bluuebunny/crossref_metadata_2025_split huggingface dataset:
The impacts of climate change, energy policy and traditional ecological practices on future firewood availability for Diné (Navajo) People
Authors: Magargal Kate , Wilson Kurt , Chee Shaniah , Campbell Michael J. , Bailey Vanessa , Dennison Philip E. , Anderegg William R. L. , Cachelin Adrienne , Brewer Simon , Codding Brian Frank 
Published: September 2023

Local-scale human–environment relationships are fundamental to energy sovereignty, and in many contexts, Indigenous ecological knowledge (IEK) is integral to such relationships. For example, Tribal leaders in southwestern USA identify firewood harvested from local woodlands as vital. For Diné people, firewood is central to cultural and physical survival and offers a reliable fuel for energy embedded in local ecological systems. However, there are two acute problems: first, climate change-induced drought will diminish local sources of firewood; second, policies aimed at reducing reliance on greenhouse-gas-emitting energy sources may limit alternatives like coal for home use, thereby increasing firewood demand to unsustainable levels. We develop an agent-based model trained with ecological and community-generated ethnographic data to assess the future of firewood availability under varying climate, demand and IEK scenarios. We find that the long-term sustainability of Indigenous firewood harvesting is maximized under low-emissions and low-to-moderate demand scenarios when harvesters adhere to IEK guidance. Results show how Indigenous ecological practices and resulting ecological legacies maintain resilient socio-environmental systems. Insights offered focus on creating energy equity for Indigenous people and broad lessons about how Indigenous knowledge is integral for adapting to climate change.
This article is part of the theme issue ‘Climate change adaptation needs a science of culture’.
Efficiency traps beyond the climate crisis: exploration–exploitation trade-offs and rebound effects
Authors: Segovia-Martin Jose , Creutzig Felix , Winters James 
Published: September 2023

Higher levels of economic activity are often accompanied by higher energy use and consumption of natural resources. As fossil fuels still account for 80% of the global energy mix, energy consumption remains closely linked to greenhouse gas (GHG) emissions and thus to climate change. Under the assumption of sufficiently elastic demand, this reality of global economic development based on permanent growth of economic activity, brings into play the Jevons Paradox, which hypothesises that increases in the efficiency of resource use leads to increases in resource consumption. Previous research on the rebound effects has limitations, including a lack of studies on the connection between reinforcement learning and environmental consequences. This paper develops a mathematical model and computer simulator to study the effects of micro-level exploration–exploitation strategies on efficiency, consumption and sustainability, considering different levels of direct and indirect rebound effects. Our model shows how optimal exploration–exploitation strategies for increasing efficiency can lead to unsustainable development patterns if they are not accompanied by demand reduction measures, which are essential for mitigating climate change. Moreover, our paper speaks to the broader issue of efficiency traps by highlighting how indirect rebound effects not only affect primary energy (PE) consumption and GHG emissions, but also resource consumption in other domains. By linking these issues together, our study sheds light on the complexities and interdependencies involved in achieving sustainable development goals.
This article is part of the theme issue ‘Climate change adaptation needs a science of culture’.
Default mode network spatio-temporal electrophysiological signature and causal role in creativity
Authors: Bartoli E. , Devara E. , Dang H.Q. , Rabinovich R. , Mathura R.K. , Anand A. , Pascuzzi B.R. , Adkinson J. , Bijanki K.R. , Sheth S.A. , Shofty B. 
Published: September 2023

