Miracle-dz/UniFAR-FTUs huggingface dataset:
Dairy consumption and risk of esophagus cancer in the prostate, lung, colorectal, and ovarian cohort

Background Epidemiological studies provide limited information on the relationship between dairy consumption and the incidence of esophagus cancer (EC). We examined whether eating dairy foods is associated with a lower risk of EC in an American population. Methods In our study, we analyzed data from the Prostate, Lung, Colorectal, and Ovarian (PLCO) cancer screening trial, which included 101,723 subjects. Dairy product consumption was assessed using a dietary history questionnaire. We used Cox regression and restricted cubic splines to assess whether dairy consumption is associated with EC incidence. Results A total of 154 EC cases were identified after a median follow-up of 12.2 years. After adjusting for confounders, we discovered no statistically significant correlation between total dairy product consumption and EC risk (HR with 95% CI for ≥1.79 servings/day vs. ≤0.6 servings/day: 0.83, 0.50–1.38; p for trend = 0.465). Additionally, no associations were found between EC risk and other dairy foods such as milk, yogurt, and cheese. Conclusion We concluded that the findings of the PLCO cohort do not suggest dairy consumption reduces the risk of EC.
Integrated transcriptome and metabolome analysis reveals the anthocyanin biosynthesis mechanisms in blueberry (Vaccinium corymbosum L.) leaves under different light qualities

Introduction Blueberry (Vaccinium corymbosum L.) is a popular fruit with an abundance of anthocyanins in its leaves and fruits. Light is one of the pivotal environmental elements that affects plant growth and development, but the regulatory mechanism between light quality and anthocyanin formation is poorly understood. Methods An integrated transcriptome and metabolome analysis was performed to investigate the effects of white (control), blue (B), red (R), and red/blue (60R/40B) light on blueberry growth and reveal the potential pathway controlling anthocyanin biosynthesis in blueberry leaves. Results The anthocyanin content was significantly improved by the blue and red/blue light when compared with white light, whereas there was a significant reduction in the photosynthesis under the blue light, showing an inverse trend to that of anthocyanin accumulation. Transcriptomic analysis resulted in the assembly of 134,709 unigenes. Of these, 22 were differentially expressed genes (DEGs) that participate in the anthocyanin biosynthesis pathway, with the majority being significantly up-regulated under the blue light. Most of the photosynthesis-related genes that were down-regulated were expressed during anthocyanin accumulation. Targeted metabolome profiling identified 44 metabolites associated with anthocyanin biosynthesis. The contents of most of these metabolites were higher under blue light than the other light conditions, which was consistent with the transcriptome results. The integrated transcriptome and metabolome analysis suggested that, under blue light, leucoanthocyanidin dioxygenase (LDOX), O-methyltransferase (OMT), and UDP-glucose flavonoid glucosyltransferase (UFGT) were the most significantly expressed, and they promoted the synthesis of cyanidin (Cy), malvidin (Mv), and pelargonidin (Pg) anthocyanidins, respectively. The expression levels of dihydroflavonol 4-reductase (DFR) and OMT, as well as the accumulation of delphinidin (Dp), peonidin (Pn), and petunidin (Pt), were significantly increased by the red/blue light. Discussion The blue and red/blue lights promoted anthocyanin biosynthesis via inducing the expression of key structural genes and accumulation of metabolites involved in anthocyanin synthesis pathway. Moreover, there was a possible feedback regulating correlation between anthocyanin biosynthesis and photosynthesis under different light qualities in blueberry leaves. This study would provide a theoretical basis for elucidating the underlying regulatory mechanism of anthocyanin biosynthesis of V. corymbosum.
Hearing loss in mice with disruption of auditory epithelial patterning in the cochlea

In the cochlear auditory epithelia, sensory hair and supporting cells are arranged in a checkerboard-like mosaic pattern, which is conserved across a wide range of species. The cell adhesion molecules nectin-1 and nectin-3 are required for this pattern formation. The checkerboard-like pattern is thought to be necessary for auditory function, but has never been examined. Here, we showed the significance of checkerboard-like cellular pattern in the survival and function of sensory hair cells in the cochlear auditory epithelia of nectin-3 knockout (KO) mice. Nectin-3 KO mice showed progressive hearing loss associated with degeneration of aberrantly attached hair cells via apoptosis. Apoptotic hair cell death was due to the disorganization of tight junctions between the hair cells. Our study revealed that the checkerboard-like cellular pattern in the auditory epithelium provides a structural basis for ensuring the survival of cochlear hair cells and hearing function.
Soil diazotrophic abundance, diversity, and community assembly mechanisms significantly differ between glacier riparian wetlands and their adjacent alpine meadows

