflectance spectra (0.35–2.65 μm) and High Resolution Imaging Science Experiment digital terrain models and images to analyze the stratigraphic location and morphology of the opaline silica‐bearing features in the SW Melas basin. We find that the basin hosts fourteen high‐relief “mounds,” eight low‐relief “patches,” and two extended layers within the sedimentary strata that are light‐toned, fractured, and often exhibit hydrated silica‐like spectral signatures. We hypothesize that the mounds are spring deposits formed by sub‐aerial hydrothermal activity, while the patches and layers correspond to sub‐lacustrine hydrothermal activity. The varied elevations of the mounds and patches indicate at least one fluctuation of lake level in the basin during its history. The combination of contemporaneous hydrothermal and lacustrine activity to form silica‐cemented sedimentary deposits in a nutrient‐rich subaqueous environment would have been conducive to forming and preserving biosignatures in the SW Melas basin.
Late Pleistocene Evolution of Tides and Tidal Dissipation
Authors: Wilmes S.‐B. , Pedersen V. K. , Schindelegger M. , Green J. A. M. 
Published: November 2023

AbstractStudies of the Last Glacial Maximum (LGM; 26.5–19 ka) tides showed strong enhancements in open ocean tidal amplitudes and dissipation rates; however, changes prior to the LGM remain largely unexplored. Using two different ice sheet and sea level reconstructions, we explicitly simulate the evolution of the leading semi‐diurnal and diurnal tidal constituents (M2, S2, K1, and O1) over the last glacial cycle with a global tide model. Both sets of simulations show that global changes, dominated by the Atlantic, take place for the semi‐diurnal constituents, while changes for the diurnal constituents are mainly regional. Irrespective of the reconstruction, open ocean dissipation peaks during the sea level lowstands of MIS 2 (∼20 ka) and MIS 4 (∼60 ka), although dissipation values prior to MIS 2 are sensitive to differences in reconstructed ice sheet extent. Using the statistically significant relationship between global mean sea level and dissipation, we apply regression analysis to infer open ocean and shelf dissipation, respectively, over the last four glacial cycles back to 430 ka. Our analysis shows that open ocean tidal energy was probably increased for most of this period, peaking during glacial maxima, and returning to near‐present‐day values during interglacials. Due to tidal resonance during glacial phases, small changes in bathymetry could have caused large changes in tidal amplitudes and dissipation, emphasizing the need for accurate ice margin reconstructions. During glacial phases, once global mean sea level decreased by more than ∼100 m, the amount of open ocean tidal energy available for ocean mixing approximately doubled.
Low-noise fluorescent detection of cardiac troponin I in human serum based on surface acoustic wave separation
Authors: Chen Xuan , Zhang Chuanyu , Liu Xianglian , Dong Yangchao , Meng Hao , Qin Xianming , Jiang Zhuangde , Wei Xueyong 
Published: November 2023

AbstractAcute myocardial infarction (AMI) is a life-threatening disease when sudden blockage of coronary artery occurs. As the most specific biomarker, cardiac troponin I (cTnI) is usually checked separately to diagnose or eliminate AMI, and achieving the accurate detection of cTnI is of great significance to patients’ life and health. Compared with other methods, fluorescent detection has the advantages of simple operation, high sensitivity and wide applicability. However, due to the strong fluorescence interference of biological molecules in body fluids, it is often difficult to obtain high sensitivity. In order to solve this problem, in this study, surface acoustic wave separation is designed to purify the target to achieve more sensitive detection performance of fluorescent detection. Specifically, the interference of background noise is almost completely removed on a microfluidic chip by isolating microbeads through acoustic radiation force, on which the biomarkers are captured by the immobilized detection probe. And then, the concentration of cTnI in human serum is detected by the fluorescence intensity change of the isolated functionalized beads. By this way, the detection limit of our biosensor calculated by 3σ/K method is 44 pg/mL and 0.34 ng/mL in PBS buffer and human serum respectively. Finally, the reliability of this method has been validated by comparison with clinical tests from the nephelometric analyzer in hospital.
Fabrication of 3D-printed molds for polydimethylsiloxane-based microfluidic devices using a liquid crystal display-based vat photopolymerization process: printing quality, drug response and 3D invasion cell culture assays
Authors: Poskus Matthew D. , Wang Tuo , Deng Yuxuan , Borcherding Sydney , Atkinson Jake , Zervantonakis Ioannis K. 
Published: November 2023

