bluuebunny/crossref_metadata_2025_split huggingface dataset:
Catching a wave: on the suitability of traveling-wave solutions in epidemiological modeling
Authors: Langmüller Anna M. , Hermisson Joachim , Murdock Courtney C. , Messer Philipp W. 
Published: June 2023

AbstractOrdinary differential equation models such as the classical SIR model are widely used in epidemiology to study and predict infectious disease dynamics. However, these models typically assume that populations are homogeneously mixed, ignoring possible variations in disease prevalence due to spatial heterogeneity. To address this issue, reaction-diffusion models have been proposed as an alternative approach to modeling spatially continuous populations in which individuals move in a diffusive manner. In this study, we explore the conditions under which such spatial structure must be explicitly considered to accurately predict disease spread, and when the assumption of homogeneous mixing remains adequate. In particular, we derive a critical threshold for the diffusion coefficient below which disease transmission dynamics exhibit spatial heterogeneity. We validate our analytical results with individual-based simulations of disease transmission across a two-dimensional continuous landscape. Using this framework, we further explore how key epidemiological parameters such as the probability of disease establishment, its maximum incidence, and its final epidemic size are affected by incorporating spatial structure into SI, SIS, and SIR models. We discuss the implications of our findings for epidemiological modeling and identify design considerations and limitations for spatial simulation models of disease dynamics.
The microenvironment dictates glycocalyx construction and immune surveillance
Authors: Tharp Kevin M. , Park Sangwoo , Timblin Greg A. , Richards Alicia L. , Berg Jordan A. , Twells Nicholas M. , Riley Nicholas M. , Peltan Egan L. , Shon D. Judy , Stevenson Erica , Tsui Kimberly , Palomba Francesco , Lefebvre Austin E. Y. T. , Soens Ross W. , Ayad Nadia M.E. , ten Hoeve-Scott Johanna , Healy Kevin , Digman Michelle , Dillin Andrew , Bertozzi Carolyn R. , Swaney Danielle L. , Mahal Lara K. , Cantor Jason R. , Paszek Matthew J. , Weaver Valerie M. 
Published: June 2023

SummaryEfforts to identify anti-cancer therapeutics and understand tumor-immune interactions are built within vitromodels that do not match the microenvironmental characteristics of human tissues. Usingin vitromodels which mimic the physical properties of healthy or cancerous tissues and a physiologically relevant culture medium, we demonstrate that the chemical and physical properties of the microenvironment regulate the composition and topology of the glycocalyx. Remarkably, we find that cancer and age-related changes in the physical properties of the microenvironment are sufficient to adjust immune surveillance via the topology of the glycocalyx, a previously unknown phenomenon observable only with a physiologically relevant culture medium.Key PointsCulture medium dictates cellular mechanoresponse signatures in vitroEpithelial glycocalyx construction is mediated by Heat Shock Factor 1 (HSF1)Sialic acid topology dictates Natural Killer cell cytotoxicityPhysiological microenvironments reveal distinct glycobiology
Fluorogenesis: Inducing Fluorescence in a Non-Fluorescent Protein Through Photoinduced Chromophore Transfer of a Genetically Encoded Chromophore
Authors: Kumar Yashwant , Singh Reman Kumar , Ojha Manisha , Pushpavanam Karthik 
Published: June 2023

ABSTRACTFluorescent proteins, while essential for bioimaging, are limited to visualizing cellular localization without offering additional functionality. We report for the first time a strategy to expand the chemical, structural, and functional diversity of fluorescent proteins by harnessing light to induce red fluorescence in a previously non-fluorescent protein. We accomplish this by inducing the transfer of the genetically encoded chromophore from a photocleavable protein (PhoCl1) to a non-fluorescent kinase (MjRibK) inducing red fluorescence in the latter. We have employed analytical and spectroscopic techniques to validate the presence of red fluorescence inMjRibK. Furthermore, molecular dynamics simulations were carried out to investigate the amino acid residues ofMjRibK involved in the generation of red fluorescence. Finally, we demonstrate the ability of the red fluorescentMjRibK to operate as a cyclable high-temperature sensor. We anticipate that this light-induced chromophore transfer strategy will open new possibilities for developing multifunctional genetically encoded fluorescent sensors.
PARP14 is a PARP with both ADP-ribosyl transferase and hydrolase activities
Authors: Đukić Nina , Strømland Øyvind , Munnur Deeksha , Zhu Kang , Schuller Marion , Chatrin Chatrin , Kar Pulak , Rack Johannes Gregor Matthias , Baretić Domagoj , Schüler Herwig , Wijngaarden Sven , Filippov Dmitri V. , Sanyal Sumana , Smith Rebecca , Ahel Dragana , Ahel Ivan 
Published: June 2023

