Evaluating the efficacy of vermicomposted products in rain-fed wetland rice and predicting potential hazards from metal-contaminated tannery sludge using novel machine learning tactic.

The study assessed the ecotoxicity and bioavailability of potential metals (PMs) from tannery waste sludge, alongside addressing the environmental concerns of overuse of chemical fertilizers, by comparing the impacts of organic vermicomposted tannery waste, chemical fertilizers, and sole application of tannery waste on soil and rice (Oryza sativa L.) plants. The results revealed that T3, which received high-quality vermicomposted tannery waste as an amendment, exhibited superior enzymatic characteristics compared to tannery sludge amended (TWS) treatments (T8, T9). After harvesting, vermicomposted tannery waste treatment (T3) showed a more significant decrease in PMs bioavailability. Accumulation of PMs in rice was minimal across all treatments except T8 and T9, where toxic tannery waste was present, resulting in a high-risk classification (class 5 < 0.01) according to the SAMOE risk assessment. Results from Fuzzy-TOPSIS, ANN, and Sobol sensitivity analyses (SSA) further indicated that elevated concentrations of PMs (Ni, Pb, Cr, Cu) adversely impacted soil-plant health synergy, with T3 showing a minimal risk in comparison to T8 and T9. According to SSA, microbial biomass carbon and acid phosphatase activity were the most sensitive factors affected by PMs concentrations in TWS. The results from the ANN assay revealed that the primary contributing factor of toxicity on the TWS was the exchangeable fraction of Cr. Correlation statistics underscored the significant detrimental effect of PMs' bioavailability on microbial and enzymatic parameters. Overall, the findings suggest that vermicomposting of tannery sludge waste shows potential as a viable organic amendment option in the near future.

Efficient and chemoselective imine synthesis catalyzed by a well-defined PN3-manganese(II) pincer system.

The highly efficient reductive amination of aldehydes with ammonia (NH3) and hydrogen (H2) to form secondary imines is described, as well as the dehydrogenative homocoupling of benzyl amines. Using an air-stable, well-defined PN3-manganese(II) pincer complex as a catalyst precursor, various aldehydes are easily converted directly into secondary imines using NH3 as a nitrogen source under H2 in a one-pot reaction. Importantly, the same catalyst facilitates the dehydrogenative homocoupling of various benzylamines, exclusively forming imine products. These reactions are conducted under very mild conditions, without the addition of any additives, yielding excellent selectivities and high yields of secondary imines in a green manner by minimizing wastes.

Phenotypic heterogeneity drives differential disease outcome in a mouse model of triple negative breast cancer.

The triple negative breast cancer (TNBC) subtype is one of the most aggressive forms of breast cancer that has poor clinical outcome and is an unmet clinical challenge. Accumulating evidence suggests that intratumoral heterogeneity or the presence of phenotypically distinct cell populations within a tumor play a crucial role in chemoresistance, tumor progression and metastasis. An increased understanding of the molecular regulators of intratumoral heterogeneity is crucial to the development of effective therapeutic strategies in TNBC. To this end, we used an unbiased approach to identify a molecular mediator of intratumoral heterogeneity in breast cancer by isolating two tumor cell populations (T1 and T2) from the 4T1 TNBC model. Phenotypic characterization revealed that the cells are different in terms of their morphology, proliferation and self-renewal ability in vitro as well as primary tumor formation and metastatic potential in vivo. Bioinformatic analysis followed by Kaplan Meier survival analysis in TNBC patients identified Metastasis associated colon cancer 1 (Macc1) as one of the top candidate genes mediating the aggressive phenotype in the T1 tumor cells. The role of Macc1 in regulating the proliferative phenotype was validated and taken forward in a therapeutic context with Lovastatin, a small molecule transcriptional inhibitor of Macc1 to target the T1 cell population. This study increases our understanding of the molecular underpinnings of intratumoral heterogeneity in breast cancer that is critical to improve the treatment of women currently living with the highly aggressive TNBC subtype.

