bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of weight loss program using prebiotics and probiotics on body composition, physique, and metabolic products: longitudinal intervention study
Authors: Hassan Nayera E. , El-Masry Sahar A. , El Shebini Salwa M. , Ahmed Nihad H. , Mehanna Nayra Sh. , Abdel Wahed Mai Magdy , Amine Darine , Hashish Adel , Selim Mohamed , Afify Mahmoud A. S. , Alian Khadija
Published: May 2024

The relationship between gut microbiota and obesity has recently been an important subject for research as the gut microbiota is thought to affect body homeostasis including body weight and composition, intervening with pro and prebiotics is an intelligent possible way for obesity management. To evaluate the effect of hypo caloric adequate fiber regimen with probiotic supplementation and physical exercise, whether it will have a good impact on health, body composition, and physique among obese Egyptian women or has no significant effect. The enrolled 58 women, in this longitudinal follow-up intervention study; followed a weight loss eating regimen (prebiotic), including a low-carbohydrate adequate-fiber adequate-protein dietary pattern with decreased energy intake. They additionally received daily probiotic supplements in the form of yogurt and were instructed to exercise regularly for 3 months. Anthropometric measurements, body composition, laboratory investigations, and microbiota analysis were obtained before and after the 3 months weight loss program. Statistically highly significant differences in the anthropometry, body composition parameters: and obesity-related biomarkers (Leptin, ALT, and AST) between the pre and post-follow-up measurements at the end of the study as they were all decreased. The prebiotic and probiotic supplementation induced statistically highly significant alterations in the composition of the gut microbiota with increased relative abundance of Lactobacillus, Bifidobacteria, and Bacteroidetes and decreased relative abundance of Firmicutes and Firmicutes/Bacteroidetes Ratio. Hypo caloric adequate fiber regimen diet with probiotics positively impacts body composition and is effective for weight loss normalizing serum Leptin and AST.
Quantitative microbiome profiling of honey bee (Apis mellifera) guts is predictive of winter colony loss in northern Virginia (USA)
Authors: Carlini David B. , Winslow Sundre K. , Cloppenborg-Schmidt Katja , Baines John F.
Published: May 2024

For the past 15 years, the proportion of honey bee hives that fail to survive winter has averaged ~ 30% in the United States. Winter hive loss has significant negative impacts on agriculture, the economy, and ecosystems. Compared to other factors, the role of honey bee gut microbial communities in driving winter hive loss has received little attention. We investigate the relationship between winter survival and honey bee gut microbiome composition of 168 honey bees from 23 hives, nine of which failed to survive through winter 2022. We found that there was a substantial difference in the abundance and community composition of honey bee gut microbiomes based on hive condition, i.e., winter survival or failure. The overall microbial abundance, as assessed using Quantitative Microbiome Profiling (QMP), was significantly greater in hives that survived winter 2022 than in those that failed, and the average overall abundance of each of ten bacterial genera was also greater in surviving hives. There were no significant differences in alpha diversity based on hive condition, but there was a highly significant difference in beta diversity. The bacterial genera Commensalibacter and Snodgrassella were positively associated with winter hive survival. Logistic regression and random forest machine learning models on pooled ASV counts for the genus data were highly predictive of winter outcome, although model performance decreased when samples from the location with no hive failures were excluded from analysis. As a whole, our results show that the abundance and community composition of honey bee gut microbiota is associated with winter hive loss, and can potentially be used as a diagnostic tool in evaluating hive health prior to the onset of winter. Future work on the functional characterization of the honey bee gut microbiome’s role in winter survival is warranted.
Cryptic diversity in southern African kelp
Authors: Madeira Pedro , Reddy Maggie M. , Assis Jorge , Bolton John J. , Rothman Mark D. , Anderson Robert J. , Kandjengo Lineekela , Kreiner Anja , Coleman Melinda A. , Wernberg Thomas , De Clerck Olivier , Leliaert Frederik , Bandeira Salomão , Ada Abdul M. , Neiva João , Pearson Gareth A. , Serrão Ester A.
Published: May 2024

The southern coast of Africa is one of the few places in the world where water temperatures are predicted to cool in the future. This endemism-rich coastline is home to two sister species of kelps of the genus Ecklonia maxima and Ecklonia radiata, each associated with specific thermal niches, and occuring primarily on opposite sides of the southern tip of Africa. Historical distribution records indicate that E. maxima has recently shifted its distribution ~ 70 km eastward, to sites where only E. radiata was previously reported. The contact of sister species with contrasting thermal affinities and the occurrence of mixed morphologies raised the hypothesis that hybridization might be occurring in this contact zone. Here we describe the genetic structure of the genus Ecklonia along the southern coast of Africa and investigate potential hybridization and cryptic diversity using a combination of nuclear microsatellites and mitochondrial markers. We found that both species have geographically discrete genetic clusters, consistent with expected phylogeographic breaks along this coastline. In addition, depth-isolated populations were found to harbor unique genetic diversity, including a third Ecklonia lineage. Mito-nuclear discordance and high genetic divergence in the contact zones suggest multiple hybridization events between Ecklonia species. Discordance between morphological and molecular identification suggests the potential influence of abiotic factors leading to convergent phenotypes in the contact zones. Our results highlight an example of cryptic diversity and hybridization driven by contact between two closely related keystone species with contrasting thermal affinities.
Inducible deletion of microRNA activity in kidney mesenchymal cells exacerbates renal fibrosis
Authors: Sakuma Hirofumi , Maruyama Keisuke , Aonuma Tatsuya , Kobayashi Yuya , Hayasaka Taiki , Kano Kohei , Kawaguchi Satoshi , Nakajima Kei-ichi , Kawabe Jun-ichi , Hasebe Naoyuki , Nakagawa Naoki
Published: May 2024