AbstractPARP14 is a mono-ADP-ribosyl transferase involved in the control of immunity, transcription and DNA replication stress management. However, little is known about the ADP-ribosylation activity of PARP14, including its substrate specificity or how PARP14-dependent ADP-ribosylation is reversed. Here we show that PARP14 is dual function enzyme with both ADP-ribosyl transferase and hydrolase activity acting on both protein and nucleic acid substrates. In particular, we show that the PARP14 macrodomain 1 is an active ADP-ribosyl hydrolase. We also demonstrate hydrolytic activity for the first macrodomain of PARP9. We reveal that expression of a PARP14 mutant with the inactivated macrodomain 1 results in a dramatic increase in mono(ADP-ribosyl)ation of proteins in human cells, including PARP14 itself and antiviral PARP13. Moreover, we demonstrate that the closely related hydrolytically active macrodomain of SARS2 Nsp3, Mac1, efficiently reverses PARP14 ADP-ribosylationin vitroand in cells, supporting the evolution of viral macrodomains to counteract PARP14-mediated antiviral response.TeaserPARP14 is an antiviral PARP that combines ADP-ribosylation writer, reader and eraser functions in one polypeptide.
Dynamic ParB-DNA interactions initiate and maintain a partition condensate for bacterial chromosome segregation
Authors: Tišma Miloš , Janissen Richard , Antar Hammam , Gonzalez Alejandro Martin , Barth Roman , Beekman Twan , van der Torre Jaco , Michieletto Davide , Gruber Stephan , Dekker Cees 
Published: June 2023

AbstractIn most bacteria, chromosome segregation is driven by the ParABSsystem where the CTPase protein ParB loads at theparSsite to trigger the formation of a large partition complex. Here, we presentin vitrostudies of the partition complex forBacillus subtilisParB, using single-molecule fluorescence microscopy and AFM imaging to show that transient ParB-ParB bridges are essential for forming DNA condensates. Molecular Dynamics simulations confirm that condensation occurs abruptly at a critical concentration of ParB and show that multimerization is a prerequisite for forming the partition complex. Magnetic tweezer force spectroscopy on mutant ParB proteins demonstrates that CTP hydrolysis at the N-terminal domain is essential for DNA condensation. Finally, we show that transcribing RNA polymerases can steadily traverse the ParB-DNA partition complex. These findings uncover how ParB forms a stable yet dynamic partition complex for chromosome segregation that induces DNA condensation and segregation while enabling replication and transcription.
Vacuolar H+-ATPase Determines Daughter Cell Fates through Asymmetric Segregation of the Nucleosome Remodeling and Deacetylase Complex
Authors: Xie Zhongyun , Chai Yongping , Zhu Zhiwen , Shen Zijie , Guo Zhengyang , Zhao Zhiguang , Xiao Long , Du Zhuo , Ou Guangshuo , Li Wei 
Published: June 2023

AbstractAsymmetric cell divisions (ACDs) generate two daughter cells with identical genetic information but distinct cell fates through epigenetic mechanisms. However, the process of partitioning different epigenetic information into daughter cells remains unclear. Here, we demonstrate that the nucleosome remodeling and deacetylase (NuRD) complex is asymmetrically segregated into the surviving daughter cell rather than the apoptotic one during ACDs inCaenorhabditis elegans. The absence of NuRD triggers apoptosis via the EGL-1-CED-9-CED-4-CED-3 pathway, while an ectopic gain of NuRD enables apoptotic daughter cells to survive. We identify the vacuolar H+–adenosine triphosphatase (V-ATPase) complex as a crucial regulator of NuRD’s asymmetric segregation. V-ATPase interacts with NuRD and is asymmetrically segregated into the surviving daughter cell. Inhibition of V-ATPase disrupts cytosolic pH asymmetry and NuRD asymmetry. We suggest that asymmetric segregation of V-ATPase may cause distinct acidification levels in the two daughter cells, enabling asymmetric epigenetic inheritance that specifies their respective life-versus-death fates.
Packaging journey from retail to home: how the meaning of sustainability for colour transforms
Authors: Sekki Sanna , Kauppinen-Räisänen Hannele , Kylkilahti Eliisa , Autio Minna 
Published: June 2023