Structural-and-dynamical similarity predicts compensatory brain areas driving the post-lesion functional recovery mechanism.

The focal lesion alters the excitation-inhibition (E-I) balance and healthy functional connectivity patterns, which may recover over time. One possible mechanism for the brain to counter the insult is global reshaping functional connectivity alterations. However, the operational principles by which this can be achieved remain unknown. We propose a novel equivalence principle based on structural and dynamic similarity analysis to predict whether specific compensatory areas initiate lost E-I regulation after lesion. We hypothesize that similar structural areas (SSAs) and dynamically similar areas (DSAs) corresponding to a lesioned site are the crucial dynamical units to restore lost homeostatic balance within the surviving cortical brain regions. SSAs and DSAs are independent measures, one based on structural similarity properties measured by Jaccard Index and the other based on post-lesion recovery time. We unravel the relationship between SSA and DSA by simulating a whole brain mean field model deployed on top of a virtually lesioned structural connectome from human neuroimaging data to characterize global brain dynamics and functional connectivity at the level of individual subjects. Our results suggest that wiring proximity and similarity are the 2 major guiding principles of compensation-related utilization of hemisphere in the post-lesion functional connectivity re-organization process.

Strategic Synthesis of Heptacoordinated FeIII Bifunctional Complexes for Efficient Water Electrolysis.

In this research, highly efficient heterogeneous bifunctional (BF) electrocatalysts (ECs) have been strategically designed by Fe coordination (CR ) complexes, [Fe2 L2 (H2 O)2 Cl2 ] (C1) and [Fe2 L2 (H2 O)2 (SO4 )].2(CH4 O) (C2) where the high seven CR number synergistically modifies the electronic environment of the Fe centre for facilitation of H2 O electrolysis. The electronic status of Fe and its adjacent atomic sites have been further modified by the replacement of -Cl- in C1 by -SO4 2- in C2. Interestingly, compared to C1, the O-S-O bridged C2 reveals superior BF activity with extremely low overpotential (η) at 10 mA cm-2 (140 mVOER , 62 mVHER ) and small Tafel slope (120.9 mV dec-1 OER , 45.8 mV dec-1 HER ). Additionally, C2 also facilitates a high-performance alkaline H2 O electrolyzer with cell voltage of 1.54 V at 10 mA cm-2 and exhibits remarkable long-term stability. Thus, exploration of the intrinsic properties of metal-organic framework (MOF)-based ECs opens up a new approach to the rational design of a wide range of molecular catalysts.

Allenyl Carbonate as a Butadiene Surrogate in Cobalt-Catalyzed Crotylation of Aldehydes.

Allenyl carbonate was used as a 1,3-butadiene surrogate to develop a photocatalytically sustainable protocol for cobalt-catalyzed crotylation of aldehydes. The developed method tolerated a wide range of aromatic and aliphatic aldehydes with retention of functional groups under mild conditions and produced good-to-excellent yields of crotylated secondary alcohols. Based on preliminary mechanistic studies and literature precedents, a plausible mechanism is proposed.

P4HA2: A link between tumor-intrinsic hypoxia, partial EMT and collective migration.

Epithelial-to-mesenchymal transition (EMT), a well-established phenomenon studied across pan-cancer types, has long been known to be a major player in driving tumor invasion and metastasis. Recent studies have highlighted the importance of partial EMT phenotypes in metastasis. Initially thought as a transitional state between epithelial and mesenchymal phenotypic states, partial EMT state is now widely recognized as a key driver of intra-tumoral heterogeneity and phenotypic plasticity, further accelerating tumor metastasis and therapeutic resistance. However, how tumor microenvironment regulates partial EMT phenotypes remains unclear. We have developed unique size-controlled three-dimensional microtumor models that recapitulate tumor-intrinsic hypoxia and the emergence of collectively migrating cells. In this study, we further interrogate these microtumor models to understand how tumor-intrinsic hypoxia regulates partial EMT and collective migration in hypoxic large microtumors fabricated from T47D breast cancer cells. We compared global gene expression profiles of hypoxic, migratory microtumors to that of non-hypoxic, non-migratory microtumors at early and late time-points. Using our microtumor models, we identified unique gene signatures for tumor-intrinsic hypoxia (early versus late), partial EMT and migration (pre-migratory versus migratory phenotype). Through differential gene expression analysis between the microtumor models with an overlap of hypoxia, partial EMT and migration signatures, we identified prolyl 4-hydroxylase subunit 2 (P4HA2), a hypoxia responsive gene, as a central regulator common to hypoxia, partial EMT and collective migration. Further, the inhibition of P4HA2 significantly blocked collective migration in hypoxic microtumors. Thus, using the integrated computational-experimental analysis, we identify the key role of P4HA2 in tumor-intrinsic hypoxia-driven partial EMT and collective migration.

