bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nagaoka ferromagnetism in an array of phosphorene quantum dots
Authors: Thakur Tanmay , Szafran Bartłomiej 
Published: November 2023

AbstractWe consider an array of four quantum dots defined in phosphorene containing three excess electrons, i.e., in the conditions of near half filling when itinerant Nagaoka ferromagnetism is expected to appear in a square array with isotropic interdot hopping. The interdot hopping in the array arranged in a square inherits the anisotropy from the form of the phosphorene conduction band. We apply the configuration interaction method for discussion of the appearance and stability of the spin-polarized ground state and discuss the compensation of the effective mass anisotropy by the geometry of the quantum dot array. Our study shows strong stability of Nagaoka ferromagnetism for optimized geometry of the array, with the Nagaoka gap as large as ∼ 230 µeV. A phase diagram for the ground-state spin ordering versus the geometric parameters of the array is presented. We study the suppression of the ferromagnetism in a transition of the $$2\times 2$$

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array to a quasi-1D chain and indicate that the shift of one of the quantum dots away from the array center is enough to transform the system to a quantum dot chain. A shift in the zigzag crystal direction induces the low-spin ground state more effectively than a shift along the armchair direction. We also discuss the robustness of the spin ordering against detuning one of the dots. The ferromagnetic ground-state survives as long as the detuning is not large enough to trap one of the electrons within a single quantum dot (for positive detuning) or remove one of the quantum dots of the accessible energy range (for negative detuning).
Exploring hydrothermal liquefaction (HTL) of digested sewage sludge (DSS) at 5.3 L and 0.025 L bench scale using experimental design
Authors: Hegdahl Stian Hersvik , Ghoreishi Solmaz , Løhre Camilla , Barth Tanja 
Published: November 2023

AbstractA common perspective within the prospect of a greener future is utilising our waste materials. One waste material of which the world has abundant resources, and where we will keep having resources, is sewage sludge. This waste material is getting an increased focus, and is commonly utilised by anaerobic digestion processes for methane production. This leaves a bioresidue of digested sewage sludge (DSS). In this study, DSS is submitted to hydrothermal liquefaction (HTL) to produce bio-oil. The studied process includes upscaling as well as considering the effects of temperature, reaction medium of water or ethanol, degree of reactor filling and stirring rate. Promising results are found as high oil yields are obtained also after upscaling. The results reported here show that stirring reduces the need of high temperatures during HTL, providing energy savings that are promising for further upscaling. In addition, a total of 18 compounds are identified and semi-quantified, showing an abundance of fatty acids and fatty acid derivatives within the oil, encouraging further studies towards separation of said fatty acids for use as biodiesel.
Statin use and outcomes of oncological treatment for castration-resistant prostate cancer
Authors: Peltomaa A. I. , Talala K. , Taari K. , Tammela T. L. J. , Auvinen A. , Murtola T. J. 
Published: November 2023

AbstractTo compare the effect of statin use in relation to castration-resistant prostate cancer (CRPC) treatment, we assessed the risk of ADT-treated PCa-patients to initiate CRPC treatment by statin use and the outcomes of CRPC treatment by statin use. Our study cohort consisted of 1169 men who participated in the Finnish Randomized Study of Screening for Prostate Cancer (FinRSPC) and initiated androgen deprivation therapy (ADT) during the follow-up (1996–2017). Statin use was associated with slightly decreased risk of initiating CRPC treatment (HR 0.68; 95% CI 0.47–0.97) with a 5.7 years’ median follow-up until CRPC for non-users and 7.5 years for statin users. The risk of discontinuation of first or second line CRPC treatment due to inefficacy was not modified by statin use and the results remained similar in subgroup analysis assessing separately patients treated with taxans or androgen receptor signaling inhibitors. We observed an inverse association between statin use and the risk of initiation of the CRPC treatment. No beneficial risk modification by statin use during CRPC treatment was observed. These results suggest that statins might be beneficial during hormone-sensitive phase but not in the later phases of prostate cancer treatment.
Roman water management impacted the hydrological functioning of wetlands during drought periods
Authors: Gázquez-Sánchez Fernando , Jiménez-Espejo Francisco , Rodríguez-Rodríguez Miguel , Martegani Lucía , Voigt Claudia , Ruíz-Lara Dolores , Moreno Ana , Valero-Garcés Blas , Morellón Mario , Martín-Puertas Celia 
Published: November 2023

