bluuebunny/crossref_metadata_2025_split huggingface dataset:
AL4GAP: Active learning workflow for generating DFT-SCAN accurate machine-learning potentials for combinatorial molten salt mixtures
Authors: Guo Jicheng , Woo Vanessa , Andersson David A. , Hoyt Nathaniel , Williamson Mark , Foster Ian , Benmore Chris , Jackson Nicholas E. , Sivaraman Ganesh 
Published: July 2023

Machine learning interatomic potentials have emerged as a powerful tool for bypassing the spatiotemporal limitations of ab initio simulations, but major challenges remain in their efficient parameterization. We present AL4GAP, an ensemble active learning software workflow for generating multicomposition Gaussian approximation potentials (GAP) for arbitrary molten salt mixtures. The workflow capabilities include: (1) setting up user-defined combinatorial chemical spaces of charge neutral mixtures of arbitrary molten mixtures spanning 11 cations (Li, Na, K, Rb, Cs, Mg, Ca, Sr, Ba and two heavy species, Nd, and Th) and 4 anions (F, Cl, Br, and I), (2) configurational sampling using low-cost empirical parameterizations, (3) active learning for down-selecting configurational samples for single point density functional theory calculations at the level of Strongly Constrained and Appropriately Normed (SCAN) exchange-correlation functional, and (4) Bayesian optimization for hyperparameter tuning of two-body and many-body GAP models. We apply the AL4GAP workflow to showcase high throughput generation of five independent GAP models for multicomposition binary-mixture melts, each of increasing complexity with respect to charge valency and electronic structure, namely: LiCl–KCl, NaCl–CaCl2, KCl–NdCl3, CaCl2–NdCl3, and KCl–ThCl4. Our results indicate that GAP models can accurately predict structure for diverse molten salt mixture with density functional theory (DFT)-SCAN accuracy, capturing the intermediate range ordering characteristic of the multivalent cationic melts.
Bond dissociation energies for Fe2+, Fe2O+, and Fe2O2+ clusters determined through threshold photodissociation in a cryogenic ion trap
Authors: Marlton Samuel J. P. , Liu Chang , Watkins Patrick , Buntine Jack T. , Bieske Evan J. 
Published: July 2023

Understanding and controlling the chemical behavior of iron and iron oxide clusters requires accurate thermochemical data, which, because of the complex electronic structure of transition metal clusters, can be difficult to calculate reliably. Here, dissociation energies for Fe2+, Fe2O+, and Fe2O2+ are measured using resonance enhanced photodissociation of clusters contained in a cryogenically cooled ion trap. The photodissociation action spectrum of each species exhibits an abrupt onset for the production of Fe+ photofragments from which bond dissociation energies are deduced for Fe2+ (2.529 ± 0.006 eV), Fe2O+ (3.503 ± 0.006 eV), and Fe2O2+ (4.104 ± 0.006 eV). Using previously measured ionization potentials and electron affinities for Fe and Fe2, bond dissociation energies are determined for Fe2 (0.93 ± 0.01 eV) and Fe2− (1.68 ± 0.01 eV). Measured dissociation energies are used to derive heats of formation ΔfH0(Fe2+) = 1344 ± 2 kJ/mol, ΔfH0(Fe2) = 737 ± 2 kJ/mol, ΔfH0(Fe2−) = 649 ± 2 kJ/mol, ΔfH0(Fe2O+) = 1094 ± 2 kJ/mol, and ΔfH0(Fe2O2+) = 853 ± 21 kJ/mol. The Fe2O2+ ions studied here are determined to have a ring structure based on drift tube ion mobility measurements prior to their confinement in the cryogenic ion trap. The photodissociation measurements significantly improve the accuracy of basic thermochemical data for these small, fundamental iron and iron oxide clusters.
The multichannel i-propyl + O2 reaction system: A model of secondary alkyl radical oxidation
Authors: Lahm Mitchell E. , Bartlett Marcus A. , Liang Tao , Pu Liang , Allen Wesley D. , Schaefer Henry F. 
Published: July 2023

