bluuebunny/crossref_metadata_2025_split huggingface dataset:
‘This Is Our Cuba’
Authors: Tendi Blessing-Miles 
Published: January 2025

Abstract
This chapter interrogates arguments that China contributed to or sponsored Zimbabwe’s 2017 coup. It maintains that arguments that point out possible Chinese involvement in, support for, or foreknowledge of the coup rest on a narrow evidential base. Scholars who pinpoint likely Chinese participation in the coup ignore informative literature on China’s approaches to coups, which tells us that China by and large does not have a history of engineering coups in Africa. The chapter also argues there was a history, going back to the early 2000s, of covert action by Britain in Zimbabwe, which sometimes sought to use military power to bring about an end to Mugabe’s presidency. This history of covert action does not, by itself, substantiate suggestions Britain was involved in Mugabe’s fall from power in 2017, but it does provide a valuable backdrop to debates about the role Britain might have played in the successful 2017 coup.
Exploring the potential of compound–protein complex structure-free models in virtual screening using BlendNet
Authors: Seo Sangmin , Kim Hwanhee , Lee Jieun , Choi Seungyeon , Park Sanghyun 
Published: January 2025

Abstract
Identifying new compounds that interact with a target is a crucial time-limiting step in the initial phases of drug discovery. Compound–protein complex structure-based affinity prediction models can expedite this process; however, their dependence on high-quality three-dimensional (3D) complex structures limits their practical application. Prediction models that do not require 3D complex structures for binding-affinity estimation offer a theoretically attractive alternative; however, accurately predicting affinity without interaction information presents significant challenges. We introduce BlendNet, a framework that employs a knowledge transfer strategy to improve affinity prediction accuracy by learning the interdependent relationships between compounds and proteins without relying on 3D complex structures. Compared with state-of-the-art models for affinity prediction, BlendNet demonstrated superior performance across various cold-start cases. The ability of BlendNet to interpret compound–protein interactions without utilizing complex structure data highlights its potential to accelerate and streamline drug development.
PHIStruct: improving phage–host interaction prediction at low sequence similarity settings using structure-aware protein embeddings
Authors: Gonzales Mark Edward M , Ureta Jennifer C , Shrestha Anish M S 
Published: January 2025

Abstract

Motivation
Recent computational approaches for predicting phage–host interaction have explored the use of sequence-only protein language models to produce embeddings of phage proteins without manual feature engineering. However, these embeddings do not directly capture protein structure information and structure-informed signals related to host specificity.

Results
We present PHIStruct, a multilayer perceptron that takes in structure-aware embeddings of receptor-binding proteins, generated via the structure-aware protein language model SaProt, and then predicts the host from among the ESKAPEE genera. Compared against recent tools, PHIStruct exhibits the best balance of precision and recall, with the highest and most stable F1 score across a wide range of confidence thresholds and sequence similarity settings. The margin in performance is most pronounced when the sequence similarity between the training and test sets drops below 40%, wherein, at a relatively high-confidence threshold of above 50%, PHIStruct presents a 7%–9% increase in class-averaged F1 over machine learning tools that do not directly incorporate structure information, as well as a 5%–6% increase over BLASTp.

Availability and implementation
The data and source code for our experiments and analyses are available at https://github.com/bioinfodlsu/PHIStruct.
Causal inference with cross-temporal design
Authors: Cao Yi , Gozalo Pedro L , Gutman Roee 
Published: January 2025

ABSTRACT
When many participants in a randomized trial do not comply with their assigned intervention, the randomized encouragement design is a possible solution. In this design, the causal effects of the intervention can be estimated among participants who would have experienced the intervention if encouraged. For many policy interventions, encouragements cannot be randomized and investigators need to rely on observational data. To address this, we propose a cross-temporal design, which uses time to mimic a randomized encouragement experiment. However, time may be confounded with temporal trends that influence the outcomes. To disentangle these trends from the intervention effects, we replace the commonly used exclusion restrictions with temporal assumptions. We develop Bayesian procedures to estimate the causal effects and compare it to instrumental variables and matching approaches in simulations. The Bayesian approach outperforms the other 2 approaches in terms of estimation accuracy, and it is relatively robust to various violations of the common trends assumption. Taking advantage of the expansion of the Medicare Advantage (MA) program between 2011 and 2017, we implement the proposed method to estimate the effects of MA enrollment on the risk of skilled nursing facility residents being re-hospitalized within 30 days after discharge from the hospital.
The impact of phenotypic heterogeneity on fungal pathogenicity and drug resistance
Authors: Kozubowski Lukasz , Berman Judith 
Published: January 2025