Global warming can trigger dramatic glacier area shrinkage and change the flux of glacial runoff, leading to the expansion and subsequent retreat of riparian wetlands. This elicits the interconversion of riparian wetlands and their adjacent ecosystems (e.g., alpine meadows), probably significantly impacting ecosystem nitrogen input by changing soil diazotrophic communities. However, the soil diazotrophic community differences between glacial riparian wetlands and their adjacent ecosystems remain largely unexplored. Here, soils were collected from riparian wetlands and their adjacent alpine meadows at six locations from glacier foreland to lake mouth along a typical Tibetan glacial river in the Namtso watershed. The abundance and diversity of soil diazotrophs were determined by real-time PCR and amplicon sequencing based on nifH gene. The soil diazotrophic community assembly mechanisms were analyzed via iCAMP, a recently developed null model-based method. The results showed that compared with the riparian wetlands, the abundance and diversity of the diazotrophs in the alpine meadow soils significantly decreased. The soil diazotrophic community profiles also significantly differed between the riparian wetlands and alpine meadows. For example, compared with the alpine meadows, the relative abundance of chemoheterotrophic and sulfate-respiration diazotrophs was significantly higher in the riparian wetland soils. In contrast, the diazotrophs related to ureolysis, photoautotrophy, and denitrification were significantly enriched in the alpine meadow soils. The iCAMP analysis showed that the assembly of soil diazotrophic community was mainly controlled by drift and dispersal limitation. Compared with the riparian wetlands, the assembly of the alpine meadow soil diazotrophic community was more affected by dispersal limitation and homogeneous selection. These findings suggest that the conversion of riparian wetlands and alpine meadows can significantly alter soil diazotrophic community and probably the ecosystem nitrogen input mechanisms, highlighting the enormous effects of climate change on alpine ecosystems.
Chickens, more than humans, focus the diversity of their immunoglobulin genes on the complementarity-determining region but utilise amino acids, indicative of a more cross-reactive antibody repertoire

The mechanisms of B-cell diversification differ greatly between aves and mammals, but both produce B cells and antibodies capable of supporting an effective immune response. To see how differences in the generation of diversity might affect overall repertoire diversity, we have compared the diversity characteristics of immunoglobulin genes from domestic chickens to those from humans. Both use V(D)J gene rearrangement and somatic hypermutation, but only chickens use somatic gene conversion. A range of diversity analysis tools were used to investigate multiple aspects of amino acid diversity at both the germline and repertoire levels. The effect of differing amino acid usages on antibody characteristics was assessed. At both the germline and repertoire levels, chickens exhibited lower amino acid diversity in comparison to the human immunoglobulin genes, especially outside of the complementarity-determining region (CDR). Chickens were also found to possess much larger and more hydrophilic CDR3s with a higher predicted protein binding potential, suggesting that the antigen-binding site in chicken antibodies is more flexible and more polyreactive than that seen in human antibodies.
Monopulse investigation of drop detachment in pulsed gas metal arc welding

The drop detachment process in pulsed welding was investigated by a novel, non-continuous method. A pendent drop was formed on a fixed electrode by a low-current arc. The drop was then detached by a single high-current pulse. The detachment process was studied by high-speed filming and by current and voltage measurements. The shielding gas was Ar with various amounts of CO2, O2, H2 and He. Comparative experiments with ordinary pulsed welding were also done. The authors found ample evidence for an upward force on the pendent drop, most likely caused by the recoil force of evaporating metal. The force increases with CO2 concentration, base current and base current duration. The recoil force gives rise to a critical concentration of the molecular additive, above which it is impossible to detach the drop almost regardless of pulse width. This critical concentration decreases with increasing base current and base current duration. It also seems to decrease with increasing dissociation energy of the molecular additive. The drop velocity decreases with increasing CO2 concentration. For 95Ar5CO2 they also present results on the effect of drop mass and pulse current on drop velocity, minimum pulse width for detachment, and shortest detachment time (tdmin). They find evidence for a minimum detachable drop mass being smallest for large pulse currents. In the pulse current range 210-350 A they observe Ip1.7 tdmin=43, and in the range 350-600 A, Ip1.2 tdmin=2.4 (basic SI-units).
Surface acoustic waves in strained media

