bluuebunny/crossref_metadata_2025 huggingface dataset:
Aircraft sequencing under the uncertainty of the runway occupancy times of arrivals during the backtrack procedure
Authors: Dönmez K.
Published: November 2022

In some small airports, a parallel taxiway is not built due to space restrictions or financial issues; hence, the runway itself is often used as a taxiway in this type of airport. After touch down, aircraft move to the U-turn area at the end of the runway and turn 180 degrees, then move back to the desired point, such as a gate or the apron, using the runway. The runway is blocked to other arrivals and departures during this process. This process, called backtrack or back-taxi, can result in high delays for both arrivals and departures. Runway occupancy times (ROTs) vary depending on numerous conditions, including pilot performance, weather conditions, aircraft type, etc. Although there are speed restrictions and procedures announced in advance, the actual performance can be uncertain. In addition, most aircraft can make a U-turn as soon as they sufficiently reduce their speed before they reach the U-turn area especially if they are already delayed. These situations bring enormous uncertainties for traffic management at such an airport. Controllers may need help to sequence aircraft, particularly in busy traffic. In this study, a stochastic mathematical model is developed to sequence arrival/departure operations at such an airport considering the ROT uncertainties of arrivals. The objective function of the developed model is determined as the minimisation of the total delay. ROT data was obtained by observing radar tracks of 120 arriving flights. Reasonable ROT scenarios with various probabilities to represent ROT uncertainties were integrated into the mathematical modeling. In addition, two different sequencing approaches are presented as well as the first come first serve (FCFS) approach. As a result, the proposed stochastic approach provides robust sequences applicable for all ROT scenarios with significant delay savings up to an average of 18.4% and 39.5% compared to deterministic and FCFS approaches, respectively.
Phonological features emerge substance-freely from the phonetics and the morphology
Authors: Boersma Paul , Chládková Kateřina , Benders Titia
Published: November 2022

Theories of phonology claim variously that phonological elements are either innate or emergent, and either substance-full or substance-free. A hitherto underdeveloped source of evidence for choosing between the four possible combinations of these claims lies in showing precisely how a child can acquire phonological elements. This article presents computer simulations that showcase a learning algorithm with which the learner creates phonological elements from a large number of sound–meaning pairs. In the course of language acquisition, phonological features gradually emerge both bottom-up and top-down, that is, both from the phonetic input (i.e., sound) and from the semantic or morphological input (i.e., structured meaning). In our computer simulations, the child's phonological features end up with emergedlinksto sounds (phonetic substance) as well as with emergedlinksto meanings (semantic substance), withoutcontainingeither phonetic or semantic substance. These simulations therefore show that emergent substance-free phonological features are learnable. In the absence of learning algorithms for linking innate features to the language-specific variable phonetic reality, as well as the absence of learning algorithms for substance-full emergence, these results provide a new type of support for theories of phonology in which features are emergent and substance-free.
Validation of a body condition scoring system in Nili Ravi dairy buffaloes (Bubalus bubalis): inter- and intra-assessor variability
Authors: Magsi Sayyad H. , Ahmad Nisar , Rashid Muhammad A. , Bah Musa , Akhter Maqsood , Shahid Muhammad Q.
Published: November 2022

The aim of the research reported in this Research Communication was to apply the 5-point body condition scoring (BCS) system to dairy buffaloes and subjectively validate it by assessing the intra- and inter-assessor agreement. For this purpose, the BCS system developed for dairy cows was applied to buffaloes. A total of 230 Nili Ravi buffaloes of varying parity, lactation stages and pregnancy status were enrolled from the Buffalo Research Institute, Pattoki, Pakistan. Four observers independently assigned BCS values to each enrolled buffalo in two phases, as follows: (1) during phase I, the assessors were trained for BCS assessment using a BCS chart developed by Elanco Animal Health Ltd.; and (2) during phase II, the assessors were trained using live buffaloes for BCS assessment. Kappa statistics (kw) were used to determine the intra- and inter-assessor agreement. The results revealed that the exact overall inter- and intra-assessor agreement was moderate (kw = 0.48–0.55) and increased to substantial levels after training on live animals (kw = 0.63–0.87). Furthermore, the intra- and inter-assessor exact agreement was higher (kw = 0.57–0.58) for buffaloes tied to the mangers compared to the buffaloes standing in the loafing area (kw = 0.50). The inter-assessor agreements within 0.25 and 0.5 points were almost perfect (kw = 0.97–1.0). The current results suggested that the 5-point BCS system (using a scale from 1 to 5 with 0.25 increments) had substantial agreement for assessment and repeatability when applied to buffaloes.
Recruitment of the endangered limpet Patella ferruginea in the Chafarinas Islands (SW Mediterranean)
Authors: Guallart Javier , Templado José , Luque Ángel A.
Published: November 2022

