bluuebunny/crossref_metadata_2025_split huggingface dataset:
TransFoxMol: predicting molecular property with focused attention
Authors: Gao Jian , Shen Zheyuan , Xie Yufeng , Lu Jialiang , Lu Yang , Chen Sikang , Bian Qingyu , Guo Yue , Shen Liteng , Wu Jian , Zhou Binbin , Hou Tingjun , He Qiaojun , Che Jinxin , Dong Xiaowu 
Published: August 2023

Abstract
Predicting the biological properties of molecules is crucial in computer-aided drug development, yet it’s often impeded by data scarcity and imbalance in many practical applications. Existing approaches are based on self-supervised learning or 3D data and using an increasing number of parameters to improve performance. These approaches may not take full advantage of established chemical knowledge and could inadvertently introduce noise into the respective model. In this study, we introduce a more elegant transformer-based framework with focused attention for molecular representation (TransFoxMol) to improve the understanding of artificial intelligence (AI) of molecular structure property relationships. TransFoxMol incorporates a multi-scale 2D molecular environment into a graph neural network + Transformer module and uses prior chemical maps to obtain a more focused attention landscape compared to that obtained using existing approaches. Experimental results show that TransFoxMol achieves state-of-the-art performance on MoleculeNet benchmarks and surpasses the performance of baselines that use self-supervised learning or geometry-enhanced strategies on small-scale datasets. Subsequent analyses indicate that TransFoxMol’s predictions are highly interpretable and the clever use of chemical knowledge enables AI to perceive molecules in a simple but rational way, enhancing performance.
Difference in respiratory syncytial virus-specific Fc-mediated antibody effector functions between children and adults
Authors: Lakerveld Anke J , Gelderloos Anne T , Schepp Rutger M , de Haan Cornelis A M , van Binnendijk Robert S , Rots Nynke Y , van Beek Josine , van Els Cécile A C M , van Kasteren Puck B 
Published: August 2023

Abstract
Respiratory syncytial virus (RSV) infections are a major cause of bronchiolitis and pneumonia in infants and older adults, for which there is no known correlate of protection. Increasing evidence suggests that Fc-mediated antibody effector functions have an important role, but little is known about the development, heterogeneity, and durability of these functional responses. In light of future vaccine strategies, a clear view of the immunological background and differences between various target populations is of crucial importance.
In this study, we have assessed both quantitative and qualitative aspects of RSV-specific serum antibodies, including IgG/IgA levels, IgG subclasses, antibody-dependent complement deposition, cellular phagocytosis, and NK cell activation (ADNKA). Samples were collected cross-sectionally in different age groups (11-, 24-, and 46-month-old children, adults, and older adults; n = 31–35 per group) and longitudinally following natural RSV infection in (older) adults (2–36 months post-infection; n = 10).
We found that serum of 24-month-old children induces significantly lower ADNKA than the serum of adults (P &lt; 0.01), which is not explained by antibody levels. Furthermore, in (older) adults we observed boosting of antibody levels and functionality at 2–3 months after RSV infection, except for ADNKA. The strongest decrease was subsequently observed within the first 9 months, after which levels remained relatively stable up to three years post-infection.
Together, these data provide a comprehensive overview of the functional landscape of RSV-specific serum antibodies in the human population, highlighting that while antibodies reach adult levels already at a young age, ADNKA requires more time to fully develop.
Effects of headgear timing on dental arch changes from 7 to 18 years of age: a follow-up study
Authors: Hannula Matti , Tolvanen Mimmi , Pirttiniemi Pertti , Pirilä-Parkkinen Kirsi , Julku Johanna 
Published: August 2023

Abstract

Background
Dental arch effects after cervical headgear (CHG) treatment have been researched from several different perspectives. However, the long-term effects of CHG timing are still unknown.

Objectives
To analyse the long-term effects of CHG timing on dental arches.