AbstractThe default mode network (DMN) is a widely distributed, intrinsic brain network thought to play a crucial role in internally-directed cognition. It subserves self-referential thinking, recollection of the past, mind wandering, and creativity. Knowledge about the electrophysiology underlying DMN activity is scarce, due to the difficulty to simultaneously record from multiple distant cortical areas with commonly-used techniques. The present study employs stereo-electroencephalography depth electrodes in 13 human patients undergoing monitoring for epilepsy, obtaining high spatiotemporal resolution neural recordings across multiple canonical DMN regions. Our results offer a rare insight into the temporal evolution and spatial origin of theta (4-8Hz) and gamma signals (30-70Hz) during two DMN-associated higher cognitive functions: mind-wandering and alternate uses. During the performance of these tasks, DMN activity is defined by a specific pattern of decreased theta coupled with increased gamma power. Critically, creativity and mind wandering engage the DMN with different dynamics: creativity recruits the DMN strongly during the covert search of ideas, while mind wandering displays the strongest modulation of DMN during the later recall of the train of thoughts. Theta band power modulations, predominantly occurring during mind wandering, do not show a predominant spatial origin within the DMN. In contrast, gamma power effects were similar for mind wandering and creativity and more strongly associated to lateral temporal nodes. Interfering with DMN activity through direct cortical stimulation within several DMN nodes caused a decrease in creativity, specifically reducing the originality of the alternate uses, without affecting creative fluency or mind wandering. These results suggest that DMN activity is flexibly modulated as a function of specific cognitive processes and supports its causal role in creative thinking. Our findings shed light on the neural constructs supporting creative cognition and provide causal evidence for the role of DMN in the generation of original connections among concepts.
A highly divergent SARS-CoV-2 lineage B.1.1 sample in a patient with long-term COVID-19
Authors: Nabieva Elena , Komissarov Andrey B. , Klink Galya V. , Zaitsev Stanislav V. , Sergeeva Maria , Fadeev Artem V. , Komissarova Kseniya , Ivanova Anna , Pisareva Maria , Kudrya Kira , Danilenko Daria , Lioznov Dmitry , Hisner Ryan , Gueli Federico , Peacock Thomas P. , Roemer Cornelius , Bazykin Georgii A. 
Published: September 2023

AbstractWe report the genomic analysis of a highly divergent SARS-CoV-2 sample obtained in October 2022 from an HIV+ patient with presumably long-term COVID-19 infection. Phylogenetic analysis indicates that the sample is characterized by a gain of 89 mutations since divergence from its nearest sequenced neighbor, which had been collected in September 2020 and belongs to the B.1.1 lineage, largely extinct in 2022. 33 of these mutations were coding and occurred in the Spike protein. Of these, 17 are lineage-defining in some of the variants of concern (VOCs) or are in sites where another mutation is lineage-defining in a variant of concern, and/or shown to be involved in antibody evasion, and/or detected in other cases of persistent COVID-19; these include some “usual suspects,” such as Spike:L452R, E484Q, K417T, Y453F, and N460K. Molecular clock analysis indicates that mutations in this lineage accumulated at an increased rate compared to the ancestral B.1.1 strain. This increase is driven by the accumulation of nonsynonymous mutations, for an average dN/dS value of 2.2, indicating strong positive selection during within-patient evolution. Additionally, there is reason to believe that the virus had persisted for at least some time in the gastrointestinal tract, as evidenced by the presence of mutations that are rare in the general population samples but common in samples from wastewater. Our analysis adds to the growing body of research on evolution of SARS-CoV-2 in chronically infected patients and its relationship to the emergence of variants of concern.
Long-term Mortality Among Hospitalized Adults with Sepsis in Uganda: a Prospective Cohort Study
Authors: Blair Paul W. , Okello Stephen , Wailagala Abdullah , Ayebare Rodgers R. , Olebo David F. , Kayiira Mubaraka , Kemigisha Stacy M. , Kayondo Willy , Gregory Melissa , Koehler Jeff W. , Schoepp Randal J. , Badu Helen , Adams CDR Nehkonti , Naluyima Prossy , Beckett Charmagne , Waitt Peter , Lamorde Mohammed , Kibuuka Hannah , Clark Danielle V. 
Published: September 2023

AbstractBackgroundTwelve-month mortality in sepsis survivors has not been previously characterized in sub-Saharan Africa.MethodsHospitalized adults with ≥ 2 modified systemic inflammatory response syndrome (SIRS) criteria (temperature < 36°C or > 38°C, heart rate ≥ 90 beats per minute, or respiratory rate ≥ 20 breaths per minute) were enrolled at a tertiary care centre from October 2017 to August 2022. Multiple clinical blood and respiratory molecular and antigen assays were used to identify infectious etiologies. Baseline demographics were evaluated for risk of death by 1 month and 12 months using Cox proportional hazards regression.ResultsAmong 435 participants, the median age was 45.0 years (interquartile range [IQR]: 28.0, 60.0) years, 57.6% were female, and 31.7% were living with HIV. Malaria (17.7%) followed by tuberculosis (4.7%), and bacteremia (4.6%) were the most common detected causes of illness. Overall, 49 (11.3%) participants died, and 24 participants died between one month and one year (49.0% of deaths and 5.5% of the cohort). Female participants had a decreased risk of death by 12-months (unadjusted hazard ratio [HR]: 0.37; 95% confidence interval [CI]: 0.21 to 0.66).ConclusionsThe burden of sepsis may be underestimated in sub-Saharan Africa due to limited long-term follow-up.
Sensitivity and Frequency Response of Biochemical Cascades
Authors: Kochen Michael A. , Hellerstein Joseph L. , Sauro Herbert M. 
Published: September 2023

