bluuebunny/crossref_metadata_2025_split huggingface dataset:
Total angular momentum conservation in Ehrenfest dynamics with a truncated basis of adiabatic states
Authors: Tao Zhen , Bian Xuezhi , Wu Yanze , Rawlinson Jonathan , Littlejohn Robert G. , Subotnik Joseph E. 
Published: February 2024

We show that standard Ehrenfest dynamics does not conserve linear and angular momentum when using a basis of truncated adiabatic states. However, we also show that previously proposed effective Ehrenfest equations of motion [M. Amano and K. Takatsuka, “Quantum fluctuation of electronic wave-packet dynamics coupled with classical nuclear motions,” J. Chem. Phys. 122, 084113 (2005) and V. Krishna, “Path integral formulation for quantum nonadiabatic dynamics and the mixed quantum classical limit,” J. Chem. Phys. 126, 134107 (2007)] involving the non-Abelian Berry force do maintain momentum conservation. As a numerical example, we investigate the Kramers doublet of the methoxy radical using generalized Hartree–Fock with spin–orbit coupling and confirm that angular momentum is conserved with the proper equations of motion. Our work makes clear some of the limitations of the Born–Oppenheimer approximation when using ab initio electronic structure theory to treat systems with unpaired electronic spin degrees of freedom, and we demonstrate that Ehrenfest dynamics can offer much improved, qualitatively correct results.
Diffusion Monte Carlo method for barrier heights of multiple proton exchanges and complexation energies in small water, ammonia, and hydrogen fluoride clusters
Authors: Zhou Xiaojun , Huang Zhiru , He Xiao 
Published: February 2024

Proton exchange reactions are of key importance in many processes in water. However, it is nontrivial to achieve reliable barrier heights for multiple proton exchanges and complexation energies in hydrogen-bonded systems theoretically. Performance of the fixed-node diffusion quantum Monte Carlo (FN-DMC) with the single-Slater–Jastrow trial wavefunction on total energies, barrier heights of multiple proton exchanges, and complexation energies of small water, ammonia, and hydrogen fluoride clusters is investigated in this study. Effects of basis sets and those of locality approximation (LA), T-move approximation (T-move), and determinant localization approximation (DLA) schemes in dealing with the nonlocal part of pseudopotentials on FN-DMC results are evaluated. According to our results, diffuse basis functions are important in achieving reliable barrier heights and complexation energies with FN-DMC, although the cardinal number of the basis set is more important than diffuse basis functions on total energies of these systems. Our results also show that the time step bias with DLA and LA is smaller than T-move; however, the time step bias of DMC energies with respect to time steps using the T-move is roughly linear up to 0.06 a.u., while this is not the case with LA and DLA. Barrier heights and complexation energies with FN-DMC using these three schemes are always within chemical accuracy. Taking into account the fact that T-move and DLA are typically more stable than LA, FN-DMC calculations with the T-move or DLA scheme and basis sets containing diffuse basis functions are suggested for barrier heights of multiple proton exchanges and complexation energies of hydrogen-bonded clusters.
Design of a high-temperature cell for cobalt-60 irradiations of aqueous solutions with in situ UV–visible spectroscopy
Authors: Conrad Jacy K. , Rollins Harry W. , Peterman Dean R. , Fox Robert V. 
Published: February 2024

To understand the speciation of solutes in aqueous solutions in high temperature radiation environments, we report the design and fabrication of a custom-built, high temperature (≤300 °C) titanium irradiation cell with in situ optical spectroscopy capabilities, as afforded by coupled fiber optic cables. The wetted surfaces of the 8-inch tall cylindrical cell with 3.5 in. diameter are entirely made of titanium, sapphire, and gold, which are chemically and radiolytically inert. The initial benchmarking results are reported, including the baseline spectrum of deionized water as a function of temperature, the stability of a spectrum over 4 h at 100 °C, and an irradiated Fricke dosimetry solution under ambient irradiator temperature conditions (27.0 ± 0.5 °C). The average gamma radiation dose rate in the cell in its current configuration is 26.1 ± 1.3 Gy min−1. This cell has application in studying several processes throughout the nuclear fuel cycle, including the reactor coolant behavior.
A novel production profile classification system for incoming calves that predicts feedlot growth performance
Authors: Hentzen Andreas H. R. , Holm Dietmar E. 
Published: February 2024

