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BACKGROUND: Bicuspid aortic valve (BAV) is often associated with a concomitant aortopathy. However, few studies have evaluated the effect of the aortic valve (AV) phenotype on the rate of dilation of the aorta. This study aimed to compare the progression rate of aorta dimensions according to AV phenotype (BAV vs tricuspid AV (TAV)), fusion type and sex in patients with aortic stenosis (AS). METHODS: 310 patients with AS (224 TAV and 86 BAV) recruited in the Metabolic Determinants of the Progression of Aortic Stenosis study (PROGRESSA, NCT01679431) were included in this analysis. Doppler echocardiography was performed annually to assess AS severity and measure ascending aorta (AA) dimensions. Baseline and last follow-up visit measurements were used to assess the annualised change. RESULTS: Median AA annualised change was larger in BAV versus TAV (0.33±0.65 mm/year vs 0.21±0.56 mm/year, p=0.04). In the whole cohort, BAV phenotype and higher low-density lipoprotein (LDL) levels were significantly associated with fast progression of AA dilation in univariate analysis (OR 1.80, 95% CI 1.08 to 2.98, p=0.02; 1.37, 95% CI 1.04 to 1.80, p=0.03, respectively). AA dilation rate did not vary according to the BAV subtype (p=0.142). Predictors of AA progression rate were different between valve phenotypes, with higher apolipoprotein B/apolipoprotein A-I ratio, higher baseline peak aortic jet velocity (Vpeak) and smaller baseline AA diameter in the TAV cohort (all p

The list of Curing Coma Campaign Collaborators included as a file in Supplementary Information has been updated. Flora Hammond, Raimund Helbok, and Naomi Niznick have been added to the list. Several spelling errors have been corrected. A revised file has been included.

BACKGROUND: Little is known about the effect of sex on functional status decline in aortic valve stenosis (AS) patients. OBJECTIVES: The purpose of this study was to examine the changes in functional status according to sex in patients with mild-to-moderate AS and its association with the composite of death or aortic valve replacement (AVR). METHODS: We included patients with mild-to-moderate AS prospectively recruited in the PROGRESSA (Metabolic Determinants of the Progression of Aortic Stenosis) study (NCT01679431). Functional status was assessed using the New York Heart Association classification and the Duke Activity Status Index (DASI). RESULTS: A total of 244 patients (mean age 64 ± 14 years, 29% women) were included. The mean follow-up was 4.3 ± 2.4 years. Women with intermediate-to-fast AS progression rate (median change in peak aortic jet velocity ≥0.11 m/s/year) had significantly faster decline in DASI score compared to men with similar progression rate (P

BACKGROUND: Aortic valve stenosis (AS) is a progressive chronic disease with progression rates that vary in patients and therefore difficult to predict. OBJECTIVES: The aim of this study was to predict the progression of AS using comprehensive and longitudinal patient data. METHODS: Machine and deep learning algorithms were trained on a data set of 303 patients enrolled in the PROGRESSA (Metabolic Determinants of the Progression of Aortic Stenosis) study who underwent clinical and echocardiographic follow-up on an annual basis. Performance of the models was measured to predict disease progression over long (next 5 years) and short (next 2 years) terms and was compared to a standard clinical model with usually used features in clinical settings based on logistic regression. RESULTS: For each annual follow-up visit including baseline, we trained various supervised learning algorithms in predicting disease progression at 2- and 5-year terms. At both terms, LightGBM consistently outperformed other models with the highest average area under curves across patient visits (0.85 at 2 years, 0.83 at 5 years). Recurrent neural network-based models (Gated Recurrent Unit and Long Short-Term Memory) and XGBoost also demonstrated strong predictive capabilities, while the clinical model showed the lowest performance. CONCLUSIONS: This study demonstrates how an artificial intelligence-guided approach in clinical routine could help enhance risk stratification of AS. It presents models based on multisource comprehensive data to predict disease progression and clinical outcomes in patients with mild-to-moderate AS at baseline.

BACKGROUND: The efficacy of avalglucosidase alfa (AVA) versus alglucosidase alfa (ALG) on forced vital capacity percent predicted (FVCpp) in patients with late-onset Pompe disease (LOPD) has been assessed in the Phase 3 COMET trial (NCT02782741). Due to the rarity of LOPD and thus small sample size in COMET, additional data were analyzed to gain further insights into the efficacy of AVA versus ALG. METHODS: Data from treatment-naive patients with LOPD were pooled from COMET and Phase 1/2 NEO1/NEO-EXT (NCT01898364/NCT02032524) trials for patients treated with AVA, and Phase 3 LOTS trial (NCT00158600) for patients treated with ALG. Regression analyses using mixed models with repeated measures consistent with those pre-specified in COMET were performed post-hoc. Analyses were adjusted for trials and differences in baseline characteristics. Four models were developed: Model 1 considered all trials; Model 2 included Phase 3 trials; Model 3 included Phase 3 trials and was adjusted for baseline ventilation use; Model 4 included COMET and NEO1/NEO-EXT (i.e., AVA trials only). RESULTS: Overall, 100 randomized patients from COMET (AVA, n = 51, ALG, n = 49), 60 from LOTS (ALG arm only), and three patients from NEO1/NEO-EXT (who received open-label AVA only) were considered for analysis. Mean age at enrollment was similar across trials (45.3-50.3 years); however, patients from LOTS had a longer mean duration of disease versus COMET and NEO1/NEO-EXT trials (9.0 years and 0.5-2.2 years, respectively) and younger mean age at diagnosis (36.2 years and 44.7-48.6 years, respectively). Least squares mean (95% confidence interval) improvement from baseline in FVCpp at Week 49-52 for AVA versus ALG was 2.43 (-0.13; 4.99) for COMET (n = 98); 2.31 (0.06; 4.57) for Model 1 (n = 160); 2.43 (0.21; 4.65) for Model 2 (n = 157); 2.80 (0.54; 5.05) for Model 3 (n = 154); and 2.27 (-0.30; 4.45) for Model 4 (n = 101). CONCLUSIONS: Models 1 to 3, which had an increased sample size versus COMET, demonstrated a nominally significant effect on FVCpp favoring AVA versus ALG after 1 year of treatment, consistent with results from COMET.

Clonal cytopenia of undetermined significance (CCUS) represents a distinct disease entity characterized by myeloid-related somatic mutations with a variant allele fraction of ≥2% in individuals with unexplained cytopenia(s) but without a myeloid neoplasm (MN). Notably, CCUS carries a risk of progressing to MN, particularly in cases featuring high-risk mutations. Understanding CCUS requires dedicated studies to elucidate its risk factors and natural history. Our analysis of 357 CCUS patients investigated the interplay between clonality, cytopenia, and prognosis. Multivariate analysis identified 3 key adverse prognostic factors: the presence of splicing mutation(s) (score = 2 points), platelet count

BACKGROUND: Prominent multi-scallop systolic leaflet displacement toward the left atrium (atrialization) is typically observed in bileaflet mitral valve prolapse (MVP) with mitral annular disjunction. We hypothesized that mitral leaflet atrialization is associated with an underlying left atrial (LA) myopathy characterized by progressive structural and functional abnormalities, irrespective of mitral regurgitation (MR) severity. METHODS: We identified 334 consecutive patients with MVP, no prior atrial fibrillation, and comprehensive clinical and echocardiographic data. LA function was assessed by LA reservoir strain, LA function index, and LA emptying fraction. We also classified the stage of LA remodeling based on LA enlargement and LA reservoir strain (stage 1: no remodeling; stage 2: mild remodeling; stage 3: moderate remodeling; and stage 4: severe remodeling). The primary end point was the composite risk of sudden arrhythmic death, heart failure hospitalization, or the new onset of atrial fibrillation. RESULTS: Bileaflet MVP with no or mild MR had a lower LA reservoir strain (P=0.04) and LA function index (P