Purpose Research has largely disregarded consumer–packaging interaction in contexts other than retail. Focusing on the powerful cue of colour and consumers’ pleas for sustainability and drawing on the customer journey and moments of consumption, this study investigates how packaging colour meanings are redefined from retail to home and how the meaning of sustainability for colour transforms.Design/methodology/approach A qualitative methodology was employed with 27 informants, who were interviewed in pairs or in small groups of three.Findings First, colour meanings emerge outside the retail context, confirming the idea of the packaging journey. Colours are dynamic, as meanings are redefined throughout the voyage. In retail, colour conveys brand, product, environmental and origin-related meanings, while at home it conveys product, food- and health-related meanings. At the end of the journey, colour communicates disposal, environmental, health and origin-related meanings. Second, the meaning of sustainability for colour transforms during the voyage from being conveyed by a colour hue to being perceived as a material and, therefore, as a waste and recycling concern.Originality/value The study adds insight into the role of colour in the packaging life cycle, wherein colour transforms from a visual packaging cue to an issue of materiality. The recyclability of colours is a prevailing sustainability issue that deserves attention within the packaging industry. The study argues that although the consumer–packaging interaction in the retail context is essential, managers should recognise that the interaction continues with colours from in-store purchase decisions to consumers’ homes (use and recycling).
Baseline knee osteoarthritis radiographic severity as a predictor of symptom response to diet and exercise program: A secondary analysis
Authors: Dissanayaka Thusharika D. , Deveza Leticia A. , Heller Gillian , Robbins Sarah R. , Hunter David J. 
Published: June 2023

AbstractObjectiveTo investigate whether baseline joint space narrowing (JSN) predicted disease remission, knee pain, and physical function changes in persons with knee osteoarthritis (OA).MethodsThis study is a secondary analysis of a two‐armed randomized controlled trial. Participants were aged ≥50 years (n = 171) with a body mass index ≥28 kg/m2 and radiographic medial tibiofemoral OA. Participants in the intervention group received diet and exercise programs and special treatment (cognitive behavioral therapy, knee brace, and muscle strengthening exercises) according to the disease remission. Remission of pain and remission of patient global assessment of disease activity and/or functional impairment were used to define the disease remission. The control group were provided with an education pamphlet. The primary outcome was disease remission at 32 weeks, and the secondary outcomes were the changes in knee pain and physical function at 20 and 32 weeks. Baseline JSN was scored from 0 to 3, and the association between baseline JSN and outcomes was assessed using multiple regression.ResultsThere was no association of baseline JSN with disease remission at 32 weeks when the disease remission has been achieved. The baseline JSN grade 3 was associated with changes in knee pain at 20 weeks (p < .05). There was no association between baseline JSN and physical function.ConclusionBaseline JSN severity predicted changes in knee pain but not the disease remission or changes in physical functions. Identification of baseline radiographic severity may be helpful in identifying differences in response to diet and exercise programs in knee OA.
Increasing rates of sars‐cov‐2 infection in newborns during the omicron variant epoch
Authors: Eid Joe , Post Sara , Guhde Heather , Basuray Rakhi Gupta , Sanchez Pablo J. , Costantine Maged M. , Rood Kara M. 
Published: June 2023

AbstractProblemTransmission of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) from infected pregnant individuals to the fetus or newborn occurs from 1.2% to 4.3%. Our aim was to determine the rate of positivity among newborns delivered to infected mothers during epochs of different variants predominance.Method of studyThis is a single academic center retrospective cohort study where we reviewed the electronic health records of pregnant individuals who tested positive for SARS‐CoV‐2 infection and their newborns from March 2020 through January 2022. Infants born to SARS‐CoV‐2‐positive mothers at the time of delivery or within 10 days of admission were tested for SARS‐CoV‐2 infection at 24–36 h of age.ResultsA total of 195 mothers were positive at delivery or within 10 days of admission and had their newborns tested for SARS‐CoV‐2. Seven newborns (3.6%) were positive. All positive infants were asymptomatic and born to unvaccinated mothers. Newborn positivity for SARS‐CoV‐2 was highest during the Omicron epoch (9.4%, p = .01).ConclusionIncreasing positivity rate was seen during the Omicron variant predominance. This could be attributed to postnatal acquisition of the virus, as Omicron has been associated with higher transmissibility in older children and adults.
Metabolic characterization of human sperm cells using the Seahorse metabolic flux analyzer
Authors: Freitas‐Martins Artur , Sousa Maria Inês , Cristo Maria Inês , Ramalho‐Santos João , Amaral Sandra 
Published: June 2023

