bluuebunny/crossref_metadata_2025_split huggingface dataset:
Blind cavefish evolved food-searching behavior without changing sensory modality compared with sighted conspecies in the dark
Authors: Kuball Kyleigh , Fernandes Vânia Filipa Lima , Takagi Daisuke , Yoshizawa Masato 
Published: June 2023

AbstractIn nature, animals must navigate to forage according to their sensory inputs. Different species use different sensory modalities to locate food efficiently. For teleosts, food emits visual, mechanical, chemical, and/or possibly weak-electrical signals, which can be detected by optic, auditory/lateral line, and olfactory/taste buds sensory systems. However, how fish respond to and use different sensory inputs when locating food, as well as the evolution of these sensory modalities, remain unclear. We examined the Mexican tetra,Astyanax mexicanus, which is composed of two different morphs: a sighted riverine (surface fish) and a blind cave morph (cavefish). Compared with surface fish, cavefish have enhanced non-visual sensory systems, including the mechanosensory lateral line system, chemical sensors comprising the olfactory system and taste buds, and the auditory system to help navigate toward food sources. We tested how visual, chemical, and mechanical stimuli evoke food-seeking behavior. In contrast to our expectations, both surface fish and cavefish did not follow a gradient of chemical stimulus (food extract) but used it as a cue for the ambient existence of food. Surface fish followed visual cues (red plastic beads and food pellets), but, in the dark, were likely to rely on mechanosensors—the lateral line and/or tactile sensor—as cavefish did. Our results indicate cavefish used similar sensory modality to surface fish in the dark, while adherence levels to stimuli were higher in cavefish. In addition, cavefish evolved an extended circling strategy to capture food, which may yield a higher chance to capture food by swimming-by the food multiple times instead of once through zigzag motion. In summary, we propose ancestors of cavefish similar to surface fish may have needed little modification in food-seeking strategy to adapt to the dark.
AMPK Drives Both Glycolytic and Oxidative Metabolism in T Cells During Graft-versus-host Disease
Authors: Ramgopal Archana , Braverman Erica L , Sun Lee-Kai , Monlish Darlene , Wittmann Christopher , Ramsey Manda J. , Caitley Richard , Hawse William , Byersdorfer Craig A. 
Published: June 2023

ABSTRACTAllogeneic T cells reprogram their metabolism during acute graft-versus-host disease (GVHD) in a process reliant on the cellular energy sensor AMP-activated protein kinase (AMPK). Deletion of AMPK in donor T cells limits GVHD but still preserves homeostatic reconstitution and graft-versus-leukemia (GVL) effects. In the current studies, murine T cells lacking AMPK decreased oxidative metabolism at early timepoints post-transplant and were also unable to mediate a compensatory increase in glycolysis following inhibition of the electron transport chain. Human T cells lacking AMPK gave similar results, with glycolytic compensation impaired bothin vitroand following expansionin vivoin a modified model of GVHD. Immunoprecipitation of proteins from day 7 allogeneic T cells, using an antibody specific to phosphorylated AMPK targets, recovered lower levels of multiple glycolysis-related proteins including the glycolytic enzymes aldolase, enolase, pyruvate kinase M (PKM), and glyceraldehyde 3-phosphate dehydrogenase (GAPDH). Functionally, murine T cells lacking AMPK exhibited impaired aldolase activity following anti-CD3/CD28 stimulation and a decrease in GAPDH activity on day 7 post-transplant. Importantly, these changes in glycolysis correlated with an impaired ability of AMPK KO T cells to produce significant amounts of interferon gamma (IFNγ) upon antigenic re-stimulation. Together these data highlight a significant role for AMPK in controlling oxidative and glycolytic metabolism in both murine and human T cells during GVHD and endorse further study of AMPK inhibition as a potential target for future clinical therapies.KEY POINTSAMPK plays a key role in driving both and oxidative and glycolytic metabolism in T cells during graft-versus-host disease (GVHD)Absence of AMPK simultaneously impairs both glycolytic enzyme activity, most notably by aldolase, and interferon gamma (IFNγ) production
The Genetics of Aerotolerant Growth in a Naturally Reduced Genome Alphaproteobacterium
Authors: Enright Amy L. , Banta Amy B. , Ward Ryan D. , Vazquez Julio Rivera , Felczak Magdalena M. , Wolfe Michael B. , TerAvest Michaela A. , Amador-Noguez Daniel , Peters Jason M. 
Published: June 2023

