bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic and morphological shifts associated with climate change in a migratory bird
Authors: Adams Nicole , Dias Tiffany , Skeen Heather R. , Pegan Teresa , Willard David E. , Winger Ben , Ruegg Kristen , Weeks Brian C. , Bay Rachael 
Published: January 2025

Abstract
Background
Rapid morphological change is emerging as a consequence of climate change in many systems. It is intuitive to hypothesize that temporal morphological trends are driven by the same selective pressures that have established well-known ecogeographic patterns over spatial environmental gradients (e.g., Bergman’s and Allen’s rules). However, mechanistic understanding of contemporary morphological shifts is lacking.

Results
We combine morphological data and whole genome sequencing from a four-decade dataset in the migratory bird hermit thrush (Catharus guttatus) to test whether morphological shifts over time are accompanied by genetic change. Using genome-wide association, we identify alleles associated with body size, bill length, and wing length. Shifts in morphology and concordant shifts in morphology-associated alleles over time would support a genetic basis for the observed changes in morphology over recent decades, potentially an adaptive response to climate change. In our data, bill size decreases were paralleled by genetic shifts in bill size-associated alleles. On the other hand, alleles associated with body size showed no shift in frequency over time.

Conclusions
Together, our results show mixed support for evolutionary explanations of morphological response to climate change. Temporal shifts in alleles associated with bill size support the hypothesis that selection is driving temporal morphological trends. The lack of evidence for genetic shifts in body size alleles could be explained by a large role of plasticity or technical limitations associated with the likely polygenic architecture of body size, or both. Disentangling the mechanisms responsible for observed morphological response to changing environments will be vital for predicting future organismal and population responses to climate change.
Understanding the dynamics driving obesity in socioeconomically deprived urban neighbourhoods: an expert-based systems map
Authors: ter Ellen Fleur , Oude Groeniger Joost , Stronks Karien , Hagenaars Luc L. , Kamphuis Carlijn B.M. , Mackenbach Joreintje D. , Beenackers Mariëlle A. , Freijer Karen , Coenen Pieter , Poelman Maartje , Oude Hengel Karen M. , van Lenthe Frank J. 
Published: January 2025

Abstract
Background
Over the past decades, the prevalence of obesity among adults has rapidly increased, particularly in socioeconomically deprived urban neighbourhoods. To better understand the complex mechanisms behind this trend, we created a system map exposing the underlying system driving obesity prevalence in socioeconomically deprived urban neighbourhoods over the last three decades in the Netherlands.

Methods
We conducted Group Model Building (GMB) sessions with a group of thirteen interdisciplinary experts to develop a Causal Loop Diagram (CLD) of the obesogenic system. Using system-based analysis, the underlying system dynamics were interpreted.

Results
The CLD demonstrates the food environment, physical activity environment, socioeconomic environment and socio-political environment, and their interactions. We identified the following overarching reinforcing dynamics in the obesogenic system in socioeconomically deprived urban neighbourhoods: (1) adverse socioeconomic conditions and an unhealthy food environment reinforced each other, (2) increased social distance between social groups and adverse socioeconomic conditions reinforced each other and (3) increased social distance between institutions and communities and the normalisation of unhealthy behaviours reinforced each other. These deeper system dynamics further reinforced chronic stress, sedentary behaviour, sleeping problems, unhealthy diets and reduced physical activity over time. In turn, these dynamics led to the emergent result of rising obesity prevalence in socioeconomically deprived urban neighbourhoods over the past decades.

Conclusions
Our study sheds light on the system dynamics leading to neighbourhoods with an unhealthy food environment, challenging socioeconomic conditions, a widening distance between social groups and an infrastructure that discouraged physical activity while promoting sedentary behaviour. Our insights can form the basis for the development of an integrated approach aimed at reshaping the obesogenic system in socioeconomically deprived urban neighbourhoods.
Perioperative infections as a prognostic risk factor in hepatocellular carcinoma and cholangiocellular carcinoma: a comparative analysis
Authors: Jördens Markus S. , Oswald Hannah C. , Heinrichs Lisa , Gassmann Nathalie , Wittig Linda , Luedde Tom , Loosen Sven H. , Roderburg Christoph , Knoefel Wolfram T. , Fluegen Georg 
Published: January 2025

Abstract
Background
Hepatocellular Carcinoma (HCC) and cholangiocellular adenocarcinoma (CCA) are the most common primary liver tumors representing a major global health burden. In early disease stages, tumor resection may provide long-term survival in selected patients. However, morbidity and mortality rates are still relatively high after extended liver surgery with perioperative bacterial infections representing major complications. In this study, we evaluate the impact of perioperative infection on the postoperative overall survival (OS) of patients undergoing resection of HCC or CCA.