The i-propyl + O2 reaction mechanism has been investigated by definitive quantum chemical methods to establish this system as a benchmark for the combustion of secondary alkyl radicals. Focal point analyses extrapolating to the ab initio limit were performed based on explicit computations with electron correlation treatments through coupled cluster single, double, triple, and quadruple excitations and basis sets up to cc-pV5Z. The rigorous coupled cluster single, double, and triple excitations/cc-pVTZ level of theory was used to fully optimize all reaction species and transition states, thus, removing some substantial flaws in reference geometries existing in the literature. The vital i-propylperoxy radical (MIN1) and its concerted elimination transition state (TS1) were found 34.8 and 4.4 kcal mol−1 below the reactants, respectively. Two β-hydrogen transfer transition states (TS2, TS2′) lie above the reactants by (1.4, 2.5) kcal mol−1 and display large Born–Oppenheimer diagonal corrections indicative of nearby surface crossings. An α-hydrogen transfer transition state (TS5) is discovered 5.7 kcal mol−1 above the reactants that bifurcates into equivalent α-peroxy radical hanging wells (MIN3) prior to a highly exothermic dissociation into acetone + OH. The reverse TS5 → MIN1 intrinsic reaction path also displays fascinating features, including another bifurcation and a conical intersection of potential energy surfaces. An exhaustive conformational search of two hydroperoxypropyl (QOOH) intermediates (MIN2 and MIN3) of the i-propyl + O2 system located nine rotamers within 0.9 kcal mol−1 of the corresponding lowest-energy minima.
Structural transformations in single-crystalline AgPd nanoalloys from multiscale deep potential molecular dynamics
Authors: Guo Longfei , Jin Tao , Shan Shuang , Tang Quan , Li Zhen , Wang Chongyang , Wang Junpeng , Pan Bowei , Wang Qiao , Chen Fuyi 
Published: July 2023

AgPd nanoalloys often undergo structural evolution during catalytic reactions; the mechanism underlying such restructuring remains largely unknown due to the use of oversimplified interatomic potentials in simulations. Herein, a deep-learning potential is developed for AgPd nanoalloys based on a multiscale dataset spanning from nanoclusters to bulk configurations, exhibits precise predictions of mechanical properties and formation energies with near-density functional theory accuracy, calculates the surface energies closer to experimental values compared to those obtained by Gupta potentials, and is applied to investigate the shape reconstruction of single-crystalline AgPd nanoalloys from cuboctahedron (Oh) to icosahedron (Ih) geometries. The Oh to Ih shape restructuring is thermodynamically favorable and occurs at 11 and 92 ps for Pd55@Ag254 and Ag147@Pd162 nanoalloys, respectively. During the shape reconstruction of Pd@Ag nanoalloys, concurrent surface restructuring of the (100) facet and internal multi-twinned phase change are observed with collaborative displacive characters. The presence of vacancies can influence the final product and reconstructing rate of Pd@Ag core–shell nanoalloys. The Ag outward diffusion on Ag@Pd nanoalloys is more pronounced in Ih geometry compared to Oh geometry and can be further accelerated by the Oh to Ih deformation. The deformation of single-crystalline Pd@Ag nanoalloys is characterized by a displacive transformation involving the collaborative displacement of a large number of atoms, distinguishing it from the diffusion-coupled transformation of Ag@Pd nanoalloys.
Cored dark matter halos in the cosmic neutrino background
Authors: Cho Wonsub , Choi Ki-Young , Kim Hee Jung 
Published: July 2023

Abstract
We study the impact of the interaction between DM and the cosmic neutrino background on
the evolution of galactic dark matter halos. The energy transfer from the cosmic background
neutrinos to galactic dark matter can heat the center of the galaxy and make it cored. The core
formation is efficient for the small galaxies such as the satellite galaxies of the Milky Way and
we can put a conservative constraint on the non-relativistic elastic scattering cross section as
σχν
≲ 10-31 cm2 for 0.1 keV dark matter.
Exploring muonphilic ALPs at muon colliders
Authors: Lu Chih-Ting , Luo Xiaoyi , Wei Xinqi 
Published: July 2023

Abstract
Axion-like particles (ALPs) are new particles that extend beyond the standard model (SM) and are extensively investigated. When considering ALPs within an effective field theory framework, their couplings with SM particles can be studied independently. It is a daunting task to search for GeV-scale ALPs coupled to muons in collider experiments because their coupling is proportional to the muon mass. However, a recent study by Altmannshofer, Dror, and Gori (2022) highlighted the importance of a four-point interaction, W-μ-

-a, as well as interactions from the chiral anomaly, whose couplings are not dependent on the muon mass. These interactions provide a new opportunity to explore muonphilic ALPs (μALPs) at the GeV scale. We explore various μALP production channels at muon colliders with μALPs decaying into a pair of muons. In particular, we find that a pair of neutrinos accompanied by a μALP is the most effective channel to search for μALPs in the electrowek violating (EWV) scenario. In contrast, a photon plus a μALP becomes a better channel to search for μALPs in the electroweak preserving (EWP) scenario because there is no W-μ-