Abstract
Phenotypic heterogeneity in genetically clonal populations facilitates cellular adaptation to adverse environmental conditions while enabling a return to the basal physiological state. It also plays a crucial role in pathogenicity and the acquisition of drug resistance in unicellular organisms and cancer cells, yet the exact contributing factors remain elusive. In this review, we outline the current state of understanding concerning the contribution of phenotypic heterogeneity to fungal pathogenesis and antifungal drug resistance.
Unveiling patterns in spatial transcriptomics data: a novel approach utilizing graph attention autoencoder and multiscale deep subspace clustering network
Authors: Zhou Liqian , Peng Xinhuai , Chen Min , He Xianzhi , Tian Geng , Yang Jialiang , Peng Lihong 
Published: January 2025

Abstract

Background
The accurate deciphering of spatial domains, along with the identification of differentially expressed genes and the inference of cellular trajectory based on spatial transcriptomic (ST) data, holds significant potential for enhancing our understanding of tissue organization and biological functions. However, most of spatial clustering methods can neither decipher complex structures in ST data nor entirely employ features embedded in different layers.

Results
This article introduces STMSGAL, a novel framework for analyzing ST data by incorporating graph attention autoencoder and multiscale deep subspace clustering. First, STMSGAL constructs ctaSNN, a cell type–aware shared nearest neighbor graph, using Louvian clustering exclusively based on gene expression profiles. Subsequently, it integrates expression profiles and ctaSNN to generate spot latent representations using a graph attention autoencoder and multiscale deep subspace clustering. Lastly, STMSGAL implements spatial clustering, differential expression analysis, and trajectory inference, providing comprehensive capabilities for thorough data exploration and interpretation. STMSGAL was evaluated against 7 methods, including SCANPY, SEDR, CCST, DeepST, GraphST, STAGATE, and SiGra, using four 10x Genomics Visium datasets, 1 mouse visual cortex STARmap dataset, and 2 Stereo-seq mouse embryo datasets. The comparison showcased STMSGAL’s remarkable performance across Davies–Bouldin, Calinski–Harabasz, S_Dbw, and ARI values. STMSGAL significantly enhanced the identification of layer structures across ST data with different spatial resolutions and accurately delineated spatial domains in 2 breast cancer tissues, adult mouse brain (FFPE), and mouse embryos.

Conclusions
STMSGAL can serve as an essential tool for bridging the analysis of cellular spatial organization and disease pathology, offering valuable insights for researchers in the field.
Unlocking the potential of palm tree starch: A review on Modification techniques and its application
Authors: Supreethee Srihari , Vashisth Rahul 
Published: January 2025

Abstract
Palm starch is an underutilised and unconventional resource gaining popularity globally due to its health-promoting properties. However, native starch often falls short in areas such as retrogradation during gelatinisation, instability at high temperatures, and acidic conditions, limiting its functionality in the food industry. Modifications are necessary to enhance the performance of native starch and broaden its applications across food and other industries. The technological implications of its underutilisation remain under investigation. This review offers a comprehensive summary of starch modifications across different palm varieties within the same family, utilising various techniques, including chemical, thermal, and non-thermal methods. It examines the resulting changes in physicochemical properties, granular and molecular structures, and the applications of these starches. Additionally, the impact of these modification techniques on starch-rich food systems such as Palmyra sprout, kithul starch, talipot starch, and sago starch is reviewed. The use of modified starches in developing biodegradable packaging film is also discussed. This review thoroughly explores the physicochemical, morphological, and rheological traits of both native and modified palm starch.
Lactobacillus fermentum KP101 fermentation broth improves high-fat diet-induced hyperlipidemia in mice by modulation of liver lipid metabolism and intestinal flora dysbiosis
Authors: Wang Chao , Nan Bo , Wang Yu , Zhang Nan , Zhang Yue , Xing Xin-yue , Wei Shan-shan , Meng Xiang-hui , Li Xia , Wang Yu-hua 
Published: January 2025