QS-21 is a potent vaccine adjuvant currently sourced by extraction from the Chilean soapbark tree. It is a key component of human vaccines for shingles, malaria, coronavirus disease 2019 and others under development. The structure of QS-21 consists of a glycosylated triterpene scaffold coupled to a complex glycosylated 18-carbon acyl chain that is critical for immunostimulant activity. We previously identified the early pathway steps needed to make the triterpene glycoside scaffold; however, the biosynthetic route to the acyl chain, which is needed for stimulation of T cell proliferation, was unknown. Here, we report the biogenic origin of the acyl chain, characterize the series of enzymes required for its synthesis and addition and reconstitute the entire 20-step pathway in tobacco, thereby demonstrating the production of QS-21 in a heterologous expression system. This advance opens up unprecedented opportunities for bioengineering of vaccine adjuvants, investigating structure-activity relationships and understanding the mechanisms by which these compounds promote the human immune response.

A key control on the magnitude of coastal eutrophication is the degree to which currents quickly transport nitrogen derived from human sources away from the coast to the open ocean before eutrophication develops. In the Southern California Bight (SCB), an upwelling-dominated eastern boundary current ecosystem, anthropogenic nitrogen inputs increase algal productivity and cause subsurface acidification and oxygen (O 2 ) loss along the coast. However, the extent of anthropogenic influence on eutrophication beyond the coastal band, and the physical transport mechanisms and biogeochemical processes responsible for these effects are still poorly understood. Here, we use a submesoscale-resolving numerical model to document the detailed biogeochemical mass balance of nitrogen, carbon and oxygen, their physical transport, and effects on offshore habitats. Despite management of terrestrial nutrients that has occurred in the region over the last 20 years, coastal eutrophication continues to persist. The input of anthropogenic nutrients promote an increase in productivity, remineralization and respiration offshore, with recurrent O 2 loss and pH decline in a region located 30-90 km from the mainland. During 2013 to 2017, the spatially averaged 5-year loss rate across the Bight was 1.3 mmol m -3 O 2 , with some locations losing on average up to 14.2 mmol m -3 O 2 . The magnitude of loss is greater than model uncertainty assessed from data-model comparisons and from quantification of intrinsic variability. This phenomenon persists for 4 to 6 months of the year over an area of 278,40 km 2 ( ∼ 30% of SCB area). These recurrent features of acidification and oxygen loss are associated with cross-shore transport of nutrients by eddies and plankton biomass and their accumulation and retention within persistent eddies offshore within the SCB.

Compositionality, or the ability to build complex representations from discrete elements, is an essential ingredient of human intelligence. Compositionality enables people to think productively, learn fast from limited experience, and generalize knowledge to new contexts without re-learning from scratch. It is also essential in information processing systems to efficiently represent structured data and has seen application in compression and symbolic Artificial Intelligence (AI). Historically, the notion of compositionality played a central role in linguistic theory and philosophy of mind. More recently, it is attracting a surge of interest throughout the domains of cognitive science. Compositional processes are leveraged for elucidating the nature of mental representations in cognition (Dehaene et al., 2022), understanding the functional organisation of the brain (Agrawal et al., 2019), or building Artificial Intelligence systems that are robust to changes in the environment (Hupkes et al., 2020).

Reducing inequality, mitigating climate change, and responding to public health crises are large-scale goals that require the cooperation and coordination of many individuals. These goals cannot be achieved by one individual alone, and contributing is not always beneficial to each individual. And yet, individuals must contribute in order to make a difference. How do we hold individuals and groups responsible for collective action?

One hallmark of human language is its combinatoriality---reusing a relatively small inventory of building blocks to create a far larger inventory of increasingly complex structures. In this paper, we explore the idea that combinatoriality in language reflects a human inductive bias toward representational efficiency in symbol systems. We develop a computational framework for discovering structure in a writing system. Built on top of state-of-the-art library learning and program synthesis techniques, our computational framework discovers known linguistic structures in the Chinese writing system and reveals how the system evolves towards simplification under pressures for representational efficiency. We demonstrate how a library learning approach, utilizing learned abstractions and compression, may help reveal the fundamental computational principles that underlie the creation of combinatorial structures in human cognition, and offer broader insights into the evolution of efficient communication systems.

We can evaluate features of problems and their potential solutions well before we can effectively solve them. When considering a game we have never played, for instance, we might infer whether it is likely to be challenging, fair, or fun simply from hearing the game rules, prior to deciding whether to invest time in learning the game or trying to play it well. Many studies of game play have focused on optimality and expertise, characterizing how people and computational models play based on moderate to extensive search and after playing a game dozens (if not thousands or millions) of times. Here, we study how people reason about a range of simple but novel connect-n style board games. We ask people to judge how fair and how fun the games are from very little experience: just thinking about the game for a minute or so, before they have ever actually played with anyone else, and we propose a resource-limited model that captures their judgments using only a small number of partial game simulations and almost no lookahead search. For more information about this project, see https://sites.google.com/view/intuitive-game-theory

Despite the fact that beliefs are mental states that cannot be directly observed, humans talk about each others' beliefs on a regular basis, often using rich compositional language to describe what others think and know. What explains this capacity to interpret the hidden epistemic content of other minds? In this paper, we take a step towards an answer by grounding the semantics of belief statements in a Bayesian theory-of-mind: By modeling how humans jointly infer coherent sets of goals, beliefs, and plans that explain an agent's actions, then evaluating statements about the agent's beliefs against these inferences via epistemic logic, our framework provides a functional role semantics for belief, explaining the gradedness and compositionality of human belief attributions, as well as their intimate connection with goals and plans. We evaluate this framework by studying how humans attribute goals and evaluate belief sentences while watching an agent solve a doors-and-keys gridworld puzzle that requires instrumental reasoning about hidden objects. In contrast to pure logical deduction, non-mentalizing baselines, and mentalizing that ignores the role of instrumental plans, our model provides a much better fit to human goal and belief attributions, demonstrating the importance of theory-of-mind for modeling how humans understand language about beliefs.

We tailor the explanations we give depending on the person asking for them – you would explain why an event happened differently depending on which of the contributing causes the listener already knows. While significant prior work focuses on how causal structure in the world influences explanation, we focus on how explanation production is modulated by listener belief. We propose a computational model framing explanation as rational communication about causal events, using a recursive theory-of-mind and language production framework to choose amongst possible explanatory utterances that minimize the divergence between speaker and listener belief about a why an event happened. We evaluate our model using some partial observer stimuli, which manipulate the listener's stated prior knowledge about an event, and find that our model well-predicts human judgements about which of several contributing causes is the best explanation for a speaker to provide by modeling their communicative value to the listener.

