Data and Knowledge Co-driving for Cancer Subtype Classification on Multi-Scale Histopathological Slides

Artificial intelligence-enabled histopathological data analysis has become a valuable assistant to the pathologist. However, existing models lack representation and inference abilities compared with those of pathologists, especially in cancer subtype diagnosis, which is unconvincing in clinical practice. For instance, pathologists typically observe the lesions of a slide from global to local, and then can give a diagnosis based on their knowledge and experience. In this paper, we propose a Data and Knowledge Co-driving (D&K) model to replicate the process of cancer subtype classification on a histopathological slide like a pathologist. Specifically, in the data-driven module, the bagging mechanism in ensemble learning is leveraged to integrate the histological features from various bags extracted by the embedding representation unit. Furthermore, a knowledge-driven module is established based on the Gestalt principle in psychology to build the three-dimensional (3D) expert knowledge space and map histological features into this space for metric. Then, the diagnosis can be made according to the Euclidean distance between them. Extensive experimental results on both public and in-house datasets demonstrate that the D&K model has a high performance and credible results compared with the state-of-the-art methods for diagnosing histopathological subtypes. Code: https://github.com/Dennis-YB/Data-and-Knowledge-Co-driving-for-Cancer-Subtypes-Classificatio

Soil Enzyme Activity and Microbial Metabolic Function Diversity in Soda Saline–Alkali Rice Paddy Fields of Northeast China

Western Jilin province has the most serious area of soda salinization in Northeast China, which affects and restricts the sustainable development of agriculture. The effects of physico-chemical properties of rhizosphere and non-rhizosphere soil on soil microbial diversity and enzyme activities (polyphenol oxidase, catalase, invertase, amylase) were evaluated in typical soda saline-alkali paddy field. Community-level physiological profile (CLPP) based on Biolog-ECO plates was used to assess the functional diversity of soil microorganisms. Exchangeable sodium percentage (ESP) and pH were negative correlated with the microbial activity (AWCD), soil enzyme activities (amylase, sucrose, and catalase, except for polyphenol oxidase) in rice rhizosphere and non-rhizosphere soil (P < 0.05). The indexes of microbial diversity in rice rhizosphere soil were significantly higher than that of non-rhizosphere soil. The utilization of amino acids by rice rhizosphere microorganisms was relatively high, while non-rhizosphere soil had relatively high utilization of carboxylic acid, phenolic acid, and amine. Among the selected physico-chemical properties, soil organic carbon (SOC) and soil water content (SWC) had the greatest influence on the variation of microbial diversity indexes and enzyme activities in rhizosphere soil. ESP and pH showed a significant positive correlation with carbon source utilization, especially for amine (AM) and phenolic acid (PA) carbon source utilization (P < 0.05) by means of RDA, and the utilization rate of AM and PA carbon sources by rice rhizosphere and non-root soil microorganisms was P1 < P2 < P3

Carbon Mineralization under Different Saline—Alkali Stress Conditions in Paddy Fields of Northeast China

Soil organic carbon (SOC) mineralization (conversion of carbonaceous material to carbon dioxide) plays a central role in global carbon cycle. However, the effects of SOC mineralization under different saline–alkali stress conditions are poorly understood. In order to understand the carbon mineralization processes, four paddy fields with different saline and alkali degrees were chosen as the experimental samples and the soil CO2 emission fluxes at nine different time steps of the whole simulation experiment were observed. The physical and chemical properties of soils of four field conditions were compared for the dynamic changes of CO2 flux in the progress of paddy field cultivation simulations. The results showed that the first three fields (P1, P2, and P3) were weakly alkaline soils and the last one (P4) was strongly alkaline soil. The SOC content of each plot was significantly different and there was a near-surface enrichment, which was significantly negatively correlated with the degree of alkalization. The accumulation process of the SOC mineralization during the incubation time was consistent with the first-order kinetic model. In the initial stage of mineralization, the amount of CO2 released massively, and then the release intensity decreased rapidly. The mineralization rate decreased slowly with time and finally reached a minimum at the end of the incubation period. This study indicates that the SOC mineralization process is affected by a variety of factors. The main factors influencing SOC mineralization in the saline–alkaline soils are the exchangeable sodium percentage (ESP), followed by enzyme activities. Salinization of the soils inhibits the rate of soil carbon cycle, which has a greater impact on the carbon sequestration than on the carbon source process. The intensity and completeness of the SOC mineralization reactions increase with increasing SOC contents and decrease with increasing ESP levels

Using expert knowledge to identify key threats and conservation strategies for wildlife: A case study with bats in China