MicroRNAs (miRNAs) are sequence-specific inhibitors of post-transcriptional gene expression. However, the physiological functions of these non-coding RNAs in renal interstitial mesenchymal cells remain unclear. To conclusively evaluate the role of miRNAs, we generated conditional knockout (cKO) mice with platelet-derived growth factor receptor-β (PDGFR-β)-specific inactivation of the key miRNA pathway gene Dicer. The cKO mice were subjected to unilateral ureteral ligation, and renal interstitial fibrosis was quantitatively evaluated using real-time polymerase chain reaction and immunofluorescence staining. Compared with control mice, cKO mice had exacerbated interstitial fibrosis exhibited by immunofluorescence staining and mRNA expression of PDGFR-β. A microarray analysis showed decreased expressions of miR-9-5p, miR-344g-3p, and miR-7074-3p in cKO mice compared with those in control mice, suggesting an association with the increased expression of PDGFR-β. An analysis of the signaling pathways showed that the major transcriptional changes in cKO mice were related to smooth muscle cell differentiation, regulation of DNA metabolic processes and the actin cytoskeleton, positive regulation of fibroblast proliferation and Ras protein signal transduction, and focal adhesion-PI3K/Akt/mTOR signaling pathways. Depletion of Dicer in mesenchymal cells may downregulate the signaling pathway related to miR-9-5p, miR-344g-3p, and miR-7074-3p, which can lead to the progression of chronic kidney disease. These findings highlight the possibility for future diagnostic or therapeutic developments for renal fibrosis using miR-9-5p, miR-344g-3p, and miR-7074-3p.
Supplemental structured surveys and pre-existing detection models improve fine-scale density and population estimation with opportunistic community science data
Authors: Hallman Tyler A. , Robinson W. Douglas
Published: May 2024

Density and population estimates aid in conservation and stakeholder communication. While free and broadly available community science data can effectively inform species distribution models, they often lack the information necessary to estimate imperfect detection and area sampled, thus limiting their use in fine-scale density modeling. We used structured distance-sampling surveys to model detection probability and calculate survey-specific detection offsets in community science models. We estimated density and population for 16 songbird species under three frameworks: (1) a fixed framework that assumes perfect detection within a specified survey radius, (2) an independent framework that calculates offsets from an independent source, and (3) a calibration framework that calculates offsets from supplemental surveys. Within the calibration framework, we examined the effects of calibration dataset size and data pooling. Estimates of density and population size were consistently biased low in the fixed framework. The independent and calibration frameworks produced reliable estimates for some species, but biased estimates for others, indicating discrepancies in detection probability between structured and community science surveys. The calibration framework produced reliable population estimates with as few as 10 calibration surveys with positive detections. Data pooling dramatically decreased bias. This study provides conservationists and managers with a cost-effective method of estimating density and population.
Major chromosome rearrangements in intergeneric wheat × rye hybrids in compatible and incompatible crosses detected by GBS read coverage analysis
Authors: Tikhenko Natalia , Haupt Max , Fuchs Jörg , Perovic Dragan , Himmelbach Axel , Mascher Martin , Houben Andreas , Rutten Twan , Nagel Manuela , Tsvetkova Natalia V. , Sehmisch Stefanie , Börner Andreas
Published: May 2024

The presence of incompatibility alleles in primary amphidiploids constitutes a reproductive barrier in newly synthesized wheat-rye hybrids. To overcome this barrier, the genome stabilization process includes large-scale chromosome rearrangements. In incompatible crosses resulting in fertile amphidiploids, the elimination of one of the incompatible alleles Eml-A1 or Eml-R1b can occur already in the somatic tissue of the wheat × rye hybrid embryo. We observed that the interaction of incompatible loci Eml-A1 of wheat and Eml-R1b of rye after overcoming embryo lethality leads to hybrid sterility in primary triticale. During subsequent seed reproductions (R1, R2 or R3) most of the chromosomes of A, B, D and R subgenomes undergo rearrangement or eliminations to increase the fertility of the amphidiploid by natural selection. Genotyping-by-sequencing (GBS) coverage analysis showed that improved fertility is associated with the elimination of entire and partial chromosomes carrying factors that either cause the disruption of plant development in hybrid plants or lead to the restoration of the euploid number of chromosomes (2n = 56) in the absence of one of the incompatible alleles. Highly fertile offspring obtained in compatible and incompatible crosses can be successfully adapted for the production of triticale pre-breeding stocks.
First insights into the age of the giant ice deposits in the Eisriesenwelt cave (Austria)
Authors: Spötl Christoph , Fohlmeister Jens , Reimer Paula , Zhang Haiwei
Published: May 2024

