bluuebunny/crossref_metadata_2025_split huggingface dataset:
3DSC - a dataset of superconductors including crystal structures
Authors: Sommer Timo , Willa Roland , Schmalian Jörg , Friederich Pascal 
Published: November 2023

AbstractData-driven methods, in particular machine learning, can help to speed up the discovery of new materials by finding hidden patterns in existing data and using them to identify promising candidate materials. In the case of superconductors, the use of data science tools is to date slowed down by a lack of accessible data. In this work, we present a new and publicly available superconductivity dataset (‘3DSC’), featuring the critical temperature TC of superconducting materials additionally to tested non-superconductors. In contrast to existing databases such as the SuperCon database which contains information on the chemical composition, the 3DSC is augmented by approximate three-dimensional crystal structures. We perform a statistical analysis and machine learning experiments to show that access to this structural information improves the prediction of the critical temperature TC of materials. Furthermore, we provide ideas and directions for further research to improve the 3DSC. We are confident that this database will be useful in applying state-of-the-art machine learning methods to eventually find new superconductors.
An Australian housing conditions data infrastructure
Authors: Baker Emma , Morey Claire , Daniel Lyrian , Beer Andrew , Bentley Rebecca , Stone Wendy , Rowley Steven , Nygaard Christian A. , London Kerry 
Published: November 2023

AbstractFor the past two decades, researchers and policy makers have known very little about conditions within Australia’s housing stock due to a lack of systematic and reliable data. In 2022, a collaboration of Australian universities and researchers commissioned a large survey of 22,550 private rental, social rental and homeowner households to build a data infrastructure on the household and demographic characteristics, housing quality and conditions in the Australian housing stock. This is the third and largest instalment in a national series of housing conditions data infrastructures.
Prediction of folding patterns for intrinsic disordered protein
Authors: Yang Jiaan , Cheng Wen-xiang , Wu Gang , Sheng Sitong , Zhang Peng 
Published: November 2023

AbstractThe conformation flexibility of natural protein causes both complexity and difficulty to understand the relationship between structure and function. The prediction of intrinsically disordered protein primarily is focusing on to disclose the regions with structural flexibility involving relevant biological functions and various diseases. The order of amino acids in protein sequence determines possible conformations, folding flexibility and biological function. Although many methods provided the information of intrinsically disordered protein (IDP), but the results are mainly limited to determine the locations of regions without knowledge of possible folding conformations. Here, the developed protein folding fingerprint adopted the protein folding variation matrix (PFVM) to reveal all possible folding patterns for the intrinsically disordered protein along its sequence. The PFVM integrally exhibited the intrinsically disordered protein with disordering regions, degree of disorder as well as folding pattern. The advantage of PFVM will not only provide rich information for IDP, but also may promote the study of protein folding problem.
Multispectral multibeam backscatter response of heterogeneous rhodolith beds
Authors: Menandro Pedro S. , Misiuk Benjamin , Brown Craig J. , Bastos Alex C. 
Published: November 2023

AbstractAcoustic backscatter has been used as a tool to map the seafloor in greater detail and plays an increasingly important role in seafloor mapping to meet multiple ocean management needs. An outstanding challenge to the use of backscatter for seafloor mapping is the distinction between acoustically similar substrates, such as mixed sediments from rhodoliths. Rhodolith beds are a biogenic substrate that provides important ecological services, and are typically classified as a single categorical substrate type—though nodules coverage may be spatially variable. Recently, multispectral acoustic backscatter has demonstrated great potential to improve thematic seafloor mapping compared to single-frequency systems. This work employs multispectral multibeam backscatter and underwater imagery to characterize and map rhodolith beds in the Costa das Algas Marine Protected Area (Brazil). A support vector machine classifier was used to classify multifrequency backscatter mosaics according to rhodolith classes identified from underwater imagery. Results suggest that multispectral backscatter is effective both in providing information for mapping different proportions of rhodolith coverage and in predicting the presence or absence of these nodules. The backscatter of the lowest frequency was the most useful for distinguishing variable proportions of rhodolith coverage, and the two higher frequencies were better predictors of presence and absence.
High-throughput analysis system of interaction kinetics for data-driven antibody design
Authors: Matsunaga Ryo , Ujiie Kan , Inagaki Mayuko , Fernández Pérez Jorge , Yasuda Yoshiki , Mimasu Shinya , Soga Shinji , Tsumoto Kouhei 
Published: November 2023

