Improving species distribution forecasts by measuring and communicating uncertainty: An invasive species case study.

Forecasting invasion risk under future climate conditions is critical for the effective management of invasive species, and species distribution models (SDMs) are key tools for doing so. However, SDM-based forecasts are uncertain, especially when correlative statistical models extrapolate to nonanalog environmental domains, such as future climate conditions. Different assumptions about the functional form of the temperature-suitability relationship can impact predicted habitat suitability under novel conditions. Hence, methods to understand the sources of uncertainty are critical when applying SDMs. Here, we use high-resolution predictions of lake water temperatures to project changes in habitat suitability under future climate conditions for an invasive macrophyte (Myriophyllym spicatum). Future suitability was predicted using five global circulation models and three statistical models that assumed different species-temperature functional responses. The suitability of lakes for M. spicatum was overall predicted to increase under future climate conditions, but the magnitude and direction of change in suitability varied greatly among lakes. Variability was most pronounced for lakes under nonanalog temperature conditions, indicating that predictions for these lakes remained highly uncertain. Integrating predictions from SDMs that differ in their species-environment response function, while explicitly quantifying uncertainty across analog and nonanalog domains, can provide a more robust and useful approach to forecasting invasive species distribution under climate change.

The IL6/JAK/STAT3 signaling axis is a therapeutic vulnerability in SMARCB1-deficient bladder cancer.

SMARCB1 loss has long been observed in many solid tumors. However, there is a need to elucidate targetable pathways driving growth and metastasis in SMARCB1-deficient tumors. Here, we demonstrate that SMARCB1 deficiency, defined as genomic SMARCB1 copy number loss associated with reduced mRNA, drives disease progression in patients with bladder cancer by engaging STAT3. SMARCB1 loss increases the chromatin accessibility of the STAT3 locus in vitro. Orthotopically implanted SMARCB1 knockout (KO) cell lines exhibit increased tumor growth and metastasis. SMARCB1-deficient tumors show an increased IL6/JAK/STAT3 signaling axis in in vivo models and patients. Furthermore, a pSTAT3 selective inhibitor, TTI-101, reduces tumor growth in SMARCB1 KO orthotopic cell line-derived xenografts and a SMARCB1-deficient patient derived xenograft model. We have identified a gene signature generated from SMARCB1 KO tumors that predicts SMARCB1 deficiency in patients. Overall, these findings support the clinical evaluation of STAT3 inhibitors for the treatment of SMARCB1-deficient bladder cancer.

Synergistic action of sumatriptan delivery and targeting magnesium deficiency using green, pH-responsive MgO nanoparticles synthesized from mahua flower extracts.

Magnesium oxide (MgO) nanoparticles were green synthesized using mahua (Madhuca longifolia) flower extracts by solvent evaporation and characterized by UV-visible spectroscopy, X-ray diffraction analysis (XRD), Fourier transform infrared spectroscopy (FTIR), Field emission scanning electron microscopy (FESEM), and Energy dispersive X-ray analysis (EDX). The drug loading of sumatriptan succinate (SS), an anti-migraine drug, was optimized using MINITAB's response surface methodology (RSM) Box Behnken model (BBD) model. The investigation of drug adsorption and release kinetics was further conducted using the optimized set obtained through RSM. The optimized parameters consisted of 23.53 mg of nanoparticles, a loading time of 6 h, and a pH of 9, yielding the experimental drug loading efficiency ~47%. The primary objective of this study is to investigate the potential of utilizing these green synthesized MgO nanoparticles for a dual purpose. The primary objective of this study is to investigate the viability of utilizing MgO nanoparticles synthesized through green route for the delivery of an anti-migraine medication. Additionally, the study aims to examine the degradation of these nanoparticles at physiological pH levels, with the intention of potentially enhancing cellular absorption. The investigation involved the assessment of drug release kinetics using various mathematical models, with a focus on the release of SS from MgO nanoparticles. This evaluation was conducted at different pH levels, specifically pH 5, 7, and 9. It has been found that the SS release increases as pH decreases, which is attributed to the dissolution of MgO nanoparticles, which therefore exhibits varied behavior at different pHs. The confirmation of the degradation of the green synthesized MgO nanoparticles was achieved through the execution of a degradation study, followed by the analysis of the obtained samples using FESEM and EDS. At neutral, the release data obtained adhered to the Higuchi model, which suggests that the release of the drug is based on diffusion. This finding is particularly advantageous for the controlled release of an anti-migraine drug. The results obtained from the study indicate that MgO nanoparticles have the potential to serve as a significant component in drug delivery systems, specifically as drug carriers. Attachment of SS over MgO nanoparticles to form SS loaded MgO nanoparticles and its possible working mechanism.

