bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sea level rise implication on small islands in Kepulauan Seribu, Jakarta
Authors: Pasaribu R. A. , Ratna Suhita N. P. A. , Gumilar G. , Choiriyah N. , Siregar R. R. , Yonatika N. O. 
Published: October 2023

Abstract
The phenomenon of sea level rise is caused by global warming, which impacts inundation in coastal areas, especially on small islands. The coastal area of small islands is very vulnerable to the impact of sea level rise, including Lancang Island (covers Lancang Besar and Lancang Kecil Island), Tidung Kecil Island, and Pramuka Island, which is part of small islands in Kepulauan Seribu, Jakarta. Sea level rise will become a problem if the seawater reaches land and causes environmental damage in coastal areas. Therefore, this study aims to create a vulnerability map for all those small islands due to coastal inundation using GIS technology. Analysis of areas affected by coastal inundation is carried out by processing DTM data derived from drone data. Based on 29 years of sea level rise data with the highest tide model, coastal inundation in 2050 is predicted to occur on all those small islands in Kepulauan Seribu and can be appropriately modelled. The results show that the affected areas on Tidung Kecil Island, Lancang Island, and Pramuka Island sequentially were 6.06 ha, 7.41 ha, and 3.47 ha. Some areas affected by coastal inundation on the three islands generally include dock and resident areas, empty land, vegetation, mangroves, forest, and road access. Mitigation efforts that can be carried out to reduce the impact of sea level rise in coastal areas include building embankments on the shoreline, dams, drainage systems, and mechanical wetlands, which must be optimized by increasing public awareness of coastal flooding.
Distribution of marine sponges based on depth area of Mesophotic Coral Ecosystems (MCEs) in North Lombok Waters, NTB Province
Authors: Arafat D , Bengen DG , Naulita Y , Subhan B , Yuliana FF , Saputra RR 
Published: October 2023

Abstract
North Lombok Waters have a fairly high level of diversity. Mesophotic Coral Ecosystems (MCEs) are light-dependent coral reef communities ranging from 30-40 meters and extending to the bottom of the photic zone to a depth of 150 meters. Sponges are the main constituent of MCEs that have many benefits, but their existence is poorly understood. This study aims to determine the distribution of marine sponges in Mesophotic Coral Ecosystems (MCEs). Data was taken in September 2020 using the Underwater Photo Transect (UPT) method. Pictures were taken at a depth of 10, 20, 30, 40, and 50 meters at 3 stations. Macroscopic identification of sponges based on underwater photos. The identification results found 32 genera of sponges spread over 3 stations in the waters of North Lombok. The deeper you go, the more genera are found at the three research stations. Out of 32 genera, sponge abundance dependent on depth only influences 5 genera. We anticipate additional factors affecting the 27 genera of sponges, but further research is necessary. The ANOVA test results showed that several sponges genera were significantly different between depths, namely Callyspongia, Theonella, Clathria, Stylotella, and Spirastrella.
Review of Marine Invasive Species Distribution Pattern in Indonesia
Authors: Zalzabil A R , Lestari D F , Fadillah S N , Maharani R S , Zulfikri M A , Farahdillah R E , Zabrina W S , Azzachra S , Lamtiur S L M , Amigunani Z W , Cahyati N A D , Nabihah N , Christy P A , Djemadjid S P , Nuzulia S R , Alfarabi F M , Zahrani S R , Hasyim M W , Sidhiq M F , Mulkiyah M D , Maysaroh S , Febridelita A , Cakasana Nadya , Madduppa H M 
Published: October 2023

Abstract
Marine invasive species may replace native species, change habitats, and affect community structures and ecological processes. The impact of introduced species can seriously damage areas and high-value biodiversity in Indonesian waters. This study aims to determine Indonesia’s distribution pattern of marine invasive species based on literature review. The data were collected through literature studies from various publications. Mollusca is the highest invasive phylum found which is 27%, followed by Echinoderms 16% and Chlorophyta 13% from all of the total data collected. The distribution of marine invasive species is influenced by ships, canals, and aquaculture activities, and introduced species to a new habitat. The publication of articles on invasive species are dominated by western part of Indonesia data as much 46 from 85 tabulated data. The habitat of invasive species is dominated by coral reefs used by various biota as a self-defence area, spawning ground, and shelter from predatory threats. As many as 64% of invasive species have Not Evaluated (NE) status at the IUCN site.
Synthesis of heparin-and-poloxamer P407-based nanogel carrying PTX for orientating in treatment of breast cancer
Authors: Nguyen Ngoc The 
Published: October 2023

