bluuebunny/crossref_metadata_2025 huggingface dataset:
The role of ribosomal protein networks in ribosome dynamics
Authors: Timsit Youri , Sergeant-Perthuis Grégoire , Bennequin Daniel
Published: January 2025

Accurate protein synthesis requires ribosomes to integrate signals from distant functional sites and execute complex dynamics. Despite advances in understanding ribosome structure and function, two key questions remain: how information is transmitted between these distant sites, and how ribosomal movements are synchronized? We recently highlighted the existence of ribosomal protein networks, likely evolved to participate in ribosome signaling. Here, we investigate the relationship between ribosomal protein networks and ribosome dynamics. Our findings show that major motion centers in the bacterial ribosome interact specifically with r-proteins, and that ribosomal RNA exhibits high mobility around each r-protein. This suggests that periodic electrostatic changes in the context of negatively charged residues (Glu and Asp) induce RNA–protein ‘distance-approach’ cycles, controlling key ribosomal movements during translocation. These charged residues play a critical role in modulating electrostatic repulsion between RNA and proteins, thus coordinating ribosomal dynamics. We propose that r-protein networks synchronize ribosomal dynamics through an ‘electrostatic domino’ effect, extending the concept of allostery to the regulation of movements within supramolecular assemblies.
New global climate actions: insight from COP29
Authors: Jiang Tong , Su Buda , Kundzewicz Zbigniew W , Zhao Weijie
Published: January 2025

The COP29 held in Baku (Azerbaijan) from 11 to 24 November 2024 passed a new climate finance goal, aiming to support the developing countries to address the climate challenges.
Considering Islamic Frameworks to Infectious Disease Prevention
Authors: Irfan Bilal , Khleif Ahmad , Badarneh Jad , Abutaqa Jana , Allam Ali , Kweis Shueib , Tarab Basel , Abu Shammala Abdallah , Nasser Elias , Shweiki Sameeha , Wajahath Muaaz , Padela Aasim
Published: January 2025

Infectious diseases remain a significant global health challenge, particularly in Muslim-majority countries, where socio-economic disparities, urbanization, and conflict exacerbate the spread of illnesses such as dengue, cholera, malaria, and COVID-19. This review explores the potential of Islamic concepts such as taharah (cleanliness), la darar wa la dirar (prevention of harm), and maslahah (communal benefit), as frameworks for infectious disease prevention. These values may align with public health goals, offering religiously resonant approaches to health promotion while addressing the ethical complexities of integrating religious beliefs with biomedical imperatives. The paper examines how community health workers (CHWs) and religious leaders can collaborate to deliver health education, promote vaccination, and manage disease outbreaks, particularly in underserved regions where trust in certain institutions is limited. Challenges arise in ensuring inclusivity, avoiding stigmatization, and balancing the utility of religion in optimal medical end-goals. The ethical implications of using religious messaging in public health campaigns are critically analyzed, emphasizing the need for careful framing to avoid coercion while addressing public benefit. By synthesizing existing literature and case studies, this review highlights how Islamic frameworks may be used to support effective, ethical, and sustainable infectious disease prevention for various stakeholders, offering valuable insights for public health strategies.
Trajectories of Resilience-Related Traits and Their Impact on Health Outcomes in Schizophrenia: Results From a 4-Year Longitudinal Study
Authors: Lee Ellen E , Wu Tsung-Chin , Ibrahim Stephanie , Van Dyne Angelina , Tu Xin M , Eyler Lisa T
Published: January 2025

Background and Hypothesis

For the rapidly growing population of older people living with schizophrenia (PLWS), psychological resilience, or the capacity to adapt to adversity, is an understudied target for improving health. Little is known about resilience and its longitudinal impact on outcomes among PLWS. This study assesses trajectories of resilience-related traits in PLWS and a nonpsychiatric comparison group (NCs) and longitudinal interactions between resilience and health.

Study Design

This sample included 166 PLWS and 155 NCs (mean age 48 years, 52% women), with a 4.1-year mean follow-up time. The groups were comparable in age, sex, and follow-up time. We assessed resilience-related traits, physical well-being, obesity, hyperglycemia, positive symptoms, and negative symptoms. We conducted linear mixed-effects models to examine linear trends over time and continuous-time structural equation models (CTSEM) to assess the longitudinal relationships (cross-lagged effects between resilience and health).

Study Results

People living with schizophrenia had lower resilience levels, compared with NCs. While resilience was stable over time for White individuals, younger non-White individuals with less education had increases in resilience over time. We found bidirectional 1-year cross-lagged effects of resilience with physical well-being and obesity, but not with hyperglycemia. Among PLWS, there were 1-year cross-lagged effects of resilience with both positive symptoms and negative symptoms.

Conclusions

These findings highlight the importance of resilience and its link to physical and mental health over time. Resilience may be a key protective factor in aging among PLWS, and the potential to improve resilience is an important and understudied approach for improving outcomes for older PLWS.
Blunted Ventral Striatal Reactivity to Social Reward Is Associated with More Severe Motivation and Pleasure Deficits in Psychosis
Authors: Shackman Alexander J , Smith Jason F , Orth Ryan D , Savage Christina L G , Didier Paige R , McCarthy Julie M , Bennett Melanie E , Blanchard Jack J
Published: January 2025

Background and Hypothesis

Among individuals living with psychotic disorders, social impairment is common, debilitating, and challenging to treat. While the roots of this impairment are undoubtedly complex, converging lines of evidence suggest that social motivation and pleasure (MAP) deficits play a central role. Yet most neuroimaging studies have focused on monetary rewards, precluding decisive inferences.