AbstractSignal transduction from a cell’s surface to cytoplasmic and nuclear targets takes place through a complex network of interconnected pathways. Phosphorylation cycles are common components of many pathways and may take the form of a multi-layered cascade of cycles or incorporate species with multiple phosphorylation sites that effectively create a sequence of cycles with increasing states of phosphorylation. This work focuses on the frequency response and sensitivity of such systems, two properties that have not been thoroughly examined. Starting with a singularly phosphorylated single-cycle system, we compare the sensitivity to perturbation at steady-state across a range of input signal strengths. This is followed by a frequency response analysis focusing on the gain and associated bandwidth. Next, we consider a two-layer cascade of single phosphorylation cycles and focus on how the two cycles interact to produce various effects on the bandwidth and damping properties. Then we consider the (ultra)sensitivity of a doubly phosphorylated system, where we describe in detail first-order ultrasensitivity, a unique property of these systems, which can be blended with zero-order ultrasensitivity to create systems with relatively constant gain over a range of signal input. Finally, we give an in-depth analysis of the sensitivity of an n-phosphorylated system.
The Impact of Martial Arts on Mental Health
Authors: Hiciano Rick A. , Piper Brian J. 
Published: September 2023

AbstractSports Psychiatry has been developing for the last three decades and is growing to be an integral part of Sports Medicine and Psychiatry. With the rising growth of mental health awareness in popular culture, and public announcements of professional athletes describing their struggles with mental health, the need for Sports Psychiatrists is becoming more apparent. However, limited data on mental health disorders amongst athletes poses issues in terms of providing standardized and reliable interventions for treatment. This is especially the case in less researched sports, such as martial arts. The current study aims to investigate the relationship between mental health and martial artists, specifically evaluating the relationship between domains of mental health, including aggression, depression, anxiety, and self-esteem, and Jeet Kune Do/mixed martial arts practitioners. The study will take place at Garcia Gung Fu, a martial arts dojo in Harlem, New York in addition to recruits from a Reddit Martial Arts form. Participants will include both adults and children. The findings in this study will contribute to the body of literature in both sports medicine and psychiatry. Additionally, this study will further illustrate the importance of the field of sports psychiatry and well as highlight the need for improved interventions for athletes.
Sharing and Reusing Computable Phenotype Definitions
Authors: Visweswaran Shyam , Zhang Louisa Yu , Bui Kevin , Sadhu Eugene M. , Samayamuthu Malarkodi J. , Morris Michele M. 
Published: September 2023

AbstractBackgroundA scalable approach for the sharing and reuse of human-readable and computer-executable phenotype definitions can facilitate the reuse of electronic health records for cohort identification and research studies.DescriptionWe developed a tool called Sharephe for the Informatics for Integrating Biology and the Bedside (i2b2) platform. Sharephe consists of a plugin for i2b2 and a cloud-based searchable repository of computable phenotypes, has the functionality to import to and export from the repository, and has the ability to link to supporting metadata.DiscussionThe i2b2 platform enables researchers to create, evaluate, and implement phenotypes without knowing complex query languages. In an initial evaluation, two sites on the Evolve to Next-Gen ACT (ENACT) network used Sharephe to successfully create, share, and reuse phenotypes.ConclusionThe combination of a cloud-based computable repository and an i2b2 plugin for accessing the repository enables investigators to store and retrieve phenotypes from anywhere and at any time and to collaborate across sites in a research network.
An International, Cross-Sectional Survey of Preprinting Attitudes Among Biomedical Researchers
Authors: Ng Jeremy Y. , Chow Valerie , Santoro Lucas J. , Armond Anna Catharina Vieira , Pirshahid Sanam Ebrahimzadeh , Cobey Kelly D. , Moher David 
Published: September 2023

