bluuebunny/crossref_metadata_2025_split huggingface dataset:
Timing the formation of the galactic thin disc with asteroseismic stellar ages
Authors: Wu Yaqian , Xiang Maosheng , Zhao Gang , Chen Yuqin , Bi Shaolan , Li Yaguang 
Published: January 2023

ABSTRACT
The formation of the extended thin disc is the most spectacular event of our Galaxy in the past ∼8 Gyr. To unveil this process, obtaining precise and accurate stellar ages for a large sample of stars is essential although challenging. In this work, we present the asteroseismic age determination of 5306 red giant branch stars using Kepler and LAMOST data, with a thorough examination of how the age determination is affected by the choice of different temperature scales and stellar models. Thanks to the high precision of the asteroseismic and spectroscopic parameters of our sample stars, we are able to achieve age determination with an average accuracy of 12 per cent. However, the age determination is sensitively dependent on the adopted temperature scale, as 50 K difference in effective temperature may cause larger than 10 per cent systematic uncertainty in the age estimates. Using the ages derived with the most plausible set of the temperature scale, we study the age distribution of the chemical thin disc stars, and present an estimate of the formation epoch of the first Galactic thin disc stars. We find that the first (oldest) thin disc stars have an age of $9.5^{+0.5(\rm rand.)+0.5(\rm sys.)}_{-0.4(\rm rand.)-0.3(\rm sys.)}$ Gyr, where the systematic uncertainties reflect ages estimated using different stellar evolutionary models. At this epoch, the Galactic thick disc was still forming stars, indicating there is a time window when both the thin and thick discs of our Galaxy were forming stars together. Moreover, we find that the first thin disc stars exhibit a broad distribution of Galactocentric radii, suggesting that the inner and outer thin discs began to form simultaneously.
The impact of weak lensing on Type Ia supernovae luminosity distances
Authors: Shah Paul , Lemos Pablo , Lahav Ofer 
Published: January 2023

ABSTRACT
When Type Ia supernovae are used to infer cosmological parameters, their luminosities are compared to those from a homogeneous cosmology. In this note, we propose a test to examine to what degree SN Ia have been observed on lines of sight where the average matter density is not representative of the homogeneous background. We apply our test to the Pantheon SN Ia compilation, and find two redshift bins which indicate a moderate bias to over-density at ∼2σ. We modify the Tripp estimator to explicitly de-lens SN Ia magnitudes, and show that this reduces scatter of Hubble diagram residuals. Using our revised Tripp estimator, the effect on cosmological parameters from Pantheon in ΛCDM is however small with a change in mean value from Ωm = 0.317 ± 0.027 (baseline) to Ωm = 0.312 ± 0.025 (de-lensed). For the Flat wCDM case, it is Ωm = 0.332 ± 0.049 and w = −1.16 ± 0.16 (baseline) versus Ωm = 0.316 ± 0.048 and w = −1.12 ± 0.15 (de-lensed). We note that the effect of lensing on cosmological parameters may be larger for future high-z surveys.
Structures of pMV158 replication initiator RepB with and without DNA reveal a flexible dual-function protein
Authors: Machón Cristina , Ruiz-Masó José A , Amodio Juliana , Boer D Roeland , Bordanaba-Ruiseco Lorena , Bury Katarzyna , Konieczny Igor , del Solar Gloria , Coll Miquel 
Published: January 2023

AbstractDNA replication is essential to all living organisms as it ensures the fidelity of genetic material for the next generation of dividing cells. One of the simplest replication initiation mechanisms is the rolling circle replication. In the streptococcal plasmid pMV158, which confers antibiotic resistance to tetracycline, replication initiation is catalysed by RepB protein. The RepB N-terminal domain or origin binding domain binds to the recognition sequence (bind locus) of the double-strand origin of replication and cleaves one DNA strand at a specific site within the nic locus. Using biochemical and crystallographic analyses, here we show how the origin binding domain recognises and binds to the bind locus using structural elements removed from the active site, namely the recognition α helix, and a β-strand that organises upon binding. A new hexameric structure of full-length RepB that highlights the great flexibility of this protein is presented, which could account for its ability to perform different tasks, namely bind to two distinct loci and cleave one strand of DNA at the plasmid origin.
Differential Expression Enrichment Tool (DEET): an interactive atlas of human differential gene expression
Authors: Sokolowski Dustin J , Ahn Jedid , Erdman Lauren , Hou Huayun , Ellis Kai , Wang Liangxi , Goldenberg Anna , Wilson Michael D 
Published: January 2023