Study Design

Here we leveraged parallel social and monetary incentive delay functional magnetic resonance imaging paradigms to test whether blunted reactivity to social incentives in the ventral striatum—a key component of the distributed neural circuit mediating appetitive motivation and hedonic pleasure—is associated with more severe MAP symptoms in a transdiagnostic adult sample enriched for psychosis. To maximize ecological validity and translational relevance, we capitalized on naturalistic audiovisual clips of an established social partner expressing positive feedback.

Study Results

Although both paradigms robustly engaged the ventral striatum, only reactivity to social incentives was associated with clinician-rated MAP deficits. This association remained significant when controlling for other symptoms, binary diagnostic status, or striatal reactivity to monetary incentives. Follow-up analyses suggested that this association predominantly reflects diminished activation during the presentation of social reward.

Conclusions

These observations provide a neurobiologically grounded framework for conceptualizing the social-anhedonia symptoms and social impairments that characterize many individuals living with psychotic disorders and underscore the need to develop targeted intervention strategies.
Influence of Digital Health Literacy on Blood Pressure and Hemoglobin A1c in Patients With Comorbid Type 2 Diabetes and Hypertension
Authors: Lee Donghwan , Silva Susan G. , Yang Qing , Crowley Matthew J. , Hatch Daniel , Pennington Gina , Matters Doreen , Urlichich Diana , Shaw Ryan J.
Published: January 2025

Digital health literacy is emerging as an important element in chronic illness management, yet its relationship with clinical outcomes remains unclear. Utilizing data from the ongoing EXpanding Technology-Enabled, Nurse-Delivered Chronic Disease Care trial, this cross-sectional, correlational study explored the association between digital health literacy, health literacy, and patient outcomes, specifically blood pressure and hemoglobin A1c levels in 76 patients managing comorbid type 2 diabetes and hypertension. Results indicate patients had moderate digital health literacy, which was not significantly correlated with health literacy (r = 0.16, P = .169). Both bivariate and covariate-adjusted regression models indicated that digital health literacy was not significantly associated with patient outcomes (all P > .05, small effects). These findings suggest that although patients from diverse sociodemographic backgrounds may possess the digital health literacy to engage with digital health tools, this alone may not improve clinical outcomes. Although digital health literacy may not be directly related to improved clinical outcomes, future research should explore how digital health tools can be optimized to enhance patient engagement and address complex challenges in diverse populations managing chronic conditions.
Risk Estimation of Carcinogenic and Noncarcinogenic Diseases from Radiation for Medical X-ray Workers
Authors: Liu Gang , Li Ye , Wu XiaoQin , Liu YinYin , Zhang Rong , Niu LiMei , Zhang Xue , Wang Jinhan , Gu Yeqing
Published: January 2025

The objective of this paper is to construct a follow-up cohort of medical x-ray workers and analyze the risk estimates of radiation-induced carcinogenic and noncarcinogenic diseases induced by chronic low-dose ionizing radiation exposure in the follow-up cohort. A fixed cohort study was used. A total of 159 medical x-ray workers working in radiology departments of hospitals in Gansu Province from 1950 to 1980 were selected as the radiology group, and 149 medical workers in internal medicine, surgery, and other departments who had not engaged in radiology work at the same hospital were selected as the control group. A fifth follow-up survey was also conducted. Information on personal radiation exposure history, lifestyle and morbidity was collected for 310 medical x-ray workers and the control group. Malignant tumors and noncancerous diseases (cataracts, diabetes, aplastic anemia, hypertension, coronary heart disease, cerebral apoplexy, etc.) were used as endpoints to analyze the risk estimates of carcinogenic and noncancerous diseases caused by low-dose radiation. There were 14 patients with malignant tumors, 8 in the radiation group and 6 in the control group (RR=1.25); 11 cases of cataract, radiation group, 8 cases, control group, 3 cases, RR:2.50; 18 patients with diabetes mellitus, 12 in the radiation group and 6 in the control group (RR = 1.87); 25 hypertensive patients, 17 in the radiation group and 8 in the control group (RR = 1.99); 23 patients with CHD, 12 in the radiation group and 11 in the control group (RR = 1.02); and 15 cerebral apoplexy patients, 5 in the radiation group and 10 in the control group (RR=0.47).Compared with the control group, the differences were statistically significant (P<0.01). The risk factors for CR and noncarcinogenic diseases associated with low-dose radiation were cataracts (RR: 2.50) > hypertension (RR: 1.99) > diabetes (RR: 1.87) > malignancy (RR: 1.25) > CHD (RR: 1.02) > cerebral apoplexy (RR: 1.02). 0.47. Compared with those in the control group, medical x-ray workers had an increased risk of developing malignant tumors and cataracts, which may be related to occupational exposure to chronic low-dose ionizing radiation. Therefore, radiation workers should pay attention to the optimization of protection in radiation work practice. The incidences of hypertension and diabetes are increased, and the incidences of CHD are basically the same; in particular, the incidence of cerebral apoplexy is significantly reduced, indicating that cerebral apoplexy has a certain protective effect on medical x-ray workers.
Stigmatized HIV Over Knowledge and Support: A Quantitative Study to Develop and Measure Bangladeshi Women's Social Support When Living With HIV-Related Stigma
Authors: Sultana Shirin , Wade Carol H. , Aguilar Jemel P.
Published: January 2025

