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We report direct measurements of the magnetic field screening at the limits of the Meissner phase for two superconducting niobium (Nb) samples. The samples are processed with two different surface treatments that have been developed for superconducting radio-frequency (SRF) cavity applications—a "baseline" treatment and an oxygen-doping ("O-doping") treatment. The measurements show: (1) that the screening length is significantly longer in the "O-doping" sample compared to the "baseline" sample; (2) that the screening length near the limits of the Meissner phase increases with applied field; (3) the evolution of the screening profile as the material transitions from the Meissner phase to the mixed phase; and (4) a demonstration of the absence of any screening profile for the highest applied field, indicative of the full flux entering the sample. Measurements are performed utilizing the β -detected nuclear magnetic resonance (β -NMR) technique that allows depth resolved studies of the local magnetic field within the first 100 nm of the surface. The study takes advantage of the β -SRF beamline, a new facility at TRIUMF, Canada, where field levels up to 200 mT are available parallel to the sample surface to replicate radio frequency fields near the Meissner breakdown limits of Nb. [ABSTRACT FROM AUTHOR]

Youth screen media activity is a growing concern, though few studies include objective usage data. Through the longitudinal, U.S.-based Adolescent Brain Cognitive Development (ABCD) Study, youth (mage = 14; n = 1415) self-reported their typical smartphone use and passively recorded three weeks of smartphone use via the ABCD-specific Effortless Assessment Research System (EARS) application. Here we describe and validate passively-sensed smartphone keyboard and app use measures, provide code to harmonize measures across operating systems, and describe trends in adolescent smartphone use. Keyboard and app-use measures were reliable and positively correlated with one another (r = 0.33) and with self-reported use (rs = 0.21–0.35). Participants recorded a mean of 5 h of daily smartphone use, which is two more hours than they self-reported. Further, females logged more smartphone use than males. Smartphone use was recorded at all hours, peaking on average from 8 to 10 PM and lowest from 3 to 5 AM. Social media and texting apps comprised nearly half of all use. Data are openly available to approved investigators (https://nda.nih.gov/abcd/). Information herein can inform use of the ABCD dataset to longitudinally study health and neurodevelopmental correlates of adolescent smartphone use. [ABSTRACT FROM AUTHOR]

Rapamycin slows cystogenesis in murine models of polycystic kidney disease (PKD) but failed in clinical trials, potentially due to insufficient drug dosing. To improve drug efficiency without increasing dose, kidney-specific drug delivery may be used. Mesoscale nanoparticles (MNP) selectively target the proximal tubules in rodents. We explored whether MNPs can target cystic kidney tubules and whether rapamycin-encapsulated-MNPs (RapaMNPs) can slow cyst growth in Pkd1 knockout (KO) mice. MNP was intravenously administered in adult Pkd1KO mice. Serum and organs were harvested after 8, 24, 48 or 72 h to measure MNP localization, mTOR levels, and rapamycin concentration. Pkd1KO mice were then injected bi-weekly for 6 weeks with RapaMNP, rapamycin, or vehicle to determine drug efficacy on kidney cyst growth. Single MNP injections lead to kidney-preferential accumulation over other organs, specifically in tubules and cysts. Likewise, one RapaMNP injection resulted in higher drug delivery to the kidney compared to the liver, and displayed sustained mTOR inhibition. Bi-weekly injections with RapaMNP, rapamycin or vehicle for 6 weeks resulted in inconsistent mTOR inhibition and little change in cyst index, however. MNPs serve as an effective short-term, kidney-specific delivery system, but long-term RapaMNP failed to slow cyst progression in Pkd1KO mice. [ABSTRACT FROM AUTHOR]

Early-life exposure to stress results in significantly increased risk of neurodevelopmental impairments with potential long-term effects into childhood and even adulthood. As a crucial step towards monitoring neonatal stress in neonatal intensive care units (NICUs), our study aims to quantify the duration, frequency, and physiological responses of care manipulation activities, based on bedside videos and physiological signals. Leveraging 289 h of video recordings and physiological data within 330 sessions collected from 27 neonates in 2 NICUs, we develop and evaluate a deep learning method to detect manipulation activities from the video, to estimate their duration and frequency, and to further integrate physiological signals for assessing their responses. With a 13.8% relative error tolerance for activity duration and frequency, our results were statistically equivalent to human annotations. Further, our method proved effective for estimating short-term physiological responses, for detecting activities with marked physiological deviations, and for quantifying the neonatal infant stressor scale scores. [ABSTRACT FROM AUTHOR]

Mood disorders are an enigmatic class of debilitating illnesses that affect millions of individuals worldwide. While chronic stress clearly increases incidence levels of mood disorders, including major depressive disorder (MDD), stress-mediated disruptions in brain function that precipitate these illnesses remain largely elusive. Serotonin-associated antidepressants (ADs) remain the first line of therapy for many with depressive symptoms, yet low remission rates and delays between treatment and symptomatic alleviation have prompted skepticism regarding direct roles for serotonin in the precipitation and treatment of affective disorders. Our group recently demonstrated that serotonin epigenetically modifies histone proteins (H3K4me3Q5ser) to regulate transcriptional permissiveness in brain. However, this non-canonical phenomenon has not yet been explored following stress and/or AD exposures. Here, we employed a combination of genome-wide and biochemical analyses in dorsal raphe nucleus (DRN) of male and female mice exposed to chronic social defeat stress, as well as in DRN of human MDD patients, to examine the impact of stress exposures/MDD diagnosis on H3K4me3Q5ser dynamics, as well as associations between the mark and depression-related gene expression. We additionally assessed stress-induced/MDD-associated regulation of H3K4me3Q5ser following AD exposures, and employed viral-mediated gene therapy in mice to reduce H3K4me3Q5ser levels in DRN and examine its impact on stress-associated gene expression and behavior. We found that H3K4me3Q5ser plays important roles in stress-mediated transcriptional plasticity. Chronically stressed mice displayed dysregulated H3K4me3Q5ser dynamics in DRN, with both AD- and viral-mediated disruption of these dynamics proving sufficient to attenuate stress-mediated gene expression and behavior. Corresponding patterns of H3K4me3Q5ser regulation were observed in MDD subjects on vs. off ADs at their time of death. These findings thus establish a neurotransmission-independent role for serotonin in stress-/AD-associated transcriptional and behavioral plasticity, observations of which may be of clinical relevance to human MDD and its treatment. Serotonin is implicated in mood-related disorders, yet direct evidence linking it to disease precipitation or treatment remains limited. Here, authors show that histone serotonylation contributes to stress- and antidepressant-mediated phenotypes, which may be of clinical relevance. [ABSTRACT FROM AUTHOR]

Background: Despite recent advancements in migraine treatment, some patients continue to endure significant disease burden. Due to the controlled nature of randomized trials in migraine prevention, many real-world patients with comorbidities or prior exposure to certain therapies are excluded. Capturing evidence of the effectiveness of treatment in real-world clinical settings can further shape treatment paradigms. The objective of this study was to develop a comprehensive understanding of both patients' and physicians' real-world experiences with eptinezumab for chronic migraine (CM). Methods: REVIEW (Real-world EVidence and Insights into Experiences With eptinezumab) is an observational, multi-site (n = 4), US-based study designed to evaluate real-world experiences of patients treated with eptinezumab and their treating physicians. Patients were ≥ 18 years of age, with a diagnosis of CM, who had completed ≥ 2 consecutive eptinezumab infusion cycles (≥ 6 months of exposure). The study included a retrospective chart review, a patient survey, and a semi-structured physician interview that assessed patient and/or physician satisfaction with elements of daily living / well-being, migraine symptomology, and perspectives of the eptinezumab infusion experience. Results: Of the 94 patients enrolled, 83% (78/94) were female, the mean age was 49.2 years, and the mean time since migraine diagnosis was 15.4 years. Before eptinezumab treatment, patients experienced a mean of 8 self-reported "good" days/month, which increased to 18 after treatment. Most patients took, on average, ≥ 10 days/month of prescription and/or over-the-counter medication (81% [75/93] and 66% [61/93], respectively) to treat migraine attacks before eptinezumab treatment, which dropped to 26% (24/93) and 23% (21/93) following eptinezumab treatment. Prior to receiving eptinezumab, 62% (58/93) of patients indicated being at least slightly concerned about infusions; after eptinezumab infusion, this dropped to 14% (13/93). These patient survey findings were consistent with physician responses. Conclusion: This real-world evidence study demonstrated high overall satisfaction with the effectiveness of eptinezumab treatment for CM among most patients and their physicians. [ABSTRACT FROM AUTHOR]