AbstractMicrofluidic platforms enable more precise control of biological stimuli and environment dimensionality than conventional macroscale cell-based assays; however, long fabrication times and high-cost specialized equipment limit the widespread adoption of microfluidic technologies. Recent improvements in vat photopolymerization three-dimensional (3D) printing technologies such as liquid crystal display (LCD) printing offer rapid prototyping and a cost-effective solution to microfluidic fabrication. Limited information is available about how 3D printing parameters and resin cytocompatibility impact the performance of 3D-printed molds for the fabrication of polydimethylsiloxane (PDMS)-based microfluidic platforms for cellular studies. Using a low-cost, commercially available LCD-based 3D printer, we assessed the cytocompatibility of several resins, optimized fabrication parameters, and characterized the minimum feature size. We evaluated the response to both cytotoxic chemotherapy and targeted kinase therapies in microfluidic devices fabricated using our 3D-printed molds and demonstrated the establishment of flow-based concentration gradients. Furthermore, we monitored real-time cancer cell and fibroblast migration in a 3D matrix environment that was dependent on environmental signals. These results demonstrate how vat photopolymerization LCD-based fabrication can accelerate the prototyping of microfluidic platforms with increased accessibility and resolution for PDMS-based cell culture assays.
Shallow whole genome sequencing approach to detect Homologous Recombination Deficiency in the PAOLA-1/ENGOT-OV25 phase-III trial
Authors: Callens Celine , Rodrigues Manuel , Briaux Adrien , Frouin Eleonore , Eeckhoutte Alexandre , Pujade-Lauraine Eric , Renault Victor , Stoppa-Lyonnet Dominique , Bieche Ivan , Bataillon Guillaume , Karayan-Tapon Lucie , Rochelle Tristan , Heitz Florian , Cecere Sabrina Chiara , Pérez Maria Jesús Rubio , Grimm Christoph , Nøttrup Trine Jakobi , Colombo Nicoletta , Vergote Ignace , Yonemori Kan , Ray-Coquard Isabelle , Stern Marc-Henri , Popova Tatiana 
Published: November 2023

AbstractThe bevacizumab (bev)/olaparib (ola) maintenance regimen was approved for BRCA1/2-mutated (BRCAmut) and Homologous Recombination Deficient (HRD) high-grade Advanced Ovarian Cancer (AOC) first line setting, based on a significantly improved progression-free survival (PFS) compared to bev alone in the PAOLA-1/ENGOT-ov25 trial (NCT02477644), where HRD was detected by MyChoice CDx PLUS test. The academic shallowHRDv2 test was developed based on shallow whole-genome sequencing as an alternative to MyChoice. Analytical and clinical validities of shallowHRDv2 as compared to MyChoice on 449 PAOLA-1 tumor samples are presented. The overall agreement between shallowHRDv2 and MyChoice was 94% (369/394). Less non-contributive tests were observed with shallowHRDv2 (15/449; 3%) than with MyChoice (51/449; 11%). Patients with HRD tumors according to shallowHRDv2 (including BRCAmut) showed a significantly prolonged PFS with bev+ola versus bev (median PFS: 65.7 versus 20.3 months, hazard ratio (HR): 0.36 [95% CI: 0.24–0.53]). This benefit was significant also for BRCA1/2 wild-type tumors (40.8 versus 19.5 months, HR: 0.45 [95% CI: 0.26–0.76]). ShallowHRDv2 is a performant, clinically validated, and cost-effective test for HRD detection.
Coupling to octahedral tilts in halide perovskite nanocrystals induces phonon-mediated attractive interactions between excitons
Authors: Yazdani Nuri , Bodnarchuk Maryna I. , Bertolotti Federica , Masciocchi Norberto , Fureraj Ina , Guzelturk Burak , Cotts Benjamin L. , Zajac Marc , Rainò Gabriele , Jansen Maximilian , Boehme Simon C. , Yarema Maksym , Lin Ming-Fu , Kozina Michael , Reid Alexander , Shen Xiaozhe , Weathersby Stephen , Wang Xijie , Vauthey Eric , Guagliardi Antonietta , Kovalenko Maksym V. , Wood Vanessa , Lindenberg Aaron M. 
Published: November 2023