Recognizing the unique context of Bangladeshi women living with HIV-related stigma in a patriarchal society is central to social scientists developing a culturally appropriate instrument for examining the impact of meaningful interventions. Working with 200 Bangladeshi women with HIV who responded to 77 items from three instruments, we used exploratory factor analysis and identified five latent constructs: emotional support, felt normative stigma, incorrect HIV transmission knowledge, correct HIV transmission knowledge, and tangible support. Confirmatory factor analysis model specifications for the Comparative Fit Index, Tucker Lewis Index (TLI), and Root Mean Square Error of Approximation (RMSEA) were analyzed and all moderately fit. We thus present the Stigmatized HIV Over Knowledge and Support (SHOKS) model as pioneering work facilitating social scientists in developing a culturally appropriate instrument to generate interventions and better support Bangladeshi women living with HIV-related stigma.
Social Determinants of Health and Unmet Needs for Services among Young Adults with HIV: Medical Monitoring Project, 2018-2021
Authors: Marcus Ruthanne , Dasgupta Sharoda , Taussig Jennifer , Tie Yunfeng , Nair Priya , Prejean Joseph
Published: January 2025

Background:

Persons aged 13-24 years are a priority population in the National HIV/AIDS Strategy. Young adults with HIV have poorer health outcomes—including not being retained in care, antiretroviral nonadherence, and not being virally suppressed—than other persons with HIV.

Setting:

Centers for Disease Control and Prevention’s Medical Monitoring Project data collected June 2018 through May 2022.

Methods:

We compared demographic characteristics, social determinants of health (SDOH), and mental health between persons aged 18-24 years with HIV versus persons aged ≥25 years with HIV. Among those aged 18-24 years, we analyzed total and unmet needs for ancillary services, defined as those that support care engagement, viral suppression, and overall health and well-being among people with HIV.

Results:

Persons aged 18-24 years were more likely to have a household income <100% of the federal poverty level (48% vs. 39%), and experience unstable housing or homelessness (37% vs. 18%) or hunger/food insecurity (29% vs. 18%) than those aged ≥25 years. Persons aged 18-24 years had higher median HIV stigma scores (40 vs. 29) and were more likely to experience symptoms of generalized anxiety disorder (21% vs. 15%) than those aged ≥25 years. Of persons aged 18-24 years, 96% had a need for ≥1 ancillary service, of whom 56% had ≥1 unmet need; unmet needs were highest for subsistence services (53%) and non-HIV medical services (41%).

Conclusions:

Addressing unmet needs for subsistence and non-HIV medical services could help reduce disparities in SDOH and mental health that drive inequities in health outcomes among persons with HIV aged 18-24 years.
Limitations of Osteocutaneous Radial Flap Despite Satisfactory Outcomes in Anterior Mandible Reconstruction With Dental Implants
Authors: Mustakim Kezia Rachellea , Eo Mi Young , Kim Soung Min
Published: January 2025

The management of oral malignancy necessitates a comprehensive approach focusing on disease eradication and patient quality of life. Surgery remains pivotal, although extensive resection can lead to aesthetic and functional challenges. Reconstruction, often with osteocutaneous radial forearm free flaps (OCRFFF), is crucial for restoring form and function. Prophylactic plating aims to prevent donor site complications, although plate selection is critical. Despite OCRFFF’s efficacy in anterior mandible reconstruction, concerns persist regarding donor site morbidity and adequacy for subsequent dental implantation. Collaborative efforts and advancements are essential to optimize outcomes and address limitations in oral cancer management.
Impact of American College of Surgeons trauma verification on statewide collaborative outcomes
Authors: Mlaver Eli , Atkins Elizabeth V. , Medeiros Regina S. , Sharma Jyotirmay , Solomon Gina , Galloway Luke , Todd Samual R. , Dunne James R. , Ashley Dennis W. ,   the Georgia Research Institute for Trauma Study Group
Published: January 2025

BACKGROUND

American College of Surgeons (ACS) trauma center verification has demonstrated improved outcomes at individual centers, but its impact on statewide Trauma Quality Improvement Program (TQIP) Collaboratives is unknown. A statewide TQIP Collaborative, founded in 2011, noted underperformance in six of eight patient cohorts identified in the TQIP Collaborative report. We hypothesized that requiring ACS verification for level I and II trauma centers would result in improved outcomes for the state collaborative.

METHODS

The ACS verification requirement was tied to ongoing Trauma Commission funding. Trauma centers were required to apply for an ACS consultative visit by 2017 and were given until 2023 to achieve ACS verification. The effect of this intervention was measured in the number of centers achieving verification and in the performance of the TQIP Collaborative semiannual reports.

RESULTS

In 2015, only 1 of 15 (7%) trauma centers were ACS verified, and 4 had undergone consultative visits. By 2023, 11 of 12 (92%) trauma centers achieved ACS verification. Following this intervention, the observed-to-expected odds ratio for all-patient morbidity and mortality improved from 1.60 to 1.17, and variation among patient-specific cohorts narrowed from 0.97–1.82 to 0.96–1.48 (Figure 2). Performance in all six underperforming patient-specific cohorts improved over the study period.

CONCLUSION

ACS verification for level I and II trauma centers improves TQIP Collaborative performance. Statewide Collaboratives should consider ACS verification as a requirement for participation.