Frozen water is the most widespread type of ice present in ice caves and forms ice stalagmites and stalactites as well as floor ice, which is often several meters thick. Organic macroremains are commonly rare in this type of cave ice, which makes it difficult to establish a chronology and severely limits the use of such ice deposits as paleoenvironmental archives. Here, the chronology of such ice deposits in the inner part of the glaciated Eisriesenwelt, one of the world’s largest ice caves located in the European Alps of Austria, is determined by a combination of radiocarbon and 230Th dating of cryogenic calcite. The data suggest that this cave ice has formed over the last three millennia, with a marked increase in the average accumulation rate during the thirteenth century, coinciding with the onset of the Little Ice Age in the Alps. Data from a second site closer to the entrance suggests that large parts of this tourist cave were likely ice-free during the Medieval Warm Period and that a substantial part of the ice is probably a relic of the Little Ice Age. The current warming has already penetrated deeper into the cave than during the Medieval Warm Period, although air exchange during the warm season is restricted by a door at the cave entrance.
TASL mediates keratinocyte differentiation by regulating intracellular calcium levels and lysosomal function
Authors: Park Ji Yeong , Kim Hyeng-Soo , Hyung Hyejin , Jang Soyeon , Ko Jiwon , Lee Jin Hong , Kim Si-Yong , Park Song , Yi Junkoo , Park Sijun , Lim Su-Geun , Kim Seonggon , Lee Sanggyu , Kim Myoung Ok , Jang Soyoung , Ryoo Zae Young
Published: May 2024

Maintaining epidermal homeostasis relies on a tightly organized process of proliferation and differentiation of keratinocytes. While past studies have primarily focused on calcium regulation in keratinocyte differentiation, recent research has shed light on the crucial role of lysosome dysfunction in this process. TLR adaptor interacting with SLC15A4 on the lysosome (TASL) plays a role in regulating pH within the endo-lysosome. However, the specific role of TASL in keratinocyte differentiation and its potential impact on proliferation remains elusive. In our study, we discovered that TASL deficiency hinders the proliferation and migration of keratinocytes by inducing G1/S cell cycle arrest. Also, TASL deficiency disrupts proper differentiation process in TASL knockout human keratinocyte cell line (HaCaT) by affecting lysosomal function. Additionally, our research into calcium-induced differentiation showed that TASL deficiency affects calcium modulation, which is essential for keratinocyte regulation. These findings unveil a novel role of TASL in the proliferation and differentiation of keratinocytes, providing new insights into the intricate regulatory mechanisms of keratinocyte biology.
Transcriptomic analysis-guided assessment of precision-cut tumor slices (PCTS) as an ex-vivo tool in cancer research
Authors: Trivedi Sumita , Tilsed Caitlin , Liousia Maria , Brody Robert M. , Rajasekaran Karthik , Singhal Sunil , Albelda Steven M. , Klampatsa Astero
Published: May 2024

With cancer immunotherapy and precision medicine dynamically evolving, there is greater need for pre-clinical models that can better replicate the intact tumor and its complex tumor microenvironment (TME). Precision-cut tumor slices (PCTS) have recently emerged as an ex vivo human tumor model, offering the opportunity to study individual patient responses to targeted therapies, including immunotherapies. However, little is known about the physiologic status of PCTS and how culture conditions alter gene expression. In this study, we generated PCTS from head and neck cancers (HNC) and mesothelioma tumors (Meso) and undertook transcriptomic analyses to understand the changes that occur in the timeframe between PCTS generation and up to 72 h (hrs) in culture. Our findings showed major changes occurring during the first 24 h culture period of PCTS, involving genes related to wound healing, extracellular matrix, hypoxia, and IFNγ-dependent pathways in both tumor types, as well as tumor-specific changes. Collectively, our data provides an insight into PCTS physiology, which should be taken into consideration when designing PCTS studies, especially in the context of immunology and immunotherapy.
Introducing the glycyrrhizic acid and glabridin rich genotypes from the cultivated Iranian licorice (Glycyrrhiza glabra L.) populations to exploit in production systems
Authors: Esmaeili Hassan , Mirjalili Mohammad Hossein , Karami Akbar , Nejad Ebrahimi Samad
Published: May 2024

Currently, the stable, uniform, and highly efficient production of raw materials for pharmaceutical companies has received special attention. To meet these criteria and reduce harvesting pressure on the natural habitats of licorice (Glycyrrhiza glabra L.), cultivation of this valuable plant is inevitable. In the present study, to introduce the glycyrrhizic acid (GA)- and glabridin-rich genotypes from cultivated Iranian licorice, forty genotypes from eight high-potential wild populations were cultivated and evaluated under the same environmental conditions. The GA content varied from 5.00 ± 0.04 mg/g DW (TF2 genotype) to 23.13 ± 0.02 mg/g DW (I5 genotype). The highest and lowest glabridin content were found in the K2 (0.72 ± 0.021 mg/g DW) and M5 (0.02 ± 0.002 mg/g DW) genotypes, respectively. The rutin content in the leaves of the studied genotypes varied from 1.27 ± 0.02 mg/g DW in E4 to 3.24 ± 0.02 mg/g DW in BO5 genotypes. The genotypes from the Ilam population were characterized by higher vegetative growth and yield traits in the aerial parts and roots. The average root dry yield was 2.44 tons per hectare (t/ha) among the studied genotypes and a genotype from Ilam (I5) yielded the maximum value (3.08 ± 0.034 t/ha). The highest coefficient of variation among the genotypes was observed for leaf width (CV = 34.9%). The GA and glabridin-rich genotypes introduced in this study can be used in the future breeding programs to release new bred licorice cultivars.
Distinct cytokine profiles in late pregnancy in Ugandan people with HIV
Authors: Bebell Lisa M. , Ngonzi Joseph , Butler Audrey , Kumbakumba Elias , Adong Julian , Loos Carolin , Boatin Adeline A. , Bassett Ingrid V. , Siedner Mark J. , Williams Paige L. , Mattie Heather , Hedt-Gauthier Bethany , Correia Katharine F. B. , Lake Erin , Alter Galit
Published: May 2024