The uncharted role of HER2 mutant alleles in breast cancer.

Somatic HER2 mutations are a novel class of therapeutic targets across different cancer types. Treatment with the tyrosine kinase inhibitor (TKI) neratinib as a single agent continues to be evaluated in HER2-mutant metastatic disease. However, responses are heterogeneous, with frequent early progression. Herein, we discuss the under-explored effects of individual HER2 mutant alleles on therapeutic response, a role for HER2 mutation in metastatic propensity, and differences in patient outcomes in ER+ invasive lobular carcinoma (ILC) versus invasive ductal carcinoma (IDC). The preclinical efficacy of additional agents is also discussed, particularly the pan-HER inhibitor poziotinib.

Disseminated Tuberculosis Presenting as Venous Thromboembolism.

Tuberculosis (TB) is one of the leading causes of morbidity and mortality throughout the world and can have both pulmonary and extrapulmonary manifestations. Among the myriad extrapulmonary manifestations of TB, deep vein thrombosis (DVT) is rare. We present the case of a 25-year-old woman who presented with progressive painful swelling of the left upper limb associated with intermittent low-grade fever. Upon evaluation, she was found to have DVT along with a subsegmental pulmonary embolism. Further workup of the patient revealed bilateral pleural effusion and constrictive pericarditis along with microbiological evidence of Mycobacterium tuberculosis. The patient was started on anti-tubercular therapy along with therapeutic anti-coagulation, after which there was a substantial clinical improvement. Though rare, this case elucidates the venous thrombosis risk associated with one of the most common diseases in developing countries.

Structures of Get3d reveal a distinct architecture associated with the emergence of photosynthesis.

Homologs of the protein Get3 have been identified in all domains yet remain to be fully characterized. In the eukaryotic cytoplasm, Get3 delivers tail-anchored (TA) integral membrane proteins, defined by a single transmembrane helix at their C terminus, to the endoplasmic reticulum. While most eukaryotes have a single Get3 gene, plants are notable for having multiple Get3 paralogs. Get3d is conserved across land plants and photosynthetic bacteria and includes a distinctive C-terminal α-crystallin domain. After tracing the evolutionary origin of Get3d, we solve the Arabidopsis thaliana Get3d crystal structure, identify its localization to the chloroplast, and provide evidence for a role in TA protein binding. The structure is identical to that of a cyanobacterial Get3 homolog, which is further refined here. Distinct features of Get3d include an incomplete active site, a "closed" conformation in the apo-state, and a hydrophobic chamber. Both homologs have ATPase activity and are capable of binding TA proteins, supporting a potential role in TA protein targeting. Get3d is first found with the development of photosynthesis and conserved across 1.2 billion years into the chloroplasts of higher plants across the evolution of photosynthesis suggesting a role in the homeostasis of photosynthetic machinery.

Structurally derived universal mechanism for the catalytic cycle of the tail-anchored targeting factor Get3.

Tail-anchored (TA) membrane proteins, accounting for roughly 2% of proteomes, are primarily targeted posttranslationally to the endoplasmic reticulum membrane by the guided entry of TA proteins (GET) pathway. For this complicated process, it remains unknown how the central targeting factor Get3 uses nucleotide to facilitate large conformational changes to recognize then bind clients while also preventing exposure of hydrophobic surfaces. Here, we identify the GET pathway in Giardia intestinalis and present the structure of the Get3-client complex in the critical postnucleotide-hydrolysis state, demonstrating that Get3 reorganizes the client-binding domain (CBD) to accommodate and shield the client transmembrane helix. Four additional structures of GiGet3, spanning the nucleotide-free (apo) open to closed transition and the ATP-bound state, reveal the details of nucleotide stabilization and occluded CBD. This work resolves key conundrums and allows for a complete model of the dramatic conformational landscape of Get3.

Poziotinib Inhibits HER2-Mutant-Driven Therapeutic Resistance and Multiorgan Metastasis in Breast Cancer.