LEVEL OF EVIDENCE

Economic and Value-Based Evaluations; Level III.
Comparison of 1-Year Food Frequency Questionnaire Data with 3-Day Food Record in Adults
Authors: Nepal Sushma , Hillman Angela R.
Published: January 2025

Food frequency questionnaires (FFQs) and 3-day food records (FRs) are widely used methods of dietary analysis and thus need to be accurate. Nutritional values obtained from 1-year FFQ and 3-day FR in 50 participants were compared. No significant differences were observed in energy, carbohydrate, protein, and fat. Differences were observed for dairy intake and 18 micronutrients. Spearman correlation showed significant relationships between 27 nutrients, the highest was cholesterol (r
s = 0.62). Bland-Altman analysis showed a wide level of agreement between the FFQ and FR indicating a need to utilize multiple methods to improve the consistency and accu-racy of dietary analysis.
Immunosuppressive Therapy Following Renal Transplant
Authors: Wallinga Melissa M. , Brody Rebecca A.
Published: January 2025

Immunosuppressive therapy, typically including steroids and immunosuppressants, is integral in graft survival following a kidney transplant but can carry significant nutrition implications for the patient. The most considerable implications include weight gain, new-onset diabetes after transplant, development of cardiovascular impacts, and osteoporosis; severity may be related to the dose and the duration of therapy. Following a transplant, individualized medical nutrition therapy should be used to monitor for adequate oral intake, appropriate weight status, and avoidance of food-medication interactions. This case report depicts the registered dietitian's involvement critical in managing patients posttransplant on immunosuppressive medications.
Protocol-Driven Insulin Regimen Improves Parenteral Nutrition-Induced Hyperglycemia and Provides Trend Toward Meeting Dextrose Calorie Goals While Posing a Low Hypoglycemic Risk
Authors: Cephas Kimberly , Nakazi Saide , Kincaid Hope , Koshy Sharmila , McCauley Robert , Perilli Gretchen
Published: January 2025

Parenteral nutrition (PN)-induced hyperglycemia is a well-documented obstacle among hospitalized patients. We retrospectively investigated the effects of a protocol-driven insulin regimen (IR) compared with provider discretion (PD) insulin management for PN-induced hyperglycemic incidents. There were no statistical differences for duration to euglycemia, proportion meeting PN dextrose goal (PN goal), or hypoglycemia; however, a trend of achieving PN goal was noted at 63.64% (IR) and 34.62% (PD) and the incidence of euglycemia was higher with IR (90.91%) compared with PD methods (42.31%, P = .01). An IR may improve PN-induced hyperglycemia with a trend of achieving PN goals compared with PD methods.
Impact of Incorporating Intuitive Eating Through a Motivational Interviewing Style of Counseling on the Eating Attitudes, Laboratory Values, and Perceptions of Nutrition Counseling of Patients on Hemodialysis
Authors: Sarcona Alessandra , Follador Talia , Benson Kerry
Published: January 2025

This study evaluated the outcomes among patients on hemodialysis using motivational interviewing to implement intuitive eating (IE) principles with 38 patients compared with 27 patients who received routine nutrition counseling. The Intuitive Eating Scale-2, levels of serum potassium and phosphorus, and survey questions related to patient perceptions of nutritional counseling were used to collect data. The motivational interviewing group achieved some aspects of IE, while keeping laboratory markers close to standards, and reported feeling supported by their dietitian. Results exemplify that a positive nutrition counseling approach can improve dialysis-dependent patients’ satisfaction and confidence in managing their health through diet.
The utility of the Living Planet Index as a policy tool and for measuring nature recovery
Authors: McRae Louise , Cornford Richard , Marconi Valentina , Puleston Hannah , Ledger Sophie E.H. , Deinet Stefanie , Oppenheimer Philippa , Hoffmann Mike , Freeman Robin
Published: January 2025

The Living Planet Index (LPI) is a leading global biodiversity indicator based on vertebrate population time series. Since it was first developed over 25 years ago, the LPI has been widely used to indicate trends in biodiversity globally, primarily reported every two years in the Living Planet Report. Based on relative abundance, a sensitive metric of biodiversity change, the LPI has also been applied as a tool for informing policy and used in assessments for several multilateral conventions and agreements, including the Convention on Biological Diversity 2010 Biodiversity Target and Aichi targets. Here, we outline all current and some potential uses of the LPI as a policy tool and explore the use of the LPI in policy documents to assess the reach of the LPI geographically and over time. We present limitations to the use of this indicator in policy, primarily relating to the development of the index at the national level, and suggest clear pathways to broaden the utility of the LPI and the underlying database for temporal and spatial predictions of biodiversity change. We also provide evidence that the LPI can detect recoveries in biodiversity and suggest its suitability for measuring progress towards the goal of biodiversity recovery by 2050.