AbstractReduced genome bacteria are genetically simplified systems that facilitate biological study and industrial use. The free-living Alphaproteobacterium,Zymomonas mobilis, has a naturally reduced genome containing fewer than 2000 protein coding genes. Despite its small genome, Z. mobilis thrives in diverse conditions including the presence or absence of atmospheric oxygen. However, insufficient characterization of essential and conditionally essential genes has limited broader adoption ofZ. mobilisas a model Alphaproteobacterium. Here, we use genome-scale CRISPRi-seq to systematically identify and characterizeZ. mobilisgenes that are conditionally essential for aerotolerant or anaerobic growth, or are generally essential across both conditions. Comparative genomics revealed that the essentiality of most “generally essential” genes was shared betweenZ. mobilisand other Alphaproteobacteria, validatingZ. mobilisas reduced genome model. Among conditionally essential genes, we found that the DNA repair gene, recJ, was critical only for aerobic growth but reduced the mutation rate under both conditions. Further, we show that genes encoding the F1FOATP synthase and Rnf respiratory complex are required for anaerobic growth ofZ. mobilis. Combining CRISPRi partial knockdowns with metabolomics and membrane potential measurements, we determined that the ATP synthase generates membrane potential that is consumed by Rnf to power downstream processes. Rnf knockdown strains accumulated isoprenoid biosynthesis intermediates, suggesting a key role for Rnf in powering essential biosynthetic reactions. Our work establishesZ. mobilisas a streamlined model for alphaproteobacterial genetics, has broad implications in bacterial energy coupling, and informsZ. mobilisgenome manipulation for optimized production of valuable isoprenoid-based bioproducts.ImportanceThe inherent complexity of biological systems is a major barrier to our understanding of cellular physiology. Bacteria with markedly fewer genes than their close relatives, or reduced genome bacteria, are promising biological models with less complexity. Reduced genome bacteria can also have superior properties for industrial use, provided the reduction does not overly restrict strain robustness. Naturally reduced genome bacteria, such as the Alphaproteobacterium,Zymomonas mobilis, have fewer genes but remain environmentally robust. In this study, we show thatZ. mobilisis a simplified genetic model for Alphaproteobacteria, a class with important impacts on the environment, human health, and industry. We also identify genes that are only required in the absence of atmospheric oxygen, uncovering players that maintain and utilize the cellular energy state. Our findings have broad implications for the genetics of Alphaproteobacteria and industrial use ofZ. mobilisto create biofuels and bioproducts.
GDmicro: classifying host disease status with GCN and Deep adaptation network based on the human gut microbiome data
Authors: Liao Herui , Shang Jiayu , Sun Yanni 
Published: June 2023

AbstractMotivationWith advances in metagenomic sequencing technologies, there are accumulating studies revealing the associations between the human gut microbiome and some human diseases. These associations shed light on using gut microbiome data to distinguish case and control samples of a specific disease, which is also called host disease status classification. Importantly, using learning-based models to distinguish the disease and control samples is expected to identify important biomarkers more accurately than abundance-based statistical analysis. However, available tools have not fully addressed two challenges associated with this task: limited labeled microbiome data and decreased accuracy in cross-studies. The confounding factors such as the diet, technical biases in sample collection/sequencing across different studies/cohorts often jeopardize the generalization of the learning model.ResultsTo address these challenges, we develop a new tool GDmicro, which combines semi-supervised learning and domain adaptation to achieve a more generalized model using limited labeled samples. We evaluated GDmicro on human gut microbiome data from 10 cohorts covering 5 different diseases. The results show that GDmicro has better performance and robustness than state-of-the-art tools. In particular, it improves the AUC from 0.783 to 0.949 in identifying inflammatory bowel disease. Furthermore, GDmicro can identify potential biomarkers with greater accuracy than abundance-based statistical analysis methods. It also reveals the contribution of these biomarkers to the host’s disease status.Availability and implementationhttps://github.com/liaoherui/GDmicroContactyannisun@cityu.edu.hkSupplementary informationSupplementary data are available at XXX online
Building a genetic and epigenetic predictive model of breast cancer intrinsic subtypes using large-scale data and hierarchical structure learning
Authors: Xie Jiemin , Yang Binyu , Li Keyi , Gao Lixin , Liu Xuemei , Xiong Yunhui , Chen Wen , Xia Li C. 
Published: June 2023

