bluuebunny/crossref_metadata_2025_split huggingface dataset:
Challenges and care strategies associated with the admission to nursing homes in Germany: a scoping review
Authors: Skudlik Stefanie , Hirt Julian , Döringer Tobias , Thalhammer Regina , Lüftl Katharina , Prodinger Birgit , Müller Martin 
Published: January 2023

Abstract
Background
The admission to a nursing home is a critical life-event for affected persons as well as their families. Admission related processes are lacking adequate participation of older people and their families. To improve transitions to nursing homes, context- and country-specific knowledge about the current practice is needed. Hence, our aim was to summarize available evidence on challenges and care strategies associated with the admission to nursing homes in Germany.

Methods
We conducted a scoping review and searched eight major international and German-specific electronic databases for journal articles and grey literature published in German or English language since 1995. Further inclusion criteria were focus on challenges or care strategies in the context of nursing home admissions of older persons and comprehensive and replicable information on methods and results. Posters, only-abstract publications and articles dealing with mixed populations including younger adults were excluded. Challenges and care strategies were identified and analysed by structured content analysis using the TRANSCIT model.

Results
Twelve studies of 1,384 records were finally included. Among those, seven were qualitative studies, three quantitative observational studies and two mixed methods studies. As major challenges neglected participation of older people, psychosocial burden among family caregivers, inadequate professional cooperation and a lack of shared decision-making and evidence-based practice were identified. Identified care strategies included strengthening shared decision-making and evidence-based practice, improvement in professional cooperation, introduction of specialized transitional care staff and enabling participation for older people.

Conclusion
Although the process of nursing home admission is considered challenging and tends to neglect the needs of older people, little research is available for the German health care system. The perspective of the older people seems to be underrepresented, as most of the studies focused on caregivers and health professionals. Reported care strategies addressed important challenges, however, these were not developed and evaluated in a comprehensive and systematic way. Future research is needed to examine perspectives of all the involved groups to gain a comprehensive picture of the needs and challenges. Interventions based on existing care strategies should be systematically developed and evaluated to provide the basis of adequate support for older persons and their informal caregivers.
Prolonged anesthesia induces neuroinflammation and complement-mediated microglial synaptic elimination involved in neurocognitive dysfunction and anxiety-like behaviors
Authors: Xu Feng , Han Linlin , Wang Yafeng , Deng Daling , Ding Yuanyuan , Zhao Shuai , Zhang Qingtong , Ma Lulin , Chen Xiangdong 
Published: January 2023

Abstract
Background
Perioperative neurocognitive disorders (PND) with a high incidence frequently occur in elderly surgical patients closely associated with prolonged anesthesia-induced neurotoxicity. The neuromorphopathological underpinnings of anesthesia-induced neurotoxicity have remained elusive.

Methods
Prolonged anesthesia with sevoflurane was used to establish the sevoflurane-induced neurotoxicity (SIN) animal model. Morris water maze, elevated plus maze, and open field test were employed to track SIN rats’ cognitive behavior and anxiety-like behaviors. We investigated the neuropathological basis of SIN through techniques such as transcriptomic, electrophysiology, molecular biology, scanning electron microscope, Golgi staining, TUNEL assay, and morphological analysis. Our work further clarifies the pathological mechanism of SIN by depleting microglia, inhibiting neuroinflammation, and C1q neutralization.

Results
This study shows that prolonged anesthesia triggers activation of the NF-κB inflammatory pathway, neuroinflammation, inhibition of neuronal excitability, cognitive dysfunction, and anxiety-like behaviors. RNA sequencing found that genes of different types of synapses were downregulated after prolonged anesthesia. Microglial migration, activation, and phagocytosis were enhanced. Microglial morphological alterations were also observed. C1qa, the initiator of the complement cascade, and C3 were increased, and C1qa tagging synapses were also elevated. Then, we found that the “Eat Me” complement pathway mediated microglial synaptic engulfment in the hippocampus after prolonged anesthesia. Afterward, synapses were remarkably lost in the hippocampus. Furthermore, dendritic spines were reduced, and their genes were also downregulated. Depleting microglia ameliorated the activation of neuroinflammation and complement and rescued synaptic loss, cognitive dysfunction, and anxiety-like behaviors. When neuroinflammatory inhibition or C1q neutralization occurred, complement was also decreased, and synaptic elimination was interrupted.

