bluuebunny/crossref_metadata_2025_split huggingface dataset:
Three Adult Cases of STAT1 Gain-of-Function with Chronic Mucocutaneous Candidiasis Treated with JAK Inhibitors
Authors: Borgström Emilie W. , Edvinsson Marie , Pérez Lucía P. , Norlin Anna C. , Enoksson Sara L. , Hansen Susanne , Fasth Anders , Friman Vanda , Kämpe Olle , Månsson Robert , Estupiñán Hernando Y. , Wang Qing , Ziyang Tan , Lakshmikanth Tadepally , Smith Carl Inge E. , Brodin Petter , Bergman Peter 
Published: September 2022

Abstract
Purpose
The aim of this study was to characterize clinical effects and biomarkers in three patients with chronic mucocutaneous candidiasis (CMC) caused by gain-of-function (GOF) mutations in the STAT1 gene during treatment with Janus kinase (JAK) inhibitors.

Methods
Mass cytometry (CyTOF) was used to characterize mononuclear leukocyte populations and Olink assay to quantify 265 plasma proteins. Flow-cytometric Assay for Specific Cell-mediated Immune-response in Activated whole blood (FASCIA) was used to quantify the reactivity against Candida albicans.

Results
Overall, JAK inhibitors improved clinical symptoms of CMC, but caused side effects in two patients. Absolute numbers of neutrophils, T cells, B cells, and NK cells were sustained during baricitinib treatment. Detailed analysis of cellular subsets, using CyTOF, revealed increased expression of CD45, CD52, and CD99 in NK cells, reflecting a more functional phenotype. Conversely, monocytes and eosinophils downregulated CD16, consistent with reduced inflammation. Moreover, T and B cells showed increased expression of activation markers during treatment. In one patient with a remarkable clinical effect of baricitinib treatment, the immune response to C. albicans increased after 7 weeks of treatment. Alterations in plasma biomarkers involved downregulation of cellular markers CXCL10, annexin A1, granzyme B, granzyme H, and oncostatin M, whereas FGF21 was the only upregulated marker after 7 weeks. After 3 months, IFN-ɣ and CXCL10 were downregulated.

Conclusions
The clinical effect of JAK inhibitor treatment of CMC is promising. Several biological variables were altered during baricitinib treatment demonstrating that lymphocytes, NK cells, monocytes, and eosinophils were affected. In parallel, cellular reactivity against C. albicans was enhanced.
A comparison on the use of DEHBA or TBP as extracting agent for tetra- and hexavalent actinides in the CHALMEX Process
Authors: Authen Thea Lyseid , Tekikachew Behabitu Ergette , Foreman Mark R. St. J. , Wilden Andreas , Ekberg Christian 
Published: September 2022

AbstractThe Chalmers Grouped ActiNide EXtraction process is a solvent extraction process for the homogeneous recycling of spent nuclear fuel. The use of TBP for the extraction of tetra- and hexavalent actinides can be problematic for several reasons, including troublesome degradation products causing crud formation, decreased extraction yield and the possibility of explosive red oil reactions. Here, the substitution of TBP by a N,N-dialkyl monoamide, DEHBA, is investigated. The findings suggest that DEHBA can be a suitable extracting agent for use in the CHALMEX solvent, although identified drawbacks need to be further investigated.
Environmental hazard assessment of metals in marine sediments of Sabah and Sarawak, Malaysia
Authors: Ahmed Amel. Y. , Abdullah Md Pauzi , Siddeeg Saifeldin M. 
Published: September 2022

AbstractThe fractionation of 10 metals (As, Co, Cr, Cu, Mn, Ni, Pb, Se, V, and Zn) within labile fractions in shallow marine sediments collected from the coasts of Sabah and Sarawak, Malaysia, was evaluated. Spatial distribution revealed that coastal sediments from Sabah were approximately 10% higher in metal content than sediments from Sarawak. Risk assessment code, enrichment factor, and pollution accumulation index calculations were used to investigate the environmental hazards of elements. For the risk assessment code, the modified Tessier sequential extraction procedure was applied. The risk assessment code values showed that metal V recorded the lowest environment risk (~ 10%) while As, Co, Cr, Cu, Mn, and Zn exhibited medium risk (Risk assessment code range of 11%–30%). The element Ni displayed no risk (0.67%) to the environment, whereas Se and Pb recorded the highest risk with values of 47% and 52%, respectively. For the enrichment factor calculation, the continental crust data presented by Taylor (Taylor, Geochim Cosmochim Acta 28:1273–1285, 1964) were used as background, with metal Al used as a reference element. Results illustrated that most of the metals show enrichment (enrichment factor > 1). However, Se was considered extremely severe to the environment (enrichment factor > 50). While the pollution accumulation index calculation demonstrated that all metals under study can be considered as non-contaminant elements except for Ni, V, and Co. These findings indicated that marine sediments in Sabah are more polluted with metal contaminants than the sediments in Sarawak, despite both states having numerous active oil- and gas-related production facilities.
Application of physics-informed neural network in the analysis of hydrodynamic lubrication
Authors: Zhao Yang , Guo Liang , Wong Patrick Pat Lam 
Published: September 2022

