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This genome-wide association study (GWAS) aimed to identify sequence variants (SVs) and candidate genes associated with fertility and health in endangered German Black Pied cattle (DSN) based on whole-genome sequence (WGS) data. We used 304 sequenced DSN cattle for the imputation of 1797 genotyped DSN to WGS. The final dataset included 11,413,456 SVs of 1886 cows. Cow traits were calving-to-first service interval (CTFS), non-return after 56 days (NR56), somatic cell score (SCS), fat-to-protein ratio (FPR), and three pre-corrected endoparasite infection traits. We identified 40 SVs above the genome-wide significance and suggestive threshold associated with CTFS and NR56, and three important potential candidate genes (ARHGAP21, MARCH11, and ZNF462). For SCS, most associations were observed on BTA 25. The GWAS revealed 61 SVs, a cluster of 10 candidate genes on BTA 13, and 7 pathways for FPR, including key mediators involved in milk fat synthesis. The strongest associations for gastrointestinal nematode and Dictyocaulus viviparus infections were detected on BTA 8 and 24, respectively. For Fasciola hepatica infections, the strongest associated SVs were located on BTA 4 and 7. We detected 200 genes for endoparasite infection traits, related to 16 pathways involved in host immune response during infection.

Simple Summary New free walk housing systems such as compost-bedded pack barns might positively influence animal welfare. However, udder health can be negatively affected due to the microbial environment in the pack. Udder health depends on many factors, such as the environment, the feed, the pathogen species, and the genetic mechanisms of the cow’s immune system. For a more precise evaluation of udder health, we examined novel traits including specific mastitis pathogens and differential somatic cell fractions in milk. In order to identify possible candidate genes for udder health, a genome-wide association study, including single-nucleotide polymorphisms (SNP) by housing system interactions (compost-bedded pack barn and conventional cubicle barn), was performed. We identified two potential candidate genes for the interaction effect in relation to udder health. The identified potential candidate gene HEMK1 (HemK methyltransferase family member 1) is involved in immune system development, and CHL1 (cell adhesion molecule L1 like) has an immunosuppressive effect during stress conditions. The results suggest housing system-specific breeding strategies in order to improve udder health in compost-bedded pack and conventional cubicle barns. Abstract The aim of the present study was to detect significant SNP (single-nucleotide polymorphism) effects and to annotate potential candidate genes for novel udder health traits in two different farming systems. We focused on specific mastitis pathogens and differential somatic cell fractions from 2198 udder quarters of 537 genotyped Holstein Friesian cows. The farming systems comprised compost-bedded pack and conventional cubicle barns. We developed a computer algorithm for genome-wide association studies allowing the estimation of main SNP effects plus consideration of SNPs by farming system interactions. With regard to the main effect, 35 significant SNPs were detected on 14 different chromosomes for the cell fractions and the pathogens. Six SNPs were significant for the interaction effect with the farming system for most of the udder health traits. We inferred two possible candidate genes based on significant SNP interactions. HEMK1 plays a role in the development of the immune system, depending on environmental stressors. CHL1 is regulated in relation to stress level and influences immune system mechanisms. The significant interactions indicate that gene activity can fluctuate depending on environmental stressors. Phenotypically, the prevalence of mastitis indicators differed between systems, with a notably lower prevalence of minor bacterial indicators in compost systems.

Drug resistance to tyrosine kinase inhibitors (TKIs) is currently a clinical problem in patients with chronic myelogenous leukemia (CML). Homoharringtonine (HHT) is an approved treatment for adult patients with chronic‑ or accelerated‑phase CML who are resistant to TKIs and other therapies; however, the underlying mechanisms remain unclear. In the present study, HHT treatment demonstrated induction of apoptosis in imatinib‑resistant K562G cells by using MTS assay and western blotting, and BCR‑ABL protein was reduced. CHX chase assay revealed that HHT induced degradation of the BCR‑ABL protein, which could be reversed by autophagy lysosome inhibitors Baf‑A1 and CQ. Next, HHT treatment confirmed the induction of autophagy in K562G cells, and silencing the key autophagic proteins ATG5 and Beclin‑1 inhibited the degradation of the BCR‑ABL protein and cytotoxicity. In addition, autophagic receptor p62/SQSTM1(p62) participated during the autophagic degradation of BCR‑ABL induced by HHT, and this was confirmed by co‑immunoprecipitation, in which HHT enhanced the ubiquitination of the BCR‑ABL protein and promoted its binding to p62. In conclusion, HHT induced p62‑mediated autophagy in imatinib‑resistant CML K562G cells, thus promoting autophagic degradation of the BCR‑ABL protein and providing a novel strategy for the treatment of TKI‑resistant CML.