Material and methods
Two hundred two patients that received liver surgery for HCC (139) or CCA (63) at our tertiary referral center were included between 2008 and 2020. Infection prior or after surgery was assessed using patient documentation and correlated to patients´ survival rates and other clinical characteristics.

Results
Patients with perioperative infection displayed a significantly impaired OS compared to patients without a documented infection (419 (95% CI: 262–576) days vs. 959 (95% CI: 637–1281) days; log rank X2(1) = 10.28; p < 0.001). Subgroup analysis revealed that this effect was only observed among HCC patients, while the outcome of CCA patients was independent of pre- or postoperative infections. Moreover, non-anatomical resection of liver tumors was beneficial in patients with HCC (1541 (95%CI: 1110–1972) vs. 749 (95%CI: 0–1528) days; log rank X2(1) = 5.387; p = 0.02) but not CCA.

Conclusion
Perioperative infection is an important prognostic factor after surgery for HCC but not CCA.
From dusk to dawn: examining how adolescents engage with digital media using objective measures of screen time in a repeated measures study
Authors: Brosnan Bradley , Meredith-Jones Kim A. , Haszard Jillian J. , Wickham Shay-Ruby , Galland Barbara C. , Russell-Camp Takiwai , Taylor Rachael W. 
Published: January 2025

Abstract
Background
Although evening screen time is thought to impair subsequent sleep, current measures are limited to questionnaires which seem unlikely to accurately assess screen time in youth. Given the ubiquitous nature of digital devices, improving measurement of screen time is required before related health effects can be appropriately determined. The aim of this study was to objectively quantify screen time before sleep using video camera footage.

Methods
This repeated-measures observational study in healthy adolescents (11–14 years) from Dunedin, New Zealand measured screen time on four evenings over one week in the home environment from March-December 2021. Wearable and stationary PatrolEyes video cameras captured screen time from two hours before bedtime until sleep and manually coded for device type (phone, tablet, laptop computer, desktop computer, handheld gaming console, gaming console, television and other) and screen activity (watching, listening, reading, educational/creative, browsing, communication, social media, video gaming, multitasking) using a reliable coding schedule (κ ≥ 0.8). Descriptive findings are reported.

Findings
Among the 83 participants (mean 12.3 [SD 1.0] years, 42% female, 52% New Zealand European, 37% Māori [indigenous]), 82 used screens in the two hours before bed on 308 of 344 (90%) nights for a mean of 54.4 min (SD 25.5). Televisions (median 37 min, 56% of nights), phones (19 min, 64% nights), and multitasking using multiple devices (19 min, 48% nights) were most commonly used (> 75% of adolescents). Once in bed but before trying to sleep, 58% of adolescents engaged in screen time for 17 (26.3) minutes on 36% of nights. The most common screen activities were watching (32.5%), social media (26.5%) and communication (20.5%). Even after attempting sleep, 32.5% of participants used screens for 8.0 min (median) on 16% of nights, mostly listening on phones.

Conclusions
Objective video cameras offer detailed insight into evening screen habits, capturing frequency, content, and duration. Youth frequently engage with screens before bed and throughout the night on a range of activities, despite recommendations to restrict screen time prior to sleep.

Trial registration
Australian New Zealand Clinical Trials Registry (anzctr.org.au), AACTRN12621000193875, Registered 23 February 2021, https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=380926&isReview=true.
Mid-term outcomes of the modified Dunn procedure for slipped capital femoral epiphysis: results from a north African pediatric hip unit
Authors: Abdelnasser Mohammad Kamal , Hassan Ahmed Abdelazim , Ibrahim Mohammed , Ibrahim Abdelkhalek Hafez , Abol Oyoun Nariman 
Published: January 2025

Abstract
Background
Slipped Capital Femoral Epiphysis (SCFE) is a prevalent pediatric orthopedic condition. Treatment options range from in situ pinning to various osteotomies, with the Modified Dunn procedure gaining significant attention over the past two decades. However, the suitability of this procedure for different SCFE subtypes and the risk of avascular necrosis (AVN), particularly in moderate and severe cases, remains controversial. This study aims to report the midterm clinical and radiographic outcomes of the Modified Dunn procedure in treating SCFE, emphasizing the factors contributing to AVN development.

