bluuebunny/crossref_metadata_2025_split huggingface dataset:
Investigation of micro pit array on titanium alloy with hydrophobic surface by through-mask electrochemical micromachining
Authors: Meng Jianbing , Li Hongmei , Zhang Hongwei , Dong Xiaojuan , Tang Youquan , Zhao Yugang , Qu Linghui 
Published: July 2023

Abstract
In order to obtain higher contact angles and improve the hydrophobicity of titanium alloy, the micro pit arrays were fabricated by the through-mask electrochemical micromachining (TMEMM). The theoretical model of surface hydrophobicity between the contact angle and the geometry size of micro pit arrays was developed. Moreover, the multi physical field coupling simulation of TMEMM was carried out. Thus, the direct mapping relationship between the contact angle and the process parameters was obtained by combining the theoretical model with the simulation results. The effect of process prameters, such as electrolyte mass fraction, mask size and processing voltage, was investigated. The optimal combination of process parameters was predicted and verified by experiments. The results show that the errors of the measured values of diameter, spacing, depth and surface contact angle of the micro pit arrays are 2.49%, 6.87%, 7.40% and 6.01% respectively, which indicates that the hydrophobic textured surface with a contact angle of about 141° is successfully fabricated without the modification of low surface energy materials.
Prognostic signature analysis and survival prediction of esophageal cancer based on N6-methyladenosine associated lncRNAs
Authors: He Ting , Gao Zhipeng , Lin Ling , Zhang Xu , Zou Quan 
Published: July 2023

Abstract
Esophageal cancer (ESCA) has a bad prognosis. Long non-coding RNA (lncRNA) impacts on cell proliferation. However, the prognosis function of N6-methyladenosine (m6A)-associated lncRNAs (m6A-lncRNAs) in ESCA remains unknown. Univariate Cox analysis was applied to investigate prognosis related m6A-lncRNAs, based on which the samples were clustered. Wilcoxon rank and Chi-square tests were adopted to compare the clinical traits, survival, pathway activity and immune infiltration in different clusters where overall survival, clinical traits (N stage), tumor-invasive immune cells and pathway activity were found significantly different. Through least absolute shrinkage and selection operator and proportional hazard (Lasso-Cox) model, five m6A-lncRNAs were selected to construct the prognostic signature (m6A-lncSig) and risk score. To investigate the link between risk score and clinical traits or immunological microenvironments, Chi-square test and Spearman correlation analysis were utilized. Risk score was found connected with N stage, tumor stage, different clusters, macrophages M2, B cells naive and T cells CD4 memory resting. Risk score and tumor stage were found as independent prognostic variables. And the constructed nomogram model had high accuracy in predicting prognosis. The obtained m6A-lncSig could be taken as potential prognostic biomarker for ESCA patients. This study offers a theoretical foundation for clinical diagnosis and prognosis of ESCA.
otargen: GraphQL-based R package for tidy data accessing and processing from Open Targets Genetics
Authors: Feizi Amir , Ray Kamalika 
Published: July 2023

Abstract

Motivation
Open Target Genetics is a comprehensive resource portal that offers variant-centric statistical evidence, enabling the prioritization of causal variants and the identification of potential drug targets. The portal uses GraphQL technology for efficient data query and provides endpoints for programmatic access for R and Python users. However, leveraging GraphQL for data retrieval can be challenging, time-consuming, and repetitive, requiring familiarity with the GraphQL query language and processing outputs in nested JSON (JavaScript Object Notation) format into tidy data tables. Therefore, developing open-source tools are required to simplify data retrieval processes to integrate valuable genetic information into data-driven target discovery pipelines seamlessly.

Results
otargen is an open-source R package designed to make data retrieval and analysis from the Open Target Genetics portal as simple as possible for R users. The package offers a suite of functions covering all query types, allowing streamlined data access in a tidy table format. By executing only a single line of code, the otargen users avoid the repetitive scripting of complex GraphQL queries, including the post-processing steps. In addition, otargen contains convenient plotting functions to visualize and gain insights from complex data tables returned by several key functions.

