bluuebunny/crossref_metadata_2025_split huggingface dataset:
No evidence that shrinking and shapeshifting meaningfully affect how birds respond to warming and cooling
Authors: Tabh Joshua K.R. , Persson Elin , Correia Maria , Cuív Ciarán Ó , Thoral Elisa , Nord Andreas 
Published: March 2024

AbstractAcross the globe, birds and mammals are becoming smaller and longer-limbed. Although the cause of these changes is unclear, many argue that each provide thermoregulatory benefits in a warmer world by easing heat dissipation. Here, we show that neither body size nor limb length in a model species (the Japanese quail) influenced metabolic costs of warming during a cold challenge. In the heat, larger body sizes increased metabolic costs of thermoregulation, however, this effect was moderate and almost always negated by cooling from the limbs (>97% of cases). Rearing in the warmth (30°C) relative to the cold (10°C) reduced body sizes and increased limb lengths at adulthood but thermoregulatory benefits of these changes in later heat exposures were absent. Our findings demonstrate that shrinking and shape-shifting are unlikely to ease thermoregulation in contemporary birds or reflect selection for such. Alternative contributors, including neutral or non-adaptive plasticity, should be further investigated.TeaserUsing experimental data, we show for the first time that shrinking and shape-shifting – which has been described as the third general response to climate change in animals – does not inherently provide thermoregulatory benefits to birds in a warming world. Further research evaluating the drivers of shape-shifts (including neutral plasticity and temporal reductions in resource abundance) is needed before we can determine why animals shrink under climate change.
SERBP1 interacts with PARP1 and is present in PARylation-dependent protein complexes regulating splicing, cell division, and ribosome biogenesis
Authors: Breunig Kira , Lei Xiufen , Montalbano Mauro , Guardia Gabriela D. A. , Ostadrahimi Shiva , Alers Victoria , Kosti Adam , Chiou Jennifer , Klein Nicole , Vinarov Corina , Wang Lily , Li Mujia , Song Weidan , Kraus W. Lee , Libich David S. , Tiziani Stefano , Weintraub Susan T. , Galante Pedro A. F. , Penalva Luiz O. F. 
Published: March 2024

ABSTRACTRNA binding proteins (RBPs) containing intrinsically disordered regions (IDRs) are present in diverse molecular complexes where they function as dynamic regulators. Their characteristics promote liquid-liquid phase separation (LLPS) and the formation of membraneless organelles such as stress granules and nucleoli. IDR-RBPs are particularly relevant in the nervous system and their dysfunction is associated with neurodegenerative diseases and brain tumor development. Serpine1 mRNA-binding protein 1 (SERBP1) is a unique member of this group, being mostly disordered and lacking canonical RNA-binding domains. We defined SERBP1’s interactome, uncovered novel roles in splicing, cell division and ribosomal biogenesis, and showed its participation in pathological stress granules and Tau aggregates in Alzheimer’s brains. SERBP1 preferentially interacts with other G-quadruplex (G4) binders, implicated in different stages of gene expression, suggesting that G4 binding is a critical component of SERBP1 function in different settings. Similarly, we identified important associations between SERBP1 and PARP1/polyADP-ribosylation (PARylation). SERBP1 interacts with PARP1 and its associated factors and influences PARylation. Moreover, protein complexes in which SERBP1 participates contain mostly PARylated proteins and PAR binders. Based on these results, we propose a feedback regulatory model in which SERBP1 influences PARP1 function and PARylation, while PARylation modulates SERBP1 functions and participation in regulatory complexes.
Genetic designs for stochastic and probabilistic biocomputing
Authors: Grozinger Lewis , Miró-Bueno Jesús , Goñi-Moreño Ángel 
Published: March 2024

