Structure of Graphene Grown on Cu(111): X-Ray Standing Wave Measurement and Density Functional Theory Prediction.

We report the quantitative adsorption structure of pristine graphene on Cu(111) determined using the normal incidence x-ray standing wave technique. The experiments constitute an important benchmark reference for the development of density functional theory approximations able to capture long-range dispersion interactions. Electronic structure calculations based on many-body dispersion-inclusive density functional theory are able to accurately predict the absolute measure and variation of adsorption height when the coexistence of multiple moiré superstructures is considered. This provides a structural model consistent with scanning probe microscopy results.

Natural and anthropogenic factors influence flowering synchrony and reproduction of a dominant plant in an inter-Andean scrub.

PREMISE: Agriculture expansion, livestock, and global change have transformed biological communities and altered, through aerosols and direct deposition, N:P balance in soils of inter-Andean valleys, potentially affecting flowering phenology of many species and thereby flowering synchrony and plant reproduction. METHODS: We evaluated the influence of variation in temperature and moisture along the local elevational gradient and treatments with the addition of N and P and grazing on flowering synchrony and reproduction of Croton, a dominant shrub of the inter-Andean dry scrub. Along the elevational gradient (300 m difference between the lowest and highest site), we set up plots with and without grazing nested with four nutrient treatments: control and addition of N or P alone or combined N + P. We recorded the number of female and male flowers in bloom monthly from September 2017 to August 2019 to calculate flowering synchrony. We assessed fruiting, seed mass, and pre-dispersal seed predation. RESULTS: Higher growing-season soil temperatures, which were negatively associated with local elevation and higher nitrogen availability promoted flowering synchrony of Croton, particularly among larger plants. Greater flowering synchrony, high soil temperatures, and addition of N + P resulted in production of more fruits of Croton, but also intensified pre-dispersal seed predation. CONCLUSIONS: Temperature, availability of moisture throughout the elevational gradient, and nutrient manipulation affected flowering synchrony, which subsequently affected production of fruits in Croton. These results emphasize the critical role of current anthropogenic changes in climate and nutrient availability on flowering synchrony and reproduction of Croton, a dominant plant of the inter-Andean scrub.

Predictive Dosimetry and Outcomes of Hepatocellular Carcinoma Treated by Yttrium-90 Resin Microsphere Radioembolization: A Retrospective Analysis Using Technetium-99m Macroaggregated Albumin SPECT/CT and Planning Software.

PURPOSE: To characterize estimated mean absorbed tumor dose (ADT), objective response (OR), and estimated target dose of hepatocellular carcinoma (HCC) after resin microsphere yttrium-90 (90Y) radioembolization using partition dosimetry. MATERIALS AND METHODS: In this retrospective, single-center study, multicompartment dosimetry of index tumors receiving 90Y radioembolization between October 2015 and June 2022 was performed using a commercial software package and pretreatment technetium-99m macroaggregated albumin single photon emission computed tomography (SPECT)/computed tomography (CT). In total, 101 patients with HCC underwent 102 treatments of 127 index tumors. Patients underwent imaging every 2-3 months after treatment to determine best response per modified Response Evaluation Criteria in Solid Tumors (mRECIST). Best response was defined as the greatest response category per mRECIST and categorized as OR or nonresponse (NR). A Cox proportional hazards model evaluated the probability of tumor OR and progression-free survival using ADT. RESULTS: The median follow-up period was 148 days (interquartile range [IQR], 92-273 days). The median ADT of OR was 141.9 Gy (IQR, 89.4-215.8 Gy) compared with the median ADT of NR treatments of 70.8 Gy (IQR, 42.0-135.3 Gy; P < .001). Only ADT was predictive of response (hazard ratio = 2.79 [95% confidence interval {CI}: 1.44-5.40]; P = .003). At 6 months, an ADT of 157 Gy predicted 90.0% (95% CI: 41.3%-98.3%) probability of OR. At 1 year, an ADT of 157 Gy predicted 91.6% (95% CI: 78.3%-100%) probability of progression-free survival. Partition modeling and delivered activity were predictive of progression (P = .021 and P = .003, respectively). CONCLUSIONS: For HCC treated with resin microspheres, tumors receiving higher ADT exhibited higher rates of OR. An ADT of 157 Gy predicted 90.0% OR at 6 months.