Patients and methods
We conducted a prospective case series between 2014 and 2022, enrolling patients with moderate and severe SCFE who were treated using the Modified Dunn procedure by a single experienced hip surgeon. Patients were followed up clinically and radiologically for a minimum of two years.

Results
Thirty-six patients (29 males, 7 females) with moderate and severe SCFE were included, with an average age of 14 years and a mean follow-up of 49.28 months (range: 24–118 months). Statistically significant improvements were observed in clinical and radiographic parameters at the final follow-up compared to pre-operative data. Five patients developed AVN, though no specific risk factor reached statistical significance regarding AVN development. While most AVN cases occurred early in the learning curve, this trend was not statistically significant.

Conclusion
Modified Dunn is a safe and effective option for treating moderate to severe SCFE, offering superior femoral head realignment and patient-reported outcomes. When performed by experienced surgeons, it results in acceptable complication rates, including AVN.

Level of evidence
Level IV Prospective Case series.
Metabolic engineering of Yarrowia lipolytica for the production and secretion of the saffron ingredient crocetin
Authors: Zhou Tingan , Park Young-Kyoung , Fu Jing , Hapeta Piotr , Klemm Cinzia , Ledesma-Amaro Rodrigo 
Published: January 2025

Abstract
Background
Crocetin is a multifunctional apocarotenoid natural product derived from saffron, holding significant promises for protection against various diseases and other nutritional applications. Historically, crocetin has been extracted from saffron stigmas, but this method is hindered by the limited availability of high-quality raw materials and complex extraction processes. To overcome these challenges, metabolic engineering and synthetic biology can be applied to the sustainable production of crocetin.

Results
We constructed a Yarrowia lipolytica strain using hybrid promoters and copy number adjustment, which was able to produce 2.66 g/L of β-carotene, the precursor of crocetin. Next, the crocetin biosynthetic pathway was introduced, and we observed both the production and secretion of crocetin. Subsequently, the metabolite profiles under varied temperatures were studied and we found that low temperature was favorable for crocetin biosynthesis in Y. lipolytica. Therefore, a two-step temperature-shift fermentation strategy was adopted to optimize yeast growth and biosynthetic enzyme activity, bringing a 2.3-fold increase in crocetin titer. Lastly, fermentation media was fine-tuned for an optimal crocetin output of 30.17 mg/L, bringing a 51% higher titer compared with the previous highest report in shake flasks. Concomitantly, we also generated Y. lipolytica strains capable of achieving substantial zeaxanthin production, yielding 1575.09 mg/L, doubling the previous highest reported titer.

Conclusions
Through metabolic engineering and fermentation optimization, we demonstrated the first de novo biosynthesis of crocetin in the industrial yeast Yarrowia lipolytica. In addition, we achieved a higher crocetin titer in flasks than all our known reports. This work not only represents a high production of crocetin, but also entails a significant simultaneous zeaxanthin production, setting the stage for sustainable and cost-effective production of these valuable compounds.
Rapid isothermal molecular tests to discriminate between Leishmania braziliensis and Leishmania infantum infections in dogs
Authors: de Luna Rafaela Lira Nogueira , Sales Kamila Gaudêncio da Silva , Bonifácio Lucas Lisboa Nunes , Figueredo Luciana Aguiar , Shelite Thomas R. , Nogueira Fábio dos Santos , Otranto Domenico , Dantas-Torres Filipe 
Published: January 2025

Abstract
Background
We standardized two recombinase polymerase amplification (RPA) assays coupled with lateral flow (LF) strips for the detection of Leishmania braziliensis and Leishmania infantum kinetoplast DNA (kDNA).

Methods
The RPA-LF assays were tested at different temperatures and reaction times, using DNA from cultured L. braziliensis and L. infantum. The L. infantum RPA-LF was also tested using clinical samples (bone marrow and skin) from infected and uninfected dogs.

Results
The detection limits (analytical sensitivity) of the assays were 0.04 pg/μl and 0.04 ng/μl for L. braziliensis and L. infantum kDNA, respectively. Using clinical samples, the L. infantum RPA-LF successfully detected the parasite kDNA in bone marrow (21/30; 70.0%) and skin samples (23/30, 76.6%) from naturally infected dogs. We found an almost perfect agreement (kappa = 0.807) between RPA-LF for L. infantum and our reference quantitative real-time polymerase chain reaction (qPCR), considering clinical samples with a quantification cycle (Cq) < 30, whereas the agreement with samples with a Cq > 30 (lower parasite loads) was moderate (kappa = 0.440).