The pan-HER tyrosine kinase inhibitor (TKI) neratinib is therapeutically active against metastatic breast cancers harboring activating HER2 mutations, but responses are variable and often not durable. Here we demonstrate that recurrent HER2 mutations have differential effects on endocrine therapy responsiveness, metastasis, and pan-HER TKI therapeutic sensitivity. The prevalence and prognostic significance may also depend on whether the HER2 mutant has arisen in the context of lobular versus ductal histology. The most highly recurrent HER2 mutant, L755S, was particularly resistant to neratinib but sensitive to the pan-HER TKI poziotinib, alone or in combination with fulvestrant. Poziotinib reduced tumor growth, diminished multiorgan metastasis, and inhibited mTOR activation more effectively than neratinib. Similar therapeutic effects of poziotinib were observed in both an engineered HER2L755S MCF7 model and a patient-derived xenograft harboring a HER2G778_P780dup mutation. Overall, these findings support the need for clinical evaluation of poziotinib for the treatment of HER2-mutant metastatic breast cancer. SIGNIFICANCE: Evaluation of the functional impact of HER2 mutations on therapy-induced resistance and metastasis identifies robust antitumor activity of poziotinib and supports the clinical evaluation of poziotinib in ER+ HER2 mutant breast cancer.

Mechanisms of neratinib resistance in HER2-mutant metastatic breast cancer.

Human epidermal growth factor receptor 2 (HER2) is a major drug target and clinical biomarker in breast cancer treatment. Targeting HER2 gene amplification is one of the greatest successes in oncology, resulting in the use of a wide array of HER2-directed agents in the clinic. The discovery of HER2-activating mutations as novel therapeutic targets in breast and other cancers marked a significant advance in the field, which led to the metastatic breast and other solid tumor trials MutHER (NCT01670877), SUMMIT (NCT01953926), and one arm of plasmaMATCH (NCT03182634). These trials reported initial clinical benefit followed by eventual relapse ascribed to either primary or acquired resistance. These resistance mechanisms are mediated by additional secondary genomic alterations within HER2 itself and via hyperactivation of oncogenic signaling within the downstream signaling axis.

Quantifying Spillover of an Urban Invasive Vector of Plant Disease: Asian Citrus Psyllid (Diaphorina citri) in California Citrus.

Urban environments frequently play an important role in the initial stages of biological invasions, often serving as gateways for non-native species, which may propagate to nearby natural and agricultural ecosystems in the event of spillover. In California, citrus trees are a dominant ornamental and food plant in urban and peri-urban environments. We studied the invasion dynamics of the Asian citrus psyllid (Diaphorina citri), which became widespread in urban areas of southern California starting in 2008, to understand the factors driving its more recent invasion in commercial citrus groves. Using a multi-year monitoring database, we applied a suite of models to evaluate the rate at which groves accrued their first D. citri detection and the cumulative number of detections thereafter. Grove characteristics and landscape context proved to be important, with generally higher invasion rates and more cumulative detections in groves that were larger, had more edge, or had more perforated shapes, with greater urbanization intensity favoring more rapid invasion, but with inconsistent effects of distance to roads among models. Notably, distance to urban or other grove occurrences proved to be among the most important variables. During the early phase of D. citri invasion in the region, groves closer to urban occurrences were invaded more rapidly, whereas more recently, invasion rate depended primarily on proximity to grove occurrences. Yet, proximity to urban and grove occurrences contributed positively to cumulative D. citri detections, suggesting a continued influx from both sources. These results suggest that inherent features of agroecosystems and spatial coupling with urban ecosystems can be important, temporally dynamic, drivers of biological invasions. Further consideration of these issues may guide the development of strategic responses to D. citri's ongoing invasion.

Species distribution models for invasive Eurasian watermilfoil highlight the importance of data quality and limitations of discrimination accuracy metrics.

