Prediction of drug sensitivity based on multi-omics data using deep learning and similarity network fusion approaches

With the rapid development of multi-omics technologies and accumulation of large-scale bio-datasets, many studies have conducted a more comprehensive understanding of human diseases and drug sensitivity from multiple biomolecules, such as DNA, RNA, proteins and metabolites. Using single omics data is difficult to systematically and comprehensively analyze the complex disease pathology and drug pharmacology. The molecularly targeted therapy-based approaches face some challenges, such as insufficient target gene labeling ability, and no clear targets for non-specific chemotherapeutic drugs. Consequently, the integrated analysis of multi-omics data has become a new direction for scientists to explore the mechanism of disease and drug. However, the available drug sensitivity prediction models based on multi-omics data still have problems such as overfitting, lack of interpretability, difficulties in integrating heterogeneous data, and the prediction accuracy needs to be improved. In this paper, we proposed a novel drug sensitivity prediction (NDSP) model based on deep learning and similarity network fusion approaches, which extracts drug targets using an improved sparse principal component analysis (SPCA) method for each omics data, and construct sample similarity networks based on the sparse feature matrices. Furthermore, the fused similarity networks are put into a deep neural network for training, which greatly reduces the data dimensionality and weakens the risk of overfitting problem. We use three omics of data, RNA sequence, copy number aberration and methylation, and select 35 drugs from Genomics of Drug Sensitivity in Cancer (GDSC) for experiments, including Food and Drug Administration (FDA)-approved targeted drugs, FDA-unapproved targeted drugs and non-specific therapies. Compared with some current deep learning methods, our proposed method can extract highly interpretable biological features to achieve highly accurate sensitivity prediction of targeted and non-specific cancer drugs, which is beneficial for the development of precision oncology beyond targeted therapy.

Drought monitoring in arid and semi-arid region based on multi-satellite datasets in northwest, China

Drought is a complex natural disaster affected by multiple climate factors and underlying surface. In recent years, drought monitoring indices of remote sensing have been widely applied to monitor drought in a certain region or global. However, some remote sensing drought monitoring indices do not consider the drought-causing factors enough to reflect the comprehensive drought situation of a region fully. In this paper, a new remote sensing drought monitoring index, called Remote Sensing Drought Evaluation Index (RSDEI), was constructed by combining Vegetation Condition Index (VCI), Temperature Condition Index (TCI), Precipitation Condition Index (PCI), and Soil Moisture Condition Index (SMCI) using the spatial principal component analysis (SPCA) method. The reasonableness of RSDEI was test and verified using Net Primary Productivity (NPP), Standardized Precipitation Evapotranspiration Index (SPEI), and unit area crop yield. The RSDEI was also applied to the drought condition monitoring of the northwest arid and semi-arid region from 2001 to 2019.The result demonstrated that the results showed that the RSDEI had a high correlation coefficient with SPEI-12 (R=0.85, p<0.01). It is concluded that the correlation coefficient between RSDEI and NPP is 0.74 at 95% confidence level, which indicates that RSDEI and NPP have a strong correlation. Then, the correlation between RSDEI and crop yield per unit area is 0.89. The results of RSDEI showed that the drought in northwest China started in May and lasted in September from 2001 to 2019. The lowest value of RSDEI appeared in May, which inflected the significant difference of drought level in different month in northwest China. The result of CV (coefficient of variation) showed that the drought variation in the study area had a stable low fluctuation condition as a whole, in the northwest and northeast of study area, which indicated that the changes of drought were different in the past 19 years. The Hurst exponent analysis showed that the area with the positive evolution of Hurst index (0.5<H<1) is 1,845,046.669 km²,which accounts for 75.9% of the total area, while the area with reverse evolution characteristics (H<0.5) accounts for 24.1% of the total area. The result obtained above reflected that the drought changes in most regions are better than that in the past 19 years. The trend gradually changes from drought to humid.

Quantifying the Variability of Forest Ecosystem Vulnerability in the Largest Water Tower Region Globally

Forests are critical ecosystems for environmental regulation and ecological security maintenance, especially at high altitudes that exhibit sensitivity to climate change and human activities. The Qinghai-Tibet Plateau—the world’s largest water tower region—has been breeding many large rivers in Asia where forests play important roles in water regulation and water quality improvement. However, the vulnerability of these forest ecosystems at the regional scale is still largely unknown. Therefore, the aim of this research is to quantitatively assess the temporal–spatial variability of forest vulnerability on the Qinghai-Tibet Plateau to illustrate the capacity of forests to withstand disturbances. Geographic information system (GIS) and the spatial principal component analysis (SPCA) were used to develop a forest vulnerable index (FVI) to assess the vulnerability of forest ecosystems. This research incorporates 15 factors covering the natural context, environmental disturbances, and socioeconomic impact. Results indicate that the measure of vulnerability was unevenly distributed spatially across the study area, and the whole trend has intensified since 2000. The three factors that contribute the most to the vulnerability of natural contexts, environmental disturbances, and human impacts are slope aspect, landslides, and the distance to the farmland, respectively. The vulnerability is higher in forest areas with lower altitudes, steeper slopes, and southerly directions. These evaluation results can be helpful for forest management in high altitude water tower regions in the forms of forest conservation or restoration planning and implementation towards sustainable development goals.