Phenotypic heterogeneity driven by plasticity of the intermediate EMT state governs disease progression and metastasis in breast cancer.

The epithelial-to-mesenchymal transition (EMT) is frequently co-opted by cancer cells to enhance migratory and invasive cell traits. It is a key contributor to heterogeneity, chemoresistance, and metastasis in many carcinoma types, where the intermediate EMT state plays a critical tumor-initiating role. We isolate multiple distinct single-cell clones from the SUM149PT human breast cell line spanning the EMT spectrum having diverse migratory, tumor-initiating, and metastatic qualities, including three unique intermediates. Using a multiomics approach, we identify CBFß as a key regulator of metastatic ability in the intermediate state. To quantify epithelial-mesenchymal heterogeneity within tumors, we develop an advanced multiplexed immunostaining approach using SUM149-derived orthotopic tumors and find that the EMT state and epithelial-mesenchymal heterogeneity are predictive of overall survival in a cohort of stage III breast cancer. Our model reveals previously unidentified insights into the complex EMT spectrum and its regulatory networks, as well as the contributions of epithelial-mesenchymal plasticity (EMP) in tumor heterogeneity in breast cancer.

A Multistep Tumor Growth Model of High Grade Serous Ovarian Carcinoma Identifies Hypoxia Associated Signatures.

High-grade serous ovarian carcinoma (HGSC) is associated with late-stage disease presentation and poor prognosis, with limited understanding of early transformation events. Our study presents a comprehensive analysis of tumor progression and organ-specific metastatic dissemination to identify hypoxia-associated molecular, cellular, and histological alterations during HGSC tumor growth. H&E staining and subsequent histological assessment of tumor volume-based categories revealed recapitulation of numerous clinical features, including the prevalence of >0.0625≤0.5cm3 volume tumors and metastatic spread by orthotopic xenografts. The constant evolution of the tissue architecture concerning increased hyaluronic acid deposition, tumor vasculature, necrosis, altered proliferative potential, and gland forming ability of the tumor cells was identified. Flow cytometry and label chase-based molecular profiling across the tumor regenerative hierarchy identified the hypoxia-vasculogenic niche and the hybrid epithelial-mesenchymal tumor-cell state as determinants of self-renewal capabilities of progenitors and cancer stem cells (CSCs). A regulatory network and mathematical model based on tumor histology and molecular signatures predicted hypoxia-inducible factor 1-alpha (HIF1A) as a central node connecting epithelial-mesenchymal transition, metabolic and necrotic pathways in HGSC tumors. Thus, our findings provide a temporal resolution of hypoxia-associated events that sculpt HGSC tumor growth, and an in-depth understanding of it may aid in the early detection and treatment of HGSC.

Extended chemothromboprophylaxis use in colorectal cancer surgery: a literature review.

