bluuebunny/crossref_metadata_2025_split huggingface dataset:
Making the Case for Audience Design in Conversational AI: Users’ Pragmatic Strategies and Rapport Expectations in Interaction with a Task-Oriented Chatbot
Authors: Dippold Doris 
Published: May 2024

Abstract
With chatbots becoming more and more prevalent in commercial and service contexts, they need to be designed to provide equitable access to services for all user groups. This paper argues that insights into users’ pragmatic strategies and rapport expectations can inform the audience design of chatbots and ensure that all users can equally benefit from the services they facilitate. The argument is underpinned by the analysis of simulated user interactions with a chatbot facilitating health appointment bookings, users’ introspective comments on their interactions, and users’ qualitative survey comments. The study shows that users’ pragmatic strategies show considerable variation. It also shows the negative impact of user experiences when the chatbot’s language and interaction patterns do not align with users’ rapport expectations. In closing, the paper uses these findings to define audience design for chatbots and discuss how audience design can be realized and supported by research.
Secreted frizzled-related protein 5 overexpression reverses oxLDL-induced lipid accumulation in human vascular smooth muscle cells
Authors: Wang Xiaogao , Chen Shiyuan , Yu Chaowen , Lu Ran , Sun Yong , Guan Zeyu , Gao Yong 
Published: May 2024

ABSTRACTAtherosclerosis (AS) is the major cause of multiple cardiovascular diseases. In addition, the lipid accumulation of human vascular smooth muscle cells (HVSMCs) can cause the occurrence of AS. Secreted frizzled-related protein 5 (Sfrp5) was known to be downregulated in AS; however, the detailed function of Sfrp5 in HVSMCs remains unclear. Specifically, we found that Sfrp5 expression in oxLDL-treated HVSMCs was downregulated. Sfrp5 overexpression inhibited the viability of HVSMCs induced by oxLDL. In addition, oxLDL-induced proliferation and migration in HVSMCs were abolished by Sfrp5 overexpression. Sfrp5 overexpression reduced oxLDL-caused oxidative stress, lipid accumulation, and inflammation in HVSMCs. Meanwhile, oxLDL treatment increased the expressions of Wnt5a, c-Myc, and β-catenin in HVSMCs, while this phenomenon was rescued by Sfrp5 overexpression. Furthermore, the inhibitory effect of Sfrp5 upregulation on the viability and migration of HVSMCs was reversed by R-spondin 1. These results indicate that Sfrp5 overexpression could reverse oxLDL-induced lipid accumulation in HVSMCs through inactivating Wnt5a/β-catenin signaling pathway.
DiSMVC: a multi-view graph collaborative learning framework for measuring disease similarity
Authors: Wei Hang , Gao Lin , Wu Shuai , Jiang Yina , Liu Bin 
Published: May 2024

Abstract

Motivation
Exploring potential associations between diseases can help in understanding pathological mechanisms of diseases and facilitating the discovery of candidate biomarkers and drug targets, thereby promoting disease diagnosis and treatment. Some computational methods have been proposed for measuring disease similarity. However, these methods describe diseases without considering their latent multi-molecule regulation and valuable supervision signal, resulting in limited biological interpretability and efficiency to capture association patterns.

Results
In this study, we propose a new computational method named DiSMVC. Different from existing predictors, DiSMVC designs a supervised graph collaborative framework to measure disease similarity. Multiple bio-entity associations related to genes and miRNAs are integrated via cross-view graph contrastive learning to extract informative disease representation, and then association pattern joint learning is implemented to compute disease similarity by incorporating phenotype-annotated disease associations. The experimental results show that DiSMVC can draw discriminative characteristics for disease pairs, and outperform other state-of-the-art methods. As a result, DiSMVC is a promising method for predicting disease associations with molecular interpretability.