The recruitment of the endangered limpet Patella ferruginea in the Chafarinas Islands (SW Mediterranean) was studied over a 17-year period (1999‒2015). A total of 8115 recruits <20 mm in maximum diameter were counted in 95 transect censuses sampled during the study period. The presence of recruits began at the end of winter or beginning of spring (March‒April), when they reached a maximum shell diameter (MD) of at least 4 mm, with a peak in abundance occurring in spring. Smaller recruits were found on the lower midlittoral on the fringe of the vermetid gastropod Dendropoma lebeche and the crustose coralline algae Neogoniolithon brassica-florida, which suggests that settlement occurs at this shore level. Recruits reach 12‒27 mm at the end of their first year of life. A regular recruitment was detected for all studied years, with an average of 11.71 recruits m−1 across the study period. However, recruitment exhibited high interannual variability and did not occur evenly along the coastline of the islands. Higher recruitment was observed in 2001, 2011 and 2012, with a maximum density of 69.07 recruits m−1 in one transect in 2012. The density of recruits decreased in summer. No significant correlation was found between the density of recruits and adults. Between 1999‒2010, 29.29% of recruits were ‘phoretic’ on the shell of adults (1.81 recruits per host on average). Recruits climbed on to adults sometime after settlement, thus we suggest that ‘phoresy’ could favour the survival of young limpets instead of being due to selective settlement on adults. To improve and standardize recruitment monitoring in future studies, we propose that recruits are considered as those specimens <20 mm in MD and that recruitment censuses are carried out in spring, with additional censuses after summer to detect juvenile mortality. Additionally, we propose that 1 mm interval size classes are used for growth studies based on size‒frequency analyses.
Which patients benefit from adding short-term psychodynamic psychotherapy to antidepressants in the treatment of depression? A systematic review and meta-analysis of individual participant data
Authors: Driessen Ellen , Fokkema Marjolein , Dekker Jack J. M. , Peen Jaap , Van Henricus L. , Maina Giuseppe , Rosso Gianluca , Rigardetto Sylvia , Cuniberti Francesco , Vitriol Veronica G. , Andreoli Antonio , Burnand Yvonne , López Rodríguez Jaime , Villamil Salcedo Valerio , Twisk Jos W. R. , Wienicke Frederik J. , Cuijpers Pim
Published: November 2022

Background

Adding short-term psychodynamic psychotherapy (STPP) to antidepressants increases treatment efficacy, but it is unclear which patients benefit specifically. This study examined efficacy moderators of combined treatment (STPP + antidepressants) v. antidepressants for adults with depression.

Methods

For this systematic review and meta-analysis (PROSPERO registration number: CRD42017056029), we searched PubMed, PsycINFO, Embase.com, and the Cochrane Library from inception to 1 January 2022. We included randomized clinical trials comparing combined treatment (antidepressants + individual outpatient STPP) v. antidepressants in the acute-phase treatment of depression in adults. Individual participant data were requested and analyzed combinedly using mixed-effects models (adding Cochrane risk of bias items as covariates) and an exploratory machine learning technique. The primary outcome was post-treatment depression symptom level.

Results

Data were obtained for all seven trials identified (100%, n = 482, combined: n = 238, antidepressants: n = 244). Adding STPP to antidepressants was more efficacious for patients with high rather than low baseline depression levels [B = −0.49, 95% confidence interval (CI) −0.61 to −0.37, p < 0.0001] and for patients with a depressive episode duration of >2 years rather than <1 year (B = −0.68, 95% CI −1.31 to −0.05, p = 0.03) and than 1–2 years (B = −0.86, 95% CI −1.66 to −0.06, p = 0.04). Heterogeneity was low. Effects were replicated in analyses controlling for risk of bias.

Conclusions

To our knowledge, this is the first study that examines moderators across trials assessing the addition of STPP to antidepressants. These findings need validation but suggest that depression severity and episode duration are factors to consider when adding STPP to antidepressants and might contribute to personalizing treatment selection for depression.
Slave Resistance in Early Medieval England
Authors: Fontaine Janel M.
Published: November 2022

Considering early medieval slave resistance proves difficult, given our limited knowledge of all people of low status, especially slaves. Without oral histories, slave narratives, or strong indications of agency, we cannot confidently move beyond discussion of what slave-owners feared into what slaves intended. In lieu of broad discussion of slave agency for early medieval England, we can speak instead of the anticipated problems of slave-ownership. Elites were most concerned by behaviours which could fall into three overlapping categories of ‘problems’: those of property ownership, labour and violence. Each issue focusses heavily on legal responsibility for actions by slaves within a communal compensation-based legal system. Examination of these fears indicates that lawmakers and slave-owning elites were consistently engaged in problematizing slave-ownership, either in reaction to known slave behaviour or in anticipation of it. What emerges, then, is a situation in which both real and imagined acts of resistance helped shape ideas of power and authority both at a personal and administrative level. The expectations of slave behaviour also illuminate some aspects of slavery’s role in society.
Sleep Problems and Psychological Well-Being: Baseline Findings from the Canadian Longitudinal Study on Aging
Authors: Rodrigues Rebecca , Nicholson Kathryn , Guaiana Giuseppe , Wilk Piotr , Stranges Saverio , Anderson Kelly K.
Published: November 2022

International studies have demonstrated associations between sleep problems and poor psychological well-being; however, Canadian data are limited. This study investigated this association using cross-sectional baseline data from the Canadian Longitudinal Study on Aging, a national survey of 30,097 community-dwelling adults, 45–85 years of age. Short sleep duration, sleep dissatisfaction, insomnia symptoms, and daytime impairment were consistently associated with a higher prevalence of dissatisfaction with life, psychological distress, and poor self-reported mental health. Long sleep duration was associated with a higher prevalence of psychological distress and poor self-reported mental health, but not with dissatisfaction with life. Associations between sleep problems and psychological distress were 11–18 per cent stronger in males. With each 10-year increase in age, the association between daytime impairment and life dissatisfaction increased by 11 per cent, and insomnia symptoms and poor mental health decreased by 11 per cent. Sleep problems in middle-aged and older adults warrant increased attention as a public health problem in Canada.
A dilemma of World Heritage ideals and challenges in Southeast Asia
Authors: Miura Keiko
Published: November 2022

