bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessment of water quality, heavy metal pollution and human health risks in the Canal system of Ho Chi Minh City, Vietnam
Authors: Tong Nguyen Xuan , Thao Nguyen Thi Thanh , Anh Le Hung 
Published: June 2024

Abstract
This study was conducted to determine the surface water quality and health risks in Ho Chi Minh City (HCMC) canals. 180 water samples and 180 sediment samples were collected from 15 canal locations in HCMC in 2021 and 2022. The Water Quality Index (WQI) assessment results indicated that the water quality in 2021 ranged from unsuitable to good, with a trend towards improvement in 2022, where good quality water was predominant. TMs PCA/FA identified domestic and agricultural wastewater from HCMC residents as influencing the water quality. Most TMs detected in surface water were within the limits the Vietnamese Ministry of Natural Resources and Environment allowed, except for Pb in 2022 (> 0.02 mg l−1). For sediments, TMs concentrations were higher than in water samples but showed a decreasing trend over the survey period in the order of Hg < Cd < As < Pb < Cu. The findings show that sediments are more strongly affected by TMs than surface water, with the main sources being industrial and agricultural human activities. The non-cancer risk assessment showed that children are more exposed to TMs than adults, mainly through ingestion. Additionally, the cancer risk assessment (CR) identified As in sediments as posing an unacceptable cancer risk (TCR > 1 × 10−4). Therefore, it is necessary to establish high-frequency monitoring policies to analyze and reduce TMs concentrations in water and sediments of the canals to protect human health.
In-situ topotactic chemical reaction for spectroscopies
Authors: Kawakami Tappei , Nakayama Kosuke , Sugawara Katsuaki , Sato Takafumi 
Published: June 2024

Abstract
Topotactic chemical reaction (TCR) is a chemical process that transforms one crystalline phase to another while maintaining one or more of the original structural frameworks, typically induced by the local insertion, removal, or replacement of atoms in a crystal. The utilization of TCR in atomic-layer materials and surfaces of bulk crystals leads to exotic quantum phases, as highlighted by the control of topological phases, the emergence of two-dimensional (2D) superconductivity, and the realization of 2D ferromagnetism. Advanced surface-sensitive spectroscopies such as angle-resolved photoemission spectroscopy and scanning tunneling microscopy are leading techniques to visualize the electronic structure of such exotic states and provide us a guide to further functionalize material properties. In this review article, we summarize the recent progress in this field, with particular emphasis on intriguing results obtained by combining spectroscopies and TCR in thin films.
Experimental and finite element analysis of tensile properties of oil palm trunk im–pregnated with epoxy
Authors: Nik Wan F , Abubakar A , Suriani M J , Saat A M , Fitriadhy A , Wan Nik W M N , Abdul Majid M S , Mukhtar Z Z , Ilyas R A , Mohd Nurazzi N , Norrrahim M N F 
Published: June 2024

Abstract
This research focuses on determining the elastic properties from the development of a three-dimensional constitutive model of impregnated oil palm trunk reinforced with epoxy (OPTE) composite. The research aims to simulate the tensile behaviour of OPTE composite for finite element analysis and compared with the OPTE experimental results, respectively. The OPTE composites were manufactured by using one of the vacuum infusion techniques namely the vacuum-assisted resin transfer moulding technique. In this research, OPTE composite is considered as a unidirectional fibre due to the wood board in the resin. Tensile tests were conducted to provide the material properties as inputs into three-dimensional constitutive model. The tensile test was performed according to ASTM D3039. The test was divided into three zones including zone I (outer), zone II (middle) and zone III (inner). The three elastic constants (elastic modulus, shear modulus and Poisson’s ratio) of material properties were obtained from the tensile test data and theoretical equation. The model was developed in Abaqus software. The results from finite element method (FEM) were compared with the experimental results. There was a good agreement and promising results between FEM and the experimental data.
The futility of being selfish in vaccine distribution
Authors: Alves Felippe , Saad David 
Published: June 2024

