bluuebunny/crossref_metadata_2025 huggingface dataset:
LINC00659 exacerbates endothelial progenitor cell dysfunction in deep vein thrombosis of the lower extremities by activating DNMT3A-mediated FGF1 promoter methylation
Authors: Zhang Bo , Qin Jie
Published: March 2023

It has been shown that long non-coding RNA (lncRNA) LINC00659 was markedly upregulated in the peripheral blood of patients with deep venous thrombosis (DVT). However, the function of LINC00659 in lower extremity DVT (LEDVT) remains to be largely unrevealed. A total of 30 inferior vena cava (IVC) tissue samples and peripheral blood (60 ml per subject) were obtained from LEDVT patients (n = 15) and healthy donors (n = 15), and then LINC00659 expression was detected by RT-qPCR. The results displayed that LINC00659 is upregulated in IVC tissues and isolated endothelial group cells (EPCs) of patients with LEDVT. LINC00659 knock-down promoted the proliferation, migration, and angiogenesis ability of EPCs, while an pcDNA-eukaryotic translation initiation factor 4A3 (EIF4A3), a EIF4A3 overexpression vector, or fibroblast growth factor 1 (FGF1) small interfering RNA (siRNA) combined with LINC00659 siRNA could not enhance this effect. Mechanistically, LINC00659 bound with EIF4A3 promoter to upregulated EIF4A3 expression. Besides, EIF4A3 could facilitate FGF1 methylation and its downregulated expression by recruiting DNA methyltransferases 3A (DNMT3A) to the FGF1 promoter region. Additionally, LINC00659 inhibition could alleviate LEDVT in mice. In summary, the data indicated the roles of LINC00659 in the pathogenesis of LEDVT, and the LINC00659/EIF4A3/FGF1 axis could be a novel therapeutic target for the treatment of LEDVT.
Efficacy of intravenous tranexamic acid administration in medial opening-wedge distal tibial tuberosity osteotomy (MOWDTO) for varus knee osteoarthritis: a randomized control trial
Authors: Iseki Takuya , Iseki Tomoya , Kanto Ryo , Onishi Shintaro , Yoshiya Shinichi , Tachibana Toshiya , Nakayama Hiroshi
Published: March 2023

Background

This randomized controlled study was undertaken to investigate the efficacy of intravenous tranexamic acid (TXA) administration in reducing perioperative blood loss in patients undergoing medial opening-wedge distal tibial tuberosity osteotomy (MOWDTO). It was hypothesized that TXA would reduce perioperative blood loss in MOWDTO.

Methods

A total of 61 knees in 59 patients who underwent MOWDTO during the study period were randomly assigned to either of the groups with intravenous TXA administration (TXA group) or without TXA administration (control group). In the TXA group, patients received 1000 mg of TXA intravenously before skin incision and 6 h after the first dose. The primary outcomes was the volume of perioperative total blood loss which calculated using the blood volume and hemoglobin (Hb) drop. The Hb drop was calculated as the difference between preoperative Hb and postoperative Hb at days 1, 3, and 7.

Results

The perioperative total blood loss was significantly lower in the TXA group (543 ± 219 ml vs. 880 ± 268 ml, P < 0.001). The Hb drop was significantly lower at postoperative days 1, 3 and 7 in the TXA group than in the control group (day 1: 1.28 ± 0.68 g/dl vs. 1.91 ± 0.69 g/dl, P = 0.001; day 3: 1.54 ± 0.66 g/dl vs. 2.69 ± 1.00 g/dl, P < 0.001; day 7: 1.74 ± 0.66 g/dl vs. 2.83 ± 0.91 g/dl, P < 0.001).

Conclusion

Intravenous TXA administration in MOWDTO could reduce the perioperative blood loss.

Trial registration The study was approved by the institutional review board. (Registered on 26/02/2019 Registration Number 3136).

Level of Evidence Level I, randomized controlled trial.
HPV genotypes in high-grade cervical lesions and invasive cervical carcinoma detected in Gabonese women
Authors: Moussavou-Boundzanga Pamela , Koumakpayi Ismaël Hervé , Engohan Aloghe Corinne , Chansi Junie K. , Revignet Rose , Leroy Eric M. , Berthet Nicolas
Published: March 2023

Background

Cervical cancer is the third most common cancer among women worldwide, but particularly affects women living in sub-Saharan Africa. Screening and vaccination programs are two prevention approaches that can reduce cervical cancer incidence. However, effective vaccination campaigns require better knowledge of the prevalence of the main human papillomavirus (HPV) genotypes reported in high-grade neoplastic lesions and invasive carcinomas in women.

Methods

All samples collected in this study were processed using standard histopathological methods with haematoxylin and eosin staining of the sections. Areas with abnormal cells were then identified. The HPV genotype was determined on the DNA extracted from the same sections using nested PCR followed by amplicon sequencing and real-time PCR specific to five different HPV genotypes (16, 18, 33, 45 and 58).

Results

A total of 132 Gabonese patients with high-grade neoplastic lesions were included in this study; 81% were squamous cell carcinomas (SCC). At least one HPV was detected in 92.4% patients; HPV16 (75.4%) was the most frequent genotype, followed by HPV18, 58, 45, 33 and 35. Moreover, histological analysis showed that SCC samples had 50% and 58.2% stage III and IV tumor cells, respectively, according to the FIGO classification. Finally, 36.9% of these stage III and IV patients were less than 50 years old.

Conclusions

Our results confirm the high prevalence of HPV16 and 18 genotypes among high-grade lesions in Gabonese women. This study confirms the need for a national strategy for early screening of precancerous lesions associated with a broad national vaccination program among non-sexually active women to significantly reduce the long-term cancer burden.
Functional identification of two novel carbohydrate-binding modules of glucuronoxylanase CrXyl30 and their contribution to the lignocellulose saccharification
Authors: Liu Jiawen , Zhu Jingrong , Xu Qian , Shi Rui , Liu Cong , Sun Di , Liu Weijie
Published: March 2023

Background

Glycoside hydrolase (GH) family 30 xylanases are a distinct group of xylanases, most of which have a highly specific catalytic activity for glucuronoxylan. Since GH30 xylanases do not normally carry carbohydrate-binding modules (CBMs), our knowledge of the function of their CBMs is lacking.

