The New Buffer Salt-Protected Sodium Butyrate Promotes Growth Performance by Improving Intestinal Histomorphology, Barrier Function, Antioxidative Capacity, and Microbiota Community of Broilers.

In this study, a commercial sodium butyrate protected by a new buffer salt solution (NSB) was tested to determine whether it can be used as an antibiotic alternative in broiler production. A total of 192 1-day-old broilers were randomly allocated to three dietary treatments: soybean meal diet (CON), antibiotic diet (ANT, basal diet + 100 mg/kg aureomycin), and NSB (basal diet + 800 mg/kg NSB). The growth performance, serum anti-inflammatory cytokines, intestinal morphology, gut barrier function, antioxidative parameters, SCFAs' content, and cecal microbiota were analyzed. The result showed that NSB significantly improved ADFI and ADG (p < 0.01), and decreased FCR (p < 0.01). Serum anti-inflammatory cytokine IL-10 was up-regulated (p < 0.01), and pro-inflammatory TNF-α was down-regulated (p < 0.05) by NSB supplementation. H&E results showed that VH and the VH/CD ratio significantly increased (p < 0.05) in the jejunum and ileum in the NSB group. Furthermore, ZO-1 (p < 0.01), claudin-1 (p < 0.01), and occludin (p < 0.05) in the jejunum and claudin-1 (p < 0.01) and mucin-2 (p < 0.05) in the ileum were significantly up-regulated in the NSB group. Additionally, SOD (p < 0.05) and the T-AOC/MDA ratio (p < 0.01) in the jejunum and SOD in the ileum were significantly increased (p < 0.05) in the NSB group. The MDA level also significantly increased (p < 0.01) in the ANT group in the jejunum. Propionic acid (p < 0.05) and butyric acid (p < 0.01) content significantly increased in the NSB group in the jejunum and ileum segments. The 16S rRNA sequencing results showed no significant difference (p > 0.05) in alpha and beta diversity among the groups. LEFSe analysis also indicated that Peptostreptococcaceae, Colidextribacter, Firmicutes, Oscillospira, and Erysipelatoclostridiaceae, which promote SCFA production (p < 0.05), were identified as dominant taxon-enriched bacterial genera in the NSB group. The Spearman correlation analysis revealed that Colidextribacter with ADFI, ADG, VH, claudin-1 (p < 0.05), and unclassified_f__Peptostreptococcaceae with ADFI, IL-10, and ZO-1 were positively correlated (p < 0.05). Furthermore, ADFI and ADG with IL-10, claudin-1, SOD, T-AOC, and butyric acid (p < 0.05), and similarly, ADG with VH (p < 0.05), showed a positive correlation. In conclusion, NSB enhanced the growth performance by improving jejunum and ileum morphology, and serum anti-inflammatory cytokines, and by regulating the intestinal barrier function and antioxidant capacity, SCFAs' content, and cecum microbiota, showing its potential use as an alternative to antibiotics in poultry nutrition.

Thyroid abnormalities identified on CT screening for lung cancer.

PURPOSE: Because incidental thyroid nodules (ITNs) are common extrapulmonary findings in low-dose computed tomography (LDCT) scans for lung cancer screening, we aimed to investigate the frequency of ITNs on LDCT scans separately on baseline and annual repeat scans, the frequency of malignancy among the ITNs, and any association with demographic, clinical, CT characteristics. METHODS: Retrospective case series of all 2309 participants having baseline and annual repeat screening in an Early Lung and Cardiac Action Program (MS-ELCAP) LDCT lung screening program from January 2010 to December 2016 was performed. Frequency of ITNs in baseline and annual repeat rounds were determined. Multivariable regression analysis was performed to identify significant predictors. RESULTS: Dominant ITNs were seen in 2.5 % of 2309 participants on baseline and in 0.15 % of participants among 4792 annual repeat LDCTs. The low incidence of new ITNs suggests slow growth as it would take approximately an average of 16.8 years for a new ITN to be detected on annual rounds of screening. Newly detected ITNs on annual repeat LDCT were all smaller than 15 mm. Regression analysis showed that the increasing of age, coronary artery calcifications score and breast density grade were significant predictors for females having an ITN. No significant predictors were found for ITNs in males. CONCLUSION: ITNs are detected at LDCT however, no malignancy was found. Certain predictors for ITNs in females have been identified including breast density, which may point towards a common causal pathway.