AbstractDuring the Roman domain of the Iberian Peninsula (from 201 BCE to 460 CE) water management infrastructures were built to satisfy high water demand. However, whether the Roman activities affected the hydrological balance of Iberian wetlands remains unclear. Here, we investigate the paleo-hydrology of Lake Zóñar (southern Iberia) by using the stable isotopes (16O, 17O, 18O, 1H and 2H) of its gypsum (CaSO4·2H2O) sediments and reconstruct the isotopic composition of the lake water during Roman times. A period of recurrent lake low stand occurred between 2120 and 1890 cal. yr BP (ca. 170 BCE to 60 CE), coinciding with a relatively dry climate stage recorded by most regional paleoclimate archives. The stable isotopes and hydrochemistry of the lake water during gypsum precipitation are consistent with a shallow saline lake that evaporated under relative humidity ~ 10% lower than the present annual mean and at least 20% less rainfall amount. Our analytical and archeological findings support lake level lowering during the Roman period was probably caused by combined arid climate conditions and diversion of the inlets feeding the lake. Spring capturing was likely necessary to satisfy the high water demand of nearby Roman settlements, in the framework of a period of persistent droughts.
Bradyrhizobium ottawaense efficiently reduces nitrous oxide through high nosZ gene expression
Authors: Wasai-Hara Sawa , Itakura Manabu , Fernandes Siqueira Arthur , Takemoto Daisaku , Sugawara Masayuki , Mitsui Hisayuki , Sato Shusei , Inagaki Noritoshi , Yamazaki Toshimasa , Imaizumi-Anraku Haruko , Shimoda Yoshikazu , Minamisawa Kiwamu 
Published: November 2023

AbstractN2O is an important greenhouse gas influencing global warming, and agricultural land is the predominant (anthropogenic) source of N2O emissions. Here, we report the high N2O-reducing activity of Bradyrhizobium ottawaense, suggesting the potential for efficiently mitigating N2O emission from agricultural lands. Among the 15 B. ottawaense isolates examined, the N2O-reducing activities of most (13) strains were approximately five-fold higher than that of Bradyrhizobium diazoefficiens USDA110T under anaerobic conditions. This robust N2O-reducing activity of B. ottawaense was confirmed by N2O reductase (NosZ) protein levels and by mitigation of N2O emitted by nodule decomposition in laboratory system. While the NosZ of B. ottawaense and B. diazoefficiens showed high homology, nosZ gene expression in B. ottawaense was over 150-fold higher than that in B. diazoefficiens USDA110T, suggesting the high N2O-reducing activity of B. ottawaense is achieved by high nos expression. Furthermore, we examined the nos operon transcription start sites and found that, unlike B. diazoefficiens, B. ottawaense has two transcription start sites under N2O-respiring conditions, which may contribute to the high nosZ expression. Our study indicates the potential of B. ottawaense for effective N2O reduction and unique regulation of nos gene expression towards the high performance of N2O mitigation in the soil.
Artificial surface labelling of Escherichia coli with StrepTagII antigen to study how monoclonal antibodies drive complement-mediated killing
Authors: Muts Remy M. , den Boer Maurits A. , Bardoel Bart W. , Aerts Piet C. , de Haas Carla J. C. , Heck Albert J. R. , Rooijakkers Suzan H. M. , Heesterbeek Dani A. C. 
Published: November 2023

AbstractAntibodies play a key role in the immune defence against Gram-negative bacteria. After binding to bacterial surface antigens, IgG and IgM can activate the complement system and trigger formation of lytic membrane attack complex (MAC) pores. Molecular studies to compare functional activity of antibodies on bacteria are hampered by the limited availability of well-defined antibodies against bacterial surface antigens. Therefore, we genetically engineered E. coli by expressing the StrepTagII antigen into outer membrane protein X (OmpX) and validated that these engineered bacteria were recognised by anti-StrepTagII antibodies. We then combined this antigen–antibody system with a purified complement assay to avoid interference of serum components and directly compare MAC-mediated bacterial killing via IgG1 and pentameric IgM. While both IgG1 and IgM could induce MAC-mediated killing, we show that IgM has an increased capacity to induce complement-mediated killing of E. coli compared to IgG1. While Fc mutations that enhance IgG clustering after target binding could not improve MAC formation, mutations that cause formation of pre-assembled IgG hexamers enhanced the complement activating capacity of IgG1. Altogether, we here present a system to study antibody-dependent complement activation on E. coli and show IgM’s enhanced capacity over IgG to induce complement-mediated lysis of E. coli.
Causal effect of gallstone disease on the risk of coronary heart disease or acute myocardial infarction: a Mendelian randomization study
Authors: Fu Qingan , Shen Tianzhou , Yu Qingyun , Jiang Long , Yang Renqiang 
Published: November 2023

