bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamics and bifurcation structure of a mean-field model of adaptive exponential integrate-and-fire networks
Authors: Kusch Lionel , Depannemaecker Damien , Destexhe Alain , Jirsa Viktor 
Published: December 2023

AbstractThe study of brain activity spans diverse scales and levels of description, and requires the development of computational models alongside experimental investigations to explore integrations across scales. The high dimensionality of spiking networks presents challenges for understanding their dynamics. To tackle this, a mean-field formulation offers a potential approach for dimensionality reduction while retaining essential elements. Here, we focus on a previously developed mean-field model of Adaptive Exponential (AdEx) networks, utilized in various research works. We provide a systematic investigation of its properties and bifurcation structure, which was not available for this model. We show that this provides a comprehensive description and characterization of the model to assist future users in interpreting their results. The methodology includes model construction, stability analysis, and numerical simulations. Finally, we offer an overview of dynamical properties and methods to characterize the mean-field model, which should be useful for for other models.
DeepEnzyme: a robust deep learning model for improved enzyme turnover number prediction by utilizing features of protein 3D structures
Authors: Wang Tong , Xiang Guangming , He Siwei , Su Liyun , Yan Xuefeng , Lu Hongzhong 
Published: December 2023

AbstractTurnover numbers (kcat), which indicate an enzyme’s catalytic efficiency, have a wide range of applications in fields including protein engineering and synthetic biology. Experimentally measuring the enzymes’ kcat is always time-consuming. Recently, the prediction of kcat using deep learning models has mitigated this problem. However, the accuracy and robustness in kcat prediction still needs to be improved significantly, particularly when dealing with enzymes with low sequence similarity compared to those within the training dataset. Herein, we present DeepEnzyme, a cutting-edge deep learning model that combines the most recent Transformer and Graph Convolutional Network (GCN) architectures. To improve the prediction accuracy, DeepEnzyme was trained by leveraging the integrated features from both sequences and 3D structures. Consequently, our model exhibits remarkable robustness when processing enzymes with low sequence similarity compared to those in the training dataset by utilizing additional features from high-quality protein 3D structures. DeepEnzyme also makes it possible to evaluate how point mutations affect the catalytic activity of the enzyme, which helps identify residue sites that are crucial for the catalytic function. In summary, DeepEnzyme represents a pioneering effort in predicting enzymes’ kcat values with superior accuracy and robustness compared to previous algorithms. This advancement will significantly contribute to our comprehension of enzyme function and its evolutionary patterns across species.
Model cyanobacterial consortia reveal a consistent core microbiome independent of inoculation source or cyanobacterial host species
Authors: Kust Andreja , Zorz Jackie , Paniker Catalina Cruañas , Bouma-Gregson Keith , Krishnappa Netravathi , Banfield Jillian F. , Diamond Spencer 
Published: December 2023

AbstractCyanobacteria are central to biogeochemical cycling, climate change, and eutrophication. While they readily develop associations with environmental microorganisms, the question of whether they consistently recruit specific microbiomes remains unresolved. Here, we establishedin vitrocyanobacterial consortia by inoculating five different cyanobacterial strains with microbiomes from three freshwater environments to determine if similar non-cyanobacterial organisms were recruited into stable cyanobacteria-based communities. Using amplicon and genome-resolved metagenomic methods we determined that stable cyanobacterial communities largely share the same taxa, regardless of the host cyanobacterial species or inoculation source. Specifically, we identified a 25 species core microbiome, which was significantly enriched in functions for micronutrient biosynthesis, metabolite transport/exchange, and anoxygenic photosynthesis. Furthermore, core species were enriched in putative mobile genetic elements, including two large (> 100 kb) circularized and curated plasmids, encoding functions that may support cyanobacteria-heterotroph symbioses. The consistency observed across these systems indicate that cyanobacterial consortia maintained under similar conditions converge to a predictable structure, and support a core microbiome with taxonomic and functional similarity to core microbiomes of other phototroph-heterotroph symbiotic assemblages.
Apramycin efficacy in the treatment of carbapenem-resistantEnterobacteralesin murine blood stream infection models
Authors: Frimodt-Møller Niels , Hansen Jon U. , Plattner Michel , Huseby Douglas L. , Almind Stine Radmer , Haldimann Klara , Gysin Marina , Petersson Anna , Ercan Onur , Ganz Lea , Hughes Diarmaid , Lundberg Carina Vingsbo , Hobbie Sven N. 
Published: December 2023