Upregulation of collagen type X alpha 1 promotes the progress of triple-negative breast cancer via Wnt/ß-catenin signaling.

Triple-negative breast cancer (TNBC) is a malignant tumor with high degree of malignancy and lack of effective target treatment. The research aims to explore the role and mechanism of X collagen alpha-1 chain protein (COL10A1 gene) in TNBC. UALCAN and Kaplan-Meier were used to detect the expression of COL10A1 and its role in the prognosis of breast cancer patients. The cells with stably expressing high levels of COL10A1 were obtained by recombinant lentivirus infection. The expression of COL10A1 in cells was temporarily downregulated by siRNA interference fragments. Real-time quantitative polymerase chain reaction and western blot analysis were utilized to detect the changes of COL10A1 mRNA and protein expression. The biological functions of the cells were evaluated by colony formation, cell counting kit-8, cell invasion and wound healing experiments. In addition, the effect of COL10A1 on angiogenesis was investigated by tube formation assay. Xenograft tumor model was used to confirm the effect of COL10A1 on tumorigenicity in vivo and multiplex fluorescent immunohistochemistry to detect multiple proteins simultaneously. The possible molecular mechanism of the function of COL10A1 was speculated through the detection of proteins in functionally related pathways. COL10A1 is highly expressed and is significantly associated with worse overall survival (OS) and recurrence-free survival (RFS) in TNBC. Overexpression of COL10A1 increased the clone formation rate and cell migration capacity of TNBC cells. In the COL10A1 overexpression group, the clone formation rates of MD-MB-231 and BT-549 cells (21.5 ± 0.62, 27.83 ± 3.72)% were significantly higher than those in the control group(15.23 ± 2.79, 19.4 ± 1.47)%, and the relative migration ratio (47.40 ± 3.09, 41.26 ± 4.33)% were higher than those in the control group (34.48 ± 2.03, 21.80 ± 1.03)%. When the expression of COL10A1 was downregulated, the ability of clone formation and wound-healing migration capacity in TNBC cells was weakened. Upregulated COL10A1 in TNBC cells generated more junctions and longer total segments between vascular endothelial cells, and promoted angiogenesis of the cells, and thus enhanced the tumorigenesis. In TNBC, it was found that COL10A1 might affect epithelial-mesenchymal transition (EMT) of the cells through Wnt/ß-catenin signaling pathway by the detection of the related pathway proteins. COL10A1 is highly expressed in TNBC, and its high expression leads to poor OS and RFS. COL10A1 may enhance TNBC cell proliferation, migration and tumor-related angiogenesis, and promote tumorigenesis in vivo via Wnt/ß-catenin signaling.

Neoadjuvant Chemotherapy Is Effective in Those Infected With SARS-CoV-2: The Real-World Experience of a Large Chinese Breast Cancer Center.

PURPOSE: During the major shift in China's policies on coronavirus disease 2019 (COVID-19), many residents will be infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) over a short period, including a few patients with breast cancer undergoing neoadjuvant chemotherapy (NAC). Moreover, it is unknown whether this comorbidity affects the efficacy of NAC for breast cancer and the patient's psychological state and quality of life (QOL). This study aims to answer these questions. METHODS: The clinical data of 2,793 patients with breast cancer who received NAC at The Affiliated Hospital of Qingdao University were retrospectively collected. The infected and non-infected groups were divided according to whether they were infected with COVID-19 during NAC. Propensity score matching was used to reduce patient selection bias. The effectiveness, psychological well-being, and QOL of the two groups were compared. RESULTS: No discernible differences were observed in the pathological complete response rates (p = 0.307) and major histological responses rate (p = 0.398) between the infected and non-infected groups. Following the full course of NAC, the Functional Assessment of Cancer Treatment General (p < 0.001) and Functional Assessment of Cancer Therapy for Breast Cancer (p < 0.001) were lower in the infected group than the non-infected group, the Hospital Anxiety and Depression Scale (HADS) anxiety scale (p < 0.001) and HADS depression scale (p < 0.001) were considerably higher in the infected group than the non-infected group. CONCLUSION: With timely treatment and effective medical management, SARS-CoV-2 does not appear to affect the efficacy of NAC; however, it can significantly affect the QOL of patients and increase their psychological distress. Therefore, in addition to a timely assessment of the efficacy of NAC, it is necessary to dynamically understand the patient's psychological state and QOL.