Fifty years after the ratification of the World Heritage Convention, we have come to learn that there is a huge discrepancy between the United Nations Educational, Scientific and Cultural Organization’s (UNESCO) ideals of protecting heritage sites with outstanding universal values and unmatched realities in situ. I attempt to elucidate what World Heritage ideals of heritage protection are held in iconic sites in Southeast Asia. The studied sites are ancient monumental heritage sites of national importance – namely, Borobudur of Indonesia, Sukhothai and Ayutthaya of Thailand, and Angkor of Cambodia. The authorities in these countries have converted heritage sites into parks for visitors and for capitalization, which has placed authenticity and integrity at stake as well as converting the sites for contestation between the authorities and local communities. In order to solve the dilemma of the World Heritage ideals and their unwanted realities, I explore possible effective approaches for UNESCO and its partners to take into consideration.
Factors affecting incidental L2 vocabulary acquisition and retention in a game-enhanced learning environment
Authors: Lee Sangmin-Michelle
Published: November 2022

In recent years, the number of studies investigating the effectiveness of using digital games for incidental second language (L2) vocabulary learning has been rapidly increasing; however, there is still a lack of research identifying the factors that affect incidental L2 vocabulary learning. Hence, the current study examined vocabulary-related (word level, exposure frequency, salience) and learner-related (language proficiency, interest, viewing captions) variables and investigated factors affecting EFL students’ incidental vocabulary learning in the use of a vernacular (noneducational) murder mystery game (N = 59). The study employed a quantitative research method and descriptive and inferential statistics (repeated measures ANOVA and multiple linear regression). The results showed that playing the game greatly facilitated L2 vocabulary acquisition and retention. Among the vocabulary-related variables, the study found that only salience significantly influenced vocabulary acquisition. Regarding the learner-related variables, the students’ interest and viewing captions were positively related to vocabulary learning, whereas their language proficiency levels were negatively correlated. The study found that the students’ conscious attention, in conjunction with salience of the word, was the main facilitating factor in incidental vocabulary acquisition and retention in the game-enhanced language learning environment. The study suggested pedagogical implications for incidental vocabulary learning through game play based on the results of the study.
A novel algorithm for classification of interatrial communications within the oval fossa in the newborn
Authors: Dannesbo Sofie , Blixenkrone-Moeller Elisabeth , Pihl Christian A. , Sillesen Anne-Sophie , Voegg Ruth O. , Davidsen Agnes S. , Lind Louise E. , Jeppesen Dorthe L. , Kruse Charlotte , Noerager Betina , Dodd James K. , Jorgensen Finn S. , Raja Anna A. , Colan Steven D. , Mertens Luc , Hjortdal Vibeke E. , Vejlstrup Niels , Anderson Robert H. , Bundgaard Henning , Iversen Kasper
Published: November 2022

Background:

An interatrial communication is present in most neonates. The majority are considered the “normal” patency of the oval foramen, while a minority are abnormal atrial septal defects. Differentiation between the two with transthoracic echocardiography may be challenging, and no generally accepted method of classification is presently available. We aimed to develop and determine the reliability of a new classification of interatrial communications in newborns.

Methods and Results:

An algorithm was developed based on echocardiographic criteria from 495 newborns (median age 11[8;13] days, 51.5% females). The algorithm defines three main categories: patency of the oval foramen, atrial septal defect, and no interatrial communication as well as several subtypes. We found an interatrial communication in 414 (83.6%) newborns. Of these, 386 (93.2%) were categorised as patency of the oval foramen and 28 (6.8%) as atrial septal defects.

Echocardiograms from another 50 newborns (median age 11[8;13] days, 36.0% female), reviewed by eight experts in paediatric echocardiography, were used to assess the inter- and intraobserver variation of classification of interatrial communications into patency of the oval foramen and atrial septal defect, with and without the use of the algorithm. Review with the algorithm gave a substantial interobserver agreement (kappa = 0.66), and an almost perfect intraobserver agreement (kappa = 0.82). Without the use of the algorithm, the interobserver agreement between experienced paediatric cardiologists was low (kappa = 0.20).

Conclusion:

A new algorithm for echocardiographic classification of interatrial communications in newborns produced almost perfect intraobserver and substantial interobserver agreement. The algorithm may prove useful in both research and clinical practice.
Genetic characterization of oleaginous bottle gourd (Lagenaria siceraria) germplasm from Côte d'Ivoire using agromorphological and molecular markers
Authors: Gbotto Ahou Anique , Yao Nasser Kouadio , Kitavi Mercy , Osama Sarah Karen , Habimana Richard , Koffi Kouamé Kevin , Zoro Bi Irié Arsène
Published: November 2022

Being difficult to regenerate and maintain the seeds, the oleaginous bottle gourd was investigated using nine agromorphological traits and 31 amplified fragment length polymorphism (AFLP) markers. Specifically, the study was conducted to determine the intra-specific variability of a total of 173 accessions, which were identified from five agro-ecological regions from Côte d'Ivoire (Centre, East, North and South). Then, the genetic diversity and relationships within accessions were studied using AFLP markers. This characterization using both morphological and AFLP markers was realized in order to ultimately build a reliable core collection. The discriminant analysis, using nine quantitative traits, reveals plant length and seeds number per fruit as discriminating characteristics. From the accessions used for the agromorphological study, 148 were able to be differentiated by the AFLP markers. A range of 52 to 113 bands were amplified per primer combination. As revealed by the analysis of molecular variance (AMOVA), 28% of the total variation resides among accessions and 72% occurs within populations. The AMOVA computed in order to differentiate cultivars, displayed the same trends when no prior grouping of accessions was considered. The differentiation within cultivar (97%) was more than that, among cultivars (3%). Tree topologies inferred by neighbour-joining analysis reflected no clear cut off grouping.