Global biodiversity is in rapid decline, yet the key threats to wildlife in many regions remain uncertain. Bats are one of the most diverse mammalian groups, playing vital roles in the ecosystems. There are at least 140 bat species in China, with 30 % of being regionally threatened or data deficient. Here, we used expert elicitation to assess the key threats and conservation strategies of bats in China. We designed an online questionnaire concerning the conservation of Chinese bats, and then distributed the questionnaire to bat experts worldwide via email. All participants were asked to rank each threat and conservation strategy according to the urgency and significance. After excluding participants without some knowledge of Chinese bats and conservation biology, we gathered the opinions of 119 bat experts from China and abroad. The results showed that the scores of different threats and conservation strategies were predicted by their categories. Loss of habitat, killing and hunting, and roost disturbance were regarded as the three top threats faced by Chinese bats. Most experts recognized that banning hunting and improving the legislation were two priority strategies for bat conservation, although monitoring of bat diversity, scientific publicity, and education were also important. Nearly 98 % of the experts supported the suggestion that threatened bats should be under special state protection because of their ecological services, economic value, population decline, scientific value, and other features. These results provide valuable implications for guiding the protection and management of bats in China

Stimulated Chiral LightMatter Interactions in Biological Microlasers

Chiral light-matter interactions have emerged as a promising area in biophysics and quantum optics. Great progress in enhancing chiral light-matter interactions have been investigated through passive resonators or spontaneous emission. Nevertheless, the interaction between chiral biomolecules and stimulated emission remains unexplored. Here we introduce the concept of a biological chiral laser by amplifying chiral light-matter interactions in an active resonator through stimulated emission process. Green fluorescent proteins or chiral biomolecules encapsulated in Fabry-Perot microcavity served as the gain material while excited by either left-handed or right-handed circularly polarized pump laser. Owing to the nonlinear pump energy dependence of stimulated emission, significant enhancement of chiral light-matter interactions was demonstrated. Detailed experiments and theory revealed that a lasing dissymmetry factor is determined by molecular absorption dissymmetry factor at its excitation wavelength. Finally, chirality transfer was investigated under a stimulated emission process through resonance energy transfer. Our findings elucidate the mechanism of stimulated chiral light-matter interactions, providing better understanding of light-matter interaction in biophysics, chiral sensing, and quantum biophotonics.Agency for Science, Technology and Research (A*STAR)Ministry of Education (MOE)Nanyang Technological UniversityThis research is supported by A*STAR under its AME IRG Grant (Project No. A20E5c0085) and the Ministry of Education Singapore (Tier 1- RG 158/19(S)). We thank the Internal Grant NAP SUG - M4082308.040 from NTU

The Development and Utilization of Saline–Alkali Land in Western Jilin Province Promoted the Sequestration of Organic Carbon Fractions in Soil Aggregates

Soil samples from T (0~20 cm) and S (20~40 cm) layers of four saline–alkali rice fields (R5, R15, R20, and R35) with different reclamation years were selected to study the distribution of soil aggregates and the contents of readily oxidizable organic carbon (ROC), dissolved organic carbon (DOC), microbial biomass carbon (MBC), potentially mineralizable carbon (PMC), and soil organic carbon (SOC). The effects of large macroaggregate (>2 mm, LMA), small macroaggregate (0.25 to 2 mm, SMA), and microaggregate (<0.25 mm, MA) particle size, soil layer, and soil physicochemical properties on SOC fractions were also analyzed. The results showed that the LMA size in saline–alkali paddy fields were easily decomposed and was unstable due to the influence of the external environment. With the increase in reclamation years, the proportion of LMA in the S layer decreased gradually. The ROC, DOC, MBC and TOC contents of aggregates in the T and S layers gradually increased with the increase in reclamation years, and SOC fractions contents of aggregates in different grain sizes were SMA > LMA > MA. An effective way to increase carbon sink and improve the ecological environment in western Jilin Province is to change the soil environment by planting rice in saline–alkali land

The emergence activities of nine cave-roosting bats under different lighting conditions