A Tunable Hydrophilic-Hydrophobic, Stimulus Responsive, and Robust Iridescent Structural Color Bionic Film with Chiral Photonic Crystal Nanointerface.

Bio-inspired in nature, using nanomaterials to fabricate the vivid bionic structural color and intelligent stimulus responsive interface as smart skin or optical devices are widely concerned and remain a huge challenge. Here, the bionic flexible film is designed and fabricated with chiral nanointerface and tunable hydrophilic-hydrophobic by the ultrasonic energy perturbation strategy and crosslinking of the cellulose nanocrystals (CNC). An intelligent nanointerface with adjustable hydrophilic and hydrophobic properties is constructed by the supramolecular assembly using a smart ionic liquid molecule. The bionic flexible film possessed the variable hydrophilic-hydrophobic, stimulus responsive, and robust iridescent structural color. The reflective wavelength and the helical pitch of the film can be easily modulated through the ultrasonic energy perturbation strategy. The bionic flexible film by covalent cross-linking has excellent robustness, good elasticity and flexibility. The tunable brilliant structural color of the chiral nanointerface is attributed to the surface charge change of the CNC photonic crystal, which is disturbed by ultrasonic energy perturbation. The bionic flexible film with tunable structure color has intelligent hydrophilic and hydrophobic stimulus response properties. The chiral bionic materials have potential applications in smart skin, optical devices, bionic materials, robots, anti-counterfeiting, colorful displays, and stealth materials.

Bottom-Up Construction of Rhombic Lamellar CoNi-MOFs for the Electrochemical Sensing of H2S.

Lamellar metal-organic frameworks (MOFs) have attracted significant attention in the field of electrochemical sensing due to their abundant open active sites and specific electron conductivity. Herein, by employing a bottom-up synthesis strategy, rhombic lamellar heterometallic CoNi-MOFs with varying thicknesses are constructed. This is achieved by using 4-methylpyridine as a capping agent based on the (4,6)-linked Co2(azpy)2(bptc) (azpy = 4,4'-azopyridine, bptc = 3,3',5,5'-biphenyltetracarboxylic acid) structure with a fsc topology and by introducing Ni species simultaneously. To mitigate sulfur deposition on electrodes, the triple pulse amperometry (TPA) method is employed. Among the synthesized lamellar CoNi-MOFs, lamellar CoNi-MOF-3 with the minimum thickness exhibits an optimal electrochemical sensing performance toward hydrogen sulfide, with a sensitivity of 119.3 µA·mM-1·cm-2 in the linear range of 2-2000 µM. This study pioneers a new approach to the controlled construction and electrochemical activity modification of lamellar MOF materials.

Establishment of novel anti-TIM-3 antibodies interfering with its binding to ligands.

The T cell immunoglobulin and mucin-domain containing-3 (TIM-3) receptor has gained significant attention as a promising target for cancer immunotherapy. The inhibitory effect of T cells by TIM-3 is mediated through the interaction between TIM-3 and its ligands. Ligand-blocking anti-TIM-3 antibodies possess the potential to reactivate antigen-specific T cells and augment anti-tumor immunity. However, the precise ligand-receptor interactions disrupted by the administration of TIM-3 blocking Abs have yet to be fully elucidated. In this study, we have developed a panel of monoclonal antibodies targeting human TIM-3, namely MsT001, MsT065, MsT229, and MsT286. They exhibited high sensitivities (10 pg/mL) and affinities (3.70 × 10-9 to 4.61 × 10-11 M) for TIM-3. The TIM-3 antibodies recognized distinct epitopes, including linear epitopes (MsT001 and MsT065), and a conformational epitope (MsT229 and MsT286). Additionally, the MsT229 and MsT286 displayed reactivity towards cynomolgus TIM-3. The interactions between TIM-3/Gal-9, TIM-3/HMGB-1, and TIM-3/CEACAM-1 disrupt the binding of MsT229 and MsT286, while leaving the binding of MsT001 and MsT065 unaffected. The inhibitory effect on the interaction between Gal-9 and TIM-3 was found to be dose-dependently in the presence of either MsT229 or MsT286. The findings suggested that the involvement of conformational epitopes in TIM-3 is crucial for its interaction with ligands, and we successfully generated novel anti-TIM-3 Abs that exhibit inhibitory potential. In conclusion, our finding offers valuable insights -on the comprehension and targeting of human TIM-3.