Abstract
We study vaccine budget-sharing strategies in the SIR (Susceptible-Infected-Recovered) model given a structured community network to investigate the benefit of sharing vaccine across communities. The network studied comprises two communities, one of which controls vaccine budget and may share it with the other. Different scenarios are considered regarding the connectivity between communities, infection rates and the unvaccinated fraction of the population. Properties of the SIR model facilitates the use of dynamic message passing (DMP) and optimal control methods to investigate preventive and reactive budget-sharing scenarios. Our results show a large set of budget-sharing strategies in which the sharing community benefits from the reduced global infection rates with no detrimental impact on its local infection rate.
Operator estimates for homogenization of higher-order elliptic operators with periodic coefficients
Authors: Sloushch V. , Suslina T. 
Published: June 2024

In

L
2

(

R

d

;

C

n

)

L_2(\mathbb {R}^d;\mathbb {C}^n)

, a strongly elliptic differential operator

A

ε

{\mathcal {A}}_\varepsilon

of order

2
p

2p

is studied. Its coefficients are periodic and depend on

x

/

ε

\mathbf {x}/\varepsilon

. The resolvent

(

A

ε

+
I

)

−
1

({\mathcal {A}}_\varepsilon +I)^{-1}

is approximated in the operator norm on

L
2

(

R

d

;

C

n

)

L_2(\mathbb {R}^d;\mathbb {C}^n)

:

(

A

ε

+
I

)

−
1

=
(

A

0

+
I

)

−
1

+

∑

j
=
1

2
p
−
1

ε

j

K

j
,
ε

+
O
(

ε

2
p

)
.

\begin{equation*} ({\mathcal {A}}_\varepsilon +I)^{-1} = ({\mathcal {A}}^0+I)^{-1} + \sum _{j=1}^{2p-1} \varepsilon ^{j} {\mathcal {K}}_{j,\varepsilon } + O(\varepsilon ^{2p}). \end{equation*}

Here

A

0

{\mathcal {A}}^0

is an effective operator with constant coefficients, and

K

j
,
ε

{\mathcal {K}}_{j,\varepsilon }

,

j
=
1
,
…
,
2
p
−
1

j=1,\dots ,2p-1

, are appropriate correctors.
Chaplaincy and Seafarers
Authors: Sampson Helen , Turgo Nelson , Cadge Wendy , Gilliat-Ray Sophie 
Published: June 2024

AbstractThis book explores the faith, work, and lives of seafarers and port chaplains. These two groups of people are frequently overlooked by academics, as well as by members of wider society. Ports and ships are largely inaccessible to the public. As a result of their lack of visibility, many people are oblivious to the duties, needs, hopes, and aspirations of port chaplains and seafarers. This book therefore offers a rare insight into the life worlds of two little-known groups of workers. The book takes a broadly sociological approach and combines ethnographic and qualitative methodologies. It draws on the findings of a comprehensive study that was funded by the Economic and Social Research Council. The research involved the analysis of archive materials, fieldwork in ports and on cargo ships, and interviews with chaplains in the United Kingdom, chaplains overseas, and stakeholder organizations. Using these sources, the text provides a detailed account of seafarers’ attitudes to working in mixed-faith crews, their understandings of their own faith and its role and negotiation in a life at sea, and their needs with regard to faith and more general welfare support. In addition, it details the daily life and work of port chaplains and explains how they understand their roles in relation to their own faith, as well as how they manage their work in a multi-faith environment.
Introduction
Authors: Sampson Helen , Turgo Nelson , Cadge Wendy , Gilliat-Ray Sophie 
Published: June 2024

AbstractThe introduction begins by describing some of the key characteristics of the shipping industry. It explains the role of port chaplains in providing seafarers with support while they are working on board and the overall importance of port welfare providers to such seafarers. It describes the background, aims, and underpinning evidence for the book and describes the large, multifaceted study funded by the Economic and Social Research Council that took place in the period 2017–2021 on the life, work, faith, and welfare needs of seafarers. It outlines the structure of the book and provides a brief synopsis for each of the chapters.
The Work of Contemporary Port Chaplains
Authors: Sampson Helen , Turgo Nelson , Cadge Wendy , Gilliat-Ray Sophie 
Published: June 2024