AbstractBreast cancer subtyping is a difficult clinical and scientific challenge. The prevalent Prediction Analysis of Microarray of 50 genes (PAM50) system and its Immunohistochemistry (IHC) surrogate showed significant inconsistencies. This is because of the limited training samples, highly variable molecular features and in-efficient strategies used in these classifiers. The rapid development of early screening technologies, especially in the field of circulating tumor DNA, has also challenged the subtyping of breast cancer at the DNA level. By integrating large-scale DNA-level data and using a hierarchical structure learning algorithm, we developed Unified Genetic and Epigenetic Subtyping (UGES), a new intrinsic subtype classifier. The benchmarks showed that the use of all classes of DNA alterations worked much better than single classes, and that the multi-step hierarchical learning is crucial, which improves the overall AUC score by 0.074 compared to the one-step multi-classification method. Based on these insights, the ultimate UGES was trained as a three-step classifier on 50831 DNA features of 2065 samples, including mutations, copy number aberrations, and methylations. UGES achieved overall AUC score 0.963, and greatly improved the clinical stratification of patients, as each strata’s survival difference became statistically more significant p-value=9.7e-55 (UGES) vs 2.2e-47 (PAM50). Finally, UGES identified 52 subtype-level DNA biomarkers that can be targeted in early screening technology to significantly expand the time window for precision care. The analysis code is freely available athttps://github.com/labxscut/UGES.
What motivates viewers to purchase recommended products in live streaming? The moderating role of extroversion–introversion personality
Authors: Chang Chun-Ming , Yen Chiahui , Chou Szu-Yu , Lo Wen-Wan 
Published: June 2023

PurposeThis study aims to investigate the factors driving viewers' purchase intention in live-streaming by incorporating stimuli–organism–response (S–O–R) framework and extroversion–introversion personality perspectives.Design/methodology/approachData collected from 228 users on live-streaming platforms in Taiwan were used to test the proposed model. The partial least squares method was used to test the measurement and the structural models.FindingsProduct attractiveness and trust in streamer significantly impacts purchase intention. The results also reveal that interactivity, breadth of information and uniqueness of information significantly impact product attractiveness, whereas social presence, breadth of information and uniqueness of information positively affect trust in streamer. Furthermore, streamer attractiveness has a greater effect on the purchase intention of extroverts.Originality/valueThis study investigates how the features of media, message and streamer impact purchase intention through their reactions to live-streaming. This research is also one of the earliest studies to examine the moderating role of extroversion–introversion personality on purchase intention and its antecedents in live-streaming commerce.
A transdisciplinary framework for university-industry collaboration in establishing a social business model
Authors: Cheah Jeffrey S. S. , Amran Azlan , Kirubakaran Mahendran , Lang Daniel J. , Su Pek-Fuen , Chu Jenn-Weng 
Published: June 2023

Purpose
This study aims to illuminate the limited understanding of viable social business among corporate actors in developing countries. It addresses pressing environmental and societal problems, emphasizing the need for corporate participation in sustainable solutions. Additionally, the study explores the transformational business notion linking company achievement with social progress, an increasingly studied concept in management.

Design/methodology/approach
Based on a transdisciplinary case study (i.e. a university-industry collaboration [UIC]), this study proposed a structural framework and guiding principles to integrate the academic and practitioners’ different but complementary resources and expertise.

Findings
The outcomes could provide insights for social entrepreneurs to perform highly optimal decisions on their organisational strategies, in which the financial-then-social pathway could be an effective social business success mechanism.

