MGCT: Mutual-Guided Cross-Modality Transformer for Survival Outcome Prediction using Integrative Histopathology-Genomic Features

The rapidly emerging field of deep learning-based computational pathology has shown promising results in utilizing whole slide images (WSIs) to objectively prognosticate cancer patients. However, most prognostic methods are currently limited to either histopathology or genomics alone, which inevitably reduces their potential to accurately predict patient prognosis. Whereas integrating WSIs and genomic features presents three main challenges: (1) the enormous heterogeneity of gigapixel WSIs which can reach sizes as large as 150,000x150,000 pixels; (2) the absence of a spatially corresponding relationship between histopathology images and genomic molecular data; and (3) the existing early, late, and intermediate multimodal feature fusion strategies struggle to capture the explicit interactions between WSIs and genomics. To ameliorate these issues, we propose the Mutual-Guided Cross-Modality Transformer (MGCT), a weakly-supervised, attention-based multimodal learning framework that can combine histology features and genomic features to model the genotype-phenotype interactions within the tumor microenvironment. To validate the effectiveness of MGCT, we conduct experiments using nearly 3,600 gigapixel WSIs across five different cancer types sourced from The Cancer Genome Atlas (TCGA). Extensive experimental results consistently emphasize that MGCT outperforms the state-of-the-art (SOTA) methods.Comment: 7 pages, 4 figures, accepted by 2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2023

Biophysical controls on soil respiration in the dominant patch types of an old-growth, mixed-conifer forest

Little is known about biophysical controls on soil respiration in California’s Sierra Nevada oldgrowth, mixed-conifer forests. Using portable and automated soil respiration sampling units, we measured soil respiration rate (SRR) in three dominant patch types: closed canopy (CC), ceanothus-dominated patches (CECO), and open canopy (OC). SRR varied significantly among the patch types, ranging from 2.0 to 4.5 �μmol m�⁻² s�⁻¹ and from 0.9 to 2.9 �μmol m�⁻² s�⁻¹ during the 1999 and 2000 measuring periods, respectively, with the maximum in CECO and the minimum in OC. Multiple peaks of seasonal SRR were functions of soil temperature and moisture dynamics. The relationship between SRR and soil temperature switched from a positive to a negative correlation when soil moisture dropped from saturation to drought. Time lag, as a function of soil moisture, was included in an exponential model to assess the effects of soil moisture on SRR in this seasonal water-stressed ecosystem. The total soil C flux summed by an area-weighted average across all three patch types was 660 �± 163 g C m�⁻² from May to Oct. 2000. These results may be applicable to other water-stressed forests in the Mediterranean climate zone, and have implications for the conservation of soil carbon.Key Words: Soil CO₂ efflux, soil temperature, soil moisture, Sierra Nevada, California

Short-term effects of experimental burning and thinning on soil respiration in an old-growth, mixed-conifer forest

To understand the roles of forest management practices in meeting the goals of forest sustainability and CO2 sequestration, we evaluated the effects of burning and thinning treatments on soil respiration and soil environments in an old-growth, mixed-conifer forest in California’s southern Sierra Nevada. Six experimental treatments with two levels of burning and three levels of thinning were implemented across three dominant patch types: closed canopy (CC), Ceanothus shrub (CECO), and open canopy (OC). We measured soil respiration rate (SRR), soil temperature (T10), moisture (Ms), and litter depth (LD), in the summers of 2000 and 2002. Soil total C and total N were measured in 2002. SRR was significantly different among the three patch types. In 2000, SRR was 0.75, 0.86, and 0.26 g CO2 m-2 hr-1 in CC, CECO, and OC, respectively. In 2002, SRR was 0.79, 0.97, and 0.44 g CO2 m-2 hr-1 in CC, CECO, and OC, respectively. The analysis of variance indicated that burning and thinning significantly affected soil respiration and soil environments. In particular, SRR significantly decreased in burned CECO patches but increased in unburned and thinned CECO. SRR in CC and OC did not significantly change. T10 and Ms increased, whereas LD and soil C decreased in treated patches. We also developed pre- and posttreatment exponential models to predict SRR using soil environmental variables. The effects of burning and thinning on soil CO2 efflux and soil environments imply that forest carbon pools would be reorganized with widespread application of these forest management practices.Keywords: Thinning, Soil moisture, Soil temperature, Prescribed burning, Mixed conifer, Soil respiratio