Abstract
Non-alcoholic fatty liver disease (NAFLD) is a primary chronic liver ailment around the world, posing a significant threat to human health. Probiotics, living microorganisms that enhance intestinal flora equilibrium and mitigate blood lipid levels. This study aimed to identify probiotics with excellent antioxidant capacity from naturally fermented foods, and investigate their potential mechanisms in relieving high-fat diet (HFD)-induced liver injury and modulating intestinal flora balance. These findings fundamentally benefit the advancement of functional probiotic foods. Lactobacillus fermentum KP101, isolated from kimchi, was evaluated for its antioxidant activity. Assessment of HFD-induced liver injury was based on the biochemical markers, protein expression levels, and liver histopathology. L. fermentum KP101 remarkably reduced mice serum and liver levels of TC, TG, LDL, ALT, and AST. L. fermentum KP101 intervention effectively modulated HFD-induced dyslipidemia and activated the AMPK signalling pathway to alleviate liver injury. Specifically, the protein expression levels of SREBP-1 and p-ACC presented an obvious reduction, while the expression of p-AMPK and PPARα was notably increased following L. fermentum KP101 treatment. Moreover, L. fermentum KP101 effectively mitigated intestinal flora dysbiosis in HFD-fed mice. In summary, L. fermentum KP101 demonstrated efficacy in improving hyperlipidemia and liver metabolic disorders in mice with HFD-induced conditions.
Exploration of interprofessional collaboration for the diagnosis of infections and antibiotic prescription in nursing homes using multiple case study observational research
Authors: Gonthier Damien , Ricci Laetitia , Buzzi Marie , Birgand Gabriel , Kivits Joëlle , Agrinier Nelly 
Published: January 2025

Abstract

Background
Antibiotic resistance in nursing homes (NHs) is inconsistently tackled by antimicrobial stewardship programmes. The literature on individual determinants of antibiotic prescriptions (APs) in NHs is extensive. However, less is known about the structural determinants of AP in NHs.

Objectives
To examine how different organizational contexts influenced interprofessional collaboration in the diagnosis and treatment of infections in NHs.

Methods
We conducted multiple case study observational research through field notes and sketches from pictures of NH layouts.

Results
We observed three NHs for 10 days (i.e. 82 h). We inductively identified four successive steps: (i) trigger by an assistant nurse, (ii) internal decision-making, (iii) calling on an external general practitioner (GP) and (iv) GP intervention. Diagnosis and treatment of infections involved various degrees of interprofessional collaboration within NHs, resulting in a range of actions, more or less directly involving AP by external GPs. In the case of onsite AP, external GPs barely relied on information about residents provided by NH professionals and did not provide any feedback regarding their decision, resulting in limited interprofessional collaboration. In contrast, remote AP (through phone calls) relied on interprofessional collaboration through mandatory exchanges between external GPs and NH nurses about the resident’s symptoms and signs.

Conclusions
Diagnosis and treatment of infections through AP involved two distinct organization types (institutional versus private practices) and often lacked interprofessional collaboration. Future antimicrobial stewardship in NHs should consider (i) improving the connection between these two organizations and (ii) developing tools to support remote interprofessional collaboration to sustain prescription.
A scoping review of the reporting quality of reviews of commercially and publicly available mobile health apps
Authors: Gasteiger Norina , Norman Gill , Grainger Rebecca , van der Veer Sabine N , McGarrigle Lisa , Jones Debra , Eost-Telling Charlotte , Vercell Amy , Ford Claire R , Ali Syed Mustafa , Law Kate , Zhao Qimeng , Byerly Matthew , Shi Chunhu , Davies Alan , Hall Alex , Dowding Dawn 
Published: January 2025

Abstract

Objectives
There is no guidance to support the reporting of systematic reviews of mobile health (mhealth) apps (app reviews), so authors attempt to use/modify the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). There is a need for reporting guidance, building on PRISMA where appropriate, tailored to app reviews. The objectives were to describe the reporting quality of published mHealth app reviews, identify the need for, and develop potential candidate items for a reporting guideline.