AbstractGallstone disease (GSD) is thought to be associated with the risk of coronary heart disease (CHD) or acute myocardial infarction (AMI), which may be due to abnormal cholesterol metabolism. We used multiple Mendelian randomization (MR) methods based on publicly available genome-wide association study data to assess whether this association is genetically causal and to search for loci driving causality. Pooled data for GSD were obtained from FinnGen Biobank and Biobank Japan, while CHD and AMI were obtained as pooled data from the CARDIoGRAMplusC4D consortium. In this MR study, we found a significant negative causal effect of genetic susceptibility to GSD on AMI in the Finnish population, but no causal effect was found on CHD. This causal effect was not confounded by reverse causality and the same findings were obtained in the Japanese population. Furthermore, the negative causal effect of GSD on AMI risk may be driven by the rs4245791-regulated ABCG5/8 protein. In conclusion, the results of this MR study support a negative causal effect of GSD on AMI and suggest that rs4245791 is the causal driver locus of this effect, which provides new ideas and evidence for the prevention and etiologic study of AMI in patients with GSD.
Comparison of three bioinformatics tools in the detection of ASD candidate variants from whole exome sequencing data
Authors: Shil Apurba , Levin Liron , Golan Hava , Meiri Gal , Michaelovski Analya , Sadaka Yair , Aran Adi , Dinstein Ilan , Menashe Idan 
Published: November 2023

AbstractAutism spectrum disorder (ASD) is a heterogenous multifactorial neurodevelopmental condition with a significant genetic susceptibility component. Thus, identifying genetic variations associated with ASD is a complex task. Whole-exome sequencing (WES) is an effective approach for detecting extremely rare protein-coding single-nucleotide variants (SNVs) and short insertions/deletions (INDELs). However, interpreting these variants' functional and clinical consequences requires integrating multifaceted genomic information. We compared the concordance and effectiveness of three bioinformatics tools in detecting ASD candidate variants (SNVs and short INDELs) from WES data of 220 ASD family trios registered in the National Autism Database of Israel. We studied only rare (< 1% population frequency) proband-specific variants. According to the American College of Medical Genetics (ACMG) guidelines, the pathogenicity of variants was evaluated by the InterVar and TAPES tools. In addition, likely gene-disrupting (LGD) variants were detected based on an in-house bioinformatics tool, Psi-Variant, that integrates results from seven in-silico prediction tools. Overall, 372 variants in 311 genes distributed in 168 probands were detected by these tools. The overlap between the tools was 64.1, 22.9, and 23.1% for InterVar–TAPES, InterVar–Psi-Variant, and TAPES–Psi-Variant, respectively. The intersection between InterVar and Psi-Variant (I ∩ P) was the most effective approach in detecting variants in known ASD genes (PPV = 0.274; OR = 7.09, 95% CI = 3.92–12.22), while the union of InterVar and Psi Variant (I U P) achieved the highest diagnostic yield (20.5%).Our results suggest that integrating different variant interpretation approaches in detecting ASD candidate variants from WES data is superior to each approach alone. The inclusion of additional criteria could further improve the detection of ASD candidate variants.
Dimeric Transmembrane Structure of the SARS-CoV-2 E Protein
Authors: Zhang Rongfu , Qin Huajun , Prasad Ramesh , Fu Riqiang , Zhou Huan-Xiang , Cross Timothy A. 
Published: November 2023