This article is part of the discussion meeting issue ‘Bending the curve towards nature recovery: building on Georgina Mace's legacy for a biodiverse future’.
A global biogeographic regionalization for butterflies
Authors: Gross Collin P. , Wright April M. , Daru Barnabas H.
Published: January 2025

The partitioning of global biodiversity into biogeographic regions is critical for understanding the impacts of global-scale ecological and evolutionary processes on species assemblages as well as prioritizing areas for conservation. However, the lack of globally comprehensive data on species distributions precludes fine-scale estimation of biogeographical regionalization for numerous taxa of ecological, economic and conservation interest. Using a recently published phylogeny and novel curated native range maps for over 10 000 species of butterflies around the world, we delineated biogeographic regions for the world’s butterflies using phylogenetic dissimilarity. We uncovered 19 distinct phylogenetically delimited regions (phyloregions) nested within 6 realms. Regional boundaries were predicted by spatial turnover in modern-day temperature and precipitation seasonality, but historical climate change also left a pronounced fingerprint on deeper- (realm-) level boundaries. We use a culturally and ecologically important group of insects to expand our understanding of how historical and contemporary factors drive the distribution of organismal lineages on the Earth. As insects and global biodiversity more generally face unprecedented challenges from anthropogenic factors, our research provides the groundwork for prioritizing regions and taxa for conservation, especially with the goal of preserving the legacies of our biosphere’s evolutionary history.

This article is part of the discussion meeting issue ‘Bending the curve towards nature recovery: building on Georgina Mace's legacy for a biodiverse future’.
Clustered warming tolerances and the nonlinear risks of biodiversity loss on a warming planet
Authors: Williamson Joseph , Lu Muyang , Camus M. Florencia , Gregory Richard D. , Maclean Ilya M. D. , Rocha Juan C. , Saastamoinen Marjo , Wilson Robert J. , Bridle Jon , Pigot Alex L.
Published: January 2025

Anthropogenic climate change is projected to become a major driver of biodiversity loss, destabilizing the ecosystems on which human society depends. As the planet rapidly warms, the disruption of ecological interactions among populations, species and their environment, will likely drive positive feedback loops, accelerating the pace and magnitude of biodiversity losses. We propose that, even without invoking such amplifying feedback, biodiversity loss should increase nonlinearly with warming because of the non-uniform distribution of biodiversity. Whether these non-uniformities are the uneven distribution of populations across a species’ thermal niche, or the uneven distribution of thermal niche limits among species within an ecological community, we show that in both cases, the resulting clustering in population warming tolerances drives nonlinear increases in the risk to biodiversity. We discuss how fundamental constraints on species’ physiologies and geographical distributions give rise to clustered warming tolerances, and how population responses to changing climates could variously temper, delay or intensify nonlinear dynamics. We argue that nonlinear increases in risks to biodiversity should be the null expectation under warming, and highlight the empirical research needed to understand the causes, commonness and consequences of clustered warming tolerances to better predict where, when and why nonlinear biodiversity losses will occur.

This article is part of the discussion meeting issue ‘Bending the curve towards nature recovery: building on Georgina Mace’s legacy for a biodiverse future’.
Impacts of limits to adaptation on population and community persistence in a changing environment
Authors: Chevin Luis-Miguel , Bridle Jon
Published: January 2025

A key issue in predicting how ecosystems will respond to environmental change is understanding why populations and communities are able to live and reproduce in some parts of ecological and geographical space, but not in others. The limits to adaptation that cause ecological niches to vary in position and width across taxa and environmental contexts determine how communities and ecosystems emerge from selection on phenotypes and genomes. Ecological trade-offs mean that phenotypes can only be optimal in some environments unless these trade-offs can be reshaped through evolution. However, the amount and rate of evolution are limited by genetic architectures, developmental systems (including phenotypic plasticity) and the legacies of recent evolutionary history. Here, we summarize adaptive limits and their ecological consequences in time (evolutionary rescue) and space (species’ range limits), relating theoretical predictions to empirical tests. We then highlight key avenues for future research in this area, from better connections between evolution and demography to analysing the genomic architecture of adaptation, the dynamics of plasticity and interactions between the biotic and abiotic environment. Progress on these questions will help us understand when and where evolution and phenotypic plasticity will allow species and communities to persist in the face of rapid environmental change.

This article is part of the discussion meeting issue ‘Bending the curve towards nature recovery: building on Georgina Mace's legacy for a biodiverse future’.
LIFE: A metric for mapping the impact of land-cover change on global extinctions
Authors: Eyres Alison , Ball Thomas S. , Dales Michael , Swinfield Tom , Arnell Andy , Baisero Daniele , Durán América Paz , Green Jonathan M. H. , Green Rhys E. , Madhavapeddy Anil , Balmford Andrew
Published: January 2025

Human-driven habitat loss is recognized as the greatest cause of the biodiversity crisis, yet to date we lack robust, spatially explicit metrics quantifying the impacts of anthropogenic changes in habitat extent on species’ extinctions. Existing metrics either fail to consider species identity or focus solely on recent habitat losses. The persistence score approach developed by Durán
et al
. (Durán
et al.
2020
Methods Ecol. Evol
.
11
, 910–921 (doi:10.1111/2041-210X.13427) represented an important development by combining species’ ecologies and land-cover data while considering the cumulative and non-linear impact of past habitat loss on species’ probability of extinction. However, it is computationally demanding, limiting its global use and application. Here we couple the persistence score approach with high-performance computing to generate global maps of what we term the LIFE (Land-cover change Impacts on Future Extinctions) metric for 30 875 species of terrestrial vertebrates at 1 arc-min resolution (3.4 km
2
at the equator). These maps provide quantitative estimates, for the first time, of the marginal changes in the expected number of extinctions (both increases and decreases) caused by converting remaining natural vegetation to agriculture, and restoring farmland to natural habitat. We demonstrate statistically that this approach integrates information on species richness, endemism and past habitat loss. Our resulting maps can be used at scales from 0.5–1000 km
2
and offer unprecedented opportunities to estimate the impact on extinctions of diverse actions that affect change in land cover, from individual dietary choices through to global protected area development.