High-resolution ice core records from coastal Antarctica are particularly useful to inform our understanding of environmental changes and their drivers. Here, we present a decadally resolved record of sea-salt sodium (a proxy for open-ocean area) and non-sea salt calcium (a proxy for continental dust) from the well-dated Roosevelt Island Climate Evolution (RICE) core, focusing on the time period between 40-26 ka BP. The RICE dust record exhibits an abrupt shift towards a higher mean dust concentration at 32 ka BP. Investigating existing ice-core records, we find this shift is a prominent feature across Antarctica. We propose that this shift is linked to an equatorward displacement of Southern Hemisphere westerly winds. Subsequent to the wind shift, data suggest a weakening of Southern Ocean upwelling and a decline of atmospheric CO2 to lower glacial values, hence making this shift an important glacial climate event with potentially important insights for future projections.

BRAT1 biallelic variants are associated with rigidity and multifocal seizure syndrome, lethal neonatal (RMFSL), and neurodevelopmental disorder associating cerebellar atrophy with or without seizures syndrome (NEDCAS). To date, forty individuals have been reported in the literature. We collected clinical and molecular data from 57 additional cases allowing us to study a large cohort of 97 individuals and draw phenotype-genotype correlations. Fifty-nine individuals presented with BRAT1-related RMFSL phenotype. Most of them had no psychomotor acquisition (100%), epilepsy (100%), microcephaly (91%), limb rigidity (93%), and died prematurely (93%). Thirty-eight individuals presented a non-lethal phenotype of BRAT1-related NEDCAS phenotype. Seventy-six percent of the patients in this group were able to walk and 68% were able to say at least a few words. Most of them had cerebellar ataxia (82%), axial hypotonia (79%) and cerebellar atrophy (100%). Genotype-phenotype correlations in our cohort revealed that biallelic nonsense, frameshift or inframe deletion/insertion variants result in the severe BRAT1-related RMFSL phenotype (46/46; 100%). In contrast, genotypes with at least one missense were more likely associated with NEDCAS (28/34; 82%). The phenotype of patients carrying splice variants was variable: 41% presented with RMFSL (7/17) and 59% with NEDCAS (10/17).

BackgroundComplete closure of large mucosal defects following colorectal endoscopic submucosal dissection (ESD) with through-the-scope (TTS) clips is oftentimes not possible. We aimed to report our early experience of using a novel TTS suturing system for the closure of large mucosal defects after colorectal ESD.MethodsWe performed a retrospective multicenter cohort study of consecutive patients who underwent attempted prophylactic defect closure using the TTS suturing system after colorectal ESD. The primary outcome was technical success in achieving complete defect closure, defined as a

AbstractTwo decades of high-resolution satellite observations and climate modeling studies have indicated strong ocean–atmosphere coupled feedback mediated by ocean mesoscale processes, including semipermanent and meandrous SST fronts, mesoscale eddies, and filaments. The air–sea exchanges in latent heat, sensible heat, momentum, and carbon dioxide associated with this so-called mesoscale air–sea interaction are robust near the major western boundary currents, Southern Ocean fronts, and equatorial and coastal upwelling zones, but they are also ubiquitous over the global oceans wherever ocean mesoscale processes are active. Current theories, informed by rapidly advancing observational and modeling capabilities, have established the importance of mesoscale and frontal-scale air–sea interaction processes for understanding large-scale ocean circulation, biogeochemistry, and weather and climate variability. However, numerous challenges remain to accurately diagnose, observe, and simulate mesoscale air–sea interaction to quantify its impacts on large-scale processes. This article provides a comprehensive review of key aspects pertinent to mesoscale air–sea interaction, synthesizes current understanding with remaining gaps and uncertainties, and provides recommendations on theoretical, observational, and modeling strategies for future air–sea interaction research.Significance StatementRecent high-resolution satellite observations and climate models have shown a significant impact of coupled ocean–atmosphere interactions mediated by small-scale (mesoscale) ocean processes, including ocean eddies and fronts, on Earth’s climate. Ocean mesoscale-induced spatial temperature and current variability modulate the air–sea exchanges in heat, momentum, and mass (e.g., gases such as water vapor and carbon dioxide), altering coupled boundary layer processes. Studies suggest that skillful simulations and predictions of ocean circulation, biogeochemistry, and weather events and climate variability depend on accurate representation of the eddy-mediated air–sea interaction. However, numerous challenges remain in accurately diagnosing, observing, and simulating mesoscale air–sea interaction to quantify its large-scale impacts. This article synthesizes the latest understanding of mesoscale air–sea interaction, identifies remaining gaps and uncertainties, and provides recommendations on strategies for future ocean–weather–climate research.

OBJECTIVES: The aim of this study was to retrospectively evaluate the signalment, treatment, surgical technique and outcomes for feline symblepharon. METHODS: A retrospective medical record review and standardized grading of clinical descriptions and photographs was undertaken. RESULTS: Forty kittens (54 eyes) aged 3-46 weeks had symblepharon of five types in various combinations: eyelid deformation (24 kittens; 32 eyes); ankyloblepharon (four kittens; four eyes); conjunctiva-to-conjunctiva (11 kittens; 12 eyes); third eyelid-to-conjunctiva (24 kittens; 29 eyes); and corneoconjunctival adhesions (14 kittens; 16 eyes). At initial presentation, 23 (43%) eyes were affected by one type of symblepharon, 25 (46%) eyes by two types and six (11%) eyes by three types; 11 (20%) corneas were ulcerated. Twenty-four (44%) eyes of 18 (45%) kittens were managed medically. Surgery was performed under general anesthesia/sedation (30 occasions) or topical anesthesia (21 occasions) on 30 (56%) eyes of 22 kittens; 12 eyes (40%) underwent multiple surgeries. Four techniques were commonly employed: separation of conjunctival-to-conjunctival adhesions ± eyelid margins (14 eyes); resection of third eyelid adhesions ± temporary tacking of the third eyelid (modified Arlts pterygium technique; 18 eyes); en bloc resection of the third eyelid (two eyes); and separation of corneoconjunctival adhesions (14 eyes). Median duration of follow-up was 55 days (range 1-1051). Median symblepharon grade in kittens treated surgically improved for all types except corneoconjunctival symblepharon. Median symblepharon grade in kittens receiving medical management remained the same or improved. Corneoconjunctival symblepharon opacity decreased for eyes treated surgically but increased for eyes treated medically. Three eyes were enucleated due to complications of corneoconjunctival symblepharon. At final presentation, symblepharon persisted in 46 (85%) eyes; however, menace response was evident in 13/16 eyes and dazzle reflex in 23/23 eyes. CONCLUSIONS AND RELEVANCE: Symblepharon is a heterogeneous group of conditions with diverse anatomic involvement, clinical appearance and impact, optimal treatment and prognosis for vision.

The study of flow and particle dynamics in microfluidic cross-slot channels is of high relevance for lab-on-a-chip applications. In this work, we investigate the dynamics of a rigid spherical particle in a cross-slot junction for a channel height-to-width ratio of 0.6 and at a Reynolds number of 120 for which a steady vortex exists in the junction area. Using an in-house immersed-boundary-lattice-Boltzmann code, we analyse the effect of the entry position of the particle in the junction and the particle size on the dynamics and trajectory shape of the particle. We find that the dynamics of the particle depend strongly on its lateral entry position in the junction and weakly on its vertical entry position; particles that enter close to the centre show trajectory oscillations. Larger particles have longer residence times in the junction and tend to oscillate less due to their confinement. Our work contributes to the understanding of particle dynamics in intersecting flows and enables the design of optimised geometries for cytometry and particle manipulation.