Conclusions
The RPA-LF assays developed here may be promising diagnostic tools for point-of-care diagnosis of L. infantum and L. braziliensis infection in dogs, particularly in remote rural areas lacking laboratory infrastructure.

Graphical Abstract
Subjective cognitive decline predicts longitudinal neuropsychological test performance in an unsupervised online setting in the Brain Health Registry
Authors: Kang Jae Myeong , Manjavong Manchumad , Jin Chengshi , Diaz Adam , Ashford Miriam T. , Eichenbaum Joseph , Thorp Emily , Wragg Elizabeth , Zavitz Kenton H. , Cormack Francesca , Aaronson Anna , Mackin R. Scott , Tank Rachana , Landavazo Bernard , Cavallone Erika , Truran Diana , Farias Sarah Tomaszewski , Weiner Michael W. , Nosheny Rachel L. 
Published: January 2025

Abstract
Backgrounds
Digital, online assessments are efficient means to detect early cognitive decline, but few studies have investigated the relationship between remotely collected subjective cognitive change and cognitive decline. We hypothesized that the Everyday Cognition Scale (ECog), a subjective change measure, predicts longitudinal change in cognition in the Brain Health Registry (BHR), an online registry for neuroscience research.

Methods
This study included BHR participants aged 55 + who completed both the baseline ECog and repeated administrations of the CANTAB® Paired Associates Learning (PAL) visual learning and memory test. Both self-reported ECog (Self-ECog) and study partner-reported ECog (SP-ECog), and two PAL scores (first attempt memory score [FAMS] and total errors adjusted [TEA]) were assessed. We estimated associations between multiple ECog scoring outputs (ECog positive [same or above cut-off score], ECog consistent [report of consistent decline in any item], and total score) and longitudinal change in PAL. Additionally we assessed the ability of ECog to identify ‘decliners’, who exhibited the worst PAL progression slopes corresponding to the fifth percentile and below.

Results
Participants (n = 16,683) had an average age of 69.07 ± 7.34, 72.04% were female, and had an average of 16.66 ± 2.26 years of education. They were followed for an average of 2.52 ± 1.63 visits over a period of 11.49 ± 11.53 months. Both Self-ECog positive (estimate = -0.01, p < 0.001, R²m = 0.56) and Self-ECog consistent (estimate=-0.01, p = 0.002, R²m = 0.56) were associated with longitudinal change in PAL FAMS after adjusting demographics and clinical confounders. Those who were Self-ECog total (Odds ratio [95% confidence interval] = 1.390 [1.121–1.708]) and SP-ECog consistent (2.417 [1.591–3.655]) had higher probability of being decliners based on PAL FAMS.

Conclusion
In the BHR’s unsupervised online setting, baseline subjective change was feasible in predicting longitudinal decline in neuropsychological tests. Online, self-administered measures of subjective cognitive change might have a potential to predict objective subjective change and identify individuals with cognitive impairments.
Neuronal CD59 isoforms IRIS-1 and IRIS-2 as regulators of neurotransmitter release with implications for Alzheimer’s disease
Authors: Golec Ewelina , Olsson Robin , Tuysuz Emre Can , Karlsson Maja , Serjieh Yasmin , King Ben C. , Wennström Malin , Blom Anna M. 
Published: January 2025

AbstractWe have previously demonstrated that the intracellular, non-GPI anchored CD59 isoforms IRIS-1 and IRIS-2 (Isoforms Rescuing Insulin Secretion 1 and 2) are necessary for insulin secretion from pancreatic β-cells. While investigating their expression across human tissues, we identified IRIS-1 and IRIS-2 mRNA in the human brain, though their protein expression and function remained unclear. This study shows the presence of both IRIS-1 and 2 proteins in the human brain, specifically in neurons and astrocytes. In the neuroblastoma cell line (SH-SY5Y), both isoforms are intracellular, and their expression increases upon differentiation into mature neurons. Silencing IRIS-1 and 2 in SH-SY5Y cells reduces the SNARE complex formation, essential for synaptic vesicle exocytosis, leading to a reduction in noradrenaline secretion. Notably, we observed diminished expression of neuronal IRIS-1 and 2 in patients with Alzheimer’s disease (AD) and non-demented individuals with type 2 diabetes (T2D). In SH-SY5Y cells, knockdown of all isoforms of CD59 including IRIS-1 and 2 not only elevates phosphorylated tau but also increases cyclin-dependent kinase 5 (CDK5) expression, known promoter of hyperphosphorylation and accumulation of tau, a key pathological feature of AD. Additionally, we found that prolonged exposure to high glucose or cytokines markedly reduces the expression of IRIS-1 and 2 in SH-SY5Y cells, suggesting a link between AD pathology and metabolic stress through modulation of these isoforms.
Lethal injuries on the scaphitid ammonoid Hoploscaphites nicolletii (Morton, 1842) in the Upper Cretaceous Fox Hills Formation, South Dakota, USA
Authors: Tajika Amane , Rashkova Anastasia , Landman Neil H. , Klompmaker Adiël A. 
Published: January 2025