Two Undervalued Functions of the Golgi Apparatus: Removal of Excess Ca2+ and Biosynthesis of Farnesol-Like Sesquiterpenoids, Possibly as Ca2+-Pump Agonists and Membrane "Fluidizers-Plasticizers"

The extensive literature dealing with the Golgi system emphasizes its role in protein secretion and modification, usually without specifying from which evolutionary ancient cell physiological necessity such secretion originated. Neither does it specify which functional requirements the secreted proteins must meet. From a reinterpretation of some classical and recent data gained mainly, but not exclusively, from (insect) endocrinology, the view emerged that the likely primordial function of the rough endoplasmic reticulum (RER)–Golgi complex in all eukaryotes was not the secretion of any type of protein but the removal of toxic excess Ca²⁺ from the cytoplasm. Such activity requires the concurrent secretion of large amounts of Ca²⁺-carrying/transporting proteins acting as a micro-conveyor belt system inside the RER–Golgi. Thus, (fitness increasing) protein secretion is subordinate to Ca²⁺ removal. Milk with its high content of protein and Ca²⁺ (60–90 mM vs. 100 nM in unstimulated mammary gland cells) is an extreme example. The sarco(endo)plasmatic reticulum Ca²⁺-ATPases (SERCAs) and SPCA1a Ca²⁺/Mn²⁺ transport ATPases are major players in Ca²⁺ removal through the Golgi. Both are blocked by the sesquiterpenoid thapsigargin. This strengthens the hypothesis (2014) that endogenous farnesol-like sesquiterpenoids (FLSs) may act as the long sought for but still unidentified agonist(s) for Ca²⁺-pumps in both the ER and Golgi. A second putative function also emerges. The fusion of both the incoming and outgoing transport vesicles, respectively, at the cis- and trans- side of Golgi stacks, with the membrane system requiring high flexibility and fast self-closing of the involved membranes. These properties may—possibly partially—be controlled by endogenous hydrophobic membrane “fluidizers” for which FLSs are prime candidates. A recent reexamination of unexplained classical data suggests that they are likely synthesized by the Golgi itself. This game-changing hypothesis is endorsed by several arguments and data, some of which date from 1964, that the insect corpus allatum (CA), which is the major production site of farnesol-esters, has active Golgi systems. Thus, in addition to secreting FLS, in particular juvenile hormone(s), it also secretes a protein(s) or peptide(s) with thus far unknown function. This paper suggests answers to various open questions in cell physiology and general endocrinology.

Targeting the Calcium Signalling Machinery in Cancer

Cancer is caused by excessive cell proliferation and a propensity to avoid cell death, while the spread of cancer is facilitated by enhanced cellular migration, invasion, and vascularization. Cytosolic Ca²⁺ is central to each of these important processes, yet to date, there are no cancer drugs currently being used clinically, and very few undergoing clinical trials, that target the Ca²⁺ signalling machinery. The aim of this review is to highlight some of the emerging evidence that targeting key components of the Ca²⁺ signalling machinery represents a novel and relatively untapped therapeutic strategy for the treatment of cancer.

Functional Coupling between the Unfolded Protein Response and Endoplasmic Reticulum/Golgi Ca2+-ATPases Promotes Stress Tolerance, Cell Wall Biosynthesis, and Virulence of Aspergillus fumigatus

