bluuebunny/crossref_metadata_2025_split huggingface dataset:
Benchmarking UMI-aware and standard variant callers for low frequency ctDNA variant detection
Authors: Maruzani Rugare , Brierley Liam , Jorgensen Andrea , Fowler Anna 
Published: September 2024

Abstract
Background
Circulating tumour DNA (ctDNA) is a subset of cell free DNA (cfDNA) released by tumour cells into the bloodstream. Circulating tumour DNA has shown great potential as a biomarker to inform treatment in cancer patients. Collecting ctDNA is minimally invasive and reflects the entire genetic makeup of a patient’s cancer. ctDNA variants in NGS data can be difficult to distinguish from sequencing and PCR artefacts due to low abundance, particularly in the early stages of cancer. Unique Molecular Identifiers (UMIs) are short sequences ligated to the sequencing library before amplification. These sequences are useful for filtering out low frequency artefacts. The utility of ctDNA as a cancer biomarker depends on accurate detection of cancer variants.

Results
In this study, we benchmarked six variant calling tools, including two UMI-aware callers for their ability to call ctDNA variants. The standard variant callers tested included Mutect2, bcftools, LoFreq and FreeBayes. The UMI-aware variant callers benchmarked were UMI-VarCal and UMIErrorCorrect. We used both datasets with known variants spiked in at low frequencies, and datasets containing ctDNA, and generated synthetic UMI sequences for these datasets. Variant callers displayed different preferences for sensitivity and specificity. Mutect2 showed high sensitivity, while returning more privately called variants than any other caller in data without synthetic UMIs – an indicator of false positive variant discovery. In data encoded with synthetic UMIs, UMI-VarCal detected fewer putative false positive variants than all other callers in synthetic datasets. Mutect2 showed a balance between high sensitivity and specificity in data encoded with synthetic UMIs.

Conclusions
Our results indicate UMI-aware variant callers have potential to improve sensitivity and specificity in calling low frequency ctDNA variants over standard variant calling tools. There is a growing need for further development of UMI-aware variant calling tools if effective early detection methods for cancer using ctDNA samples are to be realised.
Evaluation of memory drought stress effects on storage compounds seedlings of cotton (Gossypium hirsutum) and in-silico analysis of glutathione reductase
Authors: Faghani Elham , Hashemi Amenehsadat , Kazemian Mina , Razzaghi Mohammad Hossein 
Published: September 2024

AbstractIn breeding programs, stress memory in plants can develop drought stress tolerance. Memory stress, as an approach, can keep stress data by activating tolerance mechanisms. This research was conducted to evaluate some physiologically effective mechanisms in inducing memory drought stress in the seeds that were exposed to water stress three times in four treatments including rainfed, 33%, 66%, and 100% of field capacity (FC). After the production of the seeds, the third-generation seeds were placed under different irrigation treatments, seed and seedling traits, starch to carbohydrate ratio in seed, protein concentration and glutathione reductase were investigatied in a factorial format based on a randomized complete block design with three replications. Results showed that percentage of changes from the lowest to the highest value for traits including seed vigor, seed endosperm weight, seed coat weight, accelerated aging, cold test, seedling biomass and seedling length were 25, 37, 65, 65, 55, 77, 55, 65 and 79, respectively and germination uniformity was 3.9 times higher than the lowest amount. According to the deterioration percentage, seed vigor and the percentage of seed germination in cold test data, it can be reported that seed production by 100% FC was not appropriate for rainfed plots. However, considering the the appropriate results in the percentage of germination for a cold test, germination uniformity percentage, and the lowest accelerated aging seeds, seed production under the rainfed conditions with 33% FC watering can be recommended. In-silico analysis was coducted on Glutathione reductase (GR) enzymes in Gossypium hirsutum. It is clear that GR has a Redox-active site and NADPH binding, and it interacts with Glutathione S transferase (GST). So, memory drought stress through inducing physiological drought tolerance mechanisms such as starch-to-carbohydrate ratio and GR can determine the suitable pattern for seed production for rainfed and low rainfall regions in a breeding program. Our study thus illustrated that seed reprduction under 33% FC equipped cotton with the tolerance against under draught stress from the seedling stage. This process is done through activating glutathione reductase and balancing the ratio of starch to carbohydrates concentration.
RNA-seq analyses on gametogenic tissues of alfalfa (Medicago sativa) revealed plant reproduction- and ploidy-related genes
Authors: Palumbo Fabio , Gabelli Giovanni , Pasquali Elisa , Vannozzi Alessandro , Farinati Silvia , Draga Samela , Ravi Samathmika , Della Lucia Maria Cristina , Bertoldo Giovanni , Barcaccia Gianni 
Published: September 2024