This article is part of the discussion meeting issue ‘Bending the curve towards nature recovery: building on Georgina Mace's legacy for a biodiverse future’.
Roseomonas cutis sp. nov., isolated from human epidermis
Authors: Son Haelim , Mun Wonsik , Mitchell Robert J. , Cho Gyu-Sung , Moon Ja-Young , Lee Kyoung
Published: January 2025

Five pink-pigmented bacterial strains, isolated from human skin and classified within the genus Roseomonas, were examined. Among them, four were identified as Roseomonas mucosa, while strain OT10T was deemed to be a potential novel species. Strain OT10T exhibited characteristics, such as Gram-stain-negative, oxidase positive, motile, strictly aerobic and rod shaped. The cells had multiple flagella at one end, arranged in a lophotrichous pattern. The predominant cellular fatty acids in OT10T were C18:1 ω7c/C18:1 ω6c and C18:1 2OH; ubiquinone (Q)-10 was identified as the sole quinone. Major polar lipids included phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylcholine and two aminolipids. The G+C content of the genome was determined to be 72.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequence similarities revealed that strain OT10T is closely related to Roseomonas gilardii subsp. gilardii ATCC 49956T (97.7%), Roseomonas gilardii subsp. rosea ATCC BAA-691T (97.7%) and R. mucosa ATCC BAA-692T (97.5%). For the comparative genomic analyses, whole-genome sequencing was also conducted for strain OT10T. Considering the chemotaxonomic, genotypic and phenotypic features, as well as the low average nucleotide identity and digital DNA–DNA hybridization values compared to its closest phylogenomic neighbours, OT10T is proposed to be a novel species named Roseomonas cutis sp. nov., with OT10T designated as the type strain (=KCTC 92087T =JCM 34968T).
Pseudoalteromonas qingdaonensis sp. nov., isolated from the intestines of Ilyoplax deschampsi
Authors: Lin Xingyue , Zhang Shuqian , Fang Suyun , Hu Xiaoke , Ma Lianju
Published: January 2025

A Gram-stain-negative, aerobic, motile, catalase-positive, oxidase-positive, short rod-shaped marine bacterium, designated as YIC-827T, was isolated from Qingdao, Shandong Province, China. The results showed that cells of strain YIC-827T could grow optimally at 25–35 °C, pH 6.5–7.5 and 2–7% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence showed that the strain YIC-827T was a member of the genus Pseudoalteromonas. The closest relative to this strain was Pseudoalteromonas ruthenica KMM 300T, with a similarity of 98.39%. The digital DNA–DNA hybridization value between the new isolate and phylogenetically related species is 19.6%. Strain YIC-827T could decompose sodium alginate, casein and esters (Tween 20, Tween 40, Tween 60 and Tween 80), but could not hydrolyse starch, cellulose and DNA. The fatty acid profile of a strain consists of a large number of C16:0, C18:1 ω7c and C16:1 ω7c/C16:1 ω6c. The G+C content of the DNA of this strain was determined to be 48.93%. Based on phenotypic characteristics, phylogenetic analysis and DNA–DNA correlation data, the strain YIC-827 T represents a novel species of the genus Pseudoalteromonas with the name Pseudoalteromonas qingdaonensis sp. nov. The type strain of P. qingdaonensis sp. is strain YIC-827T (=MCCC 1K08807T=CGMCC 1.62085T=KCTC 8212T).
Addition of Section 10, Rules 66–73 for further integration of Candidatus names into the International Code of Nomenclature of Prokaryotes
Authors: Oren Aharon
Published: January 2025

Following a proposal for further integration of Candidatus names into the International Code of Nomenclature of Prokaryotes, I here report the outcome of the ballot on this proposal by the members of the International Committee on Systematics of Prokaryotes.
8-Hydroxyquinoline derivative as a promising antifungal agent to combat ocular fungal infections
Authors: Reginatto Paula , Joaquim Angélica Rocha , Teixeira Mário Littieri , Andrade Saulo Fernandes de , Fuentefria Alexandre Meneghello
Published: January 2025

Introduction. Ocular fungal infections are pathologies of slow progression, occurring mainly in the cornea, but can also affect the entire structure of the eyeball. The main aetiological agents are species of the genera Candida and Fusarium. Both diagnosis and treatment require speed and effectiveness. However, the currently available therapy basically consists of the use of azoles and polyenes, known for their low penetration into the ocular tissue and the associated toxicity.

Hypothesis. Thus, new strategies to combat these infections are needed, such as the development of new antifungals or the use of associations.

Aim. Thus, the compound PH151, derived from a promising class of 8-hydroxyquinolines, and natamycin, amphotericin B (AMB) and voriconazole (VRC), the main antifungals used in ocular antifungal therapy, were considered against Candida spp. and Fusarium spp.

Methodology. The MICs of compound PH151 ranged from 1.0 to 16.0 µg ml−1, according to CLSI protocols.

Results. The association of PH151 with AMB and VRC showed a synergistic effect for more than 50% of the strains tested.

