bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association between ultra-processed food consumption and the incidence of type 2 diabetes: the ELSA-Brasil cohort
Authors: Canhada Scheine L. , Vigo Álvaro , Levy Renata , Luft Vivian C. , da Fonseca Maria de Jesus M. , Giatti Luana , Molina Maria del Carmen B. , Duncan Bruce B. , Schmidt Maria Inês 
Published: November 2023

AbstractBackgroundUltra-processed food (UPF) consumption increases the risk of type 2 diabetes in various high-income countries, with some variation in the magnitude across studies. Our objective was to investigate the association of UPF consumption and specific subgroups with incident type 2 diabetes in Brazilian adults.MethodsThe Brazilian Longitudinal Study of Adult Health (ELSA-Brasil) is a multicenter cohort study of 15,105 adults (35–74 years) enrolled in public institutions in Brazil (2008–2010). We followed participants with two clinic visits (2012–2014; 2017–2019) and annual telephone surveillance. After excluding those with diabetes at baseline, who died or were lost in the follow-up, with missing data, with implausible energy food intake, or reporting bariatric surgery, there were 10,202 participants. We used the NOVA classification to assess UPF consumption based on a food frequency questionnaire. We defined type 2 diabetes by self-report, medication use, or comprehensive laboratory tests. We estimated relative risks (RR) and 95% confidence intervals (95% CI) using robust Poisson regression.ResultsMedian UPF consumption was 372 g/day. Over 8.2 (0.7) years of follow-up, we detected 1799 (17.6%) incident cases. After adjustment for socio-demographics, family history of diabetes, and behavioral risk factors, comparing the fourth (≥ 566 g/day) with the first (< 236 g/day) quartile of UPF distribution, RR was 1.24 (1.10–1.39); every 150 g/day increments in UPF consumption resulted in a RR of 1.05 (1.03–1.07). Reclassifying natural beverages with added sweeteners as UPF increased risk (RR 1.40; 1.25–1.58). Among UPF subgroupings, consumption of processed meats and sweetened beverages increased diabetes risk, while yogurt and dairy sweets decreased the risk (p < 0.05).ConclusionsUPF consumption increased the incidence of type 2 diabetes in Brazilian adults, with heterogeneity across specific food items. These findings add to previous evidence for the role of UPFs in the development of diabetes and other chronic diseases, supporting recommendations to avoid their intake in diabetes prevention and management.
Long noncoding RNAs emerge from transposon-derived antisense sequences and may contribute to infection stage-specific transposon regulation in a fungal phytopathogen
Authors: Qian Jiangzhao , Ibrahim Heba M. M. , Erz Myriam , Kümmel Florian , Panstruga Ralph , Kusch Stefan 
Published: November 2023

Abstract
Background
The genome of the obligate biotrophic phytopathogenic barley powdery mildew fungus Blumeria hordei is inflated due to highly abundant and possibly active transposable elements (TEs). In the absence of the otherwise common repeat-induced point mutation transposon defense mechanism, noncoding RNAs could be key for regulating the activity of TEs and coding genes during the pathogenic life cycle.

Results
We performed time-course whole-transcriptome shotgun sequencing (RNA-seq) of total RNA derived from infected barley leaf epidermis at various stages of fungal pathogenesis and observed significant transcript accumulation and time point-dependent regulation of TEs in B. hordei. Using a manually curated consensus database of 344 TEs, we discovered phased small RNAs mapping to 104 consensus transposons, suggesting that RNA interference contributes significantly to their regulation. Further, we identified 5,127 long noncoding RNAs (lncRNAs) genome-wide in B. hordei, of which 823 originated from the antisense strand of a TE. Co-expression network analysis of lncRNAs, TEs, and coding genes throughout the asexual life cycle of B. hordei points at extensive positive and negative co-regulation of lncRNAs, subsets of TEs and coding genes.