Using CHROMagar™ STEC medium exclusively does not recover all clinically relevant Shiga toxin-producing Escherichia coli in Aotearoa, New Zealand.

Diagnostic laboratories in Aotearoa, New Zealand (NZ) refer cultures from faecal samples positive for Shiga toxin genes to the national Enteric Reference Laboratory for isolation of Shiga toxin-producing Escherichia coli (STEC) for epidemiological typing. As there was variation in the culture media being referred, a panel of 75 clinical isolates of STEC, representing 28 different serotypes, was used to assess six commercially available media and provide guidance to clinical laboratories. Recommendations were subsequently tested for a 3-month period, where STEC isolations and confirmations were assessed by whole genome sequencing analysis against the culture media referred. CHROMagar™ STEC (CH-STEC; CHROMagar Microbiology, Paris, France) or CH-STEC plus cefixime-tellurite sorbitol MacConkey agar was confirmed inferior to CH-STEC plus blood agar with vancomycin, cefsulodin, and cefixime (BVCC). The former resulted in fewer STEC types (n = 18) being confirmed compared to those from a combination of CH-STEC and BVCC (n = 42). A significant (P < .05) association with an STEC's ability to grow on CH-STEC and the presence of the ter gene cluster, and eae was observed. Culturing screen positive STEC samples onto both CH-STEC and BVCC ensures a consistently higher recovery of STEC from all clinical samples in NZ than CH-STEC alone.

Identification of immune correlates of fatal outcomes in critically ill COVID-19 patients.

Prior studies have demonstrated that immunologic dysfunction underpins severe illness in COVID-19 patients, but have lacked an in-depth analysis of the immunologic drivers of death in the most critically ill patients. We performed immunophenotyping of viral antigen-specific and unconventional T cell responses, neutralizing antibodies, and serum proteins in critically ill patients with SARS-CoV-2 infection, using influenza infection, SARS-CoV-2-convalescent health care workers, and healthy adults as controls. We identify mucosal-associated invariant T (MAIT) cell activation as an independent and significant predictor of death in COVID-19 (HR = 5.92, 95% CI = 2.49-14.1). MAIT cell activation correlates with several other mortality-associated immunologic measures including broad activation of CD8+ T cells and non-Vδ2 γδT cells, and elevated levels of cytokines and chemokines, including GM-CSF, CXCL10, CCL2, and IL-6. MAIT cell activation is also a predictor of disease severity in influenza (ECMO/death HR = 4.43, 95% CI = 1.08-18.2). Single-cell RNA-sequencing reveals a shift from focused IFNα-driven signals in COVID-19 ICU patients who survive to broad pro-inflammatory responses in fatal COVID-19 -a feature not observed in severe influenza. We conclude that fatal COVID-19 infection is driven by uncoordinated inflammatory responses that drive a hierarchy of T cell activation, elements of which can serve as prognostic indicators and potential targets for immune intervention.

Health care administration and drug policy.

The American healthcare system faces a potential reorganization of the way in which services are provided and financed. We argue that healthcare administrators need to be increasingly aware of the ways in which our nation's illicit drug policy, commonly referred to as the 'War on Drugs', affects the provision of health services. A large and growing portion of the US population uses one or more of the currently illegal drugs and some of these persons suffer from an addiction or other substance use disorder. This is clearly demonstrated by the current opioid epidemic which is not yet being adequately controlled. Providing specialty treatment for drug abuse disorders will be increasingly important for healthcare administrators thanks to recent mental health parity legislation. At the same time, drug users and abusers will be increasingly encountered while providing care not specifically tied to drug use or abuse. The character of our current national drug policy has an important impact on how drug abuse disorders are treated and how the health delivery system responds to drug users who are increasingly often encountered in primary care, emergency care, specialty care, and long-term care settings.

Selective hydrogenation of graphene on Ir(111): an X-ray standing wave study.