AbstractBackgroundPreprints are scientific manuscripts that are made available on open-access servers but are not yet peer reviewed. While preprints are becoming more prevalent uptake is not uniform or optimal. Understanding researchers’ opinions and attitudes towards preprints is valuable to their successful implementation. Understanding knowledge gaps and researchers’ attitudes toward preprinting can assist stakeholders like journals, funding agencies, and universities to implement preprints more effectively. Here, we aim to collect perceptions and behaviours regarding preprints in across an international sample of biomedical researchers.MethodsBiomedical authors were identified by a keyword-based, systematic search from the MEDLINE database, and their emails were extracted to invite them to our survey. A cross-sectional anonymous survey was distributed to all identified biomedical authors to collect their knowledge, attitudes, and opinions about preprinting.ResultsThe survey was completed by 730 biomedical researchers with a response rate of 3.20% and demonstrated a wide range of attitudes and opinions about preprints with authors from various disciplines and career stages around the world. Most respondents were familiar with the concept of preprints, but most had not published a preprint before. The lead author of the project and journal policy had the most impact on decisions to post a preprint, while employers/research institute had the least impact. Supporting open science practices was the highest ranked incentive, while increases to authors’ visibility was highest ranked motivation for publishing preprints.ConclusionWhile many biomedical researchers recognize the benefits of preprints, there is still hesitation among others to engage in this practice. This may be due to the general lack of peer review of preprints and little enthusiasm from external organizations, such as journals, funding agencies, and universities. Future work is needed to determine optimal ways to increase researcher’s attitudes through modifications to current preprint systems and policies.
Chronic respiratory symptoms and chronic obstructive pulmonary disease following completion of pulmonary tuberculosis treatment in Uganda
Authors: Namusobya Martha , Bongomin Felix , John Mukisa , Kimuli Ivan , Ddungu Ahmed , Batte Charles , Kirenga Bruce J. 
Published: September 2023

AbstractBackgroundPrior pulmonary tuberculosis (PTB) is associated with chronic lung impairment, including chronic obstructive pulmonary disease (COPD). We determined the prevalence and associations of chronic respiratory symptoms and COPD following completion of PTB treatment in Uganda.MethodsBetween August 2022 and December 2022, we consecutively enrolled post-PTB patients who had successfully completed PTB treatment between January 2016 and January 2020 at Mulago National Referral Hospital, Kampala, Uganda. Chronic respiratory symptoms were defined as the presence of at least one of the following symptoms lasting for at least three months within a year: cough or sputum production, shortness of breath, chest pain, or wheezing, along with an FEV1/FVC < 0.70 on spirometry for the definition of COPD.ResultsWe enrolled 326 participants (median age 36 years; IQR: 30 — 43), 182 (55.8%) were male, and 123 (37.7%) were living with HIV. Fifty-one (15.6%) participants had chronic respiratory symptoms, 5 (9.8%) having COPD; 4 GOLD I and 1 GOLD II. Chronic respiratory symptoms were 89% lower among participants whose PTB treatment outcome was “completed” (adjusted Odds Ratio (aOR): 0.11, 95% confidence interval (CI): 0.01 – 0.87, p<0.01) and they were 74% lower among those with alcohol use disorders (aOR: 0.26, 95% CI: 0.12 – 0.57, p <0.001). Non-HIV immunosuppressive conditions such as diabetes mellitus and chronic steroid use, were significantly associated with both chronic respiratory symptoms (aOR:7.72, 95% CI 3.13 – 19.04, p<0.001) and COPD (aOR: 8.42, 95% CI: 1.32 — 53.47, p=0.024).ConclusionChronic pulmonary symptoms, including COPD, are important and yet under recognized complications of PTB treatment in Uganda. Therefore, screening and management in key sub-groups, such as those with immunosuppressive condition, will improve morbidity and quality of life in this population.
Determinants and Patterns of Contraceptive Use among Sexually Active Women living with HIV in Ibadan, Nigeria
Authors: Akinsolu Folahanmi T. , Adegbite Zaniab O. , Bankole Samuel , Lawale Abisola , Adewole Ifeoluwa E. , Abodunrin Olunike R. , Olagunju Mobolaji T. , Ola Oluwabukola M. , Chukwuemeka Abel , Gambari Aisha O. , Njuguna Diana W. , Nwogu-Attah Jacinta N. , Salako Abideen O. , Lukwa Akim T. , Herbertson Ebiere , Eleje George U. , Ezechi Oliver C. 
Published: September 2023

