Thymic Adenocarcinoma With Metastasis to the Left Orbit: A Case Report.

We present the case of a 57-year-old female who initially presented with a chief complaint of left-sided orbital headaches and associated left eyelid swelling. Initial imaging work-up with CT head/orbit revealed soft tissue enhancement of the left orbital roof, concerning for neoplastic process (primary lymphoma versus extracranial primary tumor versus metastatic tumor). Further imaging studies with CT chest/abdomen/pelvis revealed an anterior mediastinal mass, concerning for possible thymoma versus lymphoma. The patient underwent further consultation with the Hematology/Oncology and Ophthalmology Departments, which recommended definitive biopsies from both sites, which showed matching histologic findings of moderately differentiated enteric-type adenocarcinoma with positive staining for CDX2, an intestinal marker. Thymic carcinomas are rare cancers that account for approximately 0.06% of all malignancies and require a high degree of clinical suspicion. Extrathoracic metastases from thymic carcinomas, especially to the orbit, is a rare occurrence and the exact incidence of this phenomenon is unknown. This case represents the diagnostic challenges associated with a rare cancer type and underscores the importance of a multidisciplinary approach to patient care.

SARS-COV-2 Omicron variants conformationally escape a rare quaternary antibody binding mode.

The ongoing evolution of SARS-CoV-2 into more easily transmissible and infectious variants has provided unprecedented insight into mutations enabling immune escape. Understanding how these mutations affect the dynamics of antibody-antigen interactions is crucial to the development of broadly protective antibodies and vaccines. Here we report the characterization of a potent neutralizing antibody (N3-1) identified from a COVID-19 patient during the first disease wave. Cryogenic electron microscopy revealed a quaternary binding mode that enables direct interactions with all three receptor-binding domains of the spike protein trimer, resulting in extraordinary avidity and potent neutralization of all major variants of concern until the emergence of Omicron. Structure-based rational design of N3-1 mutants improved binding to all Omicron variants but only partially restored neutralization of the conformationally distinct Omicron BA.1. This study provides new insights into immune evasion through changes in spike protein dynamics and highlights considerations for future conformationally biased multivalent vaccine designs.

Lithium Promotes Acetylide Formation on MgO During Methane Coupling Under Non-Oxidative Conditions.

A prototypical material for the oxidative coupling of methane (OCM) is Li/MgO, for which Li is known to be essential as a dopant to obtain high C2 selectivities. Herein, Li/MgO is demonstrated to be an effective catalyst for non-oxidative coupling of methane (NOCM). Moreover, the presence of Li is shown to favor the formation of magnesium acetylide (MgC2 ), while pure MgO promotes coke formation as evidenced by solid-state 13 C NMR, thus indicating that Li promotes C-C bond formation. Metadynamic simulations of the carbon mobility in MgC2 and Li2 C2 at the density functional theory (DFT) level show that carbon easily diffuses as a C2 unit at 1000 °C. These insights suggest that the enhanced C2 selectivity for Li-doped MgO is related to the formation of Li and Mg acetylides.

Role and dynamics of transition metal carbides in methane coupling.

Transition metal carbides have numerous applications and are known to excel in terms of hardness, thermal stability and conductivity. In particular, the Pt-like behavior of Mo and W carbides has led to the popularization of metal carbides in catalysis, ranging from electrochemically-driven reactions to thermal methane coupling. Herein, we show the active participation of carbidic carbon in the formation of C2 products during methane coupling at high temperature that is associated with the dynamics of Mo and W carbides. A detailed mechanistic study reveals that the catalyst performance of these metal carbides can be traced back to its carbon diffusivity and exchange capability upon interaction with methane (gas phase carbon). A stable C2 selectivity over time on stream for Mo carbide (Mo2C) can be rationalized by fast carbon diffusion dynamics, while W carbide (WC) shows loss of selectivity due to slow diffusion leading to surface carbon depletion. This finding showcases that the bulk carbidic carbon of the catalyst plays a crucial role and that the metal carbide is not only responsible for methyl radical formation. Overall, this study evidences the presence of a carbon equivalent to the Mars-Van Krevelen type mechanism for non-oxidative coupling of methane.