<p>Artificial light at night has become an emerging environmental pollutant, posing a serious threat to biodiversity. Cave-roosting animals are vulnerable to light pollution due to long-term adaptation to nocturnal niches, and the problem is especially severe in the context of cave tourism and limestone mining. Mitigating the adverse impacts of artificial light on cave-dwelling animals presents a challenge. Here, we aimed to assess the relative contribution of spectral parameters and light intensity to emergence behavior among nine bat species inhabiting a karst cave, including <em>Rhinolophus macrotis</em>, <em>Rhinolophus pearsonii</em>,<em> Rhinolophus rex</em>, <em>Rhinolophus pusillus</em>, <em>Rhinolophus siamensis</em>, <em>Rhinolophus sinicus</em>, <em>Hipposideros armiger,</em> <em>Myotis davidii</em>, and <em>Miniopterus fuliginosus</em>. We manipulated light spectra and intensities through light-emitting diode (LED) lighting and gel filters at the entrance of bat roost. We monitored nightly passes per species to quantify bat emergence under the dark control and ten lighting conditions (blue, green, yellow, red, and white light at high and low intensities) using ultrasonic recording. Our analyses showed that the number of bat passes tended to be reduced in the presence of white, green, and yellow light, independent of light intensity. In contrast, the number of bat passes showed no pronounced differences under the dark control, blue light, and red light. The number of bat passes was primarily affected by LED light's blue component, red component, peak wavelength, and half-width instead of light intensity. These results demonstrate that spectral parameters of LED light can significantly affect emergence behavior of cave-dwelling bats. Our findings highlight the importance of manipulating light colors to reduce the negative impacts of light pollution on cave-roosting bats as a function of their spectral sensitivity. We recommend the use of gel filters to manage existing artificial lighting systems in underground habitats exploited by bats.</p><p>Microsoft Excel.</p><p>Funding provided by: National Natural Science Foundation of China<br>Crossref Funder Registry ID: https://ror.org/01h0zpd94<br>Award Number: 32271561</p><p>Funding provided by: Science and Technology Department of Sichuan Province<br>Crossref Funder Registry ID: https://ror.org/04323m874<br>Award Number: 2022NSFSC1761</p><p>Funding provided by: Undergraduate Innovation and Entrepreneurship Training Program of China*<br>Crossref Funder Registry ID: <br>Award Number: 202310638011</p><p>Funding provided by: Undergraduate Innovation and Entrepreneurship Training Program of China*<br>Crossref Funder Registry ID: <br>Award Number: S202210638071</p><p>We manipulated light spectra and intensities through light-emitting diode (LED) lighting and gel filters at the entrance of a karst cave inhabited by nine bat species, including <em>Rhinolophus macrotis</em>,<em> Rhinolophus pearsonii,</em> <em>Rhinolophus rex</em>,<em> Rhinolophus pusillus</em>, <em>Rhinolophus siamensis</em>, <em>Rhinolophus sinicus</em>, <em>Hipposideros armiger</em>, <em>Myotis davidii,</em> and <em>Miniopterus fuliginosus.</em> We recorded echolocation vocalizations per species under the dark control and ten lighting conditions (blue, green, yellow, red, and white light at high and low intensities) via an ultrasonic recording system (UltrasoundGate 116; Avisoft Bioacoustics, Berlin, Germany). Using Avisoft-SASLab Pro (Avisoft Bioacoustics), we inspected bat echolocation vocalizations counted the number of passes per species under each treatment. Spectral parameters and intensity of LED light were measured using an OHSP350 spectrometer (Hangzhou Hopoo Light Color Technology Co., Ltd., China) and an SW582 illuminance meter (Frank Electronics Co., Ltd, China) held horizontally at a height of 1.7 m. The horizontal distance between an experimenter and the lamp was 1 m during luminance measurement. </p&gt

Ultrathin CoNiP@Layered Double Hydroxides Core–Shell Nanosheets Arrays for Largely Enhanced Overall Water Splitting

Electrocatalytic water splitting to give a continuous production of oxygen and hydrogen is one of goals of energy research aiming at sustainable energy demands, in which the development of bifunctional electrocatalysts toward both oxygen evolution reaction (OER) and hydrogen evolution reaction (HER) with high activity, good durability, and low cost remains a challenge. In this work, a bifunctional electrocatalyst based on transition metal phosphides CoNiP@layered double hydroxides (LDHs) core–shell nanosheets arrays for both OER and HER have been designed and synthesized. The resulting CoNiP@LDHs nanoarrays exhibit excellent electrocatalytic activity and a remarkable long-term durability (∼6 mV degradation after 500 h OER stability test). Especially, this hierarchical nanostructure needs a cell potential as low as 1.44 V at a current density of 10 mA cm^–2, which is the best performance of bifunctional electrocatalysts among transition metal phosphides to our knowledge

Light-harvesting in biophotonic optofluidic microcavities via whispering-gallery modes

Phycobiliproteins are a class of light-harvesting fluorescent proteins existing in cyanobacteria and microalgae, which harvest light and convert it into electricity. Owing to recent demands on environmental-friendly and renewable apparatuses, phycobiliproteins have attracted substantial interest in bioenergy and sustainable devices. However, converting energy from biological materials remains challenging to date. Herein, we report a novel scheme to enhance biological light-harvesting through light-matter interactions at the biointerface of whispering-gallery modes (WGMs), where phycobiliproteins were employed as the active gain material. By exploiting microdroplets as a carrier for light-harvesting biomaterials, strong local electric field enhancement and photon confinement at the cavity interface resulted in significantly enhanced bio-photoelectricity. A threshold-like behavior was discovered in photocurrent enhancement and the WGM modulated fluorescence. Systematic studies of biologically produced photoelectricity and optical mode resonance were carried out to illustrate the impact of the cavity quality factor, structural geometry, and refractive indices. Finally, a biomimetic system was investigated by exploiting cascade energy transfer in phycobiliprotein assembly composed of three light-harvesting proteins. The key findings not only highlight the critical role of optical cavity in light-harvesting but also offer deep insights into light energy coupling in biomaterials.Ministry of Education (MOE)Nanyang Technological UniversityThis research is supported by the Ministry of Education Singapore (Tier 1-RG 158/19(S)). We would like to thank Internal Grant NAP SUG -M4082308.040 from NTU