AbstractUnderstanding the origin of electron–phonon coupling in lead halide perovskites is key to interpreting and leveraging their optical and electronic properties. Here we show that photoexcitation drives a reduction of the lead–halide–lead bond angles, a result of deformation potential coupling to low-energy optical phonons. We accomplish this by performing femtosecond-resolved, optical-pump–electron-diffraction-probe measurements to quantify the lattice reorganization occurring as a result of photoexcitation in nanocrystals of FAPbBr3. Our results indicate a stronger coupling in FAPbBr3 than CsPbBr3. We attribute the enhanced coupling in FAPbBr3 to its disordered crystal structure, which persists down to cryogenic temperatures. We find the reorganizations induced by each exciton in a multi-excitonic state constructively interfere, giving rise to a coupling strength that scales quadratically with the exciton number. This superlinear scaling induces phonon-mediated attractive interactions between excitations in lead halide perovskites.
The p97/VCP adaptor UBXD1 drives AAA+ remodeling and ring opening through multi-domain tethered interactions
Authors: Braxton Julian R. , Altobelli Chad R. , Tucker Maxwell R. , Tse Eric , Thwin Aye C. , Arkin Michelle R. , Southworth Daniel R. 
Published: November 2023

Abstractp97, also known as valosin-containing protein, is an essential cytosolic AAA+ (ATPases associated with diverse cellular activities) hexamer that unfolds substrate polypeptides to support protein homeostasis and macromolecular disassembly. Distinct sets of p97 adaptors guide cellular functions but their roles in direct control of the hexamer are unclear. The UBXD1 adaptor localizes with p97 in critical mitochondria and lysosome clearance pathways and contains multiple p97-interacting domains. Here we identify UBXD1 as a potent p97 ATPase inhibitor and report structures of intact human p97–UBXD1 complexes that reveal extensive UBXD1 contacts across p97 and an asymmetric remodeling of the hexamer. Conserved VIM, UBX and PUB domains tether adjacent protomers while a connecting strand forms an N-terminal domain lariat with a helix wedged at the interprotomer interface. An additional VIM-connecting helix binds along the second (D2) AAA+ domain. Together, these contacts split the hexamer into a ring-open conformation. Structures, mutagenesis and comparisons to other adaptors further reveal how adaptors containing conserved p97-remodeling motifs regulate p97 ATPase activity and structure.
Visualizing software refactoring using radar charts
Authors: Al-Ghuwairi Abdel-Rahman , Al-Fraihat Dimah , Sharrab Yousef , Alrashidi Huda , Almujally Nouf , Kittaneh Ahmed , Ali Ahmed 
Published: November 2023

AbstractRefactoring tools have advanced greatly and are being used in many large projects. As a result, a great deal of information is now available about past refactoring and its effects on the source code. However, when multiple refactoring is performed at once, it becomes more difficult to analyze their impact. Refactoring visualization can help developers create more maintainable code that is easier to understand and modify over time. Although there is an increasing interest in visualizing code changes in software engineering research, there has been relatively little research on visualizing the process of refactoring. In this paper, we propose a Radar Chart Refactoring Visualization (RcRV) approach to visualize software refactoring of source code across multiple software releases. Radar charts are a form of 2D visualization that can show multiple variables on a single chart. The RcRv receives input from developers or through refactoring identification tools, such as Ref-Finder, to generate charts. The generated charts can show the changes made during the refactoring process, highlighting areas of the trend of refactoring over evolution for multiple refactoring, multiple methods, and multiple classes. The evaluation study conducted to assess the usefulness of the RcRV tool has shown that the proposed tool is useful to developers, appealing, and easy to use. The proposed method of visualization can be beneficial for developers and maintainers to detect design violations and potential bugs in the code, thus saving time and effort during the development and maintenance process. Therefore, this research presents a significant contribution to the software engineering field by providing developers with an efficient tool to enhance code quality and maintainability.