Rapid characterization of spike variants via mammalian cell surface display.

The SARS-CoV-2 spike protein is a critical component of vaccines and a target for neutralizing monoclonal antibodies (nAbs). Spike is also undergoing immunogenic selection with variants that increase infectivity and partially escape convalescent plasma. Here, we describe Spike Display, a high-throughput platform to rapidly characterize glycosylated spike ectodomains across multiple coronavirus-family proteins. We assayed ∼200 variant SARS-CoV-2 spikes for their expression, ACE2 binding, and recognition by 13 nAbs. An alanine scan of all five N-terminal domain (NTD) loops highlights a public epitope in the N1, N3, and N5 loops recognized by most NTD-binding nAbs. NTD mutations in variants of concern B.1.1.7 (alpha), B.1.351 (beta), B.1.1.28 (gamma), B.1.427/B.1.429 (epsilon), and B.1.617.2 (delta) impact spike expression and escape most NTD-targeting nAbs. Finally, B.1.351 and B.1.1.28 completely escape a potent ACE2 mimic. We anticipate that Spike Display will accelerate antigen design, deep scanning mutagenesis, and antibody epitope mapping for SARS-CoV-2 and other emerging viral threats.

Influenza vaccination in the elderly boosts antibodies against conserved viral proteins and egg-produced glycans.

Seasonal influenza vaccination elicits a diminished adaptive immune response in the elderly, and the mechanisms of immunosenescence are not fully understood. Using Ig-Seq, we found a marked increase with age in the prevalence of cross-reactive (CR) serum antibodies that recognize both the H1N1 (vaccine-H1) and H3N2 (vaccine-H3) components of an egg-produced split influenza vaccine. CR antibodies accounted for 73% ± 18% of the serum vaccine responses in a cohort of elderly donors, 65% ± 15% in late middle-aged donors, and only 13% ± 5% in persons under 35 years of age. The antibody response to non-HA antigens was boosted by vaccination. Recombinant expression of 19 vaccine-H1+H3 CR serum monoclonal antibodies (s-mAbs) revealed that they predominantly bound to non-HA influenza proteins. A sizable fraction of vaccine-H1+H3 CR s-mAbs recognized with high affinity the sulfated glycans, in particular sulfated type 2 N-acetyllactosamine (Galß1-4GalNAcß), which is found on egg-produced proteins and thus unlikely to contribute to protection against influenza infection in humans. Antibodies against sulfated glycans in egg-produced vaccine had been identified in animals but were not previously characterized in humans. Collectively, our results provide a quantitative basis for how repeated exposure to split influenza vaccine correlates with unintended focusing of serum antibody responses to non-HA antigens that may result in suboptimal immunity against influenza.

Methane-to-Methanol on Mononuclear Copper(II) Sites Supported on Al2 O3 : Structure of Active Sites from Electron Paramagnetic Resonance*.

The selective conversion of methane to methanol remains one of the holy grails of chemistry, where Cu-exchanged zeolites have been shown promote this reaction under stepwise conditions. Over the years, several active sites have been proposed, ranging from mono-, di- to trimeric CuII . Herein, we report the formation of well-dispersed monomeric CuII species supported on alumina using surface organometallic chemistry and their reactivity towards the selective and stepwise conversion of methane to methanol. Extensive studies using various transition alumina supports combined with spectroscopic characterization, in particular electron paramagnetic resonance (EPR), show that the active sites are associated with specific facets, which are typically found in γ- and η-alumina phase, and that their EPR signature can be attributed to species having a tri-coordinated [(Al2 O)CuIIO(OH)]- T-shape geometry. Overall, the selective conversion of methane to methanol, a two-electron process, involves two monomeric CuII sites that play in concert.

Prevalent, protective, and convergent IgG recognition of SARS-CoV-2 non-RBD spike epitopes.