AbstractThe last decade has witnessed a surge of interest in artificial neural network in many different areas of scientific research. Despite the rapid expansion in the application of neural networks, few efforts have been carried out to introduce such a powerful tool into lubrication studies. Thus, this work aims to apply the physics-informed neural network (PINN) to the hydrodynamic lubrication analysis. The 2D Reynolds equation is solved. The PINN is a meshless method and does not require big data for network training compared with classical methods. Our results are consistent with those obtained by experiments and the finite element method. Hence, we envision that the PINN method will have great application potential in lubrication and bearing research.
Stitching Womanhood in theZongo: Seamstress Apprenticeship in Accra
Authors: Cassiman Ann 
Published: September 2022

AbstractFocusing upon the daily lives of young female Muslim apprentices in the sewing shops of Accra’szongocommunities, Cassiman argues that the sewing workshop may be understood as a playground in which young women may experiment with the normative chronologies shaping women’s lives, and with ideals of female respectability, self-making, and autonomy. Opening up the possibility to subvert the chrononormativity of apprenticeship and marriage, young seamstress apprentices carve out a platform from which they can exert specific forms of agency, by suspending marriage or hastening it, while trying out various possible futures.
A categorical approach to dynamical quantum groups
Authors: Kalmykov Artem , Safronov Pavel 
Published: September 2022

Abstract
We present a categorical point of view on dynamical quantum groups in terms of categories of Harish-Chandra bimodules. We prove Tannaka duality theorems for forgetful functors into the monoidal category of Harish-Chandra bimodules in terms of a slight modification of the notion of a bialgebroid. Moreover, we show that the standard dynamical quantum groups

$F(G)$

and

$F_q(G)$

are related to parabolic restriction functors for classical and quantum Harish-Chandra bimodules. Finally, we exhibit a natural Weyl symmetry of the parabolic restriction functor using Zhelobenko operators and show that it gives rise to the action of the dynamical Weyl group.
Fast mixing of a randomized shift-register Markov chain
Authors: Levin David A. , Tankala Chandan 
Published: September 2022

AbstractWe present a Markov chain on the n-dimensional hypercube
$\{0,1\}^n$
which satisfies
$t_{{\rm mix}}^{(n)}(\varepsilon) = n[1 + o(1)]$
. This Markov chain alternates between random and deterministic moves, and we prove that the chain has a cutoff with a window of size at most
$O(n^{0.5+\delta})$
, where
$\delta>0$
. The deterministic moves correspond to a linear shift register.
Effects of parasitic freshwater mussels on their host fishes: a review
Authors: Rock Sebastian L. , Watz Johan , Nilsson P. Anders , Österling Martin 
Published: September 2022

AbstractFreshwater mussels in the order Unionida are highly adapted to parasitize fish for the primary purpose of dispersal. The parasitic larval stage affixes itself to the gills or fins of the host where it becomes encysted in the tissue, eventually excysting to develop into a free-living adult. Research on the parasitic interactions between unionids and their host fishes has garnered attention recently due to the increase in worldwide preservation efforts surrounding this highly endangered and ecologically significant order. With the exception of heavy infestation events, these mussels cause minor effects to their hosts, typically only observable effect in combination with other stressors. Moreover, the range of effect intensities on the host varies greatly with the species involved in the interaction, an effect that may arise from different evolutionary strategies between long- and short-infesting mussels; a distinction not typically made in conservation practices. Lower growth and reduced osmotic potential in infested hosts are commonly observed and correlated with infestation load. These effects are typically also associated with increases in metabolic rate and behaviour indicative of stress. Host fish seem to compensate for this through a combination of rapid wound healing in the parasitized areas and higher ventilation rates. The findings are heavily biased towardsMargaritifera margaritifera, a unique mussel not well suited for cross-species generalizations. Furthermore, the small body of molecular and genetic studies should be expanded as many conclusions are drawn from studies on the ultimate effects of glochidiosis rather than proximate studies on the underlying mechanisms.
An infrastructural account of scientific objectivity for legal contexts and bloodstain pattern analysis
Authors: Koolage W. John , Williams Lauren M. , Barroso Morgen L. 
Published: September 2022

