An AI-Ready Multiplex Staining Dataset for Reproducible and Accurate Characterization of Tumor Immune Microenvironment.

We introduce a new AI-ready computational pathology dataset containing restained and co-registered digitized images from eight head-and-neck squamous cell carcinoma patients. Specifically, the same tumor sections were stained with the expensive multiplex immunofluorescence (mIF) assay first and then restained with cheaper multiplex immunohistochemistry (mIHC). This is a first public dataset that demonstrates the equivalence of these two staining methods which in turn allows several use cases; due to the equivalence, our cheaper mIHC staining protocol can offset the need for expensive mIF staining/scanning which requires highly-skilled lab technicians. As opposed to subjective and error-prone immune cell annotations from individual pathologists (disagreement > 50%) to drive SOTA deep learning approaches, this dataset provides objective immune and tumor cell annotations via mIF/mIHC restaining for more reproducible and accurate characterization of tumor immune microenvironment (e.g. for immunotherapy). We demonstrate the effectiveness of this dataset in three use cases: (1) IHC quantification of CD3/CD8 tumor-infiltrating lymphocytes via style transfer, (2) virtual translation of cheap mIHC stains to more expensive mIF stains, and (3) virtual tumor/immune cellular phenotyping on standard hematoxylin images. The dataset is available at https://github.com/nadeemlab/DeepLIIF.

Neutral and Cationic Molybdenum Imido Alkylidene Cyclic Alkyl Amino Carbene (CAAC) Complexes for Olefin Metathesis.

The first neutral and cationic Mo imido alkylidene cyclic alkyl amino carbene (CAAC) complexes of the general formulae [Mo(N-Ar)(CHCMe2 Ph)(X)2 (CAAC)] and [Mo(N-Ar)(CHCMe2 Ph)(X)(CAAC)][B(ArF )4 ] (X=Br, Cl, OTf, OC6 F5 ; CAAC=1-(2,6-iPr2 -C6 H3 )-3,3,5,5-tetramethyltetrahydropyrrol-2-ylidene) have been synthesized from molybdenum imido bishalide alkylidene DME precursors. Different combinations of the imido and "X" ligands have been employed to understand synthetic peculiarities. Selected complexes have been characterized by single-crystal X-ray analysis. Due to the pronounced σ-donor/π-acceptor characteristics of CAACs, the corresponding neutral and cationic molybdenum imido alkylidene CAAC complexes do not require the presence of stabilizing donor ligands such as nitriles. Calculations on the PBE0-D3BJ/def2-TZVP level for PBE0-D3BJ/def2-SVP optimized geometries revealed partial charges at molybdenum similar to the corresponding molybdenum imido alkylidene N-heterocyclic carbene (NHC) complexes with a slightly higher polarization of the molybdenum alkylidene bond in the CAAC complexes. All cationic complexes have been tested in olefin metathesis reactions and showed improved activity compared to the analogous NHC complexes for hydrocarbon-based substrates, allowing for turnover numbers (TONs) up to 9500 even at room temperature. Some Mo imido alkylidene CAAC complexes are tolerant towards functional groups like thioethers and sulfonamides.

An AI-Ready Multiplex Staining Dataset for Reproducible and Accurate Characterization of Tumor Immune Microenvironment.

We introduce a new AI-ready computational pathology dataset containing restained and co-registered digitized images from eight head-and-neck squamous cell carcinoma patients. Specifically, the same tumor sections were stained with the expensive multiplex immunofluorescence (mIF) assay first and then restained with cheaper multiplex immunohistochemistry (mIHC). This is a first public dataset that demonstrates the equivalence of these two staining methods which in turn allows several use cases; due to the equivalence, our cheaper mIHC staining protocol can offset the need for expensive mIF staining/scanning which requires highly-skilled lab technicians. As opposed to subjective and error-prone immune cell annotations from individual pathologists (disagreement > 50%) to drive SOTA deep learning approaches, this dataset provides objective immune and tumor cell annotations via mIF/mIHC restaining for more reproducible and accurate characterization of tumor immune microenvironment (e.g. for immunotherapy). We demonstrate the effectiveness of this dataset in three use cases: (1) IHC quantification of CD3/CD8 tumor-infiltrating lymphocytes via style transfer, (2) virtual translation of cheap mIHC stains to more expensive mIF stains, and (3) virtual tumor/immune cellular phenotyping on standard hematoxylin images. The dataset is available at \url{https://github.com/nadeemlab/DeepLIIF}.