AbstractSurface plasmon resonance (SPR) is widely used for antigen–antibody interaction kinetics analysis. However, it has not been used in the screening phase because of the low throughput of measurement and analysis. Herein, we proposed a high-throughput SPR analysis system named “BreviA” using the Brevibacillus expression system. Brevibacillus was transformed using a plasmid library containing various antibody sequences, and single colonies were cultured in 96-well plates. Sequence analysis was performed using bacterial cells, and recombinant antibodies secreted in the supernatant were immobilized on a sensor chip to analyze their interactions with antigens using high-throughput SPR. Using this system, the process from the transformation to 384 interaction analyses can be performed within a week. This system utility was tested using an interspecies specificity design of an anti-human programmed cell death protein 1 (PD-1) antibody. A plasmid library containing alanine and tyrosine mutants of all complementarity-determining region residues was generated. A high-throughput SPR analysis was performed against human and mouse PD-1, showing that the mutation in the specific region enhanced the affinity for mouse PD-1. Furthermore, deep mutational scanning of the region revealed two mutants with > 100-fold increased affinity for mouse PD-1, demonstrating the potential efficacy of antibody design using data-driven approach.
Risk of SARS-CoV-2 infection and hospitalization in individuals with natural, vaccine-induced and hybrid immunity: a retrospective population-based cohort study from Estonia
Authors: Uusküla Anneli , Pisarev Heti , Tisler Anna , Meister Tatjana , Suija Kadri , Huik Kristi , Abroi Aare , Kalda Ruth , Kolde Raivo , Fischer Krista 
Published: November 2023

AbstractA large proportion of the world’s population has some form of immunity against SARS-CoV-2, through either infection (‘natural’), vaccination or both (‘hybrid’). This retrospective cohort study used data on SARS-CoV-2, vaccination, and hospitalization from national health system from February 2020 to June 2022 and Cox regression modelling to compare those with natural immunity to those with no (Cohort1, n = 94,982), hybrid (Cohort2, n = 47,342), and vaccine (Cohort3, n = 254,920) immunity. In Cohort 1, those with natural immunity were at lower risk for infection during the Delta (aHR 0.17, 95%CI 0.15–0.18) and higher risk (aHR 1.24, 95%CI 1.18–1.32) during the Omicron period than those with no immunity. Natural immunity conferred substantial protection against COVID-19-hospitalization. Cohort 2—in comparison to natural immunity hybrid immunity offered strong protection during the Delta (aHR 0.61, 95%CI 0.46–0.80) but not the Omicron (aHR 1.05, 95%CI 0.93–1.1) period. COVID-19-hospitalization was extremely rare among individuals with hybrid immunity. In Cohort 3, individuals with vaccine-induced immunity were at higher risk than those with natural immunity for infection (Delta aHR 4.90, 95%CI 4.48–5.36; Omicron 1.13, 95%CI 1.06–1.21) and hospitalization (Delta aHR 7.19, 95%CI 4.02–12.84). These results show that risk of infection and severe COVID-19 are driven by personal immunity history and the variant of SARS-CoV-2 causing infection.
Study on correlation between TBM tailings gradation and granitic gneiss surrounding rock stability
Authors: Liu Yuancheng , Deng Ronggui , Yang Bai , Cheng Gang , Wang Tuo , Fu Zhiqian 
Published: November 2023

AbstractIn the process of double-shield TBM excavation, it is difficult to directly observe and test the characteristics of the surrounding rock. In this paper, the screening test of the different type tailings in the wet state was carried out to obtain the gradation curve and curve evaluation index. Combining with the excavation parameters and the surrounding rock characteristics of the tailings, a comprehensive analysis was carried out to establish the evaluation system among with the tailings gradation characteristics, lithology characteristics and excavation parameters. The results showed that: Sparsely fissured rock: the tailings are extensional fractures, the tailings gradation curve is inverse “S” type and gentle, and the evaluation index value: (1.50 > lg(Cu) > 1.35), (1.90 > Cc > 1.10). Broken surrounding rock: the curve is “L” type and steep, the content of coarse particles is much more than that of fine particles and (1.10 > lg(Cu) > 1.00), (2.60 > Cc > 2.40). Fractured rock: the curve is “Step” type, the tailings particles lack the middle particle size, the minerals are mostly weathered, (2.15 > lg(Cu )> 1.95), (0.09 > Cc > 0.07). The research results have good applicability to the surrounding rock stability evaluation of the example tunnel, which verifies the feasibility of the method.
The physiological measurement and evaluation of empathy of video content
Authors: Cho Ayoung , Park Sung , Lee Hyunwoo , Whang Mincheol 
Published: November 2023