ABSTRACTBackgroundThe aminoglycoside apramycin has been proposed as a drug candidate for the treatment of critical Gram-negative systemic infections. However, its potential in the treatment of drug-resistant bloodstream infections (BSIs) has yet to be assessed.MethodsThe resistance gene annotations of 26 493 blood culture isolates were analyzed.In vitroprofiling of apramycin comprised cell-free translation assays, broth microdilution, and frequency of resistance determination. The efficacy of apramycin was studied in a mouse peritonitis model for nineE. coliandK. pneumoniaeisolates.ResultsGenotypic aminoglycoside resistance was identified in 87.8% of all 6973 carbapenem-resistantEnterobacteralesblood-culture isolates, in comparison to 46.4% of colistin and 2.1% of apramycin resistance. Apramycin activity against methylated ribosomes was > 100-fold higher than other aminoglycosides. Frequencies of resistance were < 10−9at 8 × MIC. Tentative epidemiological cutoffs (ECOFFs) were determined as 8 μg/mL forE. coliand 4 μg/mL forK. pneumoniae. A single dose of 5 to 13 mg/kg resulted in a 1-log CFU reduction in the blood and peritoneum. Two doses of 80 mg/kg, resulting in an exposure that resembles the AUC observed for a single 30 mg/kg dose in humans, resulted in complete eradication of carbapenem- and aminoglycoside-resistant bacteremias.ConclusionEncouraging coverage and potent in-vivo efficacy against a selection of highly drug-resistantEnterobacteralesisolates in the mouse peritonitis model warrants further consideration of apramycin as a drug candidate for the treatment and prophylaxis of BSI.
‘Pscore’ - A Novel Percentile-Based Metric to Accurately Assess Individual Deviations in Non-Gaussian Distributions of Quantitative MRI Metrics
Authors: Hafiz Rakibul , Irfanoglu M. Okan , Nayak Amritha , Pierpaoli Carlo 
Published: December 2023

ABSTRACTBACKGROUNDQuantitative MRI metrics could be used in personalized medicine to assess individuals against normative distributions. Conventional Zscore analysis is inadequate in the presence of non-Gaussian distributions. Therefore, if quantitative MRI metrics deviate from normality, an alternative is needed.PURPOSETo confirm non-Gaussianity of diffusion MRI (dMRI) metrics on a publicly available dataset, and to propose a novel percentile-based method, ‘Pscore’ to address this issue.STUDY TYPERetrospective cohortPOPULATION961 healthy young-adults (age:22-35 years, Females:53%) from the Human Connectome ProjectFIELD STRENGTH/SEQUENCE3-T, spin-echo diffusion echo-planar imaging, T1-weighted: MPRAGEASSESSMENTThe dMRI data were preprocessed using the TORTOISE pipeline. Forty-eight regions of interest (ROIs) from the JHU-atlas were redrawn on a study-specific diffusion tensor (DT) template and average values were computed from various DT and mean apparent propagator (MAP) metrics. For each ROI, percentile ranks across participants were computed to generate ‘Pscores’– which normalized the difference between the median and a participant’s value with the corresponding difference between the median and the 5th/95thpercentile values.STATISTICAL TESTSROI-wise distributions were assessed using Log transformations, Zscore, and the ‘Pscore’ methods. The percentages of extreme values above-95thand below-5thpercentile boundaries (PEV>95(%),PEV<5(%)) were also assessed in the overall white matter. Bootstrapping was performed to test the reliability of Pscores in small samples (n=100) using 100 iterations.RESULTSThe dMRI metric distributions were systematically non-Gaussian, including positively skewed (e.g., mean and radial diffusivity) and negatively skewed (e.g., fractional and propagator anisotropy) metrics. This resulted in unbalanced tails in Zscore distributions (PEV>95≠5%,PEV<5≠5%) whereas ‘Pscore’ distributions were symmetric and balanced (PEV>95=PEV<5=5%); even for small bootstrapped samples (average.DATA CONCLUSIONThe inherent skewness observed for dMRI metrics may preclude the use of conventional Zscore analysis. The proposed ‘Pscore’ method may help estimating individual deviations more accurately in skewed normative data, even from small datasets.
FOXA2 is essential for maintaining the urea cycle in acute liver failure
Authors: Feng Rilu , Liu Rui , Tong Chenhao , Lin Tao , Li Xiaofeng , Liu Hui , Shao Chen , Kan Kejia , Sticht Carsten , Li Yujia , Wang Sai , Munker Stefan , Wirth Ulrich , Niess Hanno , Liebe Roman , Meyer Christoph , Wang Shanshan , Ebert Matthias P , Dooley Steven , Ding Huiguo , Wang Hua , Weng Hong-Lei 
Published: December 2023