Availability and implementation
otargen is available at https://amirfeizi.github.io/otargen/.
Vascularized lymph node flaps can survive on venous blood without an arterial inflow: an experimental model describing the dynamics of venous flow using indocyanine green angiography (With video)
Authors: Li Ke , Nicoli Fabio , Cui Chunxiao , Wo Yan , Liu Ning Fei , Feng Shaoqing , Xi Wenjing , Min Peiru , Zhang Yixin 
Published: July 2023

Abstract

Background
Several surgeons have described studies of free-tissue transfers using veins instead of arteries. These innovative microsurgical techniques can offer several advantages, such as an easier dissection during flap harvesting, and represent an alternative during an accidental surgical mistake or development of new surgical procedures. The purpose of this study was to describe and explore different constructs of vascularized lymph node transfer (VLNT) only based on venous blood flow in a mouse model, evaluate their blood flow microcirculation through indocyanine green (ICG) angiography and investigate the lymphatic drainage function and the lymph nodes’ structures.

Methods
Five types of venous lymph node flaps (LNF) were created and investigated: Types IA, IB, IC, IIA and IIB were developed by ICG intraoperatively (with videos in the article). Seven weeks later, by applying methylene blue, the recanalization of the lymphatic vessels between the LNF and the recipient site was detected. Lymph nodes were collected at the same time and their structures were analyzed by hematoxylin and eosin staining analysis.

Results
All of the venous LNFs developed except Type IC. Seven weeks later, methylene blue flowed into Types IA, IB, IIA and IIB from recipient sites. When comparing with arteriovenous lymph node, the medullary sinus was diffusely distributed in venous lymph nodes. The proportion of cells was significantly reduced (p &lt; 0.05). The artery diameters were significantly smaller (p &lt; 0.05). The veins diameters and lymphatic vessels output in Types IA, IB, IIA and IIB were more dilated (p &lt; 0.05).

Conclusions
This research demonstrated that Type IA, IB, IIA and IIB venous LNFs can retrogradely receive venous blood supply; they can survive, produce a lymphatic recanalization and integrate with the surrounding tissue, despite lymph node structural changes. Our results will improve the understanding of the survival mechanism of venous LNFs and will help researchers to design new studies or lymphatic models and eventually find an alternative procedure for the surgical treatment of lymphedema.
Behind the monocyte’s mystique: uncovering their developmental trajectories and fates
Authors: Teh Ye Chean , Chooi Ming Yao , Chong Shu Zhen 
Published: July 2023

Summary
Monocytes are circulating myeloid cells that are derived from dedicated progenitors in the bone marrow. Originally thought of as mere precursors for the replacement of tissue macrophages, it is increasingly clear that monocytes execute distinct effector functions and may give rise to monocyte-derived cells with unique properties from tissue-resident macrophages. Recently, the advent of novel experimental approaches such as single-cell analysis and fate-mapping tools has uncovered an astonishing display of monocyte plasticity and heterogeneity, which we believe has emerged as a key theme in the field of monocyte biology in the last decade. Monocyte heterogeneity is now recognized to develop as early as the progenitor stage through specific imprinting mechanisms, giving rise to specialized effector cells in the tissue. At the same time, monocytes must overcome their susceptibility towards cellular death to persist as monocyte-derived cells in the tissues. Environmental signals that preserve their heterogenic phenotypes and govern their eventual fates remain incompletely understood. In this review, we will summarize recent advances on the developmental trajectory of monocytes and discuss emerging concepts that contributes to the burgeoning field of monocyte plasticity and heterogeneity.
Platelet activation and endothelial dysfunction biomarkers in acute coronary syndrome: the impact of PCSK9 inhibition
Authors: Ziogos Efthymios , Chelko Stephen P , Harb Tarek , Engel Morgan , Vavuranakis Michael A , Landim-Vieira Maicon , Walsh Elise M , Williams Marlene S , Lai Shenghan , Halushka Marc K , Gerstenblith Gary , Leucker Thorsten M 
Published: July 2023

Abstract

Aims
Platelet activation and endothelial dysfunction contribute to adverse outcomes in patients with acute coronary syndromes (ACS). The goals of this study were to assess the impact of proprotein convertase subtilisin/kexin type 9 (PCSK9) inhibition on markers of platelet activation and endothelial dysfunction in ACS patients and the interaction among PCSK9, platelets, and endothelial cells (ECs) on left internal mammary artery (LIMA) vascular endothelium using specimens obtained during coronary artery bypass surgery (CABG).