AbstractThe programming of computations in living cells can be done by manipulating information flows within genetic networks. Typically, a single bit of information is encoded by a single gene’s steady state expression. Expression is discretized into high and low levels that correspond to 0 and 1 logic values, analogous to the high and low voltages in electronic logic circuits. However, the processes of molecular signaling and computation in living systems challenge this computational paradigm with their dynamic, stochastic and continuous operation. Although there is a good understanding of these phenomena in genetic networks, and there are already stochastic and probabilistic models of computation which can take on these challenges, there is currently a lack of work which puts both together to implement computations tailored to these features of living matter. Here, we design genetic networks for stochastic and probabilistic computing paradigms and develop the theory behind their operation. Moving beyond the digital abstraction, we explore the concepts of bit-streams (sequences of pulses acting as time-based signals) and probabilistic-bits or p-bits (values that can be either 1 or 0 with an assigned probability), as more suitable candidates for the encoding and processing of information in genetic networks. Specifically, the conceptualization of signals as stochastic bit-streams allows for encoding information in the frequency of random expression pulses, offering advantages such as robustness to noise. Additionally, the notion of p-bit enables the design of genetic circuits with capabilities surpassing those of current genetic logic gates, including invertibility. We design several circuits to illustrate these advantages and provide mathematical models and computational simulations that demonstrate their functionality. Our approach to stochastic and probabilistic computing in living cells not only enhances and reflects understanding of information processing in biological systems but also presents promising avenues for designing genetic circuits with advanced functionalities.
HIV and Hepatitis B virus co-infection in Mozambique: policy review and health professionals’ knowledge and practices
Authors: dos Muchangos Vanda , Chambal Lúcia , Nilsson Charlotta , Sevene Esperança 
Published: March 2024

AbstractBackgroundHuman Immunodeficiency Virus (HIV) and Hepatitis B Virus (HBV) co-infection is a public health problem affecting 2.7 million worldwide. In Mozambique, the prevalence of this co-infection is 9.1%, calling for specific policies on prevention, diagnosis and adequate management in health facilities caring for HIV patients. This study aimed to review the existing policies and to assess the knowledge and practices of health professionals about HIV/HBV co-infection.MethodsA document and literature review to describe the existing policies and guidelines on HIV/HBV co-infection in Mozambique was performed. Key informants were contacted to clarify or add information. Health Professionals who care for HIV-positive patients in four health centers in Maputo City, the capital of Mozambique, responded to a questionnaire on knowledge and practices about this co-infection. Qualitative analysis was done to identify main themes using content analysis. Descriptive statistics of socio-demographic, knowledge and practice variables was presented using the SPSS Program version 20 and bivariate analysis was applied to describe the association between variables.ResultsTwenty-one policy documents were found, and five key informants were interviewed. Fifty-two participants answered the questionnaire. Only one policy document explicitly referred to HIV/HBV co-infection treatment. Most Health Professionals (96%) were aware of HIV/HBV co-infection. Although the only existing policy is on the treatment, few (33%) referenced antiretroviral formulations containing Tenofovir and Lamivudine. Only 29% of Health Professionals reported screening HIV patients for HBV and 21% practiced HIV/HBV co-infection counselling. No statistically significant differences were found when relating the socio-demographic variables with knowledge and practices.ConclusionPolicy documents relating to prevention, diagnosis and clinical management of HIV/HBV co-infection were rare or absent. Health Professionals had little knowledge about HIV/HBV co-infection. Defining adequate policies and training of Health Professionals may help increase awareness, increase counselling of patients for disease prevention, diagnosis and proper management of HIV/HBV co-infected patients.
A CRISPR mediated point-of-care assay for the detection of mucosal calprotectin in an animal model of ulcerative colitis
Authors: Chia Selena , Guo Tianruo , Goldys Ewa M. , Payne Sophie C. , Lovell Nigel H. , Shivdasani Mohit N. , Deng Fei 
Published: March 2024

AbstractInflammatory bowel disease (IBD) is a chronic disorder associated with inflammation in the gastrointestinal tract, leading to a range of debilitating symptoms. Fecal calprotectin is an established biomarker for ulcerative colitis (UC), one of the main IBD diseases, which provides indications of the presence and severity of inflammation in the digestive tract. Enzyme-Linked Immunosorbent Assay (ELISA) as a gold standard approach for fecal calprotectin detection is time-consuming and impractical in point-of-care settings. Moreover, obtaining fecal samples from patients is challenging and inhibits longitudinal monitoring. To overcome these limitations, we designed a new approach for detecting calprotectin which leverages clustered regularly interspaced short palindromic repeats (CRISPR)/Cas technology. We successfully developed a portable tube-based CRISPR/Cas assay for point-of-care testing of calprotectin. This assay showed a detection range from 1-10000 ng/mL (over 4 log units), using both fluorescent and colorimetric analytical techniques. The established assay was further validated through measurements in mucosal samples obtained in an anesthetised preclinical rodent model of UC, with 2-3 times higher calprotectin concentration detected in UC rat samples compared to that of healthy control animals. This point-of-care test may provide a rapid, precise, and user-friendly approach for the diagnosis and monitoring of IBD through mucosal sample testing.
Discovery and heterologous expression of functional 4-O-dimethylallyl-L-tyrosine synthases from lichen-forming fungi
Authors: Iacovelli Riccardo , He Siqi , Sokolova Nika , Lokhorst Iris , Borg Maikel , Fodran Peter , Haslinger Kristina 
Published: March 2024