AbstractThe COVID-19 pandemic has led to a surge in video content consumption, but measuring viewers' empathy towards the content has been limited to subjective evaluations or attached physiological apparatus. In this study, we introduced a novel non-contact physiological method for measuring empathy towards video content by assessing the synchronization of facial micromovements between the subject and object (i.e., person) within the media. We recorded facial micromovements and heart rate variability (HRV) remotely using a camera while 62 subjects watched one video each, designed and validated to elicit one of four two-dimensional emotions: pleasant-aroused, pleasant-relaxed, unpleasant-aroused, and unpleasant-relaxed. We also collected the subjects' self-assessed emotions and empathy using a questionnaire. The results confirmed that the stimuli effectively induced the intended arousal in the subjects, as evidenced by both self-reported emotions and HRV responses that suggested higher arousal was associated with stronger activity in the sympathetic nervous system. A closer examination of HRV indicators, such as SDNN and Total Power values, showed an amplification during the unpleasant state. We interpret this as the body's dynamic response to stressors, underlining the autonomic nervous system's proactive role in responding to such stimuli. In a broader context, our results emphasized that while subjects showcased augmented empathy during aroused conditions, the introduction of stressors, represented by unpleasant content, led to a dampening of this empathetic response. This findings demonstrate the potential of non-contact physiological methods for measuring empathy toward video content.
Recombinant inbred lines derived from wide crosses in Pisum
Authors: Ellis N. , Hofer J. , Sizer-Coverdale E. , Lloyd D. , Aubert G. , Kreplak J. , Burstin J. , Cheema J. , Bal M. , Chen Y. , Deng S. , Wouters R. H. M. , Steuernagel B. , Chayut N. , Domoney C. 
Published: November 2023

AbstractGenomic resources are becoming available for Pisum but to link these to phenotypic diversity requires well marked populations segregating for relevant traits. Here we describe two such resources. Two recombinant inbred populations, derived from wide crosses in Pisum are described. One high resolution mapping population involves cv Caméor, for which the first pea whole genome assembly was obtained, crossed to JI0281, a basally divergent P. sativum sativum landrace from Ethiopia. The other is an inter sub-specific cross between P. s. sativum and the independently domesticated P. s. abyssinicum. The corresponding genetic maps provide information on chromosome level sequence assemblies and identify structural differences between the genomes of these two Pisum subspecies. In order to visualise chromosomal translocations that distinguish the mapping parents, we created a simplified version of Threadmapper to optimise it for interactive 3-dimensional display of multiple linkage groups. The genetic mapping of traits affecting seed coat roughness and colour, plant height, axil ring pigmentation, leaflet number and leaflet indentation enabled the definition of their corresponding genomic regions. The consequence of structural rearrangement for trait analysis is illustrated by leaf serration. These analyses pave the way for identification of the underlying genes and illustrate the utility of these publicly available resources. Segregating inbred populations derived from wide crosses in Pisum, together with the associated marker data, are made publicly available for trait dissection. Genetic analysis of these populations is informative about chromosome scale assemblies, structural diversity in the pea genome and has been useful for the fine mapping of several discrete and quantitative traits.
Epidemiological trends of pyogenic spondylodiscitis in Germany: an EANS Spine Section Study
Authors: Kramer Andreas , Thavarajasingam Santhosh G. , Neuhoff Jonathan , Ponniah Hariharan Subbiah , Ramsay Daniele S. C. , Demetriades Andreas K. , Davies Benjamin M. , Shiban Ehab , Ringel Florian 
Published: November 2023