Originality/value
Besides, the case study also generates each five learning lessons and challenges coping strategies that provide practical guidance on operationalising an effective UIC. The empirical findings contribute to social entrepreneurship and sustainability science literature.
Exploring barriers and facilitators to knowledge transfer and learning processes through a cross-departmental collaborative project in a municipal organization
Authors: Sunnemark Fredrik , Lundqvist Westin Wilma , Al Saad Tamy , Assmo Per 
Published: June 2023

Purpose
This study aims to explore barriers and facilitators for knowledge transfer and learning processes by examining a cross-departmental collaborative project in the municipal organization. It is based on a R&D collaboration between University West and a Swedish municipality.

Design/methodology/approach
To explore the barriers and facilitators, the data collection was made through observation of the project implementation process, as well as 20 interviews with public servants and external actors. To conduct a systematic qualitative-oriented content analysis, the article constructs and applies a theoretical analytical framework consisting of different factors influencing knowledge transfer and learning processes within a municipal organizational setting.

Findings
This study explores the facilitators and barriers to knowledge transfer and learning processes, specifically focusing on strategic communication, individual roles, common goals, time pressure, group learning, trust and relationships and absorptive capability. Lack of communication affected the group learning process, while the close relation between time pressure, group learning and trust in colleagues is also pointed out as crucial areas. Trust developed through dialogue efforts helped overcome project fatigue. Coaching with a human rights-based approach improved organizational absorptive capabilities.

Originality/value
The study gives important insights into organizational learning within a municipality in Sweden for the successful implementation of collaborative projects. Knowledge must be transferred for the organization to learn to develop and tackle future challenges and its complex responsibilities. The theoretical analytical framework provided in this article has proven to be effective and is therefore transferable to other organizations in both the public and private sectors.
Identifying reliable ions for the statistical differentiation of structurally similar fentanyl analogs
Authors: Sacha Andrew M. , Willis Isaac C. , McGuffin Victoria L. , Waddell Smith Ruth 
Published: June 2023

AbstractDefinitive identification of fentanyl analogs based on mass spectral comparison is challenging given the high degree of structural and, hence, spectral similarity. To address this, a statistical method was previously developed in which two electron‐ionization (EI) mass spectra are compared using the unequal variance t‐test. Normalized intensities of corresponding ions are compared, testing the null hypothesis (H0) that the difference in intensity is equal to zero. If H0 is accepted at all m/z values, the two spectra are statistically equivalent at the specified confidence level. If H0 is not accepted at any m/z value, then there is a significant difference in intensity at that m/z value between the two spectra. In this work, the statistical comparison method is applied to distinguish EI spectra of valeryl fentanyl, isovaleryl fentanyl, and pivaloyl fentanyl. Spectra of the three analogs were collected over a 9‐month period and at different concentrations. At the 99.9% confidence level, the spectra of corresponding isomers were statistically associated. Spectra of different isomers were statistically distinct, and ions responsible for discrimination were identified in each comparison. To account for inherent instrument variations, discriminating ions for each pairwise comparison were ranked based on the magnitude of the calculated t‐statistic (tcalc) value. For a given comparison, ions with higher tcalc values are those with the greatest difference in intensity between the two spectra and, therefore, are considered more reliable for discrimination. Using these methods, objective discrimination among the spectra was achieved and ions considered most reliable for discrimination of these isomers were identified.
Slovakia: Political Developments and Data in 2022
Authors: LÁŠTIC ERIK 
Published: June 2023

AbstractThe war in Ukraine and its fallout dominated politics in Slovakia throughout 2022. The coalition split up after the summer, leaving the Cabinet in a fragile position in Parliament. This led to chaotic parliamentary sessions in October and November that ended on 15 December, when the Heger II Cabinet lost a no‐confidence vote initiated by a former coalition party Freedom and Solidarity, SaS. As no new parliamentary majority formed, the Heger II Cabinet continued in office under the supervision of President Z. Čaputová, with parliamentary political parties unable to compromise on early elections.
The effect of the COVID‐19 pandemic on substance use patterns and physiological dysregulation in pregnant and postpartum women
Authors: Ruyak Sharon , Roberts Melissa H. , Chambers Stephanie , Ma Xingya , DiDomenico Jared , De La Garza Richard , Bakhireva Ludmila N. 
Published: June 2023