AbstractDifferential gene expression analysis using RNA sequencing (RNA-seq) data is a standard approach for making biological discoveries. Ongoing large-scale efforts to process and normalize publicly available gene expression data enable rapid and systematic reanalysis. While several powerful tools systematically process RNA-seq data, enabling their reanalysis, few resources systematically recompute differentially expressed genes (DEGs) generated from individual studies. We developed a robust differential expression analysis pipeline to recompute 3162 human DEG lists from The Cancer Genome Atlas, Genotype-Tissue Expression Consortium, and 142 studies within the Sequence Read Archive. After measuring the accuracy of the recomputed DEG lists, we built the Differential Expression Enrichment Tool (DEET), which enables users to interact with the recomputed DEG lists. DEET, available through CRAN and RShiny, systematically queries which of the recomputed DEG lists share similar genes, pathways, and TF targets to their own gene lists. DEET identifies relevant studies based on shared results with the user's gene lists, aiding in hypothesis generation and data-driven literature review.
mSigHdp: hierarchical Dirichlet process mixture modeling for mutational signature discovery
Authors: Liu Mo , Wu Yang , Jiang Nanhai , Boot Arnoud , Rozen Steven G 
Published: January 2023

Abstract
Mutational signatures are characteristic patterns of mutations caused by endogenous or exogenous mutational processes. These signatures can be discovered by analyzing mutations in large sets of samples—usually somatic mutations in tumor samples. Most programs for discovering mutational signatures are based on non-negative matrix factorization (NMF). Alternatively, signatures can be discovered using hierarchical Dirichlet process (HDP) mixture models, an approach that has been less explored. These models assign mutations to clusters and view each cluster as being generated from the signature of a particular mutational process. Here, we describe mSigHdp, an improved approach to using HDP mixture models to discover mutational signatures. We benchmarked mSigHdp and state-of-the-art NMF-based approaches on four realistic synthetic data sets. These data sets encompassed 18 cancer types. In total, they contained 3.5 × 107 single-base-substitution mutations representing 32 signatures and 6.1 × 106 small insertion and deletion mutations representing 13 signatures. For three of the four data sets, mSigHdp had the best positive predictive value for discovering mutational signatures, and for all four data sets, it had the best true positive rate. Its CPU usage was similar to that of the NMF-based approaches. Thus, mSigHdp is an important and practical addition to the set of tools available for discovering mutational signatures.
Unexpected giant negative area compressibility in palladium diselenide
Authors: Jiang Xingxing , Zhang Shengzi , Jiang Dequan , Wang Yonggang , Molokeev Maxim S , Wang Naizheng , Liu Youquan , Zhang Xingyu , Lin Zheshuai 
Published: January 2023

ABSTRACT
Negative area compressibility (NAC) is a counterintuitive ‘squeeze–expand’ behavior in solids that is very rare but attractive due to possible pressure–response applications and coupling with rich physicochemical properties. Herein, NAC behavior is reported in palladium diselenide with a large magnitude and wide pressure range. We discover that, apart from the rigid flattening of layers that has been generally recognized, the unexpected giant NAC effect in PdSe2 largely comes from anomalous elongation of intralayer chemical bonds. Both structural variations are driven by intralayer-to-interlayer charge transfer with enhanced interlayer interactions under pressure. Our work updates the mechanical understanding of this anomaly and establishes a new guideline to explore novel compression-induced properties.
First finding of continental deep subduction in the Sesia Zone of the Western Alps and implications for subduction dynamics
Authors: Chen Yi-Xiang , Zhou Kun , He Qiang , Zheng Yong-Fei , Schertl Hans-Peter , Chen Kun 
Published: January 2023