Results

In this work, the CBM functions of CrXyl30 were investigated. CrXyl30 was a GH30 glucuronoxylanase containing tandem CBM13 (CrCBM13) and CBM2 (CrCBM2) at its C terminus, which was identified in a lignocellulolytic bacterial consortium previously. Both CBMs could bind insoluble and soluble xylan, with CrCBM13 having binding specificity for the xylan with l-arabinosyl substitutions, whereas CrCBM2 targeted l-arabinosyl side chains themselves. Such binding abilities of these two CBMs were completely different from other CBMs in their respective families. Phylogenetic analysis also suggested that both CrCBM13 and CrCBM2 belong to novel branches. Inspection of the simulated structure of CrCBM13 identified a pocket that just accommodates the side chain of 3(2)-alpha-l-arabinofuranosyl-xylotriose, which forms hydrogen bonds with three of the five amino acid residues involved in ligand interaction. The truncation of either CrCBM13 or CrCBM2 did not alter the substrate specificity and optimal reaction conditions of CrXyl30, whereas truncation of CrCBM2 decreased the kcat/Km value by 83% (± 0%). Moreover, the absence of CrCBM2 and CrCBM13 resulted in a 5% (± 1%) and a 7% (± 0%) decrease, respectively, in the amount of reducing sugar released by the synergistic hydrolysis of delignified corncob whose hemicellulose is arabinoglucuronoxylan, respectively. In addition, fusion of CrCBM2 with a GH10 xylanase enhanced its catalytic activity against the branched xylan and improved the synergistic hydrolysis efficiency by more than fivefold when delignified corncob was used as substrate. Such a strong stimulation of hydrolysis resulted from the enhancement of hemicellulose hydrolysis on the one hand, and the cellulose hydrolysis is also improved according to the lignocellulose conversion rate measured by HPLC.

Conclusions

This study identifies the functions of two novel CBMs in CrXyl30 and shows the good potential of such CBMs specific for branched ligands in the development of efficient enzyme preparations.
Cross-domain coordination of resource allocation and route planning for the edge computing-enabled multi-connected vehicles
Authors: Xue Duan , Guo Yan , Li Ning , Song Xiaoxiang , Zhang Lixiong
Published: March 2023

Multi-access edge computing (MEC) has unique interests in processing intensive and delay-critical computation tasks for vehicular application through computation offloading. However, due to the spatial inhomogeneity and dynamic mobility of connected vehicles (CVs), the edge servers (ESs) must dynamically adjust their resource allocation schemes to effectively provide computation offloading services for CVs. In this case, we propose a MEC framework supporting the collaboration of CVs, and incorporate digital twins (DTs) into wireless network to mitigate the unreliable long-distance communication between CVs and ESs. To solve the contradiction between the task change requirements of CVs and ES resources, we proactively balance the computation resources load of ESs by appropriately cooperative route planning of CVs, and achieve cross-domain load balancing between traffic flow and edge cloud resources domains. Furthermore, we jointly formulate route planning and resource allocation to balance the travel and service time delay by considering the mobility of CVs, distributed resources of ESs and the deadline sensitive vehicular tasks comprehensively. Besides, considering the coupled relationship between route planning and resource allocation, an alternating optimization algorithm is proposed to solve the formulated problem. we decompose it into two sub-problems. Firstly, a reinforcement learning method is used to optimize the route planning of CVs with fixed resource allocation. Then, an online learning and iterative algorithm is used to optimize the resource allocation strategy of edge cloud with fixed route selection. In order to demonstrate that our suggested scheme is more effective than other comparison schemes, a comprehensive series of experiments are conducted.
Genomic analysis of firework fear and noise reactivity in standard poodles
Authors: Handegård Karin Westereng , Storengen Linn Mari , Joergensen Dina , Lingaas Frode
Published: March 2023

Background

Fear of firework noises and other loud, sudden noises (noise reactivity) is a significant problem for many dogs and may have a negative effect on both welfare and, in severe cases, the life expectancy of dogs. A wide range of behavior traits, including fear-related behaviors, have high heritability estimates in dogs. The aim of this study was to estimate genomic heritability for fear of fireworks and loud noises in dogs.

Results

A genomic heritability estimate was performed based on genome-wide SNPs from standard poodles with records of fear of fireworks and noise reactivity. The study was based on questionnaires answered by owners, who also volunteered to return a cheek swab from their dog for DNA analyses. SNP-based heritability was estimated to be 0.28 for firework fear and 0.16 for noise reactivity. We also identified an interesting region on chromosome 17 that was weakly associated with both traits.

Conclusions

We have estimated low to medium genomic heritabilities for fear of fireworks and noise reactivity in standard poodles. We have also identified an interesting region on chromosome 17, which harbors genes that have been shown to be involved in different psychiatric traits with anxiety components in humans. The region was associated with both traits; however, the association was weak and need further verification from other studies.
DNA methylation analysis identifies key transcription factors involved in mesenchymal stem cell osteogenic differentiation
Authors: Gómez Rodolfo , Barter Matt J. , Alonso-Pérez Ana , Skelton Andrew J. , Proctor Carole , Herrero-Beaumont Gabriel , Young David A.
Published: March 2023

Background

Knowledge about regulating transcription factors (TFs) for osteoblastogenesis from mesenchymal stem cells (MSCs) is limited. Therefore, we investigated the relationship between genomic regions subject to DNA-methylation changes during osteoblastogenesis and the TFs known to directly interact with these regulatory regions.