Obesity is a well-established risk factor for human cancer, yet the underlying mechanisms remain elusive. Immune dysfunction is commonly associated with obesity but whether compromised immune surveillance contributes to cancer susceptibility in individuals with obesity is unclear. Here we use a mouse model of diet-induced obesity to investigate tumor-infiltrating CD8 + T cell responses in lean, obese, and previously obese hosts that lost weight through either dietary restriction or treatment with semaglutide. While both strategies reduce body mass, only dietary intervention restores T cell function and improves responses to immunotherapy. In mice exposed to a chemical carcinogen, obesity-related immune dysfunction leads to higher incidence of sarcoma development. However, impaired immunoediting in the obese environment enhances tumor immunogenicity, making the malignancies highly sensitive to immunotherapy. These findings offer insight into the complex interplay between obesity, immunity and cancer, and provide explanation for the obesity paradox observed in clinical immunotherapy settings. Obesity represents a risk factor for cancer and compromises immune function, however the mechanisms linking the two together are not fully known. Here authors show in a mouse sarcoma model that obesity increases tumour incidence, impairs intra-tumoral T cell immunity but paradoxically increases sensitivity to immune therapy via impairing immunoediting. [ABSTRACT FROM AUTHOR]

Rock textures observed via thin section are skewed from their true 3D nature. This is due to various cut effects—artifacts introduced due to the lower dimensional nature of the thin section relative to the rock. These cut effects can be corrected, and several methods have been developed to invert crystal shape and crystal size, but with each process performed separately and sequentially. With the ongoing adoption of electron backscatter diffraction (EBSD) by petrologists, an additional data stream has now become available: the 3D orientation of 2D grain sections. For EBSD analysis, no stereological corrections are typically applied for interpreting the data. This study tests whether this orientational information is skewed due to a fabric cut effect. We test this by numerically generating synthetic crystal datasets representative of several crystal shapes and population sizes. We find that EBSD orientational data has a fabric cut effect since crystals oriented with long axes perpendicular to the thin section are more likely to be sampled compared to those with long axes oriented parallel to it. This effect must be accounted for to interpret the true 3D fabric accurately. Towards this end, we develop two new tools for working with EBSD-derived fabric: (1) a simple first-order test for determining if a measured fabric exceeds that of the fabric cut effect, and (2) a method of inverting cut fabrics that provides robust error estimations. We demonstrate the applicability and accuracy of these methods using a range of synthetic examples and a natural sample. With these newly developed tools, there is clear potential for a new textural toolkit framework, to further our ability to correct for the various cut effects while also providing accurate uncertainty estimates. [ABSTRACT FROM AUTHOR]

The "dorsal pons", or "dorsal pontine tegmentum" (dPnTg), is part of the brainstem. It is a complex, densely packed region whose nuclei are involved in regulating many vital functions. Notable among them are the parabrachial nucleus, the Kölliker Fuse, the Barrington nucleus, the locus coeruleus, and the dorsal, laterodorsal, and ventral tegmental nuclei. In this study, we applied single-nucleus RNA-seq (snRNA-seq) to resolve neuronal subtypes based on their unique transcriptional profiles and then used multiplexed error robust fluorescence in situ hybridization (MERFISH) to map them spatially. We sampled ~1 million cells across the dPnTg and defined the spatial distribution of over 120 neuronal subtypes. Our analysis identified an unpredicted high transcriptional diversity in this region and pinpointed the unique marker genes of many neuronal subtypes. We also demonstrated that many neuronal subtypes are transcriptionally similar between humans and mice, enhancing this study's translational value. Finally, we developed a freely accessible, GPU and CPU-powered dashboard (http://harvard.heavy.ai:6273/) that combines interactive visual analytics and hardware-accelerated SQL into a data science framework to allow the scientific community to query and gain insights into the data. The dorsal pons in the brainstem is packed with clusters of neurons, including the parabrachial nucleus, that are involved in many vital functions. Here, authors use single nucleus RNA sequencing and MERFISH to create a spatially defined transcriptional atlas of this region. [ABSTRACT FROM AUTHOR]

Repetitive, long-term inhalation of radioactive radon gas is one of the leading causes of lung cancer, with exposure differences being a function of geographic location, built environment, personal demographics, activity patterns, and decision-making. Here, we examine radon exposure disparities across the urban-to-rural landscape, based on 42,051 Canadian residential properties in 2034 distinct communities. People living in rural, lower population density communities experience as much as 31.2% greater average residential radon levels relative to urban equivalents, equating to an additional 26.7 Bq/m3 excess in geometric mean indoor air radon, and an additional 1 mSv/year in excess alpha radiation exposure dose rate to the lungs for occupants. Pairwise and multivariate analyses indicate that community-based radon exposure disparities are, in part, explained by increased prevalence of larger floorplan bungalows in rural areas, but that a majority of the effect is attributed to proximity to, but not water use from, drilled groundwater wells. We propose that unintended radon gas migration in the annulus of drilled groundwater wells provides radon migration pathways from the deeper subsurface into near-surface materials. Our findings highlight a previously under-appreciated determinant of radon-induced lung cancer risk, and support a need for targeted radon testing and reduction in rural communities. [ABSTRACT FROM AUTHOR]

The pace of human brain development is highly protracted compared with most other species1–7. The maturation of cortical neurons is particularly slow, taking months to years to develop adult functions3–5. Remarkably, such protracted timing is retained in cortical neurons derived from human pluripotent stem cells (hPSCs) during in vitro differentiation or upon transplantation into the mouse brain4,8,9. Those findings suggest the presence of a cell-intrinsic clock setting the pace of neuronal maturation, although the molecular nature of this clock remains unknown. Here we identify an epigenetic developmental programme that sets the timing of human neuronal maturation. First, we developed a hPSC-based approach to synchronize the birth of cortical neurons in vitro which enabled us to define an atlas of morphological, functional and molecular maturation. We observed a slow unfolding of maturation programmes, limited by the retention of specific epigenetic factors. Loss of function of several of those factors in cortical neurons enables precocious maturation. Transient inhibition of EZH2, EHMT1 and EHMT2 or DOT1L, at progenitor stage primes newly born neurons to rapidly acquire mature properties upon differentiation. Thus our findings reveal that the rate at which human neurons mature is set well before neurogenesis through the establishment of an epigenetic barrier in progenitor cells. Mechanistically, this barrier holds transcriptional maturation programmes in a poised state that is gradually released to ensure the prolonged timeline of human cortical neuron maturation.The slow maturation of human neurons is regulated by epigenetic modification in nascent neurons, mediated by EZH2, EHMT1, EHMT2 and DOT1L. [ABSTRACT FROM AUTHOR]

