BET inhibitors rescue anti-PD1 resistance by enhancing TCF7 accessibility in leukemia-derived terminally exhausted CD8+ T cells.

Many acute myeloid leukemia (AML) patients exhibit hallmarks of immune exhaustion, such as increased myeloid-derived suppressor cells, suppressive regulatory T cells and dysfunctional T cells. Similarly, we have identified the same immune-related features, including exhausted CD8+ T cells (TEx) in a mouse model of AML. Here we show that inhibitors that target bromodomain and extra-terminal domain (BET) proteins affect tumor-intrinsic factors but also rescue T cell exhaustion and ICB resistance. Ex vivo treatment of cells from AML mice and AML patients with BET inhibitors (BETi) reversed CD8+ T cell exhaustion by restoring proliferative capacity and expansion of the more functional precursor-exhausted T cells. This reversal was enhanced by combined BETi and anti-PD1 treatment. BETi synergized with anti-PD1 in vivo, resulting in the reduction of circulating leukemia cells, enrichment of CD8+ T cells in the bone marrow, and increase in expression of Tcf7, Slamf6, and Cxcr5 in CD8+ T cells. Finally, we profiled the epigenomes of in vivo JQ1-treated AML-derived CD8+ T cells by single-cell ATAC-seq and found that JQ1 increases Tcf7 accessibility specifically in Tex cells, suggesting that BETi likely acts mechanistically by relieving repression of progenitor programs in Tex CD8+ T cells and maintaining a pool of anti-PD1 responsive CD8+ T cells.

Fecal microbiota and diets of muskox female adults and calves.

In mammals, the gut microbiome is vertically transmitted during maternal lactation at birth. In this study, we investigated the gut microbiome and diets of muskox, a large herbivore inhabiting in the high Arctic. We compared the microbiota composition using bacterial 16S rRNA gene sequencing and diets using stable isotope analysis of muskox feces of six female adults and four calves on Ella Island, East Greenland. Firmicutes were the most abundant bacterial phylum in both the adults and calves, comprising 94.36% and 94.03%, respectively. Significant differences were observed in the relative abundance of the two Firmicutes families. The adults were primarily dominated by Ruminococcaceae (73.90%), and the calves were dominated by both Ruminococcaceae (56.25%) and Lachnospiraceae (24.00%). Stable isotope analysis of the feces in the study area revealed that both adults and calves had similar ranges of 13C and 15N, likely derived from the dominant diet plants. Despite their similar diets, the different gut microbiome compositions in muskox adults and calves indicate that the gut microbiome of the calves may not be fully colonized to the extent of that of the adults.

Cross Encoder-Decoder Transformer with Global-Local Visual Extractor for Medical Image Captioning.

Transformer-based approaches have shown good results in image captioning tasks. However, current approaches have a limitation in generating text from global features of an entire image. Therefore, we propose novel methods for generating better image captioning as follows: (1) The Global-Local Visual Extractor (GLVE) to capture both global features and local features. (2) The Cross Encoder-Decoder Transformer (CEDT) for injecting multiple-level encoder features into the decoding process. GLVE extracts not only global visual features that can be obtained from an entire image, such as size of organ or bone structure, but also local visual features that can be generated from a local region, such as lesion area. Given an image, CEDT can create a detailed description of the overall features by injecting both low-level and high-level encoder outputs into the decoder. Each method contributes to performance improvement and generates a description such as organ size and bone structure. The proposed model was evaluated on the IU X-ray dataset and achieved better performance than the transformer-based baseline results, by 5.6% in BLEU score, by 0.56% in METEOR, and by 1.98% in ROUGE-L.

Engineered Attenuated Salmonella typhimurium Expressing Neoantigen Has Anticancer Effects.

Neoantigen vaccines are an immunotherapy strategy for treating cancer. The vaccine degrades quickly, so the strategy must include protection and precise targeting for immune cell stimulation. In this study, we engineered attenuated Salmonella typhimurium, which is highly infiltrative to tumors, to act as a carrier for Neoantigen peptide vaccine. Our system used a constitutive promoter vector, so that a single injection of Salmonella expressing Neoantigen could be used without requiring additional induction injections. In vivo experiments on bacteria-treated mice showed that Neoantigen expressed by the engineered carrier infiltrated tumors and resulted in suppressed tumor growth, higher survival rates and longer survival times, a relative increase of CD4 and CD8 T cells, and cytokine release. These results indicate that engineered Salmonella can be used as a carrier for Neoantigen immunotherapy.