-a interaction in this situation. Most importantly, we find that the future bounds for μALPs in the EWV scenario are considerably stronger than those in the EWP scenario and the existing bounds for exploring μALPs with

GeV

.
Markers of economic activity in satellite aerosol optical depth data
Authors: Kondragunta Shobha , Wei Zigang , Zhang Hai , Liu Hongqing , Laszlo Istvan , Zhang Bin , Cao Changyong , Ciren Pubu 
Published: July 2023

Abstract
This study investigated the impact of COVID-19 lockdowns on satellite aerosol optical depth (AOD), to explore the hypothesis that if changes in economic activity are seen in emissions of NO2, an aerosol precursor, then AOD should change commensurably. We developed a technique to filter AOD data to isolate changes associated with anthropogenic emissions. Overall, in 37 of the 43 cities that were identified as top oxides of nitrogen (NO
x
) emitters from their transportation sectors, AODs decreased by 21.2% ± 7.8%, 18.9% ± 11.7%, 27% ± 12.4%, 22.9% ± 7.6% in the United States, India, western Europe, and China, respectively—an average of 22.4% ± 7.4%. In contrast, AODs increased on average by 11.7% ± 8.4% in Taiwan, where economic stimulus was used as a strategy during the pandemic. This analysis implies NO
x
and volatile organic compounds emissions reductions from the transportation sector can be targeted, and by transitioning 6 million light duty vehicles from gasoline to electricity, the US can achieve 21% improvement in AOD.
Measurement-device-independent nonlinear entanglement witnesses
Authors: Sen Kornikar , Srivastava Chirag , Sen Ujjwal 
Published: July 2023

AbstractEntanglement witnesses (EWs) are one of the most effective methods to detect entanglement. It is known that nonlinear EW provide better entanglement detection than their linear counterparts, in that the former detect a strictly larger subset of entangled states than the latter. Whether linear or nonlinear, the method is measurement-device dependent, so that imperfect measurements may cause false certification of entanglement in a shared state. Measurement-device-independent EW provide an escape from such measurement dependence of the entanglement detection for linear EW. Here we present measurement-device-independent nonlinear EW for non-positive partial transpose entangled states as well as for bound entangled states with positive partial transpose. Although the witness considered herein does not detect a larger set of entangled states than other nonlinear EW, it is more efficient in that it never leads to a false detection corresponding to wrong measurements. The constructed measurement-device-independent nonlinear EW certify the entanglement of the same sets of entangled states as their device-dependent parents do, and therefore are better than the linear EW, device-independent or otherwise.
From contigs towards chromosomes: automatic improvement of long read assemblies (ILRA)
Authors: Ruiz José Luis , Reimering Susanne , Escobar-Prieto Juan David , Brancucci Nicolas M B , Echeverry Diego F , Abdi Abdirahman I , Marti Matthias , Gómez-Díaz Elena , Otto Thomas D 
Published: July 2023

Abstract
Recent advances in long read technologies not only enable large consortia to aim to sequence all eukaryotes on Earth, but they also allow individual laboratories to sequence their species of interest with relatively low investment. Long read technologies embody the promise of overcoming scaffolding problems associated with repeats and low complexity sequences, but the number of contigs often far exceeds the number of chromosomes and they may contain many insertion and deletion errors around homopolymer tracts. To overcome these issues, we have implemented the ILRA pipeline to correct long read-based assemblies. Contigs are first reordered, renamed, merged, circularized, or filtered if erroneous or contaminated. Illumina short reads are used subsequently to correct homopolymer errors. We successfully tested our approach by improving the genome sequences of Homo sapiens, Trypanosoma brucei, and Leptosphaeria spp., and by generating four novel Plasmodium falciparum assemblies from field samples. We found that correcting homopolymer tracts reduced the number of genes incorrectly annotated as pseudogenes, but an iterative approach seems to be required to correct more sequencing errors. In summary, we describe and benchmark the performance of our new tool, which improved the quality of novel long read assemblies up to 1 Gbp. The pipeline is available at GitHub: https://github.com/ThomasDOtto/ILRA.
RegCFinder: targeted discovery of genomic subregions with differential read density
Authors: Weiß Elena , Friedel Caroline C 
Published: July 2023

Abstract

Motivation
To date, no methods are available for the targeted identification of genomic subregions with differences in sequencing read distributions between two conditions. Existing approaches either only determine absolute read number changes, require predefined subdivisions of input windows or average across multiple genes.