Conclusion. Both the compound alone and its association (VRC-AMB-PH151) demonstrated promising potential as an antifungal agent in ocular infections, since the evaluated ocular toxicity profile was positive and the compounds presented low toxicity.
SRSF2 transcriptional function maintains genome integrity during cell
division
Authors: Wagner Rebecca E. , Arnetzl Leonie , Britto-Borges Thiago , Heit-Mondrzyk Anke , Bakr Ali , Sollier Etienne , Panten Jasper , Delaunay Sylvain , Sohn Daniela , Schmezer Peter , Odom Duncan T. , Müller-Decker Karin , Dieterich Christoph , Lutsik Pavlo , Bornelöv Susanne , Frye Michaela
Published: January 2025

Recurrent mutations in serine / arginine-rich splicing factor 2 (SRSF2),
particularly the proline-to-histidine substitution at position 95 (P95H), have
been proposed to drive neoplastic diseases. SRSF2 plays pivotal roles in
pre-mRNA processing and gene transcription. However, the precise impact of these
diverse functions of SRSF2 on cancer cell behaviour remains unclear. Here, we
show that deletion or homozygous P95H mutation
ofSRSF2both cause extensive DNA damage leading to
cell cycle arrestin vitroandin
vivo,regardless of cell genotype. We mechanistically
demonstrate that SRSF2 is required for efficient bi-directional transcription of
DNA replication and repair genes, independent of its function in splicing. In
contrast, SRSF2 haploinsufficiency induces DNA damage without halting the cell
cycle in cancer cells. Inducing the
heterozygousSrsf2P95H mutation leads to clonal
expansion of epidermal cells in mouse skin, but tumor formation is inhibited
following exposure to carcinogens. To survive carcinogen treatment, cells
containing theSrsf2P95H mutation undergo substantial
transcription rewiring that restores bi-directional gene expression. Thus, our
study reveals crucial roles of SRSF2 beyond splicing and underscores its
importance in regulating transcription to orchestrate the cell cycle along with
the DNA damage response.
DefensePredictor: A Machine Learning Model to Discover Novel Prokaryotic Immune Systems
Authors: DeWeirdt Peter C. , Mahoney Emily M. , Laub Michael T.
Published: January 2025

Anti-phage defense systems protect bacteria from viruses. Studying defense systems has begun to reveal the evolutionary roots of eukaryotic innate immunity and produced important biotechnologies such as CRISPR-Cas9. Dozens of new systems have been discovered by looking for systems that co-localize in genomes, but this approach cannot identify systems outside defense islands. Here, we present DefensePredictor, a machine-learning model that leverages embeddings from a protein language model to classify proteins as defensive. We applied DefensePredictor to 69 diverseE. colistrains and validated 45 previously unknown systems, with >750 additional unique proteins receiving high confidence predictions. Our model, provided as open-source software, will help comprehensively map the anti-phage defense landscape of bacteria, further reveal connections between prokaryotic and eukaryotic immunity, and accelerate biotechnology development.
Linage priming and cell type proportioning depends on the interplay between stochastic and deterministic factors
Authors: Salvidge William M. , Brimson Chris , Gruenheit Nicole , Huang Li-Yao , Pears Catherine J. , Wolf Jason B. , Thompson Christopher R.L.
Published: January 2025

Embryonic stem cells (ESCs) can break symmetry and differentiate along different lineages, even when exposed to a seemingly identical environment. It is thought that this priming of cells towards different lineages is due to cell-cell variation, although the underlying mechanisms are poorly understood. To address this, we exploit the tractability of the social amoebaDictyostelium discoideum, where cell fate choice also does not depend on spatial cues. We develop and test a model to explain quantitative experimental single cell observations of probabilistic differentiation. The model suggests that cell cycle position affects lineage choice, as previously shown, but that stochastic cell-cell variation also plays a key role. Single cell sequencing reveals genes strongly associated with fate choice exhibit extensive stochastic cell-cell expression variation. Like lineage priming genes in ESCs, they are associated with specific epigenetic modifications, which when perturbed affect their expression and disrupt fate choice. We suggest this represents an adaptive mechanism that increases developmental robustness against perturbations that affect deterministic signals.
The 2.3 Å Structure of A21, a Protein Component of the Conserved Poxvirus Entry-Fusion Complex
Authors: Diesterbeck Ulrike S. , Muslinkina Liya A. , Gittis Apostolos G. , Singh Kavita , Moss Bernard , Garboczi David N.
Published: January 2025

Poxviruses are exceptional in having an entry-fusion complex (EFC) consisting of eleven conserved proteins embedded in the membrane of mature virions. With the goal of understanding the function of the EFC, extensive efforts have been made to determine the structures and roles of its components, and to date, structures have been determined for nine of the eleven proteins. Here, we report the crystal structure of A21, the 10thEFC protein, comprising two α-helices clasping a twisted antiparallel β-sheet stabilized by two conserved disulfide bonds. The stability of each of the three A21 loops is provided by hydrogen bonds between main-chain atoms and several highly conserved residues, making the overall fold of A21 and its orthologs resilient to evolutionary change. Based on AlphaFold modeling and phylogenetic analysis of A21, we suggest that its highly conserved N-terminal transmembrane domain and C-terminal α-helix enable A21 integration into EFC, where it primarily interacts with the G3/L5 subcomplex and the smallest of EFC components, the O3 protein.

Highlights

With the structure of A21 determined by us, the structures of 10 out of the 11 proteins forming the entry-fusion complex (EFC) of the poxvirus are now known.

A21 features a highly conserved transmembrane (TM) domain, which, along with the C-α-helix, facilitates the integration of A21 and its orthologs into the EFC.