The functionalization of proteins with different cargo molecules is highly desirable for a broad range of applications. However, the reproducible production of defined conjugates with multiple functionalities is a significant challenge. Herein, we report the dual site-specific labeling of an antibody fragment, utilizing the orthogonal Sortase A and π-clamp conjugation methods, and demonstrate that binding of the antibody fragment to its target receptor is retained after dual labeling.

There is a dire need to develop more effective therapeutics to combat brain cancer such as glioblastoma multiforme (GBM). An ideal treatment is expected to target deliver chemotherapeutics to glioma cells across the blood-brain barrier (BBB). The overexpression of transferrin (Tf) receptor (TfR) on the BBB and the GBM cell surfaces but not on the surrounding cells renders TfR a promising target. While porous silicon nanoparticles (pSiNPs) have been intensely studied as a delivery vehicle due to their high biocompatibility, degradability, and drug-loading capacity, the potential to target deliver drugs with transferrin (Tf)-functionalized pSiNPs remains unaddressed. Here, we developed and systematically evaluated Tf-functionalized pSiNPs (Tf@pSiNPs) as a glioma-targeted drug delivery system. These nanoparticles showed excellent colloidal stability and had a low toxicity profile. As compared with nontargeted pSiNPs, Tf@pSiNPs were selective to BBB-forming cells and GBM cells and were efficiently internalized through clathrin receptor-mediated endocytosis. The anticancer drug doxorubicin (Dox) was effectively loaded (8.8 wt %) and released from Tf@pSiNPs in a pH-responsive manner over 24 h. Furthermore, the results demonstrate that Dox delivered by Tf@pSiNPs induced significantly enhanced cytotoxicity to GBM cells across an in vitro BBB monolayer compared with free Dox. Overall, Tf@pSiNPs offer a potential toolbox for enabling targeted therapy to treat GBM.

Metal transfer processes during double-wire double pulsed gas metal arc welding (DP-GMAW) were observed in both the double pulse synchronous (DPS) and double pulse alternating (DPA) phases using a high-speed digital camera. Meanwhile, the corresponding waveforms were acquired. The results showed that metal transfer occurred as one drop per pulse (ODPP) during both the strong and weak pulse periods, irrespective of phase. In the DPA phase, ODPP was achieved more easily compared with the DPS phase and the metal transfer stability was improved. The droplet offset distance was shorter in the DPA phase. Moreover, the desirable fish-scale appearance was more evident on surface of the weld bead created in the DPA phase. Finally, penetration achieved in the DPA phase was significantly deeper, and fluctuations in the penetration were clearly observed in longitudinal section of the weld bead.

Background B7-H4 is among the B7 family members which may serve as a new targetable immune checkpoint molecule. It was reported that high level of serum B7-H4 level may be correlated with lymphoma. Nevertheless, the role of B7-H4 in Epstein-Barr Virus-Positive diffuse large B cell lymphoma (EBV+DLBCL) has not been addressed although it has been suggested that B7-H4 could promote tumor growth and metastatic progression in certain cancers. Methods Between January 2005 and November 2017 at the department of Hematology, Shanghai Jiao Tong University School of Medicine affiliated Shanghai General Hospital 260 DLBCL samples were analyzed for EBV-encoded small RNA (EBV-EBER) by in situ hybridization. The expression level of B7-H4 in DLBCL tumor tissue was evaluated by immunohistochemistry. Furthermore, the role of B7-H4 in DLBCL was further investigated in DLBCL cell line. Results EBV+DLBCL patients suffered from markedly lower overall survival (OS) and progression-free survival (PFS) rates in our study. We showed that B7-H4 was significantly overexpressed in 16 EBV+-subgroup cases out of 260 DLBCL patients. We further found that EBV infection in lymphoblast cells led to enhanced expression of B7-H4 followed by increased cell viability and reduced apoptosis. In contrast, inhibition of B7-H4 simultaneously impaired cell viability and induced apoptosis. Mechanistically, inhibiting B7-H4 resulted in decreased phosphorylation Erk 1/2 and Akt. Conclusion Our study reveals a critical role of B7-H4 in EBV+DLBCL development by regulating cell survival and apoptosis through the Erk and Akt signalling pathways. Targetting B7-H4 may be promising in the therapy of EBV+DLBCL.