IntroductionAlthough the physiological role of the C-terminal hydrolase domain of the soluble epoxide hydrolase (sEH-H) is well investigated, the function of its N-terminal phosphatase activity (sEH-P) remains unknown.ObjectivesThis study aimed to assess in vivo the physiological role of sEH-P.MethodsCRISPR/Cas9 was used to generate a novel knock-in (KI) rat line lacking the sEH-P activity.ResultsThe sEH-P KI rats has a decreased metabolism of lysophosphatidic acids to monoacyglycerols. KI rats grew almost normally but with less weight and fat mass gain while insulin sensitivity was increased compared to wild-type rats. This lean phenotype was more marked in males than in female KI rats and mainly due to decreased food consumption and enhanced energy expenditure. In fact, sEH-P KI rats had an increased lipolysis allowing to supply fatty acids as fuel to potentiate brown adipose thermogenesis under resting condition and upon cold exposure. The potentiation of thermogenesis was abolished when blocking PPARγ, a nuclear receptor activated by intracellular lysophosphatidic acids, but also when inhibiting simultaneously sEH-H, showing a functional interaction between the two domains. Furthermore, sEH-P KI rats fed a high-fat diet did not gain as much weight as the wild-type rats, did not have increased fat mass and did not develop insulin resistance or hepatic steatosis. In addition, sEH-P KI rats exhibited enhanced basal cardiac mitochondrial activity associated with an enhanced left ventricular contractility and were protected against cardiac ischemia-reperfusion injury.ConclusionOur study reveals that sEH-P is a key player in energy and fat metabolism and contributes together with sEH-H to the regulation of cardiometabolic homeostasis. The development of pharmacological inhibitors of sEH-P appears of crucial importance to evaluate the interest of this promising therapeutic strategy in the management of obesity and cardiac ischemic complications.

Human language richly invokes our intuitive physical knowledge. We talk about physical objects, scenes, properties, and events; and we can ask questions and answer them with predictions and inferences about physical worlds described entirely in language. How does language construct meanings that connect to our general physical reasoning? In this paper, we propose PiLoT, a computational model that maps language into a probabilistic language of thought—meanings are constructed as probabilistic programs, which provide a formal basis for probabilistic and physical reasoning. Our model uses a large language model (LLM) to map from language to meanings and a probabilistic physics engine to support inferences over scenes described in language. We conduct a linguistic reasoning experiment based on prior psychophysics studies that requires reasoning about physical outcomes based on linguistic descriptions. We show that PiLoT well predicts human judgments across this experiment and outperforms baseline models which use the LLM to directly perform the same task.

Inhibitors of soluble epoxide hydrolase (sEH), which catalyzes the hydrolysis of various natural epoxides to their corresponding diols, present an opportunity for developing oral drugs for a range of human cardiovascular and inflammatory diseases, including, among others, diabetes and neuropathic pain. However, some evidence suggests that their administration may precipitate the development of pulmonary hypertension (PH). We thus evaluated the impact of chronic oral administration of the sEH inhibitor TPPU (N-[1-(1-Oxopropyl)-4-piperidinyl]-N'-[4-(trifluoromethoxy)phenyl]-urea) on hemodynamics, pulmonary vascular reactivity, and remodeling, as well as on right ventricular (RV) dimension and function at baseline and in the Sugen (SU5416) + hypoxia (SuHx) rat model of severe PH. Treatment with TPPU started 5 weeks after SU5416 injection for 3 weeks. No differences regarding the increase in pulmonary vascular resistance, remodeling, and inflammation, nor the abolishment of phenylephrine-induced pulmonary artery constriction, were noted in SuHx rats. In addition, TPPU did not modify the development of RV dysfunction, hypertrophy, and fibrosis in SuHx rats. Similarly, none of these parameters were affected by TPPU in normoxic rats. Complementary in vitro data demonstrated that TPPU reduced the proliferation of cultured human pulmonary artery-smooth muscle cells (PA-SMCs). This study demonstrates that inhibition of sEH does not induce nor aggravate the development of PH and RV dysfunction in SuHx rats. In contrast, a potential beneficial effect against pulmonary artery remodeling in humans is suggested.

The relationship between communicated language and intended meaning is often probabilistic and sensitive to context. Numerous strategies attempt to estimate such a mapping, often leveraging recursive Bayesian models of communication. In parallel, LLMs have been increasingly applied to semantic parsing applications, tasked with inferring logical representations from natural language. While existing LLM explorations have been largely restricted to literal language use, in this work, we evaluate the capacity of LLMs to infer the meanings of pragmatic utterances. Specifically, we explore the case of threshold estimation on the gradable adjective “strong”, contextually conditioned on a strength prior, then extended to composition with qualification, negation, polarity inversion, and class comparison. We find that LLMs can derive context-grounded, human-like distributions over the interpretations of several complex pragmatic utterances, yet struggle composing with negation. These results inform the inferential capacity of statistical language models, and their use in pragmatic and semantic parsing applications.

Abstraction enables humans to distill a cascade of sensory experiences into a useful format for making sense of the world and generalizing to new contexts. In developing theories of how these various forms of abstraction are discovered and used, cognitive scientists have proposed a multitude of representational formats with different properties to capture behavioral data and neural activity. However, because abstraction manifests in human cognition and behavior in so many ways, individual communities within cognitive science have generally studied these specific forms of abstraction under domain-specific representational assumptions. The goal of this workshop is to facilitate the search for unifying principles governing how humans learn, discover, and use abstractions in different domains, by providing a venue for the exchange of theoretical and empirical insights between research communities.

Integrated virus genomes (prophages) are commonly found in sequenced bacterial genomes but have rarely been described in detail for rhizobial genomes. Cupriavidus taiwanensis STM 6018 is a rhizobial Betaproteobacteria strain that was isolated in 2006 from a root nodule of a Mimosa pudica host in French Guiana, South America. Here we describe features of the genome of STM 6018, focusing on the characterization of two different types of prophages that have been identified in its genome. The draft genome of STM 6018 is 6,553,639 bp, and consists of 80 scaffolds, containing 5,864 protein-coding genes and 61 RNA genes. STM 6018 contains all the nodulation and nitrogen fixation gene clusters common to symbiotic Cupriavidus species; sharing >99.97% bp identity homology to the nod/nif/noeM gene clusters from C. taiwanensis LMG19424T and "Cupriavidus neocalidonicus" STM 6070. The STM 6018 genome contains the genomes of two prophages: one complete Mu-like capsular phage and one filamentous phage, which integrates into a putative dif site. This is the first characterization of a filamentous phage found within the genome of a rhizobial strain. Further examination of sequenced rhizobial genomes identified filamentous prophage sequences in several Beta-rhizobial strains but not in any Alphaproteobacterial rhizobia.

Salivary gland acinar cells are severely depleted after radiotherapy for head and neck cancer, leading to loss of saliva and extensive oro-digestive complications. With no regenerative therapies available, organ dysfunction is irreversible. Here, using the adult murine system, we demonstrate that radiation-damaged salivary glands can be functionally regenerated via sustained delivery of the neurogenic muscarinic receptor agonist cevimeline. We show that endogenous gland repair coincides with increased nerve activity and acinar cell division that is limited to the first week after radiation, with extensive acinar cell degeneration, dysfunction, and cholinergic denervation occurring thereafter. However, we found that mimicking cholinergic muscarinic input via sustained local delivery of a cevimeline-alginate hydrogel was sufficient to regenerate innervated acini and retain physiological saliva secretion at nonirradiated levels over the long term (>3 months). Thus, we reveal a previously unknown regenerative approach for restoring epithelial organ structure and function that has extensive implications for human patients.