Abstract
Background
In alfalfa (Medicago sativa), the coexistence of interfertile subspecies (i.e. sativa, falcata and coerulea) characterized by different ploidy levels (diploidy and tetraploidy) and the occurrence of meiotic mutants capable of producing unreduced (2n) gametes, have been efficiently combined for the establishment of new polyploids. The wealth of agronomic data concerning forage quality and yield provides a thorough insight into the practical benefits of polyploidization. However, many of the underlying molecular mechanisms regarding gene expression and regulation remained completely unexplored. In this study, we aimed to address this gap by examining the transcriptome profiles of leaves and reproductive tissues, corresponding to anthers and pistils, sampled at different time points from diploid and tetraploid Medicago sativa individuals belonging to progenies produced by bilateral sexual polyploidization (dBSP and tBSP, respectively) and tetraploid individuals stemmed from unilateral sexual polyploidization (tUSP).

Results
Considering the crucial role played by anthers and pistils in the reduced and unreduced gametes formation, we firstly analyzed the transcriptional profiles of the reproductive tissues at different stages, regardless of the ploidy level and the origin of the samples. By using and combining three different analytical methodologies, namely weighted-gene co-expression network analysis (WGCNA), tau (τ) analysis, and differentially expressed genes (DEGs) analysis, we identified a robust set of genes and transcription factors potentially involved in both male sporogenesis and gametogenesis processes, particularly in crossing-over, callose synthesis, and exine formation. Subsequently, we assessed at the same floral stage, the differences attributable to the ploidy level (tBSP vs. dBSP) or the origin (tBSP vs. tUSP) of the samples, leading to the identification of ploidy and parent-specific genes. In this way, we identified, for example, genes that are specifically upregulated and downregulated in flower buds in the comparison between tBSP and dBSP, which could explain the reduced fertility of the former compared to the latter materials.

Conclusions
While this study primarily functions as an extensive investigation at the transcriptomic level, the data provided could represent not only a valuable original asset for the scientific community but also a fully exploitable genomic resource for functional analyses in alfalfa.
Overweight and vitamin D deficiency are common in patients with irritable bowel syndrome - a cross-sectional study
Authors: Roth Bodil , Ohlsson Bodil 
Published: September 2024

Abstract
Background
Irritable bowel syndrome (IBS) is a common disease with unknown etiology. Poor dietary intake with nutritional deficiency and overweight have been described to increase the risk of IBS. The aim of the present study was to compare weight and circulating levels of micronutrients in IBS compared with healthy controls.

Design
Cross-sectional study.

Methods
Patients diagnosed with IBS and healthy volunteers were recruited. Participants had to complete a dietary diary book and the questionnaires Rome IV, IBS-severity scoring system (IBS-SSS), and visual analog scale for IBS (VAS-IBS). Weight and height were measured, and blood samples were drawn. C-reactive protein (CRP), cobalamin, folate, iron, total iron-binding capacity (TIBC), and 25-hydroxy (25-OH) vitamin D were analyzed. Differences were calculated between groups and generalized linear model for regressions was adjusted for false discovery rate (FDR).