Abstract
In this study, nanogels based on the conjugation of heparin and poloxamer P407 (HR-P407) with different grafting ratios were successfully synthesised. The structural properties of products were evaluated by Fourier-transform infrared spectroscopy (FT-IR) and proton nuclear magnetic resonance (1H-NMR). The morphology and size of nanoparticles were assessed by dynamic light scattering (DLS) method, which showed that particle size distribution was from 144 nm to 214 nm. The HR-P407 nanogel systems were biocompatible and non-toxic to healthy cells. While free PTX displayed rapid and potent cytotoxic effects, PTX released from HR-P407 (1:10)/PTX demonstrated a gradual and sustained cytotoxicity. This controlled release mechanism allowed prolonged drug exposure, reducing acute toxicity and enhancing cytotoxicity over time. The results suggest that the synthesised nanogels can be used as an effective hydrophobic anticancer drug carrier system.
Characterization of pulsed-tungsten inert gas (PTIG) welding on AA5754-H111 alloy: mechanical properties and microstructural analysis
Authors: Tamil Kumaran G , Jayakumar K S , Amala Mithin Minther Singh A 
Published: October 2023

Abstract
Aluminium and its alloys were widely used in engineering because they are lightweight, strong, and resistant to corrosion. However, using standard arc welding techniques can be difficult when dealing with such materials. Pulsed-Tungsten Inert Gas (PTIG) welding is being researched as a potential solution to this problem. This study is the first to investigate the use of the straightforward and intuitive PTIG technique on the ubiquitous AA5754 wrought aluminium alloy. Welded samples were supplied for examination of mechanical parameters such as surface hardness and strength under impact and tensile loading. The results of a statistical analysis of the mechanical characterization of a PTIG-welded permanent joint fabricated from AA5754 aluminium alloy were presented and discussed. The heat-affected zone (HAZ) on the AA5754 retracting side of the weld had a hardness of 50–70 Hv0.5, while the HAZ on the AA5756 side had a hardness of 90–100 Hv0.5, as measured by testing on the perfect weld specimen. Samples taken from different parts of the weldment all showed that the HAZ is the softest and weakest. The shattered surface of the welded sample consisted of flat facets and quasi-cleavage patterns, as revealed by scanning electron microscopy. Analysis of the HAZ microstructure revealed widespread dissolution of Mg2Si precipitates in the AA5754-H111.
Enhancing photo voltaic solar panel efficiency by using a combination of silica based and phase change material coating
Authors: Sankaran Durairaj , Pappan Balakrishnan , Balakrishnan Kirubakaran 
Published: October 2023

Abstract
This study attempts to enhance the overall efficiency of a photo voltaic solar panel by employing a dual-coating approach. The initial coating consists of a Silica-based anti-reflective material synthesized through an acid-catalyzed sol–gel process, utilizing cetyltrimethylammonium bromide as a template. Subsequently, the second coating was formulated using a phase change material, such as expanded graphite infused with paraffin jelly. The coating materials were characterized using Ultraviolet-Visual ray spectroscopy, Fourier Transform-Infrared Ray spectroscopy, Field Emission-Scanning Electron Microscopy, x-ray Diffraction sepctroscopy, and Thermogravimetry analysis. The panels’ performance had been investigated under three conditions: uncoated, single-coated, and double-coated. These panels were subjected to both indoor and outdoor experiments. Indoor tests were conducted in a laboratory with induced irradiance levels of 350, 600, and 850 W/m2. The corresponding variations in maximum power output, maximum surface temperature and peak current were recorded. For the outdoor experiments, two sets of panels were installed on a rooftop. One set underwent daily surface cleaning, while the other was left untouched, allowing dust accumulation. Over a 45-day period, outdoor experiments were carried out (daily cleaned and unclean panels) to examine the impact of dust accumulation on power loss, current, voltage, surface temperature, energy generation and panel efficiency. Upon comparing the performance of uncoated, single-coated, and double-coated solar panels, it was observed that photovoltaic solar panels coated with both silica-based anti-reflective coating and paraffin jelly-infused expanded graphite coating exhibited superior performance when compared to other coating options.
A disruptive clickable antibody design for the generation of antibody-drug conjugates
Authors: Rakotoarinoro Nathanaël , Dyck Yan F K , Krebs Simon K , Assi Miriam-Kousso , Parr Maria K , Stech Marlitt 
Published: October 2023