AIM: Availability of uniformly collected presence, absence, and abundance data remains a key challenge in species distribution modeling (SDM). For invasive species, abundance and impacts are highly variable across landscapes, and quality occurrence and abundance data are critical for predicting locations at high risk for invasion and impacts, respectively. We leverage a large aquatic vegetation dataset comprising point-level survey data that includes information on the invasive plant Myriophyllum spicatum (Eurasian watermilfoil) to: (a) develop SDMs to predict invasion and impact from environmental variables based on presence-absence, presence-only, and abundance data, and (b) compare evaluation metrics based on functional and discrimination accuracy for presence-absence and presence-only SDMs. LOCATION: Minnesota, USA. METHODS: Eurasian watermilfoil presence-absence and abundance information were gathered from 468 surveyed lakes, and 801 unsurveyed lakes were leveraged as pseudoabsences for presence-only models. A Random Forest algorithm was used to model the distribution and abundance of Eurasian watermilfoil as a function of lake-specific predictors, both with and without a spatial autocovariate. Occurrence-based SDMs were evaluated using conventional discrimination accuracy metrics and functional accuracy metrics assessing correlation between predicted suitability and observed abundance. RESULTS: Water temperature degree days and maximum lake depth were two leading predictors influencing both invasion risk and abundance, but they were relatively less important for predicting abundance than other water quality measures. Road density was a strong predictor of Eurasian watermilfoil invasion risk but not abundance. Model evaluations highlighted significant differences: Presence-absence models had high functional accuracy despite low discrimination accuracy, whereas presence-only models showed the opposite pattern. MAIN CONCLUSION: Complementing presence-absence data with abundance information offers a richer understanding of invasive Eurasian watermilfoil's ecological niche and enables evaluation of the model's functional accuracy. Conventional discrimination accuracy measures were misleading when models were developed using pseudoabsences. We thus caution against the overuse of presence-only models and suggest directing more effort toward systematic monitoring programs that yield high-quality data.

Pediatric emergency medicine fellowship point-of-care ultrasound training in 2020.

OBJECTIVES: The primary objective was to survey pediatric emergency medicine (PEM) leaders and fellows regarding point-of-care ultrasound (POCUS) training in PEM fellowship programs, including teaching methods, training requirements, and applications taught. Secondary objectives were to compare fellows' and program leaders' perceptions of fellow POCUS competency and training barriers. METHODS: This was a cross-sectional survey of U.S. PEM fellows and fellowship program leaders of the 78 fellowship programs using two online group-specific surveys exploring five domains: program demographics; training strategies and requirements; perceived competency; barriers, strengths, and weaknesses of POCUS training; and POCUS satisfaction. RESULTS: Eighty-three percent (65/78) of programs and 53% (298/558) of fellows responded. All participating PEM fellowship programs included POCUS training in their curriculum. Among the 65 programs, 97% of programs and 92% of programs utilized didactics and supervised scanning shifts as educational techniques, respectively. Sixty percent of programs integrated numerical benchmarks and 49% of programs incorporated real-time, hands-on demonstration as training requirements. Of the 19 POCUS applications deemed in the literature as core requirements for fellows, at least 75% of the 298 fellows reported training in 13 of those applications. Although less than half of fellows endorsed competency for identifying intussusception, ultrasound-guided pericardiocentesis, and transvaginal pregnancy evaluation, a higher proportion of leaders reported fellows as competent for these applications (40% vs. 68%, p ≤ 0.001; 21% vs. 39%, p = 0.003; and 21% vs. 43%, p ≤ 0.001). Forty-six percent of fellows endorsed a lack of PEM POCUS evidence as a training barrier compared to 31% of leaders (p = 0.02), and 39% of leaders endorsed a lack of local financial support as a training barrier compared to 23% of fellows (p = 0.01). CONCLUSIONS: Although most PEM fellowship programs provide POCUS training, there is variation in content and requirements. Training does conform to many of the expert recommended guidelines; however, there are some discrepancies and perceived barriers to POCUS training remain.

Thioredoxin reductase is a major regulator of metabolism in leukemia cells.

Despite the fact that AML is the most common acute leukemia in adults, patient outcomes are poor necessitating the development of novel therapies. We identified that inhibition of Thioredoxin Reductase (TrxR) is a promising strategy for AML and report a highly potent and specific inhibitor of TrxR, S-250. Both pharmacologic and genetic inhibition of TrxR impairs the growth of human AML in mouse models. We found that TrxR inhibition leads to a rapid and marked impairment of metabolism in leukemic cells subsequently leading to cell death. TrxR was found to be a major and direct regulator of metabolism in AML cells through impacts on both glycolysis and the TCA cycle. Studies revealed that TrxR directly regulates GAPDH leading to a disruption of glycolysis and an increase in flux through the pentose phosphate pathway (PPP). The combined inhibition of TrxR and the PPP led to enhanced leukemia growth inhibition. Overall, TrxR abrogation, particularly with S-250, was identified as a promising strategy to disrupt AML metabolism.