Results
IBS patients (n = 260) were elder than controls (n = 50) (44.00 (33.25-56.00) vs. 37.85 (30.18–45.48) years; p = 0.012). After adjustment for age, both weight (β: 5.880; 95% CI: 1.433–10.327; p = 0.010, FDR = 0.020) and body mass index (BMI) (β: 2.02; 95% CI: 0.68–3.36; p = 0.003, FDR = 0.012) were higher in patients. Among IBS participants, 48.1% were overweight/obese compared with 26.0% in controls (p = 0.007). Diarrhea-predominated IBS had highest weight (p < 0.001) and BMI (p = 0.077). CRP and cobalamin were higher in patients than controls (p = 0.010 vs. p = 0.007), whereas folate was highest in controls (p = 0.001). IBS patients had lower intake of vegetables (p = 0.026), dairy products (p = 0.004), and cereals (p = 0.010) compared with controls. Despite 21.5% of IBS patients were taking vitamin D supplements, 23.65% of them had vitamin D levels below 50 nmol/L, compared with 26.0% observed in the control group (p = 0.720). Vitamin D levels were lower in overweight than in normal weight IBS patients (60 (48–73) nmol/L vs. 65 (53–78) nmol/L, p = 0.022). Vitamin D correlated with cobalamin and folate but correlated inversely with TIBC and BMI. IBS patients had a high degree of gastrointestinal and extraintestinal symptoms, which were inversely associated with iron levels. Extraintestinal symptoms were associated with increased BMI.

Conclusion
IBS patients were often overweight or obese, with low vitamin D levels. High burden of extraintestinal symptoms were associated with overweight and lower iron levels.

Registration
ClinicalTrials.gov, NCT05192603 (Date of registration 11/29/2021) and NCT03306381 (Date of registration 09/18/2017), respectively.
Terminalia bellirica and Andrographis paniculata dietary supplementation in mitigating heat stress-induced behavioral, metabolic and genetic alterations in broiler chickens
Authors: Fayed Rabie H. , Ali Sara E. , Yassin Aya M. , Madian K. , Bawish Basma M. 
Published: September 2024

Abstract
Background
Heat stress (HS) is one of the most significant environmental stressors on poultry production and welfare worldwide. Identification of innovative and effective solutions is necessary. This study evaluated the effects of phytogenic feed additives (PHY) containing Terminalia bellirica and Andrographis paniculata on behavioral patterns, hematological and biochemical parameters, Oxidative stress biomarkers, and HSP70, I-FABP2, IL10, TLR4, and mTOR genes expression in different organs of broiler chickens under chronic HS conditions. A total of 208 one-day-old Avian-480 broiler chicks were randomly allocated into four treatments (4 replicate/treatment, 52 birds/treatment): Thermoneutral control treatment (TN, fed basal diet); Thermoneutral treatment (TN, fed basal diet + 1 kg/ton feed PHY); Heat stress treatment (HS, fed basal diet); Heat stress treatment (HS, fed basal diet + 1 kg/ton feed PHY).

Results
The findings of the study indicate that HS led to a decrease in feeding, foraging, walking, and comfort behavior while increasing drinking and resting behavior, also HS increased red, and white blood cells (RBCs and WBCs) counts, and the heterophile/ lymphocyte (H/L) ratio (P < 0.05); while both mean corpuscular volume (MCV), and mean corpuscular hemoglobin (MCH) were decreased (P < 0.05). In addition, HS negatively impacted lipid, protein, and glucose levels, liver and kidney function tests, and oxidative biomarkers by increasing malondialdehyde (MDA) levels and decreasing reduced glutathion (GSH) activity (P < 0.05). Heat stress (HS) caused the upregulation in HSP70, duodenal TLR4 gene expression, and the downregulation of I-FABP2, IL10, mTOR in all investigated tissues, and hepatic TLR4 (P < 0.05) compared with the TN treatment. Phytogenic feed additives (PHY) effectively mitigated heat stress’s negative impacts on broilers via an improvement of broilers’ behavior, hematological, biochemical, and oxidative stress biomarkers with a marked decrease in HSP70 expression levels while all tissues showed increased I-FABP2, IL10, TLR4, and mTOR (except liver) levels (P < 0.05).