Venous thromboembolism (VTE) is a potentially fatal condition associated with chronic morbidity. Patients undergoing colorectal cancer surgery have an especially high rate of VTE postoperatively. This risk continues to be elevated for up to 3 months after discharge, hence arises the question of extended thromboprophylaxis (ETP). The objective of this literature review is to summarize the current literature on ETP post colorectal cancer surgery. The results of five randomized controlled trials (RCT), several meta-analysis and five major guidelines are outlined and examined. The literature overwhelmingly supports the use of ETP in colorectal cancer surgery. The key limitation of the evidence base is the use of objective tests to diagnose VTE which also detect asymptomatic events. However, this surrogate marker has been reliably shown to correlate with symptomatic VTE. In other high-risk populations such as orthopaedic patients, similar research has led to the use of routinely prescribed ETP. There is evidence now that the use of ETP is cost-effective in reducing morbidity and mortality from VTE in colorectal cancer patients. However, despite strong evidence on the benefits of ETP in colorectal cancer surgery, it is not yet a routine clinical practice. Future research is required to determine the optimal duration of chemothromboprophylaxis in different subgroups within colorectal cancer patients such as patients with rectal cancer only or those undergoing minimally invasive surgery.

Iron-Catalyzed α-Methylation of Ketones Using Methanol as the C1 Source under Photoirradiation.

A mild, environmentally benign approach for α-methylation of ketones utilizing methanol as the C1 source under visible light has been developed. The reaction conditions were favorable for a wide range of ketones with both aromatic and aliphatic backbones, allowing for good-to-excellent yields of the respective products. The tentative mechanism is postulated after preliminary mechanistic and kinetic experiments.

Emergence of hybrid states of stem-like cancer cells correlates with poor prognosis in oral cancer.

Cancer cell state transitions emerged as powerful mechanisms responsible for drug tolerance and overall poor prognosis; however, evidences were largely missing in oral cancer. Here, by multiplexing phenotypic markers of stem-like cancer cells (SLCCs); CD44, CD24 and aldehyde dehydrogenase (ALDH), we characterized diversity among multiple oral tumor tissues and cell lines. Two distinct patterns of spontaneous transitions with stochastic bidirectional interconversions on 'ALDH-axis', and unidirectional non-interconvertible transitions on 'CD24-axis' were observed. Interestingly, plastic 'ALDH-axis' was harnessed by cells to adapt to a Cisplatin tolerant state. Furthermore, phenotype-specific RNA sequencing suggested the possible maintenance of intermediate hybrid cell states maintaining stemness within the differentiating subpopulations. Importantly, survival analysis with subpopulation-specific gene sets strongly suggested that cell-state transitions may drive non-genetic heterogeneity, resulting in poor prognosis. Therefore, we have described the phenotypic-composition of heterogeneous subpopulations critical for global tumor behavior in oral cancer; which may provide prerequisite knowledge for treatment strategies.

CTCF Expression and Dynamic Motif Accessibility Modulates Epithelial-Mesenchymal Gene Expression.

Epithelial-mesenchymal transition (EMT) and its reversal, mesenchymal-epithelial transition (MET) drive tissue reorganization critical for early development. In carcinomas, processing through EMT, MET, or partial states promotes migration, invasion, dormancy, and metastatic colonization. As a reversible process, EMT is inherently regulated at epigenetic and epigenomic levels. To understand the epigenomic nature of reversible EMT and its partial states, we characterized chromatin accessibility dynamics, transcriptomic output, protein expression, and cellular phenotypes during stepwise reversible EMT. We find that the chromatin insulating protein machinery, including CTCF, is suppressed and re-expressed, coincident with broad alterations in chromatin accessibility, during EMT/MET, and is lower in triple-negative breast cancer cell lines with EMT features. Through an analysis of chromatin accessibility using ATAC-seq, we identify that early phases of EMT are characterized by enrichment for AP-1 family member binding motifs, but also by a diminished enrichment for CTCF binding motifs. Through a loss-of-function analysis, we demonstrate that the suppression of CTCF alters cellular plasticity, strengthening the epithelial phenotype via the upregulation of epithelial markers E-cadherin/CDH1 and downregulation of N-cadherin/CDH2. Conversely, the upregulation of CTCF leads to the upregulation of EMT gene expression and an increase in mesenchymal traits. These findings are indicative of a role of CTCF in regulating epithelial-mesenchymal plasticity and gene expression.