Sequence-based features that are determinant for tail-anchored membrane protein sorting in eukaryotes.

The correct targeting and insertion of tail-anchored (TA) integral membrane proteins is critical for cellular homeostasis. TA proteins are defined by a hydrophobic transmembrane domain (TMD) at their C-terminus and are targeted to either the ER or mitochondria. Derived from experimental measurements of a few TA proteins, there has been little examination of the TMD features that determine localization. As a result, the localization of many TA proteins are misclassified by the simple heuristic of overall hydrophobicity. Because ER-directed TMDs favor arrangement of hydrophobic residues to one side, we sought to explore the role of geometric hydrophobic properties. By curating TA proteins with experimentally determined localizations and assessing hypotheses for recognition, we bioinformatically and experimentally verify that a hydrophobic face is the most accurate singular metric for separating ER and mitochondria-destined yeast TA proteins. A metric focusing on an 11 residue segment of the TMD performs well when classifying human TA proteins. The most inclusive predictor uses both hydrophobicity and C-terminal charge in tandem. This work provides context for previous observations and opens the door for more detailed mechanistic experiments to determine the molecular factors driving this recognition.

Mismatch repair deficiency predicts response to HER2 blockade in HER2-negative breast cancer.

Resistance to endocrine treatment occurs in ~30% of ER+ breast cancer patients resulting in ~40,000 deaths/year in the USA. Preclinical studies strongly implicate activation of growth factor receptor, HER2 in endocrine treatment resistance. However, clinical trials of pan-HER inhibitors in ER+/HER2- patients have disappointed, likely due to a lack of predictive biomarkers. Here we demonstrate that loss of mismatch repair activates HER2 after endocrine treatment in ER+/HER2- breast cancer cells by protecting HER2 from protein trafficking. Additionally, HER2 activation is indispensable for endocrine treatment resistance in MutL- cells. Consequently, inhibiting HER2 restores sensitivity to endocrine treatment. Patient data from multiple clinical datasets supports an association between MutL loss, HER2 upregulation, and sensitivity to HER inhibitors in ER+/HER2- patients. These results provide strong rationale for MutL loss as a first-in-class predictive marker of sensitivity to combinatorial treatment with endocrine intervention and HER inhibitors in endocrine treatment-resistant ER+/HER2- breast cancer patients.

Moltemplate: A Tool for Coarse-Grained Modeling of Complex Biological Matter and Soft Condensed Matter Physics.

Coarse-grained models have long been considered indispensable tools in the investigation of biomolecular dynamics and assembly. However, the process of simulating such models is arduous because unconventional force fields and particle attributes are often needed, and some systems are not in thermal equilibrium. Although modern molecular dynamics programs are highly adaptable, software designed for preparing all-atom simulations typically makes restrictive assumptions about the nature of the particles and the forces acting on them. Consequently, the use of coarse-grained models has remained challenging. Moltemplate is a file format for storing coarse-grained molecular models and the forces that act on them, as well as a program that converts moltemplate files into input files for LAMMPS, a popular molecular dynamics engine. Moltemplate has broad scope and an emphasis on generality. It accommodates new kinds of forces as they are developed for LAMMPS, making moltemplate a popular tool with thousands of users in computational chemistry, materials science, and structural biology. To demonstrate its wide functionality, we provide examples of using moltemplate to prepare simulations of fluids using many-body forces, coarse-grained organic semiconductors, and the motor-driven supercoiling and condensation of an entire bacterial chromosome.

The STI1-domain is a flexible alpha-helical fold with a hydrophobic groove.

STI1-domains are present in a variety of co-chaperone proteins and are required for the transfer of hydrophobic clients in various cellular processes. The domains were first identified in the yeast Sti1 protein where they were referred to as DP1 and DP2. Based on hidden Markov model searches, this domain had previously been found in other proteins including the mammalian co-chaperone SGTA, the DNA damage response protein Rad23, and the chloroplast import protein Tic40. Here, we refine the domain definition and carry out structure-based sequence alignment of STI1-domains showing conservation of five amphipathic helices. Upon examinations of these identified domains, we identify a preceding helix 0 and unifying sequence properties, determine new molecular models, and recognize that STI1-domains nearly always occur in pairs. The similarity at the sequence, structure, and molecular levels likely supports a unified functional role.