Results
Here, we present RegCFinder, which automatically identifies subregions of input windows with differences in read density between two conditions. For this purpose, the problem is defined as an instance of the all maximum scoring subsequences problem, which can be solved in linear time. Subsequently, statistical significance and differential usage of identified subregions are determined with DEXSeq. RegCFinder allows flexible definition of input windows to target the analysis to any regions of interests, e.g. promoters, gene bodies, peak regions and more. Furthermore, any type of sequencing assay can be used as input; thus, RegCFinder lends itself to a wide range of applications. We illustrate the usefulness of RegCFinder on two applications, where we can both confirm previous results and identify interesting gene subgroups with distinctive changes in read distributions.

Availability and implementation
RegCFinder is implemented as a workflow for the workflow management system Watchdog and available at: https://github.com/watchdog-wms/watchdog-wms-workflows/

Supplementary information
Supplementary data are available at Bioinformatics Advances online.
Lifetime risk, life expectancy, loss-of-life expectancy and lifetime healthcare expenditure for Stevens–Johnson syndrome/toxic epidermal necrolysis in Taiwan: follow-up of a nationwide cohort from 2008 to 2019
Authors: Chiu Ying-Ming , Chiu Hsien-Yi 
Published: July 2023

Abstract

Background
Stevens–Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN) not only cause acute, devastating mucocutaneous reactions but also have long-lasting implications on survivors’ lives.

Objectives
To quantify the lifetime burden of SJS/TEN.

Methods
The cumulative incidence rate (CIR), life expectancy (LE), loss-of-life expectancy (LoLE) and lifetime healthcare expenditure (HE) for SJS/TEN were estimated over the period from 2008 to 2019 using data from the National Health Insurance Research Database of Taiwan and life tables of vital statistics.

Results
In this nationwide cohort of 6552 incident SJS/TEN cases, a trend towards a decrease in the CIR was observed between 2008 and 2019. Compared with the general population, patients with SJS/TEN experience a tremendous loss of 9.43 (1.06) [mean (SEM)] years of LE after diagnosis of SJS/TEN. Male patients with SJS/TEN had higher LoLE [10.74 (1.22) vs. 7.69 (1.43) years] and annual HE than females. Younger age at diagnosis of SJS/TEN was associated with longer LE but greater LoLE and higher lifetime HE. Patients with intensive care unit admission on diagnosis, malignancy, diabetes mellitus, end-stage renal disease and SJS/TEN-associated sequelae experienced substantially greater LoLE and HE per life year.

Conclusions
Patients with SJS/TEN suffer substantial loss-of-LE and HE, particularly young patients, compared with the general population. These data provide a reference estimate of the lifetime burden of SJS/TEN to help health authorities evaluate the cost-effectiveness of future preventive and treatment strategies to minimize the burden of SJS/TEN.
Focal segmental glomerulosclerosis associated with the use of the IL-23 inhibitor guselkumab
Authors: Stryckers Marijke , Van Oevelen Stefaan , Koshy Priyanka , Sprangers Ben , Van Craenenbroeck Amaryllis H 
Published: July 2023

ABSTRACT
We report a case of a 38-year-old man who developed a nephrotic syndrome shortly after the start of guselkumab for the treatment of plaque psoriasis. Renal biopsy showed focal segmental glomerulosclerosis (FSGS). The clinical course of our case is highly suspect for drug-induced FSGS since the nephrotic syndrome resolved after cessation of the drug without relapse (2 years of follow-up). To the best of our knowledge, this is the first case describing FSGS lesions associated with the use of an interleukin-23 inhibitor.
Determinants of depressive symptoms in patients with heart failure based on the hopelessness theory of depression
Authors: Zhang Yilin , Hou Danhua , Dong Xiaoyu , Zhao Qiuge , Zhang Xiuting , Fan Xiuzhen 
Published: July 2023

Abstract

Aims
Depressive symptoms are common in patients with heart failure (HF) and are associated with adverse outcomes in this group. This study examined depressive symptoms and associated determinants in patients with HF based on the hopelessness theory of depression.

Methods and results
In this cross-sectional study, a total of 282 patients with HF were recruited from 3 cardiovascular units of a university hospital. Symptom burden, optimism, maladaptive cognitive emotion regulation strategies (MCERSs), hopelessness, and depressive symptoms were assessed using self-reported questionnaires. A path analysis model was established to evaluate the direct and indirect effects. The prevalence of depressive symptoms was 13.8% in the patients. Symptom burden had the greatest direct effect on depressive symptoms (β = 0.406; P &lt; 0.001), optimism affected depressive symptoms both directly and indirectly with hopelessness as the mediator (direct: β = −0.360; P = 0.001; indirect: β = −0.169; P &lt; 0.001), and MCERSs only had an indirect effect on depressive symptoms with hopelessness as the mediator (β = 0.035; P &lt; 0.001).