Abstract

Background
Antibody-drug conjugates are cancer therapeutics that combine specificity and toxicity. A highly cytotoxic drug is covalently attached to an antibody that directs it to cancer cells. The conjugation of the drug-linker to the antibody is a key point in research and development as well as in industrial production. The consensus is to conjugate the drug to a surface-exposed part of the antibody to ensure maximum conjugation efficiency. However, the hydrophobic nature of the majority of drugs used in antibody-drug conjugates leads to an increased hydrophobicity of the generated antibody-drug conjugates, resulting in higher liver clearance and decreased stability.

Methods
In contrast, we describe a non-conventional approach in which the drug is conjugated in a buried part of the antibody. To achieve this, a ready-to-click antibody design was created in which an azido-based non-canonical amino acid is introduced within the Fab cavity during antibody synthesis using nonsense suppression technology. The Fab cavity was preferred over the Fc cavity to circumvent issues related to cleavage of the IgG1 lower hinge region in the tumor microenvironment.

Results
This antibody design significantly increased the hydrophilicity of the generated antibody-drug conjugates compared to the current best-in-class designs based on non-canonical amino acids, while conjugation efficiency and functionality were maintained. The robustness of this native shielding effect and the versatility of this approach were also investigated.

Conclusions
This pioneer design may become a starting point for the improvement of antibody-drug conjugates and an option to consider for protecting drugs and linkers from unspecific interactions.
Normative Data for the 12-Item Sniffin’ Sticks Odor Identification Test in Older Adults
Authors: Kamath Vidyulata , Chen Honglei , Shrestha Srishti , Mechanic-Hamilton Dawn , Deal Jennifer A , Mosley Thomas H , Schneider Andrea L C 
Published: October 2023

Abstract

Objective
Quantitative olfactory assessment has demonstrated clinical utility for the evaluation of a range of neurologic, psychiatric, and sinonasal conditions. Here, we provide age, sex, race, and education-specific normative data for the 12-item Sniffin Sticks Odor Identification Test (SSOIT-12) in older Black and White U.S. adults without preclinical or clinical dementia or sinonasal disease.

Method
A sample of 2,224 Atherosclerosis Risk in Communities study participants aged 66–89 years were included. A normative regression equation was developed using a linear model for the association of age, sex, race, and education with odor identification score. Regression-based normative mean scores and percentiles were generated by age, sex, race, and education groups.

Results
Participants (mean age = 74 years, 59% women, 20% Black, 48% &gt; high school education) had a mean SSOIT-12 score of 9.8. Age, sex, race, and education were all associated with odor identification performance (all ps &lt; .05). A linear regression model for the predicted SSOIT-12 score was developed for use with an individual’s actual SSOIT-12 score in order to calculate the Z-score and corresponding percentile for a specific age, sex, race, and education group. Data are also reported in tabular format.

Conclusions
Our study provides SSOIT-12 normative data obtained from a large population of White and Black older adults without preclinical or clinical dementia or sinonasal disease living in the USA. These findings can aid clinicians in assessing the degree of olfactory loss, establishing concordance with a person’s perception of olfactory difficulties and quantitatively monitoring changes in olfactory performance over time.
JSONWP: a static website generator for protein bioinformatics research
Authors: Kilinc Mesih , Jia Kejue , Jernigan Robert L 
Published: October 2023

Abstract

Motivation
Presenting the integrated results of bioinformatics research can be challenging and requires sophisticated visualization components, which can be time-consuming to develop. This article presents a new way to effectively communicate research findings.

Results
We have developed a static web page generator, JSONWP, which is specifically designed for protein bioinformatics research. Utilizing React (a JavaScript library used to build interactive and dynamic user interfaces for web applications), we have integrated publicly available bioinformatics visualization components to provide standardized access to these components. JSON (or JavaScript Object Notation, is a lightweight textual data format often used to structure and exchange information between different software tools.) is used as the input source due to its ability to represent nearly all types of data using key and value pairs. This allows researchers to use their preferred programming language to create a JSON representation, which can then be converted into a website by JSONWP. No server or domain is required to host the website, as only the publicly accessible JSON file is required.