Conclusion
Phytogenic feed additives (PHY) containing Terminalia bellirica and Andrographis paniculata have ameliorated the HS-induced oxidative stress and improved the immunity as well as the gut health and welfare of broiler chickens.
Is artificial intelligence a hazardous technology? Economic trade-off model
Authors: Herzog Bodo 
Published: September 2024

AbstractArtificial intelligence (AI) demonstrates various opportunities and risks. Our study explores the trade-off of AI technology, including existential risks. We develop a theory and a Bayesian simulation model in order to explore what is at stake. The study reveals four tangible outcomes: (i) regulating existential risks has a boundary solution of either prohibiting the technology or allowing a laissez-faire regulation. (ii) the degree of ‘normal’ risks follows a trade-off and is dependent on AI-intensity. (iii) we estimate the probability of ‘normal’ risks to be between 0.002% to 0.006% over a century. (iv) regulating AI requires a balanced and international approach due to the dynamic risks and its global nature.
Comparison of various test methods to quantify the deterioration degree of archaeological leather
Authors: Yao Shuli , Lin Yirui , Lei Chao , Wang Ya-nan , Yu Yue , Zeng Yunhang 
Published: September 2024

Abstract
Quantifying the degree of deterioration is crucial for developing prevention strategies for archaeological leather. In this work, the morphology, chemical compositions, and physical properties of artificially aged leather samples were analyzed using a series of test methods to determine non-destructive or micro-destructive technologies for quantifying the degree of deterioration in archaeological leather. Results show that the hydroxyproline (Hyp) content of leather decreases with the increase of deterioration degree because deterioration leads to the gradual destruction of the collagen fiber network of leather. Moreover, the Hyp content of leather can be micro-destructively determined by high-performance liquid chromatography with fluorescence detection. Therefore, the determination of Hyp content is recommended to quantify the degree of deterioration in archaeological leather.
Application of CRISPR/Cas9 system to knock out GluB gene for developing low glutelin rice mutant
Authors: AlHusnain Latifa , AlKahtani Muneera D. F. , Attia Kotb A. , Sanaullah Tayyaba , Elsharnoby Dalia E. 
Published: September 2024

AbstractThe nutritional quality improvement is among the most integral objective for any rice molecular breeding programs. The seed storage proteins (SSPs) have greater role to determine the nutritional quality of any cereal grains. Rice contains relatively balanced amino acid composition and the SSPs are fractioned into albumins (ALB), globulins (GLO), prolamins (PRO) and glutelins (GLU) according to differences in solubility. GLUs are further divided into subfamilies: GluA, GluB, GluC, and GluD depending on resemblance in amino acid. The GLU protein accounts for 60–80% of total protein contents, encoded by 15 genes located on different chromosomes of rice genome. The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system was employed to knockout Glu-B (LOC-Os02g15070) gene in non-basmati rice PK386 cultivar. The mutant displayed two base pair and three base pair mutation in the targeted regions. The homozygous mutant plant displayed reduction for both in total protein contents and GLU contents whereas, elevation in GLO, ALB and PRO. Moreover, the mutant plant also displayed reduction in physio-chemical properties e.g., total starch, amylose and gel consistency. The agronomic characteristics of both mutant and wild type displayed non-significant differences along with increase in higher percentage of chalkiness in mutant plants. The results obtained from scanning electron microscopy showed the loosely packed starch granules compared to wild type. The gene expression analysis displayed the lower expression of gene at 5 days after flowering (DAF), 10 DAF, 15 DAF and 20 DAF compared to wild type. GUS sub-cellular localization showed the staining in seed which further validated the results obtained from gene expression. Based on these findings it can be concluded Glu-B gene have significant role in controlling GLU contents and can be utilized in breeding programs to enhance the nutritional quality of rice, and may serve as healthy diet for patient allergic with high GLU contents.
Enhanced photo-induced optical activity of crisscrossed self-organized gratings in photosensitive nanolayers by introducing bi-periodicity
Authors: Nahal Arashmid , Kiasatfar Ozra 
Published: September 2024

AbstractIn the present work, the enhancement of photoinduced optical activity in a photosensitive nanolayer of AgCl doped by Ag nanoparticles, using bi-periodic crisscrossed self-organized periodic nanostructures (C-SPNs) is achieved. We found that the formation of two non-identical SPNs (i.e., with different periods), which crisscrossed each other, enhances the rotation of the polarization plane of the linear polarized probe beam, compared to the case when the two nanostructures are identical (i.e., having the same period). The difference in periods of the two C-SPNs increases the anisotropy of the medium, which in turn boosts the optical chirality produced by the formation of complex crisscrossed gratings made of Ag nanoparticles. The angle between the two gratings can be a control parameter for the amount and sign of rotation of the polarization plane of the probe beam. The enhanced optical activity of the bi-periodic C-SPNs, compared to the identical C-SPNs, can be attributed to the formation of more intricate chiral building blocks at the intersections of the two gratings.
Transfemoral hepatic vein access in double vein embolization – initial experience and feasibility
Authors: Carling Ulrik , Berger Sigurd , Gjønnæss Eyvind , Røsok Bård , Yaqub Sheraz , Lassen Kristoffer , Fretland Åsmund Avdem , Dorenberg Eric 
Published: September 2024