AbstractThe SARS-CoV-2 E protein is a transmembrane (TM) protein with its N-terminus exposed on the external surface of the virus. At debate is its oligomeric state, let alone its function. Here, the TM structure of the E protein is characterized by oriented sample and magic angle spinning solid-state NMR in lipid bilayers and refined by molecular dynamics simulations. This protein was previously found to be a pentamer, with a hydrophobic pore that appears to function as an ion channel. We identify only a front-to-front, symmetric helix-helix interface, leading to a dimeric structure that does not support channel activity. The two helices have a tilt angle of only 6°, resulting in an extended interface dominated by Leu and Val sidechains. While residues Val14-Thr35 are almost all buried in the hydrophobic region of the membrane, Asn15 lines a water-filled pocket that potentially serves as a drug-binding site. The E and other viral proteins may adopt different oligomeric states to help perform multiple functions.
MELCHIORS
Authors: Royer P. , Merle T. , Dsilva K. , Sekaran S. , Van Winckel H. , Frémat Y. , Van der Swaelmen M. , Gebruers S. , Tkachenko A. , Laverick M. , Dirickx M. , Raskin G. , Hensberge H. , Abdul-Masih M. , Acke B. , Alonso M. L. , Bandhu Mahato S. , Beck P. G. , Behara N. , Bloemen S. , Buysschaert B. , Cox N. , Debosscher J. , De Cat P. , Degroote P. , De Nutte R. , De Smedt K. , de Vries B. , Dumortier L. , Escorza A. , Exter K. , Goriely S. , Gorlova N. , Hillen M. , Homan W. , Jorissen A. , Kamath D. , Karjalainen M. , Karjalainen R. , Lampens P. , Lobel A. , Lombaert R. , Marcos-Arenal P. , Menu J. , Merges F. , Moravveji E. , Nemeth P. , Neyskens P. , Ostensen R. , Pápics P. I. , Perez J. , Prins S. , Royer S. , Samadi-Ghadim A. , Sana H. , Sans Fuentes A. , Scaringi S. , Schmid V. , Siess L. , Siopis C. , Smolders K. , Sódor Á. , Thoul A. , Triana S. , Vandenbussche B. , Van de Sande M. , Van De Steene G. , Van Eck S. , van Hoof P. A. M. , Van Marle A. J. , Van Reeth T. , Vermeylen L. , Volpi D. , Vos J. , Waelkens C. 
Published: November 2023

Aims. Over the past decades, libraries of stellar spectra have been used in a large variety of science cases, including as sources of reference spectra for a given object or a given spectral type. Despite the existence of large libraries and the increasing number of projects of large-scale spectral surveys, there is to date only one very high-resolution spectral library offering spectra from a few hundred objects from the southern hemisphere (UVES-POP). We aim to extend the sample, offering a finer coverage of effective temperatures and surface gravity with a uniform collection of spectra obtained in the northern hemisphere.
Methods. Between 2010 and 2020, we acquired several thousand echelle spectra of bright stars with the Mercator-HERMES spectrograph located in the Roque de Los Muchachos Observatory in La Palma, whose pipeline offers high-quality data reduction products. We have also developed methods to correct for the instrumental response in order to approach the true shape of the spectral continuum. Additionally, we have devised a normalisation process to provide a homogeneous normalisation of the full spectral range for most of the objects.
Results. We present a new spectral library consisting of 3256 spectra covering 2043 stars. It combines high signal-to-noise and high spectral resolution over the entire range of effective temperatures and luminosity classes. The spectra are presented in four versions: raw, corrected from the instrumental response, with and without correction from the atmospheric molecular absorption, and normalised (including the telluric correction).
When the horseshoe fits: Characterizing 2023 FY3 with the 10.4 m Gran Telescopio Canarias and the Two-meter Twin Telescope
Authors: de la Fuente Marcos R. , de la Fuente Marcos C. , de León J. , Alarcon M. R. , Licandro J. , Serra-Ricart M. , García-Álvarez D. , Cabrera-Lavers A. 
Published: November 2023

Context. The Arjuna asteroid belt is loosely defined as a diverse group of small asteroids that follow dynamically cold, Earth-like orbits. Most of them are not actively engaged in resonant, co-orbital behavior with Earth. Some of them experience temporary but recurrent horseshoe episodes. Objects in horseshoe paths tend to approach Earth at a low velocity, leading to captures as Earth’s temporary satellites or mini-moons. Four such objects have already been identified: 1991 VG, 2006 RH120, 2020 CD3, and 2022 NX1. Here, we focus on 2023 FY3, a recent finding, the trajectory of which might have a co-orbital status and perhaps lead to temporary captures.
Aims. We want to determine the physical properties of 2023 FY3 and explore its dynamical evolution.
Methods. We carried out an observational study of 2023 FY3 using the OSIRIS camera spectrograph at the 10.4 m Gran Telescopio Canarias, to derive its spectral class, and time-series photometry obtained with QHY411M cameras and two units of the Two-meter Twin Telescope to investigate its rotational state. N-body simulations were also performed to examine its possible resonant behavior.
Results. The visible reflectance spectrum of 2023 FY3 is consistent with that of an S-type asteroid; its light curve gives a rotation period of 9.3±0.6 min, with an amplitude of 0.48±0.13 mag. We confirm that 2023 FY3 roams the edge of Earth’s co-orbital space.
Conclusions. Arjuna 2023 FY3, an S-type asteroid and fast rotator, currently exhibits horseshoe-like resonant behavior and in the past experienced mini-moon engagements of the temporarily captured flyby type that may repeat in the future. The spectral type result further confirms that mini-moons are a diverse population in terms of surface composition.
Can nutritional and inflammatory indices predict 90-day mortality in fragility hip fracture patients?
Authors: Rutenberg Tal Frenkel , Hershkovitz Avital , Jabareen Rana , Vitenberg Maria , Daglan Efrat , Iflah Moti , Drexler Michael , Shemesh Shai 
Published: November 2023