Conclusions
Our work suggests that similar to mammals and plants, fungal lncRNAs support the dynamic modulation of transcript levels, including TEs, during pivotal stages of host infection. The lncRNAs may support transcriptional diversity and plasticity amid loss of coding genes in powdery mildew fungi and may give rise to novel regulatory elements and virulence peptides, thus representing key drivers of rapid evolutionary adaptation to promote pathogenicity and overcome host defense.
A pangenome-guided manually curated library of transposable elements for Zymoseptoria tritici
Authors: Baril Tobias , Croll Daniel 
Published: November 2023

Abstract
Objectives
High-quality species-specific transposable element (TE) libraries are required for studies to elucidate the evolutionary dynamics of TEs and gain an understanding of their impacts on host genomes. Such high-quality TE resources are severely lacking for species in the fungal kingdom. To facilitate future studies on the putative role of TEs in rapid adaptation observed in the fungal wheat pathogen Zymoseptoria tritici, we produced a manually curated TE library. This was generated by detecting TEs in 19 reference genome assemblies representing the global diversity of the species supplemented by multiple sister species genomes. Improvements over previous TE libraries have been made on TE boundary resolution, detection of ORFs, TE domains, terminal inverted repeats, and class-specific motifs.

Data description
A TE consensus library for Z. tritici formatted for use with RepeatMasker. This data is relevant to other researchers investigating TE-host evolutionary dynamics in Z. tritici or who are interested in comparative studies of the fungal kingdom. Further, this TE library can be used to improve gene annotation. Finally, this TE library increases the number of manually curated TE datasets, providing resources to further our understanding of TE diversity.
Placental extract suppresses lipid droplet accumulation by autophagy during the differentiation of adipose-derived mesenchymal stromal/stem cells into mature adipocytes
Authors: Ando Yusuke , Odawara Eri , Sakai Hiroyasu , Sato Fumiaki , Kamei Junzo 
Published: November 2023

Abstract
Objective
Placental extract, which contains various bioactive compounds, has been used as traditional medicine. Many studies have demonstrated additional applications of placental extract and provided a scientific basis for the broad spectrum of its effects. We have previously reported that porcine placental extract (PPE) strongly suppresses adipogenesis in a 3T3-L1 preadipocyte cell line, inhibiting differentiation. This study aimed to examine the effect of PPE on the accumulation of lipid droplets (LD) in adipose-derived mesenchymal stromal/stem cells (ASC).

Results
The study findings revealed that PPE decreased the size of LD during the differentiation of ASC into mature adipocytes. RT-qPCR analysis revealed that PPE increased the gene expression of lysosomal acid lipase A (Lipa), a lipolysis-related gene, in ASC-differentiated adipocytes. However, no differences were noted in the adipocyte differentiation markers (Pparg, Cebpa, and Adipoq), or the adipogenesis-related genes (Dgat1, Dgat2, Fasn, Soat1, and Soat2). In addition, PPE promoted autophagosome formation, which was partially co-localized with the LD, indicating that PPE accelerated the degradation of LD by inducing autophagy (termed lipophagy) during the differentiation of ASC into mature adipocytes. These results suggest that the use of PPE may be a potential novel treatment for regulating adipogenesis for the treatment of obesity.
Neuronal transcriptome, tau and synapse loss in Alzheimer’s knock-in mice require prion protein
Authors: Stoner Austin , Fu Li , Nicholson LaShae , Zheng Chao , Toyonaga Takuya , Spurrier Joshua , Laird Will , Cai Zhengxin , Strittmatter Stephen M. 
Published: November 2023

Abstract
Background
Progression of Alzheimer’s disease leads to synapse loss, neural network dysfunction and cognitive failure. Accumulation of protein aggregates and brain immune activation have triggering roles in synaptic failure but the neuronal mechanisms underlying synapse loss are unclear. On the neuronal surface, cellular prion protein (PrPC) is known to be a high-affinity binding site for Amyloid-β oligomers (Aβo). However, PrPC’s dependence in knock-in AD models for tau accumulation, transcriptomic alterations and imaging biomarkers is unknown.

Methods
The necessity of PrPC was examined as a function of age in homozygous AppNL−G−F/hMapt double knock-in mice (DKI). Phenotypes of AppNL−G−F/hMapt mice with a deletion of Prnp expression (DKI; Prnp−/−) were compared with DKI mice with intact Prnp, mice with a targeted deletion of Prnp (Prnp−/−), and mice with intact Prnp (WT). Phenotypes examined included behavioral deficits, synapse loss by PET imaging, synapse loss by immunohistology, tau pathology, gliosis, inflammatory markers, and snRNA-seq transcriptomic profiling.