Abstract
Background
Hepatic vein embolization in double vein embolization (DVE) can be performed with transhepatic, transjugular or transfemoral access. This study evaluates the feasibility and technical success of using a transfemoral access for the hepatic vein embolization in patients undergoing preoperative to induce hypertrophy of the future liver remnant (FLR).

Material and methods
Retrospective analysis of single center cohort including 17 consecutive patients. The baseline standardized FLR was 18.2% (range 14.7–24.9). Portal vein embolization was performed with vascular plugs and glue through an ipsilateral transhepatic access. Hepatic vein embolization was performed using vascular plugs. Access for the hepatic vein was either transhepatic, transjugular or transfemoral. Technical success, number of hepatic veins embolized and complications were registered. In addition, volumetric data including degree of hypertrophy (DH) and kinetic growth rate (KGR), and resection data were registered.
R: Seven of the 17 patients had transfemoral hepatic vein embolization, with 100% technical success. No severe complications were registered. In the whole cohort, the median number of hepatic veins embolized was 2 (1–6). DH was 8.6% (3.0–19.4) and KGR was 3.6%/week (1.4–7.4), without significant differences between the patients having transfemoral versus transhepatic /transjugular access (p = 0.48 and 0.54 respectively). Time from DVE to surgery was median 4.8 weeks (2.6–33.9) for the whole cohort, with one patient declining surgery, two having explorative laparotomy and one patient having change of surgical strategy due to insufficient growth.

Conclusion
Transfemoral access is a feasible option with a high degree of technical success for hepatic vein embolization in patients with small future liver remnants needing DVE.
Debulking Surgery After Muscular Paraffin Oil Injections: Effects on Calcium Homeostasis and Patient Satisfaction
Authors: Yahyavi Sam Kafai , Wall-Gremstrup Gustav , Makki Ahmad , Juel Jacob , Theilade Simone , Berg Jais Oliver , Juul Anders , Momsen Ole , Eldrup Ebbe , Blomberg Jensen Martin 
Published: September 2024

Abstract

Context
Cosmetic paraffin oil injections can lead to granuloma formation, causing hypercalcemia and kidney failure.

Objective
This study explores whether debulking surgery is an effective treatment for improving calcium homeostasis, inflammation, and clinical symptoms.

Methods
In a retrospective study, we reviewed 33 patients undergoing debulking surgery. Changes in calcium, inflammatory markers, and renal function from baseline up to 12 months after surgery were assessed. Patients were interviewed after surgery.

Results
The patients were 34.6 years of age (SD 6.9) and had 1104 grams (SD 591) of granuloma tissue removed following injection of 1329 mL (SD 803) paraffin oil 7.9 years (SD 3.2) earlier. Seventeen patients had hypercalcemia and experienced a significant decline in ionized calcium from 1.48 mmol/L (SD 0.16) at baseline to 1.33 mmol/L (SD 0.03) at 12 months (P &lt; .002), although only 4 men (23.5%) became normocalcemic. Serum ferritin was reduced by 50% after 12 months (P = .048). Sixteen patients were normocalcemic and had no change in calcium homeostasis but experienced a 20% drop in serum ferritin levels (P = .025) after surgery. Fifteen patients completed all their planned surgeries within the study period and experienced a decline in serum ionized calcium (P = .031), ferritin (P = .011), and interleukin 2-receptor (P = .037). A survey showed that 55% of patients reported postoperative satisfaction scores of 10/10, and 59% of the patients reported reduced pain.

Conclusion
Surgery improved calcium homeostasis in a fraction of patients and reduced inflammation and subjective symptoms such as pain and mental well-being in a patient group left with few treatment options except high-dose prednisolone.