Conclusions
These findings illustrated that prolonged anesthesia triggered neuroinflammation and complement-mediated microglial synaptic engulfment that pathologically caused synaptic elimination in SIN. We have demonstrated the neuromorphopathological underpinnings of SIN, which have direct therapeutic relevance for PND patients.
Development of a workflow for the detection of vancomycin-resistant Enterococcus faecium and Enterococcus faecalis from rectal swabs using the spectra VRE medium
Authors: Kling Kendall , Rios Javier , Dirnberger Laura , Polanco Wanda , Fritz Kevin , Malczynski Michael , Zembower Teresa , Qi Chao 
Published: January 2023

Abstract
Background
Spectra™ VRE agar (Remel, Lenexa, KS) is a chromogenic agar that is FDA approved for screening patients for VRE colonization. The package insert recommends confirming isolates with identification and susceptibility testing, but confirming every culture delays time to result. Given the agar’s historic high specificity for E. faecium isolates, we theorized the agar could be utilized as a stand-alone screening to minimize reagents and time.

Aim
Our laboratory sought to develop a workflow to optimize the use of the medium.

Methods
We plated 3,815 rectal swabs to the Spectra VRE agar and compared results to traditional identification and susceptibility testing.

Results
Dark blue or purple colonies on the agar demonstrated a sensitivity of 98% and specificity of 85% for detection of VRE faecium, but light blue colonies were significantly less specific for E. faecalis.

Conclusions
We streamlined our workflow to accept dark blue or purple colonies as VRE faecium and plan to perform additional testing only on light blue colonies. Interestingly, higher quantity of growth increased the accuracy of the agar. In the future, growth quantity may be used to further streamline the workflow once more data is obtained.
Breastfeeding in the first hour of life in Brazilian private hospitals participating in a quality-of-care improvement project
Authors: Alves Rachael de Vasconcelos , de Oliveira Maria Inês Couto , Domingues Rosa Maria Soares Madeira , Pereira Ana Paula Esteves , Leal Maria do Carmo 
Published: January 2023

Abstract
Background
The Baby-Friendly Hospital Initiative’s Step 4 recommends: “support mothers to start breastfeeding as soon as possible after birth”, thus contributing to the reduction of neonatal mortality. The objective of this study is to estimate the prevalence of breastfeeding in the first hour of life in private maternity hospitals participating in the “Adequate Childbirth Project”, a quality-of-care improvement project, and to analyze determinants of this outcome.

Methods
Secondary analysis of data collected by the cross-sectional evaluative “Healthy Birth Study”, conducted in 2017 in 12 maternity hospitals participating in the Adequate Childbirth Project, where 4800 mothers were interviewed, and hospital records were observed. Conditions that prevented breastfeeding at birth, such as maternal HIV-infection and newborns’ severe malformations, were excluded. Multiple logistic regression was performed according to a hierarchical theoretical model.

Results
The prevalence of breastfeeding in the first hour of life was 58% (CI 95% 56.6–59.5%). Lower maternal education (aOR 0.643; CI 95% 0.528–0.782), lower economic status (aOR 0.687; CI 95% 0.504–0.935), cesarean section delivery (ORa 0.649; CI 95% 0.529–0.797), preterm birth (aOR 0.660; CI 95% 0.460–0.948) and non-rooming-in at birth (aOR 0.669; CI 95% 0.559–0.800) were negatively associated with the outcome. Receiving information during prenatal care about the importance of breastfeeding at birth (aOR 2.585; CI 95% 2.102–3.179), being target of the quality-of-care improvement project (aOR 1.273; CI 95% 1.065–1.522), skin-to-skin contact at birth (aOR 2.127; CI 95% 1.791–2.525) and female newborn (aOR 1.194; CI 95% 1.008–1.415) were factors positively associated with the outcome.