AbstractBackgroundThe concerning trend on male infertility global prevalence, together with the unexplainable causes in half of those cases, highlights that there are still aspects of this disease to be understood and solved. To address this issue, one should not only be aware of the limitations of the implemented diagnostic tools, but also understand the sperm cell in depth, structurally, biochemically, molecularly in order to develop reliable and ready‐to‐be new/improved diagnostic tools. In this sense, the sperm cells metabolism, highly related to its functionality, seems to be a promising aspect to explore. Though there is much information on the human sperm metabolism, there is still a lack of a quick integrated and comprehensive analysis that may be introduced with the potential to reveal innovative clinically relevant information.ObjectivesFind metabolic details on human sperm that can be accessed easily, in real time and using few cells, relying on the bivalent potential of the Seahorse flux analyzer (SFA).ResultsWe have obtained standard records on human sperm cells’ oxygen consumption rate (OCR) and extracellular acidification rate (ECAR), that together with the metabolic metrics provided information on sperm cells’ oxidative and glycolytic metabolism. Furthermore, a metabolic interindividual variation was observed.Discussion and conclusionAlthough the comparison with other species or cell types is not linear and warrant further studies, the metabolic profile of human sperm cells seems to be similar to that of other species. Altogether our results corroborate the value of SFA for metabolic human sperm cell analysis, warranting new studies, and anticipating several applications in the male infertility field.
‘Staying Close’: Enabling social interdependence for young people leaving residential care in England
Authors: Allen Dan 
Published: June 2023

AbstractApplying social interdependence theory as a framework for document analysis, this paper considers eight evaluations of an extended care scheme in England known as ‘Staying Close’. Findings suggest that for extended care projects like ‘Staying Close’ to work, any service offer designed to support the transition from residential care to independent living must be seen by the young person, the carer, and the wider social network, as a continuation of earlier efforts to build and nurture a genuinely committed relationship. A new interrelations model for extended care is introduced and implications are discussed for strategic responses that enable young people, their carers and wider social network to promote opportunities for social interdependence.
Cytomorphology of paediatric hepatocellular carcinoma: A useful diagnostic adjunct
Authors: Nalwa Aasma , Nakra Tripti , Yadav Rajni , Walia Ritika , Agarwala Sandeep , Jana Manisha , Jain Deepali , Das Prasenjit , Mathur Sandeep R. , Iyer Venkateswaran K. 
Published: June 2023

AbstractIntroductionHepatocellular carcinoma (HCC) is a common primary malignancy of the liver but is rare in the paediatric age group; thus, it may be misdiagnosed as the more common tumour, hepatoblastoma. Management varies in both these tumours, and pathological diagnosis thus plays an important role for definitive therapy. Only a few case reports available in the literature have described the cytological characteristics of paediatric HCC. The present study was thus planned to evaluate the cytomorphological features of paediatric HCC.MethodsCases diagnosed with HCC on ultrasound‐guided fine needle aspiration cytology over a period of 14 years were retrieved. The cases were evaluated for detailed cytological features including cellularity, architecture, sinusoidal wrapping, trabecular thickness, necrosis, anisonucleosis, chromatin, nucleoli, nuclear contours, bi‐ or multinucleation, intranuclear and intracytoplasmic inclusions, naked nuclei, extra‐medullary haematopoiesis, monomorphism, and nuclear overlapping.ResultsTwelve cases of HCC were included in the study. The median age at diagnosis was 10 years. Serum alpha‐fetoprotein level was raised in most of them. Five of the 12 cases were characterised as moderately differentiated, three as poorly differentiated, two as well differentiated, and two as the fibrolamellar type of HCC. Cytohistological correlation was performed in seven cases.ConclusionsUltrasound‐guided fine needle aspiration serves as a useful tool to diagnose paediatric HCC and differentiate it from other primary hepatic malignancies, especially hepatoblastoma which closely mimics HCC in this age group, as serum alpha protein levels and imaging findings are unable to distinguish these two tumours.
A simple ATTR‐CM score to identify transthyretin amyloid cardiomyopathy burden in HFpEF patients
Authors: Ye Min , Liu Xiao , Gu Zhenbang , Sun Junyi , Dong Yugang , Chen Yili , Liu Chen , Wu Zexuan , Zhu Wengen 
Published: June 2023