Material and methods
A total of 67 children with Angle Class II malocclusion comprised the study group in this trial. The participants were randomized into two equal-sized groups. In the early group (EG, n = 33), treatment was started after the eruption of the first upper molars. In the later-timed group (LG, n = 34), treatment was started 18 months later compared with the early group. Long-term effects were measured from dental casts taken at five time points between 7 and 18 years of age.

Results
The total maxillary dental arch length was achieved earlier, the gained length persisted better in the long term, and significantly more space was achieved in EG compared with LG (P = .048). The intermolar width in the maxillary dental arch was more stable and was reached earlier in EG compared with LG (P = .002). The results showed that in terms of total mandibular arch length increases, EG males benefited the most and LG females the least from CHG treatment (P = .031).

Conclusions
Both genders benefited from earlier CHG treatment. The maxillary dental arches remained longer, and the final width was gained earlier in EG compared with LG.
Costs and duration of orthodontic-surgical treatment with mandibular advancement surgery
Authors: Niemi Pekka , Kortelainen Mika , Harjunmaa Ulla , Waltimo-Sirén Janna 
Published: August 2023

Abstract

Objectives
The aim was to analyse the costs and duration of orthodontic-surgical treatment with mandibular advancement in the public health care sector in Finland.

Materials
The study was conducted as a retrospective registry study in a public district hospital on all nonsyndromic patients that were ethnic Finns and treated with full fixed appliances and mandibular advancement surgery in 2016–2020.

Results
The mean treatment duration of the included 45 patients was 28.1 months, including 18.9 months pre and 9.2 months postoperative orthodontics. The median number of visits was 27, including 17 visits before and 9 visits after surgery. The mean total treatment time was 14.5 h. The mean total direct costs per course of treatment were 7574 € to the municipality and 947 € to the patient. The costs positively correlated with the duration of the treatment (rho = 0.71, P = .000), but were not associated to gender or age of patient. The mean surgery time was 78 minutes, and significantly less with an experienced surgeon (P = .002). It was calculated that the mean minimum treatment costs would be 45% of the present total, achievable with a patient with optimum dental arches at the start of treatment.

Limitations
The major limitation of the study is the relatively small number of study subjects.

Conclusion
A 55% share of the costs is influenced by case- and operator-dependent factors. This indicates that the complexity and performance of the orthodontic phases of treatment are important determinants in the cost structure.
Paying for animal welfare labelling no matter what? A discrete choice experiment
Authors: Schwickert Henrike 
Published: August 2023

Abstract
Animal welfare is a credence attribute with public good characteristics. Using a discrete choice experiment, consumers’ willingness to pay (WTP) for a concretely planned state animal welfare label is derived and compared by product group (fresh vs. processed meat) and tax scenario (no tax vs. additional animal welfare tax included in price). Consumers have a positive WTP for the state label. However, label WTP is significantly lower for processed than for fresh meat. An additional tax does not impact label WTP on average. Results provide insights for both policymakers on label implementation and farmers on further investments in animal welfare.
Early mobilization after transcatheter aortic valve implantation: observational cohort study
Authors: Lauck Sandra B , Yu Maggie , Bancroft Carrie , Borregaard Britt , Polderman Jopie , Stephenson Anna L , Durand Eric , Akodad Mariama , Meier David , Andrews Holly , Achtem Leslie , Tang Erin , Wood David A , Sathananthan Janarthanan , Webb John G 
Published: August 2023

Abstract

Aims
Early mobilization is associated with improved outcomes in hospitalized older patients. We sought to determine the effect of a nurse-led protocol on mobilization 4 h after transfemoral transcatheter aortic valve implantation (TAVI) across different units of care.