The molecular composition and binding epitopes of the immunoglobulin G (IgG) antibodies that circulate in blood plasma after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are unknown. Proteomic deconvolution of the IgG repertoire to the spike glycoprotein in convalescent subjects revealed that the response is directed predominantly (>80%) against epitopes residing outside the receptor binding domain (RBD). In one subject, just four IgG lineages accounted for 93.5% of the response, including an amino (N)-terminal domain (NTD)-directed antibody that was protective against lethal viral challenge. Genetic, structural, and functional characterization of a multidonor class of "public" antibodies revealed an NTD epitope that is recurrently mutated among emerging SARS-CoV-2 variants of concern. These data show that "public" NTD-directed and other non-RBD plasma antibodies are prevalent and have implications for SARS-CoV-2 protection and antibody escape.

Antiphospholipid antibodies in critically ill COVID-19 patients with thromboembolism: cause of disease or epiphenomenon?

Coronavirus 2019 disease (COVID-19) is associated with coagulation dysfunction that predisposes patients to an increased risk for both arterial (ATE) and venous thromboembolism (VTE) and consequent poor prognosis; in particular, the incidence of ATE and VTE in critically ill COVID-19 patients can reach 5% and 31%, respectively. The mechanism of thrombosis in COVID-19 patients is complex and still not completely clear. Recent literature suggests a link between the presence of antiphospholipid antibodies (aPLs) and thromboembolism in COVID-19 patients. However, it remains uncertain whether aPLs are an epiphenomenon or are involved in the pathogenesis of the disease.

Synthetic repertoires derived from convalescent COVID-19 patients enable discovery of SARS-CoV-2 neutralizing antibodies and a novel quaternary binding modality.

The ongoing evolution of SARS-CoV-2 into more easily transmissible and infectious variants has sparked concern over the continued effectiveness of existing therapeutic antibodies and vaccines. Hence, together with increased genomic surveillance, methods to rapidly develop and assess effective interventions are critically needed. Here we report the discovery of SARS-CoV-2 neutralizing antibodies isolated from COVID-19 patients using a high-throughput platform. Antibodies were identified from unpaired donor B-cell and serum repertoires using yeast surface display, proteomics, and public light chain screening. Cryo-EM and functional characterization of the antibodies identified N3-1, an antibody that binds avidly (Kd,app = 68 pM) to the receptor binding domain (RBD) of the spike protein and robustly neutralizes the virus in vitro. This antibody likely binds all three RBDs of the trimeric spike protein with a single IgG. Importantly, N3-1 equivalently binds spike proteins from emerging SARS-CoV-2 variants of concern, neutralizes UK variant B.1.1.7, and binds SARS-CoV spike with nanomolar affinity. Taken together, the strategies described herein will prove broadly applicable in interrogating adaptive immunity and developing rapid response biological countermeasures to emerging pathogens.

Derangement of the coagulation process using subclinical markers and viscoelastic measurements in critically ill patients with coronavirus disease 2019 pneumonia and non-coronavirus disease 2019 pneumonia.

Systemic coagulation abnormalities including clotting activation and inhibition of anticoagulant factors have been observed in patients with pneumonia. In severe coronavirus disease 2019 (COVID-19) the alteration of coagulation parameters was associated with poor prognosis. We evaluated the difference in coagulopathy between critically ill patients with COVID-19 pneumonia (COVID group) and non-COVID-19 pneumonia (non-COVID group), using traditional coagulation markers and rotational thromboelastometry (ROTEM). Standard laboratory and ROTEM parameters were evaluated in 45 patients (20 COVID group patients and 25 non-COVID group patients) at time of admission to the Intensive Care Unit (ICU) (T0) and at 5 (T5) and 10 days (T10) later. In all evaluations times, platelet count was found higher in COVID group rather than in non-COVID group. At T0, COVID group revealed a fibrinogen value greater than non-COVID group. d-Dimer values were high in both groups and they were not statistically different. At T0 COVID group showed a significant reduction of clot formation time in INTEM and in EXTEM and a significant increase of maximum clot firmness in INTEM, EXTEM and FIBTEM respect to non-COVID group. Moreover, COVID group demonstrated a coagulability state with ROTEM profiles higher than non-COVID group at T5 and T10. Coagulation profiles showed that critically ill patients with COVID-19 pneumonia are characterized by a higher coagulable state than others; this greater procoagulative state persists over time.