Cationic molybdenum oxo alkylidenes stabilized by N-heterocyclic carbenes: from molecular systems to efficient supported metathesis catalysts.

Cationic d0 group 6 olefin metathesis catalysts have been recently shown to display in most instances superior activity in comparison to their neutral congeners. Furthermore, their catalytic performance is greatly improved upon immobilization on silica. In this context, we have developed the new family of molecular cationic molybdenum oxo alkylidene complexes stabilized by N-heterocyclic carbenes of the general formula [Mo(O)(CHCMe3)(IMes)(OR)[X-]] (IMes = 1,3-dimesitylimidazol-2-ylidene; R = 1,3-dimesityl-C6H3, C6F5; X- = B(3,5-(CF3)2C6H3)4 -, B(ArF)4, tetrakis(perfluoro-t-butoxy)aluminate (PFTA)). Immobilization of [Mo(O)(CHCMe3)(IMes)(O-1,3-dimesityl-C6H3)+B(ArF)4 -] on silica via surface organometallic chemistry yields an active alkene metathesis catalyst that shows the highest productivity towards terminal olefins amongst all existing molybdenum oxo alkylidene catalysts.

The Impact of Different Ventilatory Strategies on Clinical Outcomes in Patients with COVID-19 Pneumonia.

Introduction: The aim was to investigate the impact of different ventilator strategies (non-invasive ventilation (NIV); invasive MV with tracheal tube (TT) and with tracheostomy (TS) on outcomes (mortality and intensive care unit (ICU) length of stay) in patients with COVID-19. We also assessed the impact of timing of percutaneous tracheostomy and other risk factors on mortality. Methods: The retrospective cohort included 868 patients with severe COVID-19. Demographics, MV parameters and duration, and ICU mortality were collected. Results: MV was provided in 530 (61.1%) patients, divided into three groups: NIV (n = 139), TT (n = 313), and TS (n = 78). Prevalence of tracheostomy was 14.7%, and ICU mortality was 90.4%, 60.2%, and 30.2% in TT, TS, and NIV groups, respectively (p < 0.001). Tracheostomy increased the chances of survival and being discharged from ICU (OR 6.3, p < 0.001) despite prolonging ICU stay compared to the TT group (22.2 days vs. 10.7 days, p < 0.001) without differences in survival rates between early and late tracheostomy. Patients who only received invasive MV had higher odds of survival compared to those receiving NIV in ICU prior to invasive MV (OR 2.7, p = 0.001). The odds of death increased with age (OR 1.032, p < 0.001), obesity (1.58, p = 0.041), chronic renal disease (1.57, p = 0.019), sepsis (2.8, p < 0.001), acute kidney injury (1.7, p = 0.049), multiple organ dysfunction (3.2, p < 0.001), and ARDS (3.3, p < 0.001). Conclusions: Percutaneous tracheostomy compared to MV via TT significantly increased survival and the rate of discharge from ICU, without differences between early or late tracheostomy.

Cationic Group VI Metal Imido Alkylidene N-Heterocyclic Carbene Nitrile Complexes: Bench-Stable, Functional-Group-Tolerant Olefin Metathesis Catalysts.

Despite their excellent selectivities and activities, Mo-and W-based catalysts for olefin metathesis have not gained the same widespread use as Ru-based systems, mainly due to their inherent air sensitivity. Herein, we describe the synthesis of air-stable cationic-at-metal molybdenum and tungsten imido alkylidene NHC nitrile complexes. They catalyze olefin metathesis reactions of substrates containing functional groups such as (thio-) esters, (thio-) ethers and alcohols without the need for prior activation, for example, by a Lewis acid. The presence of a nitrile ligand was found to be essential for their stability towards air, while no decrease in activity and productivity could be observed upon coordination of a nitrile. Variations of the imido and anionic ligand revealed that alkoxide complexes with electron-withdrawing imido ligands offer the highest reactivities and excellent stability compared to analogous triflate and halide complexes.

Molecular Determinants of Thyroid Nodules with Indeterminate Cytology and RAS Mutations.