Methods and results
We conducted a prospective observational cohort single-centre study of consecutive patients. We implemented a standardized protocol for safe early recovery and progressive mobilization in the critical care and cardiac telemetry units. We measured the time to first mobilization and conducted descriptive statistics to identify patient and system barriers to timely ambulation. We recruited 139 patients (82.5 years, SD = 6.7; 46% women). At baseline, patients who were mobilized early (≤4 h) and late (&gt;4 h) did not differ, except for higher rates of diabetes (25.5% vs. 43.9%, P = 0.032) and peripheral arterial disease (8.2% vs. 26.8%, P = 0.003) in the late mobilization group. The median time to mobilization was 4 h [inter-quartile range (IQR) 3.25, 4]; 98 patients (70.5%) were mobilized successfully after 4 h of bedrest; 118 (84.9%) were walking by the evening of the procedure (&lt;8 h bedrest); and 21 (15.1%) were on bedrest overnight and mobilized the following day. Primary reasons for overnight bedrest were arrhythmia monitoring (n = 10, 7.2%) and haemodynamic and/or neurological instability (n = 6, 4.3%); six patients (4.3%) experienced delayed ambulation due to system issues. Procedure location in the hybrid operating room and transfer to critical care were associated with longer bedrest times.

Conclusion
Standardized nurse-led mobilization 4 h after TF TAVI is feasible in the absence of clinical complications and system barriers.
Meiotic drive does not impede success in sperm competition in the stalk-eyed fly, Teleopsis dalmanni
Authors: Bates Sadé , Meade Lara , Pomiankowski Andrew 
Published: August 2023

Abstract
Male X-linked meiotic drive systems, which cause the degeneration of Y-bearing sperm, are common in the Diptera. Sperm killing is typically associated with fitness costs that arise from the destruction of wildtype sperm and collateral damage to maturing drive sperm, resulting in poor success under sperm competition. We investigate X-linked meiotic drive fertility in the stalk-eyed fly, Teleopsis dalmanni. Drive male paternity was measured in double mating trials under sperm competition against a wildtype male. Drive males sired the same number of offspring as wildtype males, both when mated first or second. This is the first evidence that drive males can compete equally with non-drive males in double matings, challenging the assumption that drive males inevitably suffer reduced fertility. The finding is in accord with previous work showing that the number of sperm per ejaculate transferred to females during non-competitive single matings does not differ between drive and wildtype males, which is likely due to the adaptive evolution of enlarged testes in drive males. Future experiments will determine whether the competitive ability of drive males is maintained under higher rates of female remating likely to be experienced in nature.
Digest: Plastic responses to warmer climates: a seminatural experiment on lizard populations
Authors: Robertson Josephine E 
Published: August 2023

Abstract
Determining whether a phenotypic change is the result of microevolution or plasticity can be challenging. Bestion et al. investigate the contributions of plasticity (both intragenerational and intergenerational) and selection to phenotypic changes in common lizards (Zootoca vivipara) in response to a warmer climate that mirrors projections for 2080. Their results suggest that plasticity plays a more important role than selection in governing many of the phenotypic responses to temperature change.
Ca-HELP: Adaptation of a Communication Tool to Help Geriatric Cancer Patients in Rural Settings Talk to Their Doctors About Pain
Authors: Harrison Jill , Stokes Tammy , Hahne Jessica , Shen Megan 
Published: August 2023

Abstract

Background and Objectives
Among the older adult population living in the rural United States, undertreated cancer pain is very common. The need for interventions targeting pain management communication between older adults with cancer in rural communities and their doctors outpaces the current evidence base. Adaptation of existing pain interventions may improve the speed at which clinicians can respond to pain in this vulnerable population.

Research Design and Methods
The Cancer Health Empowerment for Living without Pain (Ca-HELP) is an evidence-based communication tool that coaches patients to communicate about pain by asking questions, making requests, and signaling distress to their physicians in order to achieve improved pain control. Guided by the Method for Program Adaptation through Community Engagement (M-PACE) model, which utilizes detailed stakeholder feedback to guide the adaptation of an intervention for an appropriate target audience, we proactively adapted the Ca-HELP and its delivery for use among geriatric cancer patients living in rural settings using qualitative feedback from patients, informal caregivers, and providers as a planned step in a multiphase pilot study.

