bluuebunny/crossref_metadata_2025 huggingface dataset:
Coherent structure detection and the inverse cascade mechanism in two-dimensional Navier–Stokes turbulence
Authors: Wang Jiahan , Sesterhenn Jörn , Müller Wolf-Christian
Published: May 2023

Coherent structures in two-dimensional Navier–Stokes turbulence are ubiquitously observed in nature, experiments and numerical simulations. The present study conducts a comparison between several structure detection schemes based on the Okubo–Weiss criterion, the vorticity magnitude and Lagrangian coherent structures (LCSs), focusing on the inverse cascade in two-dimensional hydrodynamic turbulence. A recently introduced vortex scaling phenomenology (Burgess & Scott, J. Fluid Mech., vol. 811, 2017, pp. 742–756) allows the quantification of the respective thresholds required by these methods based on physical properties of the flow. The resulting improved comparability allows us to identify characteristic relative differences in the detection sensitivity between the employed structure detection techniques. With respect to the inverse cascade of energy, coherent structures contribute, as expected, substantially less to the cross-scale flux than the residual incoherent parts of the flow although the energetically dominant coherent structures lead to an important large-scale deformation of the energy spectrum. This cascade inactivity can be understood by an increased misalignment of strain-rate and subgrid stress tensors within coherent structures. At the same time, the structures exhibit strong and localised nonlinear cross-scale interactions that appear to stabilise them. We quantify and interpret the resulting shape preservation of coherent structures in terms of a multi-scale gradient approach (Eyink, J. Fluid Mech., vol. 549, 2006, pp. 191–214) as the depletion of strain rotation and vorticity gradient stretching whereas the dynamics of the residual fluctuations are consistent with the vortex thinning picture.
Effects of the geothermal gradient on the convective dissolution in CO2sequestration
Authors: Hu Chenglong , Xu Ke , Yang Yantao
Published: May 2023

Convective dissolution is an important mechanism for long-term CO$_2$sequestration in deep saline aquifers. The presence of an unstable geothermal gradient can affect the process of dissolution. In this paper, we present direct numerical simulations in a three-dimensional porous medium at three different concentration Rayleigh numbers$Ra_S$with a set of thermal Rayleigh numbers$Ra_T$. Simulations reveal that the flow structures alter when${\textit {Ra}}_T$increases for a fixed${\textit {Ra}}_S$. Strong thermal gradient can yield large-scale convection rolls which change the horizontal distribution and motions of concentration fingers. The time evolution of fluxes also has different responses to different${\textit {Ra}}_T$. A theoretical model is developed and successfully describes the evolution of concentration flux and volume averaged concentration during the final shutdown stage. We further calculate the dissolved CO$_2$into the interior over time, which shows non-monotonic variations as${\textit {Ra}}_T$increases. At the end of our simulations, the maximum increment of dissolved CO$_2$occurs when density ratio is around unity for all three concentration Rayleigh numbers we have explored. We apply our results to a typical geological reservoir and discuss their implications.
“A New Non-Entity”: Border Commuters, the Peyton Strike, and the Adverse Effect Standard in Immigration Law, 1958–1972
Authors: Harvey Sean Parulian
Published: May 2023

This article uses a 1958–1962 strike at the Peyton Packing Company in El Paso, Texas, to examine how labor unions in the U.S.–Mexico borderlands used racial stereotypes and Cold War paranoia to influence the adoption of a more rigorous labor certification standard for those applying for a visa to enter the United State. Ultimately, labor unions and Mexican American workers sought to end the practice of border commuting by adopting and advancing the language of immigration restriction deployed by many Mexican American civil rights leaders of the era. This rhetoric ignored pleas for improving the minimum wage laws and protections and overlooked the fact that many border commuters wanted to migrate to the United States, but were often prevented from doing so by existing immigration laws. This case study forces historians of immigration and labor to reassess the role that labor unions played in helping to make the 1965 Hart-Cellar Act more exclusionary than previously thought.
Second-kind symmetric periodic orbits for planar perturbed Kepler problems and applications
Authors: Alberti Angelo , Vidal Claudio
Published: May 2023

We investigate the existence of families of symmetric periodic solutions of second kind as continuation of the elliptical orbits of the two-dimensional Kepler problem for certain symmetric differentiable perturbations using Delaunay coordinates. More precisely, we characterize the sufficient conditions for its existence and its type of stability is studied. The estimate on the characteristic multipliers of the symmetric periodic solutions is the new contribution to the field of symmetric periodic solutions. In addition, we present some results about the relationship between our symmetric periodic solutions and those obtained by the averaging method for Hamiltonian systems. As applications of our main results, we get new families of periodic solutions for: the perturbed hydrogen atom with stark and quadratic Zeeman effect, for the anisotropic Seeligers two-body problem and to the planar generalized Størmer problem.
Examining associations between genetic and neural risk for externalizing behaviors in adolescence and early adulthood
Authors: Brislin Sarah J. , Salvatore Jessica E. , Meyers Jacquelyn M. , Kamarajan Chella , Plawecki Martin H. , Edenberg Howard J. , Kuperman Samuel , Tischfield Jay , Hesselbrock Victor , Anokhin Andrey P. , Chorlian David B. , Schuckit Marc A. , Nurnberger John I. , Bauer Lance , Pandey Gayathri , Pandey Ashwini K. , Kramer John R. , Chan Grace , Porjesz Bernice ,   COGA Collaborators, Dick Danielle M.
Published: May 2023

Background

Researchers have identified genetic and neural risk factors for externalizing behaviors. However, it has not yet been determined if genetic liability is conferred in part through associations with more proximal neurophysiological risk markers.