AbstractBackgroundThe SARS‐CoV‐2/COVID‐19 pandemic has been associated with increased stress levels and higher alcohol use, including in pregnant and postpartum women. In the general population, alcohol use is associated with dysregulation in the autonomic nervous system (ANS), which is indexed by heart rate variability (HRV). The objectives of this study were to: (1) characterize changes in substance use during the SARS‐CoV‐2/COVID‐19 pandemic via a baseline self‐report survey followed by mobile ecological momentary assessment (mEMA) of substance use; and (2) examine the associations between momentary substance use and ambulatory HRV measures in pregnant and postpartum women.MethodsPregnant and postpartum women were identified from the ENRICH‐2 prospective cohort study. Participants were administered a baseline structured phone interview that included the Coronavirus Perinatal Experiences (COPE) survey and ascertained the prevalence of substance use. Over a 14‐day period, momentary substance use was assessed three times daily, and HRV measurements were captured via wearable electronics. Associations between momentary substance use and HRV measures (root mean square of successive differences [RMSSD] and low frequency/high frequency [LF/HF] ratio) were examined using a mixed effects model that included within‐subject (WS) and between‐subject (BS) effects and adjusted for pregnancy status and participant age.ResultsThe sample included 49 pregnant and 22 postpartum women. From a combination of a baseline and 14‐day mEMA surveys, 21.2% reported alcohol use, 16.9% reported marijuana use, and 8.5% reported nicotine use. WS effects for momentary alcohol use were associated with the RMSSD (β = −0.14; p = 0.005) and LF/HF ratio (β = 0.14; p = 0.01) when controlling for pregnancy status and maternal age. No significant associations were observed between HRV measures and instances of marijuana or nicotine use.ConclusionsThese findings highlight the negative effect of the SARS‐CoV‐2/COVID‐19 pandemic on the psychological health of pregnant and postpartum women associated with substance use, and in turn, ANS dysregulation, which potentially puts some women at risk of developing a substance use disorder.
Long‐term follow‐up of single‐visit pulp revascularisation for the dens evaginatus and dens invaginatus: Cases report
Authors: Kim Hyeon‐Cheol , Kwak Sang Won , Cheung Gary Shun‐Pan 
Published: June 2023

AbstractThis article documents cases of single‐visit pulp revascularisation for dens evaginatus and dens invaginatus, without using intracranial medicaments or antibiotics, aiming to provide a potentially applicable protocol for pulp revascularisation procedure in a single‐visit. Two patients with chief complaints of pain and swelling visited a dental hospital. Radiographs revealed that the causative teeth had an open apex and periapical radiolucency, and the teeth were diagnosed as pulp necrosis and acute apical abscess or symptomatic apical periodontitis. For both cases, single‐visit revascularisation was completed without intracanal medicaments or antibiotics. The patients were periodically recalled to evaluate periapical healing after treatment. The apical lesion healed, and the root dentin thickening was observed. The single‐visit pulp revascularisation procedure without using specific intracanal medicaments can produce clinically favourable results for these dental anomalies.
‘Fixing’ destitute children: The relational geography of an early twentieth century children's home through its archives
Authors: Cope Meghan 
Published: June 2023

AbstractDrawing from early twentieth century documents from the Home for Destitute Children in Burlington, Vermont, USA, I explore the notion of the archive as a site of knowledge, politics, and ethics. Despite the absence of children's own perspectives in this archive, I propose taking a geographical relational poverty approach to gain insights by examining power relations between middle‐class adult women and ‘destitute’ children. Specifically, I use records generated by women in charge of the Home (the matrons and the Board of Directors) to identify three dimensions of relational relevance. First, the women exerted power in constructing the Home as a place through ordering temporal rhythms, influencing sensory experiences, and imposing social boundaries and material conditions. Second, I review discourses such as the ‘desirable child’, ‘innocence’, and eugenicist notions of ‘feeblemindedness’ employed by the women to ‘fix’ children, both to repair them and to keep them in place. Third, I provide a reflection on the possibilities of combining manuscript archives with digitized sources such as the census to uncover adults' production and containment of ‘destitute children’.