An international breeding project using a wild potato relative Solanum commersonii resulted in two new frost-tolerant native potato cultivars for the Andes and the Altiplano.

This breeding project, initiated at the United States Potato Genebank (USPG) in collaboration with Peruvian partners Instituto Nacional de Innovacion Agraria (INIA), International Potato Center, Peru (CIP), and local farmers, sought to enhance cold hardiness and frost tolerance in native potato cultivars in Peru. The Andes and Altiplano are often affected by frost, which causes significant reduction in yield; creating varieties with superior resilience is a critical undertaking. The goal was to transfer outstanding non-acclimated cold tolerance and acclimation capacity found in wild potato species Solanum commersonii (cmm). Breeding families segregating for cold hardiness were created using (a) a somatic hybrid cmm + haploid Solanum tuberosum (tbr) (cv. Superior, US variety from Wisconsin) as male and (b) seven cultivars native to Peru of the species S. tuberosum sbsp. andigenum (adg) as females. All plant materials were part of the USPG germplasm collection. Sexual seeds of each family were sent to Peru for evaluations under the natural conditions of the Andean highlands and Altiplano. The plants were assessed for their response to frost, and genotypes showing exceptional tolerance were selected. Plants were also evaluated for good tuber traits and yield. Initial planting involving ~2,500 seedlings in five locations resulted in selecting 58 genotypes with exceptional frost tolerance, good recovery capacity after frost, and good tuber traits. Over the years, evaluations continued and were expanded to replicated field trials in the harsher conditions of the Altiplano (Puno). All trials confirmed consistency of frost tolerance over time and location, tuber quality, and yield. After 8 years, two advanced clones were considered for cultivar release because of their exceptional frost tolerance and superior field productivity that outyielded many of the established cultivars in the region. In November 2018, a new native cultivar named Wiñay, a Quechua word meaning "to grow" was released in Peru. In 2022, a second cultivar followed with the name Llapanchispaq (meaning "for all of us"). This project evidenced that a multinational and all-encompassing approach to deploy valuable genetic diversity can work and deliver effective results. This is even more significant when outcomes can promote food security and sustainability in very vulnerable regions of the world.

Mechanism of TLR4-Mediated Anti-Inflammatory Response Induced by Exopolysaccharide from the Probiotic Bacillus subtilis.

Intestinal inflammatory diseases affect millions of people worldwide, and one class of drugs showing promise toward treatment of several inflammatory diseases is probiotics. Numerous studies have been performed using probiotics to prevent and treat intestinal inflammatory diseases. Most of these studies used intact bacteria, and neither the active molecule nor the molecular mechanisms by which they affect immune responses are known. We have shown that the probiotic Bacillus subtilis is anti-inflammatory and can protect mice from acute colitis induced by the enteric pathogen Citrobacter rodentium. We identified and purified the active molecule, exopolysaccharide (EPS), and showed that it protects mice from C. rodentium-induced colitis by inducing anti-inflammatory M2 macrophages or inhibitory dendritic cells (DCs), both of which inhibit excessive T cell responses. We showed previously that EPS affects macrophages and DCs in a TLR4-dependent manner, and in the current study we asked how EPS induces these anti-inflammatory cells and how they function to inhibit T cells. By investigating the signaling downstream of TLR4 that leads to acquisition of inhibitory properties of macrophages and DCs, we found that EPS induces expression of the inhibitory molecule IDO in bone marrow-derived DCs, and that inhibition of T cell proliferation by IDO-expressing bone marrow-derived DCs utilizes the kynurenine/aryl hydrocarbon receptor circuit. Furthermore, unlike LPS, EPS does not induce inflammatory cytokines upon injection in vivo, directly demonstrating different outcomes induced by two different TLR4 agonists.

Roadmap on Deep Learning for Microscopy.

Through digital imaging, microscopy has evolved from primarily being a means for visual observation of life at the micro- and nano-scale, to a quantitative tool with ever-increasing resolution and throughput. Artificial intelligence, deep neural networks, and machine learning are all niche terms describing computational methods that have gained a pivotal role in microscopy-based research over the past decade. This Roadmap is written collectively by prominent researchers and encompasses selected aspects of how machine learning is applied to microscopy image data, with the aim of gaining scientific knowledge by improved image quality, automated detection, segmentation, classification and tracking of objects, and efficient merging of information from multiple imaging modalities. We aim to give the reader an overview of the key developments and an understanding of possibilities and limitations of machine learning for microscopy. It will be of interest to a wide cross-disciplinary audience in the physical sciences and life sciences.