A combined high resolution X-ray photoelectron spectroscopy and X-ray standing wave study into the adsorption structure of hydrogenated graphene on Ir(111) is presented. By exploiting the unique absorption profiles and significant modulations in signal intensity found within the X-ray standing wave results, we refine the fitting of the C 1s X-ray photoelectron spectra, allowing us to disentangle the contributions from hydrogenation of graphene in different high-symmetry regions of the moiré supercell. We clearly demonstrate that hydrogenation in the FCC regions results in the formation of a graphane-like structure, giving a standalone component that is separated from the component assigned to the similar structure in the HCP regions. The contribution from dimer structures in the ATOP regions is found to be minor or negligible. This is in contrast to the previous findings where a dimer structure was assumed to contribute significantly to the sp3 part of the C 1s spectra. The corrugation of the remaining pristine parts of the H-graphene is shown to increase with the H coverage, reflecting an increasing number and size of pinning centers of the graphene to the Ir(111) substrate with increasing H exposure.

Towards open, reliable, and transparent ecology and evolutionary biology.

Unreliable research programmes waste funds, time, and even the lives of the organisms we seek to help and understand. Reducing this waste and increasing the value of scientific evidence require changing the actions of both individual researchers and the institutions they depend on for employment and promotion. While ecologists and evolutionary biologists have somewhat improved research transparency over the past decade (e.g. more data sharing), major obstacles remain. In this commentary, we lift our gaze to the horizon to imagine how researchers and institutions can clear the path towards more credible and effective research programmes.

Using data calibration to reconcile outputs from different survey methods in long-term or large-scale studies.

Understanding the impact of management interventions on the environment over decadal and longer timeframes is urgently required. Longitudinal or large-scale studies with consistent methods are best practice, but more commonly, small datasets with differing methods are used to achieve larger coverage. Changes in methods and interpretation affect our ability to understand data trends through time or across space, so an ability to understand and adjust for such discrepancies between datasets is important for applied ecologists. Calibration or double sampling is the key to unlocking the value from disparate datasets, allowing us to account for the differences between datasets while acknowledging the uncertainties. We use a case study of livestock grazing impacts on riparian vegetation in southeastern Australia to develop a flexible and powerful approach to this problem. Using double sampling, we estimated changes in vegetation attributes over a 12-year period using a pseudo-quantitative visual method as the starting point, and the same technique plus point-intercept survey for the second round. The disparate nature of the datasets produced uncertain estimates of change over time, but accounting for this uncertainty explicitly is precisely the objective and highlights the need to look more closely at this very common problem in environmental management, as well as the potential benefits of the double sampling approach.

N-Heterocyclic Carbenes: Molecular Porters of Surface Mounted Ru-Porphyrins.

Ru-porphyrins act as convenient pedestals for the assembly of N-heterocyclic carbenes (NHCs) on solid surfaces. Upon deposition of a simple NHC ligand on a close packed Ru-porphyrin monolayer, an extraordinary phenomenon can be observed: Ru-porphyrin molecules are transferred from the silver surface to the next molecular layer. We have investigated the structural features and dynamics of this portering process and analysed the associated binding strengths and work function changes. A rearrangement of the molecular layer is induced by the NHC uptake: the NHC selective binding to the Ru causes the ejection of whole porphyrin molecules from the molecular layer on silver to the layer on top. This reorganisation can be reversed by thermally induced desorption of the NHC ligand. We anticipate that the understanding of such mass transport processes will have crucial implications for the functionalisation of surfaces with carbenes.

Misinformation, internet honey trading and beekeepers drive a plant invasion.

Biological invasions are a major human induced global change that is threatening global biodiversity by homogenizing the world's fauna and flora. Species spread because humans have moved species across geographical boundaries and have changed ecological factors that structure ecosystems, such as nitrogen deposition, disturbance, etc. Many biological invasions are caused accidentally, as a byproduct of human travel and commerce driven product shipping. However, humans also have spread many species intentionally because of perceived benefits. Of interest is the role of the recent exponential growth in information exchange via internet social media in driving biological invasions. To date, this has not been examined. Here, we show that for one such invasive species, goldenrod, social networks spread misleading and incomplete information that is enhancing the spread of goldenrod invasions into new environments. We show that the notion of goldenrod honey as a "superfood" with unsupported healing properties is driving a demand that leads beekeepers to produce goldenrod honey. Social networks provide a forum for such information exchange and this is leading to further spread of goldenrod in many countries where goldenrod is not native, such as Poland. However, this informal social information exchange ignores laws that focus on preventing the further spread of invasive species and the strong negative effects that goldenrod has on native ecosystems, including floral resources that negatively impact honeybee performance. Thus, scientifically unsupported information on "superfoods" such as goldenrod honey that is disseminated through social internet networks has real world consequences such as increased goldenrod invasions into novel geographical regions which decreases native biodiversity.