Results

The genome-wide DNA-methylation signature of MSCs differentiated to osteoblasts and adipocytes was determined using the Illumina HumanMethylation450 BeadChip array. During adipogenesis no CpGs passed our test for significant methylation changes. Oppositely, during osteoblastogenesis we identified 2462 differently significantly methylated CpGs (adj. p < 0.05). These resided outside of CpGs islands and were significantly enriched in enhancer regions. We confirmed the correlation between DNA-methylation and gene expression. Accordingly, we developed a bioinformatic tool to analyse differentially methylated regions and the TFs interacting with them. By overlaying our osteoblastogenesis differentially methylated regions with ENCODE TF ChIP-seq data we obtained a set of candidate TFs associated to DNA-methylation changes. Among them, ZEB1 TF was highly related with DNA-methylation. Using RNA interference, we confirmed that ZEB1, and ZEB2, played a key role in adipogenesis and osteoblastogenesis processes. For clinical relevance, ZEB1 mRNA expression in human bone samples was evaluated. This expression positively correlated with weight, body mass index, and PPARγ expression.

Conclusions

In this work we describe an osteoblastogenesis-associated DNA-methylation profile and, using these data, validate a novel computational tool to identify key TFs associated to age-related disease processes. By means of this tool we identified and confirmed ZEB TFs as mediators involved in the MSCs differentiation to osteoblasts and adipocytes, and obesity-related bone adiposity.
Possible mechanisms of action of Bacillus wiedmannii AzBw1, a biocontrol agent of the root-knot nematode, Meloidogyne arenaria
Authors: Fallahzadeh-Mamaghani Vahid , Shahbazi-Ezmareh Roya , Shirzad Akbar , Moslehi Shalaleh
Published: March 2023

Background

With increased environmental concerns and restrictions of chemical control, the importance of other eco-friendly strategies for management of the nematodes is being substantially grown nowadays. One of the most well-known strategies that have attracted the attentions is biological control of these deleterious agents. In our previous study (Moslehi et al. in Egypt J Biol Pest Control 31:1–11, 2021), Bacillus wiedmannii AzBw1 was introduced as a robust antagonistic agent against root-knot nematode Meloidogyne arenaria. Present study addressed the possible mechanisms of action of this strain.

Results

Based on quantitative bioassays it was shown that the strain AzBw1 is able to produce considerable amount of siderophore, protease, and chitinase. In an in vitro assay conducted by bi-plate Petri dishes, it was shown that hatching of the nematode eggs, subjected to bacterial volatile compounds (BVCs) was 34% lower than those of mock-treated control eggs. On the other hand, mortality of BVC-treated juveniles was 33.5% higher than those of mock-treated control juveniles. The secretory proteins from the medium culture of strain AzBw1 were precipitated and fractionated by anion exchange chromatography (AEC). Fractions from AEC were checked for hydrolytic activity and nematicidal effect. It was found that the fractions with the highest protease activity have a strong nematicidal effect. In contrast, significant nematicidal effect in the fraction with Chitinase activity was detected.

Conclusion

The results suggested that protease activity played a key role in strain AzBw1 antagonism against root-knot nematode, M. arenaria. Finally, nonvolatile organic compounds were also extracted from the medium culture after removing secretory proteins and enzymes. Obtained results showed that these metabolites had also a strong anti-nematode effect.
Induction of liver transplant immune tolerance in an outbred rat strain model using tacrolimus
Authors: Park Min-Jung , Na Hyun Sik , Joo Young-Shin , Cho Keun-Hyung , Kim Se-Young , Choi Jeong Won , Baek Jin-Ah , Choi Jong Young , You Young Kyoung , Cho Mi-La
Published: March 2023

Background

Orthotopic liver transplantation is the only option for patients with end-stage liver disease and hepatocellular carcinoma. Post-transplant immunosuppressive therapy is important to prevent graft failure. We investigated the effectiveness of tacrolimus (FK506) and their mechanisms for liver transplant immune tolerance in an outbred rat LT model.

Results

To investigate the therapeutic effect of the FK506 on outbred rat LT model, FK506 and postoperative therapy were administered subcutaneously once or twice daily to transplanted rats. Histopathological and immunohistochemical analyses were conducted for all groups. The regulation of inflammatory cytokine signaling in the spleen was analyzed by flow cytometry. FK506 attenuated allograft rejection and increased survival in rat orthotopic liver transplantation models. The FK506-treated group had reduced serum levels of alanine aminotransferase, aspartate aminotransferase and alkaline phosphatase. Furthermore, FK506 decreased the expression of inflammatory cytokines and the activation of pathogenic Th1 and Th17 cells in the liver.

Conclusions

Taken together, we revealed that FK506 ameliorated strong allograft rejection in outbred liver transplantation model by anti-inflammatory effect and inhibitory peroperty of pathogenic T cells.
The Severity of Congenital Hypothyroidism With Gland-In-Situ Predicts Molecular Yield by Targeted Next-Generation Sequencing
Authors: Levaillant Lucie , Bouhours-Nouet Natacha , Illouz Frédéric , Amsellem Jager Jessica , Bachelot Anne , Barat Pascal , Baron Sabine , Bensignor Candace , Brac De La Perriere Aude , Braik Djellas Yasmine , Caillot Morgane , Caldagues Emmanuelle , Campas Marie-Neige , Caquard Marylène , Cartault Audrey , Cheignon Julie , Decrequy Anne , Delemer Brigitte , Dieckmann Katherine , Donzeau Aurélie , Doye Emilie , Fradin Mélanie , Gaudillière Mélanie , Gatelais Frédérique , Gorce Magali , Hazart Isabelle , Houcinat Nada , Houdon Laure , Ister-Salome Marielle , Jozwiak Lucie , Jeannoel Patrick , Labarthe Francois , Lacombe Didier , Lambert Anne-Sophie , Lefevre Christine , Leheup Bruno , Leroy Clara , Maisonneuve Benedicte , Marchand Isis , Marquant Emeline , Muszlak Matthias , Pantalone Letitia , Pochelu Sandra , Quelin Chloé , Radet Catherine , Renoult-Pierre Peggy , Reynaud Rachel , Rouleau Stéphanie , Teinturier Cécile , Thevenon Julien , Turlotte Caroline , Valle Aline , Vierge Melody , Villanueva Carine , Ziegler Alban , Dieu Xavier , Bouzamondo Nathalie , Rodien Patrice , Prunier-Mirebeau Delphine , Coutant Régis
Published: March 2023

Introduction

Congenital hypothyroidism with gland-in-situ (CH-GIS) is usually attributed to mutations in the genes involved in thyroid hormone production. The diagnostic yield of targeted next-generation sequencing (NGS) varied widely between studies. We hypothesized that the molecular yield of targeted NGS would depend on the severity of CH.