AbstractChapter 2 presents a detailed account of the daily work of port chaplains. It describes their day-to-day activities and the assistance they provide to seafarers. The chapter describes some of the challenges they face in carrying out their work. These include the demanding nature of the work in relation to emotional labour, financial constraints, and ecumenical approaches to port welfare provision. Drawing upon field notes and the testimony of chaplains themselves (in the form of quotes from interview transcripts), the chapter offers a rich flavour of what it is that port chaplains do, how they do it, and the challenges which they face in trying to do their job.
Practical Ecumenical Cooperation amongst Organizations Providing Port Chaplaincy
Authors: Sampson Helen , Turgo Nelson , Cadge Wendy , Gilliat-Ray Sophie 
Published: June 2024

AbstractCaring for seafarers is a global collaborative effort between individuals working for organizations affiliated with secular and religious charities. Chapter 7 examines the ways that the charitable organizations supporting port chaplaincy have embraced ecumenism and ecumenical working practices and the consequences of this for the day-to-day work of port chaplains. A major initiative that has been taken by cash strapped charities has been to combine resources and co-locate service provision. Although working from the same building is economically efficient it has sometimes given rise to tensions between members of different welfare charities, which may be associated with individual personalities and also differing theologies. This chapter focuses on commonalities and differences between welfare workers from different organizations and how these play out in relation to the day-to-day work of port chaplains and the support that they provide to seafarers.
Comparison of caffeine consumption behavior with plasma caffeine levels as exposure measures in drug-target mendelian randomization
Authors: Woolf Benjamin , Cronjé Héléne T , Zagkos Loukas , Larsson Susanna C , Gill Dipender , Burgess Stephen 
Published: June 2024

Abstract
Mendelian randomization is an epidemiologic technique that can explore the potential effect of perturbing a pharmacological target. Plasma caffeine levels can be used as a biomarker to measure the pharmacological effects of caffeine. Alternatively, this can be assessed using a behavioral proxy, such as average number of caffeinated drinks consumed per day. Either variable can be used as the exposure in a Mendelian randomization investigation, and to select which genetic variants to use as instrumental variables. Another possibility is to choose variants in gene regions with known biological relevance to caffeine level regulation. These choices affect the causal question that is being addressed by the analysis, and the validity of the analysis assumptions. Further, even when using the same genetic variants, the sign of Mendelian randomization estimates (positive or negative) can change depending on the choice of exposure. Some genetic variants that decrease caffeine metabolism associate with higher levels of plasma caffeine, but lower levels of caffeine consumption, as individuals with these variants require less caffeine consumption for the same physiological effect. We explore Mendelian randomization estimates for the effect of caffeine on body mass index, and discuss implications for variant and exposure choice in drug target Mendelian randomization investigations.
Simple graphical rules for assessing selection bias in general-population and selected-sample treatment effects
Authors: Mathur Maya B , Shpitser Ilya 
Published: June 2024

Abstract
When analyzing a selected sample from a general population, selection bias can arise relative to the causal average treatment effect (ATE) for the general population, and also relative to the ATE for the selected sample itself. In this paper, we provide simple graphical rules that indicate (1) whether a selected-sample analysis will be unbiased for each ATE and (2) whether adjusting for certain covariates could eliminate selection bias. The rules can easily be checked in a standard single-world intervention graph. When the treatment could affect selection, a third estimand of potential scientific interest is the “net treatment difference”—namely the net change in outcomes that would occur for the selected sample if all members of the general population were treated versus not treated, including any effects of the treatment on which individuals are in the selected sample. We provide graphical rules for this estimand as well. We decompose bias in a selected-sample analysis relative to the general-population ATE into (1) “internal bias” relative to the net treatment difference and (2) “net-external bias,” a discrepancy between the net treatment difference and the general-population ATE. Each bias can be assessed unambiguously via a distinct graphical rule, providing new conceptual insight into the mechanisms by which certain causal structures produce selection bias.
Making proteomics accessible: Rokai
Xplorer for interactive analysis of phospho-proteomic data
Authors: Yılmaz Serhan , Blasco Tavares Pereira Lopes Filipa , Schlatzer Daniela , Ayati Marzieh , Chance Mark R , Koyutürk Mehmet 
Published: June 2024

