Miracle-dz/UniFAR-FTUs huggingface dataset:
Co-Culturing of Endothelial and Cancer Cells in a Nanofibrous Scaffold-Based Two-Layer System

Angiogenesis is critical for local tumor growth. This study aimed to develop a three-dimensional two-layer co-culture system to investigate effects of cancer cells on the growth of endothelial cells (ECs). Poly(ε-caprolactone) (PCL) nanofibrous membranes were generated via electrospinning of PCL in chloroform (C-PCL-M) and chloroform and dimethylformamide (C/DMF-PCL-M). We assembled a two-layer co-culture system using C-PCL-M and C/DMF-PCL-M for EC growth in the upper layer with co-cultured cancer cells in the lower layer. In the absence of vascular endothelial growth factor (VEGF), growth of bEND.3 ECs decreased on C/DMF-PCL-M but not on C-PCL-M with time. Growth of bEND.3 cells on C/DMF-PCL-M was enhanced through co-culturing of CT26 cancer cells and enhanced growth of bEND.3 cells was abrogated with anti-VEGF antibodies and sorafenib. However, EA.hy926 ECs displayed steady growth and proliferation on C/DMF-PCL-M, and their growth was not further increased through co-culturing of cancer cells. Moreover, chemical hypoxia in CT26 cancer cells upon treatment with CoCl2 enhanced the growth of co-cultured bEND.3 cells in the two-layer system. Thus, EC growth on the nanofibrous scaffold is dependent on the types of ECs and composition of nanofibers and this co-culture system can be used to analyze EC growth induced by cancer cells.
Sustained representation of perspectival shape

Significance Our experience of the world goes beyond the light reaching our eyes: Even when a coin is tilted in depth, we infer the circular shape it truly has, rather than the ellipse it projects. But do we ever escape the perspective from which we view the world? A centuries-old philosophical debate asks whether objects of different distal shapes bear a representational similarity to one another when their perspectival shapes match. Here, we test this question empirically. We demonstrate such representational similarity by showing that perspectival shapes influence basic mechanisms of perception and attention, even after distal shape is known. Objects are stamped with the perceiver’s perspective: We do not see the world completely separate from our point of view. Arguably the most foundational principle in perception research is that our experience of the world goes beyond the retinal image; we perceive the distal environment itself, not the proximal stimulation it causes. Shape may be the paradigm case of such “unconscious inference”: When a coin is rotated in depth, we infer the circular object it truly is, discarding the perspectival ellipse projected on our eyes. But is this really the fate of such perspectival shapes? Or does a tilted coin retain an elliptical appearance even when we know it’s circular? This question has generated heated debate from Locke and Hume to the present; but whereas extant arguments rely primarily on introspection, this problem is also open to empirical test. If tilted coins bear a representational similarity to elliptical objects, then a circular coin should, when rotated, impair search for a distal ellipse. Here, nine experiments demonstrate that this is so, suggesting that perspectival shapes persist in the mind far longer than traditionally assumed. Subjects saw search arrays of three-dimensional “coins,” and simply had to locate a distally elliptical coin. Surprisingly, rotated circular coins slowed search for elliptical targets, even when subjects clearly knew the rotated coins were circular. This pattern arose with static and dynamic cues, couldn’t be explained by strategic responding or unfamiliarity, generalized across shape classes, and occurred even with sustained viewing. Finally, these effects extended beyond artificial displays to real-world objects viewed in naturalistic, full-cue conditions. We conclude that objects have a remarkably persistent dual character: their objective shape “out there,” and their perspectival shape “from here. ”
Zooplankton at a seamount in the eastern Mediterranean: distribution and trophic interactions