To group accessions, we used a Bayesian clustering analysis which exhibited two clusters. Using the informativeness of the primer combinations analysed in the present study, an orientation was given for the choice of the accessions which would be used to build a core collection.
Taking economic and social rights earnestly: What does international human rights law offer persons with disabilities in situations of armed conflict?
Authors: de Beco Gauthier
Published: November 2022

This article studies the economic and social rights of people with disabilities in times of armed conflict. While hostilities prevent them from accessing the essential goods and services that they rely on to enjoy these rights, the topic has attracted little attention to date. Calling upon international human rights law, the article applies the Convention on the Rights of Persons with Disabilities, with a view to complementing the provisions of international humanitarian law. It focuses on the requirements above the provision of medical care and examines the legal obligations attached to economic and social rights.
Conference Committee Structure and Majority Party Bias in U.S. States
Authors: Emrich Colin
Published: November 2022

How representative are conference delegations in state legislative chambers? I argue that differing conference rules across state legislative chambers influence majority party control over conference delegations. With an original data set encompassing all state-level conference committees from 2005 to 2016, I compare the observed policy preferences between conference delegation and majority party medians when the majority party unilaterally appoints and when the minority party has influence over conferee selection. My results show that in state legislative chambers where the minority can influence conference appointments, delegations are ideologically biased away from the majority party. These findings underscore how majority parties are limited when minorities have procedural rights.
Divergent Electoral Policies: Why Some States Increase Ballot Access
Authors: Smith Kelly B. , Hill David , Ancheva Slavina
Published: November 2022

Why have some states adopted policies expanding ballot access while others have restricted access to the ballot? Since the 1990s, some states have been adopting policies restricting access to the ballot such as requiring identification. At the same time, states have been adopting a variety of registration reforms that lower the barriers to registration and voting. Using an original, 45-state dataset, we examine state innovation within the policy domain of electoral reforms in US states. We find reforms have an independent and, sometimes, negative effect on the innovation of states in electoral reforms. Next, we use dyad analysis to examine the spread of a single policy: automatic voter registration. We find that the propensity to innovate both within and across a state makes the spread of automatic voter registration more likely. Our paper contributes to the broader understanding of why states adopt electoral reforms.
A genetically informed prediction model for suicidal and aggressive behaviour in teens
Authors: Tate Ashley E. , Akingbuwa Wonuola A. , Karlsson Robert , Hottenga Jouke-Jan , Pool René , Boman Magnus , Larsson Henrik , Lundström Sebastian , Lichtenstein Paul , Middeldorp Christel M. , Bartels Meike , Kuja-Halkola Ralf
Published: November 2022

Suicidal and aggressive behaviours cause significant personal and societal burden. As risk factors associated with these behaviours frequently overlap, combined approaches in predicting the behaviours may be useful in identifying those at risk for either. The current study aimed to create a model that predicted if individuals will exhibit suicidal behaviour, aggressive behaviour, both, or neither in late adolescence. A sample of 5,974 twins from the Child and Adolescent Twin Study in Sweden (CATSS) was broken down into a training (80%), tune (10%) and test (10%) set. The Netherlands Twin Register (NTR; N = 2702) was used for external validation. Our longitudinal data featured genetic, environmental, and psychosocial predictors derived from parental and self-report data. A stacked ensemble model was created which contained a gradient boosted machine, random forest, elastic net, and neural network. Model performance was transferable between CATSS and NTR (macro area under the receiver operating characteristic curve (AUC) [95% CI] AUCCATSS(test set) = 0.709 (0.671–0.747); AUCNTR = 0.685 (0.656–0.715), suggesting model generalisability across Northern Europe. The notable exception is suicidal behaviours in the NTR, which was no better than chance. The 25 highest scoring variable importance scores for the gradient boosted machines and random forest models included self-reported psychiatric symptoms in mid-adolescence, sex, and polygenic scores for psychiatric traits. The model’s performance is comparable to current prediction models that use clinical interviews and is not yet suitable for clinical use. Moreover, genetic variables may have a role to play in predictive models of adolescent psychopathology.
An effective and chemotherapy-free strategy of all-trans retinoic acid and arsenic trioxide for acute promyelocytic leukemia in all risk groups (APL15 trial)
Authors: Wang Huai-Yu , Gong Sha , Li Guo-Hui , Yao Ya-Zhou , Zheng Yin-Suo , Lu Xiao-Hong , Wei Su-Hua , Qin Wei-Wei , Liu Hai-Bo , Wang Meng-Chang , Xi Jie-Ying , Chen Li-Mei , Zhang Mei , Zhang Xin-Xin , Zhang Hui-Yun , Zhang Cheng-Sheng , Wald David N. , Zhu Hong-Hu , Liu Li , He Peng-Cheng
Published: November 2022