Methods

Targeted NGS was performed in 103 CH-GIS patients from the French national screening program referred to the Reference Center for Rare Thyroid Diseases of Angers University Hospital. The custom targeted NGS panel contained 48 genes. Cases were classified as solved or probably solved depending on the known inheritance of the gene, the classification of the variants according to the American College of Medical Genetics and Genomics, the familial segregation, and published functional studies. Thyroid-stimulating hormone at CH screening and at diagnosis (TSHsc and TSHdg) and free T4 at diagnosis (FT4dg) were recorded.

Results

NGS identified 95 variants in 10 genes in 73 of the 103 patients, resulting in 25 solved cases and 18 probably solved cases. They were mainly due to mutations in the TG (n = 20) and TPO (n = 15) genes. The molecular yield was, respectively, 73% and 25% if TSHsc was ≥ and < 80 mUI/L, 60% and 30% if TSHdg was ≥ and < 100 mUI/L, and 69% and 29% if FT4dg was ≤ and > 5 pmol/L.

Conclusion

NGS in patients with CH-GIS in France found a molecular explanation in 42% of the cases, increasing to 70% when TSHsc was ≥ 80 mUI/L or FT4dg was ≤ 5 pmol/L.
The Role of Religious Thought in Interdisciplinary “Law and Literature” Studies
Authors: Schramm Jan-Melissa
Published: March 2023

This essay traces the intense interrelatedness of the three discourses that we now consider distinct but that ask similar questions about the existential value of life and the relationship between spiritual and temporal matters. Law, literature, and theology address crucial and complementary issues of epistemology—that is, questions of evidence-based knowledge and how we ground our ethical deliberations on these evidential foundations.
Fathers, Mothers, Saints, Martyrs: Religion as a Lineage of Belief
Authors: Coleman Dawn
Published: March 2023

Critiquing the literary-critical habit of approaching religion primarily in terms of individual belief, this essay proposes that the sociologist Danièle Hervieu-Léger’s definition of religion as a “lineage of belief” can reorient literary scholars to religion’s investment in its own survival and reproduction. Hervieu-Léger’s model emphasizes that religious institutions ensure their continuity by negotiating intracommunity conflict and intergenerational transformations. Building on this model, the essay argues that literary texts participate in religion’s collective memory and self-definition, then illustrates this point by demonstrating how Harriet Beecher Stowe’s Oldtown Folks (1869) creates a bildungsroman-like narrative to shape the story of Protestantism’s Anglican-Puritan branch from the seventeenth to nineteenth centuries. Although this representation is political in that it reinforces Protestantism as integral to American identity, Oldtown Folks prioritizes the vibrancy and longevity of Anglo-American Puritanism and Episcopalianism as relatively autonomous, family- and community-based institutions that maintain complex relationships to state violence and imperialism. For instance, while Oldtown Folks endorses Protestantism’s collaboration with North American settler colonialism, it also challenges the efficacy and desirability of the Congregational Church’s South Seas missionary work.
The Role of Prolonged Bed Rest in Postoperative Cerebrospinal Fluid Leakage After Surgery of Intradural Pathology—A Retrospective Cohort Study
Authors: Krahwinkel Sophia , Schipmann Stephanie , Spille Dorothee , Maragno Emanuele , Al Barim Bilal , Warneke Nils , Stummer Walter , Gallus Marco , Schwake Michael
Published: March 2023

BACKGROUND:

Postoperative cerebrospinal fluid leakage (CSFL) is a feared complication after surgery on intradural pathologies and may cause postoperative complications and subsequently higher treatment costs.

OBJECTIVE:

To assess whether prolonged bed rest may lower the risk of CSFL.

METHODS:

We performed a retrospective cohort study including patients with intradural pathologies who underwent surgery at our department between 2013 and 2021. Cohorts included patients who completed 3 days of postoperative bed rest and patients who were mobilized earlier. The primary end point was the occurrence of clinically proven CSFL.

RESULTS:

Four hundred and thirty-three patients were included (female [51.7%], male [48.3%]) with a mean age of 48 years (SD ±20). Bed rest was ordered in 315 cases (72.7%). In 7 cases (N = 7/433, 1.6%), we identified a postoperative CSFL. Four of them (N = 4/118) did not preserve bed rest, showing no significant difference to the bed rest cohort (N = 3/315; P = .091). In univariate analysis, laminectomy (N = 4/61; odds ratio [OR] 8.632, 95% CI 1.883-39.573), expansion duraplasty (N = 6/70; OR 33.938, 95% CI 4.019-286.615), and recurrent surgery (N = 5/66; OR 14.959, 95% CI 2.838-78.838) were significant risk factors for developing CSFL. In multivariate analysis, expansion duraplasty was confirmed as independent risk factor (OR 33.937, 95% CI 4.018-286.615, P = .001). In addition, patients with CSFL had significant higher risk for meningitis (N = 3/7; 42.8%, P = .001).

CONCLUSION:

Prolonged bed rest did not protect patients from developing CSFL after surgery on intradural pathologies. Avoiding laminectomy, large voids, and minimal invasive approaches may play a role in preventing CSFL. Furthermore, special caution is indicated if expansion duraplasty was done.
Systematic radiomics analysis based on multiparameter MRI to preoperatively predict the expression of Ki67 and histological grade in patients with bladder cancer
Authors: Fan Xuhui , Yu Hongwei , Ni Xie , Chen Guihua , Li Tiewen , Chen Jingwen , He Meijuan , Liu Hao , Wang Han , Yin Xiaorui
Published: March 2023

Objectives:

Bladder cancer is among the most prevalent urothelial malignancies. Radiomics-based preoperative prediction of Ki67 and histological grade will facilitate clinical decision-making.