Methods

Participants from the Collaborative Study on the Genetics of Alcoholism, a large, family-based study of alcohol use disorders were genotyped and polygenic scores for externalizing (EXT PGS) were calculated. Associations with target P3 amplitude from a visual oddball task (P3) and broad endorsement of externalizing behaviors (indexed via self-report of alcohol and cannabis use, and antisocial behavior) were assessed in participants of European (EA; N = 2851) and African ancestry (AA; N = 1402). Analyses were also stratified by age (adolescents, age 12–17 and young adults, age 18–32).

Results

The EXT PGS was significantly associated with higher levels of externalizing behaviors among EA adolescents and young adults as well as AA young adults. P3 was inversely associated with externalizing behaviors among EA young adults. EXT PGS was not significantly associated with P3 amplitude and therefore, there was no evidence that P3 amplitude indirectly accounted for the association between EXT PGS and externalizing behaviors.

Conclusions

Both the EXT PGS and P3 amplitude were significantly associated with externalizing behaviors among EA young adults. However, these associations with externalizing behaviors appear to be independent of each other, suggesting that they may index different facets of externalizing.
The co-occurrence of manic and depressive dimensions in early psychosis: a latent transition analysis
Authors: Ramain Julie , Abrahamyan Empson Lilith , Alameda Luis , Solida Alessandra , Elowe Julien , Mebdouhi Nadir , Conus Philippe , Golay Philippe
Published: May 2023

Background

Frequently associated with early psychosis, depressive and manic dimensions may play an important role in its course and outcome. While manic and depressive symptoms can alternate and co-occur, most of the studies in early intervention investigated these symptoms independently. The aim of this study was therefore to explore the co-occurrence of manic and depressive dimensions, their evolution and impact on outcomes.

Methods

We prospectively studied first-episode psychosis patients (N = 313) within an early intervention program over 3 years. Based on latent transition analysis, we identified sub-groups of patients with different mood profiles considering both manic and depressive dimensions, and studied their outcomes.

Results

Our results revealed six different mood profiles at program entry and after 1.5 years follow-up (absence of mood disturbance, co-occurrence, mild depressive, severe depressive, manic and hypomanic), and four after 3 years (absence of mood disturbance, co-occurrence, mild depressive and hypomanic). Patients with absence of mood disturbance at discharge had better outcomes. All patients with co-occurring symptoms at program entry remained symptomatic at discharge. Patients with mild depressive symptoms were less likely to return to premorbid functional level at discharge than the other subgroups. Patients displaying a depressive component had poorer quality of physical and psychological health at discharge.

Conclusions

Our results confirm the major role played by mood dimensions in early psychosis, and show that profiles with co-occurring manic and depressive dimensions are at risk of poorer outcome. An accurate assessment and treatment of these dimensions in people with early psychosis is crucial.
Proinflammatory indicators and the relevance of echocardiography in children with cystic fibrosis
Authors: Yagci Ovgu Ozenli , Sulu Ayşe , Kosger Pelin , Yildirim Gonca Kilic , Anil Hulya , Ucar Birsen , Harmanci Koray
Published: May 2023

As the life expectancy improves in cystic fibrosis, cardiac dysfunction is becoming an important risk factor for morbidity and mortality. Here, the association of cardiac dysfunction with proinflammatory markers and neurohormones between cystic fibrosis patients and healthy children was investigated. Echocardiographic measurements of right and left ventricular morphology and functions together with levels of proinflammatory markers and neurohormones (renin, angiotensin-II, and aldosterone) were obtained and analysed in a study group of 21 cystic fibrosis children aged 5–18 years and compared with age- and gender-matched healthy children. It was shown that patients had significantly higher interleukin-6, C-reactive protein, renin and aldosterone levels (p < 0.05), dilated right ventricles, decreased left ventricle sizes, as well as both right and left ventricular dysfunction. These echocardiographic changes correlated with hypoxia, interleukin-1 α, interleukin-6, C-reactive protein, and aldosterone (p < 0.05) levels. The current study revealed that hypoxia, proinflammatory markers, and neurohormones are major determinants of subclinical changes in ventricular morphology and function. While the right ventricle anatomy was affected by cardiac remodeling, the left ventricle changes were induced by right ventricle dilation and hypoxia. A significant but subclinical systolic and diastolic right ventricle dysfunction in our patients was associated with hypoxia and inflammatory markers. Systolic left ventricle function was affected by hypoxia and neurohormones. Echocardiography is a reliable and non-invasive method that is used safely in cystic fibrosis children for screening and detection of cardiac anatomical and functional changes. Extensive studies are needed to determine the time and frequency of screening and treatment suggestions for such changes.
Development of the data registry for the Cardiac Neurodevelopmental Outcome Collaborative
Authors: Sadhwani Anjali , Sood Erica , Van Bergen Andrew H. , Ilardi Dawn , Sanz Jacqueline H. , Gaynor J. William , Seed Michael , Ortinau Cynthia M. , Marino Bradley S. , Miller Thomas A. , Gaies Michael , Cassidy Adam R. , Donohue Janet E. , Ardisana Amy , Wypij David , Goldberg Caren S.
Published: May 2023