Conclusion
In patients with HF, symptom burden, decreased optimism, and hopelessness contribute to depressive symptoms directly. What is more, decreased optimism and MCERS lead to depressive symptoms indirectly via hopelessness. Accordingly, interventions aimed at decreasing symptom burden, enhancing optimism, and reducing the use of MCERSs, while declining hopelessness, may be conducive to relieving depressive symptoms in patients with HF.
Driver Mutations of Pancreatic Cancer Affect Ca2+ Signaling and ATP Production
Authors: Stopa Kinga B , Łoziński Filip , Kusiak Agnieszka A , Litewka Jacek , Krzysztofik Daria , Mosiołek Sylwester , Morys Jan , Ferdek Paweł E , Jakubowska Monika A 
Published: July 2023

AbstractGlandular pancreatic epithelia of the acinar or ductal phenotype may seem terminally differentiated, but they are characterized by remarkable cell plasticity. Stress-induced trans-differentiation of these cells has been implicated in the mechanisms of carcinogenesis. Current consensus links pancreatic ductal adenocarcinoma with onco-transformation of ductal epithelia, but under the presence of driver mutations in Kras and Trp53, also with trans-differentiation of pancreatic acini. However, we do not know when, in the course of cancer progression, physiological functions are lost by mutant acinar cells, nor can we assess their capacity for the production of pancreatic juice components. Here, we investigated whether two mutations—KrasG12D and Trp53R172H—present simultaneously in acinar cells of KPC mice (model of oncogenesis) influence cytosolic Ca2+ signals. Since Ca2+ signals control the cellular handling of digestive hydrolases, any changes that affect intracellular signaling events and cell bioenergetics might have an impact on the physiology of the pancreas. Our results showed that physiological doses of acetylcholine evoked less regular Ca2+ oscillations in KPC acinar cells compared to the control, whereas responses to supramaximal concentrations were markedly reduced. Menadione elicited Ca2+ signals of different frequencies in KPC cells compared to control cells. Finally, Ca2+ extrusion rates were significantly inhibited in KPC cells, likely due to the lower basal respiration and ATP production. Cumulatively, these findings suggest that driver mutations affect the signaling capacity of pancreatic acinar cells even before the changes in the epithelial cell morphology become apparent.
Compound heterozygous IFT81 variations in a skeletal ciliopathy patient cause Bardet–Biedl syndrome-like ciliary defects
Authors: Tasaki Koshi , Zhou Zhuang , Ishida Yamato , Katoh Yohei , Nakayama Kazuhisa 
Published: July 2023

AbstractOwing to their crucial roles in development and homeostasis, defects in cilia cause ciliopathies with diverse clinical manifestations. The intraflagellar transport (IFT) machinery, containing the IFT-A and IFT-B complexes, mediates not only the intraciliary bidirectional trafficking but also import and export of ciliary proteins together with the kinesin-2 and dynein-2 motor complexes. The BBSome, containing eight subunits encoded by causative genes of Bardet–Biedl syndrome (BBS), connects the IFT machinery to ciliary membrane proteins to mediate their export from cilia. Although mutations in subunits of the IFT-A and dynein-2 complexes cause skeletal ciliopathies, mutations in some IFT-B subunits are also known to cause skeletal ciliopathies. We here show that compound heterozygous variations of an IFT-B subunit, IFT81, found in a patient with skeletal ciliopathy cause defects in its interactions with other IFT-B subunits, and in ciliogenesis and ciliary protein trafficking when one of the two variants was expressed in IFT81-knockout (KO) cells. Notably, we found that IFT81-KO cells expressing IFT81(Δ490–519), which lacks the binding site for the IFT25-IFT27 dimer, causes ciliary defects reminiscent of those found in BBS cells and those in IFT74-KO cells expressing a BBS variant of IFT74, which forms a heterodimer with IFT81. In addition, IFT81-KO cells expressing IFT81(Δ490–519) in combination with the other variant, IFT81 (L645*), which mimics the cellular conditions of the above skeletal ciliopathy patient, demonstrated essentially the same phenotype as those expressing only IFT81(Δ490–519). Thus, our data indicate that BBS-like defects can be caused by skeletal ciliopathy variants of IFT81.