Conclusions
The private maternities participating in the Healthy Birth Study showed a good prevalence of breastfeeding in the first hour of life, according to WHO parameters. Prenatal guidance on breastfeeding at birth, being target of the quality-of-care improvement project and skin-to-skin contact at birth contributed to breastfeeding in the first hour of life.
Gut microbiome and stages of diabetes in middle-aged adults: CARDIA microbiome study
Authors: Hu Yi-Han , Meyer Katie , Lulla Anju , Lewis Cora E. , Carnethon Mercedes R. , Schreiner Pamela J. , Sidney Stephen , Shikany James M. , Meirelles Osorio , Launer Lenore J. 
Published: January 2023

AbstractBackgroundAnimal and human studies suggest the gut microbiome is linked to diabetes but additional data are needed on the associations of the gut microbiome to specific diabetes characteristics. The aim of this study was to examine the associations of gut microbiome composition to insulin resistance [Homeostatic Model Assessment of Insulin Resistance (HOMA-IR)], duration of diabetes, and 4 stages of diabetes [normoglycemia, pre-diabetes, and diabetes with (+) and without (−) medication for diabetes].MethodsData are from a sub-sample (n = 605) of Black and White participants from the 30-year follow-up exam of the prospectively followed community-based Coronary Artery Risk Development in Young Adults cohort (2015–2016; aged 48–60 years). Stool samples were collected and sequenced using the 16S ribosomal RNA method. Microbial measures included: α diversity (within-person), β diversity (between-person), and taxonomies. All analyses were adjusted for demographic, clinical, lifestyle factors, and use of relevant medications (full adjustment). Multivariate linear regression models were used to assess the association of diabetes characteristics with α diversity and genera abundance, while the association with β diversity was analyzed using permutational multivariate analysis of variance. Statistical significance was set top-value < 0.05 for α and β diversity analyses and to q-value < 0.1 for genera abundance analyses.ResultsThere were 16.7% of participants with pre-diabetes, and 14.4% with diabetes (9% diabetes+) with median (interquartile range) diabetes duration of 5 (5–10) years. In the fully adjusted models, compared to those with no diabetes, longer diabetes duration and the diabetes + group had a lower α diversity. There were significant differences in β diversity across diabetes-related characteristics. A significantly reduced abundance of butyrate-producing genera was associated with higher HOMA-IR (ex.,AnaerostipesandLachnospiraceae_UCG.004), longer diabetes duration (ex.,AgathobacterandRuminococcus), and diabetes + (ex.,FaecalibacteriumandRomboutsia).ConclusionsOur results suggest that an adverse alteration of gut microbiome composition is related to higher insulin resistance, longer diabetes duration, and is present in those persons with diabetes using medications. These diabetes-related characteristics were also associated with lower levels of certain butyrate-producing bacteria that produce health-promoting short‐chain fatty acids. Understanding the role of gut microbiota in glucose regulation may provide new strategies to reduce the burden of diabetes.
Towards the rate limit of heterologous biotechnological reactions in recombinant cyanobacteria
Authors: Barone Giovanni Davide , Hubáček Michal , Malihan-Yap Lenny , Grimm Hanna C. , Nikkanen Lauri , Pacheco Catarina C. , Tamagnini Paula , Allahverdiyeva Yagut , Kourist Robert 
Published: January 2023

AbstractBackgroundCyanobacteria have emerged as highly efficient organisms for the production of chemicals and biofuels. Yet, the productivity of the cell has been low for commercial application. Cyanobacterial photobiotransformations utilize photosynthetic electrons to form reducing equivalents, such as NADPH-to-fuel biocatalytic reactions. These photobiotransformations are a measure to which extent photosynthetic electrons can be deviated toward heterologous biotechnological processes, such as the production of biofuels. By expressing oxidoreductases, such as YqjM fromBacillus subtilisinSynechocystissp. PCC 6803, a high specific activity was obtained in the reduction of maleimides. Here, we investigated the possibility to accelerate the NAD(P)H-consuming redox reactions by addition of carbohydrates as exogenous carbon sources such as D-Glucose under light and darkness.ResultsA 1.7-fold increase of activity (150 µmol min−1gDCW−1) was observed upon addition of D-Glucose at an OD750 = 2.5 (DCW = 0.6 g L−1) in the biotransformation of 2-methylmaleimide. The stimulating effect of D-Glucose was also observed at higher cell densities in light and dark conditions as well as in the reduction of other substrates. No increase in both effective photosynthetic yields of Photosystem II and Photosystem I was found upon D-Glucose addition. However, we observed higher NAD(P)H fluorescence when D-Glucose was supplemented, suggesting increased glycolytic activity. Moreover, the system was scaled-up (working volume of 200 mL) in an internally illuminated Bubble Column Reactor exhibiting a 2.4-fold increase of specific activity under light-limited conditions.ConclusionsResults show that under photoautotrophic conditions at a specific activity of 90 µmol min−1 gDCW−1, the ene-reductase YqjM inSynechocystissp. PCC 6803 is not NAD(P)H saturated, which is an indicator that an increase of the rates of heterologous electron consuming processes for catalysis and biofuel production will require funnelling further reducing power from the photosynthetic chain toward heterologous processes.
Afoxolaner (NexGard®) in pet snakes for the treatment and control of Ophionyssus natricis (Mesostigmata: Macronyssidae)
Authors: Mendoza-Roldan Jairo Alfonso , Napoli Ettore , Perles Livia , Marino Matteo , Spadola Filippo , Berny Philippe , España Bernadette , Brianti Emanuele , Beugnet Frederic , Otranto Domenico 
Published: January 2023