Children with congenital heart disease (CHD) can face neurodevelopmental, psychological, and behavioural difficulties beginning in infancy and continuing through adulthood. Despite overall improvements in medical care and a growing focus on neurodevelopmental screening and evaluation in recent years, neurodevelopmental disabilities, delays, and deficits remain a concern. The Cardiac Neurodevelopmental Outcome Collaborative was founded in 2016 with the goal of improving neurodevelopmental outcomes for individuals with CHD and pediatric heart disease. This paper describes the establishment of a centralised clinical data registry to standardize data collection across member institutions of the Cardiac Neurodevelopmental Outcome Collaborative. The goal of this registry is to foster collaboration for large, multi-centre research and quality improvement initiatives that will benefit individuals and families with CHD and improve their quality of life. We describe the components of the registry, initial research projects proposed using data from the registry, and lessons learned in the development of the registry.
The popular Algerian barley landraces Saïda and Tichedrett are autochthonous – evidence from RAPD, SSR and agrophenological markers
Authors: Guetteche Hamama , Jarrar Ali Akram , Khiyel Ines , Djekkoun Narimane , Rouabah Leila , Rouabah Abdelkader , Benbelkacem Abdelkader , Nick Peter
Published: May 2023

The characterisation of traditional barley varieties from North Africa is promising with respect to detect traits linked with resilience to drought. Nine Algerian barley varieties comprising the economically relevant local landraces Saïda183 and Tichedrett were genotyped by random amplifying polymorphic DNA (RAPD) and by Simple Sequence Repeat (SSR) markers to get insight into their phylogenetic relationship and to compare the efficiency of the two approaches. The SSR markers were chosen such that all chromosomes of barley were represented by at least one marker. In addition, a principal component analysis (PCA) of morpho-agronomical traits was conducted. We found that the phylogeny based on the RAPD markers reflected the geographical distribution of the tested varieties, while the phylogeny based on the SSR markers reflected the pedigree. Among the RAPD markers, the maximal polymorphism information content was obtained for BY14 with a value of 0.82, for the SSR markers, Bmg13 was most informative with a value of 0.60. The similarity matrix used to the construct the phylogenetic tree, inferred a close relationship (Jaccard Index 0.8 based on RAPD markers) between the accessions Fouara and Oued-Athmania occurring in close vicinity. The SSR markers group the autochthonous varieties Saïda183 and Tichedrett together with a Jaccard Index of 0.8. The close phylogenetic relationship between Saïda183 and Tichedrett is also supported by the PCA of morphological and agronomic traits. Our data underpin the diversity of Algerian barley varieties and lend support to the autochthonous origin of these two Algerian landraces.
Uncertainty Analysis Related to Beach Morphology and Storm Duration for More Reliable Early Warning Systems for Coastal Hazards
Authors: Garzon J. L. , Plomaritis T. A. , Ferreira Ó.
Published: May 2023

Early warning systems (EWSs) for coastal erosion are cost‐effective instruments for risk reduction. Among other aspects, the selection of the pre‐storm beach morphology and the definition of storm characteristics can affect EWS reliability. Here, XBeach simulations were used to assess the uncertainties in beach‐dune erosion related to the variability of storm severity and duration and pre‐storm morphology. Wave height return periods (from 5 to 50 years) determined the severity and the duration variability was established from confidence intervals after an adjustment with wave height. The variability of steep profiles included different berm morphologies (from fully developed to eroded berms). Three indicators, relative eroded volume, proportional berm retreat and proportional dune retreat, were evaluated. The experiments revealed that: (a) Relative eroded volume uncertainties related to the pre‐storm morphology variability were slightly lower (maximum 8%) than the uncertainties related to storm duration (11%–18%). (b) Pre‐storm profile variability can induce large uncertainties in the proportional berm retreat (up to 88%) for moderate events such as the 5‐ and 10‐year events. Storm duration variability had less influence on this indicator (maximum 12%). (c) The uncertainties in the proportional dune retreat increased with storm severity and they ranged between 14% and 41% for pre‐storm profile variability and between 2% and 40% for storm duration variability. Duration variability even governed the occurrence of dune breaching on eroded berm profiles in the most extreme event. Hence, the uncertainties related to initial/forcing conditions, namely pre‐storm morphology and storm duration, must be assessed to develop reliable coastal erosion EWSs.
Outcomes of a hypertension care program based on task-sharing with private pharmacies: a retrospective study from two blocks in rural India
Authors: Das Hemanshu , Sachdeva Ashish , Kumar Harish , Krishna Ashish , Moran Andrew E. , Pathni Anupam K. , Sharma Bhawna , Singh Bhanu P. , Ranjan Manish , Deo Sarang
Published: May 2023