Non-oxidative Methane Coupling over Silica versus Silica-Supported Iron(II) Single Sites.

Non-oxidative CH4 coupling is promoted by silica with incorporated iron sites, but the role of these sites and their speciation under reaction conditions are poorly understood. Here, silica-supported iron(II) single sites, prepared via surface organometallic chemistry and stable at 1020 °C in vacuum, are shown to rapidly initiate CH4 coupling at 1000 °C, leading to 15-22 % hydrocarbons selectivity at 3-4 % conversion. During this process, iron reduces and forms carburized iron(0) nanoparticles. This reactivity contrasts with what is observed for (iron-free) partially dehydroxylated silica, that readily converts methane, albeit with low hydrocarbon selectivity and after an induction period. This study supports that iron sites facilitate faster initiation of radical reactions and tame the surface reactivity.

Prevalent, protective, and convergent IgG recognition of SARS-CoV-2 non-RBD spike epitopes in COVID-19 convalescent plasma.

Although humoral immunity is essential for control of SARS-CoV-2, the molecular composition, binding epitopes and effector functions of the immunoglobulin G (IgG) antibodies that circulate in blood plasma following infection are unknown. Proteomic deconvolution of the circulating IgG repertoire (Ig-Seq 1 ) to the spike ectodomain (S-ECD 2 ) in four convalescent study subjects revealed that the plasma response is oligoclonal and directed predominantly (>80%) to S-ECD epitopes that lie outside the receptor binding domain (RBD). When comparing antibodies directed to either the RBD, the N-terminal domain (NTD) or the S2 subunit (S2) in one subject, just four IgG lineages (1 anti-S2, 2 anti-NTD and 1 anti-RBD) accounted for 93.5% of the repertoire. Although the anti-RBD and one of the anti-NTD antibodies were equally potently neutralizing in vitro , we nonetheless found that the anti-NTD antibody was sufficient for protection to lethal viral challenge, either alone or in combination as a cocktail where it dominated the effect of the other plasma antibodies. We identified in vivo protective plasma anti-NTD antibodies in 3/4 subjects analyzed and discovered a shared class of antibodies targeting the NTD that utilize unmutated or near-germline IGHV1-24, the most electronegative IGHV gene in the human genome. Structural analysis revealed that binding to NTD is dominated by interactions with the heavy chain, accounting for 89% of the entire interfacial area, with germline residues uniquely encoded by IGHV1-24 contributing 20% (149 Å 2 ). Together with recent reports of germline IGHV1-24 antibodies isolated by B-cell cloning 3,4 our data reveal a class of shared IgG antibodies that are readily observed in convalescent plasma and underscore the role of NTD-directed antibodies in protection against SARS-CoV-2 infection.

Separating distinct structures of multiple macromolecular assemblies from cryo-EM projections.

Single particle analysis for structure determination in cryo-electron microscopy is traditionally applied to samples purified to near homogeneity as current reconstruction algorithms are not designed to handle heterogeneous mixtures of structures from many distinct macromolecular complexes. We extend on long established methods and demonstrate that relating two-dimensional projection images by their common lines in a graphical framework is sufficient for partitioning distinct protein and multiprotein complexes within the same data set. The feasibility of this approach is first demonstrated on a large set of synthetic reprojections from 35 unique macromolecular structures spanning a mass range of hundreds to thousands of kilodaltons. We then apply our algorithm on cryo-EM data collected from a mixture of five protein complexes and use existing methods to solve multiple three-dimensional structures ab initio. Incorporating methods to sort single particle cryo-EM data from extremely heterogeneous mixtures will alleviate the need for stringent purification and pave the way toward investigation of samples containing many unique structures.