Variations of elastic constants and density with strain and the introduction of stresses can significantly affect the propagation velocity of surface acoustic waves. Digital computation using iterative methods is employed to obtain the variations of propagation velocity with strain. It is found that while the individual contributions of the initial stresses, changes in elastic constants, and changes in density with strain can be considerable, their combined effect in some materials may be reduced by mutual cancellation. Computed results for YX quartz YZ LiNbO3 are compared with experimentally measured values.Variations of elastic constants and density with strain and the introduction of stresses can significantly affect the propagation velocity of surface acoustic waves. Digital computation using iterative methods is employed to obtain the variations of propagation velocity with strain. It is found that while the individual contributions of the initial stresses, changes in elastic constants, and changes in density with strain can be considerable, their combined effect in some materials may be reduced by mutual cancellation. Computed results for YX quartz YZ LiNbO3 are compared with experimentally measured values.
Evi5 is required for Xenopus limb and tail regeneration

Amphibians such as salamanders and the African clawed frog Xenopus are great models for regeneration studies because they can fully regenerate their lost organs. While axolotl can regenerate damaged organs throughout its lifetime, Xenopus has a limited regeneration capacity after metamorphosis. The ecotropic viral integrative factor 5 (Evi5) is of great interest because its expression is highly upregulated in the limb blastema of axolotls, but remains unchanged in the fibroblastema of post-metamorphic frogs. Yet, its role in regeneration-competent contexts in Xenopus has not been fully analyzed. Here we show that Evi5 is upregulated in Xenopus tadpoles after limb and tail amputation, as in axolotls. Down-regulation of Evi5 with morpholino antisense oligos (Mo) impairs limb development and limb blastema formation in Xenopus tadpoles. Mechanistically, we show that Evi5 knockdown significantly reduces proliferation of limb blastema cells and causes apoptosis, blocking the formation of regeneration blastema. RNA-sequencing analysis reveals that in addition to reduced PDGFα and TGFβ signaling pathways that are required for regeneration, evi5 Mo downregulates lysine demethylases Kdm6b and Kdm7a. And knockdown of Kdm6b or Kdm7a causes defective limb regeneration. Evi5 knockdown also impedes tail regeneration in Xenopus tadpoles and axolotl larvae, suggesting a conserved function of Evi5 in appendage regeneration. Thus, our results demonstrate that Evi5 plays a critical role in appendage regeneration in amphibians.
An immune risk score predicts progression-free survival of melanoma patients in South China receiving anti-PD-1 inhibitor therapy—a retrospective cohort study examining 66 circulating immune cell subsets

Introduction Immune checkpoint blockade inhibitor (ICI) therapy offers significant survival benefits for malignant melanoma. However, some patients were observed to be in disease progression after the first few treatment cycles. As such, it is urgent to find convenient and accessible indicators that assess whether patients can benefit from ICI therapy. Methods In the training cohort, flow cytometry was used to determine the absolute values of 66 immune cell subsets in the peripheral blood of melanoma patients (n=29) before treatment with anti-PD-1 inhibitors. The least absolute shrinkage and selection operator (LASSO) Cox regression model was followed for the efficacy of each subset in predicting progression-free survival. Then we validated the performance of the selected model in validation cohorts (n=20), and developed a nomogram for clinical use. Results A prognostic immune risk score composed of CD1c+ dendritic cells and three subsets of T cells (CD8+CD28+, CD3+TCRab+HLA-DR+, CD3+TCRgd+HLA-DR+) with a higher prognostic power than individual features (AUC = 0.825). Using this model, patients in the training cohort were divided into high- and low-risk groups with significant differences in mean progression-free survival (3.6 vs. 12.3 months), including disease control rate (41.2% vs. 91.7%), and objective response rate (17.6% vs. 41.6%). Integrating four-immune cell-subset based classifiers and three clinicopathologic risk factors can help to predict which patients might benefit from anti-PD-1 antibody inhibitors and remind potential non-responders to pursue effective treatment options in a timely way. Conclusions The prognostic immune risk score including the innate immune and adaptive immune cell populations could provide an accurate prediction efficacy in malignant melanoma patients with ICI therapy.
Carbonate system data tracing freshwater inflow into the Ross Sea through the eastern gate and along the Ross Ice Shelf (Antarctica)