Robust Copper Metal-Organic Framework-Embedded Polysiloxanes for Biomedical Applications: Its Antibacterial Effects on MRSA and In Vitro Cytotoxicity.

Polysiloxanes (PSs) have been widely utilized in the industry as lubricants, varnishes, paints, release agents, adhesives, and insulators. In addition, their applications have been expanded to include the development of new biomedical materials. To modify PS for application in therapeutic purposes, a flexible antibacterial Cu-MOF (metal-organic framework) consisting of glutarate and 1,2-bis(4-pyridyl)ethane ligands was embedded in PS via a hydrosilylation reaction of vinyl-terminated and H-terminated PSs at 25 °C. The bactericidal activities of the resulting Cu-MOF-embedded PS (PS@Cu-MOF) and the control polymer (PS) were tested against Escherichia coli, Staphylococcus aureus, and methicillin-resistant Staphylococcus aureus. PS@Cu-MOF exhibited more than 80% bactericidal activity toward the tested bacteria at a concentration of 100 µg⋅mL-1 and exhibited a negligible cytotoxicity toward mouse embryonic fibroblasts at the same concentration. Release tests of the Cu(II) ion showed PS@Cu-MOF to be particularly stable in a phosphate-buffered saline solution. Furthermore, its physical and thermal properties, including the phase transition, rheological measurements, swelling ratio, and thermogravimetric profile loss, were similar to those of the control polymer. Moreover, the low cytotoxicity and bactericidal activities of PS@Cu-MOF render it a promising candidate for use in medicinal applications, such as in implants, skin-disease treatment, wound healing, and drug delivery.

Distinct gut microbiotas between southern elephant seals and Weddell seals of Antarctica.

The gut microbiome provides ecological information about host animals, but we still have limited knowledge of the gut microbiome, particularly for animals inhabiting remote locations, such as Antarctica. Here, we compared fecal microbiota between southern elephant seals (Mirounga leonina) and Weddell seals (Leptonychotes weddelli), that are top predatory marine mammals in the Antarctic ecosystem, using 16S rRNA amplicon sequencing and assessed the relationships of the gut microbial communities to functional profiles using gut metabolite analysis. The bacterial community did not differ significantly by host species or sex at the phylum level, but the distinction at the family level was obvious. The family Ruminococcaceae (Firmicutes) was more abundant in southern elephant seals than in Weddell seals, and the families Acidaminococcaceae (Firmicutes) and Pasteurellaceae (Gammaproteobacteria) were uniquely present in Weddell seals. The fecal bacterial community structure was distinctively clustered by host species, with only 6.7% of amplicon sequence variants (ASVs) shared between host species. This result implies that host phylogeny rather than other factors, such as diet or age, could be the major driver of fecal microbiotic diversification. Interestingly, there was no apparent sex effect on bacterial community structure in Weddell seals, but the effect of sex was pronounced in adult southern elephant seals mainly due to the prevalence of Edwardsiella sp., suggesting that extreme sexual dimorphism may modulate the gut microbiota of southern elephant seals. Unlike the clear distinction in the taxonomic composition of fecal bacterial communities, there were no discernible differences in the profiles of potential microbial functions and gut metabolites between host species or sexes, indicating that functional redundancy dominates the gut microbiota of seals surveyed in this study.

Interspecific comparison of the fecal microbiota structure in three Arctic migratory bird species.

