bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of metabolism terms significantly affecting hepatocellular carcinoma immune microenvironment and immunotherapy response
Authors: Tan Xijuan , Chen Sizong , Luo Qiyi , You Shenglin , Yuan Hankun , Wang Jianchu 
Published: November 2023

AbstractMetabolic pathways exert a significant influence on the onset and progression of cancer. Public data on hepatocellular carcinoma (HCC) patients were obtained from The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) databases. Analysis was performed in R software using different R packages. Here, we integrated the data from multiple independent HCC cohorts, including TCGA‐LIHC, ICGC‐FR and ICGC‐JP. Then, the enrichment score of 21 metabolism‐related pathways was quantified using the ssGSEA algorithm. Next, univariate Cox regression analysis was applied to identify the metabolic terms with significant correlation to patient survival. Finally, a prognosis model based on linoleic acid metabolism, sphingolipid metabolism and regulation of lipolysis in adipocytes was established, which showed good performance in predicting patients' survival. Furthermore, we conducted a biological enrichment analysis to delineate the biological disparities between high‐ and low‐risk patients. Notably, we discerned differences in the microenvironments between these two patient groups. We also found that low‐risk patients could potentially respond better to immunotherapy. Drug sensitivity analysis suggested that low‐risk patients are more susceptible to bexarotene and erlotinib, yet exhibit resistance to ATRA and bleomycin. Furthermore, through the use of LASSO logistic regression analysis, we identified 19 characteristic genes, which could robustly indicate the risk groups. Our research underscores the role of linoleic acid metabolism, sphingolipid metabolism and the regulation of lipolysis in adipocytes in HCC, pointing towards potential avenues for future research.
How chromosomal inversions reorient the evolutionary process
Authors: Berdan Emma L. , Barton Nicholas H. , Butlin Roger , Charlesworth Brian , Faria Rui , Fragata Inês , Gilbert Kimberly J. , Jay Paul , Kapun Martin , Lotterhos Katie E. , Mérot Claire , Durmaz Mitchell Esra , Pascual Marta , Peichel Catherine L. , Rafajlović Marina , Westram Anja M. , Schaeffer Stephen W. , Johannesson Kerstin , Flatt Thomas 
Published: November 2023

AbstractInversions are structural mutations that reverse the sequence of a chromosome segment and reduce the effective rate of recombination in the heterozygous state. They play a major role in adaptation, as well as in other evolutionary processes such as speciation. Although inversions have been studied since the 1920s, they remain difficult to investigate because the reduced recombination conferred by them strengthens the effects of drift and hitchhiking, which in turn can obscure signatures of selection. Nonetheless, numerous inversions have been found to be under selection. Given recent advances in population genetic theory and empirical study, here we review how different mechanisms of selection affect the evolution of inversions. A key difference between inversions and other mutations, such as single nucleotide variants, is that the fitness of an inversion may be affected by a larger number of frequently interacting processes. This considerably complicates the analysis of the causes underlying the evolution of inversions. We discuss the extent to which these mechanisms can be disentangled, and by which approach.AbstractInversions often play key roles in adaptation and speciation, but the processes that direct their evolution are obscured by the characteristic that makes them so unique (reduced recombination between arrangements). In this review, we examine how different mechanisms can impact inversion evolution, weaving together both theoretical and empirical studies. We emphasize that most patterns are overdetermined (i.e. can be caused by multiple processes), but we highlight new technologies that provide a path forward towards disentangling these mechanisms.
A digital approach to create a virtual implant preliminary cast for the fabrication of a splinted framework and custom open tray for multiple implants impression making: A dental technique
Authors: Yang Shengtao , Lin Pochun , Gu Yiping , Yue Li , Yuan Quan 
Published: November 2023

AbstractA digital approach is described for fabricating a splinted framework and custom open tray for the impression of multiple implants based on a virtually created implant cast with the digital prediction of the future impression coping positions. In this technique, impression copings to be used in the definitive impression‐making process were digitally scanned and aligned to a preliminary cast using installed protective caps of screw‐retained abutments as references, which resulted in a virtual cast that offers information both about the impression coping positions and their surrounding tissues and could allow a splinted framework and custom open tray to be digitally designed and fabricated. Creation of a virtual cast through digital technologies eliminates the traditional manual splinted framework and custom tray fabrication procedures. Additionally, only one set of impression copings and analogs is needed in this technique, thereby reducing treatment time and cost. It also offers a splinted framework and custom open tray with consistent quality.
Is there a latitudinal diversity gradient for symbiotic microbes? A case study with sensitive partridge peas
Authors: Harrison Tia L. , Parshuram Zoe A. , Frederickson Megan E. , Stinchcombe John R. 
Published: November 2023