AbstractHepatic encephalopathy is a lethal complication of acute liver failure (ALF), and is caused by hyperammonemia. Ammonia clearance by the liver requires an intact and complete urea cycle comprising six enzymes, including the rate-limiting enzyme carbamoyl phosphate synthetase I (CPS1). To date, the detailed regulation of CPS1 transcription in order to maintain urea cycle in physiological condition and ALF remains largely unknown. This study scrutinizes the role of pioneer factor forkhead box A 2 (FOXA2) in the regulation of CPS1 transcription, urea cycle performance and hyperammonemia. Physiologically, CPS1 transcription requires FOXA2 to maintain chromatin accessibility on its enhancers, which is essential for CCAAT enhancer-binding protein-alpha (C/EBPα) binding to activate gene transcription. In ALF, hepatic C/EBPα expression is inhibited by inflammatory mediators such as TGF-β and TNF-α. In this setting, retinoic acid receptor synergizes with FOXA2 to maintain CPS1 transcriptions. Once ALF patients suffer from massive hepatic necrosis, liver progenitor cells initiate a transcription network comprising FOXA2 and C/EBPα to perform the urea cycle and prevent hyperammonemia. In ALF, hepatic encephalopathy occurs in patients lacking hepatic FOXA2 expression. In mice with acetaminophen-induced ALF, injection of Foxa2-AAV8 maintains urea cycle and prevents hyperammonemia. Taken together, FOXA2 is essential for maintaining the urea cycle. Pharmaceutical induction of hepatic FOXA2 expression might represent a novel approach to treat hepatic encephalopathy in ALF.One Sentence SummaryPioneer factor FOXA2 synergizes with C/EBPα or RAR to maintain urea cycle in acute liver failure
Short-run dynamics and long-run effects of monetary policy on residential property prices in South Africa
Authors: Mwanyepedza Robert , Mishi Syden 
Published: December 2023

Purpose
The study aims to estimate the short- and long-run effects of monetary policy on residential property prices in South Africa. Over the past decades, there has been a monetary policy shift, from targeting money supply and exchange rate to inflation. The shifts have affected residential property market dynamics.

Design/methodology/approach
The Johansen cointegration approach was used to estimate the effects of changes in monetary policy proxies on residential property prices using quarterly data from 1980 to 2022.

Findings
Mortgage finance and economic growth have a significant positive long-run effect on residential property prices. The consumer price index, the inflation targeting framework, interest rates and exchange rates have a significant negative long-run effect on residential property prices. The Granger causality test has depicted that exchange rate significantly influences residential property prices in the short run, and interest rates, inflation targeting framework, gross domestic product, money supply consumer price index and exchange rate can quickly return to equilibrium when they are in disequilibrium.