Corneal endothelium assessment in specular microscopy images with Fuchs' dystrophy via deep regression of signed distance maps.

Specular microscopy assessment of the human corneal endothelium (CE) in Fuchs' dystrophy is challenging due to the presence of dark image regions called guttae. This paper proposes a UNet-based segmentation approach that requires minimal post-processing and achieves reliable CE morphometric assessment and guttae identification across all degrees of Fuchs' dystrophy. We cast the segmentation problem as a regression task of the cell and gutta signed distance maps instead of a pixel-level classification task as typically done with UNets. Compared to the conventional UNet classification approach, the distance-map regression approach converges faster in clinically relevant parameters. It also produces morphometric parameters that agree with the manually-segmented ground-truth data, namely the average cell density difference of -41.9 cells/mm2 (95% confidence interval (CI) [-306.2, 222.5]) and the average difference of mean cell area of 14.8 µm 2 (95% CI [-41.9, 71.5]). These results suggest a promising alternative for CE assessment.

Single-shot self-supervised object detection in microscopy.

Object detection is a fundamental task in digital microscopy, where machine learning has made great strides in overcoming the limitations of classical approaches. The training of state-of-the-art machine-learning methods almost universally relies on vast amounts of labeled experimental data or the ability to numerically simulate realistic datasets. However, experimental data are often challenging to label and cannot be easily reproduced numerically. Here, we propose a deep-learning method, named LodeSTAR (Localization and detection from Symmetries, Translations And Rotations), that learns to detect microscopic objects with sub-pixel accuracy from a single unlabeled experimental image by exploiting the inherent roto-translational symmetries of this task. We demonstrate that LodeSTAR outperforms traditional methods in terms of accuracy, also when analyzing challenging experimental data containing densely packed cells or noisy backgrounds. Furthermore, by exploiting additional symmetries we show that LodeSTAR can measure other properties, e.g., vertical position and polarizability in holographic microscopy.

Sphingosine Phosphate Lyase Is Upregulated in Duchenne Muscular Dystrophy, and Its Inhibition Early in Life Attenuates Inflammation and Dystrophy in Mdx Mice.

Duchenne muscular dystrophy (DMD) is a congenital myopathy caused by mutations in the dystrophin gene. DMD pathology is marked by myositis, muscle fiber degeneration, and eventual muscle replacement by fibrosis and adipose tissue. Satellite cells (SC) are muscle stem cells critical for muscle regeneration. Sphingosine-1-phosphate (S1P) is a bioactive sphingolipid that promotes SC proliferation, regulates lymphocyte trafficking, and is irreversibly degraded by sphingosine phosphate lyase (SPL). Here, we show that SPL is virtually absent in normal human and murine skeletal muscle but highly expressed in inflammatory infiltrates and degenerating fibers of dystrophic DMD muscle. In mdx mice that model DMD, high SPL expression is correlated with dysregulated S1P metabolism. Perinatal delivery of the SPL inhibitor LX2931 to mdx mice augmented muscle S1P and SC numbers, reduced leukocytes in peripheral blood and skeletal muscle, and attenuated muscle inflammation and degeneration. The effect on SC was also observed in SCID/mdx mice that lack mature T and B lymphocytes. Transcriptional profiling in the skeletal muscles of LX2931-treated vs. control mdx mice demonstrated changes in innate and adaptive immune functions, plasma membrane interactions with the extracellular matrix (ECM), and axon guidance, a known function of SC. Our cumulative findings suggest that by raising muscle S1P and simultaneously disrupting the chemotactic gradient required for lymphocyte egress, SPL inhibition exerts a combination of muscle-intrinsic and systemic effects that are beneficial in the context of muscular dystrophy.

Benign tumors in TSC are amenable to treatment by GD3 CAR T cells in mice.