Targeting protein for Xenopus kinesin-like protein 2 (TPX2) is a microtubule-associated protein required for mitosis and spindle assembly. Previous studies showed that TPX2 is overexpressed in various human cancers and promotes cancer progression. In this study, the differentially expressed genes including TPX2 were screened in GEO database for gene expression microarray of breast cancer. The TPX2 expression level was significantly increased in breast cancer cells and the breast malignant tissues compared with those controls. In vitro experiment further confirmed that knockdown of TPX2 by small hairpin RNA inhibited breast cancer cell proliferatio, migration, and induced cell apoptosis. TPX2 silencing decreased the expression of PI3K and extent of AKT phosphorylation, as well as increased expression of p53 and p21. Taken together, our findings indicate that TPX2 silencing negatively regulates the PI3K/AKT and activates p53 signaling pathway by which breast cancer cells proliferation were inhibited whereas cellulars apoptosis were accelerated, suggesting that TPX2 may be a potential target for anticancer therapy in breast cancer.

The effect of non-cytotoxic doses of epigallocatechin-3-gallate (EGCG) on the metastatic capability of human hepatocellular carcinoma (HCC) cells was investigated in vitro and in vivo. miR483-3p, a microRNA whose expression correlates inversely with survival and positively with disease progression in HCC patients, was found to promote HCC cell migration and invasion in vitro as well as lung metastasis in nude mice established by the tail-vein injection of HCC cells. The induction of reactive oxygen species (ROS) and downregulation of antioxidant defense factors Nrf2 and SOD2 appeared to be an important underlying mechanism and treatment with a non-cytotoxic dose of EGCG effectively reversed the miR483-3p-induced enhancement of HCC cell migration and invasion in vitro. Moreover, administration through drinking water at doses (0.1% and 0.5% EGCG solution, respectively) equivalent to the intake of regular to heavy tea drinkers could also significantly inhibit lung metastasis of HCC cells based on the estimation from the USDA Database for the Flavonoid Content of Selected Foods and FDA guidelines for the conversion of animal dose to human equivalent dose. EGCG also significantly counteracted the miR483-3p-induced alteration in the expression of epithelial–mesenchymal transition (EMT) markers, E-cadherin and vimentin, and downregulated the endogenous expression of miR483-3p in HCC cells through an epigenetic mechanism that led to the hypermethylation of the miR483-3p promoter region. The data from our study illustrate that miR483-3p promotes HCC metastasis likely through the induction of oxidative stress and uncover a novel role of EGCG for protection against miR483-3p-mediated HCC metastasis via the epigenetic modulation of miR483-3p expression. These findings therefore provide further evidence supporting that regular tea consumption may contribute to protection against miR-483-3p-induced ROS and the associated HCC progression.

High plasma lactate is associated with poor prognosis of many malignancies, but its role in virally mediated cancer progression and underlying molecular mechanisms are unclear. Epstein-Barr virus (EBV), the first human oncogenic virus, causes several cancers, including B-cell lymphoma. Here, we report that lactate dehydrogenase A (LDH-A) expression and lactate production are elevated in EBV-immortalized B lymphoblastic cells, and lactic acid (LA; acidic lactate) at low concentration triggers EBV-infected B-cell adhesion, morphological changes, and proliferation in vitro and in vivo. Moreover, LA-induced responses of EBV-infected B cells uniquely occurs in viral latency type III, and it is dramatically associated with the inhibition of global viral microRNAs, particularly the miR-BHRF1 cluster, and the high expression of SMAD3, JUN, and COL1A genes. The introduction of miR-BHRF1-1 blocks the LA-induced effects of EBV-infected B cells. Thus, this may be a novel mechanism to explain EBV-immortalized B lymphoblastic cell malignancy in an LA microenvironment.

The consensusability and global optimality problems are solved for the discrete-time linear multiagent system (MAS) with marginally stable and strictly unstable dynamics. A unified framework is proposed by capturing the maximal disc-guaranteed gain margin (GGM) of the discrete-time linear quadratic regulator (LQR). Sufficient and necessary conditions on consensusability are established. Two bounds of the consensus region are derived only in terms of the unstable eigenvalues of the agent' dynamics. For the single-input MAS, by proving that the radius of the consensus region exactly equals the reciprocal of the Mahler measure of the agent' dynamics, we incidentally reveal the relation between the maximal GGM and the intrinsic entropy rate of the system dynamics for single-input discrete-time linear systems. By employing the inverse optimal control approach, it is proved that the globally optimal consensus is achieved, if and only if the associated Laplacian matrix is a simple matrix and all its nonzero eigenvalues can be radially projected into a specific subset of the consensus region. Moreover, the limitation on the eigenvalues vanishes for the marginally stable MAS. As an application of the global optimality, the minimum-energy-distributed consensus control problem is solved for the marginally stable MAS. Finally, a numerical example is given to demonstrate the effectiveness of the obtained results.