Results
By 9 months age, DKI mice showed learning and memory impairment, but DKI; Prnp−/− and Prnp−/− groups were indistinguishable from WT. Synapse loss in DKI brain, measured by [18F]SynVesT-1 SV2A PET or anti-SV2A immunohistology, was prevented by Prnp deletion. Accumulation of Tau phosphorylated at aa 217 and 202/205, C1q tagging of synapses, and dystrophic neurites were all increased in DKI mice but each decreased to WT levels with Prnp deletion. In contrast, astrogliosis, microgliosis and Aβ levels were unchanged between DKI and DKI; Prnp−/− groups. Single-nuclei transcriptomics revealed differential expression in neurons and glia of DKI mice relative to WT. For DKI; Prnp−/− mice, the majority of neuronal genes differentially expressed in DKI mice were no longer significantly altered relative to WT, but most glial DKI-dependent gene expression changes persisted. The DKI-dependent neuronal genes corrected by Prnp deletion associated bioinformatically with synaptic function. Additional genes were uniquely altered only in the Prnp−/− or the DKI; Prnp−/− groups.

Conclusions
Thus, PrPC-dependent synapse loss, phospho-tau accumulation and neuronal gene expression in AD mice can be reversed without clearing Aβ plaque or preventing gliotic reaction. This supports targeting the Aβo-PrPC interaction to prevent Aβo-neurotoxicity and pathologic tau accumulation in AD.
Hyperthermia elevates brain temperature and improves behavioural signs in animal models of autism spectrum disorder
Authors: Lopez-Rodriguez Ana Belen , Murray Carol L. , Kealy John , Towns Clodagh , Roche Andrew , Nazmi Arshed , Doran Michelle , Lowry John P. , Cunningham Colm 
Published: November 2023

Abstract
Background
Autism spectrum disorders (ASD) are predominantly neurodevelopmental and largely genetically determined. However, there are human data supporting the idea that fever can improve symptoms in some individuals, but those data are limited and there are almost no data to support this from animal models. We aimed to test the hypothesis that elevated body temperature would improve function in two animal models of ASD.

Methods
We used a 4 h whole-body hyperthermia (WBH) protocol and, separately, systemic inflammation induced by bacterial endotoxin (LPS) at 250 µg/kg, to dissociate temperature and inflammatory elements of fever in two ASD animal models: C58/J and Shank3B- mice. We used one- or two-way ANOVA and t-tests with normally distributed data and Kruskal–Wallis or Mann–Whitney with nonparametric data. Post hoc comparisons were made with a level of significance set at p < 0.05. For correlation analyses, data were adjusted by a linear regression model.

Results
Only LPS induced inflammatory signatures in the brain while only WBH produced fever-range hyperthermia. WBH reduced repetitive behaviours and improved social interaction in C58/J mice and significantly reduced compulsive grooming in Shank3B- mice. LPS significantly suppressed most activities over 5–48 h.

Limitations
We show behavioural, cellular and molecular changes, but provide no specific mechanistic explanation for the observed behavioural improvements.

Conclusions
The data are the first, to our knowledge, to demonstrate that elevated body temperature can improve behavioural signs in 2 distinct ASD models. Given the developmental nature of ASD, evidence that symptoms may be improved by environmental perturbations indicates possibilities for improving function in these individuals. Since experimental hyperthermia in patients would carry significant risks, it is now essential to pursue molecular mechanisms through which hyperthermia might bring about the observed benefits.
Validation of scoring systems for the prediction of complicated appendicitis in adults using clinical and computed tomographic findings
Authors: Kaewlai Rathachai , Tongsai Sasima , Teerasamit Wanwarang , Wongsaengchan Dhanawin , Noppakunsomboon Napakadol , Khamman Pramuk , Chatkaewpaisal Anchisa , Apisarnthanarak Piyaporn 
Published: November 2023

Abstract
Objectives
The study aimed to evaluate scoring systems for predicting complicated appendicitis in adults diagnosed with acute appendicitis on computed tomography.

Methods
Three hundred twenty-five consecutive adult patients (mean age 51.9 ± 19.6 years, 212 women) diagnosed with acute appendicitis on computed tomography were retrospectively included. Clinical and imaging findings were compared between patients with and without complicated appendicitis, and independent associations were identified. As C-reactive protein was not available for most patients, 5 out of 8 scoring systems were modified. They, and a newly proposed system, were compared via area under the receiver operating characteristics (ROC) curve (AUC), Additionally, the latter was internally validated. Pairwise comparison was performed, and diagnostic performance of these scoring systems was obtained.