Results
All stakeholders agreed that the Ca-HELP was a promising candidate intervention to improve pain among older adults with cancer. They suggested modifications to the delivery, context, and content of the intervention. A multidisciplinary team of nurse leaders and researchers evaluated stakeholder feedback and recommendations before determining which adaptations were made. Adaptations were cataloged and reported using the Framework for Reporting Adaptations and Modifications-Enhanced model.

Discussion and Implications
Our multistakeholder team proactively modified the Ca-HELP intervention tool using end-user feedback with a goal to optimize fit for use by older adults with cancer in rural settings without compromising the active ingredients. Documenting and reporting modifications to interventions are critical to their implementation and will lay the groundwork for further testing of the efficacy of the adapted Ca-HELP intervention.
Learning with real data without real labels: a strategy for extrapolated full-waveform inversion with field data
Authors: Sun Hongyu , Sun Yen , Nammour Rami , Rivera Christian , Williamson Paul , Demanet Laurent 
Published: August 2023

SUMMARY
Full-waveform inversion (FWI) relies on low-frequency data to succeed if a good initial model is unavailable. However, field seismic data excited by active sources are typically band-limited above 3 Hz. By extrapolated FWI, we can start inversion from computational low frequencies extrapolated from band-limited data. However, low-frequency extrapolation with deep learning is challenging for field data since a neural network trained on synthetic data usually generalizes poorly on real seismic data. Here we use a semi-supervised learning method to extrapolate low frequencies for field data by training with real data without real labels. Specifically, by training CycleGAN with unpaired images of field 4–10 Hz band-limited and synthetic 0–4 Hz low-frequency shot gathers, we can extrapolate the 0–4 Hz low frequencies for the field data band-limited above 4 Hz. The source wavelet for the simulation of synthetic low-frequency data is used as the source in FWI using the extrapolated data. The inverted velocity model using only the extrapolated low frequencies is comparable to the tomography model. Our method strengthens the ability of FWI for mapping fine Earth structures by mitigating the cycle-skipping problem effectively.
Genome-wide identification of dominant polyadenylation hexamers for use in variant classification
Authors: Shiferaw Henoke K , Hong Celine S , Cooper David N , Johnston Jennifer J , NISC  , Biesecker Leslie G 
Published: August 2023

Abstract
Polyadenylation is an essential process for the stabilization and export of mRNAs to the cytoplasm and the polyadenylation signal hexamer (herein referred to as hexamer) plays a key role in this process. Yet, only 14 Mendelian disorders have been associated with hexamer variants. This is likely an under-ascertainment as hexamers are not well defined and not routinely examined in molecular analysis. To facilitate the interrogation of putatively pathogenic hexamer variants, we set out to define functionally important hexamers genome-wide as a resource for research and clinical testing interrogation. We identified predominant polyA sites (herein referred to as pPAS) and putative predominant hexamers across protein coding genes (PAS usage &gt;50% per gene). As a measure of the validity of these sites, the population constraint of 4532 predominant hexamers were measured. The predominant hexamers had fewer observed variants compared to non-predominant hexamers and trimer controls, and CADD scores for variants in these hexamers were significantly higher than controls. Exome data for 1477 individuals were interrogated for hexamer variants and transcriptome data were generated for 76 individuals with 65 variants in predominant hexamers. 3′ RNA-seq data showed these variants resulted in alternate polyadenylation events (38%) and in elongated mRNA transcripts (12%). Our list of pPAS and predominant hexamers are available in the UCSC genome browser and on GitHub. We suggest this list of predominant hexamers can be used to interrogate exome and genome data. Variants in these predominant hexamers should be considered candidates for pathogenic variation in human disease, and to that end we suggest pathogenicity criteria for classifying hexamer variants.
Atlantic Oceanic Squids in the “Grey Speciation Zone”
Authors: Fernández-Álvarez Fernando Á , Sanchez Gustavo , Deville Diego , Taite Morag , Villanueva Roger , Allcock A Louise 
Published: August 2023