Availability and implementation
Datasets and source codes are available at https://github.com/Biohang/DiSMVC.
greenPipes: an integrated data analysis pipeline for greenCUT&RUN and CUT&RUN genome-localization datasets
Authors: Nizamuddin Sheikh , Timmers H T Marc 
Published: May 2024

Abstract

Motivation
To study gene regulation through transcription factors and chromatin modifiers, a variety of genome-wide techniques are used. Recently, CUT&RUN-based technologies have become popular, but a pipeline for the comprehensive analysis of CUT&RUN datasets is currently lacking. Here, we present the “greenPipes” package, which includes fine-tuned parameters specifically for bioinformatic analyses of greenCUT&RUN and CUT&RUN datasets. greenPipes provides additional functionalities for data analysis and data integration with other -omics technologies, which are either not available in other pipelines developed for CUT&RUN datasets or scattered in the literature as individual packages.

Availability and implementation
Source code and a manual of the greenPipes are freely available on GitHub website (https://github.com/snizam001/greenPipes). The test datasets, comprehensive annotation files, and other datasets are available at https://osf.io/ruhj9/.

Contact
n.sheikh@dkfz-heidelberg.de or m.timmers@dkfz-heidelberg.de

Supplementary information
The handbook of greenPipes is available online at Bioinformatics as Supplementary text.
Asynchronous behavioral and neurophysiological changes in word production in the adult lifespan
Authors: Krethlow Giulia , Fargier Raphaël , Atanasova Tanja , Ménétré Eric , Laganaro Marina 
Published: May 2024

Abstract
Behavioral and brain-related changes in word production have been claimed to predominantly occur after 70 years of age. Most studies investigating age-related changes in adulthood only compared young to older adults, failing to determine whether neural processes underlying word production change at an earlier age than observed in behavior. This study aims to fill this gap by investigating whether changes in neurophysiological processes underlying word production are aligned with behavioral changes. Behavior and the electrophysiological event-related potential patterns of word production were assessed during a picture naming task in 95 participants across five adult lifespan age groups (ranging from 16 to 80 years old). While behavioral performance decreased starting from 70 years of age, significant neurophysiological changes were present at the age of 40 years old, in a time window (between 150 and 220 ms) likely associated with lexical-semantic processes underlying referential word production. These results show that neurophysiological modifications precede the behavioral changes in language production; they can be interpreted in line with the suggestion that the lexical-semantic reorganization in mid-adulthood influences the maintenance of language skills longer than for other cognitive functions.
Oxidative DNA damage promotes vascular ageing associated with changes in extracellular matrix-regulating proteins
Authors: Foote Kirsty , Rienks Marieke , Schmidt Lukas , Theofilatos Konstantinos , Yasmin  , Ozols Matiss , Eckersley Alexander , Shah Aarti , Figg Nichola , Finigan Alison , O’Shaughnessy Kevin , Wilkinson Ian , Mayr Manuel , Bennett Martin 
Published: May 2024

Abstract

Aims
Vascular ageing is characterized by vessel stiffening, with increased deposition of extracellular matrix (ECM) proteins including collagens. Oxidative DNA damage occurs in vascular ageing, but how it regulates ECM proteins and vascular stiffening is unknown. We sought to determine the relationship between oxidative DNA damage and ECM regulatory proteins in vascular ageing.

Methods and results
We examined oxidative DNA damage, the major base excision repair (BER) enzyme 8-Oxoguanine DNA Glycosylase (Ogg1) and its regulators, multiple physiological markers of ageing, and ECM proteomics in mice from 22 to 72 w. Vascular ageing was associated with increased oxidative DNA damage, and decreased expression of Ogg1, its active acetylated form, its acetylation regulatory proteins P300 and CBP, and the transcription factor Foxo3a. Vascular stiffness was examined in vivo in control, Ogg1−/−, or mice with vascular smooth muscle cell-specific expression of Ogg1+ (Ogg1) or an inactive mutation (Ogg1KR). Ogg1−/− and Ogg1KR mice showed reduced arterial compliance and distensibility, and increased stiffness and pulse pressure, whereas Ogg1 expression normalized all parameters to 72 w. ECM proteomics identified major changes in collagens with ageing, and downregulation of the ECM regulatory proteins Protein 6-lysyl oxidase (LOX) and WNT1-inducible-signaling pathway protein 2 (WISP2). Ogg1 overexpression upregulated LOX and WISP2 both in vitro and in vivo, and downregulated Transforming growth factor β1 (TGFb1) and Collagen 4α1 in vivo compared with Ogg1KR. Foxo3a activation induced Lox, while Wnt3 induction of Wisp2 also upregulated LOX and Foxo3a, and downregulated TGFβ1 and fibronectin 1. In humans, 8-oxo-G increased with vascular stiffness, while active OGG1 reduced with both age and stiffness.