AbstractBackgroundTransthyretin amyloid cardiomyopathy (ATTR‐CM) is often found in patients with heart failure with preserved ejection fraction (HFpEF). However, the evidence regarding ATTR‐CM and prognosis in HFpEF remains scarce. This study sought to determine whether the ATTR‐CM burden was associated with clinical outcomes in HFpEF patients.MethodsWe evaluated the associations of baseline ATTR‐CM score with adverse outcomes in HFpEF patients from the TOPCAT trial using the Cox proportional hazards model or the competing risk regression model. The discriminatory ability of the ATTR‐CM score was assessed using the area under the time‐dependent receiver operating characteristic curve (AUC).ResultsWe included 870 HFpEF patients, 18.9% of which had an ATTR‐CM score ≥6. Per 1 increment in the ATTR‐CM score was significantly associated with an increased risk of the primary outcome (adjusted hazard ratio [HR] 1.19, 95% confidence interval [CI] 1.12–1.27) with an AUC of 0.652 (0.594–0.711), whereas patients with ATTR‐CM score ≥6 presented higher risks of the primary outcome (adjusted HR 2.20, 95% CI 1.65–2.95). Similar results were observed toward the secondary outcomes.ConclusionsThe simple ATTR‐CM score identified an 18.9% ATTR‐CM burden in HFpEF patients, and a higher ATTR‐CM burden might predict adverse outcomes with moderate discriminatory abilities in HFpEF.
Birth outcomes in pregnant women with epilepsy: A Nationwide multicenter study from Türkiye
Authors: Pekoz Mehmet Taylan , Aslan‐Kara Kezban , Tekin Betül , Gurses Candan , Yeni Seher Naz , Bozdemir Hacer , Keskin‐Guler Selda , Ataklı Dilek , Gul Gunay , Eren Fulya , Sarı Hüseyin , Gul Zeynep Baştug , Ceyhan‐Dirican Ayten , Genc Fatma , Bicer‐Gomceli Yasemin , Ozkara Cigdem , Delil Sakir , Atalar Arife Cimen , Bebek Nerses , Baykan Betül , Bora İbrahim , Bican‐Demir Aylin , Mısırlı Cemile Handan , Tutkavul Kemal , Velioglu Sibel K. , Ilhan‐Algin Demet , Erdinc Oguz , Saygi Serap , Tezer‐Fılık Irsel , Apaydın‐Dogan Ebru , Akyol Ali , Kamisli Ozden , Yalcın A. Destina , Cakmak Gonul , Ersoy Alevtina , Ustun‐Ozek Sibel , Halac Gulistan , Kutlu Gulnihal , Tantik‐Pak Aygul , Yücel Sevinc P. 
Published: June 2023

AbstractObjectiveThe present study was aimed at investigating the effects of anti‐seizure medications (ASMs), patient demographic characteristics, and the seizure type and frequency on the development of congenital malformations (CMs) in the infants of pregnant women with epilepsy (PWWE).MethodsPWWE followed up at the neurology outpatient clinic of 21 centers between 2014 and 2019 were included in this prospective study. The follow‐up of PWWE was conducted using structured, general pregnant follow‐up forms prepared by the Pregnancy and Epilepsy Study Committee. The newborns were examined by a neonatologist after delivery and at 1 and 3 months postpartum.ResultsOf the infants of 759 PWWE, 7.2% had CMs, with 5.6% having major CMs. Polytherapy, monotherapy, and no medications were received by 168 (22.1%), 548 (72.2 %), and 43 (5.7 %) patients, respectively. CMs were detected at an incidence of 2.3% in infants of PWWE who did not receive medication, 5.7% in infants of PWWE who received monotherapy, and 13.7% in infants of PWWE who received polytherapy. The risk of malformation was 2.31‐fold (95% confidence interval (CI): 1.48–4.61, p < .001) higher in infants of PWWE who received polytherapy. Levetiracetam was the most frequently used seizure medication as monotherapy, with the highest incidence of CMs occurring with valproic acid (VPA) use (8.5%) and the lowest with lamotrigine use (2.1%). The incidence of CMs was 5% at a carbamazepine dose <700 mg, 10% at a carbamazepine dose ≥700 mg, 5.5% at a VPA dose <750 mg, and 14.8% at a VPA dose ≥750 mg. Thus the risk of malformation increased 2.33 times (p = .041) in infants of PWWE receiving high‐dose ASMs.SignificanceBirth outcomes of PWWE receiving and not receiving ASMs were evaluated. The risk of CMs occurrence was higher, particularly in infants of PWWE using VPA and receiving polytherapy. The incidence of CMs was found to be lower in infants of PWWE receiving lamotrigine.