The gut microbiota of birds is known to be characterized for different species, although it may change with feeding items. In this study, we compared the gut microbiota of birds with different feeding behaviors in the same habitat. We collected fecal samples from three Arctic species, snow buntings Plectrophenax nivalis, sanderlings Calidris alba, and pink-footed geese Anser brachyrhynchus that are phylogenetically quite distant in different families to evaluate effects of diet on gut microbiota. Also, we characterized the prevalence of fecal bacteria using the Illumina MiSeq platform to sequence bacterial 16S rRNA genes. Our NMDS results showed that fecal bacteria of snow buntings and sanderlings were significantly distant from those of pink-footed geese. Although all three birds were occupied by three bacterial phyla, Proteobacteria, Firmicutes, and Bacteroidetes, dominant taxa still varied among the species. Our bacterial sequences showed that snow buntings and sanderlings were dominated by Firmicutes and Bacteroidetes, while pink-footed geese were dominated by Proteobacteria. In addition, the bacterial diversity in snow buntings and sanderlings was significantly higher than that in pink-footed geese. Our results suggest that insectivorous feeding diet of snow buntings and sanderlings could be responsible for the similar bacterial communities between the two species despite the distant phylogenetic relationship. The distinctive bacterial community in pink-footed geese was discussed to be related with their herbivorous diet.

Overcoming evanescent field decay using 3D-tapered nanocavities for on-chip targeted molecular analysis.

Enhancement of optical emission on plasmonic nanostructures is intrinsically limited by the distance between the emitter and nanostructure surface, owing to a tightly-confined and exponentially-decaying electromagnetic field. This fundamental limitation prevents efficient application of plasmonic fluorescence enhancement for diversely-sized molecular assemblies. We demonstrate a three-dimensionally-tapered gap plasmon nanocavity that overcomes this fundamental limitation through near-homogeneous yet powerful volumetric confinement of electromagnetic field inside an open-access nanotip. The 3D-tapered device provides fluorescence enhancement factors close to 2200 uniformly for various molecular assemblies ranging from few angstroms to 20 nanometers in size. Furthermore, our nanostructure allows detection of low concentration (10 pM) biomarkers as well as specific capture of single antibody molecules at the nanocavity tip for high resolution molecular binding analysis. Overcoming molecule position-derived large variations in plasmonic enhancement can propel widespread application of this technique for sensitive detection and analysis of complex molecular assemblies at or near single molecule resolution.

Influence of Pd Doping on Electrical and Thermal Properties of n-Type Cu0.008Bi2Te2.7Se0.3 Alloys.

Doping is known as an effective way to modify both electrical and thermal transport properties of thermoelectric alloys to enhance their energy conversion efficiency. In this project, we report the effect of Pd doping on the electrical and thermal properties of n-type Cu0.008Bi2Te2.7Se0.3 alloys. Pd doping was found to increase the electrical conductivity along with the electron carrier concentration. As a result, the effective mass and power factors also increased upon the Pd doping. While the bipolar thermal conductivity was reduced with the Pd doping due to the increased carrier concentration, the contribution of Pd to point defect phonon scattering on the lattice thermal conductivity was found to be very small. Consequently, Pd doping resulted in an enhanced thermoelectric figure of merit, zT, at a high temperature, due to the enhanced power factor and the reduced bipolar thermal conductivity.

Faecal microbiota changes associated with the moult fast in chinstrap and gentoo penguins.

In many seabirds, individuals abstain from eating during the moult period. Penguins have an intense moult that lasts for weeks, during which they are confined to land. Despite the importance for survival, it is still unclear how the faecal microbiota of Antarctic penguins changes in response to the moult fast. Here, we investigated the faecal microbiota of chinstrap (Pygoscelis antarcticus) and gentoo penguins (Pygoscelis papua) on King George Island, Antarctica. The bacterial community compositions during the feeding and moulting stages were compared for both species using bacterial 16S rRNA gene amplicon on an Illumina MiSeq platform. Our results showed that the moult fast altered the bacterial community structures in both penguin species. Interestingly, the bacterial community composition shifted in the same direction in response to the moult fast but formed two distinct clusters that were specific to each penguin species. A significant increase in bacterial diversity was observed in gentoo penguins, whereas no such change was observed for chinstrap penguins. By analysing the contribution of the ecological processes that determine bacterial community assembly, we observed that processes regulating community turnover were considerably different between the feeding and moulting stages for each penguin. At the phylum level, the relative abundances of Fusobacteria, Firmicutes and Proteobacteria were dominant in chinstrap penguins, and no significant changes were detected in these phyla between the feeding and moulting periods. Our results suggest that moult fast-induced changes in the faecal microbiota occur in both species.