Conclusion
Vascular ageing is associated with oxidative DNA damage, downregulation of major BER proteins, and changes in multiple ECM structural and regulatory proteins. Ogg1 protects against vascular ageing, associated with changes in ECM regulatory proteins including LOX and WISP2.
Influence of sticky trap color, host plant species, and weather factors on the population dynamics of thrips species in Southern Ghana
Authors: Nkafu Ngosong Therese , Fening Ken Okwae , Ajonglefac Martin Fonyi , Afreh-Nuamah Kwame 
Published: May 2024

Abstract
It is essential to correctly identify and keep track of the abundance of thrips species on infested host crops to understand their population dynamics and implement control measures promptly. The current study was conducted to evaluate the performance of sticky traps in monitoring thrips species in exporters’ eggplant and chili farms and to assess the impact of weather factors on thrips population dynamics. Thrips species were monitored using blue, yellow, and white sticky traps on chili and eggplant farms in Tuba, respectively, in 2020 and 2021. Each field was divided into 8 blocks, and in each replicate, all colors representing 3 treatments were randomly tied to stakes at the center of the respective crop. Data loggers were installed to record hourly weather variables. Three thrips species [Thrips parvispinus Karny (Thysanoptera: Thripidae), Franklinella schultzei Trybom (Thysanoptera: Thripidae), and Thrips tabaci Lindeman (Thysanoptera: Thripidae)] were identified from both farms and the different species showed varied attractiveness to trap color for both seasons, with white proving more attractive to T. parvispinus. The population dynamics of the species varied significantly with the season and weather but not with the crop. Optimum temperatures (28–31 °C) and relative humidity (60%–78%) showed a positive linear relationship between the trapped insects with temperature and RH, while extreme temperatures (35 °C) negatively affected their abundance. All sticky trap colors attracted several nontarget organisms; however, yellow colors had higher populations, including the predator, Orius insidiosus. White sticky traps are recommended for inclusion in the country-wide monitoring for thrips, especially T. parvispinus.
Dynamic risk stratification of worsening heart failure using a deep learning-enabled implanted ambulatory single-lead electrocardiogram
Authors: Howard James Philip , Vasudevan Neethu , Sarkar Shantanu , Landman Sean , Koehler Jodi , Keene Daniel 
Published: May 2024

Abstract

Aims
Implantable loop recorders (ILRs) provide continuous single-lead ambulatory electrocardiogram (aECG) monitoring. Whether these aECGs could be used to identify worsening heart failure (HF) is unknown.

Methods and results
We linked ILR aECG from Medtronic device database to the left ventricular ejection fraction (LVEF) measurements in Optum® de-identified electronic health record dataset. We trained an artificial intelligence (AI) algorithm [aECG-convolutional neural network (CNN)] on a dataset of 35 741 aECGs from 2247 patients to identify LVEF ≤ 40% and assessed its performance using the area under the receiver operating characteristic curve. Ambulatory electrocardiogram-CNN was then used to identify patients with increasing risk of HF hospitalization in a real-world cohort of 909 patients with prior HF diagnosis. This dataset provided 12 467 follow-up monthly evaluations, with 201 HF hospitalizations. For every month, time-series features from these predictions were used to categorize patients into high- and low-risk groups and predict HF hospitalization in the next month. The risk of HF hospitalization in the next 30 days was significantly higher in the cohort that aECG-CNN identified as high risk [hazard ratio (HR) 1.89; 95% confidence interval (CI) 1.28–2.79; P = 0.001] compared with low risk, even after adjusting patient demographics (HR 1.88; 95% CI 1.27–2.79 P = 0.002).