AbstractBackgroundOphionyssus natricisis the main species of mite that infests captive reptiles. High infestations may result in the host experiencing general discomfort and deleterious effects, even death. Moreover,O. natricisis an important vector of reptile vector-borne diseases and is considered to be the putative vector of theReptarenavirus,the causal agent of the inclusion body disease. Despite the cosmopolitan distribution ofO. natricisin captive reptiles, treatment options are limited. The aim of the present study was to assess the efficacy of afoxolaner (NexGard®; Boehringer Ingelheim, Ingelheim, Germany) in heavily infested, privately owned snakes, evaluate the prevalence of mites and drug availability in the plasma of treated snakes (pharmacokinetics) and perform a clinical examination of animals.MethodsThe study was conducted in two snake breeding facilities, where many snakes were infested with mites. Each animal was clinically examined and weighed, and mite infestations were assessed on the animals and in their enclosures (environment). Animals were treated with a dose of 2.5 mg afoxolaner per kilogram body weight (2.5 mg/kg) administered orally. All animals were examined pre-treatment (T0) and at various time points post-treatment (T1, 6 h; T2, 24 h; T3, 14 days; T4, 28 days). The collected mites were morphologically identified at the species level and the species identity also confirmed molecularly.ResultsOverall, 81 snakes from the two participating facilities (i.e. 70 from site 1 and 11 from site 2) were screened, and 31 (38.3%) snakes were found to have at least one mite. All mites were identified morphologically and molecularly asO. natricis. Lampropeltiswas the genus of snakes with highest number of infested individuals. Mites were found to be alive on snakes at T1, but at T2 only dead mites were observed, and at T3 and T4 mites were no longer present on the animals or in their environment. No side effects were observed in the treated snakes.ConclusionsA single oral administration of afoxolaner at 2.5 mg/kg was a safe treatment for snakes and 100% effective for the eradication of naturalO. natricisinfestation without the need to treat the environment of the snake.Graphical Abstract
Papyrus: a large-scale curated dataset aimed at bioactivity predictions
Authors: Béquignon O. J. M. , Bongers B. J. , Jespers W. , IJzerman A. P. , van der Water B. , van Westen G. J. P. 
Published: January 2023

AbstractWith the ongoing rapid growth of publicly available ligand–protein bioactivity data, there is a trove of valuable data that can be used to train a plethora of machine-learning algorithms. However, not all data is equal in terms of size and quality and a significant portion of researchers’ time is needed to adapt the data to their needs. On top of that, finding the right data for a research question can often be a challenge on its own. To meet these challenges, we have constructed the Papyrus dataset. Papyrus is comprised of around 60 million data points. This dataset contains multiple large publicly available datasets such as ChEMBL and ExCAPE-DB combined with several smaller datasets containing high-quality data. The aggregated data has been standardised and normalised in a manner that is suitable for machine learning. We show how data can be filtered in a variety of ways and also perform some examples of quantitative structure–activity relationship analyses and proteochemometric modelling. Our ambition is that this pruned data collection constitutes a benchmark set that can be used for constructing predictive models, while also providing an accessible data source for research.
Graphical Abstract
XSMILES: interactive visualization for molecules, SMILES and XAI attribution scores
Authors: Heberle Henry , Zhao Linlin , Schmidt Sebastian , Wolf Thomas , Heinrich Julian 
Published: January 2023