During pregnancy, multiple immune regulatory mechanisms establish an immune-tolerant environment for the allogeneic fetus, including cellular signals called cytokines that modify immune responses. However, the impact of maternal HIV infection on these responses is incompletely characterized. We analyzed paired maternal and umbilical cord plasma collected during labor from 147 people with HIV taking antiretroviral therapy and 142 HIV-uninfected comparators. Though cytokine concentrations were overall similar between groups, using Partial Least Squares Discriminant Analysis we identified distinct cytokine profiles in each group, driven by higher IL-5 and lower IL-8 and MIP-1α levels in pregnant people with HIV and higher RANTES and E-selectin in HIV-unexposed umbilical cord plasma (P-value < 0.01). Furthermore, maternal RANTES, SDF-α, gro $$\mathrm{\alpha }$$
α
-KC, IL-6, and IP-10 levels differed significantly by HIV serostatus (P < 0.01). Although global maternal and umbilical cord cytokine profiles differed significantly (P < 0.01), umbilical cord plasma profiles were similar by maternal HIV serostatus. We demonstrate that HIV infection is associated with a distinct maternal plasma cytokine profile which is not transferred across the placenta, indicating a placental role in coordinating local inflammatory response. Furthermore, maternal cytokine profiles in people with HIV suggest an incomplete shift from Th2 to Th1 immune phenotype at the end of pregnancy.
Serum ApoB/ApoA1 ratio in patients with CHB and the occurrence of HBV related cirrhosis and HBV related hepatocellular carcinoma
Authors: Cai Xin , Peng Shi , Xiao Xuan , Huang Zhaoyang , Zhang Pingan
Published: May 2024

Clinical research has suggested that chronic HBV infection exerts a certain effect on the occurrence of cardiovascular disease by regulating cholesterol metabolism in liver cells. High serum apolipoprotein B/apolipoprotein A1 (ApoB/ApoA1) ratio plays a certain role in the above regulation, and it serves as a risk factor for cardiovascular disease. However, whether the ApoB/ApoA1 ratio is correlated with chronic HBV infection and its disease progression remains unclear. In accordance with the inclusion and exclusion criteria, all 378 participants administrated at Renmin Hospital of Wuhan University from March 2021 to March 2022, fell into Healthy Control (HC) group (50 participants), Hepatocellular carcinoma (HCC) group (107 patients), liver cirrhosis (LC) group (64 patients), chronic hepatitis B (CHB) group (62 patients), chronic hepatitis C (CHC) group (46 patients) and Hepatitis E Virus (HEV) group (49 patients). Serum ApoA1 and ApoB concentrations were measured at admission, and the ApoB/ApoA1 ratio was determined. The levels of laboratory parameters in the respective group were compared and ApoB/ApoA1 ratios in HCC patients and LC patients with different severity were further analyzed. ROC curves were plotted to analyze the early diagnostic ability of ApoB/ApoA1 ratio for HBV-associated HCC. Logistic regression and restricted cubic spline analysis were used to explore the correlation between ApoB/ApoA1 ratio and LC and HCC risk. A comparison was drawn in terms of ApoB/ApoA1 ratio between the groups, and the result was expressed in descending sequence: HEV group > CHB group > LC group > HCC group > CHC group > HC group, early-stage HCC < middle-stage HCC < advanced-stage HCC, Class A LC < Class B LC < Class C LC. Serum ApoB/ApoA1 ratio combined diagnosis with AFP exhibited the capability of increasing the detection efficacy and specificity of AFP for HCC and AFP-negative HCC. The incidence of LC and HCC in the respective logistic regression model showed a negative correlation with the serum ApoB/ApoA1 ratio in CHB patients (P < 0.05). After all confounding factors covered in this study were regulated, the result of the restricted cubic spline analysis suggested that in a certain range, serum ApoB/ApoA1 ratio showed an inverse correlation with the prevalence of LC or HCC in CHB patients. Serum ApoB/ApoA1 ratio in CHB patients may be conducive to identifying high-risk patients for HCC or LC, such that LC and HCC can be early diagnosed and treated.
Experimental study on mechanical and hydraulic properties of xanthan gum improved low liquid limit silty soil
Authors: Zhang Xutao , Cao Wenyue , Zhang Xiao
Published: May 2024

The low liquid limit silty soil in the North China plain area is generally unsuitable for direct use as roadbed and slope soil. In order to improve the performance of low liquid limit silty soil, xanthan gum was used as an improver. Through a series of tests, the improvement effect of xanthan gum on low liquid limit silty soil was studied. The test results showed that Xanthan gum as an improver could significantly improve the unconfined compressive strength of silty soil. With the increase in dosage and curing age, the unconfined compressive strength of improved silty soil continued to improve and eventually tended to stabilize. The optimal dosage and curing period were 2% and 7 days, respectively. In addition, Xanthan gum could greatly improve the permeability and disintegration of low liquid limit silty soil. The permeability coefficient of improved silty soil with a content of 0.75% Xanthan gum and a 7-day curing period was 4.73 × 10−4 m·s−1, which was only 1.10% of that of plain silty soil at the same curing period. After immersion in water for 12 h, the soil only experienced slight disintegration. The scanning electron microscope image showed that the gel generated by the hydration reaction of Xanthan gum could improve the compactness and integrity of the soil by filling the voids, thus significantly improving the mechanical and hydraulic properties of the low liquid limit silty soil.
Clinical usefulness of NT-proBNP as a prognostic factor for septic shock patients presenting to the emergency department
Authors: Choi Yunhyung , Lee Jae Hee
Published: May 2024