Conclusions
Overall, JSONWP provides a useful new tool for bioinformatics researchers to effectively communicate their findings. The open-source implementation is located at https://github.com/MesihK/react-json-wpbuilder, and the tool can be used at jsonwp.onrender.com.
An evolution strategy approach for the balanced minimum evolution problem
Authors: Gasparin Andrea , Camerota Verdù Federico Julian , Catanzaro Daniele , Castelli Lorenzo 
Published: October 2023

Abstract

Motivation
The Balanced Minimum Evolution (BME) is a powerful distance based phylogenetic estimation model introduced by Desper and Gascuel and nowadays implemented in popular tools for phylogenetic analyses. It was proven to be computationally less demanding than more sophisticated estimation methods, e.g. maximum likelihood or Bayesian inference while preserving the statistical consistency and the ability to run with almost any kind of data for which a dissimilarity measure is available. BME can be stated in terms of a nonlinear non-convex combinatorial optimization problem, usually referred to as the Balanced Minimum Evolution Problem (BMEP). Currently, the state-of-the-art among approximate methods for the BMEP is represented by FastME (version 2.0), a software which implements several deterministic phylogenetic construction heuristics combined with a local search on specific neighbourhoods derived by classical topological tree rearrangements. These combinations, however, may not guarantee convergence to close-to-optimal solutions to the problem due to the lack of solution space exploration, a phenomenon which is exacerbated when tackling molecular datasets characterized by a large number of taxa.

Results
To overcome such convergence issues, in this article, we propose a novel metaheuristic, named PhyloES, which exploits the combination of an exploration phase based on Evolution Strategies, a special type of evolutionary algorithm, with a refinement phase based on two local search algorithms. Extensive computational experiments show that PhyloES consistently outperforms FastME, especially when tackling larger datasets, providing solutions characterized by a shorter tree length but also significantly different from the topological perspective.

Availability and implementation
The software and the data are available at https://github.com/andygaspar/PHYLOES.
TT3D: Leveraging precomputed protein 3D sequence models to predict protein–protein interactions
Authors: Sledzieski Samuel , Devkota Kapil , Singh Rohit , Cowen Lenore , Berger Bonnie 
Published: October 2023

Abstract

Motivation
High-quality computational structural models are now precomputed and available for nearly every protein in UniProt. However, the best way to leverage these models to predict which pairs of proteins interact in a high-throughput manner is not immediately clear. The recent Foldseek method of van Kempen et al. encodes the structural information of distances and angles along the protein backbone into a linear string of the same length as the protein string, using tokens from a 21-letter discretized structural alphabet (3Di).

Results
We show that using both the amino acid sequence and the 3Di sequence generated by Foldseek as inputs to our recent deep-learning method, Topsy-Turvy, substantially improves the performance of predicting protein–protein interactions cross-species. Thus TT3D (Topsy-Turvy 3D) presents a way to reuse all the computational effort going into producing high-quality structural models from sequence, while being sufficiently lightweight so that high-quality binary protein–protein interaction predictions across all protein pairs can be made genome-wide.

Availability and Implementation
TT3D is available at https://github.com/samsledje/D-SCRIPT. An archived version of the code at time of submission can be found at https://zenodo.org/records/10037674.
Training Pearl: Welcome to the CC360 Fellow’s Corner
Authors: Michel Hilary K , Malter Lisa 
Published: October 2023

Abstract
The Crohn’s & Colitis Foundation has grown to appreciate the needs of gastroenterology trainees with numerous initiatives designed to provide education, academic opportunities, and mentoring in inflammatory bowel disease (IBD) in recent years. The editors and staff at Crohn’s and Colitis 360 (CC360) have launched 2 new initiatives, the Fellow’s Corner and the CC360 Editorial Fellowship, to support trainees in gaining knowledge and skills regarding peer review and publication as well as offering guidance on training in IBD and an opportunity for publication in this peer-reviewed, open access, quarterly online journal. These opportunities are described in this manuscript.
Diagnostic and prognostic value of the sex-specific 99th percentile of four high-sensitivity cardiac troponin assays in patients with suspected myocardial infarction
Authors: Lehmacher Jonas , Sörensen Nils Arne , Twerenbold Raphael , Goßling Alina , Haller Paul Michael , Hartikainen Tau Sarra , Schock Alina , Toprak Betül , Zeller Tanja , Westermann Dirk , Neumann Johannes Tobias 
Published: October 2023