Monomeric Copper(II) Sites Supported on Alumina Selectively Convert Methane to Methanol.

Monomeric CuII sites supported on alumina, prepared using surface organometallic chemistry, convert CH4 to CH3 OH selectively. This reaction takes place by formation of CH3 O surface species with the concomitant reduction of two monomeric CuII sites to CuI , according to mass balance analysis, infrared, solid-state nuclear magnetic resonance, X-ray absorption, and electron paramagnetic resonance spectroscopy studies. This material contains a significant fraction of Cu active sites (22 %) and displays a selectivity for CH3 OH exceeding 83 %, based on the number of electrons involved in the transformation. These alumina-supported CuII sites reveal that C-H bond activation, along with the formation of CH3 O- surface species, can occur on pairs of proximal monomeric CuII sites in a short reaction time.

Causal Economics: A new pluralist framework for behavioral economics that advances theoretical and applied foundations.

This paper introduces Causal Economics, a new pluralist framework for Behavioral Economics that allows for deep incorporation of psychological drivers at a level not possible in existing models. Its core theoretical breakthrough is the replacement of conventional single-value (net cost OR net benefit), single-period exogenous lottery outcomes as utilized within mainstream economics, with endogenous multi-period outcomes that always contain both personal total benefit (B) and personal total cost (C), including certain (deliberate) and uncertain components, with cause and effect running in at least one direction. Agents optimize an overall cumulative rank dependent weighted outcome value function against internal personal psychological trade-off constraints. Its core applied breakthrough is the introduction of the Causal Coefficient and four Causal Coupling Mechanisms to evaluate and guide development of effective economic and social activities, policies and institutions. Sustainable Pareto Optimal outcomes are predicted whenever causal coupling of B and C across involved or impacted agents is achieved via a Causal Coefficient ≥ 1. It provides a powerful pluralist framework for additional research into the optimality of concepts that prioritize individual freedom of choice and responsibility to society.

Persistent Antibody Clonotypes Dominate the Serum Response to Influenza over Multiple Years and Repeated Vaccinations.

Humans are repeatedly exposed to influenza virus via infections and vaccinations. Understanding how multiple exposures and pre-existing immunity impact antibody responses is essential for vaccine development. Given the recent prevalence of influenza H1N1 A/California/7/2009 (CA09), we examined the clonal composition and dynamics of CA09 hemagglutinin (HA)-reactive IgG repertoire over 5 years in a donor with multiple influenza exposures. The anti-CA09 HA polyclonal response in this donor comprised 24 persistent antibody clonotypes, accounting for 72.6% ± 10.0% of the anti-CA09 HA repertoire over 5 years. These persistent antibodies displayed higher somatic hypermutation relative to transient serum antibodies detected at one time point. Additionally, persistent antibodies predominantly demonstrated cross-reactivity and potent neutralization toward a phylogenetically distant H5N1 A/Vietnam/1203/2004 (VT04) strain, a feature correlated with HA stem recognition. This analysis reveals how "serological imprinting" impacts responses to influenza and suggests that once elicited, cross-reactive antibodies targeting the HA stem can persist for years.

Aggregated occurrence records of the federally endangered Poweshiek skipperling (Oarisma poweshiek).