Methods and Results
Acute coronary syndromes patients enrolled in the Evolocumab in ACS trials were randomized to placebo or a single dose of 420 mg evolocumab within 24 h of hospitalization. Serum samples for analysis of platelet factor 4 (PF4) and P-selectin, markers of platelet activation, and von Willebrand factor (vWF), a marker of endothelial dysfunction, were obtained at baseline and 30 days. Additionally, LIMA segments obtained during CABG from patients who were and were not receiving evolocumab were immunostained with PCSK9; CD61, a platelet-specific marker; and CD31, an endothelial cell-specific marker. Forty-six participants were randomized to placebo or to evolocumab. Controlling for baseline levels, PF4 and vWF were significantly lower in the evolocumab, than in the placebo, group at 30 days. Immunostaining of LIMA specimens from twelve participants undergoing CABG revealed colocalization of PCSK9, CD61, and CD31 at the vascular endothelium. Administration of evolocumab was associated with decreased overlap of PCSK9, CD61, and CD31.

Conclusions
Proprotein Convertase Subtilisin/Kexin 9 inhibition decreases markers of platelet activation and endothelial dysfunction in ACS patients. PCSK9 is associated with platelets and vascular ECs in LIMA segments and PCSK9 inhibition decreases that interaction.
Intravascular imaging during percutaneous coronary intervention: temporal trends and clinical outcomes in the USA
Authors: Fazel Reza , Yeh Robert W , Cohen David J , Rao Sunil V , Li Siling , Song Yang , Secemsky Eric A 
Published: July 2023

Abstract

Aims
Prior trials have demonstrated that intravascular imaging (IVI)-guided percutaneous coronary intervention (PCI) results in less frequent target lesion revascularization and major adverse cardiovascular events (MACEs) compared with standard angiographic guidance. The uptake and associated outcomes of IVI-guided PCI in contemporary clinical practice in the USA remain unclear. Accordingly, temporal trends and comparative outcomes of IVI-guided PCI relative to PCI with angiographic guidance alone were examined in a broad, unselected population of Medicare beneficiaries.

Methods and results
Retrospective cohort study of Medicare beneficiary data from 1 January 2013, through 31 December 2019 to evaluate temporal trends and comparative outcomes of IVI-guided PCI as compared with PCI with angiography guidance alone in both the inpatient and outpatient settings. The primary outcomes were 1 year mortality and MACE, defined as the composite of death, myocardial infarction (MI), repeat PCI, or coronary artery bypass graft surgery. Secondary outcomes were MI or repeat PCI at 1 year. Multivariable Cox regression was used to estimate the adjusted association between IVI guidance and outcomes. Falsification endpoints (hospitalized pneumonia and hip fracture) were used to assess for potential unmeasured confounding. The study population included 1 189 470 patients undergoing PCI (38.0% female, 89.8% White, 65.1% with MI). Overall, IVI was used in 10.5% of the PCIs, increasing from 9.5% in 2013% to 15.4% in 2019. Operator IVI use was variable, with the median operator use of IVI 3.92% (interquartile range 0.36%–12.82%). IVI use during PCI was associated with lower adjusted rates of 1 year mortality [adjusted hazard ratio (aHR) 0.96, 95% confidence interval (CI) 0.94–0.98], MI (aHR 0.97, 95% CI 0.95–0.99), repeat PCI (aHR 0.74, 95% CI 0.73–0.75), and MACE (aHR 0.85, 95% CI 0.84–0.86). There was no association with the falsification endpoint of hospitalized pneumonia (aHR 1.02, 95% CI 0.99–1.04) or hip fracture (aHR 1.02, 95% CI 0.94–1.10).