Introduction: Hip fractures in the elderly are related to increased mortality. The identification of patients at risk is essential. Several nutritional and inflammatory parameters were investigated in an effort to find a prognostic indicator for mortality following fragility hip fractures (FHF) surgery. We aim to evaluate their utility and compare between the different factors. Methods: A retrospective cohort study of patients 65 years and older, who underwent surgery following fragility hip fractures between January 2012 and June 2020, was conducted. Patients who died within 90 days were matched at a 1:1 ratio with surviving controls, based on age, gender, fracture type, and comorbidities. Nutritional and inflammatory indices, including serum albumin, protein energy malnutrition (PEM), albumin-to-globulin ratio (AGR), prognostic nutritional index (PNI), the systemic immune-inflammation index (SII), platelet-to-lymphocyte ratio (PLR), and the neutrophile-to-lymphocyte ratio (NLR), were compared between groups. Results: 304 patients were included, 152 in each group. Patients’ demographics were similar. Among all indices evaluated, only the PLR significantly differed between the study groups (236.9 ± 193.5 for the study group vs. 186.6 ± 119.3 for the control group (p = 0.007). In patients who survived the initial hospitalization, the PEM was also found to be correlated with 90 days mortality. Discussion: The PLR was found to be correlated with mortality risk following FHF surgery. As it can be easily calculated from accessible blood tests, we recommend its’ routine assessment as a screening tool for personalized management of patients at high risk for mortality.
Utility of Clinical and Radiological Markers in Diagnosing Cerebral Tuberculoma and Neurocysticercosis
Authors: Patra Chandrakanta , Paul Shabeer Ahmad , Mondal Gouranga Prosad , Bhattacharyya Ramesh , Ghosh Kartik Chandra 
Published: November 2023

Abstract
Background Ring-enhancing lesion is one of the most common radiological findings in a spectrum of diseases affecting the central nervous system (CNS) including infectious, inflammatory, demyelinating, and neoplastic pathologies.
Objective The aim of this study was to analyze the clinical and radiological parameters of pathologies presenting as ring-enhancing lesions in the brain, especially tuberculoma and neurocysticercosis.
Materials and Methods In this study, 58 patients with ring-enhancing lesions on brain magnetic resonance imaging (MRI) were recruited. Cases were studied for different clinical and radiological variables. Data were analyzed using SPSS 20 version.
Results Tuberculoma is the most common pathology accounting for ring-enhancing lesions in the brain, followed by neurocysticercosis. Seizures were present in the majority of cases, with focal onset seizures being more common than generalized seizures. Multiple ring-enhancing lesions were present in the majority of cases, with the cerebral cortex being the most frequently involved site. On T2 fluid-attenuated inversion recovery (FLAIR) sequence, 2/3rds of the neurocysticercosis cases showed full suppression, whereas only 1/10th of tuberculoma cases showed full suppression. On diffusion-weighted imaging (DWI), a minority of neurocysticercosis cases showed diffusion restriction, while more than one-fifth of tuberculoma cases showed diffusion restriction. MR spectroscopy (MRS) results showed that a normal lipid lactate peak was observed in the majority of neurocysticercosis cases, whereas more than half of tuberculoma cases had a high lipid lactate peak. The choline-to-creatine ratio (Chol/Cre ratio) was less than 1.2 in one-third of neurocysticercosis cases and between 1.2 and 2.0 in two-thirds of the cases. In contrast, more than half of tuberculoma cases showed a Chol/Cre ratio between 1.2 and 2.0.
Conclusion Tuberculoma and NCC are the two most common causes of ring-enhancing lesions in developing world. Radiological characteristics like FLAIR suppression and diffusion restriction on MRI and Chol/Cre ratio and lipid peak on MRS can substantiate the clinical parameters in distinguishing the two pathologies to a good extent.