Miracle-dz/UniFAR-FTUs huggingface dataset:
Exploring associations of non-coding RNAs in human diseases via three-matrix factorization with hypergraph-regular terms on center kernel alignment

Relationship of accurate associations between non-coding RNAs and diseases could be of great help in the treatment of human biomedical research. However, the traditional technology is only applied on one type of non-coding RNA or a specific disease, and the experimental method is time-consuming and expensive. More computational tools have been proposed to detect new associations based on known ncRNA and disease information. Due to the ncRNAs (circRNAs, miRNAs and lncRNAs) having a close relationship with the progression of various human diseases, it is critical for developing effective computational predictors for ncRNA-disease association prediction. In this paper, we propose a new computational method of three-matrix factorization with hypergraph regularization terms (HGRTMF) based on central kernel alignment (CKA), for identifying general ncRNA-disease associations. In the process of constructing the similarity matrix, various types of similarity matrices are applicable to circRNAs, miRNAs and lncRNAs. Our method achieves excellent performance on five datasets, involving three types of ncRNAs. In the test, we obtain best area under the curve scores of $0.9832$, $0.9775$, $0.9023$, $0.8809$ and $0.9185$ via 5-fold cross-validation and $0.9832$, $0.9836$, $0.9198$, $0.9459$ and $0.9275$ via leave-one-out cross-validation on five datasets. Furthermore, our novel method (CKA-HGRTMF) is also able to discover new associations between ncRNAs and diseases accurately. Availability: Codes and data are available: https://github.com/hzwh6910/ncRNA2Disease.git. Contact: fguo@tju.edu. cn.
Modulators of Mortality Benefit From Peri-Angioplasty Adjunctive Tirofiban in Patients With ST-Elevation Myocardial Infarction Undergoing Primary Percutaneous Coronary Intervention.

BACKGROUND Studies investigating the modulators of mortality benefit conferred by peri-angioplasty glycoprotein IIb/IIIa inhibitors in ST-elevation myocardial infarction (STEMI) are still lacking.Methods and Results:A prospective database (n=1,025) of consecutive cases undergoing primary percutaneous coronary intervention for STEMI was retrospectively analyzed. For patients in Killip class I, II or III, IV, the multivariate-adjusted hazard ratios of 30-day all-cause mortality associated with adjunctive tirofiban were 3.873 (95% CI 0.504-29.745; P=0.193), 0.550 (95% CI 0.188-1.609; P=0.275), and 0.264 (95% CI 0.099-0.704; P=0.008), respectively. The P value for a linear trend was 0.032. Patients who had a body mass index (BMI) within 22.9-25.0 kg/m2had a significant benefit from tirofiban (adjusted HR 0.344; 95% CI 0.145-0.814; P=0.015) compared to other BMI groups. The P value for a quadratic trend was 0.012. A novel Killip-BMI score (KBS = 2.5 × Killip category - | BMI - 24 |) was calculated to select the beneficial population. A KBS ≥2 was associated with significant mortality benefit, whereas a KBS <0 predicted increased 30-day mortality with tirofiban use. CONCLUSIONS Survival benefit from peri-angioplasty tirofiban therapy for STEMI was positively correlated with the Killip class. Tirofiban should be used cautiously in either underweight or overweight patients. The novel KBS used in this study can guide peri-angioplasty use of adjunctive tirofiban in patients with STEMI undergoing primary angioplasty.
Adaptively Learning Facial Expression Representation via C-F Labels and Distillation

Facial expression recognition is of significant importance in criminal investigation and digital entertainment. Under unconstrained conditions, existing expression datasets are highly class-imbalanced, and the similarity between expressions is high. Previous methods tend to improve the performance of facial expression recognition through deeper or wider network structures, resulting in increased storage and computing costs. In this paper, we propose a new adaptive supervised objective named AdaReg loss, re-weighting category importance coefficients to address this class imbalance and increasing the discrimination power of expression representations. Inspired by human beings’ cognitive mode, an innovative coarse-fine (C-F) labels strategy is designed to guide the model from easy to difficult to classify highly similar representations. On this basis, we propose a novel training framework named the emotional education mechanism (EEM) to transfer knowledge, composed of a knowledgeable teacher network (KTN) and a self-taught student network (STSN). Specifically, KTN integrates the outputs of coarse and fine streams, learning expression representations from easy to difficult. Under the supervision of the pre-trained KTN and existing learning experience, STSN can maximize the potential performance and compress the original KTN. Extensive experiments on public benchmarks demonstrate that the proposed method achieves superior performance compared to current state-of-the-art frameworks with 88.07% on RAF-DB, 63.97% on AffectNet and 90.49% on FERPlus.
Nannochloropsis spp. as Feed Additive for the Pacific White Shrimp: Effect on Midgut Microbiology, Thermal Shock Resistance and Immunology