The high potential of siRNAs to silence oncogenic drivers remains largely untapped due to the challenges of tumor cell delivery. Here, divalent lipid-conjugated siRNAs are optimized for in situ binding to albumin to improve pharmacokinetics and tumor delivery. Systematic variation of the siRNA conjugate structure reveals that the location of the linker branching site dictates tendency toward albumin association versus self-assembly, while the lipid hydrophobicity and reversibility of albumin binding also contribute to siRNA intracellular delivery. The lead structure increases tumor siRNA accumulation 12-fold in orthotopic triple negative breast cancer (TNBC) tumors over the parent siRNA. This structure achieves approximately 80% silencing of the anti-apoptotic oncogene MCL1 and yields better survival outcomes in three TNBC models than an MCL-1 small molecule inhibitor. These studies provide new structure-function insights on siRNA-lipid conjugate structures that are intravenously injected, associate in situ with serum albumin, and improve pharmacokinetics and tumor treatment efficacy. Limited tumor cell delivery is a major challenge for the efficacious delivery of siRNAs to silence traditionally undruggable oncogenes. Here the authors optimize siRNAs for in situ binding to albumin through C18 lipid modifications and show the application of the lead conjugate structure for targeting MCL1 in orthotopic breast tumors in mice. [ABSTRACT FROM AUTHOR]

Cancer can be conceptualized as arising from somatic mutations resulting in a single renegade cell escaping from the constraints of multicellularity. Thus, the era of precision medicine has led to intense focus on the cancer cell to target these mutations that result in oncogenic signaling and sustain malignancy. However, in pancreatic ductal adenocarcinoma (PDAC) there are only four abundantly common driver mutations (KRAS, CDKN2A, TP53, and SMAD4), which are not currently actionable. Thus, precision therapy for PDAC must look beyond the cancer cell. In fact, PDAC is more than a collection of renegade cells, instead representing an extensive, supportive ecosystem, having developed over several years, and consisting of numerous interactions between the cancer cells, normal mesenchymal cells, immune cells, and the dense extracellular matrix. In this issue, Huang and colleagues demonstrate how elucidation of these complex relationships within the tumor microenvironment (TME) can be exploited for therapeutic intervention in PDAC. They identify in a subset of PDAC with mutations in TGFβ signaling, that a paracrine signaling axis can be abrogated to modulate the TME and improve outcomes.

Purpose: To assess the outcome and safety of radiofrequency (RF) wire recanalization in patients with end-stage renal disease (ESRD) and chronic central venous occlusions (CVO). Materials and Methods: A retrospective review of ESRD patients who underwent RF-wire recanalization of symptomatic chronic thoracic CVO from January 2017 to August 2022 yielded 20 patients who underwent 21 procedures. All patients had undergone at least one prior unsuccessful attempt at central venous recanalization using conventional catheter-based techniques. Technical success was defined by the ability to cross the CVO using RF-wire recanalization enabling endovascular treatment. Access circuit patency was evaluated based on follow-up imaging and symptomatic improvement. Results: Radiofrequency wire recanalization was successful in 17/21 procedures (81%) with all patients (100%) reporting resolution of arm ± facial swelling. Three major complications occurred (14%): two hemothoraces and one hemopericardium. Medial stent diameter was 13 mm (range, 9–14 mm). Mean duration of hospital stay was 2 days ± 3 days. Mean procedure time was 158 ± 46 min with a mean fluoroscopy time of 31.7 ± 16.3 min. Primary unassisted patency at 6 and 12 months was 94 ± 6% and 85 ± 10%, respectively. Additional interventions resulted in significantly increased stent graft patency (P = 0.006). Conclusion: Radiofrequency wire-enabled recanalization of CVO in symptomatic dialysis patients has a high rate of technical success with resolution of arm and facial swelling and resumed use of the ipsilateral dialysis access. Although a superior safety profile was seen than with needle-based techniques such as sharp recanalization, major complications were not infrequent indicating that this RF-wire procedure should be performed in centers equipped to manage central venous perforations. [ABSTRACT FROM AUTHOR]

The ability to distinguish between the abdominal conditions of adult female mosquitoes has important utility for the surveillance and control of mosquito-borne diseases. However, doing so requires entomological training and time-consuming manual effort. Here, we design computer vision techniques to determine stages in the gonotrophic cycle of female mosquitoes from images. Our dataset was collected from 139 adult female mosquitoes across three medically important species—Aedes aegypti, Anopheles stephensi, and Culex quinquefasciatus—and all four gonotrophic stages of the cycle (unfed, fully fed, semi-gravid, and gravid). From these mosquitoes and stages, a total of 1959 images were captured on a plain background via multiple smartphones. Subsequently, we trained four distinct AI model architectures (ResNet50, MobileNetV2, EfficientNet-B0, and ConvNeXtTiny), validated them using unseen data, and compared their overall classification accuracies. Additionally, we analyzed t-SNE plots to visualize the formation of decision boundaries in a lower-dimensional space. Notably, ResNet50 and EfficientNet-B0 demonstrated outstanding performance with an overall accuracy of 97.44% and 93.59%, respectively. EfficientNet-B0 demonstrated the best overall performance considering computational efficiency, model size, training speed, and t-SNE decision boundaries. We also assessed the explainability of this EfficientNet-B0 model, by implementing Grad-CAMs—a technique that highlights pixels in an image that were prioritized for classification. We observed that the highest weight was for those pixels representing the mosquito abdomen, demonstrating that our AI model has indeed learned correctly. Our work has significant practical impact. First, image datasets for gonotrophic stages of mosquitoes are not yet available. Second, our algorithms can be integrated with existing citizen science platforms that enable the public to record and upload biological observations. With such integration, our algorithms will enable the public to contribute to mosquito surveillance and gonotrophic stage identification. Finally, we are aware of work today that uses computer vision techniques for automated mosquito species identification, and our algorithms in this paper can augment these efforts by enabling the automated detection of gonotrophic stages of mosquitoes as well. [ABSTRACT FROM AUTHOR]

Environmental stimuli trigger rapid transcriptional reprogramming of gene networks. These responses occur in the context of the local chromatin landscape, but the contribution of organ-specific dynamic chromatin modifications in responses to external signals remains largely unexplored. We treated tomato seedlings with a supply of nitrate and measured the genome-wide changes of four histone marks, the permissive marks H3K27ac, H3K4me3, and H3K36me3 and repressive mark H3K27me3, in shoots and roots separately, as well as H3K9me2 in shoots. Dynamic and organ-specific histone acetylation and methylation were observed at functionally relevant gene loci. Integration of transcriptomic and epigenomic datasets generated from the same organ revealed largely syngenetic relations between changes in transcript levels and histone modifications, with the exception of H3K27me3 in shoots, where an increased level of this repressive mark is observed at genes activated by nitrate. Application of a machine learning approach revealed organ-specific rules regarding the importance of individual histone marks, as H3K36me3 is the most successful mark in predicting gene regulation events in shoots, while H3K4me3 is the strongest individual predictor in roots. Our integrated study substantiates a view that during plant environmental responses, the relationships between histone code dynamics and gene regulation are highly dependent on organ-specific contexts. Analysis of ChIP-Seq of multiple histone modifications across shoots and roots in two nutrient supply conditions, coupled with machine learning, reveals new organ-specific patterns of epigenetic regulation in response to nitrate in tomatoes. [ABSTRACT FROM AUTHOR]

Prime editing in vivo is systematically improved with an eye to clinical translation. [ABSTRACT FROM AUTHOR]