Abstract: The Santa Barbara Channel is one of the most productive regions of the California Current System. Yet, the physical processes that sustain this high productivity remain unclear. We use a high‐resolution physical‐biogeochemical model to show that submesoscale eddies generated by islands are energized by orographic effects on the wind, with significant impacts on nutrient, carbon, and oxygen cycles. These eddies are modulated by two co‐occurring air‐sea‐land interactions: transfer of wind energy to ocean currents that intensifies ocean eddies, and a wind‐current feedback that tends to dampen them. Here we show that the dampening is overwhelmed by fine scale wind patterns induced by the presence of surrounding capes and islands. The fine‐scale winds cause an additional transfer of momentum from the atmosphere to the ocean that energizes submesoscale eddies. This drives upward doming of isopycnals in the center of the channel, allowing a more efficient injection of nutrients to the surface, and triggering intense phytoplankton blooms that nearly double productivity relative to the case without fine‐scale winds. The intensification of the doming effect by the wind‐curl and submesoscale eddies pumps deep low oxygen, acidic waters to the center of the cyclonic eddies. These eddies are then transported away from the Channel into the California Current, where they impact a wider area along the central coast, with potential ecological consequences. Our study highlights the important role of air‐sea‐land interactions in modulating coastal processes, and suggests that submesoscale resolving models are required to correctly represent coastal processes and their ecological impacts.

BackgroundImaging features obtained with Fourier-domain optical coherence tomography (FD-OCT) and in vivo confocal microscopy (IVCM) for corneal stromal disorders have been sparsely reported in dogs. This case report is a compilation of imaging features for three cases of different stromal disorders of the canine cornea which have not yet been reported elsewhere.Case presentationLipid deposition in case 1 appeared as needle-shaped hyperreflective lines along the collagen lamellae, which correlated histologically with lipid clefts. In case 2, glycosaminoglycan accumulation by mucopolysaccharidosis type 1 caused diffuse stromal hyperreflectivity and depletion of keratocytes on IVCM and was associated with secondary corneal degeneration presumed to be calcium deposition. In case 3, posterior corneal stromal opacities in the absence of ocular inflammation were identified. Hyperreflective particles were scattered in the middle and posterior corneal stroma on FD-OCT. With IVCM, hyperreflective deposits were identified within keratocytes and the number of enlarged keratocytes containing hyperreflective deposits increased towards the posterior stroma. The bilateral, non-inflammatory nature and unique appearance with IVCM is most consistent with a posterior stromal dystrophy reminiscent of pre-Descemet corneal dystrophy described in humans.ConclusionsIn vivo multimodal corneal imaging facilitated instantaneous microstructural analysis and may be valuable in the differential diagnosis of corneal stromal disorders in veterinary clinical practice. The non-specific nature of imaging findings occurs in some conditions such as mucopolysaccharidosis, thus in vivo corneal imaging should be complemented with other gold standard methods of definitive diagnosis.

Through an expansive international effort that involved data collection on 12 small-angle X-ray scattering (SAXS) and four small-angle neutron scattering (SANS) instruments, 171 SAXS and 76 SANS measurements for five proteins (ribonuclease A, lysozyme, xylanase, urate oxidase and xylose isomerase) were acquired. From these data, the solvent-subtracted protein scattering profiles were shown to be reproducible, with the caveat that an additive constant adjustment was required to account for small errors in solvent subtraction. Further, the major features of the obtained consensus SAXS data over the q measurement range 0-1 Å-1 are consistent with theoretical prediction. The inherently lower statistical precision for SANS limited the reliably measured q-range to 2.2 Å-1 showed good mutual agreement, affirming that this region has interpretable features for structural modelling. SAS measurements with inline size-exclusion chromatography (SEC) proved to be generally superior for eliminating sample heterogeneity, but with unavoidable sample dilution during column elution, while batch SAS data collected at higher concentrations and for longer times provided superior statistical precision. Careful merging of data measured using inline SEC and batch modes, or low- and high-concentration data from batch measurements, was successful in eliminating small amounts of aggregate or interparticle interference from the scattering while providing improved statistical precision overall for the benchmarking data set.

BackgroundTeclistamab is a T-cell-redirecting bispecific antibody that targets both CD3 expressed on the surface of T cells and B-cell maturation antigen expressed on the surface of myeloma cells. In the phase 1 dose-defining portion of the study, teclistamab showed promising efficacy in patients with relapsed or refractory multiple myeloma.MethodsIn this phase 1-2 study, we enrolled patients who had relapsed or refractory myeloma after at least three therapy lines, including triple-class exposure to an immunomodulatory drug, a proteasome inhibitor, and an anti-CD38 antibody. Patients received a weekly subcutaneous injection of teclistamab (at a dose of 1.5 mg per kilogram of body weight) after receiving step-up doses of 0.06 mg and 0.3 mg per kilogram. The primary end point was the overall response (partial response or better).ResultsAmong 165 patients who received teclistamab, 77.6% had triple-class refractory disease (median, five previous therapy lines). With a median follow-up of 14.1 months, the overall response rate was 63.0%, with 65 patients (39.4%) having a complete response or better. A total of 44 patients (26.7%) were found to have no minimal residual disease (MRD); the MRD-negativity rate among the patients with a complete response or better was 46%. The median duration of response was 18.4 months (95% confidence interval [CI], 14.9 to not estimable). The median duration of progression-free survival was 11.3 months (95% CI, 8.8 to 17.1). Common adverse events included cytokine release syndrome (in 72.1% of the patients; grade 3, 0.6%; no grade 4), neutropenia (in 70.9%; grade 3 or 4, 64.2%), anemia (in 52.1%; grade 3 or 4, 37.0%), and thrombocytopenia (in 40.0%; grade 3 or 4, 21.2%). Infections were frequent (in 76.4%; grade 3 or 4, 44.8%). Neurotoxic events occurred in 24 patients (14.5%), including immune effector cell-associated neurotoxicity syndrome in 5 patients (3.0%; all grade 1 or 2).ConclusionsTeclistamab resulted in a high rate of deep and durable response in patients with triple-class-exposed relapsed or refractory multiple myeloma. Cytopenias and infections were common; toxic effects that were consistent with T-cell redirection were mostly grade 1 or 2. (Funded by Janssen Research and Development; MajesTEC-1 ClinicalTrials.gov numbers, NCT03145181 and NCT04557098.).