ArgumentIn the United States, scientific knowledge is brought before the courts by way of testimony – the testimony of scientific experts. We argue that this expertise is best understoodfirstas related to the quality of the underlying scienceand thenin terms of who delivers it. Bloodstain pattern analysis (BPA), a contemporary forensic science, serves as the vaulting point for our exploration of objectivity as a metric for the quality of a science in judicial contexts. We argue that BPA fails to meet the minimal standard set by Helen Longino’s social-procedural account of objectivity (1990, 2002). In light of some pressing issues for social-procedural accounts, we offer an infrastructural account of objectivity. This account offers what amounts to a friendly amendment to Longino’s account and adds to the ways in which we might analyze social-procedural objectivity. Finally, we address an issue that is pressing in the legal context: given that scientific knowledge is delivered by individuals, not communities, at least in U.S. courts, we (may) need a way to evaluate individual scientific and epistemic agents. We suggest a means for making this evaluation that is derived from our infrastructural account of objectivity.
Animism and natural teleology from Avicenna to Boyle
Authors: Kochan Jeff 
Published: September 2022

ArgumentHistorians have claimed that the two closely related concepts of animism and natural teleology were both decisively rejected in the Scientific Revolution. They tout Robert Boyle as an early modern warden against pre-modern animism. Discussing Avicenna, Aquinas, and Buridan, as well as Renaissance psychology, I instead suggest that teleology went through a slow and uneven process of rationalization. As Neoplatonic theology gained influence over Aristotelian natural philosophy, the meaning of animism likewise grew obscure. Boyle, as some historians have shown, exemplifies this uneven process. There is an unresolved tension between his religious convictions and the implicit animism of his empirical practice.
Using one’s talents in honor of God: Lambert ten Kate (1674-1731) and Isaac Newton’s natural philosophy
Authors: Ducheyne Steffen 
Published: September 2022

ArgumentLambert ten Kate (1674-1731), the scholar of language, religious writer, art theoretician and collector, and natural philosophy enthusiast, was part of an informal network of Amsterdam-based mathematics and natural philosophy enthusiasts who played a pivotal role in the early diffusion of Newton’s natural philosophical ideas in the Dutch Republic. Because Ten Kate contributed to several areas of research, it is worth asking whether connections can be found between his different scholarly activities and, more specifically, whether his oeuvre as a whole was shaped by his religious views, as has been suggested. In this essay, I shall argue that his oeuvre was indeed shaped by his religious beliefs, which reflect elements typical of Dutchdoperdom, but also reflect a more general Christian orientation that transcends confessional divides. More particularly, I aim to show that, if we want to understand why Ten Kate was drawn to the natural philosophy of his day, and especially to Isaac Newton’s (1642-1727), and why he sought to promote it, we also need to pay attention to this broader Christian orientation in his thought. Along the way, I shall add nuance to earlier characterizations of how ten Kate mobilized Isaac Newton’s natural philosophy according to his own agenda.
Establishing the Domains of a Hospital Disaster Preparedness Evaluation Tool: A Systematic Review
Authors: Munasinghe Nimali Lakmini , O’Reilly Gerard , Cameron Peter 
Published: September 2022

AbstractIntroduction:Recent disasters emphasize the need for disaster risk mitigation in the health sector. A lack of standardized tools to assess hospital disaster preparedness hinders the improvement of emergency/disaster preparedness in hospitals. There is very limited research on evaluation of hospital disaster preparedness tools.Objective:This study aimed to determine the presence and availability of hospital preparedness tools across the world, and to identify the important components of those study instruments.Method:A systematic review was performed using three databases, namely Ovid Medline, Embase, and CINAHL, as well as available grey literature sourced by Google, relevant websites, and also from the reference lists of selected articles. The studies published on hospital disaster preparedness across the world from 2011-2020, written in English language, were selected by two independent reviewers. The global distribution of studies was analyzed according to the World Health Organization’s (WHO) six geographical regions, and also according to the four categories of the United Nations Human Development Index (UNHDI). The preparedness themes were identified and categorized according to the 4S conceptual framework: space, stuff, staff, and systems.Result:From a total of 1,568 articles, 53 met inclusion criteria and were selected for data extraction and synthesis. Few published studies had used a study instrument to assess hospital disaster preparedness. The Eastern Mediterranean region recorded the highest number of such publications. The countries with a low UNHDI were found to have a smaller number of publications. Developing countries had more focus on preparedness for natural disasters and less focus on chemical, biological, radiological, and nuclear (CBRN) preparedness. Infrastructure, logistics, capacity building, and communication were the priority themes under the space, stuff, staff, and system domains of the 4S framework, respectively. The majority of studies had neglected some crucial aspects of hospital disaster preparedness, such as transport, back-up power, morgue facilities and dead body handling, vaccination, rewards/incentive, and volunteers.Conclusion:Important preparedness themes were identified under each domain of the 4S framework. The neglected aspects should be properly addressed in order to ensure adequate preparedness of hospitals. The results of this review can be used for planning a comprehensive disaster preparedness tool.
Distinct Microbial Communities in the Soils, Waters, and Speleothems of a Hyperalkaline Cave System
Authors: Shen Jianxun , Smith Andrew C. , Barnett Megan J. , Morgan Alistair , Wynn Peter M. 
Published: September 2022