AbstractPyogenic spondylodiscitis presents significant diagnostic and therapeutic challenges. In Germany, a comprehensive understanding of its epidemiology and inpatient management outcomes is limited, hindering the optimisation of therapeutic strategies. This study aimed to characterise the evolving epidemiological trends of pyogenic spondylodiscitis in Germany, and concurrently evaluate inpatient management strategies and outcomes. We performed a retrospective population-based study of spondylodiscitis cases in Germany from 2005 to 2021, utilising data from the German Federal Statistical Office database. The parameters assessed were incidence trends, demographic characteristics, inpatient management strategies, and inpatient mortality. The study found a significant rise in the population-adjusted incidence of spondylodiscitis in Germany from 2005 to 2021, increasing by 104% from 5.4 to 11.0 cases per 100,000 individuals (p < 0.001). The highest number of diagnoses was recorded in 2019. Age group-adjusted data revealed the largest relative changes in the “90 + ” age group, followed by the “80–89” and “70–79” age groups. These increases were not solely attributable to population changes but were also confirmed after calculating the age-group-adjusted incidence rates. Additionally, our statistical analysis demonstrated that both age and year significantly influenced the incidence of spondylodiscitis. Over the same period, inpatient mortality also surged significantly by 347% (p < 0.001), with the highest increase recorded in the 90 + age group, observing a 2450% rise (p < 0.001). The mean length of inpatient stay decreased by 15% (p < 0.05). Concurrently, there was a significant increase in surgical interventions using spinal stabilisation procedures (p < 0.001), which might suggest a shift in the treatment paradigm for spondylodiscitis. The results underscore a concerning rise in spondylodiscitis incidence and mortality in Germany, particularly affecting the ageing population. A notable shift towards surgical intervention was observed. The data highlights the urgent necessity for high-level evidence studies comparing surgical versus conservative treatment, thereby guiding optimised therapeutic strategies.
A novel subject-wise dictionary learning approach using multi-subject fMRI spatial and temporal components
Authors: Khalid Muhammad Usman , Nauman Malik Muhammad 
Published: November 2023

AbstractThe conventional dictionary learning (DL) algorithms aim to adapt the dictionary/sparse code to individual functional magnetic resonance imaging (fMRI) data. Thus, lacking the capability to consolidate the spatiotemporal diversities offered by other subjects. Considering that subject-wise (sw) data matrix can be decomposed into the sparse linear combination of multi-subject (MS) time courses and MS spatial maps, two new algorithms, sw sequential DL (swsDL) and sw block DL (swbDL), have been proposed. They are based on the novel framework, defined by the mixing model, where base matrices prepared by operating a computationally fast sparse spatiotemporal blind source separation method over multiple subjects are employed to adapt the mixing matrices to sw training data. They solve the optimization models formulated using $$l_0$$

l
0

/$$l_1$$

l
1

-norm penalization/constraints through dictionary/sparse code pair update and alternating minimization approach. They are unique because no existing sparse DL method can incorporate MS spatiotemporal components while updating sw atoms/sparse codes, which can eventually be assembled using neuroscience knowledge to extract group-level dynamics. Various fMRI datasets are used to evaluate and compare the performance of the proposed algorithms with existing state-of-the-art algorithms. Specifically, overall, a $$14\%$$

14
%

increase in the mean correlation value and $$39\%$$

39
%

reduction in the mean computation time exhibited by swsDL and swbDL, respectively, over the adaptive consistent sequential dictionary algorithm.
Placebo hypoalgesia induced by operant conditioning: a comparative study on the effects of verbal, token-based, and social rewards and punishers
Authors: Bieniek Helena , Bąbel Przemysław 
Published: November 2023

AbstractOperant conditioning was shown to be a mechanism of placebo hypoalgesia; however, only verbal rewards and punishers were applied in the previous study. We aimed to induce placebo hypoalgesia using more clinically relevant consequences: token-based and social. Participants were divided into three experimental groups (with verbal, social, and token-based rewards and punishers); and two control groups (with and without placebo application). During operant conditioning, participants in the experimental groups received thermal stimuli of equal intensity and were rewarded for reporting lower pain and punished for reporting higher pain compared to their pretest pain levels. The control groups did not receive any consequences. Our results revealed placebo hypoalgesia was induced by operant conditioning only in the experimental groups with social and token-based reinforcement, compared to the control groups. The hypoalgesic effect found in the group that received verbal reinforcement did not differ significantly from the control group with the placebo application. Moreover, expectations about upcoming pain intensity were found to be a mediator, and the number of reinforcers received during conditioning was a predictor of placebo hypoalgesia. These findings highlight the potential benefits of incorporating token-based and social consequences for optimizing treatment outcomes in pain management.
Efficacy of ibuprofen and indomethacin as prophylaxis of heterotopic ossification: a comparative study
Authors: Schneider Jens , Maffulli Nicola , Eschweiler Jörg , Bell Andreas , Hildebrand Frank , Migliorini Filippo 
Published: November 2023