Low density of formal care providers in rural India results in restricted and delayed access to standardized management of hypertension. Task-sharing with pharmacies, typically the first point of contact for rural populations, can bridge the gap in access to formal care and improve health outcomes. In this study, we implemented a hypertension care program involving task-sharing with twenty private pharmacies between November 2020 and April 2021 in two blocks of Bihar, India. Pharmacists conducted free hypertension screening, and a trained physician offered free consultations at the pharmacy. We calculated the number of subjects screened, initiated on treatment (enrolled) and the change in blood pressure using the data collected through the program application. Of the 3403 subjects screened at pharmacies, 1415 either reported having a history of hypertension or had elevated blood pressure during screening. Of these, 371 (26.22%) were enrolled in the program. Of these, 129 (34.8%) made at least one follow-up visit. For these subjects, the adjusted average difference in systolic and diastolic blood pressure between the screening and follow-up visits was −11.53 (−16.95 to −6.11, 95% CI) and −4.68 (−8.53 to −0.82, 95% CI) mmHg, respectively. The adjusted odds of blood pressure being under control in this group during follow-up visits compared to screening visit was 7.07 (1.29 to 12.85, 95% CI). Task-sharing with private pharmacies can lead to early detection and improved control of blood pressure in a resource-constrained setting. Additional strategies to increase patient screening and retention rates are needed to ensure sustained health benefits.
Safety, pharmacokinetics, and pharmacodynamics of intravenous ferric carboxymaltose in children with iron deficiency anemia
Authors: Korczowski Bartosz , Farrell Colm , Falone Mark , Blackman Nicole , Rodgers Trudy
Published: May 2023

Background

Iron deficiency is the primary cause of anemia in children. Intravenous (IV) iron formulations circumvent malabsorption and rapidly restore hemoglobin.

Methods

This Phase 2, non-randomized, multicenter study characterized the safety profile and determined appropriate dosing of ferric carboxymaltose (FCM) in children with iron deficiency anemia. Patients aged 1–17 years with hemoglobin <11 g/dL and transferrin saturation <20% received single IV doses of undiluted FCM 7.5 mg/kg (n = 16) or 15 mg/kg (n = 19).

Results

The most common drug-related treatment-emergent adverse event was urticaria (in three recipients of FCM 15 mg/kg). Systemic exposure to iron increased in a dose-proportional manner with approximate doubling of mean baseline-corrected maximum serum iron concentration (157 µg/mL with FCM 7.5 mg/kg; and 310 µg/mL with FCM 15 mg/kg) and area under the serum concentration–time curve (1901 and 4851 h·µg/mL, respectively). Baseline hemoglobin was 9.2 and 9.5 g/dL in the FCM 7.5 and 15 mg/kg groups, respectively, with mean maximum changes in hemoglobin of 2.2 and 3.0 g/dL, respectively.

Conclusions

In conclusion, FCM was well tolerated by pediatric patients. Improvements in hemoglobin were greater with the higher dose, supporting use of the FCM 15 mg/kg dose in pediatric patients (Clinicaltrials.gov NCT02410213).

Impact

This study provided information on the pharmacokinetics and safety of intravenous ferric carboxymaltose for treatment of iron deficiency anemia in children and adolescents.

In children aged 1–17 years with iron deficiency anemia, single intravenous doses of ferric carboxymaltose 7.5 or 15 mg/kg increased systemic exposure to iron in a dose-proportional manner, with clinically meaningful increases in hemoglobin.

The most common drug-related treatment-emergent adverse event was urticaria.

The findings suggest that iron deficiency anemia in children can be corrected with a single intravenous dose of ferric carboxymaltose and support use of a 15 mg/kg dose.
Evolving cognition of the JAK-STAT signaling pathway: autoimmune disorders and cancer
Authors: Xue Chen , Yao Qinfan , Gu Xinyu , Shi Qingmiao , Yuan Xin , Chu Qingfei , Bao Zhengyi , Lu Juan , Li Lanjuan
Published: May 2023

The Janus kinase (JAK) signal transducer and activator of transcription (JAK-STAT) pathway is an evolutionarily conserved mechanism of transmembrane signal transduction that enables cells to communicate with the exterior environment. Various cytokines, interferons, growth factors, and other specific molecules activate JAK-STAT signaling to drive a series of physiological and pathological processes, including proliferation, metabolism, immune response, inflammation, and malignancy. Dysregulated JAK-STAT signaling and related genetic mutations are strongly associated with immune activation and cancer progression. Insights into the structures and functions of the JAK-STAT pathway have led to the development and approval of diverse drugs for the clinical treatment of diseases. Currently, drugs have been developed to mainly target the JAK-STAT pathway and are commonly divided into three subtypes: cytokine or receptor antibodies, JAK inhibitors, and STAT inhibitors. And novel agents also continue to be developed and tested in preclinical and clinical studies. The effectiveness and safety of each kind of drug also warrant further scientific trials before put into being clinical applications. Here, we review the current understanding of the fundamental composition and function of the JAK-STAT signaling pathway. We also discuss advancements in the understanding of JAK-STAT–related pathogenic mechanisms; targeted JAK-STAT therapies for various diseases, especially immune disorders, and cancers; newly developed JAK inhibitors; and current challenges and directions in the field.
General framework for E(3)-equivariant neural network representation of density functional theory Hamiltonian
Authors: Gong Xiaoxun , Li He , Zou Nianlong , Xu Runzhang , Duan Wenhui , Xu Yong
Published: May 2023