Complete mitochondrial genome of the Greenland wolf, Canis lupus orion.

The Greenland wolf, Canis lupus orion as s subspecies of the gray wolf, is native to Greenland. Here, we assembled a complete 16,650 bp genome for the C. l. orion mitochondrion by employing Illumina HiSeq platform. The complete mitochondrial genome contained 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and one control region. Overall DNA sequence of the C. l. orion mitochondrion was identical to that of gray wolf C. l. lupus, although slight difference was observed in their control regions. The genomic structure of C. l. orion mitochondrion was conserved with the gene arrangements of mitogenomes published in Canidae, and phylogenetic analysis confirmed the sister relationship among Canis sp. This information will provide essential molecular reference to elucidate biogeography, phylogenetic distance, and evolutionary history in gray wolves.

Soil pH rather than elevation determines bacterial phylogenetic community assembly on Mt. Norikura.

There is considerable interest in the factors which may explain variation in microbial community assembly processes. In this study, we investigated bacterial community assembly, phylogenetic diversity and the relative role of deterministic and stochastic processes along environmental gradients on Mt. Norikura, Japan. DNA extracted from soil samples collected at a range of elevations was PCR-amplified targeting the V3 and V4 regions of the bacterial 16S rRNA gene, and sequenced using Illumina MiSeq. We hypothesized that elevation would be a strong predictor of phylogenetic community assembly, with communities being more phylogenetically clustered towards higher elevations, due to more extreme physiological conditions. We also hypothesized a greater role of stochasticity at the highest elevations, due to more frequent soil disturbance. Contrary to our hypotheses, we found that the strength of phylogenetic clustering and the role of stochasticity were strongly related to soil pH, with phylogenetic clustering and deterministic processes being strongest at lower soil pH values. Moreover, there was no trend towards stronger influence of phylogenetic clustering and stochasticity in the upper elevations of Mt. Norikura. These results reveal an overwhelming influence of soil pH on phylogenetic community assembly of soil bacteria, even when a range of other environmental gradients are present.

Glucose Sensing Using Surface-Enhanced Raman-Mode Constraining.

Diabetes mellitus is a chronic disease, and its management focuses on monitoring and lowering a patient's glucose level to prevent further complications. By tracking the glucose-induced shift in the surface-enhanced Raman-scattering (SERS) emission of mercaptophenylboronic acid (MPBA), we have demonstrated fast and continuous glucose sensing in the physiologically relevant range from 0.1 to 30 mM and verified the underlying mechanism using numerical simulations. Bonding of glucose to MPBA suppresses the "breathing" mode of MPBA at 1071 cm-1 and energizes the constrained-bending mode at 1084 cm-1, causing the dominant peak to shift from 1071 to 1084 cm-1. MPBA-glucose bonding is also reversible, allowing continuous tracking of ambient glucose concentrations, and the MPBA-coated substrates showed very stable performance over a 30 day period, making the approach promising for long-term continuous glucose monitoring. Using Raman-mode-constrained, miniaturized SERS implants, we also successfully demonstrated intraocular glucose measurements in six ex vivo rabbit eyes within ±0.5 mM of readings obtained using a commercial glucose sensor.

Surface-Enhanced Raman Spectroscopy-Based Label-Free Insulin Detection at Physiological Concentrations for Analysis of Islet Performance.

Label-free optical detection of insulin would allow in vitro assessment of pancreatic cell functions in their natural state and expedite diabetes-related clinical research and treatment; however, no existing method has met these criteria at physiological concentrations. Using spatially uniform 3D gold-nanoparticle sensors, we have demonstrated surface-enhanced Raman sensing of insulin in the secretions from human pancreatic islets under low and high glucose environments without the use of labels such as antibodies or aptamers. Label-free measurements of the islet secretions showed excellent correlation among the ambient glucose levels, secreted insulin concentrations, and measured Raman-emission intensities. When excited at 785 nm, plasmonic hotspots of the densely arranged 3D gold-nanoparticle pillars as well as strong interaction between sulfide linkages of the insulin molecules and the gold nanoparticles produced highly sensitive and reliable insulin measurements down to 100 pM. The sensors exhibited a dynamic range of 100 pM to 50 nM with an estimated detection limit of 35 pM, which covers the reported concentration range of insulin observed in pancreatic cell secretions. The sensitivity of this approach is approximately 4 orders of magnitude greater than previously reported results using label-free optical approaches, and it is much more cost-effective than immunoassay-based insulin detection widely used in clinics and laboratories. These promising results may open up new opportunities for insulin sensing in research and clinical applications.