The study focuses on the question, how a seamount in the oligotrophic eastern Mediterranean affects the zooplankton community, as compared to the open water. Zooplankton samples were taken with 333 µm nets at two sites, the Rhodes Basin and the Anaximenes Mountain, in December 2006. The samples were sieved into size fractions, and the composition, biomass, abundance and stable isotope signatures were analysed. In general, biomass and abundance of zooplankton were low, reflecting the oligotrophic character of the eastern Mediterranean, but zooplankton standing stocks were higher at the Rhodes Basin than at the Anaximenes Mountain. Stable isotope signatures showed, at a generally low level, enrichment in zooplankton taxa along the food chain within the different pelagic zones and from the surface to the deep-sea, but no significant differences between Rhodes Basin and the seamount were evident in the food web structure. The zooplankton community in the Anaximenes Mountain region in the northern Levantine Basin seems not to be influenced by a local seamount effect, despite the difference in standing stocks between the seamount and the Rhodes Basin. This seems to be driven by larger-scale upwelling and downwelling structures of cyclones and anticyclones, dominating the circulation in the area.
Negshell casting: 3D-printed structured and sacrificial cores for soft robot fabrication

Soft robot fabrication by casting liquid elastomer often requires multiple steps of casting or skillful manual labor. We present a novel soft robotic fabrication technique: negshell casting (negative-space eggshell casting), that reduces the steps required for fabrication by introducing 3D-printed thin-walled cores for use in casting that are meant to be left in place instead of being removed later in the fabrication process. Negshell casting consists of two types of cores: sacrificial cores (negshell cores) and structural cores. Negshell cores are designed to be broken into small pieces that have little effect on the mechanical structure of the soft robot, and can be used for creating fluidic channels and bellows for actuation. Structural cores, on the other hand, are not meant to be broken, and are for increasing the stiffness of soft robotic structures, such as endoskeletons. We describe the design and fabrication concepts for both types of cores and report the mechanical characterization of the cores embedded in silicone rubber specimens. We also present an example use-case of negshell casting for a single joint soft robotic finger, along with an experiment to demonstrate how negshell casting concepts can aid in force transmission. Finally, we present real-world usage of negshell casting in a 6 degree-of-freedom three-finger soft robotic gripper, and a demonstration of the gripper in a robotic pick-and-place task. A companion website with further details about fabrication (as well as an introduction to molding and casting for those who are unfamiliar with the terms), engineering file downloads, and experimental data is provided at https://negshell.github. io/.
Seasonal roosts of Red‐lored Amazons in Ecuador provide information about population size and structure

Data from roosts of Amazona parrots may be useful in creating demographic models, because these birds exhibit high roost fidelity and pairs are conspicuous in flight. However, few investigators have attempted to track changes in the number of pairs using such roosts. We studied Red-lored Amazons (Amazona autumnalis) at a communal roost in southwest Ecuador over a 1-yr period to understand better their population structure. Population size was estimated at 214 individuals. Counts revealed seasonal variation in numbers, but the occurrence of pairs and singles was seldom correlated. The number of paired individuals using the roost was lower during the breeding period. In contrast, the number of single birds at the roost nearly doubled during the breeding period. Overall, our data suggest that parental responsibilities during the nesting period explain fluctuations in the number of birds at the roost, and such fluctuations can be used to estimate the reproductive portion of the population. Protection of the small mangrove islands where the parrots roost would likely benefit a population that occupies a much larger area and would, at the same time, provide a useful tool for demographic studies of this poorly known neotropical parrot. SINOPSIS Datos colectados desde dormideros de los loros de Amazona podrian ser aptos para modelos demograficos, porque suelen ser fieles a los dormideros y vuelan en pareja. Apesar de la apreciacion general de esto, pocos estudios han atentado documentar los cambios en el numero de parejas que visiten los dormideros a menudo. Realizamos un censo del Loro Frentirrojo (Amazona autumnalis) en un dormidero comunal durante un ano en el suroeste del Ecuador para obtener datos sobre la estructura de la poblacion. El tamano de la poblacion fue estimado en 214 individuos. Los datos indicaron una variacion estacional y fuerte, sin embargo, la incidencia de parejas e solitarios no siempre estuvieron correlados. El numero de parejas fue mucho mas bajo durante el periodo de la anidacion. Por otro lado, la cantidad de solitarios fue casi el doble durante la epoca de anidacion. En conjunto, los datos sugieren que las responsibilidades asociadas con la reproduccion podrian explicar las fluctuaciones grandes en el dormidero y asi proveer una estimacion de la proporcion reproductiva. Proteccion de las islas pequenas del manglar podria proveer beneficios a una poblacion que ocupan a un area de habitat mucho mas grande y a la vez conservar una herramienta util para estudios demograficos de un loro neotropical y poco conocido.
ABC transporters in gills of rainbow trout (Oncorhynchus mykiss)