Conclusion
An AI algorithm trained to detect LVEF ≤40% using ILR aECGs can also readily identify patients at increased risk of HF hospitalizations by monitoring changes in the probability of HF over 30 days.
Digest: When sexual selection hits the wall of natural selection
Authors: O’Loughlin Brendan S , Marcondes Rafael S 
Published: May 2024

Abstract
Sexual selection often drives traits in a direction that is disfavored by natural selection. The balance between these two types of selection can shift rapidly in response to environmental changes. Gallagher et al. (2024) report such a shift in the cricket population following the introduction of a parasitoid fly. The ancestral male morph, though still preferred by females, has been supplanted by multiple novel morphs that are more difficult for the parasitoid to detect.
An investigation of the effect of the universal model of family-centered care on patient and family outcomes in patients under home invasive mechanical ventilation
Authors: Kavand Babak , Asgari Parvaneh 
Published: May 2024

Abstract

Background
The number of patients under home mechanical ventilation is increasing worldwide. The unique nature of these patients and their complex health needs exposes home caregivers to various needs and challenges regarding different dimensions of care.

Objective
The present study was conducted to investigate the effect of the universal model of family-centered care on the clinical outcomes of the patient and the family.

Methods
This clinical trial was conducted between 2020 and 2021. A total of 60 patients under invasive mechanical ventilation was selected and divided into control (routine training that is usually given by hospital staff to families to care for patients) and intervention (comprehensive pre-discharge training program to post-discharge follow-up using the universal model of family-centered care) groups using random block design and universal model of family-centered care. Home caregivers’ functional skills and burden, as well as patients’ readmission and mortality rates, were compared in the two groups.

Results
Implementing the intervention 1 and 3 months later effectively increased home caregivers’ functional skills. Moreover, a statistically significant difference was observed between the two groups in terms of the psychological burden of caregiving (P &lt; .001); the implementation of the intervention could highly reduce the psychological burden of caregiving in the intervention group (EF = 0.94). The hospital readmission and mortality rate in the intervention group was significantly lower than in the control group (P = .02 and P = .03, respectively).

Conclusions
Given the significant impact of the universal model of family-centered care on the clinical outcomes of the patient and the family, pre-discharge training and its post-discharge follow-up and continuity of education with an active presence of nurses, as one of the main pillars of the treatment, seems essential.
Sensitivity of Salmonella Typhimurium to nisin in vitro and in orange juice under refrigeration
Authors: Fernandes da Silva Carla Gabriela , Santos Lopes Flávio , Cardoso Vieira Valois Álissy Fernanda , Vieira Prudêncio Cláudia 
Published: May 2024

Abstract
The influence of environmental factors on Salmonella sensitivity to nisin in vitro and in refrigerated orange juice were investigated. Nisin activity was observed in the different conditions, but the highest efficiency was achieved at lower pH (4.0) and with higher bacteriocin concentration (174 µM). Moreover, the bactericidal action was directly proportional to the incubation period. When tested in orange juice, nisin caused a reduction of up to 4.05 logarithm cycles in the Salmonella population. So, environmental factors such as low pH and low temperature favored the sensitization of Salmonella cells to the bactericidal action of nisin. Therefore, this may represent an alternative to control Salmonella in refrigerated foods.
Colonization of vancomycin-resistant Enterococcus faecium in human-derived colonic epithelium: unraveling the transcriptional dynamics of host–enterococcal interactions
Authors: Stege Paul B , Beekman Jeffrey M , Hendrickx Antoni P A , van Eijk Laura , Rogers Malbert R C , Suen Sylvia W F , Vonk Annelotte M , Willems Rob J L , Paganelli Fernanda L 
Published: May 2024