Materials and Methods
A scoping review following the Joanna Briggs Institute and Arksey and O’Malley approaches. App reviews were identified in January 2024 from SCOPUS, CINAHL, AMED, EMBASE, Medline, PsycINFO, ACM Digital Library, snowballing reference lists, and forward citation searches. Data were extracted into Excel and analyzed using descriptive statistics and content synthesis, using PRISMA items as a framework.

Results
One hundred and seventy-one app reviews were identified, published from 2013 to 2024. Protocols were developed for 11% of the reviews, and only 52% reported the geographical location of the app markets. Few reported the duplicate removal process (12%), device and operating system used (30%), or made clear recommendations for the best-rated apps (18%). Nineteen PRISMA items were not reported by most (&gt;85%) reviews, and 4 were modified by &gt;30% of the reviews. Involvement of patient/public contributors (4%) or other stakeholders (11%) was infrequent. Overall, 34 candidate items and 10 subitems were identified to be considered for a new guideline.

Discussion and Conclusion
App reviews were inconsistently reported, and many PRISMA items were not deemed relevant. Consensus work is needed to revise and prioritize the candidate items for a reporting guideline for systematic app reviews.
The effect of calcium supplementation on bone calcium balance and calcium and bone metabolism during load carriage in women: a randomised controlled crossover trial
Authors: Coombs Charlotte V , Greeves Julie P , Young Christina D , Irving Alice S , Eisenhauer Anton , Kolevica Ana , Heuser Alexander , Tang Jonathan C Y , Fraser William D , O’Leary Thomas J 
Published: January 2025

Abstract
Calcium supplementation before exercise attenuates the decrease in serum calcium and increase in PTH and bone resorption. This study investigated the effect of calcium supplementation on calcium and bone metabolism during load carriage in women. Forty-eight women completed two load carriage sessions (load carriage 1 n = 48; load carriage 2 n = 40) (12.8 km in 120 min carrying 20 kg) 60 min after consuming either 1000 mg calcium (Calcium) or nothing (Control) in a randomised order. Pre- and post-exercise urine samples were analysed for calcium isotope ratio (δ44/42Ca). Fasted blood samples were taken before (pre-exercise), during (0, 20, 40, 60, 80, 100, 120 min), and after (+15, +30, +60, +90 min) exercise and analysed for markers of calcium and bone metabolism. There was no effect of load carriage or supplementation on urine δ44/42Ca (P≥.110). Serum δ44/42Ca did not change with load carriage in Control (P=.617) but increased in Calcium (P=.003) and was higher at 120 min in Calcium vs Control (P=.018). Ionised calcium (iCa) decreased from pre-exercise to all exercise time-points (P&lt;.001); iCa was higher in Calcium than Control throughout (P&lt;.001). PTH increased from pre-exercise to 120 min in Control (P&lt;.001) but decreased from pre-exercise to all time-points in Calcium (P&lt;.001). PTH was higher in Control than Calcium from 0 to +90 min (P&lt;.001). βCTX decreased from pre-exercise to 20 to +15 min in Control (P≤.004); βCTX decreased from pre-exercise to 0 to +90 min in Calcium (P&lt;.001). βCTX was lower in Calcium than Control from 20 to +90 min (P≤.036). A 1000 mg calcium supplement before load carriage promotes bone calcium balance and prevents disruptions to bone and calcium homeostasis.
Treating Opium Addiction in China: Medical Missionaries, Chinese Medicine, and the State, 1830-1910
Authors: Zheng Shihan 
Published: January 2025