Simple Summary We evaluated Nannochloropsis spp. as a feed additive for the Pacific white shrimp by testing for thermal shock resistance, immunology, and midgut microbiology. Nannochlorpsis spp. are rich in Eicosapentaenoic acid, an n-3 fatty acid. This study demonstrated that the inclusion of these microalgae in the diet increased shrimp resistance to thermal shock and stimulated shrimp immune defense. Abstract This work aimed to evaluate Nannochloropsis spp. as feed additive in the diet of Pacific white shrimp for their effect on midgut microbiology, thermal shock resistance and immunological parameters. Initially, the digestibility of the microalgae meal was assessed, and the apparent digestibility coefficient (ADC) was determined. The ADC was, in general, high in lipids (78.88%) and eicosapentaenoic fatty acid (73.86%). Then, Nannochloropsis spp. were included in diets at four levels (0, 0.5, 1 and 2% inclusion). The shrimp were reared in 500 L clear water tanks containing 20 shrimp per tank with an initial weight of 6.05 ± 0.06 g and fed four times a day. Shrimp fed with supplemented diets containing Nannochloropsis spp. (0.5 and 2%) presented higher resistance to thermal shock when compared to the non-supplemented group (control). Shrimp fed with 1 and 2% of algae inclusion had a higher production of reactive oxygen species (ROS) when compared to other treatments. No statistical difference was observed in the immunological parameters and microbiology of the intestinal tract. Thus, the inclusion of Nannochloropsis spp. in shrimp diets at 0.5 and 2% levels increases resistance to thermal shock and ROS production in shrimp.
Next-Generation Profiling of Medulloblastoma: Old Drugs Are an Elegant Weapon in a Civilized Age

Personalized therapies have remained elusive in medulloblastoma, resulting in treatment paradigms that have been largely stagnant for almost four decades. A recent study by Rusert and colleagues applies a novel integrated approach to the identification of new targets in medulloblastoma by combining genomics, transcriptomics, and high-throughput drug screening across a panel of molecularly characterized patient-derived models. Actinomysin D, a common chemotherapeutic agent, was identified as highly active in the most aggressive form of medulloblastoma, highlighting the power of this approach over genomic paradigms alone. See related article by Rusert et al.; Cancer Res 80(23):5393–407.
Metagenome-Assembled Genome Sequences of a Biofilm Derived from Marsberg Copper Mine

We sequenced the metagenome of a biofilm collected near a leachate stream of the Marsberg copper mine (Germany) and reconstructed eight metagenome-assembled genomes. These genomes yield copper resistance through Cu(I) oxidation via multiple copper oxidases and extrusion through copper-exporting P-type ATPases. ABSTRACT We sequenced the metagenome of a biofilm collected near a leachate stream of the Marsberg copper mine (Germany) and reconstructed eight metagenome-assembled genomes. These genomes yield copper resistance through Cu(I) oxidation via multiple copper oxidases and extrusion through copper-exporting P-type ATPases.
SIGACT News Online Algorithms Column 36

In this column, we will discuss some papers in online algorithms that appeared in 2020. As usual, we make no claim at complete coverage here, and have instead made a selection. If we have unaccountably missed your favorite paper and you would like to write about it or about any other topic in online algorithms, please don't hesitate to contact us!
Elements of nanocrystal high-field carrier transport modeling

Embedded semiconductor nanocrystals (NCs) within wide bandgap oxide materials are being considered for light emission and solar cell applications. One of the fundamental issues is the high-field transport in NCs. This requires the combination of a number of tools: ensemble Monte Carlo carrier transport simulation, ab initio band structure of the bulk oxide, Fermi's golden rule modeling of impact ionization and Auger processes and the pseudopotential-based atomistic description of the confined NC states. These elements are outlined in this brief report. (© 2007 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)
Light through the fog: using precision fMRI data to disentangle the neural substrates of cognitive control

Cognitive control, the ability to engage in goal-related behavior, is linked to frontal, parietal, and cingulate brain regions. However, the underlying function(s) of these regions is still in question, with ongoing discussions about their specificity and/or multifunctionality. These brain regions are also among the most variable across individuals, which may confound multi-functionality with inter-individual heterogeneity. Precision fMRI-extended data acquisition from single individuals-allows for reliable individualized mapping of brain organization. We review examples of recent studies that use precision fMRI to surmount inter-individual variability in functional neuroanatomy. These studies provide evidence of interleaved specialized and multifunctional regions in the frontal cortex. We discuss the potential for these techniques to address outstanding controversies on the neural underpinnings of cognitive control.
Can Extra Daytime Light Exposure Improve Well-Being and Sleep? A Pilot Study of Patients With Glaucoma