The combination of all-trans retinoic acid (ATRA) and arsenic trioxide (ATO) has been demonstrated to have comparable effectiveness or better to ATRA and chemotherapy (CHT) in non-high-risk acute promyelocytic leukemia (APL). However, the efficacy of ATRA-ATO compared to ATRA-ATO plus CHT in high-risk APL remains unknown. Here we performed a randomized multi-center non-inferiority phase III study to compare the efficacy of ATRA-ATO and ATRA-ATO plus CHT in newly diagnosed all-risk APL to address this question. Patients were assigned to receive ATRA-ATO for induction, consolidation, and maintenance or ATRA-ATO plus CHT for induction followed by three cycles of consolidation therapy, and maintenance therapy with ATRA-ATO. In the non-CHT group, hydroxyurea was used to control leukocytosis. A total of 128 patients were treated. The complete remission rate was 97% in both groups. The 2-year disease-free, event-free survival rates in the non-CHT group and CHT group in all-risk patients were 98% vs 97%, and 95% vs 92%, respectively (P = 0.62 and P = 0.39, respectively). And they were 94% vs 87%, and 85% vs 78% in the high-risk patients (P = 0.52 and P = 0.44, respectively). This study demonstrated that ATRA-ATO had the same efficacy as the ATRA-ATO plus CHT in the treatment of patients with all-risk APL.
Validation of the revised diagnostic criteria for primary plasma cell leukemia by the Korean Multiple Myeloma Working Party
Authors: Jung Sung-Hoon , Kim Kihyun , Yoon Sang Eun , Moon Joon Ho , Kim Dajung , Kim Hyo Jung , Kim Min Kyoung , Kim Kyoung Ha , Lee Hyun Jung , Lee Ji Hyun , Kim Sung-Hyun , Yoo Kawi Han , Lee Jae Hoon , Lee Je-Jung
Published: November 2022

The International Myeloma Working Group has recently revised the diagnostic criteria for primary plasma cell leukemia (PCL) to circulating plasma cells (CPCs) ≥ 5% in a peripheral blood smear. The present study validated new criteria in patients with multiple myeloma or PCL diagnosed using the previous diagnostic criteria, who were administered immunomodulatory drugs or proteasome inhibitors as induction therapy. We analyzed the medical records of 1357 patients from eight hospitals in South Korea. The median age of the all patients was 64 years, and 187 (13.8%) had CPCs at diagnosis. Only 79 (5.8%) of the patients had ≥ 5% CPCs. The median overall survival (OS) of patients with CPCs ≥ 5% and ≥ 20% was similar, but had significantly inferior median progression-free survival (PFS) and median OS than those with CPCs < 5% (13.1 vs. 21.5 months, P < 0.001, and 21.5 vs. 60.9 months, P < 0.001, respectively). Primary PCL diagnosed using the revised criteria presented with higher total calcium levels and serum creatinine levels, lower platelet counts and frequent organomegaly and plasmacytoma at diagnosis. Univariate and multivariate analyses demonstrated that the presence of plasmacytoma and elevated serum β2-microglobulin were significantly associated with OS in primary PCL. In conclusion, the revised criterion of CPCs ≥ 5% in a peripheral blood smear is appropriate for PCL diagnosis.
Retinoic acid-induced 1 gene haploinsufficiency alters lipid metabolism and causes autophagy defects in Smith-Magenis syndrome
Authors: Turco Elisa Maria , Giovenale Angela Maria Giada , Sireno Laura , Mazzoni Martina , Cammareri Alessandra , Marchioretti Caterina , Goracci Laura , Di Veroli Alessandra , Marchesan Elena , D’Andrea Daniel , Falconieri Antonella , Torres Barbara , Bernardini Laura , Magnifico Maria Chiara , Paone Alessio , Rinaldo Serena , Della Monica Matteo , D’Arrigo Stefano , Postorivo Diana , Nardone Anna Maria , Zampino Giuseppe , Onesimo Roberta , Leoni Chiara , Caicci Federico , Raimondo Domenico , Binda Elena , Trobiani Laura , De Jaco Antonella , Tata Ada Maria , Ferrari Daniela , Cutruzzolà Francesca , Mazzoccoli Gianluigi , Ziviani Elena , Pennuto Maria , Vescovi Angelo Luigi , Rosati Jessica
Published: November 2022

Smith-Magenis syndrome (SMS) is a neurodevelopmental disorder characterized by cognitive and behavioral symptoms, obesity, and sleep disturbance, and no therapy has been developed to alleviate its symptoms or delay disease onset. SMS occurs due to haploinsufficiency of the retinoic acid-induced-1 (RAI1) gene caused by either chromosomal deletion (SMS-del) or RAI1 missense/nonsense mutation. The molecular mechanisms underlying SMS are unknown. Here, we generated and characterized primary cells derived from four SMS patients (two with SMS-del and two carrying RAI1 point mutations) and four control subjects to investigate the pathogenetic processes underlying SMS. By combining transcriptomic and lipidomic analyses, we found altered expression of lipid and lysosomal genes, deregulation of lipid metabolism, accumulation of lipid droplets, and blocked autophagic flux. We also found that SMS cells exhibited increased cell death associated with the mitochondrial pathology and the production of reactive oxygen species. Treatment with N-acetylcysteine reduced cell death and lipid accumulation, which suggests a causative link between metabolic dyshomeostasis and cell viability. Our results highlight the pathological processes in human SMS cells involving lipid metabolism, autophagy defects and mitochondrial dysfunction and suggest new potential therapeutic targets for patient treatment.
Hydrogen atom collisions with a semiconductor efficiently promote electrons to the conduction band
Authors: Krüger Kerstin , Wang Yingqi , Tödter Sophia , Debbeler Felix , Matveenko Anna , Hertl Nils , Zhou Xueyao , Jiang Bin , Guo Hua , Wodtke Alec M. , Bünermann Oliver
Published: November 2022