BackgroundFor the surgical treatment of single-level degenerative spondylolisthesis (DS), patients can be treated with either an anterior or posterior interbody fusion. Prior studies have shown that patients with symptomatic degenerative spondylolisthesis treated surgically maintain substantially greater pain relief and improvement in function when compared to those treated non-operatively, but no consensus has emerged between which approach results in the best outcomes.MethodsThe PearlDiver MARINER database was queried for patients with single-level DS who underwent either an anterior or posterior lumbar interbody fusion. Both populations were compared on multiple outcomes, including reoperation, post-operative complications, and readmission rates at 90 days, as well as rates of reoperation and cauda equina syndrome two-years postoperatively.ResultsAt 90 days patients who underwent anterior interbody were found to have higher rates of DVT (OR 2.53, 95% CI 1.74 - 3.70, p

BACKGROUND Serious mental illnesses (SMI) are common, disabling, and challenging to treat, requiring years of monitoring and treatment adjustments. Stress or reduced medication adherence can lead to rapid worsening of symptoms and behaviors. Illness exacerbations and relapses generally occur with little or no clinician awareness in real time, leaving limited opportunity to modify treatments. Previous research suggests that passive mobile sensing may be beneficial for individuals with SMI by helping them monitor mental health status, behaviors, and quickly detect worsening mental health for prompt assessment and intervention. However, there is too little research on its feasibility and acceptability in patients with SMI, and the extent to which passive data can predict changes in behaviors and symptoms. OBJECTIVE To study the feasibility, acceptability and safety of passive mobile sensing for tracking behaviors and symptoms of patients in treatment for SMI, as well as developing analytics that utilize passive data to predict changes in behaviors and symptoms. METHODS A mobile application (app) monitors and transmits passive mobile sensor and phone utilization data to track activity, sociability and sleep in patients with SMI. The study consists of a user-centered design phase and a mobile sensing phase. In the design phase, focus groups, interviews and in-lab usability testing inform further app development. In the mobile sensing phase, passive mobile sensing occurs with participants engaging in weekly assessments for up to nine months. Three and nine month interviews study the perceptions of passive mobile sensing and ease of app use. Clinician interviews before and after the mobile sensing phase study the usefulness and feasibility of app utilization in clinical care. Predictive analytic models are built, trained and selected, and make use of machine learning methods. Models use sensor and phone utilization data to predict behavioral changes and symptoms. RESULTS The study was funded in October 2020 and has received IRB approval. The user-centered design phase, consisting of focus groups, usability testing, and pre-intervention clinician interviews has been completed. Recruitment and enrollment for the mobile sensing phase are ongoing. CONCLUSIONS Findings may inform the development of passive sensing apps and self-tracking in patients with SMI, and integration into care to improve assessment, treatment, and patient outcomes. CLINICALTRIAL ClinicalTrials.gov NCT05023252; https://clinicaltrials.gov/ct2/show/NCT05023252

Conflicts between transcription and replication machinery are a potent source of replication stress and genome instability; however, no technique currently exists to identify endogenous genomic locations prone to transcription-replication interactions. Here, we report a novel method to identify genomic loci prone to transcription-replication interactions termed transcription-replication immunoprecipitation on nascent DNA sequencing, TRIPn-Seq. TRIPn-Seq employs the sequential immunoprecipitation of RNA polymerase 2 phosphorylated at serine 5 (RNAP2s5) followed by enrichment of nascent DNA previously labeled with bromodeoxyuridine. Using TRIPn-Seq, we mapped 1009 unique transcription-replication interactions (TRIs) in mouse primary B cells characterized by a bimodal pattern of RNAP2s5, bidirectional transcription, an enrichment of RNA:DNA hybrids, and a high probability of forming G-quadruplexes. TRIs are highly enriched at transcription start sites and map to early replicating regions. TRIs exhibit enhanced Replication Protein A association and TRI-associated genes exhibit higher replication fork termination than control transcription start sites, two marks of replication stress. TRIs colocalize with double-strand DNA breaks, are enriched for deletions, and accumulate mutations in tumors. We propose that replication stress at TRIs induces mutations potentially contributing to age-related disease, as well as tumor formation and development.

Class switch recombination generates distinct antibody isotypes critical to a robust adaptive immune system, and defects are associated with autoimmune disorders and lymphomagenesis. Transcription is required during class switch recombination to recruit the cytidine deaminase AID-an essential step for the formation of DNA double-strand breaks-and strongly induces the formation of R loops within the immunoglobulin heavy-chain locus. However, the impact of R loops on double-strand break formation and repair during class switch recombination remains unclear. Here, we report that cells lacking two enzymes involved in R loop removal-senataxin and RNase H2-exhibit increased R loop formation and genome instability at the immunoglobulin heavy-chain locus without impacting its transcriptional activity, AID recruitment, or class switch recombination efficiency. Senataxin and RNase H2-deficient cells also exhibit increased insertion mutations at switch junctions, a hallmark of alternative end joining. Importantly, these phenotypes were not observed in cells lacking senataxin or RNase H2B alone. We propose that senataxin acts redundantly with RNase H2 to mediate timely R loop removal, promoting efficient repair while suppressing AID-dependent genome instability and insertional mutagenesis.

BackgroundSerious mental illnesses (SMI) are common, disabling, and challenging to treat, requiring years of monitoring and treatment adjustments. Stress or reduced medication adherence can lead to rapid worsening of symptoms and behaviors. Illness exacerbations and relapses generally occur with little or no clinician awareness in real time, leaving limited opportunity to modify treatments. Previous research suggests that passive mobile sensing may be beneficial for individuals with SMI by helping them monitor mental health status and behaviors, and quickly detect worsening mental health for prompt assessment and intervention. However, there is too little research on its feasibility and acceptability and the extent to which passive data can predict changes in behaviors or symptoms.ObjectiveThe aim of this research is to study the feasibility, acceptability, and safety of passive mobile sensing for tracking behaviors and symptoms of patients in treatment for SMI, as well as developing analytics that use passive data to predict changes in behaviors and symptoms.MethodsA mobile app monitors and transmits passive mobile sensor and phone utilization data, which is used to track activity, sociability, and sleep in patients with SMI. The study consists of a user-centered design phase and a mobile sensing phase. In the design phase, focus groups, interviews, and usability testing inform further app development. In the mobile sensing phase, passive mobile sensing occurs with participants engaging in weekly assessments for 9 months. Three- and nine-month interviews study the perceptions of passive mobile sensing and ease of app use. Clinician interviews before and after the mobile sensing phase study the usefulness and feasibility of app utilization in clinical care. Predictive analytic models are built, trained, and selected, and make use of machine learning methods. Models use sensor and phone utilization data to predict behavioral changes and symptoms.ResultsThe study started in October 2020. It has received institutional review board approval. The user-centered design phase, consisting of focus groups, usability testing, and preintervention clinician interviews, was completed in June 2021. Recruitment and enrollment for the mobile sensing phase began in October 2021.ConclusionsFindings may inform the development of passive sensing apps and self-tracking in patients with SMI, and integration into care to improve assessment, treatment, and patient outcomes.Trial registrationClinicalTrials.gov NCT05023252; https://clinicaltrials.gov/ct2/show/NCT05023252.International registered report identifier (irrid)DERR1-10.2196/39010.

We conducted a phase I clinical trial of H3B-8800, an oral small molecule that binds Splicing Factor 3B1 (SF3B1), in patients with MDS, CMML, or AML. Among 84 enrolled patients (42 MDS, 4 CMML and 38 AML), 62 were red blood cell (RBC) transfusion dependent at study entry. Dose escalation cohorts examined two once-daily dosing regimens: schedule I (5 days on/9 days off, range of doses studied 1-40 mg, n = 65) and schedule II (21 days on/7 days off, 7-20 mg, n = 19); 27 patients received treatment for ≥180 days. The most common treatment-related, treatment-emergent adverse events included diarrhea, nausea, fatigue, and vomiting. No complete or partial responses meeting IWG criteria were observed; however, RBC transfusion free intervals >56 days were observed in nine patients who were transfusion dependent at study entry (15%). Of 15 MDS patients with missense SF3B1 mutations, five experienced RBC transfusion independence (TI). Elevated pre-treatment expression of aberrant transcripts of Transmembrane Protein 14C (TMEM14C), an SF3B1 splicing target encoding a mitochondrial porphyrin transporter, was observed in MDS patients experiencing RBC TI. In summary, H3B-8800 treatment was associated with mostly low-grade TAEs and induced RBC TI in a biomarker-defined subset of MDS.