AbstractMutualism is thought to be more prevalent in the tropics than temperate zones and may therefore play an important role in generating and maintaining high species richness found at lower latitudes. However, results on the impact of mutualism on latitudinal diversity gradients are mixed, and few empirical studies sample both temperate and tropical regions. We investigated whether a latitudinal diversity gradient exists in the symbiotic microbial community associated with the legume Chamaecrista nictitans. We sampled bacteria DNA from nodules and the surrounding soil of plant roots across a latitudinal gradient (38.64–8.68 °N). Using 16S rRNA sequence data, we identified many non‐rhizobial species within C. nictitans nodules that cannot form nodules or fix nitrogen. Species richness increased towards lower latitudes in the non‐rhizobial portion of the nodule community but not in the rhizobial community. The microbe community in the soil did not effectively predict the non‐rhizobia community inside nodules, indicating that host selection is important for structuring non‐rhizobia communities in nodules. We next factorially manipulated the presence of three non‐rhizobia strains in greenhouse experiments and found that co‐inoculations of non‐rhizobia strains with rhizobia had a marginal effect on nodule number and no effect on plant growth. Our results suggest that these non‐rhizobia bacteria are likely commensals—species that benefit from associating with a host but are neutral for host fitness. Overall, our study suggests that temperate C. nictitans plants are more selective in their associations with the non‐rhizobia community, potentially due to differences in soil nitrogen across latitude.
Intra‐uterine programming of future fertility
Authors: Chavatte‐Palmer Pascale , Couturier‐Tarrade Anne , Rousseau‐Ralliard Delphine 
Published: November 2023

AbstractThe developmental origins of health and disease (DOHaD) shows that a relationship exists between parental environment at large, foeto‐placental development and the risk for the offspring to develop non‐transmittable disease(s) in adulthood. This concept has been validated in both humans and livestock. In mammals, after fertilization and time spent free in the maternal reproductive tract, the embryo develops a placenta that, in close relationship with maternal endometrium, is the organ responsible for exchanges between dam and foetus. Any modification of the maternal environment can lead to adaptive mechanisms affecting placental morphology, blood flow, foetal‐maternal exchanges (transporters) and/or endocrine function, ultimately modifying placental efficiency. Among deleterious environments, undernutrition, protein restriction, overnutrition, micronutrient deficiencies and food contaminants can be outlined. When placental adaptive capacities become insufficient, foetal growth and organ formation is no longer optimal, including foetal gonadal formation and maturation, which can affect subsequent offspring fertility. Since epigenetic mechanisms have been shown to be key to foetal programming, epigenetic modifications of the gametes may also occur, leading to inter‐generational effects. After briefly describing normal gonadal development in domestic species and inter‐species differences, this review highlights the current knowledge on intra‐uterine programming of offspring fertility with a focus on domestic animals and underlines the importance to assess transgenerational effects on offspring fertility at a time when new breeding systems are developed to face the current climate changes.
Evaluation of an Unloading Concept for Knee Osteoarthritis: A Pilot Study in a Small Patient Group
Authors: Stoltze Jonas S. , Oliveira Anderson S. C. , Rasmussen John , Andersen Michael S. 
Published: November 2023

Abstract
Joint compressive forces have been identified as a risk factor for osteoarthritis disease progression. Therefore, unloader braces are a common treatment with the aim of relieving pain, but their effects are not clearly documented in the literature. A knee brace concept was tested with the aim of reducing joint loads and pain in knee osteoarthritis patients by applying an extension moment exclusively during the stance phase. The ideal effects were evaluated during gait based on musculoskeletal modeling of six patients, and experimental tests with a prototype brace were conducted on one patient. The effects were evaluated using electromyography measurements and musculoskeletal models to evaluate the muscle activation and knee compressive forces, respectively. The ideal brace simulations revealed a varying reduction of the first peak knee force between 3.5% and 33.8% across six patients whereas the second peak was unaffected. The prototype reduced the peak vasti muscle activation with 7.9% and musculoskeletal models showed a reduction of the first peak knee compressive force of up to 26.3%. However, the prototype brace increased the knee joint force impulse of up to 17.1% and no immediate pain reduction was observed. The reduction of the first peak knee compressive force, using a prototype on a single patient, indicates a promising effect from an applied knee extension moment for reducing knee joint loads during normal gait. However, further clinical experiments with this brace method are required to evaluate the long-term effects on both pain and disease progression in knee osteoarthritis patients.
A First Step Toward a Family of Morphed Human Body Models Enabling Prediction of Population Injury Outcomes
Authors: Larsson Karl-Johan , Östh Jonas , Iraeus Johan , Pipkorn Bengt 
Published: November 2023