AbstractCaves are complex ecosystems with various microbial habitats. Understanding the individual community structures in the key source environments (soils, waters) and those in the sinks (speleothems, cave muds) can help elucidate the extent to which in‐cave communities are a function of their source communities, or if they can successfully adapt and diversify locally. Here, we assess the network of microbial communities existing within a unique British cave system. Poole's Cavern is characterized by alkalinity or even hyperalkalinity (pH > 9) in its drip waters, creating a series of challenging ecological niches for microbes to survive. Samples of soil, drip water, speleothem, and cave sediment were collected for chemical characterization, cell culture assays and DNA sequencing analysis. We show that microbial abundance and diversity were highest in the soils proximal to the cave, and the microbiotas of the hyperalkaline cave chamber were less abundant and less diverse than the cave chamber with lower pH. Proteobacteria and Planctomycetota were the most prevalent bacterial phyla throughout the cave system irrespective of pH, indicating their members are comparatively more metabolically versatile. Predicted essential metabolic pathways were still dominant within all sampling sites, and microorganisms were shown to be capable of utilizing various inorganic or simple organic compounds to survive. Interestingly, co‐occurrence between Poole's samples was limited, never demonstrating more than 50% similarity. This work highlights the diversity of microbial communities within this extreme environment and the development of microbial niches which reflects the adaptation strategy of microorganisms under alkaline‐hyperalkaline conditions.
Non‐Local Parameterization of Atmospheric Subgrid Processes With Neural Networks
Authors: Wang Peidong , Yuval Janni , O’Gorman Paul A. 
Published: September 2022

AbstractSubgrid processes in global climate models are represented by parameterizations which are a major source of uncertainties in simulations of climate. In recent years, it has been suggested that machine‐learning (ML) parameterizations based on high‐resolution model output data could be superior to traditional parameterizations. Currently, both traditional and ML parameterizations of subgrid processes in the atmosphere are based on a single‐column approach, which only use information from single atmospheric columns. However, single‐column parameterizations might not be ideal since certain atmospheric phenomena, such as organized convective systems, can cross multiple grid boxes and involve slantwise circulations that are not purely vertical. Here we train neural networks (NNs) using non‐local inputs spanning over 3 × 3 columns of inputs. We find that including the non‐local inputs improves the offline prediction of a range of subgrid processes. The improvement is especially notable for subgrid momentum transport and for atmospheric conditions associated with mid‐latitude fronts and convective instability. Using an interpretability method, we find that the NN improvements partly rely on using the horizontal wind divergence, and we further show that including the divergence or vertical velocity as a separate input substantially improves offline performance. However, non‐local winds continue to be useful inputs for parameterizating subgrid momentum transport even when the vertical velocity is included as an input. Overall, our results imply that the use of non‐local variables and the vertical velocity as inputs could improve the performance of ML parameterizations, and the use of these inputs should be tested in online simulations in future work.
Correcting a 200 km Resolution Climate Model in Multiple Climates by Machine Learning From 25 km Resolution Simulations
Authors: Clark Spencer K. , Brenowitz Noah D. , Henn Brian , Kwa Anna , McGibbon Jeremy , Perkins W. Andre , Watt‐Meyer Oliver , Bretherton Christopher S. , Harris Lucas M. 
Published: September 2022

AbstractBretherton et al. (2022, https://doi.org/10.1029/2021MS002794) demonstrated a successful approach for using machine learning (ML) to help a coarse‐resolution global atmosphere model with real geography (a ∼200 km version of NOAA's FV3GFS) evolve more like a fine‐resolution model, at the scales resolved by both. This study extends that work for application in multiple climates and multi‐year ML‐corrected simulations. Here four fine‐resolution (∼25 km) 2 year reference simulations are run using FV3GFS with climatological sea surface temperatures perturbed uniformly by −4, 0, +4, and +8 K. A data set of state‐dependent corrective tendencies is then derived through nudging the ∼200 km model to the coarsened state of the fine‐resolution simulations in each climate. Along with the surface radiative fluxes, the corrective tendencies of temperature and specific humidity are machine‐learned as functions of the column state. ML predictions for the fluxes and corrective tendencies are applied in 5.25 years ∼200 km resolution simulations in each climate, and improve the spatial pattern errors of land precipitation by 8%–28% and land surface temperature by 19%–25% across the four climates. The ML has a neutral impact on the pattern error of oceanic precipitation.