BACKGROUND: Primary biodiversity data records that are open access and available in a standardised format are essential for conservation planning and research on policy-relevant time-scales. We created a dataset to document all known occurrence data for the Federally Endangered Poweshiek skipperling butterfly [Oarisma poweshiek (Parker, 1870; Lepidoptera: Hesperiidae)]. The Poweshiek skipperling was a historically common species in prairie systems across the upper Midwest, United States and Manitoba, Canada. Rapid declines have reduced the number of verified extant sites to six. Aggregating and curating Poweshiek skipperling occurrence records documents and preserves all known distributional data, which can be used to address questions related to Poweshiek skipperling conservation, ecology and biogeography. Over 3500 occurrence records were aggregated over a temporal coverage from 1872 to present. Occurrence records were obtained from 37 data providers in the conservation and natural history collection community using both "HumanObservation" and "PreservedSpecimen" as an acceptable basisOfRecord. Data were obtained in different formats and with differing degrees of quality control. During the data aggregation and cleaning process, we transcribed specimen label data, georeferenced occurrences, adopted a controlled vocabulary, removed duplicates and standardised formatting. We examined the dataset for inconsistencies with known Poweshiek skipperling biogeography and phenology and we verified or removed inconsistencies by working with the original data providers. In total, 12 occurrence records were removed because we identified them to be the western congener Oarisma garita (Reakirt, 1866). This resulting dataset enhances the permanency of Poweshiek skipperling occurrence data in a standardised format. NEW INFORMATION: This is a validated and comprehensive dataset of occurrence records for the Poweshiek skipperling (Oarisma poweshiek) utilising both observation and specimen-based records. Occurrence data are preserved and available for continued research and conservation projects using standardised Darwin Core formatting where possible. Prior to this project, much of these occurrence records were not mobilised and were being stored in individual institutional databases, researcher datasets and personal records. This dataset aggregates presence data from state conservation agencies, natural heritage programmes, natural history collections, citizen scientists, researchers and the U.S. Fish & Wildlife Service. The data include opportunistic observations and collections, research vouchers, observations collected for population monitoring and observations collected using standardised research methodologies. The aggregated occurrence records underwent cleaning efforts that improved data interoperablitity, removed transcription errors and verified or removed uncertain data. This dataset enhances available information on the spatiotemporal distribution of this Federally Endangered species. As part of this aggregation process, we discovered and verified Poweshiek skipperling occurrence records from two previously unknown states, Nebraska and Ohio.

Identification of tumor-reactive B cells and systemic IgG in breast cancer based on clonal frequency in the sentinel lymph node.

A better understanding of antitumor immune responses is the key to advancing the field of cancer immunotherapy. Endogenous immunity in cancer patients, such as circulating anticancer antibodies or tumor-reactive B cells, has been historically yet incompletely described. Here, we demonstrate that tumor-draining (sentinel) lymph node (SN) is a rich source for tumor-reactive B cells that give rise to systemic IgG anticancer antibodies circulating in the bloodstream of breast cancer patients. Using a synergistic combination of high-throughput B-cell sequencing and quantitative immunoproteomics, we describe the prospective identification of tumor-reactive SN B cells (based on clonal frequency) and also demonstrate an unequivocal link between affinity-matured expanded B-cell clones in the SN and antitumor IgG in the blood. This technology could facilitate the discovery of antitumor antibody therapeutics and conceivably identify novel tumor antigens. Lastly, these findings highlight the unique and specialized niche the SN can fill in the advancement of cancer immunotherapy.

Middle-Down 193-nm Ultraviolet Photodissociation for Unambiguous Antibody Identification and its Implications for Immunoproteomic Analysis.

Mass spectrometry (MS) has emerged as a powerful tool within the growing field of immunoproteomics, which aims to understand antibody-mediated immunity at the molecular-level based on the direct determination of serological antibody repertoire. To date, these methods have relied on the use of high-resolution bottom-up proteomic strategies that require effective sampling and characterization of low abundance peptides derived from the antigen-binding domains of polyclonal antibody mixtures. Herein, we describe a method that uses restricted Lys-C enzymatic digestion to increase the average mass of proteolytic IgG peptides (≥4.5 kDa) and produce peptides which uniquely derive from single antibody species. This enhances the capacity to discriminate between very similar antibodies present within polyclonal mixtures. Furthermore, our use of 193-nm ultraviolet photodissociation (UVPD) improves spectral coverage of the antibody sequence relative to conventional collision- and electron-based fragmentation methods. We apply these methods to both a monoclonal and an antibody mixture. By identifying from a database search of approximately 15 000 antibody sequences those which compose the mixture, we demonstrate the analytical potential of middle-down UVPD for MS-based serological repertoire analysis.