Mutations underlying disease in tuberous sclerosis complex (TSC) give rise to tumors with biallelic mutations in TSC1 or TSC2 and hyperactive mammalian target of rapamycin complex 1 (mTORC1). Benign tumors might exhibit de novo expression of immunogens, targetable by immunotherapy. As tumors may rely on ganglioside D3 (GD3) expression for mTORC1 activation and growth, we compared GD3 expression in tissues from patients with TSC and controls. GD3 was overexpressed in affected tissues from patients with TSC and also in aging Tsc2+/- mice. As GD3 overexpression was not accompanied by marked natural immune responses to the target molecule, we performed preclinical studies with GD3 chimeric antigen receptor (CAR) T cells. Polyfunctional CAR T cells were cytotoxic toward GD3-overexpressing targets. In mice challenged with Tsc2-/- tumor cells, CAR T cells substantially and durably reduced the tumor burden, correlating with increased T cell infiltration. We also treated aged Tsc2+/- heterozygous (>60 weeks) mice that carry spontaneous Tsc2-/- tumors with GD3 CAR or untransduced T cells and evaluated them at endpoint. Following CAR T cell treatment, the majority of mice were tumor free while all control animals carried tumors. The outcomes demonstrate a strong treatment effect and suggest that targeting GD3 can be successful in TSC.

Active droploids.

Active matter comprises self-driven units, such as bacteria and synthetic microswimmers, that can spontaneously form complex patterns and assemble into functional microdevices. These processes are possible thanks to the out-of-equilibrium nature of active-matter systems, fueled by a one-way free-energy flow from the environment into the system. Here, we take the next step in the evolution of active matter by realizing a two-way coupling between active particles and their environment, where active particles act back on the environment giving rise to the formation of superstructures. In experiments and simulations we observe that, under light-illumination, colloidal particles and their near-critical environment create mutually-coupled co-evolving structures. These structures unify in the form of active superstructures featuring a droplet shape and a colloidal engine inducing self-propulsion. We call them active droploids-a portmanteau of droplet and colloids. Our results provide a pathway to create active superstructures through environmental feedback.

Amelioration of Graft-versus-Host Disease by Exopolysaccharide from a Commensal Bacterium.

Acute graft-versus-host disease (aGvHD) is a severe, often lethal, complication of hematopoietic stem cell transplantation, and although prophylactic regimens are given as standard pretransplantation therapy, up to 60% of these patients develop aGvHD, and require additional immunosuppressive intervention. We treated mice with a purified probiotic molecule, exopolysaccharide (EPS) from Bacillus subtilis, shortly before and after induction of aGvHD and found that, whereas only 10% of control mice survived to day 80, 70% of EPS-treated mice survived to 80 d. EPS treatment of donor-only mice resulted in ∼60% survival. Using a biosensor mouse model to assess inflammation in live mice during aGvHD, we found that EPS prevented the activation of alloreactive donor T cells. In vitro, EPS did not affect T cells directly but, instead, induced bone marrow-derived dendritic cells (BMDCs) that displayed characteristics of inhibitory dendritic cells (DCs). Development of these BMDCs required TLR4 signaling through both MyD88 and TRIF pathways. Using BMDCs derived from IDO knockout mice, we showed that T cell inhibition by EPS-treated BMDCs was mediated through the suppressive effects of IDO. These studies describe a bacterial molecule that modulates immune responses by inducing inhibitory DCs in a TLR4-dependent manner, and these cells have the capacity to inhibit T cell activation through IDO. We suggest that EPS or EPS-treated DCs can serve as novel agents for preventing aGvHD.

Extracting quantitative biological information from bright-field cell images using deep learning.

Quantitative analysis of cell structures is essential for biomedical and pharmaceutical research. The standard imaging approach relies on fluorescence microscopy, where cell structures of interest are labeled by chemical staining techniques. However, these techniques are often invasive and sometimes even toxic to the cells, in addition to being time consuming, labor intensive, and expensive. Here, we introduce an alternative deep-learning-powered approach based on the analysis of bright-field images by a conditional generative adversarial neural network (cGAN). We show that this is a robust and fast-converging approach to generate virtually stained images from the bright-field images and, in subsequent downstream analyses, to quantify the properties of cell structures. Specifically, we train a cGAN to virtually stain lipid droplets, cytoplasm, and nuclei using bright-field images of human stem-cell-derived fat cells (adipocytes), which are of particular interest for nanomedicine and vaccine development. Subsequently, we use these virtually stained images to extract quantitative measures about these cell structures. Generating virtually stained fluorescence images is less invasive, less expensive, and more reproducible than standard chemical staining; furthermore, it frees up the fluorescence microscopy channels for other analytical probes, thus increasing the amount of information that can be extracted from each cell. To make this deep-learning-powered approach readily available for other users, we provide a Python software package, which can be easily personalized and optimized for specific virtual-staining and cell-profiling applications.