Conclusion
Among Medicare beneficiaries undergoing PCI, use of IVI has increased over the previous decade but remains relatively infrequent. IVI-guided PCI was associated with lower risk-adjusted mortality, acute MI, repeat PCI, and MACE.
Patent term extension and test data protection obligations: identifying the gap in policy, research, and practice of implementing free trade agreements
Authors: Mercurio Bryan , Upreti Pratyush Nath 
Published: July 2023

Abstract
Much of the academic literature criticizes the inclusion of patent term extensions (PTE) and test data protection into the pharmaceutical provisions and/or intellectual property (IP) chapters of free trade agreements (FTAs), with many arguing that such provisions will increase the cost of pharmaceuticals for the implementing government. Such arguments are often backed by studies conducted prior to the conclusion of the relevant FTA. This is problematic for several reasons, most notably that the studies make assumptions that subsequently turn out not to be false and that the claims are not revisited and supported with empirical data following implementation. This article reviews the experience of two jurisdictions – Canada and Australia – in order to provide an analysis of legislative and judicial practices with a focus on implications and the cost of FTAs. The article examines how Canada and Australia have implemented their FTA obligations domestically and on the hereto ignored but important role of courts. One key finding is how courts in both countries are vigilant in narrowing the scope of obligations under FTAs to accommodate the need of the domestic market. The article ultimately concludes by calling on governments to conduct a detailed analysis of PTE and test data protection so as to better inform and prepare policymakers and, ultimately, improved FTA provisions and health outcomes.
Fatty acid based antimicrobials from Streptomyces sp. SORS-24, an endophyte isolated from Sonchus oleraceus
Authors: Tanvir Rabia , Sajid Imran , Rehman Yasir , Hasnain Shahida 
Published: July 2023

Abstract
Due to the rise in bacterial resistance towards various therapeutic agents, interest is now developing towards fatty acid based antimicrobials because of their non-specific mode of action. A strain SORS 24 isolated from Sonchus oleraceus (Sow thistle) showed significant activity against Escherichia coli ATCC 25922 (25 mm), Chlorella vulgaris (20 mm), Bacillus subtilis DSM 10 (ATCC 6051) and Pseudomonas sp. (15 mm). It displayed an LC50 value of 10 µg/ml against Artemia salina (Brine shrimp) nauplii and an EC50 value of 0.8 µg/ml in the (DPPH) diphenylpicrylhydrazyl antioxidant assay. The strain also displayed genotoxicity against a PolA deficient strain, E. coli K-12 AB 3027 (15 mm). Mass spectrometry (HPLC-MS) showed that the strain produced oleamide (9-Octadecenamide) and erucamide (13-Docosenamide). Both of the purified fatty acid amides showed prominent activity against B. subtilis DSM 10 (ATCC 6051) (20 mm) and E. coli ATCC 25922 (15 mm). Significant genotoxicity was observed against E. coli K-12 AB 3027 (15 mm). The 16S gene sequencing revealed that the strain belonged to species, Streptomyces tanashiensis. As far as our understanding, this is the first report of this species producing these fatty acid based antimicrobials.
Characterizing and understanding galaxies with two parameters
Authors: Cooray Suchetha , Takeuchi Tsutomu T , Kashino Daichi , Yoshida Shuntaro A , Ma Hai-Xia , Kono Kai T 
Published: July 2023

ABSTRACT
We report the discovery of a 2D Galaxy Manifold within the multidimensional luminosity space of local galaxies. The multidimensional luminosity space is constructed using 11 bands that span from far ultraviolet to near-infrared for redshift &lt; 0.1 galaxies observed with GALEX, SDSS, and UKIDSS. The manifold captures the diversity of observed galaxies in terms of stellar-dominated emissions and ties the correlations of various physical properties to the manifold. We find that two latent parameters are sufficient to express 93.2 per cent of the variance in the galaxy sample, suggesting that this Galaxy Manifold is one of the most efficient representations of galaxies. The transformation between the observed luminosities and the manifold parameters as an analytic mapping is provided. The manifold representation provides accurate (precision = 0.85) morphological classifications with a simple linear boundary, and galaxy properties can be estimated with minimal scatter (0.12 and 0.04 dex for star formation rate and stellar mass, respectively) by calibrating with the 2D manifold location. Under the assumption that the manifold expresses the possible parameter space of galaxies, the evolution on the manifold is considered. We find that constant and exponentially decreasing star formation histories form almost orthogonal modes of evolution on the manifold. Through these simple models, we understand that the two modes are closely related to gas content, which suggests the close relationship of the manifold to gas accretion. Lastly, the found manifold suggests a paradigm where galaxies are characterized by their mass/scale and specific SFR, which agrees with previous studies of dimensionality reduction.
The force explosion condition is consistent with spherically symmetric CCSN explosions
Authors: Gogilashvili Mariam , Murphy Jeremiah W , O’Connor Evan P 
Published: July 2023