Abstract
From the 1830s onward, Euro-American medicine began addressing opium addiction among the Chinese population. Drawing upon records from medical missionaries, medical journals, and related Chinese sources, this article examines the transformation of opium addiction treatment in late Qing China (1830-1910). Despite their pioneering efforts, medical missionaries encountered various challenges in gaining cooperation from patients and Chinese authorities. In contrast, Chinese medical practitioners, particularly elite scholar-physicians, enjoyed favor with the Qing government throughout much of the nineteenth century. By the turn of the twentieth century, the scientific knowledge introduced by the missionaries had gained greater acceptance in the country. By creatively translating this knowledge, Chinese medical practitioners began to recognize new theories for addressing the opium problem.
Physics-Based Synthetic Data Model for Automated Segmentation in Catalysis Microscopy
Authors: Vuijk Maurits , Ducci Gianmarco , Sandoval Luis , Pietsch Markus , Reuter Karsten , Lunkenbein Thomas , Scheurer Christoph 
Published: January 2025

Abstract
In catalysis research, the amount of microscopy data acquired when imaging dynamic processes is often too much for nonautomated quantitative analysis. Developing machine learned segmentation models is challenged by the requirement of high-quality annotated training data. We thus substitute expert-annotated data with a physics-based sequential synthetic data model. We study environmental scanning electron microscopy (ESEM) data collected from isopropanol oxidation to acetone over cobalt oxide as an example. Upon applying a temperature program during the reaction a phase transition occurs, reducing the catalyst selectivity toward acetone. This is accompanied on the micrometer ESEM scale by the formation of cracks between the pores of the catalyst surface. We aim to generate synthetic data to train a neural network capable of semantic segmentation (pixel-wise labeling) of this ESEM data. This analysis will lead to insights into this phase transition. To generate synthetic data that approximates this transition, our algorithm composes the ESEM images of the room-temperature catalyst with dynamically evolving synthetic cracks satisfying physical construction principles, gathered from qualitative knowledge accessible in the ESEM data. We mimic the surface crack growth propagation along surface paths, avoiding close vicinity to nearby pores. This physics-based approach results in a lowered rate of false positives compared to a random approach.
Maternal exercise before and during pregnancy protects against genotoxicity and promotes offspring hippocampal health in mice prenatally exposed to high fructose
Authors: Magenis Marina Lummertz , de Oliveira Monteiro Isadora , Damiani Adriani Paganini , Dagostin Ligia Salvan , Possamai Otávio Lúcio , Medeiros Eduarda Behenck , Budni Josiane , Bittencourt João Vitor Silvano , Mendes Carolini , Silveira Paulo Cesar Lock , Garcia Ana Letícia Hilario , da Silva Juliana , de Feveri Wanessa , Langie Sabine A S , Godschalk Roger , de Andrade Vanessa Moraes 
Published: January 2025

Abstract
The fetal brain is susceptible to programming effects during pregnancy, potentially leading to long-term consequences for offspring’s cognitive health. Fructose (FRU) intake is thought to adversely affect fetal brain development, whereas physical exercise before and during pregnancy may be protective. Therefore, this study aimed to assess biochemical and genotoxic changes in maternal hippocampi and behavioral, genotoxic, and biochemical alterations in offspring hippocampi. Seventy female mice were exposed to FRU (20%/L) and/or voluntary physical exercise (VPE) pre-pregnancy for eight weeks, and then mated and exposure was continued until weaning. Offspring were evaluated at 60 days old using behavioral test, genotoxic, and biochemical markers. FRU-induced long-term memory impairment in male offspring, which was alleviated by VPE. VPE mitigated DNA damage from maternal FRU consumption in both maternal and offspring hippocampi in female offspring, VPE increased levels of apurine/apyrimidinic endonuclease 1, erythroid nuclear factor 2, and cAMP response element binding proteins, whereas in males, 8-oxoguanine DNA glycosylase-1 levels upregulate. FRU consumption led to oxidative stress and antioxidant defense alterations in offspring, while VPE mitigated these effects. Telomere shortening was observed in male offspring from mothers who consumed FRU during pregnancy. Our findings suggest that exposure to FRU during (pre)pregnancy and lactation has adverse effects on offspring’s hippocampi later in life, and VPE has a protective effect. Overall, the study underscores the significance of maternal dietary and physical habits on long-term offspring health, with an emphasis on implications for adult cognitive function.