The human brain extracts meaning using an extensive neural system for semantic knowledge. Whether broadly distributed systems depend on or can compensate after losing a highly interconnected hub is controversial. We report intracranial recordings from two patients during a speech prediction task, obtained minutes before and after neurosurgical treatment requiring disconnection of the left anterior temporal lobe (ATL), a candidate semantic knowledge hub. Informed by modern diaschisis and predictive coding frameworks, we tested hypotheses ranging from solely neural network disruption to complete compensation by the indirectly affected language-related and speech-processing sites. Immediately after ATL disconnection, we observed neurophysiological alterations in the recorded frontal and auditory sites, providing direct evidence for the importance of the ATL as a semantic hub. We also obtained evidence for rapid, albeit incomplete, attempts at neural network compensation, with neural impact largely in the forms stipulated by the predictive coding framework, in specificity, and the modern diaschisis framework, more generally. The overall results validate these frameworks and reveal an immediate impact and capability of the human brain to adjust after losing a brain hub. The human brain is a distributed system composed of highly interconnected hubs. Here, patients undergoing a rare operation reveal the immediate impact and compensatory brain network changes that occur when a key hub is removed. [ABSTRACT FROM AUTHOR]

Through infection and lysis of their coexisting bacterial hosts, viruses impact the biogeochemical cycles sustaining globally significant pelagic oceanic ecosystems. Currently, little is known of the ecological interactions between lytic viruses and their bacterial hosts underlying these biogeochemical impacts at ecosystem scales. This study focused on populations of lytic viruses carrying the B12-dependent Class II monomeric ribonucleotide reductase (RNR) gene, ribonucleotide-triphosphate reductase (Class II RTPR), documenting seasonal changes in pelagic virioplankton and bacterioplankton using amplicon sequences of Class II RTPR and the 16S rRNA gene, respectively. Amplicon sequence libraries were analyzed using compositional data analysis tools that account for the compositional nature of these data. Both virio- and bacterioplankton communities responded to environmental changes typically seen across seasonal cycles as well as shorter term upwelling–downwelling events. Defining Class II RTPR-carrying viral populations according to major phylogenetic clades proved a more robust means of exploring virioplankton ecology than operational taxonomic units defined by percent sequence homology. Virioplankton Class II RTPR populations showed positive associations with a broad phylogenetic diversity of bacterioplankton including dominant taxa within pelagic oceanic ecosystems such as Prochlorococcus and SAR11. Temporal changes in Class II RTPR virioplankton, occurring as both free viruses and within infected cells, indicated possible viral–host pairs undergoing sustained infection and lysis cycles throughout the seasonal study. Phylogenetic relationships inferred from Class II RTPR sequences mirrored ecological patterns in virio- and bacterioplankton populations demonstrating possible genome to phenome associations for an essential viral replication gene. [ABSTRACT FROM AUTHOR]

In optic neuropathies, including glaucoma, retinal ganglion cells (RGCs) die. Cell transplantation and endogenous regeneration offer strategies for retinal repair, however, developmental programs required for this to succeed are incompletely understood. To address this, we explored cellular reprogramming with transcription factor (TF) regulators of RGC development which were integrated into human pluripotent stem cells (PSCs) as inducible gene cassettes. When the pioneer factor NEUROG2 was combined with RGC-expressed TFs (ATOH7, ISL1, and POU4F2) some conversion was observed and when pre-patterned by BMP inhibition, RGC-like induced neurons (RGC-iNs) were generated with high efficiency in just under a week. These exhibited transcriptional profiles that were reminiscent of RGCs and exhibited electrophysiological properties, including AMPA-mediated synaptic transmission. Additionally, we demonstrated that small molecule inhibitors of DLK/LZK and GCK-IV can block neuronal death in two pharmacological axon injury models. Combining developmental patterning with RGC-specific TFs thus provided valuable insight into strategies for cell replacement and neuroprotection. [ABSTRACT FROM AUTHOR]

Purpose: The Adverse Childhood Experiences (ACEs) screening tool captures some experiences of childhood adversity, ranging from abuse to parental separation. Research has shown a correlation between ACEs and both adult and childhood disease. This study evaluated the feasibility of conducting ACE screening in the pediatric intensive care unit (PICU) and investigated associations with markers for severity of illness and utilization of resources. Methods: This was a cross sectional study screening for ACEs among children admitted to a single quaternary medical-surgical PICU. Children age 0–18 years old admitted to the PICU over a one-year period were considered for enrollment. A 10-question ACE screen was used to evaluate children for exposure to ACEs. Chart review was used to collect demographic and clinical data. Results: Of the 432 parents approached for enrollment, 400 (92.6%) agreed to participate. Most parents reported an ACE score of zero (68.9%) while 31% of participants experienced at least 1 ACE, of whom 14.8% experienced ≥ 2 ACEs. There was not a statistically significant association between ACE score and length of stay (p-value = 0.26) or level of respiratory support in patients with asthma (p-value = 0.15) or bronchiolitis (p-value = 0.83). The primary reasons for not approaching families were parent availability, non-English speaking parents, and social work concerns. Conclusions: This study demonstrates feasibility to collect sensitive psychosocial data in the PICU and highlights challenges to enrollment. [ABSTRACT FROM AUTHOR]

Estrogen and progesterone, acting through their cognate receptors the estrogen receptor α (ERα) and the progesterone receptor (PR) respectively, regulate uterine biology. Using rapid immunoprecipitation and mass spectrometry (RIME) and co-immunoprecipitation, we identified TRIM28 (Tripartite motif containing 28) as a protein which complexes with ERα and PR in the regulation of uterine function. Impairment of TRIM28 expression results in the inability of the uterus to support early pregnancy through altered PR and ERα action in the uterine epithelium and stroma by suppressing PR and ERα chromatin binding. Furthermore, TRIM28 ablation in PR-expressing uterine cells results in the enrichment of a subset of TRIM28 positive and PR negative pericytes and epithelial cells with progenitor potential. In summary, our study reveals the important roles of TRIM28 in regulating endometrial cell composition and function in women, and also implies its critical functions in other hormone regulated systems. This paper identifies Tripartite motif-containing 28 (TRIM28) as a novel modulator of steroid hormone signaling. TRIM28 deficiency disrupts uterine cell functions and composition leading to fertility defects [ABSTRACT FROM AUTHOR]

Introduction: Pediatric subglottic stenosis (SGS) results from prolonged intubation where scar tissue leads to airway narrowing that requires invasive surgery. We have recently discovered that modulating the laryngotracheal microbiome can prevent SGS. Herein, we show how our patent-pending antimicrobial peptide-eluting endotracheal tube (AMP-ET) effectively modulates the local airway microbiota resulting in reduced inflammation and stenosis resolution. Materials and Methods: We fabricated mouse-sized ETs coated with a polymeric AMP-eluting layer, quantified AMP release over 10 days, and validated bactericidal activity for both planktonic and biofilm-resident bacteria against Staphylococcus aureus and Pseudomonas aeruginosa. Ex vivo testing: we inserted AMP-ETs and ET controls into excised laryngotracheal complexes (LTCs) of C57BL/6 mice and assessed biofilm formation after 24 h. In vivo testing: AMP-ETs and ET controls were inserted in sham or SGS-induced LTCs, which were then implanted subcutaneously in receptor mice, and assessed for immune response and SGS severity after 7 days. Results: We achieved reproducible, linear AMP release at 1.16 µg/day resulting in strong bacterial inhibition in vitro and ex vivo. In vivo, SGS-induced LTCs exhibited a thickened scar tissue typical of stenosis, while the use of AMP-ETs abrogated stenosis. Notably, SGS airways exhibited high infiltration of T cells and macrophages, which was reversed with AMP-ET treatment. This suggests that by modulating the microbiome, AMP-ETs reduce macrophage activation and antigen specific T cell responses resolving stenosis progression. Conclusion: We developed an AMP-ET platform that reduces T cell and macrophage responses and reduces SGS in vivo via airway microbiome modulation. [ABSTRACT FROM AUTHOR]

We have collectively been spoiled by the astounding clinical benefit of antimicrobials. Much like the discovery and use of penicillin to eradicate once deadly infections, we continue to desperately search for the next “magic bullet” to kill cancer while sparing the non‐transformed cells. Greater appreciation for the molecular intricacies of malignancy has resulted in dedicated pursuit of cancer genomics and large‐scale informatics to identify “drugable” targets within the cancer cell itself. However, studies at the bench elucidating a dynamic relationship between tumor and microenvironment have become more common and demonstrate promise for novel therapeutic intervention.