AbstractBackgroundContraception is a strategy to meet the family planning goals of women living with human immunodeficiency virus (WLHIV) as well as to reduce the transmission of HIV. There is limited data from Nigeria, where HIV prevalent is the second-largest in the world. This study aimed to examine contraceptive use and identify factors influencing its use among sexually active WLHIV in Ibadan, Nigeria.MethodsA facility-based cross-sectional study was conducted involving 443 sexually active WLHIV. The inclusion criteria were WLHIV, aged 18–49 years, who asserted being fecund and sexually active. An adopted questionnaire was used to collect data, and the data was analyzed using the Statistical Package for Social Sciences (SPSS) Windows version 25. Statistical significance was set at p < 0.05.ResultsAmong sexually active WLHIV (n = 443), 73.1% used contraceptives, with 26.9% having unmet needs. The results revealed a significant association between employment status and the use of contraceptives (AOR] = 2.150; 95% CI 1.279–3.612 p=0.004); accessibility to contraceptive methods and the use of contraceptives (AOR = 21.483; 95% CI 7.279–63.402 p=0.00). Also, a significant association was found between payment for service and contraceptive use (AOR = 14.343; 95% CI 2.705-76.051; p = 0.003). Previous reactions towards contraceptive use were also significantly associated with contraceptive use (AOR = 14.343; 95% CI 2.705-76.051 p = 0.003). The dual contraceptives usage rate was 30.7%.ConclusionsAlthough contraceptive use among sexually active WLHIV was high, the study highlighted the need for increased adoption of dual contraceptive methods to mitigate the risk of unintended pregnancy and HIV re-infection among this population. It emphasized the importance of continuous sensitization and counseling services healthcare providers provide to promote contraceptive use among WLHIV.
Differential effects of IL4I1 protein on lymphocytes from healthy and multiple sclerosis patients
Authors: Davis Stephanie E. , Hu Jingwen , Nanescu Sonia E. , Kumar Mahesh N. , Baydyuk Maryna , Oft Helena , Amjad Faria S. , Wellstein Anton , Huang Jeffrey K. 
Published: September 2023

ABSTRACTMultiple sclerosis (MS) is a chronic inflammatory disease characterized by immune mediated demyelination of the central nervous system, resulting in extensive neurological deficit and remyelination impairment. We have previously found that interleukin-four induced one (IL4I1) protein modulates CNS inflammation and enhances remyelination in mouse models of experimental demyelination. However, it remained unclear if IL4I1 regulates lymphocyte activity in MS. To assess the therapeutic potential of IL4I1 in MS, we investigated the impact of IL4I1 treatment on human lymphocytes from peripheral blood mononuclear cells (PBMCs) obtained from healthy individuals and MS patients. We found that IL4I1 increased the relative densities of Th2 and regulatory T-cells, while reducing Th17 cell density in healthy control samples. Furthermore, IL4I1-treated lymphocytes promoted CNS remyelination when grafted into demyelinated spinal cord lesions in mice. We found that baseline endogenousIL4I1expression was reduced in people with MS. However, unlike healthy controls, IL4I1 treatment had no significant effect onIL17orTOB1expression in lymphocytes derived from MS patients. These results suggest that IL4I1 skews CD4+T-cells to a regulatory state in healthy human lymphocytes, which may be essential for promoting remyelination. However, IL4I1 appears unable to exert its influence on lymphocytes in MS, indicating that impaired IL4I1-mediated activity may underlie MS pathology.
Attractor dynamics reflect decision confidence in macaque prefrontal cortex
Authors: Wang Siyu , Falcone Rossella , Richmond Barry , Averbeck Bruno B. 
Published: September 2023

AbstractDecisions are made with different degrees of consistency, and this consistency can be linked to the confidence that the best choice has been made. Theoretical work suggests that attractor dynamics in networks can account for choice consistency, but how this is implemented in the brain remains unclear. Here, we provide evidence that the energy landscape around attractor basins in population neural activity in prefrontal cortex reflects choice consistency. We trained two rhesus monkeys to make accept/reject decisions based on pretrained visual cues that signaled reward offers with different magnitudes and delays-to-reward. Monkeys made consistent decisions for very good and very bad offers, but decisions were less consistent for intermediate offers. Analysis of neural data showed that the attractor basins around patterns of activity reflecting decisions had steeper landscapes for offers that led to consistent decisions. Therefore, we provide neural evidence that energy landscapes predict decision consistency, which reflects decision confidence.