The Born–Oppenheimer approximation is the keystone of modern computational chemistry and there is wide interest in understanding under what conditions it remains valid. Hydrogen atom scattering from insulator, semi-metal and metal surfaces has helped provide such information. The approximation is adequate for insulators and for metals it fails, but not severely. Here we present hydrogen atom scattering from a semiconductor surface: Ge(111)c(2 × 8). Experiments show bimodal energy-loss distributions revealing two channels. Molecular dynamics trajectories within the Born–Oppenheimer approximation reproduce one channel quantitatively. The second channel transfers much more energy and is absent in simulations. It grows with hydrogen atom incidence energy and exhibits an energy-loss onset equal to the Ge surface bandgap. This leads us to conclude that hydrogen atom collisions at the surface of a semiconductor are capable of promoting electrons from the valence to the conduction band with high efficiency. Our current understanding fails to explain these observations.
Global patterns in marine organic matter stoichiometry driven by phytoplankton ecophysiology
Authors: Inomura Keisuke , Deutsch Curtis , Jahn Oliver , Dutkiewicz Stephanie , Follows Michael J.
Published: November 2022

The proportion of major elements in marine organic matter links cellular processes to global nutrient, oxygen and carbon cycles. Differences in the C:N:P ratios of organic matter have been observed between ocean biomes, but these patterns have yet to be quantified from the underlying small-scale physiological and ecological processes. Here we use an ecosystem model that includes adaptive resource allocation within and between ecologically distinct plankton size classes to attribute the causes of global patterns in the C:N:P ratios. We find that patterns of N:C variation are largely driven by common physiological adjustment strategies across all phytoplankton, while patterns of N:P are driven by ecological selection for taxonomic groups with different phosphorus storage capacities. Although N:C varies widely due to cellular adjustment to light and nutrients, its latitudinal gradient is modest because of depth-dependent trade-offs between nutrient and light availability. Strong latitudinal variation in N:P reflects an ecological balance favouring small plankton with lower P storage capacity in the subtropics, and larger eukaryotes with a higher cellular P storage capacity in nutrient-rich high latitudes. A weaker N:P difference between southern and northern hemispheres, and between the Atlantic and Pacific oceans, reflects differences in phosphate available for cellular storage. Despite simulating only two phytoplankton size classes, the emergent global variability of elemental ratios resembles that of all measured species, suggesting that the range of growth conditions and ecological selection sustain the observed diversity of stoichiometry among phytoplankton.
Structures of transcription preinitiation complex engaged with the +1 nucleosome
Authors: Wang Haibo , Schilbach Sandra , Ninov Momchil , Urlaub Henning , Cramer Patrick
Published: November 2022

The preinitiation complex (PIC) assembles on promoters of protein-coding genes to position RNA polymerase II (Pol II) for transcription initiation. Previous structural studies revealed the PIC on different promoters, but did not address how the PIC assembles within chromatin. In the yeast Saccharomyces cerevisiae, PIC assembly occurs adjacent to the +1 nucleosome that is located downstream of the core promoter. Here we present cryo-EM structures of the yeast PIC bound to promoter DNA and the +1 nucleosome located at three different positions. The general transcription factor TFIIH engages with the incoming downstream nucleosome and its translocase subunit Ssl2 (XPB in human TFIIH) drives the rotation of the +1 nucleosome leading to partial detachment of nucleosomal DNA and intimate interactions between TFIIH and the nucleosome. The structures provide insights into how transcription initiation can be influenced by the +1 nucleosome and may explain why the transcription start site is often located roughly 60 base pairs upstream of the dyad of the +1 nucleosome in yeast.
Prediction of $$\beta $$-Thalassemia carriers using complete blood count features
Authors: Rustam Furqan , Ashraf Imran , Jabbar Shehbaz , Tutusaus Kilian , Mazas Cristina , Barrera Alina Eugenia Pascual , de la Torre Diez Isabel
Published: November 2022

$$\beta $$
β
-Thalassemia is one of the dangerous causes of the high mortality rate in the Mediterranean countries. Substantial resources are required to save a $$\beta $$
β
-Thalassemia carriers’ life and early detection of thalassemia patients can help appropriate treatment to increase the carrier’s life expectancy. Being a genetic disease, it can not be prevented however the analysis of several indicators in parents’ blood can be used to detect disorders causing Thalassemia. Laboratory tests for Thalassemia are time-consuming and expensive like high-performance liquid chromatography, Complete Blood Count (CBC) with peripheral smear, genetic test, etc. Red blood indices from CBC can be used with machine learning models for the same task. Despite the available approaches for Thalassemia carriers from CBC data, gaps exist between the desired and achieved accuracy. Moreover, the data imbalance problem is studied well which makes the models less generalizable. This study proposes a highly accurate approach for $$\beta $$
β
-Thalassemia detection using red blood indices from CBC augmented by supervised machine learning. In view of the fact that all the features do not carry predictive information regarding the target variable, this study employs a unified framework of two features selection techniques including Principal Component Analysis (PCA) and Singular Vector Decomposition (SVD). The data imbalance between $$\beta $$
β
-Thalassemia carrier and non-carriers is handled by Synthetic Minority Oversampling Technique (SMOTE) and Adaptive Synthetic (ADASYN). Extensive experiments are performed using many state-of-the-art machine learning models and deep learning models. Experimental results indicate the superiority of the proposed approach over existing approaches with an accuracy score of 0.96.
Monitoring of magmatic–hydrothermal system by noble gas and carbon isotopic compositions of fumarolic gases
Authors: Obase Tomoya , Sumino Hirochika , Toyama Kotaro , Kawana Kaori , Yamane Kohei , Yaguchi Muga , Terada Akihiko , Ohba Takeshi
Published: November 2022