The combination of deep learning and ab initio calculation has shown great promise in revolutionizing future scientific research, but how to design neural network models incorporating a priori knowledge and symmetry requirements is a key challenging subject. Here we propose an E(3)-equivariant deep-learning framework to represent density functional theory (DFT) Hamiltonian as a function of material structure, which can naturally preserve the Euclidean symmetry even in the presence of spin–orbit coupling. Our DeepH-E3 method enables efficient electronic structure calculation at ab initio accuracy by learning from DFT data of small-sized structures, making the routine study of large-scale supercells (>104 atoms) feasible. The method can reach sub-meV prediction accuracy at high training efficiency, showing state-of-the-art performance in our experiments. The work is not only of general significance to deep-learning method development but also creates opportunities for materials research, such as building a Moiré-twisted material database.
Three-dimensional covalent organic frameworks with pto and mhq-z topologies based on Tri- and tetratopic linkers
Authors: Zhu Dongyang , Zhu Yifan , Chen Yu , Yan Qianqian , Wu Han , Liu Chun-Yen , Wang Xu , Alemany Lawrence B. , Gao Guanhui , Senftle Thomas P. , Peng Yongwu , Wu Xiaowei , Verduzco Rafael
Published: May 2023

Three-dimensional (3D) covalent organic frameworks (COFs) possess higher surface areas, more abundant pore channels, and lower density compared to their two-dimensional counterparts which makes the development of 3D COFs interesting from a fundamental and practical point of view. However, the construction of highly crystalline 3D COF remains challenging. At the same time, the choice of topologies in 3D COFs is limited by the crystallization problem, the lack of availability of suitable building blocks with appropriate reactivity and symmetries, and the difficulties in crystalline structure determination. Herein, we report two highly crystalline 3D COFs with pto and mhq-z topologies designed by rationally selecting rectangular-planar and trigonal-planar building blocks with appropriate conformational strains. The pto 3D COFs show a large pore size of 46 Å with an extremely low calculated density. The mhq-z net topology is solely constructed from totally face-enclosed organic polyhedra displaying a precise uniform micropore size of 1.0 nm. The 3D COFs show a high CO2 adsorption capacity at room temperature and can potentially serve as promising carbon capture adsorbents. This work expands the choice of accessible 3D COF topologies, enriching the structural versatility of COFs.
A rapid theta network mechanism for flexible information encoding
Authors: Johnson Elizabeth L. , Lin Jack J. , King-Stephens David , Weber Peter B. , Laxer Kenneth D. , Saez Ignacio , Girgis Fady , D’Esposito Mark , Knight Robert T. , Badre David
Published: May 2023

Flexible behavior requires gating mechanisms that encode only task-relevant information in working memory. Extant literature supports a theoretical division of labor whereby lateral frontoparietal interactions underlie information maintenance and the striatum enacts the gate. Here, we reveal neocortical gating mechanisms in intracranial EEG patients by identifying rapid, within-trial changes in regional and inter-regional activities that predict subsequent behavioral outputs. Results first demonstrate information accumulation mechanisms that extend prior fMRI (i.e., regional high-frequency activity) and EEG evidence (inter-regional theta synchrony) of distributed neocortical networks in working memory. Second, results demonstrate that rapid changes in theta synchrony, reflected in changing patterns of default mode network connectivity, support filtering. Graph theoretical analyses further linked filtering in task-relevant information and filtering out irrelevant information to dorsal and ventral attention networks, respectively. Results establish a rapid neocortical theta network mechanism for flexible information encoding, a role previously attributed to the striatum.
The FAIR Cookbook - the essential resource for and by FAIR doers
Authors: Rocca-Serra Philippe , Gu Wei , Ioannidis Vassilios , Abbassi-Daloii Tooba , Capella-Gutierrez Salvador , Chandramouliswaran Ishwar , Splendiani Andrea , Burdett Tony , Giessmann Robert T. , Henderson David , Batista Dominique , Emam Ibrahim , Gadiya Yojana , Giovanni Lucas , Willighagen Egon , Evelo Chris , Gray Alasdair J. G. , Gribbon Philip , Juty Nick , Welter Danielle , Quast Karsten , Peeters Paul , Plasterer Tom , Wood Colin , van der Horst Eelke , Reilly Dorothy , van Vlijmen Herman , Scollen Serena , Lister Allyson , Thurston Milo , Granell Ramon ,   the FAIR Cookbook Contributors, Backianathan Gabriel , Baier Sebastian , Thomsen Anne Cambon , Cook Martin , Courtot Melanie , d’Arcy Mike , Dauth Kurt , del Piico Eva Marin , Garcia Leyla , Goldmann Ulrich , Grouès Valentin , Clarke Daniel J. B. , Lefloch Erwan , Liyanage Isuru , Papadopoulos Petros , Pommier Cyril , Reynares Emiliano , Ronzano Francesco , Delfin-Rossaro Alejandra , Sagatopam Venkata , Sedani Ashni , Sedlyarov Vitaly , Shilova Liubov , Singh Sukhi , Strubel Jolanda , van Bochove Kees , Warnes Zachary , Woollard Peter , Xu Fuqi , Zaliani Andrea , Sansone Susanna-Assunta
Published: May 2023