AbstractThe injury risk in a vehicle crash can depend on occupant specific factors. Virtual crash testing using finite element human body models (HBMs) to represent occupant variability can enable the development of vehicles with improved safety for all occupants. In this study, it was investigated how many HBMs of different sizes that are needed to represent a population crash outcome through a metamodel. Rib fracture risk was used as an example occupant injury outcome. Morphed HBMs representing variability in sex, height, and weight within defined population ranges were used to calculate population variability in rib fracture risk in a frontal and a side crash. Two regression methods, regularized linear regression with second-order terms and Gaussian process regression (GPR), were used to metamodel rib fracture risk due to occupant variability. By studying metamodel predictive performance as a function of training data, it was found that constructing GPR metamodels using 25 individuals of each sex appears sufficient to model the population rib fracture risk outcome in a general crash scenario. Further, by utilizing the known outcomes in the two crashes, an optimization method selected individuals representative for population outcomes across both crash scenarios. The optimization results showed that 5–7 individuals of each sex were sufficient to create predictive GPR metamodels. The optimization method can be extended for more crashes and vehicles, which can be used to identify a family of HBMs that are generally representative of population injury outcomes in future work.
Comparison of Two Contact Detection Methods for Ground Reaction Forces and Moment Estimation During Sidestep Cuts, Runs, and Walks
Authors: Morin Pauline , Muller Antoine , Dumont Georges , Pontonnier Charles 
Published: November 2023

Abstract
Force platforms often limit the analysis of human movement to the laboratory. Promising methods for estimating ground reaction forces and moments (GRF&M) can overcome this limitation. The most effective family of methods consists of minimizing a cost, constrained by the subject's dynamic equilibrium, for distributing the force over the contact surface on the ground. The detection of contact surfaces over time is dependent on numerous parameters. This study proposes to evaluate two contact detection methods: the first based on foot kinematics and the second based on pressure sole data. Optimal parameters for these two methods were identified for walking, running, and sidestep cut tasks. The results show that a single threshold in position or velocity is sufficient to guarantee a good estimate. Using pressure sole data to detect contact improves the estimation of the position of the center of pressure (CoP). Both methods demonstrated a similar level of accuracy in estimating ground reaction forces.
Expression and engineering of PET-degrading enzymes from
Microbispora, Nonomuraea
, and
Micromonospora
Authors: Tiong Elaine , Koo Ying Sin , Bi Jiawu , Koduru Lokanand , Koh Winston , Lim Yee Hwee , Wong Fong Tian 
Published: November 2023

ABSTRACT

Low recycling rates coupled with increased production have resulted in an alarming rapid accumulation of a widely used plastic material, polyethylene terephthalate (PET). With the buildup of plastics in our environment, there is an urgent need for more sustainable solutions to process them. Biological methods such as enzyme-catalyzed PET recycling or bioprocessing are potential solutions to this problem. Actinobacteria, known for producing enzymes involved in the degradation of complex organic molecules, are of particular interest due to their potential to produce enzymes that may assimilate plastics. This work expands on the discovery and characterization of new PET-degrading enzymes from the
Microbispora, Nonomuraea,
and
Micromonospora
genera. Within the
Micromonospora
genus, we analyzed enzymes from the polyesterase-lipase-cutinase family with ~60% similarity to leaf-branch compost cutinase (LCC), in which one of the enzymes was found to be capable of breaking down PET and bis(2-hydroxyethyl) terephthalate (BHET) at 45°C–50°C. Moreover, we were able to enhance the enzyme’s depolymerization rate through further engineering, resulting in a two-fold increase in activity.

IMPORTANCE
Mismanagement of PET plastic waste significantly threatens human and environmental health. Together with the relentless increase in plastic production, plastic pollution is an issue of rising concern. In response to this challenge, scientists are investigating eco-friendly approaches, such as bioprocessing and microbial factories, to sustainably manage the growing quantity of plastic waste in our ecosystem. Industrial applicability of enzymes capable of degrading PET is limited by numerous factors, including their scarcity in nature. The objective of this study is to enhance our understanding of this group of enzymes by identifying and characterizing novel enzymes that can facilitate the breakdown of PET waste. This data will expand the enzymatic repertoire and provide valuable insights into the prerequisites for successful PET degradation.
Phage Milagro: a platform for engineering a broad host range virulent phage for
Burkholderia
Authors: Yao Guichun , Le Tram , Korn Abby M. , Peterson Hannah N. , Liu Mei , Gonzalez Carlos F. , Gill Jason J. 
Published: November 2023