Penaeid shrimp genome provides insights into benthic adaptation and frequent molting

Crustacea, the subphylum of Arthropoda which dominates the aquatic environment, is of major importance in ecology and fisheries. Here we report the genome sequence of the Pacific white shrimp Litopenaeus vannamei, covering similar to 1.66 Gb (scaffold N50 605.56 Kb) with 25,596 protein-coding genes and a high proportion of simple sequence repeats (>23.93%). The expansion of genes related to vision and locomotion is probably central to its benthic adaptation. Frequent molting of the shrimp may be explained by an intensified ecdysone signal pathway through gene expansion and positive selection. As an important aquaculture organism, L. vannamei has been subjected to high selection pressure during the past 30 years of breeding, and this has had a considerable impact on its genome. Decoding the L. vannamei genome not only provides an insight into the genetic underpinnings of specific biological processes, but also provides valuable information for enhancing crustacean aquaculture

Native circulating Brucella melitensis lineages causing a brucellosis epidemic in Qinghai, China

Since 2010, the cases and incidences of human brucellosis have been increasing annually in Qinghai (QH) Province. Molecular epidemiology and phylogenetic analyses of strains from this region are crucial to better understand the transmission of the disease and the evolutionary patterns of Brucella strains. In this study, classical bio-typing assay, multilocus variable-number tandem repeat analysis, and the whole-genome sequencing–single-nucleotide polymorphism approach were used to illustrate the epidemiological and evolutionary patterns of Brucella melitensis. A total of 54 B. melitensis bv. 3 strains were isolated and molecularly characterized, with all strains belonging to the East Mediterranean lineages. Cross-regional transmission events (i.e., between counties) were caused by common sources of infection, suggesting that predominant circulating genotypes are endemic in different regions. Strengthening surveillance in animal brucellosis and controlling infected animals’ cross-border movement are necessary. Two strains isolated from humans and marmots were clustered in the same sub-clade, implying the possible existence of direct and/or indirect contact between sheep (and goats) and wildlife (marmots), but this needs to be verified by further investigations. The global-scale phylogenetic analysis indicated that 54 strains sorted into six subclades, four of which formed independent lineages, suggesting that the increase in the incidence rate of human brucellosis may be caused by local circulating lineages. Further strengthening the serology and pathogen surveillance of animals (wildlife) and humans will contribute to an in-depth understanding of the transmission chain of human brucellosis in this region

What eddy-covariance measurements tell us about prior land flux errors in CO2-flux inversion schemes

0.2 after 200 km). Separating out the plant functional types did not increase the spatial correlations, except for the deciduous broad-leaved forests. Using the statistics of the flux measurements as a proxy for the statistics of the prior flux errors was shown not to be a viable approach. A statistical model allowed us to upscale the site-level flux error statistics to the coarser spatial and temporal resolutions used in regional or global models. This approach allowed us to quantify how aggregation reduces error variances, while increasing correlations. As an example, for a typical inversion of grid point (300 km × 300 km) monthly fluxes, we found that the prior flux error follows an approximate e-folding correlation length of 500 km only, with correlations from one month to the next as large as 0.6

Vegetation and ecological characteristics of mixed-conifer and Red Fir forests at the Teakettle Experimental Forest

Detailed analysis of mixed-conifer and red fir forests were made from extensive, large vegetation sampling, systematically conducted throughout the Teakettle Experimental Forest. Mixed conifer is characterized by distinct patch conditions of closed-canopy tree clusters, persistent gaps and shrub thickets. This heterogeneous spatial structure provides contrasting microclimate, habitat and resource conditions probably associated with the high diversity of understory plants, fungi, and invertebrates found in ongoing studies in the Teakettle Experiment. In contrast, red fir forests are more homogeneous with continuous high canopy cover, cooler, more consistent microclimate conditions and fewer plant species. In both forests, annual fluctuations in available soil moisture resulting from El Niño influences on snow pack depth may have a significant influence on tree establishment and understory diversity. In depth descriptions of Teakettle’s mixed conifer may provide a target of historic old-growth conditions for forest management