ABSTRACTFungal DMATS-type aromatic prenyltransferases are a family of biosynthetic enzymes that catalyze the prenylation of a range of aromatic substrates during the biosynthesis of bioactive indole alkaloids, diketopiperazines, and meroterpenoids. Together with their broad substrate scope and soluble nature, this makes DMATS-type prenyltransferases particularly adept for applications in biocatalysis, for example to derivatize aromatic drug leads and improve their bioactivity. Here, we investigated four putative DMATS-type prenyltransferases from lichen-forming fungi, an underexplored group of organisms that produce more than 1,000 unique metabolites. We were able to successfully express two functional lichen prenyltransferases in the heterologous hostA. oryzae, which allowed us to identify them as 4-O-dimethylallyltyrosine synthases. Our extensive bioinformatic analysis shows that related lichen prenyltransferases are likely not active on indoles but rather on aromatic polyketides and phenylpropanoids, common metabolites in these organisms. Overall, our work not only provides new insights into fungal DMATS-type prenyltransferases at the family level, but it also enables future efforts aimed at identifying new candidates for biocatalytic transformations of aromatic compounds.
Selective Posterior Cerebral Artery Wada Better Predicts Good Memory and Naming Outcomes Following Selective Stereotactic Thermal Ablation for Medial Temporal Lobe Epilepsy Than Internal Carotid Artery Wada
Authors: Drane Daniel L. , Acerbo Emma , Rogers Anna , Pedersen Nigel P. , Williamson Adam , Stern Matthew A. , Dickey Adam S. , Howard Brian M. , Bearden Donald J. , Okada Noah , Staikova Ekaterina , Gutekunst Claire Anne , Alwaki Abdulrahman , Gershon Timothy , Jirsa Viktor , Gross Robert E. , Loring David W. , Kheder Ammar , Willie Jon T. 
Published: March 2024

AbstractThe conventional intracarotid amobarbital (Wada) test has been used to assess memory function in patients being considered for temporal lobe epilepsy (TLE) surgery. Minimally invasive approaches that target the medial temporal lobe (MTL) and spare neocortex are increasingly used, but a knowledge gap remains in how to assess memory and language risk from these procedures. We retrospectively compared results of two versions of the Wada test, the intracarotid artery (ICA-Wada) and posterior cerebral artery (PCA-Wada) approaches, with respect to predicting subsequent memory and language outcomes, particularly after stereotactic laser amygdalohippocampotomy (SLAH). We included all patients being considered for SLAH who underwent both ICA-Wada and PCA-Wada at a single institution. Memory and confrontation naming assessments were conducted using standardized neuropsychological tests to assess pre- to post-surgical changes in cognitive performance. Of 13 patients who initially failed the ICA-Wada, only one patient subsequently failed the PCA-Wada (p=0.003, two-sided binomial test withp0=0.5) demonstrating that these tests assess different brain regions or networks. PCA-Wada had a high negative predictive value for the safety of SLAH, compared to ICA-Wada, as none of the patients who underwent SLAH after passing the PCA-Wada experienced catastrophic memory decline (0 of 9 subjects,p<.004, two-sided binomial test withp0=0.5), and all experienced a good cognitive outcome. In contrast, the single patient who received a left anterior temporal lobectomy after failed ICA- and passed PCA-Wada experienced a persistent, near catastrophic memory decline. On confrontation naming, few patients exhibited disturbance during the PCA-Wada. Following surgery, SLAH patients showed no naming decline, while open resection patients, whose surgeries all included ipsilateral temporal lobe neocortex, experienced significant naming difficulties (Fisher’s exact test,p<.05). These findings demonstrate that (1) failing the ICA-Wada falsely predicts memory decline following SLAH, (2) PCA-Wada better predicts good memory outcomes of SLAH for MTLE, and (3) the MTL brain structures affected by both PCA-Wada and SLAH are not directly involved in language processing.
Can motion capture improve task-based fMRI studies of motor function post-stroke? A systematic review
Authors: Belkacemi Zakaria , van Dokkum Liesjet E.H. , Tchechmedjiev Andon , Lepetit-Coiffe Matthieu , Mottet Denis , Le Bars Emmanuelle 
Published: March 2024