Synopsis
Cryptic species complexes represent an important challenge for the adequate characterization of Earth’s biodiversity. Oceanic organisms tend to have greater unrecognized cryptic biodiversity since the marine realm was often considered to lack hard barriers to genetic exchange. Here, we tested the effect of several Atlantic and Mediterranean oceanic barriers on 16 morphospecies of oceanic squids of the orders Oegopsida and Bathyteuthida using three mitochondrial and one nuclear molecular marker and five species delimitation methods. Number of species recognized within each morphospecies differed among different markers and analyses, but we found strong evidence of cryptic biodiversity in at least four of the studied species (Chtenopteryx sicula, Chtenopteryx canariensis, Ancistrocheirus lesueurii, and Galiteuthis armata). There were highly geographically structured units within Helicocranchia navossae that could either represent recently diverged species or population structure. Although the species studied here can be considered relatively passive with respect to oceanic currents, cryptic speciation patterns showed few signs of being related to oceanic currents. We hypothesize that the bathymetry of the egg masses and duration of the paralarval stage might influence the geographic distribution of oceanic squids. Because the results of different markers and different species delimitation methods are inconsistent and because molecular data encompassing broad geographic sampling areas for oceanic squids are scarce and finding morphological diagnostic characters for early life stages is difficult, it is challenging to assess the species boundaries for many of these species. Thus, we consider many to be in the “grey speciation zone.” As many oceanic squids have cosmopolitan distributions, new studies combining genomic and morphological information from specimens collected worldwide are needed to correctly assess the actual oceanic squid biodiversity.
Integrating survey and observer data improves the predictions of New Zealand spatio-temporal models
Authors: Grüss A , Charsley A R , Thorson J T , Anderson O F , O'Driscoll R L , Wood B , Breivik O N , O’Leary C A 
Published: August 2023

AbstractIn many situations, species distribution models need to make use of multiple data sources to address their objectives. We developed a spatio-temporal modelling framework that integrates research survey data and data collected by observers onboard fishing vessels while accounting for physical barriers (islands, convoluted coastlines). We demonstrated our framework for two bycatch species in New Zealand deepwater fisheries: spiny dogfish (Squalus acanthias) and javelinfish (Lepidorhynchus denticulatus). Results indicated that employing observer-only data or integrated data is necessary to map fish biomass at the scale of the New Zealand exclusive economic zone, and to interpolate local biomass indices (e.g., for the east coast of the South Island) in years with no survey but available observer data. Results also showed that, if enough survey data are available, fisheries analysts should: (1) develop both an integrated model and a model relying on survey-only data; and (2) for a given geographic area, ultimately choose the index produced with integrated data or the index produced with survey-only data based on the reliability of the interannual variability of the index. We also conducted a simulation experiment, which indicated that the predictions of our spatio-temporal models are virtually insensitive to the consideration of physical barriers.
Digital assets and inheritance law: How to create fundamental principles of digital succession system?
Authors: Szwajdler Paweł 
Published: August 2023

Abstract
Currently, there are no generally applicable legal regulations in the field of digital succession in the majority of legal orders. However, such legal provisions are needed because digital assets are getting more and more significant in the contemporary world. Entry into force of legal regulations in this area should be preceded by creation of legal theory of digital succession. Therefore, it is necessary to consider fundamental principles of digital asset inheritance system. The author of this work reviews current theoretical and practical approaches to the matters of digital succession. Considerations included in this work lead to answer to the question how to create fundamental principles of digital succession system. Furthermore, there are separate recommendations for legislators, end-users, digital service providers and judiciary in this work. Hence, this article seems not only theoretical but also practical.