Molecular basis of tail-anchored integral membrane protein recognition by the cochaperone Sgt2.

The targeting and insertion of tail-anchored (TA) integral membrane proteins (IMPs) into the correct membrane is critical for cellular homeostasis. The fungal protein Sgt2, and its human homolog SGTA, is the entry point for clients to the guided entry of tail-anchored protein (GET) pathway, which targets endoplasmic reticulum-bound TA IMPs. Consisting of three structurally independent domains, the C terminus of Sgt2 binds to the hydrophobic transmembrane domain (TMD) of clients. However, the exact binding interface within Sgt2 and molecular details that underlie its binding mechanism and client preference are not known. Here, we reveal the mechanism of Sgt2 binding to hydrophobic clients, including TA IMPs. Through sequence analysis, biophysical characterization, and a series of capture assays, we establish that the Sgt2 C-terminal domain is flexible but conserved and sufficient for client binding. A molecular model for this domain reveals a helical hand forming a hydrophobic groove approximately 15 Å long that is consistent with our observed higher affinity for client TMDs with a hydrophobic face and a minimal length of 11 residues. This work places Sgt2 into a broader family of TPR-containing cochaperone proteins, demonstrating structural and sequence-based similarities to the DP domains in the yeast Hsp90 and Hsp70 coordinating protein, Sti1.

High quality imaging and dosimetry for yttrium-90 (90Y) liver radioembolization using a SiPM-based PET/CT scanner.

PURPOSE: Transarterial radioembolization (TARE) with yttrium-90 (90Y) microspheres is a liver-directed treatment for primary and secondary hepatic malignancies. Personalized dosimetry aims for maximum treatment effect and reduced toxicity. We aimed to compare pre-treatment voxel-based dosimetry from 99mTc macroaggregated albumin (MAA) SPECT/CT with post-treatment 90Y PET/CT for absorbed dose values, and to evaluate image quality of 90Y SiPM-based PET/CT. METHODS: Forty-two patients (28 men, 14 women, mean age: 67 ± 11 years) with advanced hepatic malignancies were prospectively enrolled. Twenty patients were treated with glass and 22 with resin microspheres. Radiation absorbed doses from planning 99mTc-MAA SPECT/CT and post-therapy 90Y PET/CT were assessed. 90Y PET/CT images were acquired for 20 min and reconstructed to produce 5-, 10-, 15-, and 20-min datasets, then evaluated using the 5-point Likert scale. RESULTS: The mean administered activity was 3.44 ± 1.5 GBq for glass and 1.62 ± 0.7 GBq for resin microspheres. The mean tumor absorbed doses calculated from 99mTc-MAA SPECT/CT and 90Y PET/CT were 175.69 ± 113.76 Gy and 193.58 ± 111.09 Gy (P = 0.61), respectively for glass microspheres; they were 60.18 ± 42.20 Gy and 70.98 ± 49.65 Gy (P = 0.37), respectively for resin microspheres. The mean normal liver absorbed doses from 99mTc-MAA SPECT/CT and 90Y PET/CT were 32.70 ± 22.25 Gy and 30.62 ± 20.09 Gy (P = 0.77), respectively for glass microspheres; they were 18.33 ± 11.08 Gy and 24.32 ± 15.58 Gy (P = 0.17), respectively for resin microspheres. Image quality of 90Y PET/CT at 5-, 10-, 15-, and 20-min scan time showed a Likert score of 3.6 ± 0.54, 4.57 ± 0.58, 4.84 ± 0.37, and 4.9 ± 0.3, respectively. CONCLUSIONS: 99mTc-MAA SPECT/CT demonstrated great accuracy for treatment planning dosimetry. SiPM-based PET/CT scanner showed good image quality at 10-min scan time, acquired in one bed position. A PET/CT scan time of 5 min showed acceptable image quality and suffices for dosimetry and treatment verification. This allows for inclusion of 90Y PET/CT in busy routine clinical workflows. Studies with larger patient cohorts are needed to confirm these findings.