We repeatedly measured isotopic compositions of noble gases and CO2 in volcanic gases sampled at six fumaroles around the Kusatsu-Shirane volcano (Japan) between 2014 and 2021 to detect variations reflecting recent volcanic activity. The synchronous increases in 3He/4He at some fumaroles suggest an increase in magmatic gas supply since 2018. The increase in magmatic gas supply is also supported by the temporal variations in 3He/CO2 ratios and carbon isotopic ratios of CO2. The 3He/40Ar* ratios (40Ar*: magmatic 40Ar) show significant increases in the period of high 3He/4He ratios. The temporal variation in 3He/40Ar* ratios may reflect changes in magma vesicularity. Therefore, the 3He/40Ar* ratio of fumarolic gases is a useful parameter to monitor the current state of degassing magma, which is essential for understanding the deep process of volcanic unrest and may contribute to identifying precursors of a future eruption. These results provide additional validation for the use of noble gas and carbon isotopic compositions of fumarolic gases for monitoring magmatic–hydrothermal systems.
Left ventricular T1-mapping in diastole versus systole in patients with mitral regurgitation
Authors: Liu Boyang , Sharma Harish , Su Khin Kyaw , Wesolowski Roman , Hothi Sandeep S. , Myerson Saul G. , Steeds Richard P.
Published: November 2022

Cardiovascular magnetic resonance T1-mapping enables myocardial tissue characterisation, and is capable of quantifying both intracellular and extracellular volume. T1-mapping is conventionally performed in diastole, however, we hypothesised that systolic readout would reduce variability due to a reduction in myocardial blood volume. This study investigated whether T1-mapping in systole alters T1 values compared to diastole and whether reproducibility alters in atrial fibrillation compared to sinus rhythm. We prospectively identified 103 consecutive patients recruited to the Mitral FINDER study who had T1 mapping in systole and diastole. These patients had moderate or severe mitral regurgitation and a high incidence of ventricular dilatation and atrial fibrillation. T1, ECV and goodness-of-fit (R2) values of the T1 times were calculated offline using Circle cvi42 and in house-developed software. Systolic T1 mapping was associated with fewer myocardial segments being affected by artefact compared to diastolic T1 mapping [217/2472 (9%) vs 515/2472 (21%)]. Mean native T1 values were not significantly different when measured in systole and diastole (985 ± 26 ms vs 988 ± 29 respectively; p = 0.061) and mean post-contrast values showed similar good agreement (462 ± 32 ms vs 459 ± 33 respectively, p = 0.052). No clinically significant differences in ECV, native T1 and post-contrast T1 were identified between diastolic and systolic T1 maps in males versus females, or in patients with permanent atrial fibrillation versus sinus rhythm. A statistically significant improvement in R2 value was observed with systolic over diastolic T1 mapping in all analysed maps (n = 411) (96.2 ± 1.4% vs 96.0 ± 1.4%; p < 0.001) and in subgroup analyses [Sinus rhythm: 96.1 ± 1.4 vs 96.3 ± 1.4 (n = 327); p < 0.001. AF: 95.5 ± 1.3 vs 95.9 ± 1.2 (n = 80); p < 0.001] [Males: 95.8 ± 1.4 vs 96.1 ± 1.3 (n = 264); p < 0.001; Females: 96.2 ± 1.3 vs 96.4 ± 1.4 (n = 143); p = 0.009]. In conclusion, myocardial T1 mapping is associated with similar T1 and ECV values in systole and diastole. Furthermore, systolic acquisition is less prone to gating artefact in arrhythmia.
Development of a novel electroporation method for the oyster parasite Perkinsus marinus
Authors: Sakamoto Hirokazu , Lin Xiaoxia X. , Bai Yun D. , Chen Xue F. , Zhang Ziyue Z. , Honjo Yui , Hikosaka Kenji
Published: November 2022

Gene manipulation techniques are fundamental to molecular biology and are continuously being improved. However, gene transfection methods are not established for many unicellular eukaryotes (protists), thereby hindering molecular biological investigations. The oyster parasite Perkinisus marinus is one of the few protists with established gene transfection and drug selection. Nevertheless, the present protocols are tedious, requiring a specific electroporator and pulse conditions which limits the accessibility of this technique across different research groups. Here, we present alternative buffer and electroporation conditions that make the protocol less restrictive. We revealed the pulse condition that enables the introduction of plasmids into P. marinus cell using Ingenio electroporation buffer and NEPA21 electroporator. We found that number of cells and plasmid concentration were critical parameters for the electroporation system. We also constructed a simpler expression plasmid that is removed needless regions for gene expression in the parasite. Our findings resolved the equipment restriction in electroporation of P. marinus and would be a good reference for electroporation in other protists, in particular other Perkinsozoa parasites and core dinoflagellates.
Dark-field chest X-ray imaging for the assessment of COVID-19-pneumonia
Authors: Frank Manuela , Gassert Florian T. , Urban Theresa , Willer Konstantin , Noichl Wolfgang , Schick Rafael , Schultheiss Manuel , Viermetz Manuel , Gleich Bernhard , De Marco Fabio , Herzen Julia , Koehler Thomas , Engel Klaus Jürgen , Renger Bernhard , Gassert Felix G. , Sauter Andreas , Fingerle Alexander A. , Haller Bernhard , Makowski Marcus R. , Pfeiffer Daniela , Pfeiffer Franz
Published: November 2022

Background

Currently, alternative medical imaging methods for the assessment of pulmonary involvement in patients infected with COVID-19 are sought that combine a higher sensitivity than conventional (attenuation-based) chest radiography with a lower radiation dose than CT imaging.