Context Mitigating financial risk in the feedlot environment is an ongoing occurrence, and good production is a key risk mitigator. However, production protocols are based on historic averages because of the inability to predict growth potential of incoming calves. Production profiling of individual incoming feeder calves could address these limitations. Aims The aim of this study was to establish criteria for optimal sorting of incoming feeder calves into various cattle groups in a feedlot that maximises feedlot profit. Methods South African feeder calves (n = 436) were classified into four production-profile (PP) categories according to a predetermined set of phenotypic traits: PP 3 (n = 72) representing feeder calves with the poorest feedlot growth potential, PP 2− (n = 191) with below-average potential, PP 2+ (n = 139) with above-average potential and PP 1 (n = 34) with above-average feedlot growth potential. After combining the data of PP 2− and PP 2+ into PP 2, mixed modelling of economically important feedlot growth traits (average daily gain (ADG), carcass ADG, and carcass exit weight) was performed to evaluate the effect of PP classification (PP 1 and PP 3), while adjusting for potential confounding effects such as starting weight (entry weight) and gender. Key results Carcass weights for calves with a PP classification of 3 and 1 were 15.54 kg less (P < 0.000), and 11.34 kg more (P = 0.007) respectively, than those with a PP classification of 2 (261.27 kg, 95% CI 257.94–264.57), after adjusting for entry weight, calf gender and the random effect of the feeding pen. Similar to carcass weight, calves with a PP 3 classification were outperformed by other classifications in all the measured traits (P < 0.05). Conclusions This is the first report demonstrating the ability of subjective production-profile classification to predict growth performance of individual feeder calves. Implications The opportunity of the PP classification system lies in value-based procurement of incoming feeder calves based on their growth potential at the start of the feeding period, and then to use technology to improve and finalise the current subjective PP classification system.
Ability of wheat genotypes to form large rhizosheaths may enhance survival of false-break events in rainfed production
Authors: Emebiri Livinus , Rohan Maheswaran , Hildebrand Shane , Pitt Wayne 
Published: February 2024

Context Crop production is one of the agricultural sectors most vulnerable to climate change. In order to minimise risks, innovative technologies and management strategies are continually being developed. Early sowing is a strategy used in wheat production; however, with irregular rainfall patterns, false breaks can occur. Aims We sought to determine the optimal volume of autumn-break rainfall for the start of season, and whether formation of a larger rhizosheath (i.e. the thick layer of soil adhering to roots) can buffer wheat seedlings from false-break conditions, thereby keeping plants alive until the next rainfall. Methods In glasshouse experiments, six varieties of common wheat (Triticum aestivum L.), two with contrasting rhizosheath-forming ability and the other four untested, were grown on two soil types (Kandosol and Vertosol) under simulated autumn-break rainfall and false-break durations. Rhizosheath size and plant establishment traits were measured. Key results The ability to form large rhizosheaths explained ~80% of the variability in crop establishment under various scenarios of false-break conditions. Comparative growth performance of the cultivars forming the largest (cv. Flanker) and smallest (cv. Westonia) rhizosheaths showed that they were largely similar for the first 28 days of drought but differed significantly thereafter. Flanker was progressively better able to establish as false-break duration increased and showed significantly greater tiller and leaf production than Westonia. Conclusions We demonstrate that genotype selection for formation of large rhizosheaths can help to reduce plant seedling death under false-break conditions. Implications Although the amount of starting rainfall is critical, cultivars differ significantly with regard to how far they can develop without follow-up rain. Future research is suggested for a field-scale study of the potential for selection for larger rhizosheaths to improve wheat crop establishment under harsh conditions.
Pair of dyon production near magnetized dyonic Reissner-Nordstrom black holes*
Authors: Siahaan Haryanto M. 
Published: February 2024

Abstract
We investigate the phenomenon of pair production of massive scalar particles with magnetic charge near the horizon of a magnetized dyonic Reissner-Nordstrom black hole. The intrinsic symmetry between the electric and magnetic quantities in the Einstein-Maxwell equations suggests that the pair can be generated through Hawking radiation and the Schwinger effect, provided that the Dirac quantization condition is satisfied.
Effects of Resilience and Emotion Regulation on Perceptions of Positive and Negative Life Changes in Cancer Survivors: A Longitudinal Study
Authors: Fritzson Emily , Bellizzi Keith M , Zhang Na , Park Crystal L 
Published: February 2024

Abstract

Background
While many studies have investigated the sociodemographic, clinical, and psychosocial factors associated with perceived positive change after cancer, longitudinal work examining how emotion regulation, and resilience impact perceptions of life change among newly diagnosed cancer survivors is lacking.