ABSTRACTContinental deep subduction after the closure of large oceanic basins is commonly ascribed to the gravitational pull of the subducting oceanic slab. However, it is not clear how continental lithosphere adjacent to small oceanic basins was subducted to mantle depths. The Sesia Zone in the Western Alps provides an excellent target for exploration of subduction dynamics in such a tectonic setting. Here we report the first finding of coesite in a jadeite-bearing orthogneiss from the Sesia Zone, providing the first evidence for deep subduction of the continental crust to mantle depths for ultrahigh-pressure (UHP) metamorphism in this zone. Three coesite inclusions were identified by laser Raman spectroscopy in two garnet grains. Based on zircon U-Pb dating and trace element analysis, the UHP metamorphic age was constrained to be 76.0 ± 1.0 Ma. The phase equilibrium modeling yields peak metamorphic pressures of 2.8–3.3 GPa, demonstrating the continental deep subduction to mantle depths of &gt;80 km. The subducted continental crust was a rifted hyperextended continental margin, which was converted to the passive continental margin during seafloor spreading and then deeply subducted during the oblique convergence between the Adria microplate and Eurasian plate in the Late Cretaceous. Because the slab pull could only play a limited role in closing small oceanic basins for continental collision, the distal push of either continental breakup or seafloor spreading is suggested as the major driving force for the deep subduction of continental crust in the Western Alps. Therefore, deep subduction of the continental crust bordering small oceanic basins would have been induced by the far-field stress of compression, whereas that bordering large oceanic basins was spontaneous due to the oceanic slab pull. This provides a new insight into the geodynamic mechanism of continental deep subduction.
Candidate Selection in Portugal
Authors: Jalali Carlos , Sanches Edalina Rodrigues 
Published: January 2023

Abstract
Candidate selection is one of the most important tasks performed by political parties in a democracy, and all the more so in closed-list proportional representation (CLPR) systems such as the one in Portugal. The choice of which individual politicians are included in the party lists and their chances of being elected rests in the hands of parties, shaping the make-up of parliament and of democratic representation. This chapter analyses the dynamics of candidate selection in Portugal, highlighting the parties’ combination of exclusive and centralized selection rules with more inclusive practices. Portugal is profiled as a crucial case that defies the expectations of centralized and exclusive selectorates with CLPR systems.
Autoregulation of blood flow drives early hypotension in a rat model of systemic inflammation induced by bacterial lipopolysaccharide
Authors: Moretti Eduardo H , Rodrigues Abner C , Marques Bruno V , Totola Leonardo T , Ferreira Caroline B , Brito Camila F , Matos Caroline M , da Silva Filipe A , Santos Robson A S , Lopes Luciana B , Moreira Thiago S , Akamine Eliana H , Baccala Luiz A , Fujita André , Steiner Alexandre A 
Published: January 2023

Abstract
Uncontrolled vasodilation is known to account for hypotension in the advanced stages of sepsis and other systemic inflammatory conditions, but the mechanisms of hypotension in earlier stages of such conditions are not clear. By monitoring hemodynamics with the highest temporal resolution in unanesthetized rats, in combination with ex-vivo assessment of vascular function, we found that early development of hypotension following injection of bacterial lipopolysaccharide is brought about by a fall in vascular resistance when arterioles are still fully responsive to vasoactive agents. This approach further uncovered that the early development of hypotension stabilized blood flow. We thus hypothesized that prioritization of the local mechanisms of blood flow regulation (tissue autoregulation) over the brain-driven mechanisms of pressure regulation (baroreflex) underscored the early development of hypotension in this model. Consistent with this hypothesis, an assessment of squared coherence and partial-directed coherence revealed that, at the onset of hypotension, the flow–pressure relationship was strengthened at frequencies (&lt;0.2 Hz) known to be associated with autoregulation. The autoregulatory escape to phenylephrine-induced vasoconstriction, another proxy of autoregulation, was also strengthened in this phase. The competitive demand that drives prioritization of flow over pressure regulation could be edema-associated hypovolemia, as this became detectable at the onset of hypotension. Accordingly, blood transfusion aimed at preventing hypovolemia brought the autoregulation proxies back to normal and prevented the fall in vascular resistance. This novel hypothesis opens a new avenue of investigation into the mechanisms that can drive hypotension in systemic inflammation.
Evaluation of sterilisation techniques for 3D-printed implantable devices
Authors: Stewart Sarah A , Domínguez-Robles Juan , Donnelly Ryan F , Larrañeta Eneko 
Published: January 2023

Abstract

Objectives
This article investigates the potential use of microwave (MW) radiation, ultraviolet (UV)-light and gamma radiation for the sterilisation of 3D-printed implantable devices prepared using poly(lactic acid) (PLA) and poly(vinyl alcohol) (PVA).

Methods
Samples were sterilised using MW, UV and gamma radiation. Subsequently, the sterility of these samples was tested following the British Pharmacopeia test for sterility and controlled contamination test. Finally, sterilised samples were characterised (DSC, FTIR and drug release studies) to evaluate potential changes in their physicochemical properties during sterilisation.