The notion that data should be Findable, Accessible, Interoperable and Reusable, according to the FAIR Principles, has become a global norm for good data stewardship and a prerequisite for reproducibility. Nowadays, FAIR guides data policy actions and professional practices in the public and private sectors. Despite such global endorsements, however, the FAIR Principles are aspirational, remaining elusive at best, and intimidating at worst. To address the lack of practical guidance, and help with capability gaps, we developed the FAIR Cookbook, an open, online resource of hands-on recipes for “FAIR doers” in the Life Sciences. Created by researchers and data managers professionals in academia, (bio)pharmaceutical companies and information service industries, the FAIR Cookbook covers the key steps in a FAIRification journey, the levels and indicators of FAIRness, the maturity model, the technologies, the tools and the standards available, as well as the skills required, and the challenges to achieve and improve data FAIRness. Part of the ELIXIR ecosystem, and recommended by funders, the FAIR Cookbook is open to contributions of new recipes.
The iratebirds Citizen Science Project: a Dataset on Birds’ Visual Aesthetic Attractiveness to Humans
Authors: Haukka Anna , Lehikoinen Aleksi , Mammola Stefano , Morris William , Santangeli Andrea
Published: May 2023

Amidst a global biodiversity crisis, shedding light on the factors that make us like a species can help us understand human’s nature-related attitudes and inform conservation actions, e.g. by leveraging flagship potential and helping identify threats. Despite scattered attempts to quantify birds’ aesthetic attractiveness to humans, there is no large-scale database providing homogeneous measures of aesthetic attractiveness that are comparable across bird species. We present data on the visual aesthetic attractiveness of bird species to humans, generated through an internet browser-based questionnaire. Respondents (n = 6,212) were asked to rate the appearance of bird species on a scale from 1 (low) to 10 (high) based on photographs from the Cornell Lab of Ornithology’s Macaulay Library. The rating scores were modeled to obtain final scores of visual aesthetic attractiveness for each bird. The data covers 11,319 bird species and subspecies, with respondents from multiple backgrounds providing over 400,000 scores. This is the first attempt to quantify the overall visual aesthetic attractiveness of the world’s bird species to humans.
An interprovincial input–output database distinguishing firm ownership in China from 1997 to 2017
Authors: Chen Quanrun , Gao Yuning , Pan Chen , Xu Dingyi , Cai Kun , Guan Dabo , He Qi , Li Shantong , Liu Wanqi , Meng Bo , Wang Zhi , Wang Yang , Xu Xianchun , Yang Peihao , Zhang Meichen , Zhou Yuanqi
Published: May 2023

Input-Output (IO) data describing supply-demand relationships between buyers and sellers for goods and services within an economy have been used not only in economics but also in scientific, environmental, and interdisciplinary research. However, most conventional IO data are highly aggregated, resulting in challenges for researchers and practitioners who face complex issues in large countries such as China, where firms within the same IO sector may have significant differences in technologies across subnational regions and different ownerships. This paper is the first attempt to compile China’s interprovincial IO (IPIO) tables with separate information for mainland China-, Hong Kong, Macau, Taiwan-, and foreign-owned firms inside each province/industry pair. To do this, we collect relevant Chinese economic census data, firm surveys, product level Custom trade statistics, and firm value-added tax invoices and consistently integrate them into a 42-sector, 31-province IO account covering 5 benchmark years between 1997–2017. This work provides a solid foundation for a diverse range of innovative IO-based research in which firm heterogeneity information about location and ownership matters.
Flora diversity survey and establishment of a plant DNA barcode database of Lomas ecosystems in Peru
Authors: Song Feng , Deng Yun-Fei , Yan Hai-Fei , Lin Zhe-Li , Delgado Amalia , Trinidad Huber , Gonzales-Arce Paúl , Riva Sebastián , Cano-Echevarría Asunción , Ramos Elmer , Aroni Yaquelin Pamela , Rivera Soledad , Arakaki Mónica , Ge Xue-Jun
Published: May 2023

Lomas formations or “fog oases” are islands of vegetation in the desert belt of the west coast of South America, with a unique vegetation composition among the world’s deserts. However, plant diversity and conservation studies have long been neglected, and there exists a severe gap in plant DNA sequence information. To address the lack of DNA information, we conducted field collections and laboratory DNA sequencing to establish a DNA barcode reference library of Lomas plants from Peru. This database provides 1,207 plant specimens and 3,129 DNA barcodes data corresponding with collections from 16 Lomas locations in Peru, during 2017 and 2018. This database will facilitate both rapid species identification and basic studies on plant diversity, thereby enhancing our understanding of Lomas flora’s composition and temporal variation, and providing valuable resources for conserving plant diversity and maintaining the stability of the fragile Lomas ecosystems.
An external validation of coding for childhood maltreatment in routinely collected primary and secondary care data
Authors: John Ann , McGregor Joanna , Marchant Amanda , DelPozo-Baños Marcos , Farr Ian , Nurmatov Ulugbek , Kemp Alison , Naughton Aideen
Published: May 2023