Assembly and Manipulation of a Prototypical N-Heterocyclic Carbene with a Metalloporphyrin Pedestal on a Solid Surface.

The controlled arrangement of N-heterocyclic carbenes (NHCs) on solid surfaces is a current challenge of surface functionalization. We introduce a strategy of using Ru porphyrins in order to control both the orientation and lateral arrangement of NHCs on a planar surface. The coupling of the NHC to the Ru porphyrin is a facile process which takes place on the interface: we apply NHCs as functional, robust pillars on well-defined, preassembled Ru porphyrin monolayers on silver and characterize these interfaces with atomic precision via a battery of experimental techniques and theoretical considerations. The NHCs assemble at room temperature modularly and reversibly on the Ru porphyrin arrays. We demonstrate a selective and complete functionalization of the Ru centers. With its binding, the NHC modifies the interaction of the Ru porphyrin with the Ag surface, displacing the Ru atom by 1 Å away from the surface. This arrangement of NHCs allows us to address individual ligands by controlled manipulation with the tip of a scanning tunneling microscope, creating patterned structures on the nanometer scale.

Indigenous plants promote insect biodiversity in urban greenspaces.

The contribution of urban greenspaces to support biodiversity and provide benefits for people is increasingly recognized. However, ongoing management practices favor vegetation oversimplification, often limiting greenspaces to lawns and tree canopy rather than multi-layered vegetation that includes under- and midstorey, and the use of nonnative species. These practices hinder the potential of greenspaces to sustain indigenous biodiversity, particularly for taxa like insects that rely on plants for food and habitat. Yet, little is known about which plant species may maximize positive outcomes for taxonomically and functionally diverse insect communities in greenspaces. Additionally, while cities are expected to experience high rates of introductions, quantitative assessments of the relative occupancy of indigenous vs. introduced insect species in greenspace are rare, hindering understanding of how management may promote indigenous biodiversity while limiting the establishment of introduced insects. Using a hierarchically replicated study design across 15 public parks, we recorded occurrence data from 552 insect species on 133 plant species, differing in planting design element (lawn, midstorey, and tree canopy), midstorey growth form (forbs, lilioids, graminoids, and shrubs) and origin (nonnative, native, and indigenous), to assess (1) the relative contributions of indigenous and introduced insect species and (2) which plant species sustained the highest number of indigenous insects. We found that the insect community was overwhelmingly composed of indigenous rather than introduced species. Our findings further highlight the core role of multi-layered vegetation in sustaining high insect biodiversity in urban areas, with indigenous midstorey and canopy representing key elements to maintain rich and functionally diverse indigenous insect communities. Intriguingly, graminoids supported the highest indigenous insect richness across all studied growth forms by plant origin groups. Our work highlights the opportunity presented by indigenous understory and midstorey plants, particularly indigenous graminoids, in our study area to promote indigenous insect biodiversity in urban greenspaces. Our study provides a blueprint and stimulus for architects, engineers, developers, designers, and planners to incorporate into their practice plant species palettes that foster a larger presence of indigenous over regionally native or nonnative plant species, while incorporating a broader mixture of midstorey growth forms.

Experimental measurement and prediction of ionic liquid ionisation energies.