Key findings
MW-radiation failed the British Pharmacopeia test for sterility. UV-light did not pass the British Pharmacopoeia test for sterility, but it showed promising results for the controlled contamination test (bacterial-contamination reduction &gt;99.9%). These techniques did not modify the physicochemical properties of PLA. On the other hand, samples treated with gamma radiation passed the British Pharmacopeia sterility tests. However, the Tg and mechanical properties of the resulting samples were affected by gamma radiation. It is important to note that none of the sterilisation methods investigated in this article resulted in any change in the in vitro release results.

Conclusions
Only gamma radiation passed the British Pharmacopeia test for sterility. However, the UV method showed potential and should be further investigated.
Howard P. Roffwarg: sleep pioneer, legend, and ontogenetic hypothesis author
Authors: Shaffery James P , Marks Gerald A 
Published: January 2023

Abstract
Narrated in this article are accounts of the many contributions Howard P. Roffwarg, MD, made to the field of sleep research and sleep medicine across his entire professional career as a student, a mentor, a leader in the Sleep Research Society, a sleep medicine clinician, and a scientist who performed experimental investigations in humans and animals. Dr Roffwarg was the originator of what is known as the “Ontogenetic Hypothesis” of sleep. His research over many years on physiology has contributed greatly to much of the experimental support substantiating a role for rapid eye-movement sleep (REMS) in the early development of the brain. Though much is still unknown, the Ontogenetic Hypothesis, still to this day, inspires many neuroscientists in their investigations. These studies have demonstrated roles for both REMS and NREMS in development as well as on brain function throughout his life span. Dr Howard P. Roffwarg, is one of the legends in the field of sleep research.
Mesenchymal Stem Cell-Derived Exosomes Ameliorate Diabetic Kidney Disease Through the NLRP3 Signaling Pathway
Authors: Wang Yinghui , Liu Jiaxi , Wang Honggang , Lv Shasha , Liu Qingzhen , Li Shan , Yang Xue , Liu Gang 
Published: January 2023

Abstract
Diabetic kidney disease (DKD) is the leading cause of end-stage renal disease worldwide. Exosomes (Exo) derived from human umbilical cord mesenchymal stem cells (HUC-MSCs) have been demonstrated to be an effective therapy for DKD, but the underlying mechanisms of this action remain poorly defined. We investigated the association of DKD with inflammasome activation and the pathophysiological relevance of Exo-mediated inflammation relief as well as damage repair in this progression. We co-cultured podocytes and HUC-MSCs derived Exo (MSCs-Exo) under high glucose (HG) and injected MSCs-Exo into diabetic mice, then we detected the NLRP3 inflammasome both in vitro and in vivo. We found that HG reduced the viability of podocytes, activated the NLRP3 signaling pathway and increased inflammation in podocytes and diabetic mice. MSCs-Exo attenuated the inflammation, including the expression of IL-6, IL-1β, IL-18, TNF-α; depressed the activation of NLRP3 signaling pathway in podocytes under HG and diabetic mice, ameliorated kidney injury. Furthermore, miR-22-3p, which is relatively highly expressed miRNAs in exosomes of MSCs, may be the key point in this progress, by suppressing the expression of its known target, NLRP3. Knocking down miR-22-3p from MSCs-Exo abolished their anti-inflammation activity and beneficial function both in vitro and in vivo. Collectively, our results have demonstrated that exosomes transferring miR-22-3p protected the podocytes and diabetic mice from inflammation by mediating NLRP3 inflammasome, indicating that MSC-derived exosomes may be a promising therapeutic cell-free strategy for DKD.
Lactation performance and feed utilization of Rahmani ewes fed with either a newly produced bacteriocin-like substance or a commercial bacteriocin
Authors: Azzaz Hossam H , Kholif Ahmed E , Abd El Tawab Ahmed M , El-Sherbiny Mohamed , Murad Hussein A , Hassaan Noha A , Vargas-Bello-Pérez Einar 
Published: January 2023