Purpose
This study examined the prevalence of perceived positive and negative life changes following cancer and explored the role of emotion regulation and resilience on perceived change over 6 months.

Methods
Data from 534 recent survivors of breast, prostate, or colorectal cancer (Mage = 59.3, 36.5% male) collected at baseline (Time 1) and 6-month follow-up (Time 2) were analyzed. Multivariate linear regressions were estimated separately to examine if resilience or emotion regulation were associated with perceived change at Time 2 after controlling for relevant sociodemographic and psychosocial measures.

Results
At both time points, greater than 90% of participants reported at least one perceived positive change while fewer than a third reported a negative change. Indices of emotion regulation and resilience were positively related to perceived positive change at both time points and negatively related to perceived negative change at Time 1. Emotion regulation but not resilience was negatively associated with perceived negative change at Time 2.

Conclusions
Findings suggest that cancer survivors who are less resilient and struggle with emotion regulation are more susceptible to perceptions of fewer positive and greater negative life changes after cancer. As such, psychosocial interventions should be developed to promote resilience and emotional regulation in cancer survivors.
PERSEUS: an interactive and intuitive web-based tool for pedigree visualization
Authors: Pradas Nicole , Jurado-Ruiz Federico , Onielfa Carles , Arús Pere , Aranzana Maria José 
Published: February 2024

Abstract

Summary
Pedigree-based analyses’ prime role is to unravel relationships between individuals in breeding programs and germplasms. This is critical information for decoding the genetics underlying main inherited traits of relevance, and unlocking the genotypic variability of a species to carry out genomic selections and predictions. Despite the great interest, current lineage visualizations become quite limiting in terms of public display, exploration, and tracing of traits up to ancestral donors. PERSEUS is a user-friendly, intuitive, and interactive web-based tool for pedigree visualizations represented as directed graph networks distributed using a force-repulsion method. The visualizations do not only showcase individual relationships among accessions, but also facilitate a seamless search and download of phenotypic traits along the pedigrees. PERSEUS is a promising tool for breeders and scientists, advantageous for evolutionary, genealogy, and diversity analyses among related accessions and species.

Availability and implementation
PERSEUS is freely accessible at https://bioinformatics.cragenomica.es/perseus and GitHub code is available at https://github.com/aranzana-lab/PERSEUS.
Expanding the coverage of spatial proteomics: a machine learning approach
Authors: Sun Huangqingbo , Li Jiayi , Murphy Robert F 
Published: February 2024

Abstract

Motivation
Multiplexed protein imaging methods use a chosen set of markers and provide valuable information about complex tissue structure and cellular heterogeneity. However, the number of markers that can be measured in the same tissue sample is inherently limited.

Results
In this paper, we present an efficient method to choose a minimal predictive subset of markers that for the first time allows the prediction of full images for a much larger set of markers. We demonstrate that our approach also outperforms previous methods for predicting cell-level protein composition. Most importantly, we demonstrate that our approach can be used to select a marker set that enables prediction of a much larger set than could be measured concurrently.

Availability and implementation
All code and intermediate results are available in a Reproducible Research Archive at https://github.com/murphygroup/CODEXPanelOptimization.
On the failure of the bootstrap for Chatterjee’s rank correlation
Authors: Lin Zhexiao , Han Fang 
Published: February 2024