Soil nematodes show a mid-elevation diversity maximum and elevational zonation on Mt. Norikura, Japan.

Little is known about how nematode ecology differs across elevational gradients. We investigated the soil nematode community along a ~2,200 m elevational range on Mt. Norikura, Japan, by sequencing the 18S rRNA gene. As with many other groups of organisms, nematode diversity showed a high correlation with elevation, and a maximum in mid-elevations. While elevation itself, in the context of the mid domain effect, could predict the observed unimodal pattern of soil nematode communities along the elevational gradient, mean annual temperature and soil total nitrogen concentration were the best predictors of diversity. We also found nematode community composition showed strong elevational zonation, indicating that a high degree of ecological specialization that may exist in nematodes in relation to elevation-related environmental gradients and certain nematode OTUs had ranges extending across all elevations, and these generalized OTUs made up a greater proportion of the community at high elevations - such that high elevation nematode OTUs had broader elevational ranges on average, providing an example consistent to Rapoport's elevational hypothesis. This study reveals the potential for using sequencing methods to investigate elevational gradients of small soil organisms, providing a method for rapid investigation of patterns without specialized knowledge in taxonomic identification.

Simple, Large-Scale Fabrication of Uniform Raman-Enhancing Substrate with Enhancement Saturation.

It is well-known that gold nanoparticle (AuNP) clusters generate strong surface-enhanced Raman scattering (SERS). In order to produce spatially uniform Raman-enhancing substrates at a large scale, we synthesized vertically perforated three-dimensional (3D) AuNP stacks. The 3D stacks were fabricated by first hydrothermally synthesizing ZnO nanowires perpendicular to silicon wafers followed by repetitively performing liquid-phase deposition of AuNPs on the tops and side surfaces of the nanowires. During the deposition process, the nanowires were shown to gradually dissolve away, leaving hollow vestiges or perforations surrounded by stacks of AuNPs. Simulation studies and experimental measurements reveal these nanoscale perforations serve as light paths that allow the excitation light to excite deeper regions of the 3D stacks for stronger overall Raman emission. Combined with properly sized nanoparticles, this feature maximizes and saturates the Raman enhancement at 1-pM sensitivity across the entire wafer-scale substrate, and the saturation improves the wafer-scale uniformity by a factor of 6 when compared to nanoparticle layers deposited directly on a silicon wafer substrate. Using the 3D-stacked substrates, quantitative sensing of adenine molecules yielded concentrations measurements within 10% of the known value. Understanding the enhancing mechanisms and engineering the 3D stacks have opened a new method of harnessing the intense SERS observed in nanoparticle clusters and realize practical SERS substrates with significantly improved uniformity suitable for quantitative chemical sensing.

Changes in Soil Fungal Community Structure with Increasing Disturbance Frequency.

Although disturbance is thought to be important in many ecological processes, responses of fungal communities to soil disturbance have been little studied experimentally. We subjected a soil microcosm to physical disturbance, at a range of frequencies designed to simulate ecological disturbance events. We analyzed the fungal community structure using Illumina HiSeq sequencing of the ITS1 region. Fungal diversity was found to decline with the increasing disturbance frequencies, with no sign of the "humpback" pattern found in many studies of larger sedentary organisms. There is thus no evidence of an effect of release from competition resulting from moderate disturbance-which suggests that competition and niche overlap may not be important in limiting soil fungal diversity. Changing disturbance frequency also led to consistent differences in community composition. There were clear differences in OTU-level composition, with different disturbance treatments each having distinct fungal communities. The functional profile of fungal groups (guilds) was changed by the level of disturbance frequency. These predictable differences in community composition suggest that soil fungi can possess different niches in relation to disturbance frequency, or time since last disturbance. Fungi appear to be most abundant relative to bacteria at intermediate disturbance frequencies, on the time scale we studied here.