Abstract
Background
Explainable artificial intelligence (XAI) methods have shown increasing applicability in chemistry. In this context, visualization techniques can highlight regions of a molecule to reveal their influence over a predicted property. For this purpose, some XAI techniques calculate attribution scores associated with tokens of SMILES strings or with atoms of a molecule. While an association of a score with an atom can be directly visually represented on a molecule diagram, scores computed for SMILES non-atom tokens cannot. For instance, a substring [N+] contains 3 non-atom tokens, i.e., [, $$+$$
+
, and ], and their attributions, depending on the model, are not necessarily revealing an influence of the nitrogen atom over the predicted property; for that reason, it is not possible to represent the scores on a molecule diagram. Moreover, SMILES’s notation is complex, foregrounding the need for techniques to facilitate the analysis of explanations associated with their tokens.

Results
We propose XSMILES, an interactive visualization technique, to explore explainable artificial intelligence attributions scores and support the interpretation of SMILES. Users can input any type of score attributed to atom and non-atom tokens and visualize them on top of a 2D molecule diagram coordinated with a bar chart that represents a SMILES string. We demonstrate how attributions calculated for SMILES strings can be evaluated and better interpreted through interactivity with two use cases.

Conclusions
Data scientists can use XSMILES to understand their models’ behavior and compare multiple modeling approaches. The tool provides a set of parameters to adapt the visualization to users’ needs and it can be integrated into different platforms. We believe XSMILES can support data scientists to develop, improve, and communicate their models by making it easier to identify patterns and compare attributions through interactive exploratory visualization.
Multi-omics analysis of sarcospan overexpression in mdx skeletal muscle reveals compensatory remodeling of cytoskeleton-matrix interactions that promote mechanotransduction pathways
Authors: McCourt Jackie L. , Stearns-Reider Kristen M. , Mamsa Hafsa , Kannan Pranav , Afsharinia Mohammad Hossein , Shu Cynthia , Gibbs Elizabeth M. , Shin Kara M. , Kurmangaliyev Yerbol Z. , Schmitt Lauren R. , Hansen Kirk C. , Crosbie Rachelle H. 
Published: January 2023

Abstract
Background
The dystrophin-glycoprotein complex (DGC) is a critical adhesion complex of the muscle cell membrane, providing a mechanical link between the extracellular matrix (ECM) and the cortical cytoskeleton that stabilizes the sarcolemma during repeated muscle contractions. One integral component of the DGC is the transmembrane protein, sarcospan (SSPN). Overexpression of SSPN in the skeletal muscle of mdx mice (murine model of DMD) restores muscle fiber attachment to the ECM in part through an associated increase in utrophin and integrin adhesion complexes at the cell membrane, protecting the muscle from contraction-induced injury. In this study, we utilized transcriptomic and ECM protein-optimized proteomics data sets from wild-type, mdx, and mdx transgenic (mdxTG) skeletal muscle tissues to identify pathways and proteins driving the compensatory action of SSPN overexpression.

Methods
The tibialis anterior and quadriceps muscles were isolated from wild-type, mdx, and mdxTG mice and subjected to bulk RNA-Seq and global proteomics analysis using methods to enhance capture of ECM proteins. Data sets were further analyzed through the ingenuity pathway analysis (QIAGEN) and integrative gene set enrichment to identify candidate networks, signaling pathways, and upstream regulators.

Results
Through our multi-omics approach, we identified 3 classes of differentially expressed genes and proteins in mdxTG muscle, including those that were (1) unrestored (significantly different from wild type, but not from mdx), (2) restored (significantly different from mdx, but not from wild type), and (3) compensatory (significantly different from both wild type and mdx). We identified signaling pathways that may contribute to the rescue phenotype, most notably cytoskeleton and ECM organization pathways. ECM-optimized proteomics revealed an increased abundance of collagens II, V, and XI, along with β-spectrin in mdxTG samples. Using ingenuity pathway analysis, we identified upstream regulators that are computationally predicted to drive compensatory changes, revealing a possible mechanism of SSPN rescue through a rewiring of cell-ECM bidirectional communication. We found that SSPN overexpression results in upregulation of key signaling molecules associated with regulation of cytoskeleton organization and mechanotransduction, including Yap1, Sox9, Rho, RAC, and Wnt.

Conclusions
Our findings indicate that SSPN overexpression rescues dystrophin deficiency partially through mechanotransduction signaling cascades mediated through components of the ECM and the cortical cytoskeleton.