Abstract

Summary
We present RokaiXplorer, an intuitive web tool designed to address the scarcity of user-friendly solutions for proteomics and phospho-proteomics data analysis and visualization. RokaiXplorer streamlines data processing, analysis, and visualization through an interactive online interface, making it accessible to researchers without specialized training in proteomics or data science. With its comprehensive suite of modules, RokaiXplorer facilitates phospho-proteomic analysis at the level of phosphosites, proteins, kinases, biological processes, and pathways. The tool offers functionalities such as data normalization, statistical testing, activity inference, pathway enrichment, subgroup analysis, automated report generation, and multiple visualizations, including volcano plots, bar plots, heat maps, and network views. As a unique feature, RokaiXplorer allows researchers to effortlessly deploy their own data browsers, enabling interactive sharing of research data and findings. Overall, RokaiXplorer fills an important gap in phospho-proteomic data analysis by providing the ability to comprehensively analyze data at multiple levels within a single application.

Availability and implementation
Access RokaiXplorer at: http://explorer.rokai.io.
DDN3.0: determining significant rewiring of biological network structure with differential dependency networks
Authors: Fu Yi , Lu Yingzhou , Wang Yizhi , Zhang Bai , Zhang Zhen , Yu Guoqiang , Liu Chunyu , Clarke Robert , Herrington David M , Wang Yue 
Published: June 2024

Abstract

Motivation
Complex diseases are often caused and characterized by misregulation of multiple biological pathways. Differential network analysis aims to detect significant rewiring of biological network structures under different conditions and has become an important tool for understanding the molecular etiology of disease progression and therapeutic response. With few exceptions, most existing differential network analysis tools perform differential tests on separately learned network structures that are computationally expensive and prone to collapse when grouped samples are limited or less consistent.

Results
We previously developed an accurate differential network analysis method—differential dependency networks (DDN), that enables joint learning of common and rewired network structures under different conditions. We now introduce the DDN3.0 tool that improves this framework with three new and highly efficient algorithms, namely, unbiased model estimation with a weighted error measure applicable to imbalance sample groups, multiple acceleration strategies to improve learning efficiency, and data-driven determination of proper hyperparameters. The comparative experimental results obtained from both realistic simulations and case studies show that DDN3.0 can help biologists more accurately identify, in a study-specific and often unknown conserved regulatory circuitry, a network of significantly rewired molecular players potentially responsible for phenotypic transitions.

Availability and implementation
The Python package of DDN3.0 is freely available at https://github.com/cbil-vt/DDN3. A user’s guide and a vignette are provided at https://ddn-30.readthedocs.io/.
GENTANGLE: integrated computational design of gene entanglements
Authors: Martí Jose Manuel , Hsu Chloe , Rochereau Charlotte , Xu Chenling , Blazejewski Tomasz , Nisonoff Hunter , Leonard Sean P , Kang-Yun Christina S , Chlebek Jennifer , Ricci Dante P , Park Dan , Wang Harris , Listgarten Jennifer , Jiao Yongqin , Allen Jonathan E 
Published: June 2024

Abstract

Summary
The design of two overlapping genes in a microbial genome is an emerging technique for adding more reliable control mechanisms in engineered organisms for increased stability. The design of functional overlapping gene pairs is a challenging procedure, and computational design tools are used to improve the efficiency to deploy successful designs in genetically engineered systems. GENTANGLE (Gene Tuples ArraNGed in overLapping Elements) is a high-performance containerized pipeline for the computational design of two overlapping genes translated in different reading frames of the genome. This new software package can be used to design and test gene entanglements for microbial engineering projects using arbitrary sets of user-specified gene pairs.