Ionic liquid (IL) valence electronic structure provides key descriptors for understanding and predicting IL properties. The ionisation energies of 60 ILs are measured and the most readily ionised valence state of each IL (the highest occupied molecular orbital, HOMO) is identified using a combination of X-ray photoelectron spectroscopy (XPS) and synchrotron resonant XPS. A structurally diverse range of cations and anions were studied. The cation gave rise to the HOMO for nine of the 60 ILs presented here, meaning it is energetically more favourable to remove an electron from the cation than the anion. The influence of the cation on the anion electronic structure (and vice versa) were established; the electrostatic effects are well understood and demonstrated to be consistently predictable. We used this knowledge to make predictions of both ionisation energy and HOMO identity for a further 516 ILs, providing a very valuable dataset for benchmarking electronic structure calculations and enabling the development of models linking experimental valence electronic structure descriptors to other IL properties, e.g. electrochemical stability. Furthermore, we provide design rules for the prediction of the electronic structure of ILs.

Conformational Control of Chemical Reactivity for Surface-Confined Ru-Porphyrins.

We assess the crucial role of tetrapyrrole flexibility in the CO ligation to distinct Ru-porphyrins supported on an atomistically well-defined Ag(111) substrate. Our systematic real-space visualisation and manipulation experiments with scanning tunnelling microscopy directly probe the ligation, while bond-resolving atomic force microscopy and X-ray standing-wave measurements characterise the geometry, X-ray and ultraviolet photoelectron spectroscopy the electronic structure, and temperature-programmed desorption the binding strength. Density-functional-theory calculations provide additional insight into the functional interface. We unambiguously demonstrate that the substituents regulate the interfacial conformational adaptability, either promoting or obstructing the uptake of axial CO adducts.

The Role of Kinetics versus Thermodynamics in Surface-Assisted Ullmann Coupling on Gold and Silver Surfaces.

Surface-assisted Ullmann coupling is the workhorse of on-surface synthesis. Despite its obvious relevance, many fundamental and mechanistic aspects remain elusive. To shed light on individual reaction steps and their progression with temperature, temperature-programmed X-ray photoelectron spectroscopy (TP-XPS) experiments are performed for a prototypical model system. The activation of the coupling by initial dehalogenation is tracked by monitoring Br 3d core levels, whereas the C 1s signature is used to follow the emergence of metastable organometallic intermediates and their conversion to the final covalent products upon heating in real time. The employed 1,3,5-tris(4-bromophenyl)benzene precursor is comparatively studied on Ag(111) versus Au(111), whereby intermolecular bonds and network topologies are additionally characterized by scanning tunneling microscopy (STM). Besides the well-comprehended differences in activation temperatures for debromination, the thermal progression shows marked differences between the two surfaces. Debromination proceeds rapidly on Ag(111), but is relatively gradual on Au(111). While on Ag(111) debromination is well explained by first-order reaction kinetics, thermodynamics prevail on Au(111), underpinned by a close agreement between experimentally deduced and density functional theory (DFT) calculated reaction enthalpies. Thermodynamically controlled debromination on Au(111) over a large temperature range implies an unexpectedly long lifetime of surface-stabilized radicals prior to covalent coupling, as corroborated by TP-XPS of C 1s core levels. These insights are anticipated to play an important role regarding our ability to rationally synthesize atomically precise low-dimensional covalent nanostructures on surfaces.

Adsorption Behavior of Organic Molecules: A Study of Benzotriazole on Cu(111) with Spectroscopic and Theoretical Methods.

The adsorption of organic molecules on solid substrates is important to applications in fields such as catalysis, photovoltaics, corrosion inhibition, adhesion, and sensors. The molecular level description of the surface-molecule interaction and of the adsorption structures in these complex systems is crucial to understand their properties and function. Here, we present an investigation of one such system, benzotriazole (BTAH) on single-crystal Cu(111) in vacuum conditions. BTAH is the most widely used corrosion inhibitor for copper and thus a molecule of great industrial relevance. We show that the co-application of a wide range of spectroscopic techniques with theoretical methods provides unique insight in the description of the atomistic details of the adsorbed structures. Specifically, spectroscopic photoemission, absorption, and standing wave experiments combined with ab initio computational modeling allowed us to identify that benzotriazole forms overlayers of intact BTAH when deposited at low temperature, and it dissociates into BTA and H at room temperature and above. The dissociated molecule then forms complex structures of mixed chains and dimers of BTA bound to copper adatoms. Our work also reveals that copper adatoms at low concentrations, such as the theoretically predicted superstructures, cannot be resolved by means of current X-ray photoelectron spectroscopy as the modeled Cu 2p spectra are practically indistinguishable from those for a Cu surface without adatoms. Overall this study significantly deepens understanding of BTAH on Cu, a system studied for more than 50 years, and it highlights the benefits of combining spectroscopic and computational methods to obtain a complete picture of a complex adsorption system.