The eastern Ross Sea is a key area to understand the role of the Amundsen Sea inflow of freshwater that can influence the Ross Sea water properties and salt budget. A survey was carried out in the eastern Ross Sea during the austral summer 2019–20 to evaluate the contribution of the Amundsen Sea Water (ASW) to the salinity variability. A total of 248 seawater samples were collected f\or the analysis of total alkalinity (AT) and pH. The data collected were used together with temperature and salinity to obtain a full description of the carbonate system properties including total inorganic carbon (CT), CO2 partial pressure (pCO2), calcium carbonate saturation state of aragonite and calcite (Ω), and Revelle factor. Moreover, we estimated the anthropogenic carbon (Cant) throughout the TrOCA method to better understand the carbon cycle, also considering the effect of atmospheric CO2 uptake on ocean acidification. We used principal component analysis (PCA) to investigate the major controls on the carbonate system parameters with the aim of defining their sensitivity as chemical tracers. The changes in carbonate chemistry in surface waters were mainly due to the physical properties. AT and pH traced the entry of the ASW showing limited mixing between water masses on the shelf area. Shelf waters were enriched in Cant, which resulted lower than the estimated value for shelf waters produced in western Ross Sea.
Surveillance of osteoarticular infections caused by Staphylococcus aureus in a paediatric hospital in Mexico City

Staphylococcus aureus is the main aetiologic agent of osteoarticular infections (OAIs) in paediatric patients. The aim of this prospective unicenter study was to describe the phenotypic and genotypic characteristics of S. aureus isolates obtained from OAIs in paediatric patients admitted to tertiary care hospital. Through a surveillance program called OsteoCode, a multidisciplinary team was created and we identified 27 patients with OAIs caused by S. aureus from 2019 to 2021. The susceptibility profile, virulence factors, biofilm formation, pulsed-field gel electrophoresis (PFGE), clonal complex (CC) and sequence type (ST) were determined. In addition, the clinical characteristics and evolution of the patients presented six months after the diagnosis of OAIs were described. Ninety-two percent of the isolates were methicillin-sensitive S. aureus (MSSA). In methicillin-resistant S. aureus (MRSA), SCCmec-II and SCCmec-V were detected. The pvl gene was only observed in MSSA (18.5%) and was associated with highest fever (p=0.015), multiple localization (p=0.017), and soft tissue sites of infection beyond the bone (pyomyositis, pulmonary abscess) (p=0.017). Biofilm formation was detected in 55.6% of isolates. The most common CC were CC5 and CC30 which represent the most common linages for bone and joint infections worldwide. The isolates were distributed in different STs, and ST672 was predominant. MRSA were associated with a longer duration of intravenous treatment and a prolonged hospital stay (p=0.023). Recurrent infection occurred in five children and orthopaedic complications in 33.3% of patients. This is the first study that reflects the epidemiology of S. aureus in OAIs in paediatric patients in Mexico; a clear predominance of MSSA distributed in different STs was observed. Our findings highlight that a multidisciplinary team is required for the diagnosis and treatment of OAIs.
Investigating Bayesian optimization for expensive-to-evaluate black box functions: Application in fluid dynamics