Plasma N-terminal prohormone of brain natriuretic peptide (NT-proBNP) level is primarily used as a biomarker for left ventricular (LV) dysfunction. It is influenced by various conditions, such as myocardial strain and situations affecting the clearance of NT-proBNP, including sepsis and shock. In this study, we investigated the appropriateness of NT-proBNP as a prognostic factor for septic shock. Patients with septic shock who visited the emergency department of the Ewha Womans’ University Mokdong Hospital between January 1, 2018, and December 31, 2020, were classified into the survival group (those who survived in the hospital and were discharged) and the death group (those who died in the hospital). The effectiveness of NT-proBNP, lactate, and blood urea nitrogen as predictive factors of in-hospital mortality was evaluated using the area under the receiver operating characteristic (AUROC) curve. The AUROC curve was 0.678 and 0.648 for lactate and NT-proBNP, respectively, with lactate showing the highest value. However, there was no significant difference between lactate and NT-proBNP levels in the comparison of their AUROC curve (p = 0.6278). NT-proBNP could be a useful predictor of in-hospital mortality in patients with septic shock who present to the emergency department.
Hydraulic property variations with depth in a loess mudstone landslide
Authors: Liu Wei , Lin Gaochao , Liu Qingpeng , Su Xing
Published: May 2024

In areas where loess is distributed, landslides represent a significant geohazard with severe implications. Among these events, loess-mudstone landslides are particularly prevalent, posing substantial risks to the safety and property of local residents, and moisture plays a pivotal role as a key factor in causing these disasters. In this study, the hydraulic properties of the soils along the longitudinal section of an ongoing loess-mudstone landslide are investigated through the variation of soil water characteristic curves, which are subsequently fitted by utilizing van Genuchten model. Moreover, a comprehensive experimental investigation was conducted on the loess, mudstone, and loess-mudstone mixtures to facilitate analysis, including X-ray diffraction (XRD) analysis, scanning electron microscopy (SEM) observation, particle size distribution (PSD) analysis, along with fundamental geotechnical tests for parameter determination. It is found that mudstone and loess have distinct SWCC distribution. The SWCC of loess at various depths exhibits a similar distribution pattern due to the occurrence of landslide. The SWCC distribution of loess-mudstone mixture displays a transitional trend between the SWCC of mudstone and that of loess, and the water retention capacity increases as the mudstone content increases. The experimental findings have demonstrated notable agreement between each other and exhibited a satisfactory level of concurrence with the observed phenomena in geological surveys.
Unveiling the potential of A. fabrum and γ-aminobutyric acid for mitigation of nickel toxicity in fenugreek
Authors: Danish Subhan , Hussain Ghulam Sabir , Hussain Muhammad Baqir , Elgorban Abdallah M. , Datta Rahul
Published: May 2024

Nickel (Ni) is a heavy metal that adversely affects the growth of different crops by inducing oxidative stress and nutrient imbalance. The role of rhizobacteria (RB) is vital to resolve this issue. They can promote root growth and facilitate the uptake of water and nutrients, resulting in better crop growth. On the other hand, γ-aminobutyric acid (GABA) can maintain the osmotic balance and scavenge the reactive oxygen species under stress conditions. However, the combined effect of GABA and RB has not been thoroughly explored to alleviate Ni toxicity, especially in fenugreek plants. Therefore, in the current pot study, four treatments, i.e., control, A. fabrum (RB), 0.40 mM GABA, and 0.40 mM GABA + RB, were applied under 0Ni and 80 mg Ni/kg soil (80Ni) stress. Results showed that RB + 0.40 mM GABA caused significant improvements in shoot length (~ 13%), shoot fresh weight (~ 47%), shoot dry weight (~ 47%), root length (~ 13%), root fresh weight (~ 60%), and root dry weight (~ 15%) over control under 80 Ni toxicity. A significant enhancement in total chlorophyll (~ 14%), photosynthetic rate (~ 17%), stomatal CO2 concentration (~ 19%), leaves and roots N (~ 10 and ~ 37%), P (~ 18 and ~ 7%) and K (~ 11 and ~ 30%) concentrations, while a decrease in Ni (~ 83 and ~ 49%) concentration also confirmed the effectiveness of RB + 0.40 mM GABA than control under 80Ni. In conclusion, fabrum + 0.40 mM GABA can potentially alleviate the Ni toxicity in fenugreek plants. The implications of these findings extend to agricultural practices, environmental remediation efforts, nutritional security, and ecological impact. Further research is recommended to elucidate the underlying mechanisms, assess long-term effects, and determine the practical feasibility of using A. fabrum + 0.40GABA to improve growth in different crops under Ni toxicity.
Spatial health risk assessments of nickel in the groundwater sources of a mining-impacted area
Authors: Salehi Fatemeh , Esmaeilbeigi Milad , Kazemi Ali , Sharafi Saeed , Sahebi Zahra , Asl Ali Ghanavati
Published: May 2024