Methods:

This retrospective study recruited 283 bladder cancer patients between 2012 and 2021. Multiparameter MRI sequences included: T1WI, T2WI, diffusion-weighted imaging (DWI), and dynamic contrast-enhanced (DCE) imaging. The radiomics features of intratumoral and peritumoral regions were extracted simultaneously. Max-Relevance and Min-Redundancy (mRMR) and least absolute shrinkage and selection operator (LASSO) algorithms were employed to select the features. Six machine learning-based classifiers were adopted to construct the radiomics models, and the best was chosen for the model construction.

Results:

The mRMR and LASSO algorithms were more suitable for Ki67 and histological grade, respectively. Additionally, Ki67 had a higher proportion of intratumoral features, while peritumoral features accounted for a greater proportion of the histological grade. Random forests performed the best in predicting both pathological outcomes. Consequently, the multiparameter MRI (MP-MRI) models achieved area under the curve (AUC) values of 0.977 and 0.852 for Ki67 in training and test sets, respectively, and 0.972 and 0.710 for the histological grade.

Conclusion:

Radiomics holds the potential to predict multiple pathological outcomes of bladder cancer preoperatively and are expected to provide clinical decision-making guidance. Furthermore, our work inspired the process of radiomics research.

Advances in knowledge:

This study demonstrated that different feature selection techniques, segmentation regions, classifiers, and MRI sequences will affect the performance of the model. We systematically demonstrated that radiomics can predict histological grade and Ki67.
No evidence for epitranscriptomic m5C modification of SARS-CoV-2, HIV and MLV viral RNA
Authors: Huang Anming , Riepler Lydia , Rieder Dietmar , Kimpel Janine , Lusser Alexandra
Published: March 2023

The addition of chemical groups to cellular RNA to modulate RNA fate and/or function is summarized under the term epitranscriptomic modification. More than 170 different modifications have been identified on cellular RNA, such as tRNA, rRNA and, to a lesser extent, on other RNA types. Recently, epitranscriptomic modification of viral RNA has received considerable attention as a possible additional mechanism regulating virus infection and replication.N6-methyladenosine (m6A) and C5-methylcytosine (m5C) have been most broadly studied in different RNA viruses. Various studies, however, reported varying results with regard to number and extent of the modification. Here we investigated the m5C methylome of SARS-CoV-2, and we reexamined reported m5C sites in HIV and MLV. Using a rigorous bisulfite-sequencing protocol and stringent data analysis, we found no evidence for the presence of m5C in these viruses. The data emphasize the necessity for optimizing experimental conditions and bioinformatic data analysis.
The genome sequence of the Kite-tailed Robberfly, Machimus atricapillus (Fallén, 1814)
Authors: Thomas Sam , Mitchell Ryan , Crowley Liam M. ,   Natural History Museum Genome Acquisition Lab,   University of Oxford and Wytham Woods Genome Acquisition Lab,   Darwin Tree of Life Barcoding collective,   Wellcome Sanger Institute Tree of Life programme,   Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective,   Tree of Life Core Informatics collective,   Darwin Tree of Life Consortium
Published: March 2023

We present a genome assembly from an individual male Machimus atricapillus (the Kite-tailed Robberfly; Arthropoda; Insecta; Diptera; Asilidae). The genome sequence is 268.6 megabases in span. Most of the assembly is scaffolded into six chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 16.3 kilobases in length. Gene annotation of this assembly on Ensembl identified 10,978 protein coding genes.
Dissolving Constraints for Riemannian Optimization
Authors: Xiao Nachuan , Liu Xin , Toh Kim-Chuan
Published: March 2023

In this paper, we consider optimization problems over closed embedded submanifolds of [Formula: see text], which are defined by the constraints c(x) = 0. We propose a class of constraint-dissolving approaches for these Riemannian optimization problems. In these proposed approaches, solving a Riemannian optimization problem is transferred into the unconstrained minimization of a constraint-dissolving function ( CDF ). Different from existing exact penalty functions, the exact gradient and Hessian of CDF are easy to compute. We study the theoretical properties of CDF and prove that the original problem and CDF have the same first-order and second-order stationary points, local minimizers, and Łojasiewicz exponents in a neighborhood of the feasible region. Remarkably, the convergence properties of our proposed constraint-dissolving approaches can be directly inherited from the existing rich results in unconstrained optimization. Therefore, the proposed constraint-dissolving approaches build up short cuts from unconstrained optimization to Riemannian optimization. Several illustrative examples further demonstrate the potential of our proposed constraint-dissolving approaches.

Funding: The research of N. Xiao and K.-C. Toh is supported by the Ministry of Education of Singapore Academic Research Fund Tier 3 [Grant MOE-2019-T3-1-010]. The research of X. Liu is supported in part by the National Natural Science Foundation of China [Grants 12125108, 11971466, 12288201, 12021001, and 11991021]; the National Key R&D Program of China [Grants 2020YFA0711900 and 2020YFA0711904]; and the Key Research Program of Frontier Sciences, Chinese Academy of Sciences [Grant ZDBS-LY-7022].
The Dual Effects of Team Contest Design on On-Demand Service Work Schedules
Authors: Dong Tingting , Sun Xiaotong , Luo Qi , Wang Jian , Yin Yafeng
Published: March 2023

Emerging on-demand service platforms (OSPs) have recently embraced teamwork as a strategy for stimulating workers’ productivity and mediating temporal supply and demand imbalances. This research investigates the team contest scheme design problem considering work schedules. Introducing teams on OSPs creates a hierarchical single-leader multi-follower game. The leader (platform) establishes rewards and intrateam revenue-sharing rules for distributing workers’ payoffs. Each follower (team) competes with others by coordinating the schedules of its team members to maximize the total expected utility. The concurrence of interteam competition and intrateam coordination causes dual effects, which are captured by an equilibrium analysis of the followers’ game. To align the platform’s interest with workers’ heterogeneous working-time preferences, we propose a profit-maximizing contest scheme consisting of a winner’s reward and time-varying payments. A novel algorithm that combines Bayesian optimization, duality, and a penalty method solves the optimal scheme in the nonconvex equilibrium-constrained problem. Our results indicate that teamwork is a useful strategy with limitations. Under the proposed scheme, team contest always benefits workers. Intrateam coordination helps teams strategically mitigate the negative externalities caused by overcompetition among workers. For the platform, the optimal scheme can direct teams’ schedules toward more profitable market equilibria when workers have inaccurate perceptions of the market.