Within the EFC, A21 primarily interacts with the G3/L5 subcomplex and the O3 peptide.
Design and characterization of HIV-1 vaccine candidates to elicit antibodies targeting multiple epitopes
Authors: Gristick Harry B. , Hartweger Harald , Nishimura Yoshiaki , Gavor Edem , Nagashima Kaito , Koranda Nicholas S. , Gnanapragasam Priyanthi N.P. , Kakutani Leesa M. , Segovia Luisa , Donau Olivia , Keeffe Jennifer R. , West Anthony P. , Martin Malcolm A. , Nussenzweig Michel C. , Bjorkman Pamela J.
Published: January 2025

A primary goal in the development of an AIDS vaccine is the elicitation of broadly neutralizing antibodies (bNAbs) that protect against diverse HIV-1 strains. To this aim, germline-targeting immunogens have been developed to activate bNAb precursors and initiate the induction of bNAbs. While most pre-clinical germline-targeting HIV-1 vaccine candidates only target a single bNAb precursor epitope, an effective HIV-1 vaccine will likely require bNAbs that target multiple epitopes on Env. Here, we report a newly designed germline-targeting Env SOSIP trimer, named 3nv.2, that targets three bNAb epitopes on Env: the CD4bs, V3, and V2 epitopes. 3nv.2 forms a stable trimeric Env and binds to bNAb precursors from each one of the desired epitopes. Importantly, immunization experiments in rhesus macaques and mice demonstrate 3nv.2 elicits the combined effects of its parent immunogens. Our results reported here provide a proof-of-concept for using a germline-targeting immunogen that targets three or more bNAb precursors and present a framework to develop improved next-generation HIV-1 vaccine candidates.
Stochastic dark matter: Covariant Brownian motion from Planckian discreteness
Authors: Albertini Emma , Nasiri Arad , Panella Emanuele
Published: January 2025

Quantum gravity has long remained elusive from an observational standpoint. Developing effective cosmological models motivated by the fundamental aspects of quantum gravity is crucial for bridging theory with observations. One key aspect is the granularity of spacetime, which suggests that free particles would deviate from classical geodesics by following a covariant Brownian motion. This notion is further supported by swerves models in causal set theory, a discrete approach to quantum gravity. At an effective level, such deviations are described by a stochastic correction to the geodesic equation. We show that the form of this correction is strictly restricted by covariance and the mass-shell condition. Under minimal coupling to curvature, the resulting covariant Brownian motion is unique. The process is equivalently described by a covariant diffusion equation for the distribution of massive particles in their relativistic phase space. When applied to dark matter particles, covariant Brownian motion results in spontaneous warming at late times, suppressing the matter power spectrum at small scales in a time-dependent manner. Using bounds on the diffusion rate from CMB and growth history measurements of fσ8, we show that the model offers a resolution to the S8 tension. Future studies on the model’s behavior at nonlinear cosmological scales will provide further constraints and, therefore, critical tests for the viability of stochastic dark matter.

Published by the American Physical Society
2025
Impact of the phase transition on quark-gluon plasma with an extremely strong magnetic field in holographic QCD
Authors: Cao Xuanmin , Liu Hui
Published: January 2025

We investigate the phase transition within an extremely strong magnetic background field, employing a holographic quantum chromodynamics (QCD) model with a focus on the entropy, pressure, and Polyakov loop properties. At relatively modest magnetic field strengths, our study discerns a crossover transition between the normal phase and the quark-gluon plasma (QGP) phase as the temperature rises. In contrast, under the influence of an extremely strong magnetic field, a first-order phase transition is observed. A critical point is identified at (eBc,Tc)≈(2.8623  GeV2,0.1191  GeV), which corresponds to a second-order phase transition. This phase structure is found to be in qualitative agreement with lattice simulation predictions reported in D’Elia []. Furthermore, we explore the impact of the magnetic field on the jet quenching parameter across various phases. At zero magnetic field (eB=0), the normalized jet quenching parameter q^/T3 exhibits a monotonic increase with temperature. However, in the presence of a magnetic background field, the normalized jet quenching parameters not only display directional anisotropy but also experience a universal enhancement, particularly in the vicinity of the critical temperature region. This observation suggests that the jet quenching parameter could potentially act as an indicator of phase transitions.

Published by the American Physical Society
2025
Analytical-based investigation of consequent poles permanent magnet machine: improved air gap flux density formulation
Authors: Jmal Hajer , Souissi Amal , Abdennadher Imen
Published: January 2025

Purpose

This paper aims to an analytical investigation of a consequent poles (CP) permanent magnet machine, to enhance the accuracy of the predicted air gap flux density and thus of the machine performance.

Design/methodology/approach

The machine under study is obtained by the substitution of the poles machines (PMs) that corresponds to south poles, of a conventional surface PM (SPM) machine, by iron pieces of same geometry. First, the analytical model of the air gap flux density generated by a SPM topology is presented. To fit the CP concept, such model has been rearranged based on a virtual SPM machine. Then, an improved prediction of the CP machine air gap flux density is addressed by the incorporation of a south pole rotor correction function.

Findings

An improved prediction of the consequent pole PM machines air gap flux density is addressed by the incorporation of a south pole rotor correction function.

Originality/value

The paper proposes an original approach to enhance the prediction of the air gap flux density of consequent pole machines despite the different magnetic permeability of the north and south poles.