AbstractPredator–prey relationships are considered a major driver for the evolution of organisms, and thus contributed to shaping morphology, ecology, and diversity. During the Late Cretaceous of North America, ammonoid cephalopods were one of the most abundant and diverse marine invertebrates. Despite frequent reports of shell breakage in ammonoids, little is known pertaining to the frequency, position, and size of the shell break through a stratigraphic succession. In this study, we analyze an extensive collection of the scaphitid ammonoid Hoploscaphites nicolletii, which exhibits shell breakage, from the Upper Cretaceous (Maastrichtian) Fox Hills Formation in South Dakota, USA. We focus on four upper Maastrichtian assemblage zones listed stratigraphically from bottom to top—the lower nicolletii Assemblage Zone (LNAZ), the Limopsis-Gervillia Assemblage Zone (LGAZ), the upper nicolletii Assemblage Zone (UNAZ), and the Protocardia-Oxytoma Assemblage Zone (POAZ). Within the collection, we observed two primary types of breakage: ventral and lateral, each displaying a relatively consistent geometry. Lateral breaks, measuring a few centimeters, represent about 20–40% of the maximum conch diameter. Ventral breaks are slightly larger, representing 30–70% of the diameter. Both breakage types occur in the body chamber at approximately 90° from the aperture extending to near the last septum. We find that the incidence of injury increased from 6.6 to 13.7% with some fluctuation across the zones. The breakage size relative to body size does not exhibit a clear change across the assemblage zones. Additionally, no significant difference is apparent in the body size between injured and uninjured specimens within each zone. A weak positive correlation between the size of lateral breaks and maximum conch diameter in LNAZ suggests a tendency for larger predators to target larger individuals. Given the consistency of geometry and size, we presume that these breaks represent lethal injuries from durophagous predators. We propose coleoid cephalopods as the likely culprits for ventral injuries, although fish and crustaceans are plausible alternatives. Concerning lateral injuries, decapod crustaceans appear to be the most probable durophagous predators.
3-bromo-4-(2-hydroxyethyl)-7-methoxy-2H-chromen-2-one inhibits allergic reactions in IgE-mediated RBL-2H3 cells and a passive cutaneous anaphylaxis mouse model
Authors: Kim Moonsu , Kim Huiji , Moon Sun Young , Shin Seong-Ah , Kim Minji , Choi Seyeon , Gwon Sugeun , Lee Jun Hyuck , Park Hyun Ho , Lee Chang Sup 
Published: January 2025

AbstractAllergic reactions occur when the immune system overreacts to generally harmless substances, leading to both acute and chronic diseases, which can be fatal. Mast cells are critical mediators of allergic reactions as they bind allergens and trigger the release of inflammatory mediators. In this study, we investigated the anti-allergic effects of the coumarin derivative 3-bromo-4-(2-hydroxyethyl)-7-methoxy-2H-chromen-2-one in rat basophilic leukemia (RBL)-2H3 cells sensitized to dinitrophenyl (DNP)-immunoglobulin E (IgE) and human serum albumin (HSA). Our results demonstrated that 3-bromo-4-(2-hydroxyethyl)-7-methoxy-2H-chromen-2-one effectively reduces the release of β-hexosaminidase and histamine, inhibiting mast cell degranulation. Additionally, 3-bromo-4-(2-hydroxyethyl)-7-methoxy-2H-chromen-2-one suppressed the production of allergy-related pro-inflammatory cytokines (IL-4, IL-13, and TNF-α) and inhibited key signaling pathways, including MAPK, AKT, and NF-κB. Furthermore, in a passive cutaneous anaphylaxis (PCA) mouse model, 3-bromo-4-(2-hydroxyethyl)-7-methoxy-2H-chromen-2-one reduced ear edema and Evans blue infiltration, further confirming its anti-allergic effects. Collectively, these findings suggest that 3-bromo-4-(2-hydroxyethyl)-7-methoxy-2H-chromen-2-one is a promising candidate for the development of anti-allergic therapeutics.