Originality/value
There are limited arguments whether the inflation targeting monetary policy framework in South Africa has prevented residential property market boom and bust scenarios. The study has found that the implementation of inflation targeting framework has successfully reduced booms in residential property prices in South Africa.
Students' mathematization in mathematics classrooms using the Thailand lesson study incorporated open approach model
Authors: Bunlang Sunti , Inprasitha Maitree , Changsri Narumon 
Published: December 2023

PurposeThe purpose of this paper is to explore students' mathematization through a flow of lessons using the Thailand Lesson Study Incorporated Open Approach (TLSOA) to improve the excellence of instruction.Design/methodology/approachA total of 16 Grade 4 students were selected because they have been taught using the TLSOA model for four years. Six Lesson Study (LS) team members participated, and two instruments were utilized, namely student worksheets, and field notes. An ethnographic research design was employed.FindingsThe results revealed that the students' mathematical ideas were developed from the real world to the mathematical world through a flow of lessons based on the four phases of the Open Approach (OA).Practical implicationsFirstly, the students demonstrated their ability to represent the real world independently when the teacher posed an open-ended problem. Secondly, the students demonstrated their ability to use semi-concrete aids to develop their ideas while self-learning. Thirdly, the students showed how they developed their ideas to solve the open-ended problem using relevant objects or related concepts as part of a whole-class discussion and comparison exercise. Finally, the students demonstrated their abilities to represent the mathematical world using numbers and symbols to communicate their ideas when they were required to make a summary by connecting their mathematical ideas.Originality/valueThis study adds new insight to the literature on students' mathematization using the TLSOA model.
“I can't look at you while talking!” – fear of missing out and smartphone addiction as predictors of consumer's phubbing behavior
Authors: Paul Justin , Manchanda Parul , Arora Nupur , Aggarwal Aanchal 
Published: December 2023

PurposeSmartphones have become a vital element of daily life and because of this ongoing reliance, consumer' attention is drawn to online platforms, which may harm societal communications. Therefore, this paper investigates a behavioral addiction known as “fear of missing out” (FoMO), which causes anxiety and leads to more problematic smartphone usage and phubbing behavior (PB). In addition, this paper examines the multidimensional perspective of smartphone addiction (SMA) and the moderating role of Big 5 personality types in the aforesaid relationship.Design/methodology/approachAn online questionnaire was administered, to collect data from 468 smartphone users from universities across India. Partial least squares structural equation modeling and Hayes' PROCESS macros were employed as statistical tools for analysis.FindingsResults highlight that there is a significant association between FoMO and PB with SMA as a significant mediator with partial mediation effect.Originality/valueConscientiousness, neuroticism and extroversion were found to be significant moderators in the model. Further, the findings raise awareness regarding smartphone etiquette and additional technology literacy required in this field.
Systemic therapy timing and use in patients with advanced melanoma at the end of life: A retrospective cohort study
Authors: van Lith P. E. A. , Schreuder K. , Jalving M. , Reyners A. K. L. , Been L. B. , Rácz E. , Fransen H. P. , Louwman M. W. J. 
Published: December 2023

AbstractNovel systemic therapies for advanced melanoma improve survival, but carry potential serious side effects and high costs. This study aimed to assess the timing and use of systemic therapies in the months before death. Patients diagnosed with advanced melanoma (July 2017–June 2020) who died before July 2020 were selected from the Netherlands Cancer Registry. We evaluated the timing of systemic therapies within 30 days and 3 months before death, and studied patient and tumor characteristics associated with systemic therapy use between diagnosis and death. Out of 1097 patients 68% received systemic therapy. Almost 25% and 10% started a new therapy within 90 days and within 30 days before death, respectively. Female sex, elevated LDH, BRAF mutation, poor ECOG performance status (≥3), and high comorbidity index reduced the odds of receiving immune therapy. Poor performance status and high comorbidity decreased the odds for both therapies. A considerable number of patients started systemic therapy shortly before death, emphasizing the importance of considering potential benefits and drawbacks through shared decision‐making.
Intimate networks of care: Perceptions of intergenerational family care and experiences of ageing among Chinese midlife and older lesbians and gay men
Authors: Lo Iris Po Yee , Liu Emma H. , Lai Daniel W. L. , Yan Elsie 
Published: December 2023