AbstractBackgroundVariability in motor recovery after stroke represents a major challenge in its understanding and management. While functional MRI has traditionally been used to address post-stroke motor function in relation to clinical outcome, it lacks details about movement characteristics linked to observed brain activations. Combining fMRI with detailed information of motor function by using motion capture (mocap) might provide clinicians with additional information about mechanisms of motor impairment after stroke.ObjectivesWe aimed to identify fMRI and mocap coupling approaches and to evaluate their potential contribution to the understanding of motor function post-stroke.MethodA systematic literature review was performed according to PRISMA guidelines, on studies using fMRI and mocap in post-stroke individuals. We assessed the internal, external, statistical, and technological validity of each study. Data extraction included study design and analysis procedures used to couple brain activity with movement characteristics.ResultsOf the 404 studies found, 23 were included in the final review. The overall study quality was moderate (0.6/1). The majority of studies focused on the upper limb, using a wide variety of motor tasks. Half of the studies performed a statistical analysis between movement and brain activity by either using kinematics as variables during group or individual level regression or correlation. This permitted establishing a link between motor characteristics and brain activations. Mocap was also integrated without statistical confrontation, to compare results between fMRI and kinematics, or to incorporate real-time movement information to supply external devices, like motor feedback.ConclusionOur review suggests that the simultaneous use of fMRI and Mocap provides new insights compared with conventional fMRI analysis. It allows a better understanding of post-stroke motor function, although being still subject to practical and technological limitations. Further research is needed to optimize and standardize both data measurement and processing procedures.
Global, Regional, and National Survey on Burden and Quality of Care Index (QCI) of Orofacial Clefts: Global Burden of Disease Systematic Analysis 1990–2019
Authors: Sofi-Mahmudi Ahmad , Shamsoddin Erfan , Khademioore Sahar , Khazaei Yeganeh , Tovani-Palone Marcos Roberto 
Published: March 2024

AbstractBackgroundOrofacial clefts are the most common craniofacial anomalies that include a variety of conditions affecting the lips and oral cavity. They remain a significant global public health challenge. Despite this, the quality of care for orofacial clefts has not been investigated in global and country level.ObjectiveWe aimed to measure the quality of care index (QCI) for orofacial clefts worldwide.MethodsWe used the 2019 Global Burden of Disease data to create a multifactorial index (QCI) to assess orofacial clefts globally and nationally. By utilizing data on incidence, prevalence, years of life lost, and years lived with disability, we defined four ratios aimed at indirectly reflecting the quality of healthcare. Subsequently, we conducted a principal component analysis to identify the most critical variables that could account for the observed variability. The outcome of this analysis was defined as the QCI for orofacial clefts. Following this, we tracked the QCI trends among males and females worldwide, across various regions and countries, considering factors such as the socio-demographic index and World Bank classifications.ResultsGlobally, the QCI for orofacial clefts exhibited a consistent upward trend from 1990 to 2019 (66.4 to 90.2) overall and for females (82.9 to 94.3) and males (72.8 to 93.6). In the year 2019, the top five countries with the highest QCI scores were as follows: Norway (QCI=99.9), Ireland (99.4), France (99.4), Germany (99.3), the Netherlands (99.3), and Malta (99.3). Conversely, the five countries with the lowest QCI scores on a global scale in 2019 were Somalia (59.1), Niger (67.6), Burkina Faso (72.6), Ethiopia (73.0), and Mali (74.4). Gender difference showed a converging trend from 1990 to 2019 (optimize gender disparity ratio (GDR): 123 vs. 163 countries), and the GDR showed a move toward optimization (between 0.95 and 1.05) in the better and worse parts of the world.ConclusionDespite the positive results regarding the QCI for orofacial clefts worldwide, some countries showed a slight negative trend.
Cross sectional study on behavioral determinants associated with sugary foods and beverages and its corelates with body mass index among adolescents
Authors: Gautam Laxmi , Thapa Milan , Pokhrel Poonam , Sapkota Parash Mani , Bhatt Anjali , Paudel Kiran 
Published: March 2024