History: This paper has been accepted for the Service Science Special Issue on Innovation in Transportation-Enabled Urban Services.

Funding: This work was supported by the National Science Foundation [Grant FW-HTF-P 2222806].

Supplemental Material: The online appendices are available at https://doi.org/10.1287/serv.2023.0320 .
DEDE KORKUT OĞUZNAMELERİNDE SAVAŞ VE SAVAŞ HUKUKU
Authors: KESKİN Ahmet
Published: March 2023

Türk dil, kültür ve edebiyat tarihi üzerine gerçekleştirilen çalışmalar içinde Dede Korkut Oğuznameleri oldukça özel bir yere sahiptir. Bunun en belirgin nedeni elbette ki bu eserin Türkoloji çalışmaları için eşsiz bir öneme ve değere sahip olmasından ileri gelmektedir. Buna bağlı olarak Dede Korkut üzerinde yapılan çalışmalar günümüzde de büyük bir yoğunlukta devam etmekte ve gerçekleştirilen her yeni çalışma daha başka çalışmalara kapı aralamaktadır. Bu çalışmalar kapsamında Dede Korkut Oğuznamelerinin Türk kültür tarihi için önemi ve özellikle de Türk töresi, gündelik yaşamı, inançları, mücadeleleri hakkında çok sayıda bilgi edinilebilmektedir. Türklerin tarihi süreçte uzun asırlar sürdürdükleri yaşam biçimleri doğrultusunda mevcut ve olası düşmanlarla sürekli ve kesin olarak, bazen de kendi içlerindeki mücadelelerinin inanç ve eylem, dil ve kültür, düşünce ve söylem gibi alanlarda doğrudan ya da dolaylı olarak Dede Korkut anlatmalarına da çeşitli boyutlarda yansıdığı görülmektedir. Bu çalışmada Dede Korkut Oğuznameleri savaş ve savaş hukuku bağlamında ele alınmıştır. Bu çerçevede Türklerin savaş hakkındaki düşünce, değerlendirme, tutum, eylem ve söylem biçimleri ile Türk kültüründe, tarihinde ve töresinde savaş kurallarının ve savaş hukukunun nasıl belirlendiği, işletildiği ve bunların başlıca görünümleri Türk dili, kültürü ve edebiyatının önemli metinlerinden biri olan Dede Korkut Oğuznameleri örnekleminde incelenmiştir.
Timestamp Based OTP and Enhanced RSA Key Exchange Scheme with SIT Encryption to Secure IoT Devices
Authors: Kollipara V. N. Hemanth , Kalakota Sai Koushik , Chamarthi Sujith , Ramani S. , Malik Preeti , Karuppiah Marimuthu
Published: March 2023

The Internet of Things (IoT) has become an emerging technology and is expected to connect billions of more devices to the internet in the near future. With time, more and more devices like wearables, intelligent home systems, and industrial automation devices are getting connected to the internet. IoT devices primarily transfer data using wireless communication networks, introducing more vulnerabilities like man-in-the-middle-attacks and eavesdropping. These security concerns are customary for any device communicating over the internet because of its intrinsic open nature. These problems are usually subdued by conventional cryptographic algorithms used in typical systems that are power-hungry and computationally intensive, making them infeasible to be used in IoT devices since they run on low-powered chips, limiting performance, memory, and bandwidth. Hence, there is a requirement to adopt lightweight cryptographic algorithms that can abate the security issues while using low computational resources, which is the constraint in the given scenario. Hence, we propose an end-to-end secured IoT system that ensures the system’s integrity is never compromised using lightweight cryptographic algorithms. We propose a three-module system, where the first module handles user authentication using a time-based one-time password, the second secures communication using lightweight enhanced RSA, and the third performs data encryption using Feistel-based enhanced SIT. This kind of system is designed to deal with security challenges in IoT devices, ensuring adequate data security while reducing the computational footprint using lightweight cryptography.
From hedonism to frugality: consumption desires in different age groups across 20 years
Authors: Wilska Terhi-Anna , Silinskas Gintautas , Nyrhinen Jussi
Published: March 2023

This article examines different kinds of consumption desires of Finnish consumers by asking how they would change their consumption habits if they had more money at their disposal. As previous research on consumption desires has been mainly based on the essence of desires and the cycle of fulfilling hedonistic desires and creating new ones, this study analyses the desires in the context of the ages of both consumers and consumer society. The focus was differences in consumption desires between age groups and changes across 20 years. The data were derived from three repeated surveys collected in 1999, 2009 and 2019 in Finland (N = 5,459), which were analysed with principal-axis factor analysis and ANCOVA. The factor analysis extracted three types of consumption desires: hedonistic, charitable-cultural and materialistic. Saving-oriented desires were analysed as a single item. Hedonistic consumption desires were the most typical for the youngest age group (18–25), and materialistic desires were the highest for young adults aged 26–35 across all three years of measurement. Older people had the most charitably and culturally oriented desires in 1999, but older age groups’ orientation to saving and charitable giving and culture decreased across 20 years. Hedonistic consumption desires generally decreased over 20 years, particularly in young age groups. Conversely, young people’s desire to save increased significantly, whereas the oldest age groups saved less. The research shows that both changes in consumer values and economic circumstances are manifested in people’s consumption desires.
Multiphonon-Assisted Emission of Rare-Earth Ions: Towards Pulse Shortening in Mode-Locked Lasers
Authors: Loiko Pavel , Chen Weidong , Wang Li , Griebner Uwe , Zhang Ge , Mateos Xavier , Bae Ji Eun , Rotermund Fabian , Braud Alain , Camy Patrice , Petrov Valentin
Published: March 2023