Chemically-resolved determination of hydrogenated graphene-substrate interaction.

Functionalization of graphene on Ir(111) is a promising route to modify graphene by chemical means in a controlled fashion at the nanoscale. Yet, the nature of such functionalized sp3 nanodots remains unknown. Density functional theory (DFT) calculations alone cannot differentiate between two plausible structures, namely true graphane and substrate stabilized graphane-like nanodots. These two structures, however, interact dramatically differently with the underlying substrate. Discriminating which type of nanodots forms on the surface is thus of paramount importance for the applications of such prepared nanostructures. By comparing X-ray standing wave measurements against theoretical model structures obtained by DFT calculations we are able to exclude the formation of true graphane nanodots and clearly show the formation graphane-like nanodots.

Genome Comparisons of Wild Isolates of Caulobacter crescentus Reveal Rates of Inversion and Horizontal Gene Transfer.

Since previous interspecies comparisons of Caulobacter genomes have revealed extensive genome rearrangements, we decided to compare the nucleotide sequences of four C. crescentus genomes, NA1000, CB1, CB2, and CB13. To accomplish this goal, we used PacBio sequencing technology to determine the nucleotide sequence of the CB1, CB2, and CB13 genomes, and obtained each genome sequence as a single contig. To correct for possible sequencing errors, each genome was sequenced twice. The only differences we observed between the two sets of independently determined sequences were random omissions of a single base in a small percentage of the homopolymer regions where a single base is repeated multiple times. Comparisons of these four genomes indicated that horizontal gene transfer events that included small numbers of genes occurred at frequencies in the range of 10-3 to 10-4 insertions per generation. Large insertions were about 100 times less frequent. Also, in contrast to previous interspecies comparisons, we found no genome rearrangements when the closely related NA1000, CB1, and CB2 genomes were compared, and only eight inversions and one translocation when the more distantly related CB13 genome was compared to the other genomes. Thus, we estimate that inversions occur at a rate of one per 10 to 12 million generations in Caulobacter genomes. The inversions seem to be complex events that include the simultaneous creation of indels.

Characterization of intramuscular calf vein thrombosis on routine knee MRI.

OBJECTIVE: Literature regarding intramuscular calf vein thrombosis (IMCVT) or infrapopliteal deep vein thrombosis (DVT) evaluation by magnetic resonance imaging (MRI) is limited, particularly with regard to routine unenhanced knee examinations. We attempt to correlate routine unenhanced MRI findings with ultrasound evaluations of the lower extremity deep venous system. MATERIALS AND METHODS: The radiology information system was searched, yielding a total of 67 patients who had undergone both routine knee MRI and duplex ultrasound examinations within 14 days. The MRI examination findings recorded were the presence and pattern of edema, segmental vein dilation, intraluminal signal on fluid-sensitive sequences, and abnormal hyperintense signal on axial T1-weighted sequences. The presence and extent of thrombus more centrally (i.e., intramuscular calf vein thrombosis with or without extension into the popliteal vein) was reassessed on ultrasound. RESULTS: When comparing patients with positive (n = 13) and negative (n = 54) ultrasound, there were significant differences in each of these parameters: perivascular edema, intramuscular edema, focal vein dilation, and abnormal fluid-sensitive signal. In the subset of patients with popliteal extension of the intramuscular calf vein thrombosis compared with those without any deep vein thrombosis, there was a statistically significant increase in peripopliteal edema, abnormal fluid-sensitive signal, and abnormal hyperintense T1 signal. CONCLUSION: Imaging findings on routine unenhanced MRI have a high rate of concordance with duplex ultrasound performed through the calf in the detection of intramuscular calf vein thrombosis.