The growth kinetics of localized corrosion, e.g. pits, in corrosive environments often controls the service life of metallic components. Yet, our understanding of these kinetics is largely based on coupon-level, e.g. mass-loss, studies which provide limited insights into the evolution of individual damage events. It is critical to relate observed cumulative loss trends, such as links between changing humidity and mass loss rates, to the growth kinetics of individual pits. Towards this goal, we leverage in-situ X-ray computed tomography to measure the growth rates of over sixty pits in aluminum in four different humid, chloride environments over ≈3 days of exposure. Pit growth rates and final volumes increased with increasing droplet volume, which was observed to increase with increasing humidity and salt loading. Two factors, droplet spreading and oxide jacking, dramatically increased pit growth rates and final volumes. [ABSTRACT FROM AUTHOR]

Rift Valley fever virus (RVFV) is an emerging mosquito-transmitted virus that circulates in livestock and humans in Africa and the Middle East. Outbreaks lead to high rates of miscarriages in domesticated livestock. Women are also at risk of vertical virus transmission and late-term miscarriages. MAb RVFV-268 is a highly potent recombinant neutralizing human monoclonal antibody that targets RVFV. Here we show that mAb RVFV-268 reduces viral replication in rat placenta explant cultures and prevents vertical transmission in a rat model of congenital RVF. Passive transfer of mAb RVFV-268 from mother to fetus occurs as early as 6 h after administration and persists through 24 h. Administering mAb RVFV-268 2 h prior to RVFV challenge or 24 h post-challenge protects the dams and offspring from RVFV infection. These findings support mAb RVFV-268 as a pre- and post-infection treatment to subvert RVFV infection and vertical transmission, thus protecting the mother and offspring. Rift valley fever virus (RVFV) infection during pregnancy has been associated with late-term fetal loss. Here, the authors show that a neutralizing monoclonal antibody can prevent vertical transmission of RVFV when administered either pre- or post-infection in a rodent model. [ABSTRACT FROM AUTHOR]

Quantifying neural activity in natural conditions (i.e. conditions comparable to the standard clinical patient experience) during the administration of psychedelics may further our scientific understanding of the effects and mechanisms of action. This data may facilitate the discovery of novel biomarkers enabling more personalized treatments and improved patient outcomes. In this single-blind, placebo-controlled study with a non-randomized design, we use time-domain functional near-infrared spectroscopy (TD-fNIRS) to measure acute brain dynamics after intramuscular subanesthetic ketamine (0.75 mg/kg) and placebo (saline) administration in healthy participants (n = 15, 8 females, 7 males, age 32.4 ± 7.5 years) in a clinical setting. We found that the ketamine administration caused an altered state of consciousness and changes in systemic physiology (e.g. increase in pulse rate and electrodermal activity). Furthermore, ketamine led to a brain-wide reduction in the fractional amplitude of low frequency fluctuations, and a decrease in the global brain connectivity of the prefrontal region. Lastly, we provide preliminary evidence that a combination of neural and physiological metrics may serve as predictors of subjective mystical experiences and reductions in depressive symptomatology. Overall, our study demonstrated the successful application of fNIRS neuroimaging to study the physiological effects of the psychoactive substance ketamine in humans, and can be regarded as an important step toward larger scale clinical fNIRS studies that can quantify the impact of psychedelics on the brain in standard clinical settings. [ABSTRACT FROM AUTHOR]

Urocortin 2 (UCN2) acts as a ligand for the G protein-coupled receptor corticotropin-releasing hormone receptor 2 (CRHR2). UCN2 has been reported to improve or worsen insulin sensitivity and glucose tolerance in vivo. Here we show that acute dosing of UCN2 induces systemic insulin resistance in male mice and skeletal muscle. Inversely, chronic elevation of UCN2 by injection with adenovirus encoding UCN2 resolves metabolic complications, improving glucose tolerance. CRHR2 recruits Gs in response to low concentrations of UCN2, as well as Gi and β-Arrestin at high concentrations of UCN2. Pre-treating cells and skeletal muscle ex vivo with UCN2 leads to internalization of CRHR2, dampened ligand-dependent increases in cAMP, and blunted reductions in insulin signaling. These results provide mechanistic insights into how UCN2 regulates insulin sensitivity and glucose metabolism in skeletal muscle and in vivo. Importantly, a working model was derived from these results that unifies the contradictory metabolic effects of UCN2. UCN2 acts as a ligand for the GPCR CRHR2 and there have been conflicting reports on whether UCN2 treatment improves or worsens glucose tolerance. Here, the authors show that acute UCN2 recruits Gs and decreases glucose uptake, while chronic treatment desensitizes CRHR2 and improves glucose uptake. [ABSTRACT FROM AUTHOR]

Alcohol is one of the most commonly used substances and frequently abused, yet little is known about the neural underpinnings driving variability in inhibitory control performance after ingesting alcohol. This study was a single-blind, placebo-controlled, randomized design with participants (N = 48 healthy, social drinkers) completing three study visits. At each visit participants received one of three alcohol doses; namely, a placebo dose [equivalent Blood Alcohol Concentration (BAC) = 0.00%], a low dose of alcohol (target BAC = 0.04%), or a moderate dose of alcohol (target BAC = 0.08%). To measure inhibitory control, participants completed a Go/No-go task paradigm twice during each study visit, once immediately before dosing and once after, while their brain activity was measured with time-domain functional near-infrared spectroscopy (TD-fNIRS). BAC and subjective effects of alcohol were also assessed. We report decreased behavioral performance for the moderate dose of alcohol, but not the low or placebo doses. We observed right lateralized inhibitory prefrontal activity during go-no-go blocks, consistent with prior literature. Using standard and novel metrics of lateralization, we were able to significantly differentiate between all doses. Lastly, we demonstrate that these metrics are not only related to behavioral performance during inhibitory control, but also provide complementary information to the legal gold standard of intoxication (i.e. BAC). [ABSTRACT FROM AUTHOR]

NAD is an essential co-factor for cellular energy metabolism and multiple other processes. Systemic NAD+ deficiency has been implicated in skeletal deformities during development in both humans and mice. NAD levels are maintained by multiple synthetic pathways but which ones are important in bone forming cells is unknown. Here, we generate mice with deletion of Nicotinamide Phosphoribosyltransferase (Nampt), a critical enzyme in the NAD salvage pathway, in all mesenchymal lineage cells of the limbs. At birth, NamptΔPrx1 exhibit dramatic limb shortening due to death of growth plate chondrocytes. Administration of the NAD precursor nicotinamide riboside during pregnancy prevents the majority of in utero defects. Depletion of NAD post-birth also promotes chondrocyte death, preventing further endochondral ossification and joint development. In contrast, osteoblast formation still occurs in knockout mice, in line with distinctly different microenvironments and reliance on redox reactions between chondrocytes and osteoblasts. These findings define a critical role for cell-autonomous NAD homeostasis during endochondral bone formation. Deficiency in NAD+ has been implicated in skeletal deformities during development in both humans and mice. Here, the authors use mice that lack the critical enzyme of the NAD+ salvage pathway Nampt in mesenchymal lineage cells to show that the NAD salvage pathway is indispensable for endochondral but not intramembranous bone development. [ABSTRACT FROM AUTHOR]