Background Approximately 80% of brain tumours are gliomas. Despite treatment, patient mortality remains high due to local metastasis and relapse. It has been shown that transferrin-functionalised porous silicon nanoparticles (Tf@pSiNPs) can inhibit the migration of U87 glioma cells. However, the underlying mechanisms and the effect of glioma cell heterogeneity, which is a hallmark of the disease, on the efficacy of Tf@pSiNPs remains to be addressed. Results Here, we observed that Tf@pSiNPs inhibited heterogeneous patient-derived glioma cells’ (WK1) migration across small perforations (3 μm) by approximately 30%. A phenotypical characterisation of the migrated subpopulations revealed that the majority of them were nestin and fibroblast growth factor receptor 1 positive, an indication of their cancer stem cell origin. The treatment did not inhibit cell migration across large perforations (8 μm), nor cytoskeleton formation. This is in agreement with our previous observations that cellular-volume regulation is a mediator of Tf@pSiNPs’ cell migration inhibition. Since aquaporin 9 (AQP9) is closely linked to cellular-volume regulation, and is highly expressed in glioma, the effect of AQP9 expression on WK1 migration was investigated. We showed that WK1 migration is correlated to the differential expression patterns of AQP9. However, AQP9-silencing did not affect WK1 cell migration across perforations, nor the efficacy of cell migration inhibition mediated by Tf@pSiNPs, suggesting that AQP9 is not a mediator of the inhibition. Conclusion This in vitro investigation highlights the unique therapeutic potentials of Tf@pSiNPs against glioma cell migration and indicates further optimisations that are required to maximise its therapeutic efficacies. Graphic Abstract

For high-density metro traffic, nowadays the time-variant passenger flow is the main cause of train delays and stranded passengers. Typically, the main objective of automatic metro traffic regulation methods is to minimize the delay time of trains while passengers' satisfaction is not considered. Instead, in this work, a novel framework that integrates a passenger flow module (PFM) and a train operation module (TOM) is proposed with the aim of simultaneously minimizing traffic delays and passengers' discomfort. In particular, the PFM is devoted to the optimization of the headway time in case of platform overcrowding, so as to reduce the passengers waiting time at platforms and increase the load rate of trains; while the TOM is devoted to the minimization of trains' delays. The two modules interact with each other so that the headway time is automatically adjusted when a platform is overcrowded, and the train traffic is immediately regulated according to the new headway time. As a result, the number of passengers on the platform and their total waiting time can be significantly reduced. Numerical results are provided to show the effectiveness of the proposed method in improving the operation performance while minimizing the passengers' discomfort., Comment: This work has been submitted to the 2021 IEEE International Intelligent Transportation Systems Conference (ITSC)