Glaucoma damages retinal ganglion cells, including intrinsically photosensitive retinal ganglion cells (ipRGCs). These cells modulate various non-visual physiological and psychological functions which are modulated by light. In patients with glaucoma, we assessed the effect of daily bright light exposure (LE) on several melanopsin-dependent functions, such as the pupil constriction, circadian rest-activity cycles, sleep and subjective well-being including relaxation, alertness and mood. Twenty patients participated in the study (9 women, 11 men, mean age = 67.6 ± 7.5 y). Pupillometry was performed before the LE weeks and repeated on the last day of LE. The post-illumination pupil response (PIPR) was calculated as a proxy for melanopsin-dependent activation. Participants continuously wore an activity monitor and self-assessed sleep quality, well-being and visual comfort for 7 days before and during 4 weeks of daily bright LE (30 min to 10,000 lux polychromatic bright white light). After the LE, there was a significantly greater PIPR and higher subjective sleep quality when compared to the pre-LE week (p < 0.05), but no significant changes in 24-h rhythms or sleep parameters. A greater PIPR was correlated with an increase in circadian amplitude and higher inter-daily stability (derived from rest-activity cycles; p < 0.05). In a small group of patients with glaucoma, scheduled daily bright light exposure could improve subjective sleep quality. These findings highlight the importance to evaluate and maintain non-visual functions at different levels in patients with progressive loss of ipRGCs.
Immunosenescence in Testicular Cancer Survivors: Potential Implications of Cancer Therapies and Psychological Distress

Testicular cancer (TC) is the most frequent solid tumor diagnosed in young adult males. Although it is a curable tumor, it is frequently associated with considerable short-term and long-term morbidity. Both biological and psychological stress experienced during cancer therapy may be responsible for stimulating molecular processes that induce premature aging and deterioration of immune system (immunosenescence) in TC survivors, leading to an increased susceptibility to infections, cancer, and autoimmune diseases. Immunosenescence is a remodeling of immune cell populations with inversion of the CD4:CD8 ratio, accumulation of highly differentiated memory cells, shrinkage of telomeres, shift of T-cell response to Th2 type, and release of pro-inflammatory signals. TC survivors exposed to chemotherapy show features of immunological aging, including an increase in memory T-cells (CD4+ and CD8+) and high expression of the senescence biomarker p16INK4a in CD3+ lymphocytes. However, the plethora of factors involved in the premature aging of TC survivors make the situation more complex if we also take into account the psychological stress and hormonal changes experienced by patients, as well as the high-dose chemotherapy and hematopoietic stem cell transplantation that some individuals may be required to undergo. The relatively young age and the long life expectancy of TC patients bear witness to the importance of improving quality of life and of alleviating long-term side-effects of cancer treatments. Within this context, the present review takes an in-depth look at the molecular mechanisms of immunosenescence, describing experimental evidence of cancer survivor aging and highlighting the interconnected relationship between the many factors modulating the aging of the immune system of TC survivors.
Modification of Transfer RNA Levels Affects Cyclin Aggregation and the Correct Duplication of Yeast Cells

Codon usage bias (the preferential use of certain synonymous codons (optimal) over others is found at the organism level (intergenomic) within specific genomes (intragenomic) and even in certain genes. Whether it is the result of genetic drift due to GC/AT content and/or natural selection is a topic of intense debate. Preferential codons are mostly found in genes encoding highly-expressed proteins, while lowly-expressed proteins usually contain a high proportion of rare (lowly-represented) codons. While optimal codons are decoded by highly expressed tRNAs, rare codons are usually decoded by lowly-represented tRNAs. Whether rare codons play a role in controlling the expression of lowly- or temporarily-expressed proteins is an open question. In this work we approached this question using two strategies, either by replacing rare glycine codons with optimal counterparts in the gene that encodes the cell cycle protein Cdc13, or by overexpression the tRNAGly that decodes rare codons from the fission yeast, Schizosaccharomyces pombe. While the replacement of synonymous codons severely affected cell growth, increasing tRNA levels affected the aggregation status of Cdc13 and cell division. These lead us to think that rare codons in lowly-expressed cyclin proteins are crucial for cell division, and that the overexpression of tRNA that decodes rare codons affects the expression of proteins containing these rare codons. These codons may be the result of the natural selection of codons in genes that encode lowly-expressed proteins.
Livestock Mobility Through Integrated Beef Production-Scapes Supports Rangeland Livestock Production and Conservation