Planets with short orbital periods (roughly under 10 days) are common around stars like the Sun1,2. Stars expand as they evolve and thus we expect their close planetary companions to be engulfed, possibly powering luminous mass ejections from the host star3–5. However, this phase has never been directly observed. Here we report observations of ZTF SLRN-2020, a short-lived optical outburst in the Galactic disk accompanied by bright and long-lived infrared emission. The resulting light curve and spectra share striking similarities with those of red novae6,7—a class of eruptions now confirmed8 to arise from mergers of binary stars. Its exceptionally low optical luminosity (approximately 1035 erg s−1) and radiated energy (approximately 6.5 × 1041 erg) point to the engulfment of a planet of fewer than roughly ten Jupiter masses by its Sun-like host star. We estimate the Galactic rate of such subluminous red novae to be roughly between 0.1 and several per year. Future Galactic plane surveys should routinely identify these, showing the demographics of planetary engulfment and the ultimate fate of planets in the inner Solar System.Observations of ZTF SLRN-2020, a short-lived optical outburst in the Galactic disk accompanied by bright, long-lived infrared emission, show that the resulting light curve and spectra are consistent with the signatures of a planet being engulfed by its host star. [ABSTRACT FROM AUTHOR]

Background: We investigated the association of body mass index (BMI) modeled as a continuous variable with survival outcomes in advanced non-small cell lung cancer (NSCLC) patients treated with immune checkpoint inhibitors (ICI). Methods: We performed a single-institution retrospective analysis of consecutively diagnosed locally advanced or metastatic NSCLC patients treated with single-agent ICI in the first line or recurrent setting. The primary outcome was overall survival (OS). Secondary outcomes were progression-free survival (PFS) and objective response rate (ORR). BMI was modeled using a four-knot restricted cubic spline. Multiple Cox regression was used for survival analysis. Results: Two hundred patients were included (female 54%; never smoker 12%). Adenocarcinoma was the most common histology (61%). Median age was 67 years, median BMI was 25.9 kg/m2, and 65% of patients had Eastern Cooperative Oncology Group performance status (ECOG PS) of 0–1. On multivariable analysis, only BMI and ECOG PS were independently associated with OS (p < 0.01). Mortality risk decreased as the BMI increased from 20 to 30 kg/m2 (HR 0.49, 95% CI 0.28–0.84); however, it was reversed as the BMI surpassed ~ 30 kg/m2. Compared to ECOG PS ≥ 2, patients with ECOG PS of 0–1 had a longer OS (HR 0.42, 95% CI 0.28–0.63). Similar trends were observed with PFS and ORR, but the strength of the association was weaker. Conclusion: We observed a nonlinear association between BMI and OS following treatment with ICI in advanced NSCLC. Risk of death increases at both extremes of BMI with a nadir that exists around 30 kg/m2. [ABSTRACT FROM AUTHOR]

Leukocyte telomere length (LTL) gets shorter with each cell division and is also sensitive to reactive oxygen species damage and inflammatory processes. Studies in adults with non-alcoholic fatty liver disease (NAFLD) have found that increased fibrosis but not ALT levels are associated with shorter LTL. Few pediatric studies have been conducted; as such, we sought to evaluate potential associations between LTL and liver disease and liver disease progression in pediatric patients. Using data from the Treatment of NAFLD in Children (TONIC) randomized controlled trial, we assessed the potential predictive relationship between LTL and liver disease progression based on two successive liver biopsies over 96 weeks. We assessed the potential relationship between LTL and child age, sex, and race/ethnicity and features of liver disease including components of histology. We subsequently evaluated predictors for improvement in non-alcoholic steatohepatitis (NASH) at 96 weeks including LTL. We also assessed predictors of lobular inflammation improvement at 96 weeks using multivariable models. Mean LTL at baseline was 1.33 ± 0.23 T/S. Increasing lobular and portal inflammation were associated with longer LTL. In multivariable models, greater lobular inflammation at baseline was associated with longer LTL (Coeff 0.03, 95% CI 0.006–0.13; p = 0.03). Longer LTL at baseline was associated with worsening lobular inflammation at 96 weeks (Coeff 2.41, 95% CI 0.78–4.04; p < 0.01). There was no association between liver fibrosis and LTL. The association between LTL and pediatric NASH does not parallel adults with no association between fibrosis stage and NASH. Conversely, longer LTL was associated with more lobular inflammation at baseline and increased lobular inflammation over the 96-week period. Longer LTL in children may indicate greater risk for future complications from NASH. [ABSTRACT FROM AUTHOR]

Background: Colorectal cancer (CRC) primary tumours are molecularly classified into four consensus molecular subtypes (CMS1–4). Genetically engineered mouse models aim to faithfully mimic the complexity of human cancers and, when appropriately aligned, represent ideal pre-clinical systems to test new drug treatments. Despite its importance, dual-species classification has been limited by the lack of a reliable approach. Here we utilise, develop and test a set of options for human-to-mouse CMS classifications of CRC tissue. Methods: Using transcriptional data from established collections of CRC tumours, including human (TCGA cohort; n = 577) and mouse (n = 57 across n = 8 genotypes) tumours with combinations of random forest and nearest template prediction algorithms, alongside gene ontology collections, we comprehensively assess the performance of a suite of new dual-species classifiers. Results: We developed three approaches: MmCMS-A; a gene-level classifier, MmCMS-B; an ontology-level approach and MmCMS-C; a combined pathway system encompassing multiple biological and histological signalling cascades. Although all options could identify tumours associated with stromal-rich CMS4-like biology, MmCMS-A was unable to accurately classify the biology underpinning epithelial-like subtypes (CMS2/3) in mouse tumours. Conclusions: When applying human-based transcriptional classifiers to mouse tumour data, a pathway-level classifier, rather than an individual gene-level system, is optimal. Our R package enables researchers to select suitable mouse models of human CRC subtype for their experimental testing. [ABSTRACT FROM AUTHOR]

While STING-activating agents have shown limited efficacy in early-phase clinical trials, multiple lines of evidence suggest the importance of tumor cell-intrinsic STING function in mediating antitumor immune responses. Although STING signaling is impaired in human melanoma, its restoration through epigenetic reprogramming can augment its antigenicity and T cell recognition. In this study, we show that reversal of methylation silencing of STING in murine melanoma cell lines using a clinically available DNA methylation inhibitor can improve agonist-induced STING activation and type-I IFN induction, which, in tumor-bearing mice, can induce tumor regression through a CD8+ T cell-dependent immune response. These findings not only provide mechanistic insight into how STING signaling dysfunction in tumor cells can contribute to impaired responses to STING agonist therapy, but also suggest that pharmacological restoration of STING signaling through epigenetic reprogramming might improve the therapeutic efficacy of STING agonists. STING agonists have shown limited efficacy in early-phase clinical trials despite promising pre-clinical data. This study shows the potential clinical relevance of the use of combination STING agonists and demethylating agent therapies to induce the expression of STING. [ABSTRACT FROM AUTHOR]