Bayesian optimization (BO) provides an effective method to optimize expensive-to-evaluate black box functions. It has been widely applied to problems in many fields, including notably in computer science, e.g., in machine learning to optimize hyperparameters of neural networks, and in engineering, e.g., in fluid dynamics to optimize control strategies that maximize drag reduction. This paper empirically studies and compares the performance and the robustness of common BO algorithms on a range of synthetic test functions to provide general guidance on the design of BO algorithms for specific problems. It investigates the choice of acquisition function, the effect of different numbers of training samples, the exact and Monte Carlo (MC) based calculation of acquisition functions, and both single-point and multi-point optimization. The test functions considered cover a wide selection of challenges and therefore serve as an ideal test bed to understand the performance of BO to specific challenges, and in general. To illustrate how these findings can be used to inform a Bayesian optimization setup tailored to a specific problem, two simulations in the area of computational fluid dynamics (CFD) are optimized, giving evidence that suitable solutions can be found in a small number of evaluations of the objective function for complex, real problems. The results of our investigation can similarly be applied to other areas, such as machine learning and physical experiments, where objective functions are expensive to evaluate and their mathematical expressions are unknown.
Low red/far-red ratio can induce cytokinin degradation resulting in the inhibition of tillering in wheat (Triticum aestivum L.)

Shoot branching is inhibited by a low red/far-red ratio (R/FR). Prior studies have shown that the R/FR suppressed Arabidopsis thaliana branching by promotes bud abscisic acid (ABA) accumulation directly. Given that wheat tiller buds are wrapped in leaf sheaths and may not respond rapidly to a R/FR, systemic cytokinin (CTK) may be more critical. Here, systemic hormonal signals including indole-3-acetic acid (IAA), gibberellins (GA) and CTK and bud ABA signals in wheat were tested under a low R/FR. The results showed that a low R/FR reduced the percentage of tiller occurrence of tiller IV and the tiller number per plant. The low R/FR did not rapidly induced ABA accumulation in the tiller IV because of the protection of the leaf sheath and had little effect on IAA content and signaling in the tiller nodes. The significant change in the CTK levels was observed earlier than those of other hormone (ABA, IAA and GA) and exogenous cytokinin restored the CTK levels and tiller number per plant under low R/FR conditions. Further analysis revealed that the decrease in cytokinin levels was mainly associated with upregulation of cytokinin degradation genes (TaCKX5, TaCKX11) in tiller nodes. In addition, exposure to a decreased R/FR upregulated the expression of GA biosynthesis genes (TaGA20ox1, TaGA3ox2), resulting in elevated GA levels, which might further promote CTK degradation in tiller nodes and inhibit tillering. Therefore, our results provide evidence that the enhancement of cytokinin degradation is a novel mechanism underlying the wheat tillering response to a low R/FR.
Impact of total marrow/lymphoid irradiation dose to the intestine on graft-versus-host disease in allogeneic hematopoietic stem cell transplantation for hematologic malignancies

Background and purpose Graft-versus-host disease (GvHD) is a leading cause of non-relapse mortality in patients undergoing allogeneic hematopoietic stem cell transplantation. The Perugia Bone Marrow Transplantation Unit designed a new conditioning regimen with total marrow/lymphoid irradiation (TMLI) and adaptive immunotherapy. The present study investigated the impact of radiotherapy (RT) doses on the intestine on the incidence of acute GvHD (aGvHD) in transplant recipients, analyzing the main dosimetric parameters. Materials and methods Between August 2015 and April 2021, 50 patients with hematologic malignancies were enrolled. All patients underwent conditioning with TMLI. Dosimetric parameters (for the whole intestine and its segments) were assessed as risk factors for aGvHD. The RT dose that was received by each intestinal area with aGvHD was extrapolated from the treatment plan for each patient. Doses were compared with those of the whole intestine minus the affected area. Results Eighteen patients (36%) developed grade ≥2 aGvHD (G2 in 5, G3 in 11, and G4 in 2). Median time to onset was 41 days (range 23–69 days). The skin was involved in 11 patients, the intestine in 16, and the liver in 5. In all 50 TMLI patients, the mean dose to the whole intestine was 7.1 Gy (range 5.07–10.92 Gy). No patient developed chronic GvHD (cGvHD). No dosimetric variable emerged as a significant risk factor for aGvHD. No dosimetric parameter of the intestinal areas with aGvHD was associated with the disease. Conclusion In our clinical setting and data sample, we have found no clear evidence that current TMLI dosages to the intestine were linked to the development of aGvHD. However, due to some study limitations, this investigation should be considered as a preliminary assessment. Findings need to be confirmed in a larger cohort and in preclinical models.