Many species of pathogenic fungi deploy the unfolded protein response (UPR) to expand the folding capacity of the endoplasmic reticulum (ER) in proportion to the demand for virulence-related proteins that traffic through the secretory pathway. Although Ca²⁺ plays a pivotal role in ER function, the mechanism by which transcriptional upregulation of the protein folding machinery is coordinated with Ca²⁺ homeostasis is incompletely understood. In this study, we investigated the link between the UPR and genes encoding P-type Ca²⁺-ATPases in the human-pathogenic mold Aspergillus fumigatus We demonstrate that acute ER stress increases transcription of the srcA gene, encoding a member of the sarco/endoplasmic reticulum Ca²⁺-ATPase (SERCA) family, as well as that of pmrA, encoding a secretory pathway Ca²⁺-ATPase (SPCA) in the Golgi membrane. Loss of the UPR transcription factor HacA prevented the induction of srcA and pmrA transcription during ER stress, defining these ER/Golgi Ca²⁺ pumps as novel downstream targets of this pathway. While deletion of srcA alone caused no major deficiencies, a ΔsrcA/ΔpmrA mutant displayed a severe polarity defect, was hypersensitive to ER stress, and showed attenuated virulence. In addition, cell wall analyses revealed a striking reduction in mannose levels in the absence of both Ca²⁺ pumps. The ΔhacA mutant was hypersensitive to agents that block calcineurin-dependent signaling, consistent with a functional coupling between the UPR and Ca²⁺ homeostasis. Together, these findings demonstrate that the UPR integrates the need for increased levels of chaperone and folding enzymes with an influx of Ca²⁺ into the secretory pathway to support fungal growth, stress adaptation, and pathogenicity.IMPORTANCE The UPR is an intracellular signal transduction pathway that maintains homeostasis of the ER. The pathway is also tightly linked to the expression of virulence-related traits in diverse species of human-pathogenic and plant-pathogenic fungal species, including the predominant mold pathogen infecting humans, Aspergillus fumigatus Despite advances in the understanding of UPR signaling, the linkages and networks that are governed by this pathway are not well defined. In this study, we revealed that the UPR is a major driving force for stimulating Ca²⁺ influx at the ER and Golgi membranes and that the coupling between the UPR and Ca²⁺ import is important for virulence, cell wall biosynthesis, and resistance to antifungal compounds that inhibit Ca²⁺ signaling.

Understanding Preferences for Humane and Cruel Treatment of Pest Rodents in Site C, Khayelitsha, South Africa

The cruel treatment of pest rodents is a neglected area of study. This paper uses a representative survey from Khayelitsha (Cape Town) to show that a minority of residents preferred rodent control to be humane but that most did not care how rats are killed and almost a fifth said they would be 'happy' if the rats suffered. Agreeing that animal welfare is important and having become used to the presence of rats raised the probability of support for humane rodent control and decreased support for cruel rodent control. Being concerned that rats might be linked to witchcraft increased the probability of a pro-cruel stance. These results were robust to the inclusion of measures of rodent presence in the household and socio-economic status. This highlights the importance of values (notably concern about animal welfare) and cultural beliefs - in this case concerns that rodents might be linked to witchcraft - in predicting whether respondents are likely to have a pro-cruel stance on rodent control or not. Promoting the humane treatment of pest animals in this context thus requires engaging with local culture.

A putative calcium-ATPase of the secretory pathway family may regulate calcium/manganese levels in the Golgi apparatus of Entamoeba histolytica

Calcium regulates many cellular processes in protozoa, including growth, differentiation, programmed cell death, exocytosis, endocytosis, phagocytosis, fusion of the endosomes of distinct stages with phagosomes, fusion of phagosomes with lysosomes, and recycling the membrane. In Entamoeba histolytica, the protozoa responsible for human amoebiasis, calcium ions are essential for signaling pathways that lead to growth and development. In addition, calcium is crucial in the modulation of gene expression in this microorganism. However, there is scant information about the proteins responsible for regulating calcium levels in this parasite. In this work, we characterized a protein of E. histolytica that shows a close phylogenetic relationship with Ca²⁺ pumps that belong to the family of secretory pathway calcium ATPases (SPCA), which for several organisms are located in the Golgi apparatus. The amoeba protein analyzed herein has several amino acid residues that are characteristic of SPCA members. By an immunofluorescent technique using specific antibodies and immunoelectron microscopy, the protein was detected on the membrane of some cytoplasmic vacuoles. Moreover, this putative calcium-ATPase was located in vacuoles stained with NBD C6-ceramide, a Golgi marker. Overall, the current findings support the hypothesis that the presently analyzed protein corresponds to the SPCA of E. histolytica.

Constitutive calcium entry and cancer: updated views and insights

Tight control of basal cytosolic Ca²⁺ concentration is essential for cell survival and to fine-tune Ca²⁺-dependent cell functions. A way to control this basal cytosolic Ca²⁺ concentration is to regulate membrane Ca²⁺ channels including store-operated Ca²⁺ channels and secondary messenger-operated channels linked to G-protein-coupled or tyrosine kinase receptor activation. Orai, with or without its reticular STIM partner and Transient Receptor Potential (TRP) proteins, were considered to be the main Ca²⁺ channels involved. It is well accepted that, in response to cell stimulation, opening of these Ca²⁺ channels contributes to Ca²⁺ entry and the transient increase in cytosolic Ca²⁺ concentration involved in intracellular signaling. However, in various experimental conditions, Ca²⁺ entry and/or Ca²⁺ currents can be recorded at rest, without application of any experimental stimulation. This led to the proposition that some plasma membrane Ca²⁺ channels are already open/activated in basal condition, contributing therefore to constitutive Ca²⁺ entry. This article focuses on direct and indirect observations supporting constitutive activity of channels belonging to the Orai and TRP families and on the mechanisms underlying their basal/constitutive activities.