Abstract
While researchers commonly use the bootstrap to quantify the uncertainty of an estimator, it has been noticed that the standard bootstrap, in general, does not work for Chatterjee’s rank correlation. In this paper, we provide proof of this issue under an additional independence assumption, and complement our theory with simulation evidence for general settings. Chatterjee’s rank correlation thus falls into a category of statistics that are asymptotically normal, but bootstrap inconsistent. Valid inferential methods in this case are Chatterjee’s original proposal for testing independence and the analytic asymptotic variance estimator of Lin & Han (2022) for more general purposes.
[Received on 5 April 2023. Editorial decision on 10 January 2024]
Identification and quantitation of multiple variants in RNA virus genomes
Authors: Sena Johnny , Karwal Lovkesh , Bell Callum , Devitt Nicholas , Schilkey Faye , Huang Claire , Livengood Jill , Das Subash , Dean Hansi J 
Published: February 2024

Abstract
The goal of the study was to identify and characterize RNA virus variants containing mutations spread over genomic distances &gt;5 kb. As proof of concept, high-quality viral RNA of the Dengue 2 component of Takeda’s tetravalent dengue vaccine candidate (TDV-2) was used to develop a reverse transcription–polymerase chain reaction protocol to amplify a ∼5.3 kb cDNA segment that contains the three genetic determinants of TDV-2 attenuation. Unique molecular identifiers were incorporated into each viral cDNA molecule for PacBio library preparation to improve the quantitative precision of the observed variants at the attenuation loci. Following assay optimization, PacBio long-read sequencing was validated with multiple clone-derived TDV-2 revertant variants and four complex revertant mixtures containing various compositions of TDV-2 and revertant viruses. PacBio sequencing analysis correctly identified and quantified variant composition in all tested samples, demonstrating that TDV-2 revertants could be identified and characterized and supporting the use of this method in the differentiation and quantification of complex variants of other RNA viruses. Long-read sequencing can identify complex RNA virus variants containing multiple mutations on a single-genome molecule, which is useful for in-depth genetic stability and revertant detection of live-attenuated viral vaccines, as well as research in virus evolution to reveal mechanisms of immune evasion and host cell adaption.
The CT and MRI features of benign calvarium and skull base osteoblastoma
Authors: Li Yulin , Wang Bing , Feng Chenya , Cheng Guanxun , Luo Zhendong 
Published: February 2024

Abstract

Objective
We retrospectively reviewed the CT and MRI features of patients with benign osteoblastoma in the calvarium and skull base (CSBOB).

Methods
Nine cases of pathologically confirmed benign CSBOB were analysed retrospectively. The patients had undergone CT and/or MRI. Tumour location, size, and imaging features were reviewed and recorded.

Results
The patients included four males and five females with a mean age of 27.0 years (age 14-40 years). The tumours were located in the frontal bone in 3 patients, the occipital bone in 3 patients, and in the parietal bone, sphenoid bone, and skull base in 1 patient each. On CT, the tumours measured 5.1 ± 3.3 (1.8-8.4) cm. Seven tumours were shown to have caused expansile bony destruction with an eggshell appearance and varying degrees of calcification or matrix mineralization. Multiple septa were observed in 5 tumours. Intracranial growth was observed in 5 tumours. On MRI, 7 tumours showed heterogeneous hypo- to isointensity on T1WI. Heterogeneous high signal patterns with low signal rims and septa were observed in 6 tumours on T2WI, and 4 showed a fluid-fluid level. On contrast-enhanced imaging, 6 tumours showed peripheral and septal enhancement, and 2 showed the dural tail sign.

Conclusions
Benign CSBOB is a rare tumour characterized by expansile bony destruction, septa, a sclerotic rim and calcification or matrix mineralization on CT and MRI.

Advances in knowledge
The findings from this study contribute to a better understanding of benign CSBOB and provide valuable imaging features that can aid in its diagnosis and differentiation from other tumours in the calvarium and skull base.
Minimally invasive treatment of early, good prognosis breast cancer—is this feasible?
Authors: Mactier Mhairi , McIntosh Stuart A , Sharma Nisha 
Published: February 2024