This thesis focused on the estimation of genetic parameters for novel functional traits in dairy and dual-propose cattle populations including heat stress responses, methane emissions, longitudinal body weights and respective growth curve parameters as well as electronically recorded behavior pattern. In this regard, quantitative-genetics and genomic modelling approaches were applied. Moreover, genetic architectures for body weight and behavior traits were inferred, i.e., via GWAS for direct-genetic as well as maternal-genetic effects, and ongoing pathway analyses to identify potential candidate genes and their functional annotations. Possible G×E were studied, considering simultaneously continuous time (e.g., aging) and environmental descriptors (e.g., THI). As a novelty, genetic (co)variance components were estimated via RRM on genetic and genomic herd scales, aiming on a deeper understanding of G×E. In the original research paper 1, we stochastically simulated longitudinal phenotypic cow records at five THI levels, as well as genotypes from the 2,000 cows, aiming on the evaluation of the effects of heritabilities, LD, maker density and the proportion of phenotypic records for extreme THI, on prediction accuracies in genomic RRM. As expected, prediction accuracies increased with increasing heritability, LD and SNP density. In order to improve accuracies of genomic predictions, it was imperative to consider a proportion of cows with phenotypic records in heat stress environments (i.e., THI larger than 75), when estimating genomic breeding values of remaining genotyped but not phenotyped cows. In all scenarios, prediction accuracies were larger when modelling the G matrix instead of the A matrix. The advantage of RRM considering genotyped cows and heat stress interactions with regard to prediction accuracies for test-day milk yield and SCS was confirmed in original research paper 2. Four RRM, i.e., RRM with or without genotyped cattle combined with or without G×E interaction terms, were evaluated using 5-fold cross-validations. The highest prediction accuracies for both traits were identified when applying genomic RRM, and modelling THI as an environmental descriptor. Such modelling superiority was stronger for milk yield than for SCS. For test-day milk yield, a quite large range in genetic correlation estimates for days in milk × THI combinations were identified, indicating GxE interactions. For test-day SCS, genetic correlations were more stable and throughout larger than 0.80. In conclusion, for traits showing sensitive responses to heat stress such as milk yield, it is imperative to include a heat stress indicator in genetic evaluation models, which also contributes to the improved identification of robust dairy cattle in harsh environments. Genetic parameters for test-day CH4, which were predicted through a deterministic approach as well as an approach combining deterministic equations and stochastic simulations, were estimated on a time scale via RRM in original research paper 3. The heritabilities for daily CH4 ranged from 0.15 to 0.37. Genetic correlations between CH4 from different prediction equations were larger than 0.90. Antagonistic genetic correlations in the range from 0.70 to 0.92 were estimated between CH4 and milk yield. Genetic correlations with other functional breeding goal traits were close to zero, but altered in the course of lactation. The simulated data basis for CH4 was used to determine the size of a cow calibration group for genomic selection. A calibration group including 2,581 cows with own measurements for CH4 (a heritability of 0.44 and an effective population size of 100) was competitive with conventional breeding strategies in terms of prediction accuracy. Genetic parameters and genetic architectures for body weight from different ages were studied in the original research papers 4 and 5, respectively. Body weight from birth to calving had moderate to high direct heritabilities. The maternal genetic component was detectable for body weights of calves in the period from birth to an age of 5 months, but later on, maternal genetic variances were close to zero. Body weights for calves and heifers were weakly correlated with production, female fertility and health traits in first parity cow. Genetic correlations between production and fertility traits with insemination body weight were stronger than with birth weight. Considering genomic data of genotyped cows, heritabilities as presented in the original research paper 5 verified the genetic parameter estimates (original research paper 4). Furthermore, in the original research paper 5, GWAS for birth weight, weaning weight and body weight at the first insemination date inferred significantly associated SNP and underlying potential candidate genes. With regard to GWAS for maternal-genetic effects, three SNP were significantly associated with birth weight according to the threshold based on 5% false discovery rate. No SNP significantly contributed to maternal-genetic effects on body weight recorded at weaning and at first insemination. Gene annotations identified 76 potential candidate genes for body weight, and these genes were involved in 12 biological processes. Hence, weight development is a very complex biological process, which is controlled by many genes with minor effects. Original research paper 6 focused on the estimation of genetic parameters and on prediction accuracies for growth curve parameters from three non-linear growth models, i.e., the Logistic, the Gompertz and the Richards functions, in combination with different kernel similarity matrices. Moderate heritabilities for growth curve parameters confirmed the pronounced genetic background for body weight with aging. Prediction accuracies for genomic growth curve parameters from different similarity matrices, including two genomic relationship matrices and three kernel matrices, combined with same non-linear functions, were very similar. In combination with all genomic relationship and kernel matrices, model superiority and largest prediction accuracies were observed when fitting the non-linear Richards function. Heritabilities for novel behavior traits, which were electronically recorded via ear tag sensors, ranged from 0.04 for rumination to 0.20 for feeding and high active. Differences in heritabilities and genetic variances indicate a diverse genetic background for different behavior traits. The underlying genetic mechanisms were unraveled through multi-breed GWAS in original research paper 7. According to a very relaxed threshold based on 20% false discovery rate, only five SNP were significantly associated with rumination, one SNP with feeding and one SNP with “not active”. The reason for the quite small number of significantly associated SNP with natural cattle behavior might be short-range LD when pooling breeds or limited conserved mutations across breeds. Mendelian randomization based on genomic variants (i.e., the instrumental variables) was used to infer causal inference between an exposure and an outcome. For example, the regression coefficients of rumination and feeding on milk yield were 0.10 kg/% and 0.12 kg/%, respectively, indicating their positive influences on dual-purpose cow productivity. Genomically, an improved welfare behavior of grazing cattle, i.e., a higher score for welfare indices, was significantly associated with increased fat and protein percentages. The original research paper 8 depicted possible G×E for production traits and SCS along phenotypic, quantitative-genetic and genomic herd descriptors. Hence, we provided the proof that genetic covariances and correlations between same traits from different herds strongly depend on genetic and genomic herd characteristics, such as inbreeding coefficients or LD within specific chromosomal segments. Apart from the herd variable “allele frequency for the SNP ARS-BFGL-NGS-4939 within the DGAT1 gene”, genetic correlations between milk yield at minimal and maximal levels for the other descriptors were always lower than 0.6, indicating environmental sensitivity. Especially for low heritability SCS, low genetic correlations were estimated when considering extreme herd classes according to LD of a genomic region on chromosome 6 at herd level, herd size, intra-herd percentage of non-EU sires, and the herd average for non-return rate. Alterations of estimated breeding values of sires in dependency of phenotypic, genetic and genomic herd structures suggest utilization of specific sires for specific herds, indicating further possibilities to optimize mating programs. Original research paper 9 addressed the importance of genotyped cows from a commercial herd perspective, including economic aspects and phenotype predictions. For different herd replacement strategies and a herd breeding goal aiming on antagonistically related production and functionality, genetic gain was maximized when focusing on large-scale female cattle genotyping. Especially selection response on the cow-dam pathway increased, through improved replacement and mating designs. From a literature review perspective, the original research paper 9 discussed further opportunities of cow training sets and commercial cow genotyping. Several studies and theoretical derivations highlighted the importance to including genotyped female cattle in training sets, because cow training sets avoid biased genomic predictions due to intensively pre-selected sires. Additionally, long-term genetic gain in novel functional traits is only possible when implementing the cow training sets. Detection of non-additive genetic effects as well as the control of inbreeding and genetic relationships (to avoid lethal defects) were further arguments to genotype cows in commercial herd. In conclusion, mainly based on studies using comprehensive datasets for genotyped cows recorded for novel traits, the habilitation thesis presented results for broad genetic mechanisms and identified potential candidate genes for various functional traits. Additionally, G×E were detected along novel continuous “environmental” gradients for both production and functional traits. These findings are important for future improvements of dairy cattle breeding programs, e.g., when expanding breeding goals with further functional trait categories (e.g., behavior traits), and simultaneously considering environmental sensitivity (e.g., heat stress response).