SPUD: simultaneous phase unwrapping and denoising algorithm for phase imaging.

Recent methods for phase unwrapping in the presence of noise include denoising algorithms to filter out noise as a preprocessing stage. However, including a denoising stage increases the overall computational complexity resulting in long execution times. In this paper, we present a noniterative simultaneous phase unwrapping and denoising algorithm for phase imaging, referred to as SPUD. The proposed method relies on the least squares discrete cosine transform (DCT) solution for phase unwrapping with an additional sparsity constraint on the DCT coefficients of the unwrapped solution. Simulation results with different levels of noise and wrapped phase fringe density reveal the suitability of the proposed method for accurate phase unwrapping and restoration. When compared to the 2D windowed Fourier transform filter, SPUD performs better in terms of phase error and execution times. The processing of experimental data from synthetic aperture radar showed the capability for processing real images, including removing phase dislocations. An implementation of the proposed algorithm can be accessed and executed through a Code Ocean compute capsule.

Actividad de adiestramiento en cardioversión eléctrica en la unidad de electrocardiología del CCR-ASCARDIO / Training program on electrical cardioversion at the electrocardiology unit of the CCR-ASCARDIO

Las enfermedades cardiovasculares son una de las principales causas de mortalidad siendo los trastornos del ritmo cardiaco una de las patologías cardiacas más frecuentes. La cardioversión eléctrica es una técnica a través de la cual se realiza una transferencia de electrones al miocardio con la finalidad de interrumpir arritmias con mecanismos de reentrada permitiendo al nodo sinusal retomar el control de la frecuencia cardiaca. La correcta selección de los casos susceptibles de cardioversión eléctrica y experiencia en cardioversión aumenta la tasa de éxito y disminuye el número de choques fallidos. En el CCR- ASCARDIO, la Unidad de Electrocardiología cuenta con experiencia en el estudio y tratamiento de arritmias. En este artículo se presenta la elaboración de un programa de adiestramiento en la técnica de cardioversión eléctrica siendo esta terapia una herramienta imprescindible para la práctica clínica del cardiólogo, facilitando la prevención de complicaciones derivadas de los trastornos del ritmo cardiaco(AU)

Cardiovascular diseases are one of the main causes of mortality worldwide being heart rhythm disorders one of the most frequent cardiac pathologies. Electrical cardioversion is a technique that allows the transfer of electrons to the myocardium in order to interrupt arrhythmias with reentry mechanisms allowing the sinus node to take control of heart rate. The appropriate selection of cases susceptible to electrical cardioversion as well as experience on this technique increases the success rate and decreases the number of failed attempts. The Electrocardiology unit of the CCR-ASCARDIO has experience in the study and treatment of arrhythmias. In this article we present the development of a training program on electrical cardioversion, essential tool for cardiologists, with the aim to increase the correct use of this technique in order to prevent complications due to heart rhythm disorders(AU)

Robust automated reading of the skin prick test via 3D imaging and parametric surface fitting.

The conventional reading of the skin prick test (SPT) for diagnosing allergies is prone to inter- and intra-observer variations. Drawing the contours of the skin wheals from the SPT and scanning them for computer processing is cumbersome. However, 3D scanning technology promises the best results in terms of accuracy, fast acquisition, and processing. In this work, we present a wide-field 3D imaging system for the 3D reconstruction of the SPT, and we propose an automated method for the measurement of the skin wheals. The automated measurement is based on pyramidal decomposition and parametric 3D surface fitting for estimating the sizes of the wheals directly. We proposed two parametric models for the diameter estimation. Model 1 is based on an inverted Elliptical Paraboloid function, and model 2 on a super-Gaussian function. The accuracy of the 3D imaging system was evaluated with validation objects obtaining transversal and depth accuracies within ± 0.1 mm and ± 0.01 mm, respectively. We tested the method on 80 SPTs conducted in volunteer subjects, which resulted in 61 detected wheals. We analyzed the accuracy of the models against manual reference measurements from a physician and obtained that the parametric model 2 on average yields diameters closer to the reference measurements (model 1: -0.398 mm vs. model 2: -0.339 mm) with narrower 95% limits of agreement (model 1: [-1.58, 0.78] mm vs. model 2: [-1.39, 0.71] mm) in a Bland-Altman analysis. In one subject, we tested the reproducibility of the method by registering the forearm under five different poses obtaining a maximum coefficient of variation of 5.24% in the estimated wheal diameters. The proposed method delivers accurate and reproducible measurements of the SPT.