Background:RAS gene family mutations are the most prevalent in thyroid nodules with indeterminate cytology and are present in a wide spectrum of histological diagnoses. We evaluated differentially expressed genes and signaling pathways across the histological/clinical spectrum of RAS-mutant nodules to determine key molecular determinants associated with a high risk of malignancy. Methods: Sixty-one thyroid nodules with RAS mutations were identified. Based on the histological diagnosis and biological behavior, the nodules were grouped into five categories indicating their degree of malignancy: non-neoplastic appearance, benign neoplasm, indeterminate malignant potential, low-risk cancer, or high-risk cancer. Gene expression profiles of these nodules were determined using the NanoString PanCancer Pathways and IO 360 Panels, and Angiopoietin-2 level was determined by immunohistochemical staining. Results: The analysis of differentially expressed genes using the five categories as supervising parameters unearthed a significant correlation between the degree of malignancy and genes involved in cell cycle and apoptosis (BAX, CCNE2, CDKN2A, CDKN2B, CHEK1, E2F1, GSK3B, NFKB1, and PRKAR2A), PI3K pathway (CCNE2, CSF3, GSKB3, NFKB1, PPP2R2C, and SGK2), and stromal factors (ANGPT2 and DLL4). The expression of Angiopoietin-2 by immunohistochemistry also showed the same trend of increasing expression from non-neoplastic appearance to high-risk cancer (p < 0.0001). Conclusions: The gene expression analysis of RAS-mutant thyroid nodules suggests increasing upregulation of key oncogenic pathways depending on their degree of malignancy and supports the concept of a stepwise progression. The utility of ANGPT2 expression as a potential diagnostic biomarker warrants further evaluation.

Reversible N-Heterocyclic Carbene-Induced α-H Abstraction in Tungsten(VI) Imido Dialkyl Dialkoxide Complexes.

The first reversible N-heterocyclic carbene (NHC) induced α-H abstraction in tungsten(VI) imido-dialkyl dialkoxide complexes is reported. Treatment of W(NAr)(CH2 Ph)2 (OtBu)2 (Ar=2,6-dichlorophenyl, 2,6-dimethylphenyl, 2,6-diisopropylphenyl) with different NHCs leads to the formation of complexes of the type W(NAr)(CHPh)(NHC)(CH2 Ph)(OtBu) in excellent isolated yields of up to 96 %. The highly unusual release of the tert-butoxide ligand as tBuOH in the course of the reaction was observed. The formed alkylidene complexes and tBuOH are in an equilibrium with the NHC and the dialkyl complexes. Reaction kinetics were monitored by 1 H NMR spectroscopy. A correlation between the steric and electronic properties of the NHC and the reaction rates was observed. Kinetics of a deuterium-labeled complex in comparison to its non-deuterated counterpart revealed the presence of a strong primary kinetic isotope effect (KIE) of 4.2, indicating that α-H abstraction is the rate-determining step (RDS) of the reaction.

Effects of Tobacco Smoking on the Tumor Immune Microenvironment in Head and Neck Squamous Cell Carcinoma.

PURPOSE: Patients with head and neck squamous cell carcinoma (HNSCC) who actively smoke during treatment have worse survival compared with never-smokers and former-smokers. We hypothesize the poor prognosis in tobacco smokers with HNSCC is, at least in part, due to ongoing suppression of immune response. We characterized the tumor immune microenvironment (TIM) of HNSCC in a retrospective cohort of 177 current, former, and never smokers. EXPERIMENTAL DESIGN: Tumor specimens were subjected to analysis of CD3, CD8, FOXP3, PD-1, PD-L1, and pancytokeratin by multiplex immunofluorescence, whole-exome sequencing, and RNA sequencing. Immune markers were measured in tumor core, tumor margin, and stroma. RESULTS: Our data indicate that current smokers have significantly lower numbers of CD8+ cytotoxic T cells and PD-L1+ cells in the TIM compared with never- and former-smokers. While tumor mutation burden and mutant allele tumor heterogeneity score do not associate with smoking status, gene-set enrichment analyses reveal significant suppression of IFNα and IFNγ response pathways in current smokers. Gene expression of canonical IFN response chemokines, CXCL9, CXCL10, and CXCL11, are lower in current smokers than in former smokers, suggesting a mechanism for the decreased immune cell migration to tumor sites. CONCLUSIONS: These results suggest active tobacco use in HNSCC has an immunosuppressive effect through inhibition of tumor infiltration of cytotoxic T cells, likely as a result of suppression of IFN response pathways. Our study highlights the importance of understanding the interaction between smoking and TIM in light of emerging immune modulators for cancer management.

Perturbation theory of a superconducting 0 - π impurity quantum phase transition.