Abstract
Breast cancer screening programmes frequently detect early, good prognosis breast cancers with significant treatment burden for patients, and associated health-cost implications. Emerging evidence suggests a role for minimally invasive techniques in the management of these patients enabling many women to avoid surgical intervention. Minimally invasive techniques include vacuum-assisted excision, cryoablation, and radiofrequency ablation. We review published evidence in relation to the risks and benefits of each technique and discuss ongoing trials. Data to date are promising, and we predict a trend towards minimally invasive treatment for early, good-prognosis breast cancer as technical skills, suitability criteria, and follow-up protocols are established.
Safety of Ustekinumab in Inflammatory Bowel Disease: Pooled Safety Analysis Through 5 Years in Crohn’s Disease and 4 Years in Ulcerative Colitis
Authors: Ghosh Subrata , Feagan Brian G , Ott Elyssa , Gasink Christopher , Godwin Bridget , Marano Colleen , Miao Ye , Ma Tony , Loftus Edward V , Sandborn William J , Danese Silvio , Abreu Maria T , Sands Bruce E 
Published: February 2024

Abstract

Background and Aims
Previously published long-term safety data reported a favourable ustekinumab safety profile for the treatment of inflammatory bowel disease [IBD]. We present the final cumulative safety data from pooled ustekinumab IBD phase 2/3 clinical studies through 5 years in Crohn’s disease [CD] and 4 years in ulcerative colitis [UC].

Methods
In phase 3 studies, patients received a single intravenous placebo or ustekinumab [130 mg or ~6 mg/kg] induction dose followed by subcutaneous maintenance doses of placebo or ustekinumab [90 mg q8w or q12w]. Analyses included all patients who received one dose of study treatment and included patients who were biologic-naïve and patients with a history of biologic failure. Safety outcomes are summarized and presented using number of events per 100 patient-years of follow-up and corresponding 95% confidence intervals.

Results
In this final pooled safety analysis, 2575 patients were treated with ustekinumab with 4826 patient-years of follow-up. Rates of key safety events, including major adverse cardiac events and malignancies, were similar between placebo and ustekinumab or not higher for ustekinumab. Opportunistic infections, including tuberculosis, and malignancies were reported infrequently. Rates of key safety events in the IBD group were no higher in the ustekinumab group than in the placebo group for both patients who were biologic-naïve or who had a history of biologic failure. No lymphomas or cases of posterior reversible encephalopathy syndrome [formerly known as reversible posterior leukoencephalopathy syndrome] were reported.

Conclusion
The final cumulative ustekinumab safety data through 5 years in CD and 4 years in UC demonstrated favourable safety compared to placebo and continue to support the well-established safety profile across all approved indications.

Clinical trials.gov numbers
NCT00265122, NCT00771667, NCT01369329, NCT01369342, NCT01369355, NCT02407236
Pheromone traps and climate variations influence populations of Sahlbergella singularis (Hemiptera: Miridae) and associated damage of cocoa in Cameroon
Authors: Mahot Hermine C , Bagny-Beilhe Leïla , Mahob Raymond J , Begoudé Aimé-Didier B , Fotso Kuate Apollin , Membang Gertrude , Ewane Nathalie , Kemga Adolph , Bilong Charles F B , Hall David R , Fiaboe Komi K M , Hanna Rachid 
Published: February 2024

Abstract
Knowledge of insect pest ecology and biology is important for maximizing crop protection and reducing crop losses. Currently, we lack an efficient control program for the cocoa mirid Sahlbergella singularis Haglund (Hemiptera: Miridae), the principal insect pest of cocoa in West and Central Africa. A 2-yr study was conducted in 11 plantations across Ayos and Konye, two of the largest cocoa growing areas of Cameroon. We evaluated the effects of mirid sex pheromone and climatic variations on mirid population dynamics and their associated cocoa damage. Sex pheromone traps caught 1.5-fold higher mirids in Ayos than in Konye, with more overall counts in 2015 than in 2016. Cocoa pod counts were also significantly higher in 2015 than in 2016 and were negatively correlated with temperature and relative humidity. In both localities, mirid populations and associated cocoa pod damage were suppressed in plantations where sex pheromone traps were used. Damage incidence was positively correlated with mirid counts, confirming that the cocoa pod is the preferential site for mirid feeding and reproduction. As such, damage incidence could be used as proxy for comparative mirid population level due to the mirid’s cryptic habit. Of the recorded weather variables, only relative humidity was correlated (negatively) with damage severity. Our data on the relationships between damage caused by mirids and their population dynamics and sex pheromone trap catches suggest that an effective control strategy using mass trapping could be developed for mirid management in cocoa plantations.