C-H bond functionalization by dual catalysis: merging of high-valent cobalt and photoredox catalysis.

The merger of transition metal catalysis and photocatalysis has emerged as a versatile platform that opened the gateway to diverse low-energy pathways for several synthetic transformations. However, amidst the first-row transition metals, directed C-H bond functionalization mediated by high-valent cobalt catalysis has advanced with rising momentum owing to its unique reactivity and the ability to participate in both one- and two-electron transfer reactions. However, the use of expensive, privileged Cp* ligands or use of stoichiometric silver(I) or manganese(III) is unavoidable. Despite significant advances in their respective fields, the combination of these two "green" approaches to further the vested interest of the scientific research community towards the development of ecofriendly and sustainable protocols is noticeably limited. Thus, the methodology based on high-cobalt-photoredox dual-catalytic strategy has high dormant potential and is worthy to explore. Herein, we highlight the recent advances in the high-valent cobalt-catalyzed sustainable catalytic approach by harnessing light energy for oxidative C-H bond functionalization. With this, we hope to inspire the development of unexplored cobalt-photoredox-catalyzed reactions with improved efficiency and selectivity.

Efficient and chemoselective hydrogenation of aldehydes catalyzed by well-defined PN3-pincer manganese(II) catalyst precursors: an application in furfural conversion.

Well-defined and air-stable PN3-pincer manganese(II) complexes were synthesized and used for the hydrogenation of aldehydes into alcohols under mild conditions using MeOH as a solvent. This protocol is applicable for a wide range of aldehydes containing various functional groups. Importantly, α,ß-unsaturated aldehydes, including ynals, are hydrogenated with the CC double bond/CC triple bond intact. Our methodology was demonstrated for the conversion of biomass derived feedstocks such as furfural and 5-formylfurfural to furfuryl alcohol and 5-(hydroxymethyl)furfuryl alcohol respectively.

Calcium signaling induces a partial EMT.

Epithelial plasticity, or epithelial-to-mesenchymal transition (EMT), is a well-recognized form of cellular plasticity, which endows tumor cells with invasive properties and alters their sensitivity to various agents, thus representing a major challenge to cancer therapy. It is increasingly accepted that carcinoma cells exist along a continuum of hybrid epithelial-mesenchymal (E-M) states and that cells exhibiting such partial EMT (P-EMT) states have greater metastatic competence than those characterized by either extreme (E or M). We described recently a P-EMT program operating in vivo by which carcinoma cells lose their epithelial state through post-translational programs. Here, we investigate the underlying mechanisms and report that prolonged calcium signaling induces a P-EMT characterized by the internalization of membrane-associated E-cadherin (ECAD) and other epithelial proteins as well as an increase in cellular migration and invasion. Signaling through Gαq-associated G-protein-coupled receptors (GPCRs) recapitulates these effects, which operate through the downstream activation of calmodulin-Camk2b signaling. These results implicate calcium signaling as a trigger for the acquisition of hybrid/partial epithelial-mesenchymal states in carcinoma cells.

Analysis of immune subtypes across the epithelial-mesenchymal plasticity spectrum.

Epithelial-mesenchymal plasticity plays a critical role in many solid tumor types as a mediator of metastatic dissemination and treatment resistance. In addition, there is also a growing appreciation that the epithelial/mesenchymal status of a tumor plays a role in immune evasion and immune suppression. A deeper understanding of the immunological features of different tumor types has been facilitated by the availability of large gene expression datasets and the development of methods to deconvolute bulk RNA-Seq data. These resources have generated powerful new ways of characterizing tumors, including classification of immune subtypes based on differential expression of immunological genes. In the present work, we combine scoring algorithms to quantify epithelial-mesenchymal plasticity with immune subtype analysis to understand the relationship between epithelial plasticity and immune subtype across cancers. We find heterogeneity of epithelial-mesenchymal transition (EMT) status both within and between cancer types, with greater heterogeneity in the expression of EMT-related factors than of MET-related factors. We also find that specific immune subtypes have associated EMT scores and differential expression of immune checkpoint markers.