Greenhouse gas emissions from livestock farming and in particular enteric methane (CH4) from ruminants are criticized for being one of the main contributors to climate change. Different breeding, feeding and management strategies are tested to decrease these emissions, but a status quo analysis is also relevant to implement such measures. The present study aimed to analyze the concentration of CH4 in air exhaled by dairy cows along a rural-urban gradient of Bangalore, India. Urban, mixed and rural areas were defined based on a survey stratification index (SSI) comprising build-up density and distance to the city center. Using a laser methane detector (LMD), CH4 concentration was determined in 2-min spot measurements of exhaled air of 448 cows at three equally spaced visits between June 2017 and April 2018. Mean, maximum and CH4 concentration per duration of the overall measurement, eructation and respiration bouts were calculated. For the overall mean and respiration bouts, CH4 concentration was higher in cows from urban areas, which had also higher milk yield than cows from mixed and rural areas. Although no differences were found in terms of the intake level of fibrous diet components, the type of measurement location (indoor, half-outdoor or outdoor) and pasture access had an impact on CH4 concentration. To our knowledge, this is the first study using the LMD on-farm and in an urbanizing environment. The LMD measurements show variations in enteric CH4 emissions along the rural-urban gradient of Bangalore that reflect differences in dairy husbandry systems governed by the social-ecological context.

Tumor heterogeneity plays a key role in cancer relapse and metastasis, however, the distinct cellular behaviors and kinetics of interactions among different cancer cell subclones and the tumor microenvironment are poorly understood. By profiling an isogenic model that resembles spontaneous human ovarian cancer metastasis with an highly metastatic (HM) and non-metastatic (NM) tumor cell pair, one finds an upregulation of Wnt/β-catenin signaling uniquely in HM. Using humanized immunocompetent mice, one shows for the first time that activated β-catenin acts nonautonomously to modulate the immune microenvironment by enhancing infiltrating tumor-associated macrophages (TAM) at the metastatic site. Single-cell time-lapse microscopy further reveals that upon contact with macrophages, a significant subset of HM, but not NM, becomes polyploid, a phenotype pivotal for tumor aggressiveness and therapy resistance. Moreover, HM, but not NM, polarizes macrophages to a TAM phenotype. Mechanistically, β-catenin upregulates cancer cell surface metadherin, which communicates through CEACAM1 expressed on macrophages to produce CCL3. Tumor xenografts in humanized mice and clinical patient samples both corroborate the relevance of enhanced metastasis, TAM activation, and polyploidy in vivo. The results thus suggest that targeting the β-catenin-metadherin/CEACAM1-CCL3 positive feedback cascade holds great therapeutic potential to disrupt polyploidization of the cancer subclones that drive metastasis.