ABSTRACT Fish gills are a structurally and functionally complex organ at the interface between the organism and the aquatic environment. Gill functions include the transfer of organic molecules, both natural ones and xenobiotic compounds. Whether the branchial exchange of organic molecules involves active transporters is currently not known. Here, we investigated the presence, diversity and functional activity of ATP-binding cassette (ABC) transporters in gills of juvenile rainbow trout. By means of RT-qPCR, gene transcripts of members from the abcb, abcc and abcg subfamilies were identified. Comparisons with mRNA profiles from trout liver and kidney revealed that ABC transporters known to have an apical localization in polarized epithelia, especially abcc2 and abcb1, were under-represented in the gills. In contrast, ABC transporters with mainly basolateral localization showed comparable gene transcript levels in the three organs. The most prominent ABC transporter in gills was an abcb subfamily member, which was annotated as abcb5 based on the synteny and phylogeny. Functional in vivo assays pointed to a role of branchial ABC transporters in branchial solute exchange. We further assessed the utility of primary gill cell cultures to characterize transporter-mediated branchial exchange of organic molecules, by examining ABC transporter gene transcript patterns and functional activity in primary cultures. The gill cultures displayed functional transport activity, but the ABC mRNA expression patterns were different to those of the intact gills. Overall, the findings of this study provide evidence for the presence of functional ABC transporter activity in gills of fish. Summary: The gills of rainbow trout as a key organ in solute exchange harbor a diversity of functional ABC transporters.
Effect of the activation of germination processes on the sensitivity of seeds towards physical sanitation treatments

Physical treatments of seeds to eradicate pathogens have the risk of reducing vitality of the seeds. Seed lots may differ in sensitivity to these treatments, therefore factors influencing this sensitivity, including the physiological condition of the seeds, should be identified. In this study priming was used to mimic the effect of pre-harvest onset of germination on the sensitivity to these treatments. The effect of humidification, by incubation for one day at 100% RH, followed by drying back, on the sensitivity was also analysed. Primed, humidified and control seeds were subjected to hot water, aerated steam or electron beam treatments at various levels. Two seed lots from Daucus carota (carrot), two seed lots from Brassica oleracea (kohlrabi) and one seed lot from Allium cepa (onion) were used in the tests. Primed seeds from all seed lots were more sensitive to the aerated steam treatment and the B. oleracea and A. cepa seed lots were also more sensitive to the hot water treatment after priming. Priming had no effect on the sensitivity towards the electron beam treatment. Humidification had no effect on the sensitivity towards the physical seed treatments, with the exception of the humidified onion seeds, which were clearly more tolerant towards the aerated steam treatment. It is concluded that seed companies should be aware that the onset seed germination processes prior to harvest may increase the sensitivity of the seeds towards aerated steam and hot water treatments.
Stretch-induced sarcoplasmic reticulum calcium leak is causatively associated with atrial fibrillation in pressure-overloaded hearts.