Long-wave multiphonon-assisted emission of rare-earth ions provides broadband gain which is essential for the generation of few-optical-cycle pulses. A phonon-terminated Kerr-lens mode-locked Tm,Ho:CALGO laser generates 37-fs pulses with an ultrabroadband spectrum (1870 - 2337 nm).
Optical Skyrmions with Tunable Topological Textures
Authors: Shen Yijie
Published: March 2023

We generated a family of structured light beams and pulses with skyrmionic configuration, as exact solutions of Maxwell’s equations, allowing tunable textures, subwavelength super-resolution and propagation-robust topologies in space and time.
Efficient Continuous-Wave Tm,Ho:CaF2 Laser at ~2.1 μm
Authors: Eremeev Kirill , Loiko Pavel , Benayad Abdelmjid , Elabedine Ghassen Zin , Solé Rosa Maria , Mateos Xavier , Aguiló Magdalena , Díaz Francesc , Camy Patrice , Braud Alain
Published: March 2023

Tm3+,Ho3+-codoped CaF2 crystals were grown by the Bridgman method and their spectroscopic properties were studied. A continuous-wave Tm,Ho:CaF2 laser generated an output power of 465 mW at 2.08 μm with a slope efficiency of 24.0%.
Novel Ho3+-doped Low-Phonon Single Crystals and Chalcogenide Glass for Mid-IR Source Application
Authors: Brown Ei Ei , Fleischman Zackery D. , McKay Jason , Dubinskii Mark , Hömmerich Uwe , Palosz Witold , Trivedi Sudhir B.
Published: March 2023

Spectroscopic characterization of Ho3+-doped low-phonon fluoride and chloride single crystals as well as Ga2Ge5S13 sulfide glass, with reduced multiphonon relaxation rates, is performed to assess materials potential for Mid-IR laser application.
Hybrid Amplification of THz-Repetition-Frequency Bursts
Authors: Stummer Vinzenz , Flöry Tobias , Kitzler-Zeiler Markus , Pugzlys Audrius , Baltuska Andrius
Published: March 2023

We propose and demonstrate experimentally hybrid two-step amplification of bursts, in which spectral modulations are deliberately suppressed in a femtosecond chirped-pulse-amplifier and then recovered in an optical-parametric-amplifier, opening up prospects of several exciting resonant-nonlinear multiphoton applications.
Pulse shaping in a midwave-IR OPCPA for multi-µJ few-cycle pulse generation at 12 µm via DFG
Authors: Bock Martin , Duda Martin , Roškot Lukáš , Smrž Martin , Novák Ondřej , von Grafenstein Lorenz , Fürtjes Pia Johanna , Griebner Uwe
Published: March 2023

Sub-4 optical cycle pulse generation around 12 µm with >10 µJ energy by difference- frequency generation in GaSe and AgGaSe2 is reported, driven by the signal and idler of a high power 1 kHz OPCPA.
Seeded growth of BaGa4S7 and BaGa4Se7 for mid-IR frequency conversion
Authors: Schunemann Peter G. , Zawilski Kevin T.
Published: March 2023

Here we demonstrate seeded horizontal gradient freeze growth of the nonlinear crystals BaGa4S7 and BaGa4Se7 along crystallographic directions optimized for simplified fabrication and maximum yield of oriented device crystals for mid-IR frequency generation.
Excited-State Absorption and Upconversion Pumping of Monoclinic Tm:KLu(WO4)2 Crystals
Authors: Tyazhev Aleksey , Loiko Pavel , Guillemot Lauren , Kouta Alexandre , Solé Rosa Maria , Mateos Xavier , Aguiló Magdalena , Díaz Francesc , Dupont Hippolyte , Georges Patrick , Druon Frédéric , Braud Alain , Hideur Ammar , Camy Patrice
Published: March 2023

Excited-state absorption of Tm3+ ions (3F4→3F2,3 and 3H4) in the KLu(WO4)2 crystal is studied. Mid-infrared laser operation (3H4→3H5) is achieved with this crystal under upconversion pumping at 1.06 μm yielding 433 mW at 2291 nm. © 2022 The Author(s)
Detailed Thermal Lensing Characterization of Cryogenically Cooled Yb:YLF Crystals
Authors: Kilinc Muharrem , Demirbas Umit , Gonzalez Juan B. , Thesinga Jelto , Kellert Martin , Palmer Guido , Pergament Mikhail , Kärtner Franz X.
Published: March 2023

We have studied thermal lensing strength of cryogenic Yb:YLF lasers in rod-geometry in detail. Overall thermal lensing is axis dependent; thermo-optic and photo-elastic effects are rather dominant while bulging and electronic lensing are quite weak.
Role of Yb2+ in Yb:CaF2 for Lasing and Optical Refrigeration
Authors: Tanaka Hiroki , Püschel Stefan , Kränkel Christian
Published: March 2023

We investigated the influence of Yb2+ on the spectroscopic properties of Yb:CaF2. A strong nonradiative decay of Yb3+ was observed in an Yb2+-rich crystal, so Yb2+ is highly detrimental for lasing and optical refrigeration.
Inspection of the First Chirped Volume Bragg Gratings Realized by Means of fs Laser Phase Mask Inscription in Fused Silica
Authors: Perevezentsev Evgeny A. , Mukhin Ivan B. , Gorokhov Anton I. , Volkov Mikhail R. , Richter Daniel , Siems Malte Per , Nolte Stefan
Published: March 2023

Study of optical and spectral properties of the first fs-laser-inscribed fused silica chirped volume Bragg gratings is performed. The perspective of the new technology, and agreement between the calculated and measured parameters, are demonstrated.
High-power, femtosecond, ultra-broadband, non-collinear optical parametric oscillator in the visible (VIS-NOPO)
Authors: Mevert Robin , Binhammer Yuliya , Dietrich Christian M. , Cardoso de Andrade José R. , Beichert Luise , Binhammer Thomas , Fan Jintao , Morgner Uwe
Published: March 2023