The aim of the present study was to infer phenotypic trait expressions via mixed modeling considering both social and ecological continuous descriptors simultaneously. In this regard, we selected a challenging heterogeneous social-ecological environment, with focus on the rising megacity Bangalore, located in southern India. Dairy traits from 517 dairy cattle were recorded in 121 herds, equally distributed along a southern and a northern rural&ndash, urban gradient of Bangalore, distinguishing between urban, mixed, and rural areas. Repeated records from three visits per herd included production traits (daily milk yield in liter: MY), energy efficiency indicators (body condition score: BCS), cow wellbeing indicators (udder hygiene score: UddHS, upper leg hygiene score: ULHS, hock assessment score: HAS, rectal temperature in &deg, C: RT), and health traits (locomotion score: LS, subclinical mastitis: SubMast). Associations between a continuous rural&ndash, urban gradient and phenotypic trait expressions were analyzed via mixed modeling, additionally considering &ldquo, classic&rdquo, environmental explanatory variables such as climatic conditions. MY and BCS were higher in urban than in rural areas, associated with reduced SubMast and improved hygiene scores for UddHS and ULHS. Scores for wellbeing indicators HAS and LS were unfavorable for cows in urban areas, indicating poor leg health conditions in that area. In rural areas, least-squares means for RT were quite large, probably due to the scarcity of shading and heat insulation of the barns. To the best of our knowledge, this is the first study disentangling phenotypic trait expressions in the context of social-ecological heterogeneity, contributing to a deeper understanding of physiological mechanisms underlying genotype by environment interactions.

The feasibility of train operation plans is an important issue in the field of railway transportation. The train operation plan provides departure, arrival and passing time of the train at each station. This paper not only studies the feasibility of train operation plans, but also considers dispatching operations in stations. Based on a given track layout including stations and block sections, its Petri net model is constructed to verify the feasibility of block section operations and station dispatch. According to the time constraints of the train operation, time factors are assigned to corresponding transitions in the Petri net model. We have further developed a feasibility verification algorithm. Petri net simulation tool TINA is used to verify the feasibility of the proposed train operation plan. We have shown that the proposed feasibility verification algorithm can identify the faults and provide amendments if a train operation plan is not feasible.

Train punctuality and safe operation are two of the most basic requirements for rail transport. As train speeds and operating densities continue to increase, trains cannot operate in accordance with operational plans sometimes. Feasibility verification of train operation plans is particularly important. In this paper, Petri nets are used as a formalization tool. The basic Petri net models of the trains in the different situations: overtaking, following and station avoidance are established. Based on the idea of modularly modeling and the evolution law of Petri nets, the algorithm of constructing the Petri net model for the potential operation plan is proposed. Then according to the time constraints of the train operation, the time factors are assigned to the corresponding transitions in the Petri net model. Finally, the time Petri net simulation software TINA is used to calculate the reachability graph of the Petri net model and to determine whether the given train operations scheduling meets the station requirements.

Different strategies were taken to make virotherapy more effective at killing cancer cells. Among them, oncolytic virus which arms the therapeutic gene to enhance antitumor activity is a prevalent approach. In this study, a newly developed oncolytic vaccinia virus (OVV) that expresses Beclin-1 (OVV-BECN1) was tested for its in vitro and in vivo oncolytic activity in blood cancer. Results showed that the OVV exhibited higher infectivity for leukemia cells. OVV-BECN1 induced significant apoptosis-independent cell death either in wild-type leukemia and multiple myeloma (MM) cell lines or caspase-3 shRNA leukemia cell lines, and had a superior antitumor activity compared to the parent OVV. Autophagic cell death induced by OVV-BECN1 was demonstrated in vitro and in vivo experiments. Finally, upregulation of SIRT-1, a member of class III histone deacetylases, by OVV-BECN1 resulted in the deacetylation of LC3 and its distribution from the nucleus toward the cytoplasm, which might contribute to induction of autophagy. Overall, our data showed a favorable therapeutic effect of the oncolytic vaccinia virus on blood cancers through oncolytic and autophagic mechanisms, and may therefore constitute a promising and effective therapeutic strategy for treating human leukemia and MM. However, further studies are warranted for its reliable clinical translation.

High plasma lactate is emerging as a critical regulator in development and progression of many human malignancies. Small RNAs derived from cleavage of mature tRNAs have been implicated in many cellular stresses, but the detailed mechanisms that respond to lactic acid (LA; acidic lactate) are not well defined. Here, using an Epstein-Barr virus (EBV)-immortalized B lymphoblastic cell line (LCL) as a model, we report that LA induces cleavage of mature tRNA at the anticodon loop, particularly production of three 5′-tRNA halves (5′-HisGUG, 5′-ValAAC, and 5′-GlyGCC), along with increased expression of RNA polymerase III and angiogenin (ANG). Of these, only the 5′-HisGUG half binds to the chromatin regulator argonaute-2 (AGO2) instead of the AGO1 protein for stability. Notably, the levels of ANG and 5′-HisGUG half expression in peripheral blood mononuclear cells from B cell lymphoma patients are tightly correlated with lactate dehydrogenase (LDH; a lactate indicator) in plasma. Silencing production of the 5′-HisGUG half by small interfering RNA or inhibition of ANG significantly reduces colony formation and growth of LA-induced tumor cells in vitro and in vivo using a murine xenograft model. Overall, our findings identify a novel molecular therapeutic target for the diagnosis and treatment of B cell lymphoma.