ABSTRACTBackgroundAdolescence is the period that demands high nutrients with changes in dietary habits making them vulnerable. Foods high in calories and deficit in essential nutrients increases risk for overweight. The habits are guided by multiple factors including behavioral determinants. Therefore, this study aims to identify the status of and factors associated with behavioral determinants on adolescents in regard to sugary items.MethodsA cross-sectional study was conducted among 768 adolescents of Nagarjun Municipality, Kathmandu from September 2022 to January 2023. This study used a multistage random sampling. The chi square test and logistic regression were applied to analyze the results in SPSS V.16 and p-value ≤ 0.05 was considered as statistically significance.ResultAdequate level of knowledge was found among 84.11% (95% CI: 81.52 to 86.70) of the adolescents. Positive attitude was seen among 60% of the adolescents (95% CI: 56.55 to 63.49). The percentage of adolescent consuming items was 84.50% (95% CI: 81.94 to 87.07). Odds of having adequate knowledge among respondents was twice (AOR=2.05, 95% CI: 1.12 to 3.76) more likely for those who were living with their parents. Female adolescents (AOR=2.51, 95% CI: 1.61 to 3.89), whose mother are homemaker (AOR=1.99, 95% CI: 1.04 to 3.58) and father are engaged in foreign employment (AOR = 2.09, 95% CI: 1.04 to 4.21) were more likely to consume sugary items. Prevalence of overweight was seen among 6.38% (95% CI: 4.64 to 8.11) of respondents. Consumption was seen to be significant to the model overweight versus normal [OR=11.95 (95% CI: 1.61 to 88.42)].ConclusionPresence of adequate knowledge wasn’t the only and adequate factor for food selection. Family indulged interventions can be useful as familial factors seem to be affecting behavioral characteristics. Sugary foods and beverages are associated with overweight. Hence interventions focusing on dietary discipline is also recommended.STRENGTHS AND LIMITATIONS OF THE STUDYThis study deviates the primary focus from range of processed foods items to sugary foods and beverages only. No such studies with sole focus on high calorie sugary foods have been found conducted in Nepal.Study was limited to a single municipality, whose results cannot be generalized for national context. However, it can apply in case of urban settings.Majority of the findings are based on self-reporting, which leaves enough space for under-reporting and recall bias. On the other hand, anthropometric measurements taken by research team was positive part of the study.Difficult to gauge the impact of the findings, because weight gain in adolescence phase varies as a function of age, maturation, and growth velocity not just consumption of sugary foods and beverages.
Using electronic health records to evaluate the adherence to cervical cancer prevention guidelines: a cross-sectional study
Authors: Mooses Kerli , Šavrova Aleksandra , Pajusalu Maarja , Oja Marek , Tamm Sirli , Haug Markus , Padrik Lee , Laanpere Made , Uusküla Anneli , Kolde Raivo 
Published: March 2024

ABSTRACTObjectiveThe fight against cervical cancer requires effective screening together with optimal and on-time treatment along the care continuum. We aimed to examine the impact of cervical cancer screening and treatment guidelines on screening, and follow-up adherence to guidelines.MethodsData from electronic health records and healthcare provision claims for 50 702 women was used. The annual rates of PAP tests, HPV tests and colposcopies during two guideline periods (2nd version 2012–2014 vs 3rd version 2016–2019) were compared. To assess the adherence to guidelines, the subjects were classified as adherent, over- or undertested based on the timing of the appropriate follow-up test.ResultsThe number of PAP tests decreased and HPV tests increased during the 3rd guideline period (p < 0.01). During the 3rd guideline period, among 21–29-year-old women, the adherence to guidelines ranged from 38.7% (44.4…50.1) for ASC-US to 73.4% (62.6…84.3) for HSIL, and among 30–59-year-old from 49.0% (45.9…52.2) for ASC-US to 65.7% (58.8…72.7) for ASC-H. The highest rate of undertested women was for ASC-US (21–29y: 25.7%; 30–59y: 21.9%). The rates of over-tested women remained below 12% for all cervical pathologies observed. There were 55.2% (95% CI 49.7…60.8) of 21–24-year-old and 57.1% (95% CI 53.6…60.6) of 25–29-year-old women who received an HPV test not adherent to the guidelines.ConclusionsOur findings highlighted some shortcomings in the adherence to guidelines, especially among women under 30. The insights gained from this study helps to improve the quality of care and thus, reduce cervical cancer incidence and mortality.