AbstractThe prophylactic action of non-steroidal anti-inflammatory drugs (NSAIDs) in heterotopic ossification (HO) was first described following analgesic therapy with indomethacin. Following that evidence, several compounds have been successfully used for prophylaxes of HO. Ibuprofen has been also proposed for the prevention of HO following THA. The present study compared the administration of ibuprofen for three weeks versus indomethacin as prophylaxis for HO following primary THA. In all THA procedures, pre- and post-operative protocols were conducted in a highly standardized fashion. The type of HO prophylaxis (indomethacin 100 mg/daily or ibuprofen 100 mg/daily) was chosen according to a chronological criterion: from 2017 to 2019 indomethacin was used, whereas from 2019 to 2022 ibuprofen was administered. In case of allergy or intolerance to NSAIDs, no prophylaxis was performed, and patients were included as a control group. All patients who underwent an anteroposterior radiography of the pelvis at a minimum of 12 months following THA were considered for inclusion. On admission, the age and sex of the patients were recorded. Moreover, the causes of osteoarthritis and the date of surgery were recorded. The grade of HO was assigned by a blinded assessor who was not involved in the clinical management of the patients. The modified Brooker Staging System was used to rate the efficacy of the interventions. Data from 1248 patients were collected. 62% (767 of 1248 patients) were women. The mean age was 67.0 ± 2.9 years. The mean follow-up was 21.1 ± 10.8 months. In the ibuprofen group, 73% of patients evidenced Brooker 0, 17% Brooker I, and 10% Brooker II. In the indomethacin group, 77% of patients evidenced Brooker 0, 16% Brooker I, 6% Brooker II. No patient in the ibuprofen and indomethacin group developed Brooker III or IV. In the control group, 64% of patients evidenced Brooker 0, 21% Brooker I, 3% Brooker II, and 12% Brooker III. No patient in the control group developed Brooker IV HO. Concluding, three weeks of administration of ibuprofen demonstrated similar efficacy to indomethacin in preventing HO following primary THA. The prophylaxis with ibuprofen or indomethacin was more effective in preventing HO compared to a control group who did not receive any pharmacological prophylaxis.
Survival following complete resection of neuroblastoma in novel orthotopic rat xenograft model
Authors: Sever ReidAnn E. , Rosenblum Lauren Taylor , Reyes-Múgica Miguel , Edwards W. Barry , Malek Marcus M. , Kohanbash Gary 
Published: November 2023

AbstractNeuroblastoma accounts for 15% of pediatric cancer deaths, despite multimodal therapy including surgical resection. Current neuroblastoma rodent models are insufficient for studying the impact of surgery and combination treatments, largely due to the small size of mouse models. Human neuroblastoma SK-N-BE(2) cells were injected into the left adrenal gland of 5–6-week-old RNU homozygous nude rats. Rats were either monitored by MRI until humane endpoint was reached or after 5 weeks underwent operative tumor resection, followed by monitoring for recurrence and survival. Following neuroblastoma cell implantation, the majority of tumors grew to greater than 5000 mm3 within 5.5–6.5 weeks, meeting the humane endpoint. Surgical resection was successfully done in 8 out of 9 rats, extending survival following tumor implantation from a median of 42 days to 78 days (p < 0.005). Pathology was consistent with human neuroblastoma, showing small round blue cell tumors with Homer-Wright rosettes, high mitoses and karyorrhectic index, and strong PHOX2B staining. Thus, we have established a novel orthotopic xenograft rat model of neuroblastoma and demonstrated increased survival of rats after surgical tumor resection. This model can be used for the development of surgical techniques, such as the use of intraoperative molecular imaging or assessment of combination therapies that include surgery.