Development of Soil Bacterial Communities in Volcanic Ash Microcosms in a Range of Climates.

There is considerable interest in understanding the processes of microbial development in volcanic ash. We tested the predictions that there would be (1) a distinctive bacterial community associated with soil development on volcanic ash, including groups previously implicated in weathering studies; (2) a slower increase in bacterial abundance and soil C and N accumulation in cooler climates; and (3) a distinct communities developing on the same substrate in different climates. We set up an experiment, taking freshly fallen, sterilized volcanic ash from Sakurajima volcano, Japan. Pots of ash were positioned in multiple locations, with mean annual temperature (MAT) ranging from 18.6 to -3 °C. Within 12 months, bacteria were detectable by qPCR in all pots. By 24 months, bacterial copy numbers had increased by 10-100 times relative to a year before. C and N content approximately doubled between 12 and 24 months. HiSeq and MiSeq sequencing of the 16S rRNA gene revealed a distinctive bacterial community, different from developed vegetated soils in the same areas, for example in containing an abundance of unclassified bacterial groups. Community composition also differed between the ash pots at different sites, while showing no pattern in relation to MAT. Contrary to our predictions, the bacterial abundance did not show any relation to MAT. It also did not correlate to pH or N, and only C was statistically significant. It appears that bacterial community development on volcanic ash can be a rapid process not closely sensitive to temperature, involving distinct communities from developed soils.

Nasogastric tube insertion using airway tube exchanger in anesthetized and intubated patients.

BACKGROUND: A nasogastric tube (NGT) is commonly inserted into patients undergoing abdominal surgery to decompress the stomach during or after surgery. However, for anatomic reasons, the insertion of NGTs into anesthetized and intubated patients may be challenging. We hypothesized that the use of a tube exchanger for NGT insertion could increase the success rate and reduce complications. METHODS: One hundred adult patients, aged 20-70 years, who were scheduled for gastrointestinal surgeries with general anesthesia and NGT insertion were enrolled in our study. The patients were randomly allocated to the tube-exchanger group or the control group. The number of attempts, the time required for successful NGT insertion, and the complications were noted for each patient. RESULTS: In the tube-exchanger group, the success rate of NGT insertion on the first attempt was 92%, which is significantly higher than 68%, the rate in the control group (P = 0.007). The time required for successful NGT insertion in the tube-exchanger group was 18.5 ± 8.2 seconds, which is significantly shorter than the control group, 75.1 ± 9.8 seconds (P < 0.001). Complications such as laryngeal bleeding and the kinking and knotting of the NGT occurred less often in the tube-exchanger group. CONCLUSIONS: There were many advantages in using a tube-exchanger as a guide to inserting NGTs in anesthetized and intubated patients. Compared to the conventional technique, the use of a tube-exchanger resulted in a higher the success rate of insertion on the first attempt, a shorter procedure time, and fewer complications.

Acoustofluidic particle manipulation inside a sessile droplet: four distinct regimes of particle concentration.

In this study, we have investigated the motion of polystyrene microparticles inside a sessile droplet of water actuated by surface acoustic waves (SAWs), which produce an acoustic streaming flow (ASF) and impart an acoustic radiation force (ARF) on the particles. We have categorized four distinct regimes (R1-R4) of particle aggregation that depend on the particle diameter, the SAW frequency, the acoustic wave field (travelling or standing), the acoustic waves' attenuation length, and the droplet volume. The particles are concentrated at the centre of the droplet in the form of a bead (R1), around the periphery of the droplet in the form of a ring (R2), at the side of the droplet in the form of an isolated island (R3), and close to the centre of the droplet in the form of a smaller ring (R4). The ASF-based drag force, the travelling or standing SAW-based ARF, and the centrifugal force are utilized in various combinations to produce these distinct regimes. For simplicity, we fixed the fluid volume at 5 µL, varied the SAW actuation frequency (10, 20, 80, and 133 MHz), and tested several particle diameters in the range 1-30 µm to explicitly demonstrate the regimes R1-R4. We have further demonstrated the separation of particles (1 and 10 µm, 3 and 5 µm) using mixed regime configurations (R1 and R2, R2 and R4, respectively).