Copper homeostasis is crucial for cellular physiology and development, and its dysregulation leads to disease. The Menkes ATPase ATP7A plays a key role in copper efflux, by trafficking from the Golgi to the plasma membrane upon cell exposure to elevated copper, but the mechanisms that target ATP7A to the cell periphery are poorly understood. PDZD11 interacts with the C-terminus of ATP7A, which contains sequences involved in ATP7A trafficking, but the role of PDZD11 in ATP7A localization is unknown. Here we identify PLEKHA5 and PLEKHA6 as new interactors of PDZD11 that bind to the PDZD11 N-terminus through their WW domains similarly to the junctional protein PLEKHA7. Using CRISPR-KO kidney epithelial cells, we show by immunofluorescence microscopy that WW-PLEKHAs (PLEKHA5, PLEKHA6, PLEKHA7) recruit PDZD11 to distinct plasma membrane localizations and that they are required for the efficient anterograde targeting of ATP7A to the cell periphery in elevated copper conditions. Pull-down experiments show that WW-PLEKHAs promote PDZD11 interaction with the C-terminus of ATP7A. However, WW-PLEKHAs and PDZD11 are not necessary for ATP7A Golgi localization in basal copper, ATP7A copper-induced exit from the Golgi, and ATP7A retrograde trafficking to the Golgi. Finally, measuring bioavailable and total cellular copper, metallothionein-1 expression, and cell viability shows that WW-PLEKHAs and PDZD11 are required for maintaining low intracellular copper levels when cells are exposed to elevated copper. These data indicate that WW-PLEKHAs-PDZD11 complexes regulate the localization and function of ATP7A to promote copper extrusion in elevated copper.

Dengue virus serotypes 1 to 4 (DENV1–4) and Zika virus (ZIKV) are mosquito-borne flaviviruses that induce both virus-specific and broadly reactive antibodies. A first DENV infection is thought to induce antibodies that wane over 2 years to titers that can subsequently enhance severe dengue disease. Secondary DENV infection with a different serotype is thought to induce stable, cross-serotype protective antibodies. Low dengue disease incidence after the recent Zika pandemic led to the hypothesis that ZIKV infection is also transiently cross protective. We investigated antibody kinetics in 4189 children up to 11 years after one and multiple DENV and ZIKV infections in longitudinal cohorts in Nicaragua. We used a DENV inhibition enzyme-linked immunosorbent assay (iELISA), which measures antibodies associated with protection against dengue and Zika disease and with enhancement of dengue disease severity. Unexpectedly, we found that overall DENV iELISA titers stabilized by 8 months after primary DENV infection to a half-life longer than a human life and waned, although gradually, after secondary DENV infection. Similarly, DENV iELISA titers were stable or rose after primary ZIKV infection but declined in individuals with histories of DENV and ZIKV infection. In contrast, kinetics of anti-ZIKV antibodies after ZIKV infection were similar regardless of prior DENV immunity. We observed heterogeneity in DENV iELISA titer, suggesting that individual antibody titer set point, rather than waning, is important for future dengue disease risk. Together, these findings change our understanding of anti-flavivirus antibody kinetics and have implications for measuring vaccine efficacy and for predicting future dengue and Zika outbreaks.

Influenza is associated with primary viral and secondary bacterial pneumonias; however, the dynamics of this relationship in populations with varied levels of pneumococcal vaccination remain unclear. We conducted nested matched case-control studies in 2 prospective cohorts of Nicaraguan children aged 2-14 years: 1 before pneumococcal conjugate vaccine introduction (2008-2010) and 1 following introduction and near universal adoption (2011-2018). The association between influenza and pneumonia was similar in both cohorts. Participants with influenza (across types/subtypes) had higher odds of developing pneumonia in the month following influenza infection. These findings underscore the importance of considering influenza in interventions to reduce global pneumonia burden.

R-loops constitute a prevalent class of transcription-driven non-B DNA structures that occur in all genomes depending on both DNA sequence and topological favorability. In recent years, R-loops have been implicated in a variety of adaptive and maladaptive roles and have been linked to genomic instability in the context of human disorders. As a consequence, the accurate mapping of these structures in genomes is of high interest to many investigators. DRIP-seq (DNA:RNA Immunoprecipitation followed by high throughput sequencing) is described here. It is a robust and reproducible technique that permits accurate and semi-quantitative mapping of R-loops. A recent iteration of the method is also described in which fragmentation is accomplished using sonication (sDRIP-seq), which allows strand-specific and high-resolution mapping of R-loops. sDRIP-seq thus addresses some of the common limitations of the DRIP-seq method in terms of resolution and strandedness, making it a method of choice for R-loop mapping.

Pancreatic ductal adenocarcinoma (PDAC) is an aggressive cancer that has remained clinically challenging to manage. Here we employ an RNAi-based in vivo functional genomics platform to determine epigenetic vulnerabilities across a panel of patient-derived PDAC models. Through this, we identify protein arginine methyltransferase 1 (PRMT1) as a critical dependency required for PDAC maintenance. Genetic and pharmacological studies validate the role of PRMT1 in maintaining PDAC growth. Mechanistically, using proteomic and transcriptomic analyses, we demonstrate that global inhibition of asymmetric arginine methylation impairs RNA metabolism, which includes RNA splicing, alternative polyadenylation, and transcription termination. This triggers a robust downregulation of multiple pathways involved in the DNA damage response, thereby promoting genomic instability and inhibiting tumor growth. Taken together, our data support PRMT1 as a compelling target in PDAC and informs a mechanism-based translational strategy for future therapeutic development.Statement of significancePDAC is a highly lethal cancer with limited therapeutic options. This study identified and characterized PRMT1-dependent regulation of RNA metabolism and coordination of key cellular processes required for PDAC tumor growth, defining a mechanism-based translational hypothesis for PRMT1 inhibitors.

The S9.6 antibody is broadly used to detect RNA:DNA hybrids but has significant affinity for double-stranded RNA. The impact of this off-target RNA binding activity has not been thoroughly investigated, especially in the context of immunofluorescence microscopy. We report that S9.6 immunofluorescence signal observed in fixed human cells arises predominantly from ribosomal RNA, not RNA:DNA hybrids. S9.6 staining was unchanged by pretreatment with the RNA:DNA hybrid-specific nuclease RNase H1, despite verification in situ that S9.6 recognized RNA:DNA hybrids and that RNase H1 was active. S9.6 staining was, however, significantly sensitive to RNase T1, which specifically degrades RNA. Additional imaging and biochemical data indicate that the prominent cytoplasmic and nucleolar S9.6 signal primarily derives from ribosomal RNA. Importantly, genome-wide maps obtained by DNA sequencing after S9.6-mediated DNA:RNA immunoprecipitation (DRIP) are RNase H1 sensitive and RNase T1 insensitive. Altogether, these data demonstrate that imaging using S9.6 is subject to pervasive artifacts without pretreatments and controls that mitigate its promiscuous recognition of cellular RNAs.