One of the most crucial components of regenerative medicine is the controlled differentiation of embryonic or adult stem cells into the desired cell lineage. Although most of the reported protocols of stem cell differentiation involve the use of soluble growth factors, it is increasingly evident that stem cells also undergo differentiation when cultured in the appropriate microenvironment. When cultured in decellularized tissues, for instance, stem cells can recapitulate the morphogenesis and functional specialization of differentiated cell types with speed and efficiency that often surpass the traditional growth factor-driven protocols. This suggests that the tissue microenvironment (TME) provides stem cells with a holistic "instructive niche" that harbors signals for cellular reprogramming. The translation of this into medical applications requires the decoding of these signals, but this has been hampered by the complexity of TME. This problem is often addressed by a reductionist approach, in which cells are exposed to substrates decorated with simple, empirically designed geometries, textures, and chemical compositions ("bottom-up" approach). Although these studies are invaluable in revealing the basic principles of mechanotransduction mechanisms, their physiological relevance is often uncertain. This review examines the recent progress of an alternative, "top-down" approach, in which the TME is treated as a holistic biological entity. This approach is made possible by recent advances in systems biology and fabrication technologies that enable the isolation, characterization, and reconstitution of TME. It is hoped that these new techniques will elucidate the nature of niche signals so that they can be extracted, replicated, and controlled. This review summarizes these emerging techniques and how the data they generated are changing our view on TME. Impact statement This review summarizes the current state of art of the understanding of instructive niche in the field of tissue microenvironment. Not only did we survey the use of different biochemical preparations as stimuli of stem cell differentiation and summarize the recent effort in dissecting the biochemical composition of these preparations, through the application of extracellular matrix (ECM) arrays and proteomics, but we also introduce the use of open-source, high-content immunohistochemistry projects in contributing to the understanding of tissue-specific composition of ECM. We believe this review would be highly useful for our peer researching in the same field. "Mr. Tulkinghorn is always the same… so oddly out of place and yet so perfectly at home." -Charles Dickens, Bleak House.

Mortality of glioblastoma multiforme (GBM) has not improved over the last two decades despite medical breakthroughs in the treatment of other types of cancers. Nanoparticles hold tremendous promise to overcome the pharmacokinetic challenges and off-target adverse effects. However, an inhibitory effect of nanoparticles by themselves on metastasis has not been explored. In this study, we developed transferrin-conjugated porous silicon nanoparticles (Tf@pSiNP) and studied their effect on inhibiting GBM migration by means of a microfluidic-based migration chip. This platform, designed to mimic the tight extracellular migration tracts in brain parenchyma, allowed high-content time-resolved imaging of cell migration. Tf@pSiNP were colloidally stable, biocompatible, and their uptake into GBM cells was enhanced by receptor-mediated internalisation. The migration of Tf@pSiNP-exposed cells across the confined microchannels was suppressed, but unconfined migration was unaffected. The pSiNP-induced destabilisation of focal adhesions at the leading front may partially explain the migration inhibition. More corroborating evidence suggests that pSiNP uptake reduced the plasticity of GBM cells in reducing cell volume, an effect that proved crucial in facilitating migration across the tight confined tracts. We believe that the inhibitory effect of Tf@pSiNP on cell migration, together with the drug-delivery capability of pSiNP, could potentially offer a disruptive strategy to treat GBM.

This paper summarizes the origin of the Mass Maker Space and the development of the Mass Maker Space in colleges and universities and discuss the necessity of co-building Mass Maker Space in colleges and universities from many aspects, such as the local government support, fund and financial institution support, cooperation with professional Mass Maker Space companies, cooperation with enterprises, cooperation with scientific research institutions, etc. This paper then introduces the specific cases of the cooperation of the Mass Maker Space in colleges and universities, including South China University of Technology, Guangdong University of Technology, South China Agricultural University, Shenzhen University, Guangzhou University of Science and Technology, Guangdong College of Business and Technology, and so on. Last but not the least, this paper analyzes the existing problems and general countermeasures of Mass Maker Space in colleges and universities, and proposes to improve the whole process of the innovation service "Mass Maker Space + Incubator + Accelerator".

Additional file 1: Figure S1. Scatterplots for the first four linear discriminant functions (LDF) included as covariates in GWAS model for population stratification in the four Beninese indigenous cattle breeds. The coloring represents the original breed assignment of samples.