Abstract
The aim of the present study was to compare the effect of feeding a newly produced bacteriocin-like substance from Lactococcus lactis ssp. lactis (PNP) with a commercial bacteriocin (NISEEN-S; CNP) in lactating Rahmani ewe diets. In experiment 1, the effects of four levels (500, 1,000, 1,500, and 2,000 unit/kg substrate, dry matter (DM) basis) of both bacteriocins on in vitro ruminal fermentation kinetics, total gas production (TGP), methane production (CH4), and nutrient degradability were determined. In experiment 2, 2 wk before the expected parturition, 30 multiparous lactating Rahmani ewes (mean ± SD: 2 ± 0.3 parity, 46.8 ± 2.5 kg body weight, 23 ± 2.7 mo of age, and 370 ± 13 g/d of previous milk production) were equally divided into three treatments in a complete randomized design for 90 d. The ewes in the control treatment were offered a diet composed of 600 g of concentrate feed mixture, 300 g berseem hay, and 100 g of faba bean straw (Control), or supplemented with produced bacteriocin like substance (PNP) or commercial (CNP) bacteriocin at 500 unit/kg feed (DM basis). In experiment 1, both PNP and CNP linearly and quadratically decreased (P &lt; 0.001) CH4 production; however, PNP and CNP at 500 unit/kg feed quadratically increased fiber degradability (P &lt; 0.01). In experiment 2, both PNP and CNP increased (P &lt; 0.05) nutrient digestibility, and ruminal total volatile fatty acids, acetate, and propionate, while decreasing ruminal ammonia-N. The PNP treatment increased (P &lt; 0.05) blood total proteins and albumin, while PNP and CNP treatments increase serum glucose. Both PNP and CNP treatments increased (P &lt; 0.05) daily milk production and milk efficiency, without affecting the concentration of milk components. Both PNP and CNP are recommended to improve feed utilization and milk production, with superior results detected for PNP at 500 unit/kg feed daily.
QuPath Analysis for CD30+ Cutaneous T-Cell Lymphoma
Authors: Cieslak Cassandra , Mitteldorf Christina , Krömer-Olbrisch Tanja , Kempf Werner , Stadler Rudolf 
Published: January 2023

Background:
Mycosis fungoides is the most common subtype of cutaneous T-cell lymphoma, in which the expression of cluster of differentiation 30 (CD30)+ subtype can now be treated with the CD30 antibody conjugate brentuximab vedotin. Diagnostic methods are based on immunohistochemical (IHC) staining followed by manual assessment by pathologists, which is always a subjective calculation. QuPath, an open-source software for digital pathology image analysis, satisfies the requirements of objective approaches.

Methods:
Ten samples from mycosis fungoides patients with CD30 expression at different stages were stained for CD3 and CD30 by IHC staining, scanned, and quantitative analysis was performed using QuPath (version 2.1). Each slide was independently assessed by 3 board-certified dermatopathologists.

Results:
Individual estimates for CD30+/CD3+ cells varied among the individual histopathologists (mean coefficient of variation, 0.46; range, 0–0.78). QuPath analysis showed excellent separation between the positively stained cells for CD3 and CD30 IHC and other cells and tissue structures, although the results correlated strongly with the respective mean estimates of the 3 histopathologists (Pearson-R 0.93).

Conclusions:
The results show a high interobserver variability evaluation of IHC markers, although quantitative image analysis offer a significant advantage for comparison. This is not only relevant for clinical routine but also especially critical in therapeutic studies addressing targeted molecules.
Chondrosarcoma of the Chest Wall
Authors: Laitinen Minna K. , Kask Gilber , Laurila Katariina , Tukiainen Erkki J. , Rönty Mikko , Haapamäki Ville , Salo Juho T.K. 
Published: January 2023

Introduction
Chondrosarcoma (CS) is most common primary osseous tumor of the chest wall. The aim of this study was to report results from surgical procedures and evaluate clinical factors predicting survival of patients with chest wall CSs treated in a single tertiary sarcoma center.

Materials and Methods
Fifty patients with primary CS located in the ribs and sternum were included. Details of the clinical data and oncological outcomes, including local recurrence (LR) and disease-specific survival (DSS), were collected.

Results
The tumor was primarily originated in the sternum in 6 patients (12.5%) and in ribs 2 to 11 in the remaining patients. Specimens were histologically graded 1 in 13 patients (26%), 2 in 28 (56%), 3 in 8 (16%), and 1 (2%) as mesenchymal grade 3 CS. R0 margins were obtained in all cases. Reconstruction was warranted in 47 (94%) cases. Local recurrence developed in 3 (6%) patients, and the median time to LR was 17 (range, 16–68) months. Eight (16%) patients developed metastasis. Increasing tumor volume was a statistically significant factor for reduction of DSS.

Conclusions
Chondrosarcoma of the chest wall can be treated effectively with clear margins, resulting in lower LR rate and higher DSS than CS of the extremities and pelvis. Metastasis of the chest wall mostly occurs in high-grade tumors, and the locations of the metastases differ greatly from those observed in CS of the extremities and pelvis. Metastases are commonly extrapulmonary, indicating the need for postoperative follow-up with multiple imaging modalities to monitor recurrence and metastases.