Lessons learnedFulvestrant is a selective estrogen receptor (ER)-downregulating antiestrogen that blocks ER transcriptional activity and is approved for ER-positive breast cancer. Fulvestrant also induces accumulation of insoluble ER and activates an unfolded protein response; proteasome inhibitors have been shown to enhance these effects in preclinical models.BackgroundFulvestrant is a selective estrogen receptor (ER)-downregulating antiestrogen that blocks ER transcriptional activity and is approved for ER-positive (+) breast cancer. Fulvestrant also induces accumulation of insoluble ER and activates an unfolded protein response; proteasome inhibitors have been shown to enhance these effects in preclinical models.MethodsThis is a single-center phase Ib study with a 3+3 design of fulvestrant and the proteasome inhibitor ixazomib (MLN9708) in patients with advanced ER+ breast cancer that was progressing on fulvestrant. A dose-escalation design allowed establishment of the ixazomib maximum tolerated dose (MTD). Secondary objectives included progression-free survival, pharmacokinetics, and tumor molecular analyses.ResultsAmong nine evaluable subjects, treatment was well-tolerated without dose-limiting toxicities The MTD of ixazomib was 4 mg in combination with fulvestrant. Plasma concentrations of the active form of ixazomib (MLN2238) in the 4-mg dose cohort had a median (range) maximal concentration (Cmax ) of 155 (122-171) ng/mL, time of maximal concentration (Tmax ) of 1 (1-1.5) hour, terminal elimination half-life of 66.6 (57.3-102.6) hour after initial dose, and area under the curve (AUC) of 5,025 (4,160-5,345) ng*h/mL. One partial response was observed, and median progression-free survival was 51 days (range, 47-137).ConclusionThis drug combination has a favorable safety profile and antitumor activity in patients with fulvestrant-resistant advanced ER+ breast cancer that justifies future testing.

ObjectivesThe aim of this retrospective case-control study was to report the efficacy of subcutaneous triamcinolone as part of a regimen for feline eosinophilic keratoconjunctivitis (FEK).MethodsRecords and clinical photographs were reviewed and lesions semiquantitatively graded for cats with cytologically confirmed FEK. Clinical data were compared between a study population of nine cats (11 eyes) treated with, and a reference population of seven cats (eight eyes) treated without, a median of 0.11 mg/kg (range 0.10-0.20 mg/kg) of triamcinolone acetonide subcutaneously.ResultsBreed, sex, age and prevalence of corneal ulceration at presentation; corneal disease severity before and at the initiation of immunomodulation; and duration of antiviral treatment before immunomodulation did not differ significantly between populations (P ⩾0.059). Corneal plaques resolved in five cats each from the study and reference populations (P = 0.366). Median (range) time from immunomodulation to corneal plaque resolution did not significantly differ (P = 0.246) between the study (median 14 days; range 8-38 days) and reference (median 28 days, range 14-46 days) populations. No adverse reactions were attributed to triamcinolone administration, and all corneal ulcers in the study population re-epithelialized within 14 days (range 8-38 days) following triamcinolone injection. Time to corneal ulcer re-epithelialization following triamcinolone injection varied minimally in those receiving antivirals prior to (8 or 30 days until re-epithelialization), simultaneously with (38 days) or after (14 or 24 days) triamcinolone.Conclusions and relevanceIn otherwise healthy cats with FEK, subcutaneous administration of triamcinolone appears to be well tolerated and as efficacious as conventional topical immunomodulatory therapies. It may be especially useful in ulcerated eyes where topical immunomodulation is contraindicated.

ObjectivesThe aim of this retrospective case-control study was to report the efficacy of subcutaneous triamcinolone as part of a regimen for feline eosinophilic keratoconjunctivitis (FEK).MethodsRecords and clinical photographs were reviewed and lesions semiquantitatively graded for cats with cytologically confirmed FEK. Clinical data were compared between a study population of nine cats (11 eyes) treated with, and a reference population of seven cats (eight eyes) treated without, a median of 0.11 mg/kg (range 0.10-0.20 mg/kg) of triamcinolone acetonide subcutaneously.ResultsBreed, sex, age and prevalence of corneal ulceration at presentation; corneal disease severity before and at the initiation of immunomodulation; and duration of antiviral treatment before immunomodulation did not differ significantly between populations (P ⩾0.059). Corneal plaques resolved in five cats each from the study and reference populations (P = 0.366). Median (range) time from immunomodulation to corneal plaque resolution did not significantly differ (P = 0.246) between the study (median 14 days; range 8-38 days) and reference (median 28 days, range 14-46 days) populations. No adverse reactions were attributed to triamcinolone administration, and all corneal ulcers in the study population re-epithelialized within 14 days (range 8-38 days) following triamcinolone injection. Time to corneal ulcer re-epithelialization following triamcinolone injection varied minimally in those receiving antivirals prior to (8 or 30 days until re-epithelialization), simultaneously with (38 days) or after (14 or 24 days) triamcinolone.Conclusions and relevanceIn otherwise healthy cats with FEK, subcutaneous administration of triamcinolone appears to be well tolerated and as efficacious as conventional topical immunomodulatory therapies. It may be especially useful in ulcerated eyes where topical immunomodulation is contraindicated.

Global change is leading to warming, acidification, and oxygen loss in the ocean. In the Southern California Bight, an eastern boundary upwelling system, these stressors are exacerbated by the localized discharge of anthropogenically enhanced nutrients from a coastal population of 23 million people. Here, we use simulations with a high-resolution, physical-biogeochemical model to quantify the link between terrestrial and atmospheric nutrients, organic matter, and carbon inputs and biogeochemical change in the coastal waters of the Southern California Bight. The model is forced by large-scale climatic drivers and a reconstruction of local inputs via rivers, wastewater outfalls, and atmospheric deposition; it captures the fine scales of ocean circulation along the shelf; and it is validated against a large collection of physical and biogeochemical observations. Local land-based and atmospheric inputs, enhanced by anthropogenic sources, drive a 79% increase in phytoplankton biomass, a 23% increase in primary production, and a nearly 44% increase in subsurface respiration rates along the coast in summer, reshaping the biogeochemistry of the Southern California Bight. Seasonal reductions in subsurface oxygen, pH, and aragonite saturation state, by up to 50 mmol m-3, 0.09, and 0.47, respectively, rival or exceed the global open-ocean oxygen loss and acidification since the preindustrial period. The biological effects of these changes on local fisheries, proliferation of harmful algal blooms, water clarity, and submerged aquatic vegetation have yet to be fully explored.

R-loops represent an abundant class of large non-B DNA structures in genomes. Even though they form transiently and at modest frequencies, interfering with R-loop formation or dissolution has significant impacts on genome stability. Addressing the mechanism(s) of R-loop-mediated genome destabilization requires a precise characterization of their distribution in genomes. A number of independent methods have been developed to visualize and map R-loops, but their results are at times discordant, leading to confusion. Here, we review the main existing methodologies for R-loop mapping and assess their limitations as well as the robustness of existing datasets. We offer a set of best practices to improve the reproducibility of maps, hoping that such guidelines could be useful for authors and referees alike. Finally, we propose a possible resolution for the apparent contradictions in R-loop mapping outcomes between antibody-based and RNase H1-based mapping approaches.