ABSTRACT

The
Burkholderia cepacia
complex (Bcc) causes life-threatening respiratory tract infections in persons with cystic fibrosis (CF). In CF patients, end-stage pulmonary disease often requires lung transplantation, and pre-transplant colonization with antibiotic-resistant
Burkholderia
is predictive of poor post-transplant outcomes. To address this issue, phage therapy has been proposed as a treatment for these infections. However, the majority of characterized Bcc phages are temperate and are therefore difficult to use as therapeutics, and the few obligately lytic phages that have been isolated have limited host ranges. To overcome these limitations, we have produced a virulent, broad-host range derivative of the temperate
Burkholderia cenocepacia
phage Milagro. Phage Milagro is a 39.1-kb temperate myophage related to phage KL3 and the paradigm coliphage P2. This phage showed a phenotype of spontaneous autoplaquing on lawns of Milagro lysogens, and these autoplaques were found to be produced by virulent mutants of the parental phage Milagro. Mutations associated with virulence were identified as single base changes, insertions or deletions in the phage lysogeny control region that define potential operator sites required for lysogen maintenance. To improve phage host range, the C-terminal domain of the Milagro tail fiber was replaced with the receptor-binding domain of the broad-host range tailocin (high molecular weight bacteriocin) BceTMilo. A spontaneous virulent mutant of this engineered phage, designated Milagro
vir gp20:Milo
, exhibited an expanded host range over the parental phage and is able to infect multiple Bcc species including
B. cenocepacia
,
Burkholderia multivorans
,
Burkholderia gladioli, Burkholderia dolosa
, and
Burkholderia vietnamensis
.

IMPORTANCE

Burkholderia
infections are a significant concern in people with CF and other immunocompromising disorders, and are difficult to treat with conventional antibiotics due to their inherent drug resistance. Bacteriophages, or bacterial viruses, are now seen as a potential alternative therapy for these infections, but most of the naturally occurring phages are temperate and have narrow host ranges, which limit their utility as therapeutics. Here we describe the temperate
Burkholderia
phage Milagro and our efforts to engineer this phage into a potential therapeutic by expanding the phage host range and selecting for phage mutants that are strictly virulent. This approach may be used to generate new therapeutic agents for treating intractable infections in CF patients.
Smyd3 negatively regulates the anti-viral pathway by promoting TAK1 degradation in teleost fish
Authors: Qu Zhili , Sun Yuqin , Zhou Xuefeng , Yan Xiaolong , Xu Tianjun 
Published: November 2023

ABSTRACT

Transforming growth factor beta kinase 1 (TAK1, also known as MAP3K7) has been identified as an adaptor protein in the NF-κB and IRF3 signaling pathways in teleost fishes, and it plays a crucial role in both inflammatory responses and anti-viral actions. SET and MYND domain protein 3 (Smyd3) belongs to the Smyd3 lysine methylase family and possess significant functions in the methylation process of diverse histone and non-histone targets. However, the exact role of Smyd3 in innate immune regulation has not yet been fully elucidated.
Siniperca chuatsi
rhabdovirus (SCRV) is a negative single-stranded RNA virus that has the potential to cause widespread fish diseases. In this study, we discovered that overexpression of Smyd3 facilitates the replication of SCRV, enabling the virus to evade detection of the immune system through Smyd3. Furthermore, we observed that Smyd3 promotes the degradation of TAK1 by inducing K48-linked ubiquitination of TAK1. As a result, Smyd3 exerts a negative regulatory effect on the TAK1-mediated NF-κB signaling pathway and the IRF3 signaling pathway. Thus, our findings demonstrate that Smyd3 plays a role in promoting the degradation of the TAK1 protein. Moreover, we discovered that the degradation of TAK1 by Smyd3 occurs independently of its methyltransferase activity. This study not only enhances our understanding of anti-viral immunity in fish but also offers a novel perspective for investigating anti-viral immunity in mammals.

IMPORTANCE
In this study, we have found that the existence of Smyd3 promoted the replication of SCRV. Additionally, we report that Smyd3 negatively regulates the NF-κB and IRF3 signaling pathway by facilitating the degradation of TAK1 in fish. Our findings suggest that Smyd3 interacts with TAK1. Further investigations have revealed that Smyd3 specifically mediates K48-linked ubiquitination of TAK1 and enhances TAK1 degradation, resulting in a significant inhibition of the NF-κB and IRF3 signaling pathway. These results not only contribute to the advancement of fish anti-viral immunity but also provide new evidence for understanding the mechanism of TAK1 in mammals.