Broadband fast-tunable laser sources are crucial elements for various spectroscopic applications. In this work we demonstrate a fast-tunable ultra-broadband non-collinear optical parametric oscillator which covers nearly the entire visible spectral range.
Rapidly Tunable Femtosecond UV Laser Pulses through Non-collinear Sum-frequency Generation in a Visible NOPO
Authors: Geesmann Fridolin , Mevert Robin , Zuber David , Morgner Uwe
Published: March 2023

Non-collinear SFG in a NOPO producing visible light can be used to generate quickly tunable ultraviolet radiation from 348-409 nm with output powers up to 23 mW and pulse durations of about 200 fs.
Non-Competitive Cascade Lasing at 1.8 and 2.3 µm Using a Tm:CALGO Crystal
Authors: Dupont Hippolyte , Loiko Pavel , Pan Zhongben , Chu Hongwei , Li Dechun , Viana Bruno , Hideur Ammar , Braud Alain , Guillemot Lauren , Camy Patrice , Georges Patrick , Druon Frédéric
Published: March 2023

Cascade lasing in a Tm:CALGO crystal at 1.8 µm (3F4→3H6) and 2.3 μm (3H4→3H5) is demonstrated with the originality of lacking a competition between the two laser channels, owing to dual-wavelength (direct and upconversion) pumping.
Improvement of 1 µm upconversion pumping of mid-infrared Tm:YLF laser at 2.3 µm by dual-wavelength-pumping
Authors: Dupont Hippolyte , Guillemot Lauren , Loiko Pavel , Braud Alain , Doualan Jean-Louis , Camy Patrice , Georges Patrick , Druon Frédéric
Published: March 2023

We present studies about upconversion pumping at 1.05 µm for Tm:YLF lasers emitting at 2.3 μm. To improve the performance of this pump, we explore the possibility dual pumping with 780 nm.
Dual-Comb Spectroscopy of C2H2 in the SWIR Using a 250-MHz Optical Parametric Oscillator
Authors: Bauer Carolin P. , Pupeikis Justinas , Willenberg Benjamin , Phillips Christopher R. , Keller Ursula
Published: March 2023

We demonstrate coherent dual-comb spectroscopy of C2H2 at 1520 nm using a spatially- multiplexed dual-comb 250-MHz OPO from a linear single-cavity. The repetition-rate difference is 15.4 kHz. Each signal comb has >125-mW average power.
Femtosecond 1.8 µm fiber laser system for in-vivo three- and four-photon fluorescence microscopy
Authors: Fuji Takao , Hamada Kosuke , Goto Ryuichiro , Ueda Hiromi H. , Murakoshi Hideji
Published: March 2023

We have developed a femtosecond 1.8 µm fiber laser system and observed 0.8 mm deep inside the cortex of a living mouse using a multi-photon fluorescence micro- scope based on the light source.
High-Energy Solitonic Source of High Harmonics
Authors: Jedidi M. , Leventoux Y. , Ferhat L. , Jimenez C. , Tilouine I. , Granger G. , Orlianges J.-C. , Crunteanu A. , Lavoute L. , Gaponov D. , Boullet J. , Froidevaux M. , Boutu W. , Merdji H. , Couderc V. , Février S.
Published: March 2023

We report on high harmonics generation in zinc oxide thin-films driven by an all-solid fiber-based architecture. The laser delivers 41 nJ 70 fs solitonic pulses at 1764 nm and drives harmonics generation up to H7.
Watt-level Erbium-Doped Dual-Wavelength Pumped All-Fiber Laser at 3.8 µm
Authors: Lemieux-Tanguay Maxime , Paradis Pascal , Vallée Réal , Bernier Martin
Published: March 2023

A dual-wavelength pumped Er3+:ZrF4 all-fiber laser generating a maximum output power of 1.2 W at 3.8 µm is reported. Experimental results supported by a numerical modeling based on the population dynamics are presented.
kW average power operation of 10 J, 100 Hz, conductive-cooled active-mirror laser
Authors: Ogino Jumpei , Tsubakimoto Koji , Yoshida Hidetsugu , Motokoshi Shinji , Morio Noboru , Matsumoto Keiko , Fujioka Kana , Tokita Shigeki , Miyanaga Noriaki , Ueda Ken-ichi , Kodama Ryousuke , Yogo Akifumi
Published: March 2023

We report highest power conductive-cooled Yb:YAG active-mirror amplifier (CcAMA) delivering 1 kW average power in 10 J, 100 Hz.
Upgrades of L1 Allegra Laser at ELI-Beamlines Facility for the Extended User Experiment Capabilities
Authors: Antipenkov Roman , Erdman Emily , Novák Jakub , Boge Robert , Hubka Zbyněk , Green Jonathan Tyler , Špaček Alexander , Indra Lukáš , Szuba Wojciech , Grenfell Annika , Tykalewicz Boguslaw , Šobr Václav , Torun Murat , Mazůrek Petr , Naylon Jack Alexander , Bakule Pavel , Rus Bedřich
Published: March 2023

We report on the performance improvements of the L1 Allegra laser system. The pump laser upgrade with the thin-disk multipass amplifier allows for the energy ramp-up, while a newly developed synchronized auxiliary laser system provides the capability of the pump-probe experiments at arbitrary delays.
Coherent spectral combining of two pulse-shaped fiber channels with compression to 54 fs
Authors: Chen Siyun , Du Qiang , Wang Dan , Gilardi Antonio , Cooper Lauren , Logantha Mahek , van Tilborg Jeroen , Schroeder Carl , Esarey Eric , Li Derun , Geddes Cameron , Wilcox Russell , Zhou Tong
Published: March 2023

We demonstrate coherent spectral synthesis of two pulse shapers in a two-channel, spectrally-combined, fiber chirped-pulse system. The combined pulses are compressed to 54 fs, the shortest from a spectrally-combined fiber system at one-micron wavelength.