Detection of retrobulbar blood vessels in optical coherence tomography angiographic images in eyes with pathologic myopia

Purpose

To report the detection of retrobulbar blood vessel in the optical coherence tomography angiographic (OCTA) images of two eyes with pathologic myopia.

Observations

Two eyes of 2 cases with pathologic myopia were examined by OCTA (RTVue XR Avanti, Optovue, and Cirrus 5000, Zeiss). Case 1 was a 64-year-old man, and Case 2 was a 65-year-old woman. In Case 1, the thickness of the subfoveal choroid was 38 μm and the sclera was 274 μm, and they were 17 μm and 214 μm, respectively, in Case 2. The axial length was 35.8 mm in Case 1 and 29.5 mm in Case 2. The choroidal vessels were clearly visible in the choriocapillary slab in both the RTVue and the Cirrus images. The vessels were visible in the area of the retinal pigment epithelial and choriocapillaris atrophy due to the pathologic myopia. The retrobulbar blood vessels temporal to fovea were seen in the OCTA images at the level of the outer aspect of the sclera in both cases. Cross sectional images of the retrobulbar blood vessel in both cases were observed under the sclera in serial scan images overlaid with blood flow.

Conclusions

and Importance: These in situ images of the retrobulbar blood vessels that were obtained by OCTA was possible because of the thinness of the choroid and sclera and atrophy of the choriocapillaris in these eyes with pathologic myopia. We conclude that OCTA might have utility to study the retrobulbar vascular alterations in eyes with pathologic myopia.

Prion infection in cells is abolished by a mutated manganese transporter but shows no relation to zinc

The cellular prion protein has been identified as a metalloprotein that binds copper. There have been some suggestions that prion protein also influences zinc and manganese homeostasis. In this study we used a series of cell lines to study the levels of zinc and manganese under different conditions. We overexpressed either the prion protein or known transporters for zinc and manganese to determine relations between the prion protein and both manganese and zinc homeostasis. Our observations supported neither a link between the prion protein and zinc metabolism nor any effect of altered zinc levels on prion protein expression or cellular infection with prions. In contrast we found that a gain of function mutant of a manganese transporter caused reduction of manganese levels in prion infected cells, loss of observable PrP(Sc) in cells and resistance to prion infection. These studies strengthen the link between manganese and prion disease.

Policing Farm Animal Welfare in Federated Nations: The Problem of Dual Federalism in Canada and the USA

Simple Summary

In any federation of states, societal oversight of farm animal welfare (agriculture policy arena, prevention) is more difficult to achieve than providing punishment of individuals abusing of companion animals (post injury). The constitutional division of powers and historical policy related to animal agriculture and non-government organization policing cruelty of companion animals may be entrenched. With changing societal expectations of agriculture production, each level of government may hesitate to take the lead, due to financial or ideological beliefs and simultaneously, obstruct the other government level from taking the lead, based on constitutional grounds. The tradition of private policing of companion animal abuse offences may be unworkable in the provision of protection for animals used in industrial production.

Abstract

In recent European animal welfare statutes, human actions injurious to animals are new “offences” articulated as an injury to societal norms in addition to property damage. A crime is foremost a violation of a community moral standard. Violating a societal norm puts society out of balance and justice is served when that balance is returned. Criminal law normally requires the presence of mens rea, or evil intent, a particular state of mind; however, dereliction of duties towards animals (or children) is usually described as being of varying levels of negligence but, rarely can be so egregious that it constitutes criminal societal injury. In instrumental justice, the “public goods” delivered by criminal law are commonly classified as retribution, incapacitation and general deterrence. Prevention is a small, if present, outcome of criminal justice. Quazi-criminal law intends to establish certain expected (moral) standards of human behavior where by statute, the obligations of one party to another are clearly articulated as strict liability. Although largely moral in nature, this class of laws focuses on achieving compliance, thereby resulting in prevention. For example, protecting the environment from degradation is a benefit to society; punishing non-compliance, as is the application of criminal law, will not prevent the injury. This paper will provide evidence that the integrated meat complex of Canada and the USA is not in a good position to make changes to implement a credible farm animal protection system.