Much of the world's rangelands contribute to food production through extensive grazing systems. In these systems, livestock producers, pastoralists, and ranchers move grazing animals to access variable feed and water resources to create value while supporting numerous other ecosystem services. Loss of mobility due to political, social, ecological, and economic factors is documented throughout the world and poses a substantial risk to rangeland livestock production and conservation of rangeland resources. The integration of production-scapes can facilitate livestock mobility through transportation and trade. This paper describes the beef cattle production system in California, where transporting and marketing animals integrate an extensive grazing system with intensive production systems, including feeding operations. Analysis of livestock inspection data quantifies the magnitude of livestock movements in the state and the scope of production-system integration. Over 500,000 head−47 percent of the state's calf crop—leave California rangelands and are moved to new pastures or feedyards seasonally over a 12 week period each year. Most ranchers in California, from small-scale producers (1 to 50 head) to larger producers (more than 5,000), participate in the integrated beef production system. Less than 1% of steers and heifers go from rangeland to meat processing. Like pastoralists, ranchers strategically move cattle around (and off) rangeland to optimize production within a variable climate. Ranchers indicate that their movements result from changes in forage quality and quantity and support their desire to manage for conservation objectives, including reducing fire fuels, controlling weeds, and managing for wildlife habitat. Inspection data, as well as direct observation, interviews, and surveys within the San Francisco Bay area, reveal the extent to which the region's ranchers rely on saleyards to facilitate the movement of cattle and integration of production systems. Saleyards and cattle buyers drive beef production efficiency by sorting, pricing, and moving cattle and matching them to feed resources in more intensive production systems. However, transactions lack traceability to inform policy and consumer choice. New data technologies like blockchain can provide traceability through integrated production-scapes and facilitate market development to support grazing landscapes and consumer choice.
Links Between Testosterone, Oestrogen, and the Growth Hormone/Insulin-Like Growth Factor Axis and Resistance Exercise Muscle Adaptations

Maintenance of skeletal muscle mass throughout the life course is key for the regulation of health, with physical activity a critical component of this, in part, due to its influence upon key hormones such as testosterone, estrogen, growth hormone (GH), and insulin-like growth factor (IGF). Despite the importance of these hormones for the regulation of skeletal muscle mass in response to different types of exercise, their interaction with the processes controlling muscle mass remain unclear. This review presents evidence on the importance of these hormones in the regulation of skeletal muscle mass and their responses, and involvement in muscle adaptation to resistance exercise. Highlighting the key role testosterone plays as a primary anabolic hormone in muscle adaptation following exercise training, through its interaction with anabolic signaling pathways and other hormones via the androgen receptor (AR), this review also describes the potential importance of fluctuations in other hormones such as GH and IGF-1 in concert with dietary amino acid availability; and the role of estrogen, under the influence of the menstrual cycle and menopause, being especially important in adaptive exercise responses in women. Finally, the downstream mechanisms by which these hormones impact regulation of muscle protein turnover (synthesis and breakdown), and thus muscle mass are discussed. Advances in our understanding of hormones that impact protein turnover throughout life offers great relevance, not just for athletes, but also for the general and clinical populations alike.
Neuromesodermal Progenitors: A Basis for Robust Axial Patterning in Development and Evolution

During early development the vertebrate embryo elongates through a combination of tissue shape change, growth and progenitor cell expansion across multiple regions of the body axis. How these events are coordinated across the length of the embryo to generate a well-proportioned body axis is unknown. Understanding the multi-tissue interplay of morphogenesis, growth and cell fate specification is essential for us to gain a complete understanding how diverse body plans have evolved in a robust manner. Within the posterior region of the embryo, a population of bipotent neuromesodermal progenitors generate both spinal cord and paraxial mesoderm derivatives during the elongation of the vertebrate body. Here we summarize recent data comparing neuromesodermal lineage and their underlying gene-regulatory networks between species and through development. We find that the common characteristic underlying this population is a competence to generate posterior neural and paraxial mesoderm cells, with a conserved Wnt/FGF and Sox2/T/Tbx6 regulatory network. We propose the hypothesis that by maintaining a population of multi-germ layer competent progenitors at the posterior aspect of the embryo, a flexible pool of progenitors is maintained whose contribution to the elongating body axis varies as a consequence of the relative growth rates occurring within anterior and posterior regions of the body axis. We discuss how this capacity for variation in the proportions and rates of NM specification might have been important allowing for alterations in the timing of embryo growth during evolution.
Visible light induced photocatalytic degradation of some xanthene dyes using immobilized anthracene

Photocatalytic degradation of eosin and erythrosin-B (xanthene dyes) has been carried out using anthracene semiconductor immobilized on polyethylene films. Effect of various parameters like pH, concentration of dyes, amount of semiconductor and light intensity have been studied on the rate of reaction. Various control experiments were carried out which indicated that semiconductor anthracene played a key role in photocatalytic degradation of dyes. A suitable tentative mechanism has been proposed for photocatalytic degradation of dyes. KEY WORDS: Photocatalytic, Degradation, Xanthene dyes, Immobilized anthracene Bull. Chem. Soc. Ethiop. 2008 , 22(3), 361-368.