Efficacy of allogeneic tendon material coracoclavicular ligament reconstruction combined with Kirschner wire and titanium alloy hook plate material fixation in the treatment of acromioclavicular joint dislocation.

Objective: To compare the effects of allogeneic tendon coracoclavicular ligament reconstruction combined with Kirschner wire fixation and clavicular hook plate fixation on early postoperative pain, postoperative shoulder joint function score and shoulder joint mobility in patients with acromioclavicular joint dislocation. Methods: From January 2020 to January 2023, 43 patients with acromioclavicular joint dislocation admitted to Xi 'an Honghui Hospital were included. Among them, 24 patients were treated with the clavicular hook plate technique (Hook Plate,HP) group, and 19 patients were treated with allogeneic tendon coracoclavicular ligament reconstruction combined with the Kirschner wire technique (Allogeneic Tendon, AT) group. The Constant-Murley score of shoulder joint function 6 months after operation, postoperative shoulder joint activity, preoperative and postoperative pain, operation time, intraoperative blood loss and complications were compared between the two groups. Results: All 43 patients were followed up for an average of 9.7 (9-12) months. The intraoperative blood loss in the allogeneic tendon group was less than in the hook plate group. The Constant-Murley shoulder function score was higher than that in the hook plate group 6 months after the operation. The abduction and lifting activity was greater than that in the hook plate group. The visual analogue scale scores at 3 days and 14 days after operation were lower than those in the hook plate group. The difference was statistically significant (p < 0.001). There was 1 case (5.3%) of exudation around the Kirschner needle track in the allogeneic tendon reconstruction group, and 5 cases (20.8%) of complications in the hook plate group, including 1 case of internal fixation stimulation, 2 cases of acromion impingement syndrome, 1 case of acromioclavicular joint osteoarthritis, and 1 case of shoulder joint stiffness. The complication rate of the allogeneic tendon group was lower than that of the hook plate group. Conclusion: The clinical efficacy of allogeneic tendon coracoclavicular ligament reconstruction combined with Kirschner wire fixation in treating acromioclavicular joint dislocation (Rockwood type III-V) is better than hook plate internal fixation. The patients have less early postoperative pain and better recovery of shoulder joint function and shoulder joint mobility.

Biomechanical evaluation of a modified intramedullary nail for the treatment of unstable femoral trochanteric fractures.

Background: The Proximal Femoral Nail Antirotation (PFNA) device is the most commonly used implant to fix unstable femoral trochanteric fractures (UFTFs), but it has a relatively high incidence of complications. Due to this factor, the modified intramedullary nail (MIN) was created to treat patients with UFTFs. The aim was to exhibit the MIN and make a comparison with PFNA and InterTAN using biomechanical methods. Methods: An adult UFTF model was developed using Mimics software. The PFNA, InterTAN nail, and MIN models were drawn referring to the corresponding parameters and installed in the fracture models. Vertical, anteroposterior (AP) bending, and torsion loads of the femoral head were set in advance and loaded onto the fracture models. The value of maximal displacement and von Mises stress was evaluated via finite element analysis (FEA). Results: The MIN model had smaller values for maximal displacement than that of the PFNA model, and the increase in displacement was less pronounced for the MIN compared to PFNA under increasing vertical loads. For the indicator of von Mises stress, the MIN model showed lower stress compared with the PFNA model in vertical loads ranging from 300 N to 2100 N. Except for the maximal stress at implants under AP bending loads, the MIN demonstrated the most superior biomechanical properties under AP bending and torsional loads. Conclusion: The MIN offered obvious advantages in terms of mechanical stability and stress distribution among the three studied implants, providing a promising implant option for patients with UFTFs.

Determination of high-risk factors and related spatially influencing variables of heavy metals in groundwater.

Identifying high-risk factors (heavy metals (HMs) and pollution sources) by coupling receptor models and health risk assessment model (HRA) is a novel approach within the field of risk assessment. However, this coupled model ignores the contribution of spatial differentiation to high-risk factors, resulting in the assessment being subjective. Taking Dongting Plain (DTP) as an example, a coupling framework by jointly using the positive matrix factorization model (PMF), HRA, Monte Carlo simulation, and geo-detector was developed, aiming to identify high-risk factors in groundwater, and further explore key environmental variables influencing the spatial heterogeneity of high-risk factors. The results showed that at least 82.86 % of non-carcinogenic risks and 97.41 % of carcinogenic risks were unacceptable for people of all ages, especially infants and children. According to the relationships among HMs, pollution sources, and health risks, As and natural sources were defined as high-risk HMs and sources, respectively. The interactions among Holocene thickness, oxidation-reduction potential, and dissolved organic carbon emerged as the primary drivers of spatial variability in high-risk factors, with their combined explanatory power reaching up to 74%. This proposed framework provides a scientific reference for future studies and a practical reference for environmental authorities in developing effective pollution management measures.