Mining activities have increased the potential risks of metal pollution to the groundwater resources in arid areas across the globe. Therefore, this study aimed to examine the health risk associated with nickel (Ni) in the groundwater sources of a mining-impacted area, South Khorasan, Eastern Iran. A total of 110 stations were included in the study, comprising 62 wells, 40 qanats, and 8 springs in summer, 2020. Initially, the collected samples were tested for temperature, pH, and electrical conductivity (EC). Subsequently, the samples were filtered and treated with nitric acid (HNO3) to measure the concentration of Ni using Inductively Coupled Plasma Mass Spectrometry (ICP-MS). Hazard quotient (HQ) and non-carcinogenic risk assessments were employed to evaluate the potential risks of Ni to the inhabitants. The findings revealed that the concentration of Ni ranged from 0.02 to 132.39 μg l−1, and only two stations exhibited Ni concentrations above the WHO standards (20 μg l−1). The results demonstrated that 98.21% of the sampled locations had HQ values below one, indicating negligible risk, while 1.78% of the stations exhibited HQ values of one or higher, representing a high non-carcinogenic risk for water consumers. Overall, the concentration of nickel in the groundwater of South Khorasan exceeded the World Health Organization (WHO) limit solely in the Halvan station, posing a non-carcinogenic risk for the residents in that area, and therefore, additional efforts should be made to provide healthier groundwater to consumers in this region.
Redox balance and immunity of piglets pre- and post-E. coli challenge after treatment with hemp or fish oil, and vitamin E
Authors: Madsen Pernille A. , Jensen Søren K. , Lauridsen Charlotte
Published: May 2024

This study investigated the influence of polyunsaturated fatty acid composition and vitamin E supplementation on oxidative status and immune responses in weanling piglets pre- and post-E. coli challenge. Suckling piglets (n = 24) were randomly selected from two litters for an oral supplementation (1 mL/day) with fish oil or hemp oil and vitamin E supplementation (60 mg natural vitamin E/mL oil) from day 10 to 28 of age. At day 29 and 30 of age, each piglet was orally inoculated with 6.7 × 108 and 3.96 × 108 CFU of F4 and F18 E. coli, respectively. Blood was sampled from all piglets on day 28 before E. coli challenge and on day 35 of age to investigate immunological and oxidative stress markers in plasma. One week after weaning and exposure to E. coli, a general reduction in the α-tocopherol concentration and activity of GPX1 was obtained. Vitamin E supplementation lowered the extent of lipid peroxidation and improved the antioxidative status and immune responses after E. coli challenge. Hemp oil had the greatest effect on antioxidant enzyme activity. Provision of hemp oil and vitamin E to suckling piglets may reduce the incidence of post-weaning diarrhea.
Alternative 3′UTR expression induced by T cell activation is regulated in a temporal and signal dependent manner
Authors: Blake Davia , Gazzara Matthew R. , Breuer Isabel , Ferretti Max , Lynch Kristen W.
Published: May 2024

The length of 3′ untranslated regions (3′UTR) is highly regulated during many transitions in cell state, including T cell activation, through the process of alternative polyadenylation (APA). However, the regulatory mechanisms and functional consequences of APA remain largely unexplored. Here we present a detailed analysis of the temporal and condition-specific regulation of APA following activation of primary human CD4+ T cells. We find that global APA changes are regulated temporally and CD28 costimulatory signals enhance a subset of these changes. Most APA changes upon T cell activation involve 3′UTR shortening, although a set of genes enriched for function in the mTOR pathway exhibit 3′UTR lengthening. While upregulation of the core polyadenylation machinery likely induces 3′UTR shortening following prolonged T cell stimulation; a significant program of APA changes occur prior to cellular proliferation or upregulation of the APA machinery. Motif analysis suggests that at least a subset of these early changes in APA are driven by upregulation of RBM3, an RNA-binding protein which competes with the APA machinery for binding. Together this work expands our understanding of the impact and mechanisms of APA in response to T cell activation and suggests new mechanisms by which APA may be regulated.
A systematic review and meta-analysis of artificial intelligence versus clinicians for skin cancer diagnosis
Authors: Salinas Maria Paz , Sepúlveda Javiera , Hidalgo Leonel , Peirano Dominga , Morel Macarena , Uribe Pablo , Rotemberg Veronica , Briones Juan , Mery Domingo , Navarrete-Dechent Cristian
Published: May 2024

Scientific research of artificial intelligence (AI) in dermatology has increased exponentially. The objective of this study was to perform a systematic review and meta-analysis to evaluate the performance of AI algorithms for skin cancer classification in comparison to clinicians with different levels of expertise. Based on PRISMA guidelines, 3 electronic databases (PubMed, Embase, and Cochrane Library) were screened for relevant articles up to August 2022. The quality of the studies was assessed using QUADAS-2. A meta-analysis of sensitivity and specificity was performed for the accuracy of AI and clinicians. Fifty-three studies were included in the systematic review, and 19 met the inclusion criteria for the meta-analysis. Considering all studies and all subgroups of clinicians, we found a sensitivity (Sn) and specificity (Sp) of 87.0% and 77.1% for AI algorithms, respectively, and a Sn of 79.78% and Sp of 73.6% for all clinicians (overall); differences were statistically significant for both Sn and Sp. The difference between AI performance (Sn 92.5%, Sp 66.5%) vs. generalists (Sn 64.6%, Sp 72.8%), was greater, when compared with expert clinicians. Performance between AI algorithms (Sn 86.3%, Sp 78.4%) vs expert dermatologists (Sn 84.2%, Sp 74.4%) was clinically comparable. Limitations of AI algorithms in clinical practice should be considered, and future studies should focus on real-world settings, and towards AI-assistance.
Shortcut learning in medical AI hinders generalization: method for estimating AI model generalization without external data
Authors: Ong Ly Cathy , Unnikrishnan Balagopal , Tadic Tony , Patel Tirth , Duhamel Joe , Kandel Sonja , Moayedi Yasbanoo , Brudno Michael , Hope Andrew , Ross Heather , McIntosh Chris
Published: May 2024