Validated methods of identifying childhood maltreatment (CM) in primary and secondary care data are needed. We aimed to create the first externally validated algorithm for identifying maltreatment using routinely collected healthcare data. Comprehensive code lists were created for use within GP and hospital admissions datasets in the SAIL Databank at Swansea University working with safeguarding clinicians and academics. These code lists build on and refine those previously published to include an exhaustive set of codes. Sensitivity, specificity and positive predictive value of previously published lists and the new algorithm were estimated against a clinically assessed cohort of CM cases from a child protection service secondary care-based setting—‘the gold standard’. We conducted sensitivity analyses to examine the utility of wider codes indicating Possible CM. Trends over time from 2004 to 2020 were calculated using Poisson regression modelling. Our algorithm outperformed previously published lists identifying 43–72% of cases in primary care with a specificity ≥ 85%. Sensitivity of algorithms for identifying maltreatment in hospital admissions data was lower identifying between 9 and 28% of cases with high specificity (> 96%). Manual searching of records for those cases identified by the external dataset but not recorded in primary care suggest that this code list is exhaustive. Exploration of missed cases shows that hospital admissions data is often focused on the injury being treated rather than recording the presence of maltreatment. The absence of child protection or social care codes in hospital admissions data poses a limitation for identifying maltreatment in admissions data. Linking across GP and hospital admissions maximises the number of cases of maltreatment that can be accurately identified. Incidence of maltreatment in primary care using these code lists has increased over time. The updated algorithm has improved our ability to detect CM in routinely collected healthcare data. It is important to recognize the limitations of identifying maltreatment in individual healthcare datasets. The inclusion of child protection codes in primary care data makes this an important setting for identifying CM, whereas hospital admissions data is often focused on injuries with CM codes often absent. Implications and utility of algorithms for future research are discussed.
Wafer map failure pattern classification using geometric transformation-invariant convolutional neural network
Authors: Jeong Iljoo , Lee Soo Young , Park Keonhyeok , Kim Iljeok , Huh Hyunsuk , Lee Seungchul
Published: May 2023

Wafer map defect pattern classification is essential in semiconductor manufacturing processes for increasing production yield and quality by providing key root-cause information. However, manual diagnosis by field experts is difficult in large-scale production situations, and existing deep-learning frameworks require a large quantity of data for learning. To address this, we propose a novel rotation- and flip-invariant method based on the labeling rule that the wafer map defect pattern has no effect on the rotation and flip of labels, achieving class discriminant performance in scarce data situations. The method utilizes a convolutional neural network (CNN) backbone with a Radon transformation and kernel flip to achieve geometrical invariance. The Radon feature serves as a rotation-equivariant bridge for translation-invariant CNNs, while the kernel flip module enables the model to be flip-invariant. We validated our method through extensive qualitative and quantitative experiments. For qualitative analysis, we suggest a multi-branch layer-wise relevance propagation to properly explain the model decision. For quantitative analysis, the superiority of the proposed method was validated with an ablation study. In addition, we verified the generalization performance of the proposed method to rotation and flip invariants for out-of-distribution data using rotation and flip augmented test sets.
Multiple quantum interrogation to determine the position of an object in a serial array of ring resonators
Authors: Nakamura Keigo , Sugio Daiki , Manabe Takahiro , Kageyama Akari , Matsumoto Takahiro , Tomita Makoto
Published: May 2023

We propose quantum interaction-free measurements to determine not only whether an object exists, but also where it is situated among possible interrogation positions. In the first configuration, the object exists at one of several possible positions, and the other positions are empty. We regard this as multiple quantum trap interrogation. In the second configuration, the object does not exist in any possible interrogation position, but other positions are occupied by objects. We refer to this as multiple quantum loophole interrogation. It is possible to determine the position of a trap or loophole with almost 100% certainty, without any real interaction between the photon and the objects. We performed a preliminary experiment using a serial array of add-drop ring resonators and confirmed that multiple trap and loophole interrogations are possible. We discuss the detuning of resonators from the critical coupling condition, the loss effects in the resonator, the frequency detuning effect of incident light, and the effect of object semitransparency on the interrogation systems.
Mir-183 functions as an oncogene via decreasing PTEN in breast cancer cells
Authors: Mohammaddoust Samaneh , Sadeghizadeh Majid
Published: May 2023

Regarding the important role of microRNAs in breast cancer, investigating the molecular mechanisms of miRs and their impacts on breast cancer progression is critical. Thus, the present work aimed to investigate the molecular mechanism of miR-183 in breast cancer. PTEN was validated by dual luciferase assay as a target gene of miR-183. Through qRT-PCR analysis, miR-183 and PTEN mRNA levels in breast cancer cell lines were measured. To determine the impacts of miR-183 on cell viability, the MTT assay was used. Moreover, flowcytometry was applied to analyze the effects of miR-183 on the cell cycle progression. To detect the effects of miR-183 on the migration of BC cell lines, wound healing was used along with a Trans-well migration assay. Western blot was utilized to assess the effect of miR-183 on PTEN protein expression. MiR-183 can exert an oncogenic effect by promoting cell viability, migration, and cell cycle progression. It was revealed that cellular oncogenicity is positively regulated by miR-183 by inhibiting the expression of PTEN. According to the present data, miR-183 may play a vital role in the progression of breast cancer by reducing PTEN expression. It may be also a potential therapeutic target for this disease.
Correlated variability in primate superior colliculus depends on functional class
Authors: Katz Leor N. , Yu Gongchen , Herman James P. , Krauzlis Richard J.
Published: May 2023