ABSTRACT
One of the major challenges in core-collapse supernova (CCSN) theory is to predict which stars explode and which collapse to black holes. The analytic force explosion condition (FEC) shows promise in predicting which stars explode in that the FEC is consistent with CCSN simulations that use the light-bulb approximation for neutrino heating and cooling. In this follow-up manuscript, we take the next step and show that the FEC is consistent with the explosion condition when using actual neutrino transport in gr1d simulations. Since most 1D simulations do not explode, to facilitate this test, we enhance the heating efficiency within the gain region. To compare the analytic FEC and radiation-hydrodynamic simulations, this manuscript also presents a practical translation of the physical parameters. For example: we replace the neutrino power deposited in the gain region, Lντg, with the net neutrino heating in the gain region; rather than assuming that $\dot{M}$ is the same everywhere, we calculate $\dot{M}$ within the gain region; and we use the neutrino opacity at the gain radius. With small, yet practical modifications, we show that the FEC predicts the explosion conditions in spherically symmetric CCSN simulations that use neutrino transport.
Discordance of dipole asymmetries seen in recent large radio surveys with the cosmological principle
Authors: Singal Ashok K 
Published: July 2023

ABSTRACT
In recent years, large radio surveys of active galactic nuclei, comprising millions of sources, have become available where one could investigate dipole asymmetries, assumedly arising due to a peculiar motion of the Solar system. Investigations of such dipoles have yielded in past much larger amplitudes than the cosmic microwave background (CMB) dipole, though their directions seem to lie close to the CMB dipole. Here we investigate dipole asymmetries in two recent large radio surveys, Very Large Array sky survey (VLASS) containing 1.9 million sources, covering the sky north of −40° declination, and the Rapid ASKAP Continuum Survey (RACS) containing 2.1 million sources, covering the sky south of +30° declination We find dipoles determined from the VLASS and RACS surveys to be significantly larger than the CMB dipole. Dipole directions from the VLASS and RACS data differ significantly from each other. Nevertheless, along with a number of other previously determined dipoles, including the CMB, they all appear to lie in a narrow sky region, which argues for the various dipoles to be related somehow. However, significant differences in their derived peculiar velocities, including that of the CMB, cannot be explained by a peculiar motion of the Solar system, which should necessarily be a single value. Instead, their discordant peculiar velocities may be indicating that different cosmic reference frames are moving relative to each other or that the matter distribution on cosmic scales is not homogeneous and isotropic, either scenario being in contravention of what expected from the cosmological principle.
A bioinformatic analysis of zinc transporters in intestinal Lactobacillaceae
Authors: Huynh Uyen , Nguyen Hazel N , Trinh Brittany K , Elhaj Joanna , Zastrow Melissa L 
Published: July 2023

Abstract
As the second most abundant transition element and a crucial cofactor for many proteins, zinc is essential for the survival of all living organisms. To maintain required zinc levels and prevent toxic overload, cells and organisms have a collection of metal transport proteins for uptake and efflux of zinc. In bacteria, metal transport proteins are well defined for model organisms and many pathogens, but fewer studies have explored metal transport proteins, including those for zinc, in commensal bacteria from the gut microbiota. The healthy human gut microbiota comprises hundreds of species and among these, bacteria from the Lactobacillaceae family are well documented to have various beneficial effects on health. Furthermore, changes in dietary metal intake, such as for zinc and iron, are frequently correlated with changes in abundance of Lactobacillaceae. Few studies have explored zinc requirements and zinc homeostasis mechanisms in Lactobacillaceae, however. Here we applied a bioinformatics approach to identify and compare predicted zinc uptake and efflux proteins in several Lactobacillaceae genera of intestinal relevance. Few Lactobacillaceae had zinc transporters currently annotated in proteomes retrieved from the UniProt database, but protein sequence-based homology searches revealed that high-affinity ABC transporter genes are likely common, albeit with genus-specific domain features. P-type ATPase transporters are probably also common and some Lactobacillaceae genera code for predicted zinc efflux cation diffusion facilitators. This analysis confirms that Lactobacillaceae harbor genes for various zinc transporter homologs, and provides a foundation for systematic experimental studies to elucidate zinc homeostasis mechanisms in these bacteria.