A single-level quantum dot with Coulomb repulsion attached to two superconducting leads is studied via the perturbation expansion in the interaction strength. We use the Nambu formalism and the standard many-body diagrammatic representation of the impurity Green functions to formulate the Matsubara self-consistent perturbation expansion. We show that at zero temperature second order of the expansion in its spin-symmetric version yields a nearly perfect agreement with the numerically exact calculations for the position of the 0 - π phase boundary at which the Andreev bound states reach the Fermi energy as well as for the values of single-particle quantities in the 0-phase. We present results for phase diagrams, level occupation, induced local superconducting gap, Josephson current, and energy of the Andreev bound states with the precision surpassing any (semi)analytical approaches employed thus far.

Vertex corrections to the mean-field electrical conductivity in disordered electron systems.

The mean-field theory for noninteracting disordered electron systems is widely and successfully used to describe equilibrium properties of alloys over the whole range of disorder strengths. However, it fails to take into account the effects of quantum coherence and localizing backscattering effects when applied to transport phenomena. Vertex corrections due to multiple backscatterings may turn the electrical conductivity negative and make expansions around the mean field in strong disorder problematic. We show how to stabilize such an expansion with the inverse of the number of nearest neighbors on hypercubic lattices as a small parameter and how to include vertex corrections to the mean-field approximation in such a way that the conductivity remains non-negative in all disorder regimes.

Equilibrium state of the mean-field Potts glass.

We investigate the low-temperature equilibrium state of the p-state mean-field Potts glass. It is the presently believed that there is a temperature interval T(2) < T < T(c) within which the equilibrium state for p > p(*) approximately 2.82 is described by the cavity method corresponding to the first level of replica-symmetry breaking. We demonstrate that this locally stable solution is globally unstable and that true equilibrium in the region of instability of the replica-symmetric solution (T < T(c)), marked by the highest free energy, is a state displaying a continuous replica-symmetry breaking.

Women and women of color in leadership: complexity, identity, and intersectionality.

This article describes the challenges that women and women of color face in their quest to achieve and perform in leadership roles in work settings. We discuss the barriers that women encounter and specifically address the dimensions of gender and race and their impact on leadership. We identify the factors associated with gender evaluations of leaders and the stereotypes and other challenges faced by White women and women of color. We use ideas concerning identity and the intersection of multiple identities to understand the way in which gender mediates and shapes the experience of women in the workplace. We conclude with suggestions for research and theory development that may more fully capture the complex experience of women who serve as leaders.

Integrability of the diffusion pole in the diagrammatic description of noninteracting electrons in a random potential.

We discuss restrictions on the existence of the diffusion pole in the translationally invariant diagrammatic treatment of disordered electron systems. We analyze Bethe-Salpeter equations for the two-particle vertex in the electron-hole and the electron-electron scattering channels and derive for systems with electron-hole symmetry a nonlinear integral equation that the two-particle irreducible vertices from both channels must obey. We use this equation and a parquet decomposition of the full vertex to set restrictions on an admissible form of the two-particle singularity induced by probability conservation. We find that such a singularity in two-particle functions can exist only if it is integrable, that is, only in the metallic phase in dimensions d>2.

Effects of HIV-1 infection on lymphocyte phenotypes in blood versus lymph nodes.

Most immunopathogenesis studies of HIV-1 use peripheral blood. Most lymphocytes reside in lymphoid tissues, however, and the extent to which blood mirrors tissues is unclear. Here, we analyze lymphocytes in blood and lymph nodes of HIV-1-uninfected and -infected persons. Baseline comparison of node and blood lymphocytes in seronegative persons demonstrates a lower ratio of CD8+ versus CD4+ T lymphocytes, a lower number of effector cells (CD28-) within the CD8+ compartment, and greater activation (D-receptor [DR+]) within the CD4+ compartment. In infected versus uninfected persons, nodes exhibit elevated CD8+ T lymphocytes with an increased memory-effector phenotype (CD62L-/CD45RA-) and activation (CD38+ and DR+) but minimal differences in the CD4+ compartment. Changes attributable to HIV-1 infection are markedly greater in node lymphocytes than in blood. Comparisons of CD8+ T-lymphocyte parameters and viremia in infected persons reveal positive correlations of CD38+ expression on cells in blood and nodes and a negative correlation of terminal effector cells (CD62L-/CD45RA+) in the nodes to viremia. Multiple linear regression analysis indicates that CD38 expression on node (not blood) CD8+ T lymphocytes is the sole independent predictor for viremia. Thus, blood indirectly reflects processes in lymphoid tissues, and caution should be applied when interpreting immunopathogenesis studies of blood.

Dynamical correlations in multiorbital Hubbard models: fluctuation exchange approximations.