Diversity and distribution of nearshore barnacle cyprids in southern California through the 2015-16 El Niño.

Abundance, species diversity, and horizontal distributions of barnacle cyprids offshore of La Jolla, southern California were described from May 2014 to August 2016 to determine how the nearshore barnacle larval assemblage changed before, during, and after the 2015-16 El Niño. The entire water column was sampled at five stations located within one km of shore with water depths of 4, 6, 8, 10, and 12 m during 33 cruises that encompassed the time when El Niño conditions impacted the area. Nearshore temperature and thermal stratification was concurrently measured using a CTD. Six identified cyprid species, including Chthamalus fissus, Pollicipes polymerus, Megabalanus rosa, Tetraclita rubescens, Balanus glandula, and B. trigonus, along with four unknown species, were collected in our samples. DNA barcoding was used to confirm identifications in a subset of the larvae. C. fissus was more than eight times more abundant than any other species, and while abundance varied by species, cyprid density was highest for all species except for M. rosa before and after the El Niño event, and lower during the environmental disturbance. There were significant differences in cross-shore distributions among cyprid species, with some located farther offshore than others, along with variability in cross-shore distributions by season. C. fissus cyprids were closest to shore during spring-summer cruises when waters were the most thermally stratified, which supports previous findings that C. fissus cyprids are constrained nearshore when thermal stratification is high. Relative species proportions varied throughout the study, but there was no obvious change in species assemblage or richness associated with El Niño. We speculate that barnacle cyprid species diversity did not increase at our study site during the 2015-16 El Niño, as it has in other areas during previous El Niño Southern Oscillation events, due to the lack of anomalous northward flow throughout the 2015-16 event.

S1P Lyase Regulation of Thymic Egress and Oncogenic Inflammatory Signaling.

Sphingosine-1-phosphate (S1P) is a potent lipid signaling molecule that regulates pleiotropic biological functions including cell migration, survival, angiogenesis, immune cell trafficking, inflammation, and carcinogenesis. It acts as a ligand for a family of cell surface receptors. S1P concentrations are high in blood and lymph but low in tissues, especially the thymus and lymphoid organs. S1P chemotactic gradients are essential for lymphocyte egress and other aspects of physiological cell trafficking. S1P is irreversibly degraded by S1P lyase (SPL). SPL regulates lymphocyte trafficking, inflammation and other physiological and pathological processes. For example, SPL located in thymic dendritic cells acts as a metabolic gatekeeper that controls the normal egress of mature T lymphocytes from the thymus into the circulation, whereas SPL deficiency in gut epithelial cells promotes colitis and colitis-associated carcinogenesis (CAC). Recently, we identified a complex syndrome comprised of nephrosis, adrenal insufficiency, and immunological defects caused by inherited mutations in human SGPL1, the gene encoding SPL. In the present article, we review current evidence supporting the role of SPL in thymic egress, inflammation, and cancer. Lastly, we summarize recent progress in understanding other SPL functions, its role in inherited disease, and SPL targeting for therapeutic purposes.

Dendritic cell sphingosine-1-phosphate lyase regulates thymic egress.

T cell egress from the thymus is essential for adaptive immunity and involves chemotaxis along a sphingosine-1-phosphate (S1P) gradient. Pericytes at the corticomedullary junction produce the S1P egress signal, whereas thymic parenchymal S1P levels are kept low through S1P lyase (SPL)-mediated metabolism. Although SPL is robustly expressed in thymic epithelial cells (TECs), in this study, we show that deleting SPL in CD11c+ dendritic cells (DCs), rather than TECs or other stromal cells, disrupts the S1P gradient, preventing egress. Adoptive transfer of peripheral wild-type DCs rescued the egress phenotype of DC-specific SPL knockout mice. These studies identify DCs as metabolic gatekeepers of thymic egress. Combined with their role as mediators of central tolerance, DCs are thus poised to provide homeostatic regulation of thymic export.