AbstractThis article examines how lesbians and gay men imagine and build their ‘intimate networks of care’ and negotiate moral expectations towards intergenerational family care as they age. To date, little is known about the strength and complexities of different intimate ties or the role of intergenerational dynamics in shaping ageing sexual minority people’s care needs and choices. Based on narrative interviews with ageing Chinese lesbians and gay men, the findings reveal their experiences of constantly juggling their ties with families of origin, moral values around intergenerational care and the urge to receive support from and offer support to chosen networks of people. Participants exercised agency in expanding their networks of care by building friendship and (online and offline) community networks for mutual care and support in later life. Nevertheless, as evidenced by the centrality of ageing with(out) children, and the moral obligation of caring for parents in participants’ narratives, participants experienced tensions between enacting what was considered morally right/wrong and developing networks of care that were perceived as emotionally intimate. Linking relational sociology with the sociology of morality, we discuss the conceptual utility of ‘intimate networks of care’ for sociological theorising of the linkages between sexuality, care and relational lives.
Testing the environmental Kuznets curve hypothesis in South Africa using the ARDL approach
Authors: Ganda Fortune 
Published: December 2023

AbstractIn recent years, an abundance of research has been conducted on the purported environmental Kuznets curve (EKC) hypothesis, which progressively proposed an inverted U‐shaped relationship between income and emissions. The primary objective of this research is to examine the case of South Africa, which stands as a prominent example of a highly developed industrialized economy within the African continent. This study aims to explore the potential of South Africa in reducing emissions resulting from human activities. Therefore, this study utilizes the autoregressive distributed lag (ARDL) approaches. The study's findings demonstrate the existence of both the U‐shaped curve and the inverted U‐shaped EKC when considering the parameters being examined in both short‐term and long‐term scenarios. In the short term, the inflection points of per capita GDP obtained from two regressions on carbon emissions validate values within the range of US$45.675‐US$45.72. The relationship between foreign direct investment (FDI) and financial development and their effects on environmental quality have yielded inconclusive and statistically insignificant results in both periods. The long‐term impact of renewable energy usage on environmental quality, specifically in terms of carbon emissions and ecological footprint, is substantial and exhibits a negative correlation. Nevertheless, it is evident that there exists a notable positive correlation in the immediate timeframe. In the long term, human capital has a key role in reducing the ecological footprint, since it is inversely correlated with it. However, in the near term, human capital has a substantial positive relationship with environmental quality, namely in terms of carbon emissions and ecological footprint. Therefore, the study affirms that in certain cases, it is exceedingly difficult for a nation to simultaneously uphold the preservation of its natural environment and foster economic development during the initial phases of expansion, and conversely.
Pregnancy characteristics and outcomes among birthing individuals with a diagnosis of fetal alcohol syndrome
Authors: Schellenberg Hannah , Baer Rebecca J. , Bandoli Gretchen 
Published: December 2023

AbstractBackgroundFetal alcohol syndrome (FAS) can have adverse effects on health outcomes throughout the life course. Adults with FAS have an increased risk of chronic and infectious diseases. Although these conditions can affect reproductive health, few have described perinatal outcomes among individuals with an FAS diagnosis.MethodsWe analyzed data from the Study of Mothers and Infants, an administrative birth cohort derived from California birth certificates linked with a hospital discharge database. The cohort consisted of 7.3 million singleton, live births between 2005 and 2021. FAS was identified by International Classification of Diseases (ICD) codes in maternal hospital discharge records. Pregnancy and birth outcomes were captured via ICD codes in maternal or infant records. We performed descriptive analyses for pregnancy and birth outcomes by maternal FAS diagnosis.ResultsThere were 35 babies born to 30 individuals with an FAS diagnosis between 2005 and 2021 (0.5/100,000 live births). The prevalence of births to individuals with an FAS diagnosis increased over the period. Individuals with an FAS diagnosis were more likely to identify as non‐Hispanic White, or “other/multiple” race, and less likely to be Hispanic than those without FAS. They were also more likely to be publicly insured and less than 18 years old. Birthing individuals with FAS were also more likely to use nicotine during pregnancy and to have diagnoses of mental health disorders, epilepsy, substance use disorders, preexisting or gestational hypertension, and sexually transmitted infections or other infections complicating pregnancy. Infants of individuals with FAS were more likely to be born prematurely or small for gestational age and be admitted to the neonatal intensive care unit.ConclusionsThese findings highlight the need for improved recognition of FAS among birthing people. The results suggest that individuals with FAS would benefit from early and sustained medical care prior to pregnancy to optimize perinatal outcomes.