Abstract

Aims
High-sensitivity cardiac troponin (hs-cTn) assays are used for detection of myocardial infarction (MI). Ninety-ninth percentiles show wide inter-assay variation. The use of sex-specific cut-offs is recommended as definitory cut-off for MI. We compared diagnostic performance and prognostic value of sex-specific 99th percentiles of four hs-cTn assays in patients with suspected MI.

Methods and results
Concentrations of four hs-cTn assays were measured at presentation and after 3 h in patients with suspected MI. Final diagnoses were adjudicated according to the 4th Universal Definition of MI. Unisex and sex-specific 99th percentiles were evaluated as diagnostic cut-offs following the ESC 0/3 h algorithm. These cut-offs were used in Cox-regression analyses to investigate the association with a composite endpoint of MI, revascularization, cardiac rehospitalization, and death. Non-ST-elevation MI was diagnosed in 368 of 2718 patients. Applying the unisex 99th percentile, Elecsys hs-cTnT provided highest negative predictive value (NPV) of 99.7 and a positive predictive value (PPV) of 75.9. The analysed hs-cTnI assays showed slightly lower NPVs and comparable PPVs [Architect (NPV 98.0, PPV of 71.4); Atellica (NPV 97.7, PPV of 76.1); Pathfast (NPV 97.7, PPV of 66.6)]. Application of sex-specific 99th percentiles did not significantly affect diagnostic performance. Concentrations above 99th percentile were independent predictors for impaired long-term outcome (hazard ratios 1.2–1.5, P &lt; 0.001).

Conclusion
We describe a good diagnostic accuracy of four hs-cTn assays using the assay-specific 99th percentile for detection of MI. Application of sex-specific 99th percentiles did neither affect diagnostic performance nor prognostic value significantly. Finally, values above the 99th percentile were associated with poor long-term outcome.
Triglyceride-glucose index, low-density lipoprotein levels, and cardiovascular outcomes in chronic stable cardiovascular disease: results from the ONTARGET and TRANSCEND trials
Authors: Haring Bernhard , Schumacher Helmut , Mancia Giuseppe , Teo Koon K , Lonn Eva M , Mahfoud Felix , Schmieder Roland , Mann Johannes F E , Sliwa Karen , Yusuf Salim , Böhm Michael 
Published: October 2023

Abstract

Aims
The triglyceride-glucose index (TyG) has been proposed as an alternative to insulin resistance and as a predictor of cardiovascular outcomes. Little is known on its role in chronic stable cardiovascular disease and its predictive power at controlled low density lipoprotein (LDL) levels.

Methods and results
Our study population consisted of 29 960 participants in the ONTARGET and TRANSCEND trials that enrolled patients with known atherosclerotic disease. Triglycerides and glucose were measured at baseline. TyG was calculated as the logarithmized product of fasting triglycerides and glucose divided by 2. The primary endpoint of both trials was a composite of cardiovascular death, myocardial infarction, stroke, or hospitalization for heart failure. The secondary endpoint was all-cause death and the components of the primary endpoint. Cox proportional hazards models were used to estimate hazard ratios (HRs) and 95% confidence intervals (CI) with extensive covariate adjustment for demographic, medical history, and lifestyle factors. During a mean follow-up of 4.3 years, 4895 primary endpoints and 3571 all-cause deaths occurred. In fully adjusted models, individuals in the highest compared to the lowest quartile of the TyG index were at higher risk for the primary endpoint (HR 1.14; 95% CI 1.05–1.25) and for myocardial infarction (HR 1.30; 95% CI 1.11–1.53). A higher TyG index did not associate with the primary endpoint in individuals with LDL levels &lt; 100 mg/dL.

Conclusion
A higher TyG index is associated with a modestly increased cardiovascular risk in chronic stable cardiovascular disease. This association is largely attenuated when LDL levels are controlled.

Registration
www.clinicaltrials.gov: NCT00153101