Semi-focal bone transport versus traditional bone transport technique for the management of large tibial bone defects after trauma.

How to deal with large tibial bone defects is still controversial. The purpose of this research was to compare the semi-focal bone transport (SFBT) technique with traditional bone transport (TBT) technique for treating such patients. Sixty-two patients were included and retrospectively analyzed. In all cases, after radical debridement large tibial bone defects remained. Patients were treated by the SFBT or TBT technique. The distraction, consolidation duration and complications were recorded by the patients' medical files. Based on the Association for the Study and Application of Methods of Ilizarov (ASAMI) standard, the bone and functional results were evaluated. The mean bone defect size was 7.7 ± 1.6 cm and 7.5 ± 2.1 cm for SFBT and TBT patients. The mean external fixation index (EFI) was 1.51 ± 0.14 months/cm and 1.89 ± 0.25 months/cm for SFBT and TBT patients (p < 0.05), respectively. With respect to bone and function results, there was no significant differences between the two groups (p > 0.05). The mean number of complications per patient was 1.1 ± 0.6 and 1.6 ± 0.7 for SFBT and TBT patients (p < 0.05). Compared to the traditional bone transport technique, patients using the semi-focal bone transport technique achieved better clinical effects, including shorter EFI and less complications. Therefore, the SFBT technique could be a new option for patients with large tibial bone defects.

An inorganic liquid crystalline dispersion with 2D ferroelectric moieties.

Electro-optical effect-based liquid crystal devices have been extensively used in optical modulation techniques, in which the Kerr coefficient reflects the sensitivity of the liquid crystals and determines the strength of the device's operational electric field. The Peterlin-Stuart theory and the O'Konski model jointly indicate that a giant Kerr coefficient could be obtained in a material with both a large geometrical anisotropy and an intrinsic polarization, but such a material is not yet reported. Here we reveal a ferroelectric effect in a monolayer two-dimensional mineral vermiculite. A large geometrical anisotropy factor and a large inherent electric dipole together raise the record value of Kerr coefficient by an order of magnitude, till 3.0 × 10-4 m V-2. This finding enables an ultra-low operational electric field of 102-104 V m-1 and the fabrication of electro-optical devices with an inch-level electrode separation, which has not previously been practical. Because of its high ultraviolet stability (decay <1% under ultraviolet exposure for 1000 hours), large-scale production, and energy efficiency, prototypical displayable billboards have been fabricated for outdoor interactive scenes. This work provides new insights for both liquid crystal optics and two-dimensional ferroelectrics.

Integrating Proteomics and Transcriptomics Reveals the Potential Pathways of Hippocampal Neuron Apoptosis in Dravet Syndrome Model Mice.

An important component contributing to the onset of epilepsy is the death of hippocampal neurons. Several studies have shown that Dravet syndrome model mice: Scn1a KO mice have a high number of apoptotic neurons following seizures, but the precise mechanism underlying this remains unclear. The aim of this research was to elucidate the potential molecular mechanism of neuronal apoptosis in Scn1a KO mice by integrating proteomics and transcriptomics, with the ultimate goal of offering better neuroprotection. We found that apoptotic processes were enriched in both proteomic and transcriptomic GO analyses, and KEGG results also indicated that differential proteins and genes play a role in neurotransmission, the cell cycle, apoptosis, and neuroinflammation. Then, we examined the upstream and downstream KGML interactions of the pathways to determine the relationship between the two omics, and we found that the HIF-1 signaling pathway plays a significant role in the onset and apoptosis of epilepsy. Meanwhile, the expression of the apoptosis-related protein VHL decreased in this pathway, and the expression of p21 was upregulated. Therefore, this study suggests that VHL/HIF-1α/p21 might be involved in the apoptosis of hippocampal neurons in Scn1a KO mice.

Exploring the thermal decomposition and detonation mechanisms of 2,4-dinitroanisole by TG-FTIR-MS and molecular simulations.