Identification of EMT signaling cross-talk and gene regulatory networks by single-cell RNA sequencing.

The epithelial-to-mesenchymal transition (EMT) plays a critical role during normal development and in cancer progression. EMT is induced by various signaling pathways, including TGF-ß, BMP, Wnt-ß-catenin, NOTCH, Shh, and receptor tyrosine kinases. In this study, we performed single-cell RNA sequencing on MCF10A cells undergoing EMT by TGF-ß1 stimulation. Our comprehensive analysis revealed that cells progress through EMT at different paces. Using pseudotime clustering reconstruction of gene-expression profiles during EMT, we found sequential and parallel activation of EMT signaling pathways. We also observed various transitional cellular states during EMT. We identified regulatory signaling nodes that drive EMT with the expression of important microRNAs and transcription factors. Using a random circuit perturbation methodology, we demonstrate that the NOTCH signaling pathway acts as a key driver of TGF-ß-induced EMT. Furthermore, we demonstrate that the gene signatures of pseudotime clusters corresponding to the intermediate hybrid EMT state are associated with poor patient outcome. Overall, this study provides insight into context-specific drivers of cancer progression and highlights the complexities of the EMT process.

A Theoretical Approach to Coupling the Epithelial-Mesenchymal Transition (EMT) to Extracellular Matrix (ECM) Stiffness via LOXL2.

The epithelial-mesenchymal transition (EMT) plays a critical role in cancer progression, being responsible in many cases for the onset of the metastatic cascade and being integral in the ability of cells to resist drug treatment. Most studies of EMT focus on its induction via chemical signals such as TGF-ß or Notch ligands, but it has become increasingly clear that biomechanical features of the microenvironment such as extracellular matrix (ECM) stiffness can be equally important. Here, we introduce a coupled feedback loop connecting stiffness to the EMT transcription factor ZEB1, which acts via increasing the secretion of LOXL2 that leads to increased cross-linking of collagen fibers in the ECM. This increased cross-linking can effectively increase ECM stiffness and increase ZEB1 levels, thus setting a positive feedback loop between ZEB1 and ECM stiffness. To investigate the impact of this non-cell-autonomous effect, we introduce a computational approach capable of connecting LOXL2 concentration to increased stiffness and thereby to higher ZEB1 levels. Our results indicate that this positive feedback loop, once activated, can effectively lock the cells in a mesenchymal state. The spatial-temporal heterogeneity of the LOXL2 concentration and thus the mechanical stiffness also has direct implications for migrating cells that attempt to escape the primary tumor.

Gene expression profiles of inflammatory breast cancer reveal high heterogeneity across the epithelial-hybrid-mesenchymal spectrum.

Inflammatory breast cancer (IBC) is a highly aggressive breast cancer that metastasizes largely via tumor emboli, and has a 5-year survival rate of less than 30%. No unique genomic signature has yet been identified for IBC nor has any specific molecular therapeutic been developed to manage the disease. Thus, identifying gene expression signatures specific to IBC remains crucial. Here, we compare various gene lists that have been proposed as molecular footprints of IBC using different clinical samples as training and validation sets and using independent training algorithms, and determine their accuracy in identifying IBC samples in three independent datasets. We show that these gene lists have little to no mutual overlap, and have limited predictive accuracy in identifying IBC samples. Despite this inconsistency, single-sample gene set enrichment analysis (ssGSEA) of IBC samples correlate with their position on the epithelial-hybrid-mesenchymal spectrum. This positioning, together with ssGSEA scores, improves the accuracy of IBC identification across the three independent datasets. Finally, we observed that IBC samples robustly displayed a higher coefficient of variation in terms of EMT scores, as compared to non-IBC samples. Pending verification that this patient-to-patient variability extends to intratumor heterogeneity within a single patient, these results suggest that higher heterogeneity along the epithelial-hybrid-mesenchymal spectrum can be regarded to be a hallmark of IBC and a possibly useful biomarker.