AIMS Despite numerous reports documenting an important role of hypertension in the development of atrial fibrillation (AF), the detailed mechanism underlying the pathological process remains incompletely understood. Here, we aim to test the hypothesis that diastolic sarcoplasmic reticulum (SR) Ca2+ leak in atrial myocytes, induced by mechanical stretch due to elevated pressure in the left atrium (LA), plays an essential role in the AF development in pressure-overloaded hearts. METHODS AND RESULTS Isolated mouse atrial myocytes subjected to acute axial stretch displayed an immediate elevation of SR Ca2+ leak. Using a mouse model of transverse aortic constriction (TAC), the relation between stretch, SR Ca2+ leak and AF susceptibility was further tested. At 36 hours post TAC, SR Ca2+ leak in cardiomyocytes from the LA (with hemodynamic stress), but not right atrium (without hemodynamic stress), significantly increased, which was further elevated at 4 weeks post TAC. Accordingly, AF susceptibility to atrial burst pacing in the 4-week TAC mice were also significantly increased, which was unaffected by inhibition of atrial fibrosis or inflammation via deletion of galectin-3. Western blotting revealed that type 2 ryanodine receptor (RyR2) in LA myocytes of TAC mice was oxidized due to activation and upregulation of Nox2 and Nox4. Direct rescue of dysfunctional RyR2 with dantrolene or rycal S107 reduced diastolic SR Ca2+ leak in LA myocytes and prevented atrial burst pacing stimulated AF. CONCLUSION Our study demonstrated for the first time the increased SR Ca2+ leak mediated by enhanced oxidative stress in LA myocytes that is causatively associated with higher AF susceptibility in pressure-overloaded hearts. TRANSLATIONAL PERSPECTIVE RyR2 is the major Ca2+ channel in cardiac myocytes, strongly affecting cellular activities. Several types of heart diseases, including heart failure and ventricular arrhythmias, are related to RyR2 dysfunction in ventricular myocytes. The present study expands RyR2 dysfunction as a critical contributor in pressure-overload associated AF. As AF is usually accompanied with cardiac remodeling and dysfunction in the setting of hypertension, which is a common risk factor for different cardiovascular diseases, the convergence of several pathological processes on the dysfunctional RyR2 makes it a common therapeutic target in these diseased settings.
New technical approaches for 3D morphological imaging and quantification of measurements

3D imaging is becoming more and more popular, as it allows us to identify interactions between structures in organs. Furthermore, it gives the possibility to quantify and size these structures. To allow 3D imaging, the tissue sample has to be transparent. This is usually achieved by using optical tissue clearing protocols. Although using optical tissue clearing often results in perfect 3D images, these protocols have some pitfalls, like long duration of sample preparation (up to several weeks), use of toxic substances, damage to antibody staining, fluorescent proteins or dyes, high refractive indices, and high costs of sample processing.Recently we described [Huang et al., Scientific Reports 9(1): 521 (2019)] a fast, safe, and inexpensive ethyl cinnamate (ECi) based optical tissue clearing protocol. Here, we present extensions of our protocol with respect to the deparaffinization of old paraffin‐embedded samples allowing 3D imaging of the blocks. In addition, we learned to remove ECi from the samples allowing the use of routine immunolabeling protocols. Furthermore, we demonstrate new pictures of lungs after expansion microscopy and adaptation of already existing protocols. The aim of our work is, in summary, to describe the advances in these methodologies, focusing on the morphological imaging of kidneys and lungs.
Widespread hermaphroditism in freshwater gastrotrichs

Freshwater members of the phylum Gastrotricha were long thought to lack male gametes and to exist exclusively as parthenogenetic females. The surprising 1978 discovery of sperm in the common species Lepidodermella squamata raised the question of how many other freshwater gastrotrichs might likewise be hermaphroditic. In a comparative study of species from across both major families, sperm have been found in every species examined intensively. They were detected in 19 species of Chaetonotidae (from Aspidiophorus, Chaetonotus, Heterolepidoderma, Ichthydium, Lepidodermella, and Polymerurus) and 3 species of Dasydytidae (from Haltidytes, Setopus, and Stylochaeta), characteristically occurring ventrally in single unilateral or (more often) 2–12 bilateral packets. Their shape ranges from filiform (length in Chaetonotus bisacer, ∼40 μm) to rodlike, spindlelike, oval, and possibly spherical (some in Stylochaeta scirtetica measure only 1 μm). With light microscopy, a dense nucleus appears to fill the entire volume of these aflagellate cells. Spermatogenesis within cysts (maximally, 16 sperm/clone) is evidently characteristic of both families, each cyst generating one large residual body. Sperm-bearers display oocytes with sometimes distinctive cytoplasmic elements and a posterior X-organ whose organization can be complex. Evidence supports an unusual life cycle in which parthenogenesis is followed by simultaneous hermaphroditism. These findings may illuminate the reproductive characters as well as ancestry of marine and brackish-water taxa of Chaetonotida.
Impacts of Buffelgrass (Pennisetum ciliare) on a Forb Community in South Texas