2,4-dinitroanisole (DNAN), an insensitive explosive, has replaced trinitrotoluene (TNT) in many melt-cast explosives to improve the safety of ammunition and becomes a promising material to desensitize novel explosives of high sensitivity. Here, we combine thermogravimetric-Fourier transform infrared spectrometry-Mass spectrometry (TG-FTIR-MS), density functional theory (DFT), and ReaxFF molecular dynamics (MD) to investigate its thermal decomposition and detonation mechanisms. As revealed by TG-FTIR-MS, the thermal decomposition of DNAN starts at ca. 453 K when highly active NO2 is produced and quickly converted to NO resulting in the formation of a large amount of Ph(OH)(OH2)OCH3+. DFT calculations show that the activation energy of DNAN is higher than that of TNT due to the lack of α-H. Further steps in both thermal decomposition and detonation reactions of the DNAN are dominated by bimolecular O-transfers. ReaxFF MD indicates that DNAN has a lower heat of explosion than TNT, in accordance with the observation that the activation energies of polynitroaromatic explosives are inversely proportional to their heat of explosion. The inactive -OCH3 group and less nitro groups also render DNAN higher thermal stability than TNT.

The Biological Role of Macrophage in Lung and Its Implications in Lung Cancer Immunotherapy.

The lungs are the largest surface of the body and the most important organ in the respiratory system, which are constantly exposed to the external environment. Tissue Resident Macrophages in lung constitutes the important defense against external pathogens. Macrophages connects the innate and adaptive immune system, and also plays important roles in carcinogenesis and cancer immunotherapy. Lung cancer is the leading cause of cancer-related death worldwide, with an overall five-year survival rate of only 21%. Macrophages that infiltrate or aggregate in lung tumor microenvironment are defined as tumor-associated macrophages (TAMs). TAMs are the main components of immune cells in the lung tumor microenvironment. The differentiation and maturation process of TAMs can be roughly divided into two different types: classical activation pathway produces M1 tumor-associated macrophages, and bypass activation pathway produces M2 tumor-associated macrophages. Studies have found that TAMs are related to tumor invasion, metastasis, and treatment resistance, and show potential as a new target for tumor immunotherapy. Therefore, the biological function of macrophages in lung and the role of TAMs in the occurrence, development, and treatment of lung cancer are discussed in this paper.

3D Printed Conductive Hydrogel Patch Incorporated with MSC@GO for Efficient Myocardial Infarction Repair.

Myocardial infarction (MI) results in an impaired heart function. Conductive hydrogel patch-based therapy has been considered as a promising strategy for cardiac repair after MI. In our study, we fabricated a three-dimensional (3D) printed conductive hydrogel patch made of fibrinogen scaffolds and mesenchymal stem cells (MSCs) combined with graphene oxide (GO) flakes (MSC@GO), capitalizing on GO's excellent mechanical property and electrical conductivity. The MSC@GO hydrogel patch can be attached to the epicardium via adhesion to provide strong electrical integration with infarcted hearts, as well as mechanical and regeneration support for the infarcted area, thereby up-regulating the expression of connexin 43 (Cx43) and resulting in effective MI repair in vivo. In addition, MI also triggers apoptosis and damage of cardiomyocytes (CMs), hindering the normal repair of the infarcted heart. GO flakes exhibit a protective effect against the apoptosis of implanted MSCs. In the mouse model of MI, MSC@GO hydrogel patch implantation supported cardiac repair by reducing cell apoptosis, promoting gap connexin protein Cx43 expression, and then boosting cardiac function. Together, this study demonstrated that the conductive hydrogel patch has versatile conductivity and mechanical support function and could therefore be a promising candidate for heart repair.

Whole-Genome Resequencing of Ujimqin Sheep Identifies Genes Associated with Vertebral Number.