Correlated variability in neuronal activity (spike count correlations, rSC) can constrain how information is read out from populations of neurons. Traditionally, rSC is reported as a single value summarizing a brain area. However, single values, like summary statistics, stand to obscure underlying features of the constituent elements. We predict that in brain areas containing distinct neuronal subpopulations, different subpopulations will exhibit distinct levels of rSC that are not captured by the population rSC. We tested this idea in macaque superior colliculus (SC), a structure containing several functional classes (i.e., subpopulations) of neurons. We found that during saccade tasks, different functional classes exhibited differing degrees of rSC. “Delay class” neurons displayed the highest rSC, especially during saccades that relied on working memory. Such dependence of rSC on functional class and cognitive demand underscores the importance of taking functional subpopulations into account when attempting to model or infer population coding principles.
Coulomb-free 1S0 p − p scattering length from the quasi-free p + d → p + p + n reaction and its relation to universality
Authors: Tumino Aurora , Rapisarda Giuseppe G. , La Cognata Marco , Oliva Alessandro , Kievsky Alejandro , Bertulani Carlos A. , D’Agata Giuseppe , Gattobigio Mario , Guardo Giovanni L. , Lamia Livio , Lattuada Dario , Pizzone Rosario G. , Romano Stefano , Sergi Maria L. , Spartá Roberta , Viviani Michele
Published: May 2023

The Coulomb-free 1S0 proton-proton (p-p) scattering length relies heavily on numerous and distinct theoretical techniques to remove the Coulomb contribution. Here, it has been determined from the half-off-the-energy-shell p-p scattering cross section measured at center-of-mass energies below 1 MeV using the quasi-free p + d → p + p + n reaction. A Bayesian data-fitting approach using the expression of the s-wave nucleon-nucleon scattering cross section returned a p-p scattering length $${a}_{pp}=-18.1{7}_{-0.58}^{+0.52}{| }_{stat}\pm 0.0{1}_{syst}$$

a

p
p

=
−
18.1

7

−
0.58

+
0.52

∣

s
t
a
t

±
0.0

1

s
y
s
t

fm and effective range r0 = 2.80 ± 0.05stat ± 0.001syst fm. A model based on universality concepts has been developed to interpret this result. It accounts for the short-range interaction as a whole, nuclear and residual electromagnetic, according to what the s-wave phase-shift δ does in the description of low-energy nucleon-nucleon scattering data. We conclude that our parameters are representative of the short-range physics and propose to assess the charge symmetry breaking of the short-range interaction instead of just the nuclear interaction. This is consistent with the current understanding that the charge dependence of nuclear forces is due to different masses of up-down quarks and their electromagnetic interactions. This achievement suggests that these properties have a lesser than expected impact in the context of the charge symmetry breaking.
Microfluidics and Lab-on-a-Chip
Authors: Manz Andreas , Neužil Pavel , O'Connor Jonathan S , Simone Giuseppina
Published: May 2023

Microfluidic technology is revolutionising a number of scientific fields, including chemistry, biology, diagnostics, and engineering. The ability to manipulate fluids and objects within networks of micrometre-scale channels allows reductions in processing and analysis times, reagent and sample consumption, and waste production, whilst allowing fine control and monitoring of chemical or biological processes. The integration of multiple components and processes enable “lab-on-a-chip” devices and “micro total analysis systems” that have applications ranging from analytical chemistry, organic synthesis, and clinical diagnostics to cell biology and tissue engineering.

This concise, easy-to-read book is perfectly suited for instructing newcomers on the most relevant and important aspects of this exciting and dynamic field, particularly undergraduate and postgraduate students embarking on new studies, or for those simply interested in learning about this widely applicable technology.

Written by a team with more than 20 years of experience in microfluidics research and teaching, the book covers a range of topics and techniques including fundamentals (e.g. scaling laws and flow effects), microfabrication and materials, standard operations (e.g. flow control, detection methods) and applications. Furthermore, it includes questions and answers that provide for the needs of students and teachers in the area.
The Changing Fortune of Cancer Immunotherapy
Authors: Marks Lara V.
Published: May 2023

Immunotherapy is now one of the most promising treatment modes for cancer. Such therapy boosts the immune system to fight cancer. This chapter shows that the idea behind cancer immunotherapy has a long history and began to be developed on the back of the rise of vaccines against infectious diseases. Achieving success in the clinic, however, took a long time. It grew out of new understanding about immunology and cancer that emerged on the back of the development of new inbred strains of laboratory animals from the 1950s. As this chapter shows, the progress in immunotherapy was never inevitable or straightforward.
Stem Cells: An Emerging Field for Medicine
Authors: Kraft Alison , Barry Frank
Published: May 2023

The concept of a stem cell as a progenitor cell from which all specialised cells are derived has been in existence for some 150 years. During the latter decades of the 20th century the concept became a reality, when embryonal carcinoma cells, embryonic stem cells, haematopoietic stem cells and mesenchymal stromal cells were all isolated and characterised. A great deal has been understood in recent years concerning the self-renewal and regulation of differentiation of stem cells. When it became clear that stem cells could be cultured in the laboratory and induced to differentiate into selected tissue-specific cells, it was quickly recognised that their therapeutic potential should be explored. It was the hope of many that tissues, injured as a result of trauma or disease, could be regenerated and their function restored. Following the amazing precedent set by bone marrow transplant it was assumed that many intractable diseases would now yield to stem cell therapy. Much effort has been made in evaluating the therapeutic utility of stem cell therapy, but for many diseases a definitive and unambiguous outcome has not yet been seen. This chapter describes the history of discovery of stem cells and the efforts that have been made to explore their use as a new medicine.