Availability and implementation
The GENTANGLE source code and its submodules are freely available on GitHub at https://github.com/BiosecSFA/gentangle. The DATANGLE (DATA for genTANGLE) repository contains related data and results and is freely available on GitHub at https://github.com/BiosecSFA/datangle. The GENTANGLE container is freely available on Singularity Cloud Library at https://cloud.sylabs.io/library/khyox/gentangle/gentangle.sif. The GENTANGLE repository wiki (https://github.com/BiosecSFA/gentangle/wiki), website (https://biosecsfa.github.io/gentangle/), and user manual contain detailed instructions on how to use the different components of software and data, including examples and reproducing the results. The code is licensed under the GNU Affero General Public License version 3 (https://www.gnu.org/licenses/agpl.html).
Surface-based multimodal protein–ligand binding affinity prediction
Authors: Xu Shiyu , Shen Lian , Zhang Menglong , Jiang Changzhi , Zhang Xinyi , Xu Yanni , Liu Juan , Liu Xiangrong 
Published: June 2024

Abstract

Motivation
In the field of drug discovery, accurately and effectively predicting the binding affinity between proteins and ligands is crucial for drug screening and optimization. However, current research primarily utilizes representations based on sequence or structure to predict protein–ligand binding affinity, with relatively less study on protein surface information, which is crucial for protein–ligand interactions. Moreover, when dealing with multimodal information of proteins, traditional approaches typically concatenate features from different modalities in a straightforward manner without considering the heterogeneity among them, which results in an inability to effectively exploit the complementary between modalities.

Results
We introduce a novel multimodal feature extraction (MFE) framework that, for the first time, incorporates information from protein surfaces, 3D structures, and sequences, and uses cross-attention mechanism for feature alignment between different modalities. Experimental results show that our method achieves state-of-the-art performance in predicting protein–ligand binding affinity. Furthermore, we conduct ablation studies that demonstrate the effectiveness and necessity of protein surface information and multimodal feature alignment within the framework.

Availability and implementation
The source code and data are available at https://github.com/Sultans0fSwing/MFE.
Conceptus estrogen and prostaglandins provide the maternal recognition of pregnancy signal to prevent luteolysis during early pregnancy in the pig
Authors: Sullivan Riley M , Lucas Caroline G , Sponchiado Mariana , Eitel Emily K , Spate Lee D , Lucy Matthew C , Smith Michael F , Wells Kevin D , Prather Randall S , Geisert Rodney D 
Published: June 2024

Abstract
Conceptus estrogens and prostaglandins have long been considered the primary signals for maternal recognition of pregnancy (MRP) in the pig. However, loss-of-function studies targeting conceptus aromatase genes (CYP19A1 and CYP19A2) and prostaglandin–endoperoxide synthase 2 (PTGS2) indicated that conceptuses can not only signal MRP without estrogens or prostaglandins but can maintain early pregnancy. However, complete loss of estrogen production leads to abortion after day 25 of gestation. Although neither conceptus estrogens nor prostaglandins had a significant effect on early maintenance of corpora lutea (CL) function alone, the two conceptus factors have a biological relationship. To investigate the role that both conceptus estrogens and prostaglandins have on MRP and maintenance of pregnancy, a triple loss-of function model (TKO) was generated for conceptus CYP19A1, CYP19A2, and PTGS2. In addition, a conceptus CYP19A2−/− model (A2KO) was established to determine the role of placental estrogen during later pregnancy. Estrogen and prostaglandin synthesis were greatly reduced in TKO concept uses which resulted in a failure to inhibit luteolysis after day 15 of pregnancy despite the presence of conceptuses in the uterine lumen. However, A2KO placentae not only maintained functional CL but were able to maintain pregnancy to day 32 of gestation. Despite the loss of placental CYP19A2 expression, the allantois fluid content of estrogen was not affected as the placenta compensated by expressing CYP19A1 and CYP19A3, which are normally absent in controls. Results suggest conceptuses can signal MRP through production of conceptus PGE or stimulating PGE synthesis from the endometrium through conceptus estrogen. Failure of conceptuses to produce both factors results in failure of MRP and loss of pregnancy.