The number of vertebrae is a crucial economic trait that can significantly impact the carcass length and meat production in animals. However, our understanding of the quantitative trait loci (QTLs) and candidate genes associated with the vertebral number in sheep (Ovis aries) remains limited. To identify these candidate genes and QTLs, we collected 73 Ujimqin sheep with increased numbers of vertebrae (T13L7, T14L6, and T14L7) and 23 sheep with normal numbers of vertebrae (T13L6). Through high-throughput genome resequencing, we obtained a total of 24,130,801 effective single-nucleotide polymorphisms (SNPs). By conducting a selective-sweep analysis, we discovered that the most significantly selective region was located on chromosome 7. Within this region, we identified several genes, including VRTN, SYNDIG1L, LTBP2, and ABCD4, known to regulate the spinal development and morphology. Further, a genome-wide association study (GWAS) performed on sheep with increased and normal vertebral numbers confirmed that ABCD4 is a candidate gene for determining the number of vertebrae in sheep. Additionally, the most significant SNP on chromosome 7 was identified as a candidate QTL. Moreover, we detected two missense mutations in the ABCD4 gene; one of these mutations (Chr7: 89393414, C > T) at position 22 leads to the conversion of arginine (Arg) to glutamine (Gln), which is expected to negatively affect the protein's function. Notably, a transcriptome expression profile in mouse embryonic development revealed that ABCD4 is highly expressed during the critical period of vertebral formation (4.5-7.5 days). Our study highlights ABCD4 as a potential major gene influencing the number of vertebrae in Ujimqin sheep, with promising prospects for future genome-assisted breeding improvements in sheep.

GraphPath: a graph attention model for molecular stratification with interpretability based on the pathway-pathway interaction network.

MOTIVATION: Studying the molecular heterogeneity of cancer is essential for achieving personalized therapy. At the same time, understanding the biological processes that drive cancer development can lead to the identification of valuable therapeutic targets. Therefore, achieving accurate and interpretable clinical predictions requires paramount attention to thoroughly characterizing patients at both the molecular and biological pathway levels. RESULTS: Here, we present GraphPath, a biological knowledge-driven graph neural network with multi-head self-attention mechanism that implements the pathway-pathway interaction network. We train GraphPath to classify the cancer status of patients with prostate cancer based on their multi-omics profiling. Experiment results show that our method outperforms P-NET and other baseline methods. Besides, two external cohorts are used to validate that the model can be generalized to unseen samples with adequate predictive performance. We reduce the dimensionality of latent pathway embeddings and visualize corresponding classes to further demonstrate the optimal performance of the model. Additionally, since GraphPath's predictions are interpretable, we identify target cancer-associated pathways that significantly contribute to the model's predictions. Such a robust and interpretable model has the potential to greatly enhance our understanding of cancer's biological mechanisms and accelerate the development of targeted therapies. AVAILABILITY AND IMPLEMENTATION: https://github.com/amazingma/GraphPath.

Examining the causal relationship between circulating immune cells and the susceptibility to osteomyelitis: A Mendelian randomization study.

BACKGROUND: Osteomyelitis is considered as a deleterious inflammatory condition affecting the bone, primarily attributed to pathogenic infection. However, the underlying factors predisposing individuals to osteomyelitis remain incompletely elucidated. The immune system plays a multifaceted role in the progression of this condition, yet previous observational studies and randomized controlled trials investigating the association between circulating immune cell counts and osteomyelitis have been constrained. In order to address this knowledge gap, we conducted a Mendelian randomization (MR) analysis to evaluate the impact of diverse immune cell counts on the risk of developing osteomyelitis. METHODS: In our study, we utilized single nucleotide polymorphisms (SNPs) that have been strongly linked to circulating immune cells or specific lymphocyte subtypes, as identified in large-scale genome-wide association studies (GWAS). These SNPs served as instrumental variables (IVs) for our MR analysis. We employed a more relaxed clumping threshold to conduct MR analysis on several related lymphocyte subtypes. To estimate causal effects, we utilized the Wald ratio, as well as the random-effects inverse variance weighted (IVW) and weighted median (WM) methods. To enhance the credibility of our results, we performed F-statistic calculations and a series of sensitivity analyses. RESULTS: Our findings revealed a significant correlation between the absolute count of circulating lymphocytes and the risk of osteomyelitis [odds ratio(OR) 1.20；95 % confidence interval (CI), 1.08-1.32；P = 0.0005]. Furthermore, we identified a causal relationship between the absolute count of CD8+ T cells and susceptibility to osteomyelitis (OR 1.16; 95 % CI, 1.04-1.30; P = 0.0098). Importantly, these findings remained robust across a wide range of sensitivity analyses. CONCLUSION: Through our MR analysis, we have provided evidence supporting a causal relationship between genetic predisposition to higher circulating immune cell counts and an increased risk of osteomyelitis. Specifically, our findings highlight the association between elevated CD8+ T cell counts and a heightened susceptibility to osteomyelitis. These results offer valuable insights for the future exploration of immunotherapy approaches in the management of osteomyelitis.