A crab swarm at an ecological hotspot: patchiness and population density from AUV observations at a coastal, tropical seamount.

A research cruise to Hannibal Bank, a seamount and an ecological hotspot in the coastal eastern tropical Pacific Ocean off Panama, explored the zonation, biodiversity, and the ecological processes that contribute to the seamount's elevated biomass. Here we describe the spatial structure of a benthic anomuran red crab population, using submarine video and autonomous underwater vehicle (AUV) photographs. High density aggregations and a swarm of red crabs were associated with a dense turbid layer 4-10 m above the bottom. The high density aggregations were constrained to 355-385 m water depth over the Northwest flank of the seamount, although the crabs also occurred at lower densities in shallower waters (∼280 m) and in another location of the seamount. The crab aggregations occurred in hypoxic water, with oxygen levels of 0.04 ml/l. Barcoding of Hannibal red crabs, and pelagic red crabs sampled in a mass stranding event in 2015 at a beach in San Diego, California, USA, revealed that the Panamanian and the Californian crabs are likely the same species, Pleuroncodes planipes, and these findings represent an extension of the southern endrange of this species. Measurements along a 1.6 km transect revealed three high density aggregations, with the highest density up to 78 crabs/m(2), and that the crabs were patchily distributed. Crab density peaked in the middle of the patch, a density structure similar to that of swarming insects.

Phylogeographic structure and northward range expansion in the barnacle Chthamalus fragilis.

The barnacle Chthamalus fragilis is found along the US Atlantic seaboard historically from the Chesapeake Bay southward, and in the Gulf of Mexico. It appeared in New England circa 1900 coincident with warming temperatures, and is now a conspicuous member of rocky intertidal communities extending through the northern shore of Cape Cod, Massachusetts. The origin of northern C. fragilis is debated. It may have spread to New England from the northern end of its historic range through larval transport by ocean currents, possibly mediated by the construction of piers, marinas, and other anthropogenic structures that provided new hard substrate habitat. Alternatively, it may have been introduced by fouling on ships originating farther south in its historic distribution. Here we examine mitochondrial cytochrome c oxidase I sequence diversity and the distribution of mitochondrial haplotypes of C. fragilis from 11 localities ranging from Cape Cod, to Tampa Bay, Florida. We found significant genetic structure between northern and southern populations. Phylogenetic analysis revealed three well-supported reciprocally monophyletic haplogroups, including one haplogroup that is restricted to New England and Virginia populations. While the distances between clades do not suggest cryptic speciation, selection and dispersal barriers may be driving the observed structure. Our data are consistent with an expansion of C. fragilis from the northern end of its mid-19th century range into Massachusetts.

Improvement in Serum Anti-Müllerian Hormone Levels in Infertile Patients after Hyperbaric Oxygen (preliminary results).

OBJECTIVE: To assess whether hyperbaric oxygen sessions elevate serum levels of anti-Müllerian hormone (AMH) in patients diagnosed with infertility with serum levels of less than or equal to 1 ng/dl AMH. METHODS: A study was performed on 4 patients diagnosed with infertility. Serum AMH level was measured at the beginning and end of hyperbaric oxygen sessions, and endometrial thickness was measured on endometrial cycle day 14 before and during the hyperbaric oxygen sessions. RESULTS: In two of the four patients, the serum AMH level increased by 40% and 116%. In one patient the serum AMH level was not elevated, with a serum AMH level before and after treatment of 0.1 ng/dl. The fourth patient became pregnant during the hyperbaric oxygen sessions. Endometrial thickness was not improved in any of our patients. CONCLUSIONS: This study showed that hyperbaric oxygen sessions can increase serum AMH levels, with a significant increase of 116% in one case. Therefore, this therapy can be used as an alternative treatment for patients with serum AMH levels of less than or equal to 1 ng/dl and a limited number of eggs for IVF cycles but not for patients with serum AMH levels of less than or equal to 0.1 ng/dl, as we did not observe an increase in serum AMH level in patients with an initial AMH level of 0.1 ng/dl. This study did not demonstrate improvement in endometrial growth following hyperbaric oxygen sessions.