Historical targets for country-level animal rabies testing volumes were abandoned due to ethical and welfare concerns, and interpretation challenges of testing healthy animals. To-date, no quantitative threshold has been established for evaluating adequate surveillance capacity specific to suspected rabid animals. The purpose here is to establish quantitative testing thresholds for rabies suspected animals to assess a country's rabies surveillance capacity. Animal rabies testing data was obtained from official and unofficial rabies surveillance platforms from 2010 to 2019 and supplemented with official country reports and published literature. Testing rates were determined for all-animal and domestic animals, and standardized per 100,000 estimated human population; the domestic animal rate was also standardized per 100,000 estimated dog population. There were 113 countries that reported surveillance data eligible for analysis. Countries reporting the most data were under WHO categories as having endemic human rabies or no dog rabies. The annual median all-animal testing rate for all countries was 1.53 animals/100,000 human population (IQR 0.27–8.78). Three proposed testing rate thresholds are an all-animal rate of 1.9 animals/100,000 humans, a domestic animal per human rate of 0.8 animals/100,000 humans, and a domestic animal per dog rate of 6.6 animals/100,000 dogs. These three peer-derived rabies testing thresholds for passive surveillance can be used to facilitate assessment of a country's rabies surveillance capacity. [ABSTRACT FROM AUTHOR]

Non-invasive methods to document healing anterior cruciate ligament (ACL) structural properties could potentially identify patients at risk for revision surgery. The objective was to evaluate machine learning models to predict ACL failure load from magnetic resonance images (MRI) and to determine if those predictions were related to revision surgery incidence. It was hypothesized that the optimal model would demonstrate a lower mean absolute error (MAE) than the benchmark linear regression model, and that patients with a lower estimated failure load would have higher revision incidence 2 years post-surgery. Support vector machine, random forest, AdaBoost, XGBoost, and linear regression models were trained using MRI T2* relaxometry and ACL tensile testing data from minipigs (n = 65). The lowest MAE model was used to estimate ACL failure load for surgical patients at 9 months post-surgery (n = 46) and dichotomized into low and high score groups via Youden's J statistic to compare revision incidence. Significance was set at alpha = 0.05. The random forest model decreased the failure load MAE by 55% (Wilcoxon signed-rank test: p = 0.01) versus the benchmark. The low score group had a higher revision incidence (21% vs. 5%; Chi-square test: p = 0.09). ACL structural property estimates via MRI may provide a biomarker for clinical decision making. [ABSTRACT FROM AUTHOR]

Assessing the lifetimes of alloys in humid, corrosive environments requires growth kinetic information regarding individual instances of damage, e.g. pit growth rates. Corrosion rates measured at the continuum scale using mass change convolute the rate of pit nucleation and growth, providing limited information on local kinetics. The current study used in-situ X-ray computed tomography to measure growth rates of individual pits in aluminum over 100 h of exposure in a humid, chloride environment. While pits grew at relatively constant rates over the first hours after nucleation, significant growth-rate nonlinearities subsequently occurred. These were linked to both droplet spreading, which altered the cathode size, and changes in the mode of pit growth. Pit morphology appeared to influence the dominant growth mode and the duration of pit growth. Post-mortem serial sectioning revealed pits preferentially attacked grain-boundary triple junctions and dislocation boundaries. [ABSTRACT FROM AUTHOR]

Additive manufacturing (AM) requires a significant capital investment to acquire a machine, procure raw material, and train operators to begin production. This substantial overhead means interruptions to the AM build process can become a costly event if the interruption results in significantly reduced build quality. Interruptions in the form of power outages, lack of powder feedstock, and/or loss of shielding gas can cause the machine to operate in an unintended manner, interrupting the build and potentially even stopping the entire process. An interrupted laser powder bed fusion process could result in reduced mechanical properties, localized failures, and physical characteristics that distinguish an interrupted component from a continuous one. This investigation aims to explore the effect of various build interruption conditions (i.e., duration of the interruption and air exposure) on microstructural and mechanical properties of Al-Si-10Mg fabricated via a laser powder bed fusion (LPBF) system. Seven builds were completed for this study, a control along with six interruption experiments with three distinct time lengths for the interruption periods: 15 min, 12 and 24 h. Each interruption period was repeated to explore the effects of air exposure during the stoppage. The effects of interruptions were characterized by x-ray computed tomography, optical microscopy, scanning electron microscopy, Vickers microhardness, and destructive oxide testing. Strain rate-controlled tension tests were conducted to determine mechanical properties. Results indicated no reduction in mechanical properties (i.e., tensile and micro-hardness) for any of the interrupted specimens when compared to the control and literature on LPBF-processed Al-Si-10Mg. However, the 24-h group specimens experienced the most failures near the interruption location, indicating that failure location can be influenced by prolonged stoppage and air exposure. [ABSTRACT FROM AUTHOR]

Checkpoint blockade immunotherapy has become a first-line treatment option for cancer patients, with success in increasingly diverse cancer types. Still, many patients do not experience durable responses and the reasons for clinical success versus failure remain largely undefined. Investigation of immune responses within the tumor microenvironment can be highly informative but access to tumor tissue is not always available, highlighting the need to identify biomarkers in the blood that correlate with clinical success. Here, we used single-cell RNA sequencing coupled with T cell receptor sequencing to define CD8+ T cell responses in peripheral blood of two patients with melanoma before and after immunotherapy with either anti-PD-1 (nivolumab) alone or the combination of anti-PD-1 and CTLA-4 (ipilimumab). Both treatment regimens increased transcripts associated with cytolytic effector function and decreased transcripts associated with naive T cells. These responses were further evaluated at the protein level and extended to a total of 53 patients with various cancer types. Unexpectedly, the induction of CD8+ T cell responses associated with cytolytic function was variable and did not predict therapeutic success in this larger patient cohort. Rather, a decrease in the frequency of T cells with a naive-like phenotype was consistently observed after immunotherapy and correlated with prolonged patient survival. In contrast, a more detailed clonotypic analysis of emerging and expanding CD8+ T cells in the blood revealed that a majority of individual T cell clones responding to immunotherapy acquired a transcriptional profile consistent with cytolytic effector function. These results suggest that responses to checkpoint blockade immunotherapy are evident and traceable in patients' blood, with outcomes predicted by the simultaneous loss of naive-like CD8+ T cells and the expansion of mostly rare and diverse cytotoxic CD8+ T cell clones. [ABSTRACT FROM AUTHOR]

Carbon storage in Earth’s oceans is controlled by deep-sea mixing processes, but the details have proved difficult to test. Ambitious efforts to track ocean mixing using dye have now demonstrated the pivotal role of the sea floor.Observations of upwelling in a deep-ocean canyon. [ABSTRACT FROM AUTHOR]

Background: To characterize the safety, immunogenicity, and outcomes of patients with high-grade serous ovarian cancer (HGSOC) in second or greater remission treated with a polyvalent antigen-KLH plus OPT-821 vaccine construct and bevacizumab. Methods: Patients with recurrent HGSOC were treated with the vaccine plus bevacizumab at our institution from 01/05/2011 to 03/20/2012. Follow-up continued until 03/2021. Blood/urine samples were collected. "Responders" had an immunogenic response to ≥ 3 antigens; "non-responders" to ≤ 2 antigens. Results: Twenty-one patients were treated on study. One developed a dose-limiting toxicity (grade 4 fever). Two (10%) experienced bevacizumab-related grade 3 hypertension. Thirteen (68%) and 16 (84%) of 19 responded to ≥ 3 and ≥ 2 antigens, respectively (Globo-H, GM2, TF cluster Tn, MUC-1). Four of 21 patients were alive > 5 years post-treatment. Responders and non-responders had a median PFS of 4.9 months (95% CI: 2.8–8.1) and 5.0 months (95% CI: 0.7-cannot estimate), respectively; median OS was 30.7 months (95% CI: 16.9–52.0) and 34.2 months (95% CI: 12.8-cannot estimate), respectively. On two-timepoint analysis (baseline, week 17), increased IL-8 exhibited improved PFS (HR as 10-unit increase, 0.43; p = 0.04); increased PDGF exhibited worse OS (HR as 10-unit increase, 1.01; p = 0.02). Conclusions: This is the longest follow-up of vaccine administration with bevacizumab in patients with ovarian cancer. The vaccine was well tolerated with bevacizumab. Response was not associated with improved survival. On two-timepoint analysis, increased IL-8 was associated with significant improvement in PFS; increased PDGF with significantly worse OS. For all timepoint measurements, cytokine levels were not significantly associated with survival. Trial registration: NCT01223235. [ABSTRACT FROM AUTHOR]