Abstract Since the 1950s, many south Texas rangelands have been seeded with buffelgrass, a perennial C4 bunchgrass native to Africa that is believed to contribute to reductions in biodiversity. Forb species represent a critical habitat component throughout the breeding period for many wildlife species as seed (summer to fall), as green vegetative material (spring to summer), and as habitat for arthropods (spring to summer). Reductions in richness and diversity of crucial ecosystem components such as forbs and arthropods have large implications for grassland birds and other wildlife. We sampled annual and perennial forbs within 1-m2 quadrats on 15 study plots (1 ha; n = 20 quadrats/plot) at Chaparral Wildlife Management Area, in LaSalle and Dimmit counties, Texas, during 2005 and 2006. Study plots were divided into five light-buffelgrass plots (0 to 5% buffelgrass canopy coverage), five moderate-buffelgrass plots (5 to 25% buffelgrass canopy coverage), and five heavy-buffelgrass plots (> 25% buffelgrass canopy coverage). Buffelgrass in study plots was composed of naturalized plants, and was not deliberately planted. During 2005 we observed that plots with > 25% buffelgrass had a 73% reduction in forb canopy of native species, a 64% reduction in native forb species richness, and a 77% reduction in native forb stem density compared to plots with 0 to 5% buffelgrass. These trends in native forb reduction (−79% native forb canopy, −65% forb species richness, −80% forb stem density) were nearly identical in 2006, even with greatly reduced rainfall. Simple linear regression revealed negative relationships between buffelgrass cover, total exotic grass cover (buffelgrass and Lehmann lovegrass), and total grass cover and the richness, coverage, and density of forbs/m2. Reductions in diversity may have larger implications regarding ecosystem function and available useable space and densities of desired bird species such as northern bobwhite. Nomenclature: Buffelgrass, Pennisetum ciliare (L.) Link; Lehmann lovegrass, Eragrostis lehmanniana Nees.
AGA Clinical Practice Guidelines on the Role of Probiotics in the Management of Gastrointestinal Disorders.

Division of Gastroenterology and Hepatology, University of Michigan, Ann Arbor, Michigan; Gastroenterology Section, Veterans Administration Ann Arbor Healthcare System, Ann Arbor, Michigan; Division of Gastroenterology, University of Washington Medical School, Seattle, Washington; Division of Gastroenterology, McMaster University, Hamilton, Ontario, Canada; Division of Gastroenterology, Case Western Reserve University, Cleveland, Ohio; Louis Stokes Veterans Affairs Medical Center, Cleveland, Ohio; Division of Gastroenterology, University of Minnesota, Minneapolis, Minnesota; Division of Gastroenterology, Mount Sinai Hospital, Department of Medicine, University of Toronto, Toronto, Ontario, Canada; and Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario, Canada
The Role of Single-Cell Technology in the Study and Control of Infectious Diseases

The advent of single-cell research in the recent decade has allowed biological studies at an unprecedented resolution and scale. In particular, single-cell analysis techniques such as Next-Generation Sequencing (NGS) and Fluorescence-Activated Cell Sorting (FACS) have helped show substantial links between cellular heterogeneity and infectious disease progression. The extensive characterization of genomic and phenotypic biomarkers, in addition to host–pathogen interactions at the single-cell level, has resulted in the discovery of previously unknown infection mechanisms as well as potential treatment options. In this article, we review the various single-cell technologies and their applications in the ongoing fight against infectious diseases, as well as discuss the potential opportunities for future development.