Results
One hundred twenty-seven patients (36.8%) had complicated appendicitis. Significant independent associations were found between complicated appendicitis and duration of symptoms > 12 h, appendicolith, periappendiceal fat stranding, periappendiceal fluid, and extraluminal air (p values < 0.001 to 0.037; AUCs of 0.824–0.829). AUCs of 9 scoring systems ranged from 0.692 to 0.831. Of these, modified Atema, Kim HY, and proposed scores had similarly high and non-significantly different AUCs (0.793–0.831) on pairwise comparison. Their sensitivities, specificities, and accuracies were 73.0–90.6%, 48.5–70.6%, and 64.3–72.3%, respectively. Internal validity test demonstrated high AUCs (0.826–0.844) with one of the proposed scores using odds ratio having 100% sensitivity and 100% negative predictive value.

Conclusions
Few scoring systems, including proposed ones, had high AUCs, sensitivity, and reasonable specificities, which could potentially aid in safely selecting adult patients with acute appendicitis for nonoperative management.

Critical relevance statement
The study suggests few scoring systems for predicting complicated appendicitis with high AUCs and reasonable sensitivities, potentially aiding in selecting patients for nonoperative management.

Key points
• The study evaluated existing and proposed new scoring systems to predict complicated appendicitis in adults with acute appendicitis on computed tomography.
• Several factors were found to be significantly associated with complicated appendicitis, including duration of symptoms, appendicolith, periappendiceal fat stranding, periappendiceal fluid, and extraluminal air.
• The modified Atema, Kim HY, and newly proposed scoring systems performed well, potentially aiding in nonoperative management selection.

Graphical Abstract
Mycoremediation of lead and cadmium by lignocellulosic enzymes of Pleurotus eryngii
Authors: Goligar N. , Saadatmand S. , Khavarinejad R. A. 
Published: November 2023

AbstractThis study aimed to investigate the ability of Pleurotus eryngii fungus to absorb lead and cadmium from industrial wastewater. After culturing the fungus on a potato dextrose agar (PDA) medium containing 0 (control), 150 mg L−1, 250 mg L−1, and 350 mg L−1 concentrations of lead and cademium for 30 days, the mycelia were isolated from the culture medium and their extracts were used to measure protein content and the activity of antioxidant enzymes. Also, heavy metal contents were analyzed by atomic absorption spectrometry using flame photometry. Results showed that the growth of mycelia was significantly affected by different concentrations of the two heavy metals. High tolerance of heavy metal pollution in the culture media and the ability to accumulate lead and cademium confirmed that Pleurotus eryngii is a favorable option for mycoremediation. Also, molecular studies for fungal sequencing were investigated using the trench method, the sequence of the fungus was recorded in the gene bank, and finally the fungus was identified in the study.
Correction of symbrachydactyly: a systematic review of surgical options
Authors: Bartsch A. , Nikkhah D. , Miller R. , Mende K. , Hovius S. E. R. , Kaempfen A. 
Published: November 2023

AbstractSymbrachydactyly is a rare congenital malformation of the hand characterized by short or even absent fingers with or without syndactyly, mostly unilaterally present. The hand condition can vary from a small hand to only nubbins on the distal forearm. This study aims to systematically review the surgical management options for symbrachydactyly and compare functional and aesthetic outcomes.The review was performed according to the PRISMA guidelines. Literature was systematically assessed searching the Cochrane Library, PubMed, Embase, and PROSPERO databases up to January 1, 2023. Studies were identified using synonyms for ‘symbrachydactyly’ and ‘treatment’. Inclusion criteria were the report of outcomes after surgical treatment of symbrachydactyly in humans. Studies were excluded if they were written in another language than English, German, or French. Case reports, letters to the editor, studies on animals, cadaveric, in vitro studies, biomechanical reports, surgical technique description, and papers discussing traumatic or oncologic cases were excluded.Twenty-four studies published were included with 539 patients (1037 digit corrections). Only one study included and compared two surgical techniques. The quality of the included studies was assessed using the Modified Coleman Methodology Score and ranged from 25 to 47. The range of motion was the main reported outcome and demonstrated modest results in all surgical techniques. The report on aesthetics of the hand was limited in non-vascularized transfers to 2/8 studies and in vascularized transfers to 5/8 studies, both reporting satisfactory results. On average, there was a foot donor site complication rate of 22% in non-vascularized transfers, compared to 2% in vascularized transfers. The hand-related complication rate of 54% was much higher in the vascularized group than in the non-vascularized transfer with 16%.No uniform strategy to surgically improve symbrachydactyly exists. All discussed techniques show limited functional improvement with considerable complication rates, with the vascularized transfer showing relative high hand-related complications and the non-vascularized transfer showing relative high foot-related complications.There were no high-quality studies, and due to a lack of comparing studies, the data could only be analysed qualitatively. Systematic assessment of studies showed insufficient evidence to determine superiority of any procedure to treat symbrachydactyly due to inadequate study designs and comparative studies. This systematic review was registered at the National Institute for Health Research PROSPERO International Prospective Register of Systematic Reviews number: CRD42020153590 and received no specific grant from any funding agency in the public, commercial, or not-for-profit sectors.Level of evidenceI.Systematic review registrationPROSPERO CRD42020153590.
SAMD13 serves as a useful prognostic biomarker for hepatocellular carcinoma
Authors: Yoo Wonbeak , Kim Seokho , Noh KyungHee 
Published: November 2023