Healthcare datasets are becoming larger and more complex, necessitating the development of accurate and generalizable AI models for medical applications. Unstructured datasets, including medical imaging, electrocardiograms, and natural language data, are gaining attention with advancements in deep convolutional neural networks and large language models. However, estimating the generalizability of these models to new healthcare settings without extensive validation on external data remains challenging. In experiments across 13 datasets including X-rays, CTs, ECGs, clinical discharge summaries, and lung auscultation data, our results demonstrate that model performance is frequently overestimated by up to 20% on average due to shortcut learning of hidden data acquisition biases (DAB). Shortcut learning refers to a phenomenon in which an AI model learns to solve a task based on spurious correlations present in the data as opposed to features directly related to the task itself. We propose an open source, bias-corrected external accuracy estimate, PEst, that better estimates external accuracy to within 4% on average by measuring and calibrating for DAB-induced shortcut learning.
Structural and mechanistic insights into Quinolone Synthase to address its functional promiscuity
Authors: Vijayanathan Mallika , Vadakkepat Abhinav Koyamangalath , Mahendran Kozhinjampara R. , Sharaf Abdoallah , Frandsen Kristian E. H. , Bandyopadhyay Debashree , Pillai M. Radhakrishna , Soniya Eppurath Vasudevan
Published: May 2024

Quinolone synthase from Aegle marmelos (AmQNS) is a type III polyketide synthase that yields therapeutically effective quinolone and acridone compounds. Addressing the structural and molecular underpinnings of AmQNS and its substrate interaction in terms of its high selectivity and specificity can aid in the development of numerous novel compounds. This paper presents a high-resolution AmQNS crystal structure and explains its mechanistic role in synthetic selectivity. Additionally, we provide a model framework to comprehend structural constraints on ketide insertion and postulate that AmQNS’s steric and electrostatic selectivity plays a role in its ability to bind to various core substrates, resulting in its synthetic diversity. AmQNS prefers quinolone synthesis and can accommodate large substrates because of its wide active site entrance. However, our research suggests that acridone is exclusively synthesized in the presence of high malonyl-CoA concentrations. Potential implications of functionally relevant residue mutations were also investigated, which will assist in harnessing the benefits of mutations for targeted polyketide production. The pharmaceutical industry stands to gain from these findings as they expand the pool of potential drug candidates, and these methodologies can also be applied to additional promising enzymes.
EP4-induced mitochondrial localization and cell migration mediated by CALML6 in human oral squamous cell carcinoma
Authors: Ishikawa Soichiro , Umemura Masanari , Nakakaji Rina , Nagasako Akane , Nagao Kagemichi , Mizuno Yuto , Sugiura Kei , Kioi Mitomu , Mitsudo Kenji , Ishikawa Yoshihiro
Published: May 2024

Lymph node metastasis, primarily caused by the migration of oral squamous cell carcinoma (OSCC) cells, stands as a crucial prognostic marker. We have previously demonstrated that EP4, a subtype of the prostaglandin E2 (PGE2) receptor, orchestrates OSCC cell migration via Ca2+ signaling. The exact mechanisms by which EP4 influences cell migration through Ca2+ signaling, however, is unclear. Our study aims to clarify how EP4 controls OSCC cell migration through this pathway. We find that activating EP4 with an agonist (ONO-AE1-473) increased intracellular Ca2+ levels and the migration of human oral cancer cells (HSC-3), but not human gingival fibroblasts (HGnF). Further RNA sequencing linked EP4 to calmodulin-like protein 6 (CALML6), whose role remains undefined in OSCC. Through protein-protein interaction network analysis, a strong connection is identified between CALML6 and calcium/calmodulin-dependent protein kinase kinase 2 (CaMKK2), with EP4 activation also boosting mitochondrial function. Overexpressing EP4 in HSC-3 cells increases experimental lung metastasis in mice, whereas inhibiting CaMKK2 with STO-609 markedly lowers these metastases. This positions CaMKK2 as a potential new target for treating OSCC metastasis. Our findings highlight CALML6 as a pivotal regulator in EP4-driven mitochondrial respiration, affecting cell migration and metastasis via the CaMKK2 pathway.
ALKBH5-mediated m6A modification of circFOXP1 promotes gastric cancer progression by regulating SOX4 expression and sponging miR-338-3p
Authors: Wang Shouhua , Zhu Xiang , Hao Yuan , Su Ting ting , Shi Weibin
Published: May 2024

Circular RNAs (circRNAs) have recently been suggested as potential functional modulators of cellular physiology processes in gastric cancer (GC). In this study, we demonstrated that circFOXP1 was more highly expressed in GC tissues. High circFOXP1 expression was positively associated with tumor size, lymph node metastasis, TNM stage, and poor prognosis in patients with GC. Cox multivariate analysis revealed that higher circFOXP1 expression was an independent risk factor for disease-free survival (DFS) and overall survival (OS) in GC patients. Functional studies showed that increased circFOXP1 expression promoted cell proliferation, cell invasion, and cell cycle progression in GC in vitro. In vivo, the knockdown of circFOXP1 inhibited tumor growth. Mechanistically, we observed ALKBH5-mediated m6A modification of circFOXP1 and circFOXP1 promoted GC progression by regulating SOX4 expression and sponging miR-338-3p in GC cells. Thus, our findings highlight that circFOXP1 could serve as a novel diagnostic and prognostic biomarker and potential therapeutic target for GC.
Data-driven insights can transform women’s reproductive health
Authors: Oskotsky Tomiko T. , Yin Ophelia , Khan Umair , Arnaout Leen , Sirota Marina
Published: May 2024