Abstract
Enterococcus faecium is an opportunistic pathogen able to colonize the intestines of hospitalized patients. This initial colonization is an important step in the downstream pathogenesis, which includes outgrowth of the intestinal microbiota and potential infection of the host. The impact of intestinal overgrowth on host–enterococcal interactions is not well understood. We therefore applied a RNAseq approach in order to unravel the transcriptional dynamics of E. faecium upon co-culturing with human derived colonic epithelium. Co-cultures of colonic epithelium with a hospital-associated vancomycin resistant (vanA-type) E. faecium (VRE) showed that VRE resided on top of the colonic epithelium when analyzed by microscopy. RNAseq revealed that exposure to the colonic epithelium resulted in upregulation of 238 VRE genes compared to the control condition, including genes implicated in pili expression, conjugation (plasmid_2), genes related to sugar uptake, and biofilm formation (chromosome). In total, 260 were downregulated, including the vanA operon located on plasmid_3. Pathway analysis revealed an overall switch in metabolism to amino acid scavenging and reduction. In summary, our study demonstrates that co-culturing of VRE with human colonic epithelium promotes an elaborate gene response in VRE, enhancing our insight in host–E. faecium interactions, which might facilitate the design of novel anti-infectivity strategies.
Prevalence of human respiratory pathogens and associated mucosal cytokine levels in young children and adults: a cross-sectional observational study in the Netherlands during the winter of 2012/2013
Authors: van Kasteren Puck B , Gelderloos Anne T , Nicolaie Mioara Alina , den Hartog Gerco , Vissers Marloes , Luytjes Willem , Rots Nynke Y , van Beek Josine 
Published: May 2024

Abstract
Respiratory pathogens can cause severe disease and even death, especially in the very young and very old. Studies investigating their prevalence often focus on individuals presenting to healthcare providers with symptoms. However, the design of prevention strategies, e.g. which target groups to vaccinate, will benefit from knowledge on the prevalence of, risk factors for and host response to these pathogens in the general population. In this study, upper respiratory samples (n = 1311) were collected cross-sectionally during winter from 11- and 24-month old children, their parents, and adults ≥60 years of age that were recruited irrespective of seeking medical care. Almost all children, approximately two-thirds of parents and a quarter of older adults tested positive for at least one pathogen, often in the absence of symptoms. Viral interference was evident for the combination of rhinovirus and respiratory syncytial virus. Attending childcare facilities and having siblings associated with increased pathogen counts in children. On average, children showed increased levels of mucosal cytokines compared to parents and especially proinflammatory molecules associated with the presence of symptoms. These findings may guide further research into transmission patterns of respiratory pathogens and assist in determining the most appropriate strategies for the prediction and prevention of disease.
siRNA that participates in Drosophila dosage compensation is produced by many 1.688X and 359 bp repeats
Authors: Biswas Sudeshna , Gurdziel Katherine , Meller Victoria H 
Published: May 2024

Abstract
Organisms with differentiated sex chromosomes must accommodate unequal gene dosage in males and females. Male fruit flies increase X-linked gene expression to compensate for hemizygosity of their single X chromosome. Full compensation requires localization of the Male-Specific Lethal (MSL) complex to active genes on the male X, where it modulates chromatin to elevate expression. The mechanisms that identify X chromatin are poorly understood. The euchromatic X is enriched for AT-rich, ∼359 bp satellites termed the 1.688X repeats. Autosomal insertions of 1.688X DNA enable MSL recruitment to nearby genes. Ectopic expression of dsRNA from one of these repeats produces siRNA and partially restores X-localization of MSLs in males with defective X recognition. Surprisingly, expression of double-stranded RNA from three other 1.688X repeats failed to rescue males. We reconstructed dsRNA-expressing transgenes with sequence from two of these repeats and identified phasing of repeat DNA, rather than sequence or orientation, as the factor that determines rescue of males with defective X recognition. Small RNA sequencing revealed that siRNA was produced in flies with a transgene that rescues, but not in those carrying a transgene with the same repeat but different phasing. We demonstrate that pericentromeric X heterochromatin promotes X recognition through a maternal effect, potentially mediated by small RNA from closely related heterochromatic repeats. This suggests that the sources of siRNAs promoting X recognition are highly redundant. We propose that enrichment of satellite repeats on Drosophilid X chromosomes facilitates the rapid evolution of differentiated sex chromosomes by marking the X for compensation.