We study the two-band degenerate Hubbard model using the fluctuation exchange approximation (FLEX) and compare the results with quantum Monte Carlo (QMC) calculations. Both the self-consistent and the non-self-consistent versions of the FLEX scheme are investigated. We find that, unlike in the one-band case, in the multiband case, good agreement with the quantum Monte Carlo results is obtained within the electron-electron T-matrix approximation using the full renormalization of the one-particle propagators. The crossover to strong coupling and the formation of satellites is more clearly visible in the non-self-consistent scheme. Finally we discuss the behaviour of the FLEX for higher orbital degeneracy.

Persistent alterations in the T-cell repertoires of HIV-1-infected and at-risk uninfected men.

OBJECTIVE: We examined the association between immunogenic exposure and T-cell receptor (TCR) diversity to more clearly assess the impact of HIV-1 infection on the T-cell repertoire. METHODS: : To estimate the extent of T-cell clonality attributable to HIV-1 infection, we evaluated T-cell repertoires in low-risk and at-risk seronegative men and HIV-1 seropositive men by assessment of T-cell receptor beta-chain (TCR beta) complimentary determining region 3 (CDR3) lengths. RESULTS: The frequency of T-cell clonality in both HIV-1 infected and at-risk uninfected men was elevated in comparison to low-risk uninfected men. Among low-risk and at-risk seronegative, and HIV-1 seropositive men, clonal expansions were present in 3, 8, and 10% of CD4+ CDR3 lengths, and 18, 22, and 28% of CD8+ CDR3 lengths respectively. In addition, the longitudinal conservation of clonal expansions was observed in at-risk seronegative men. Based on comparisons to at-risk seronegative men, we estimate that at-risk seropositive men with chronic HIV-1 infection exhibit a 27% increase in the number of expanded CD8+ CDR3 lengths. CONCLUSION: These findings provide an approximation of the magnitude of the T-cell response in individuals undergoing chronic HIV-1 infection and demonstrate a significant association between the history of immunogenic challenge and the magnitude of clonality within the T-cell repertoire. In addition, these findings underscore the necessity of selecting controls with similar antigenic exposure histories when investigating T-cell dynamics in HIV-infected individuals.

Immunologic profile of highly exposed yet HIV type 1-seronegative men.

The host immune factors that determine susceptibility to HIV-1 infection are poorly understood. We compared multiple immunologic parameters in three groups of HIV-1-seronegative men: 14 highly exposed (HR10), 7 previously reported possibly to have sustained transient infection (PTI), and a control group of 14 low risk blood bank donors (BB). Virus-specific cellular immune assays were performed for CD4(+) T helper cell responses, CD8(+) cytotoxic T lymphocyte activity, CD8(+) cell chemokine release, and CD8(+) cell-derived antiviral soluble factor activity. General immune parameters evaluated included CCR5 genotype and phenotype, interferon alpha production by PBMCs, leukocyte subset analysis, and detailed T lymphocyte phenotyping. Comparisons revealed no detectable group-specific differences in measures of virus-specific immunity. However, the HR10 group differed from the BB group in several general immune parameters, having higher absolute monocyte counts, higher absolute CD8(+) T cell counts and percentages, lower naive and higher terminal effector CD8(+) cells, and lower levels of CD28(+)CD8(+) cells. These changes were not associated with seropositivity for other chronic viral infections. The PTI men appeared to have normal levels of monocytes and slightly elevated levels of CD8(+) T cells (also with increased effector and decreased naive cells). Although we cannot entirely exclude the contribution of other chronic viral infections, these findings suggest that long-lived systemic cellular antiviral immunity as detected by our assays is not a common mechanism for resistance to infection, and that resistance may be multifactorial. General immune parameters reflected by CD8(+) T cell levels and activation, and monocyte concentrations may affect the risk of infection with HIV-1, and/or serve as markers of exposure.

MaGiK method of T-Cell receptor repertoire analysis.

T-cell receptor diversity enables the cellular immune response to recognize a broad range of viral and other pathogenic agents. An increasingly common method of characterizing T-cell receptor diversity and usage in response to antigenic challenges involves the identification of clonal expansions by PCR amplification of the CDR3 region of distinct TCRVbeta families. Though clonal expansions often appear evident upon visual inspection of the results, a systematic method is needed for the valid enumeration of these expansions. Here, we describe a novel analysis method, termed the MaGiK method, for systematically identifying and enumerating clonal T-cell expansions and for applying the results to investigations of the T-cell receptor repertoire.