This perspective explores the transformative potential of data-driven insights to understand and address women’s reproductive health conditions. Historically, clinical studies often excluded women, hindering comprehensive research into conditions such as adverse pregnancy outcomes and endometriosis. Recent advances in technology (e.g., next-generation sequencing techniques, electronic medical records (EMRs), computational power) provide unprecedented opportunities for research in women’s reproductive health. Studies of molecular data, including large-scale meta-analyses, provide valuable insights into conditions like preterm birth and preeclampsia. Moreover, EMRs and other clinical data sources enable researchers to study populations of individuals, uncovering trends and associations in women’s reproductive health conditions. Despite these advancements, challenges such as data completeness, accuracy, and representation persist. We emphasize the importance of holistic approaches, greater inclusion, and refining and expanding on how we leverage data and computational integrative approaches for discoveries so that we can benefit not only women’s reproductive health but overall human health.
The kinase ZYG-1 phosphorylates the cartwheel protein SAS-5 to drive centriole assembly in C. elegans
Authors: Sankaralingam Prabhu , Wang Shaohe , Liu Yan , Oegema Karen F , O’Connell Kevin F
Published: May 2024

Centrioles organize centrosomes, the cell’s primary microtubule-organizing centers (MTOCs). Centrioles double in number each cell cycle, and mis-regulation of this process is linked to diseases such as cancer and microcephaly. In C. elegans, centriole assembly is controlled by the Plk4 related-kinase ZYG-1, which recruits the SAS-5–SAS-6 complex. While the kinase activity of ZYG-1 is required for centriole assembly, how it functions has not been established. Here we report that ZYG-1 physically interacts with and phosphorylates SAS-5 on 17 conserved serine and threonine residues in vitro. Mutational scanning reveals that serine 10 and serines 331/338/340 are indispensable for proper centriole assembly. Embryos expressing SAS-5S10A exhibit centriole assembly failure, while those expressing SAS-5S331/338/340A possess extra centrioles. We show that in the absence of serine 10 phosphorylation, the SAS-5–SAS-6 complex is recruited to centrioles, but is not stably incorporated, possibly due to a failure to coordinately recruit the microtubule-binding protein SAS-4. Our work defines the critical role of phosphorylation during centriole assembly and reveals that ZYG-1 might play a role in preventing the formation of excess centrioles.
Diet-driven differential response of Akkermansia muciniphila modulates pathogen susceptibility
Authors: Wolter Mathis , Grant Erica T , Boudaud Marie , Pudlo Nicholas A , Pereira Gabriel V , Eaton Kathryn A , Martens Eric C , Desai Mahesh S
Published: May 2024

The erosion of the colonic mucus layer by a dietary fiber-deprived gut microbiota results in heightened susceptibility to an attaching and effacing pathogen, Citrobacter rodentium. Nevertheless, the questions of whether and how specific mucolytic bacteria aid in the increased pathogen susceptibility remain unexplored. Here, we leverage a functionally characterized, 14-member synthetic human microbiota in gnotobiotic mice to deduce which bacteria and functions are responsible for the pathogen susceptibility. Using strain dropouts of mucolytic bacteria from the community, we show that Akkermansia muciniphila renders the host more vulnerable to the mucosal pathogen during fiber deprivation. However, the presence of A. muciniphila reduces pathogen load on a fiber-sufficient diet, highlighting the context-dependent beneficial effects of this mucin specialist. The enhanced pathogen susceptibility is not owing to altered host immune or pathogen responses, but is driven by a combination of increased mucus penetrability and altered activities of A. muciniphila and other community members. Our study provides novel insights into the mechanisms of how discrete functional responses of the same mucolytic bacterium either resist or enhance enteric pathogen susceptibility.
GABAergic Neurotransmission and Toxicity 1: Organochlorines
Authors: Smith Andrew G.
Published: May 2024

In the 1950s, the introduction of organochlorine insecticides containing active ingredients such as lindane, dieldrin, endrin, chlordane, heptachlor, endosulfan and toxaphene was extremely effective in combating a wide variety of crop and livestock pests. In the 1980s, the inhibitory molecular action causing convulsions and neurotoxicity was identified as binding to the pre-synaptic γ-aminobutyric acid-binding receptor A (GABAA)-regulated chloride channel, near to the picrotoxinin-binding site, antagonising membrane hyperpolarisation and inward chloride current. However, it became evident that the properties that made them excellent insecticides might also make them toxic to humans and non-target animal species. Accidental, occupational and suicidal convulsions occurred in humans, and there were marked effects on wildlife, especially in birds, due to accumulation up the food chain. Differential metabolism was an important factor determining the differences between individual insecticides. After a few decades of use, these pesticides were phased out and banned. The now-established multiple aspects of their toxicity in vivo or in vitro continue to be of concern regarding their possible adverse effects on human health through environmental exposure.
Re-assessment of monoclonal antibodies against diclofenac for their application in the analysis of environmental waters
Authors: Schmidt Stephan , Hoffmann Holger , Garbe Leif-Alexander , Harrer Andrea , Steiner Markus , Himly Martin , Schneider Rudolf J.
Published: May 2024

A formerly developed antibody against diclofenac was re-assessed for its application in an indirect competitive ELISA to determine the pharmaceutical in wastewater. A series of matrix influences and cross-reactivities have been investigated.
Quantifying the dominant sources influencing the 2016 particulate matter pollution episode over northern India
Authors: Agarwal Prerita , Stevenson David S. , Heal Mathew R.
Published: May 2024

Contribution of anthropogenic, biomass-burning and natural sources to the spatiotemporal extent of the episode across northern India.