Methods

Sixty patients with COVID-19-associated lung changes in a CT scan and 40 subjects without pathologic lung changes visible in the CT scan were included (in total, 100, 59 male, mean age 58 ± 14 years). All patients gave written informed consent. We employed a clinical setup for grating-based dark-field chest radiography, obtaining both a dark-field and a conventional attenuation image in one image acquisition. Attenuation images alone, dark-field images alone, and both displayed simultaneously were assessed for the presence of COVID-19-associated lung changes on a scale from 1 to 6 (1 = surely not, 6 = surely) by four blinded radiologists. Statistical analysis was performed by evaluation of the area under the receiver–operator-characteristics curves (AUC) using Obuchowski’s method with a 0.05 level of significance.

Results

We show that dark-field imaging has a higher sensitivity for COVID-19-pneumonia than attenuation-based imaging and that the combination of both is superior to one imaging modality alone. Furthermore, a quantitative image analysis shows a significant reduction of dark-field signals for COVID-19-patients.

Conclusions

Dark-field imaging complements and improves conventional radiography for the visualisation and detection of COVID-19-pneumonia.
The effect of spin exchange interaction on protein structural stability
Authors: Levy Hadar Manis , Schneider Avi , Tiwari Satyam , Zer Hagit , Yochelis Shira , Goloubinoff Pierre , Keren Nir , Paltiel Yossi
Published: November 2022

Interactions with magnetic materials alter the structural and functional resilience of folded proteins under varying denaturing conditions. These effects are attributed to spin exchange interactions with surfaces having different magnetic properties.
Influence of the temperature-dependent dielectric constant on the photoacoustic effect of gold nanospheres
Authors: Sun Jian-Ping , Ren Ya-Tao , Gao Ren-Xi , Gao Bao-Hai , He Ming-Jian , Qi Hong
Published: November 2022

The effect of the temperature dependence of the dielectric constant on gold nanoparticles’ photoacoustic response is investigated. We find that ignoring this factor will lead to large (20 or 30%) errors in the photothermal response and the nonlinear photoacoustic signals.
Mesoporous SBA-15 supported gold nanoparticles for solvent-free oxidation of cyclohexane: superior catalytic activity with higher cyclohexanone selectivity
Authors: Bhuyan Diganta , Kalita Sanmilan Jyoti , Saikia Lakshi
Published: November 2022

Gold nanoparticles embedded on mesoporous SBA-15 is an excellent catalyst for solvent-free oxidation cyclohexane using TBHP as oxidant.
Solvent dependent triplet state delocalization in a co-facial porphyrin heterodimer
Authors: Ciuti Susanna , Toninato Jacopo , Barbon Antonio , Zarrabi Niloofar , Poddutoori Prashanth K. , van der Est Art , Di Valentin Marilena
Published: November 2022

The excited triplet state of a cofacial aluminum(iii) porphyrin–phosphorus(v) porphyrin heterodimer is investigated using transient EPR spectroscopy and quantum chemical calculations.
Performance evaluation of the balanced force field ff03CMAP for intrinsically disordered and ordered proteins
Authors: Jiang Yuxin , Chen Hai-Feng
Published: November 2022

The performance of the ff03CMAP force field is better than that of ff03 for reproducing the Ca chemical shifts for IDPs.
Insight into the effect of tetrapropylammonium hydroxide on HZSM-5 zeolite and its application in the reaction between 2,5-dimethylfuran and ethanol to p-xylene
Authors: Zhao Rongrong , Sui Juan , Wu Lianchao , Sun Xunzhen , Fu Lekai , Tan Hongzi , Cui Hongyou
Published: November 2022

Renewable synthesis of p-xylene (PX) via 2,5-dimethylfuran (2,5-DMF) and ethanol was achieved on alkali and surface modified HZSM-5 zeolite. Besides, the influence of hydrophobicity on the reaction performance was also thoroughly investigated.
Rare-earth squarate frameworks with scu topology
Authors: Wang Zhe , Liu Zhanning , Xie Changsong , Wang Rongming , Sun Daofeng
Published: November 2022

A series of rare earth squarate frameworks with the “smallest” scu type topology were synthesized.
Distinguishing the nanoplastic–cell membrane interface by polymer type and aging properties: translocation, transformation and perturbation
Authors: Li Lingzhi , Li Shixin , Xu Yan , Ren Luyao , Yang Lin , Liu Xia , Dai Yanhui , Zhao Jian , Yue Tongtao
Published: November 2022

Molecular simulations identify distinctive behaviors of nanoplastics at the cell membrane surface and reveal interfacial processes of translocation, transformation and membrane perturbation governed by the polymer type and aging properties.
Curcuminoids, a major turmeric component, have a sleep-enhancing effect by targeting the histamine H1 receptor
Authors: Um Min Young , Yoon Minseok , Kim Minji , Jung Jonghoon , Kim Seonghui , Kim Dae-Ok , Cho Suengmok
Published: November 2022

Curcuminoids (curcumin, demethoxycurcumin, and bisdemethoxycurcumin), which are the major constituents of turmeric (Curcuma longa), have sleep-promoting effects in mice through blockade of histamine H1 receptors