Short peptide sequences and bolaamphiphiles derived from natural proteins are gaining importance due to their ability to form unique nanoscale architectures for a variety of biological applications. In this work, we have designed six short peptides (triplet or monomeric forms) and two peptide bolaamphiphiles that either incorporate the bioactive collagen motif (Gly-X–Y) or sequences where Gly, Pro, or hydroxyproline (Hyp) are replaced by Ala or His. For the bolaamphiphiles, a malate moiety was used as the aliphatic linker for connecting His with Hyp to create collagen mimics. Stability of the assemblies was assessed through molecular dynamics simulations and results indicated that (Pro-Ala-His)3 and (Ala-His-Hyp)3 formed the most stable structures, while the amphiphiles and the monomers showed some disintegration over the course of the 200 ns simulation, though most regained structural integrity and formed fibrillar structures, and micelles by the end of the simulation, likely due to the formation of more thermodynamically stable conformations. Multiple replica simulations (REMD) were also conducted where the sequences were simulated at different temperatures. Our results showed excellent convergence in most cases compared to constant temperature molecular dynamics simulation. Furthermore, molecular docking and MD simulations of the sequences bound to collagen triple helix structure revealed that several of the sequences had a high binding affinity and formed stable complexes, particularly (Pro-Ala-His)3 and (Ala-His-Hyp)3. Thus, we have designed new hybrid-peptide-based sequences which may be developed for potential applications as biomaterials for tissue engineering or drug delivery. [ABSTRACT FROM AUTHOR]

Molecular phylogenetics of microbial eukaryotes has reshaped the tree of life by establishing broad taxonomic divisions, termed supergroups, that supersede the traditional kingdoms of animals, fungi and plants, and encompass a much greater breadth of eukaryotic diversity1. The vast majority of newly discovered species fall into a small number of known supergroups. Recently, however, a handful of species with no clear relationship to other supergroups have been described2–4, raising questions about the nature and degree of undiscovered diversity, and exposing the limitations of strictly molecular-based exploration. Here we report ten previously undescribed strains of microbial predators isolated through culture that collectively form a diverse new supergroup of eukaryotes, termed Provora. The Provora supergroup is genetically, morphologically and behaviourally distinct from other eukaryotes, and comprises two divergent clades of predators—Nebulidia and Nibbleridia—that are superficially similar to each other, but differ fundamentally in ultrastructure, behaviour and gene content. These predators are globally distributed in marine and freshwater environments, but are numerically rare and have consequently been overlooked by molecular-diversity surveys. In the age of high-throughput analyses, investigation of eukaryotic diversity through culture remains indispensable for the discovery of rare but ecologically and evolutionarily important eukaryotes.Provora is an ancient supergroup of microbial predators that are genetically, morphologically and behaviourally distinct from other eukaryotes, and comprise two divergent clades of predators—Nebulidia and Nibbleridia—that differ fundamentally in ultrastructure, behaviour and gene content. [ABSTRACT FROM AUTHOR]

DNA methylation is a key epigenetic property that drives gene regulatory programs in development and disease. Current single-cell methods that produce high quality methylomes are expensive and low throughput without the aid of extensive automation. We previously described a proof-of-principle technique that enabled high cell throughput; however, it produced only low-coverage profiles and was a difficult protocol that required custom sequencing primers and recipes and frequently produced libraries with excessive adapter contamination. Here, we describe a greatly improved version that generates high-coverage profiles (~15-fold increase) using a robust protocol that does not require custom sequencing capabilities, includes multiple stopping points, and exhibits minimal adapter contamination. We demonstrate two versions of sciMETv2 on primary human cortex, a high coverage and rapid version, identifying distinct cell types using CH methylation patterns. These datasets are able to be directly integrated with one another as well as with existing snmC-seq2 datasets with little discernible bias. Finally, we demonstrate the ability to determine cell types using CG methylation alone, which is the dominant context for DNA methylation in most cell types other than neurons and the most applicable analysis outside of brain tissue. Despite the importance of DNA methylation, accessible and high-throughput methods to profile methylation at the single-cell level are lacking. Here, the authors present sciMETv2, a high-throughput workflow that provides high-quality single-cell methylomes in a robust and simple workflow. [ABSTRACT FROM AUTHOR]

Point-of-care antigen-detecting rapid diagnostic tests (RDTs) to detect Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) represent a scalable tool for surveillance of active SARS-CoV-2 infections in the population. Data on the performance of these tests in real-world community settings are paramount to guide their implementation to combat the COVID-19 pandemic. We evaluated the performance characteristics of the CareStart COVID-19 Antigen test (CareStart) in a community testing site in Holyoke, Massachusetts. We compared CareStart to a SARS-CoV-2 reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) reference, both using anterior nasal swab samples. We calculated the sensitivity, specificity, and the expected positive and negative predictive values at different SARS-CoV-2 prevalence estimates. We performed 666 total tests on 591 unique individuals. 573 (86%) were asymptomatic. There were 52 positive tests by RT-qPCR. The sensitivity of CareStart was 49.0% (95% Confidence Interval (CI) 34.8–63.4) and specificity was 99.5% (95% CI 98.5–99.9). Among positive RT-qPCR tests, the median cycle threshold (Ct) was significantly lower in samples that tested positive on CareStart. Using a Ct ≤ 30 as a benchmark for positivity increased the sensitivity of the test to 64.9% (95% CI 47.5–79.8). Our study shows that CareStart has a high specificity and moderate sensitivity. The utility of RDTs, such as CareStart, in mass implementation should prioritize use cases in which a higher specificity is more important, such as triage tests to rule-in active infections in community surveillance programs. [ABSTRACT FROM AUTHOR]

Nutrient inputs to northern freshwaters are changing, potentially altering aquatic ecosystem functioning through effects on primary producers. Yet, while primary producer growth is sensitive to nutrient supply, it is also constrained by a suite of other factors, including light and temperature, which may play varying roles across stream and lake habitats. Here, we use bioassay results from 89 lakes and streams spanning northern boreal to Arctic Sweden to test for differences in nutrient limitation status of algal biomass along gradients in colored dissolved organic carbon (DOC), water temperature, and nutrient concentrations, and to ask whether there are distinct patterns and drivers between habitats. Single nitrogen (N) limitation or primary N-limitation with secondary phosphorus (P) limitation of algal biomass was the most common condition for streams and lakes. Average response to N-addition was a doubling in biomass; however, the degree of limitation was modulated by the distinct physical and chemical conditions in lakes versus streams and across boreal to Arctic regions. Overall, algal responses to N-addition were strongest at sites with low background concentrations of dissolved inorganic N. Low temperatures constrained biomass responses to added nutrients in lakes but had weaker effects on responses in streams. Further, DOC mediated the response of algal biomass to nutrient addition differently among lakes and streams. Stream responses were dampened at higher DOC, whereas lake responses to nutrient addition increased from low to moderate DOC but were depressed at high DOC. Our results suggest that future changes in nutrient availability, particularly N, will exert strong effects on the trophic state of northern freshwaters. However, we highlight important differences in the physical and chemical factors that shape algal responses to nutrient availability in different parts of aquatic networks, which will ultimately affect the integrated response of northern aquatic systems to ongoing environmental changes. [ABSTRACT FROM AUTHOR]