AbstractHepatocellular carcinoma (HCC) is the most common form of liver cancer and the 5-year relative overall survival (OS) rate is less than 20%. Since there are no specific symptoms, most patients with HCC are diagnosed in an advanced stage with poor prognosis. Therefore, identifying novel prognostic biomarkers to improve the survival of patients with HCC is urgently needed. In the present study, we attempted to identify SAMD13 (Sterile Alpha Motif Domain-Containing Protein 13) as a novel biomarker associated with the prognosis of HCC using various bioinformatics tools. SAMD13 was found to be highly expressed pan-cancer; however, the SAMD13 expression was significantly correlated with the worst prognosis in HCC. Clinicopathological analysis revealed that SAMD13 upregulation was significantly associated with advanced HCC stage and high-grade tumor type. Simultaneously, high SAMD13 expression resulted in association with various immune markers in the immune cell subsets by TIMER databases and efficacy of immunotherapy. Methylation analysis showed SAMD13 was remarkably associated with prognosis. Furthermore, a six-hub gene signature associated with poor prognosis was correlated with the cell cycle, transcription, and epigenetic regulation and this analysis may support the connection between SAMD13 expression and drug-resistance. Our study illustrated the characteristics of SAMD13 role in patients with HCC using various bioinformatics tools and highlights its potential role as a therapeutic target and promising biomarker for prognosis in HCC.
Partitioning survival during early marine migration of wild and hatchery-reared Atlantic salmon (Salmo salar L.) smolts using acoustic telemetry
Authors: Doogan Aisling , Cotter Deirdre , Bond Nigel , Ó’Maoiléidigh Niall , Brophy Deirdre 
Published: November 2023

AbstractThe marine migration of Atlantic salmon (Salmo salar) has been prioritised for research internationally as populations of S. salar have declined significantly throughout the species’ range. The main objectives of this study were to use acoustic telemetry to partition survival during the early migration phase, investigate potential causes of mortality and establish diurnal and tidal influences on movements. In 2017 and 2018 wild (n = 49) and hatchery (n = 81) S. salar smolts were tagged with acoustic transmitters. Migration was monitored through a brackish tidal lake, which discharges through a short estuary into northeast Clew Bay in Ireland situated in the northeast Atlantic. Partitioned survival through each area was similar for both wild and hatchery smolts and both groups followed the same migration routes, travelling along the main current out of Clew Bay. Total survival was high within the brackish lake (wild = 98% ± 1.21 and hatchery = 100%) and estuary (wild = 98% ± 1.01 and hatchery = 89% ± 9.28) compared to the marine environment (wild = 67% ± 4.39 and hatchery = 66% ± 7.91). Leaving the brackish lake during an ebb tide and entering the marine environment during daylight increased the probability of survival through the early marine period. The majority of smolts transited through the study area during ebb tides. Migration of hatchery smolts occurred mainly during hours of daylight while wild smolt migration showed no diel patterns. High mortality rates during the initial stages of the marine migration have consequences for the persistence of salmon populations and should be addressed through regionally tailored management measures and conservation efforts aimed at increasing the resilience of salmon stocks.