Miracle-dz/UniFAR-FTUs huggingface dataset:
Visualizing the periodic Ribo-seq reads with RiboPlotR

Background Ribo-seq has revolutionized the study of mRNA translation in a genome-wide scale. High-quality Ribo-seq data display strong 3-nucleotide (nt) periodicity, which corresponds to translating ribosomes decipher three nucleotides each time. While the 3-nt periodicity has been widely used to study novel translation events and identify small open reading frames on presumed non-coding RNAs, tools which allow the visualization of those events remain underdeveloped. Findings RiboPlotR is a visualization package written in R that presents both RNA-seq coverage and Ribo-seq reads for all annotated transcript isoforms in a context of a given gene. In particular, RiboPlotR plots Ribo-seq reads mapped in three reading frames using three colors for one isoform model at a time. Moreover, RiboPlotR shows Ribo-seq reads on upstream ORFs, 5’ and 3’ untranslated regions and introns, which is critical for observing new translation events and potential regulatory mechanisms. Conclusions RiboPlotR is freely available (https://github.com/hsinyenwu/RiboPlotR) and allows the visualization of the translating features in Ribo-seq data.
DNA base excision repair genes variants rs25487 (X-ray repair cross-complementing 1) and rs1052133 (human 8-oxoguanine glycosylase 1) with susceptibility to ovarian cancer in the population of the Jammu region, India

Background: Ovarian cancer is highly prevalent in the population of Jammu, in India; the ovarian cancer ranks third among other types of cancer prevalent in females. However, association studies on ovarian cancer are lacking in this region. We aimed to investigate the disease susceptible variants rs1052133 (human 8-oxoguanine glycosylase 1 [hOGG1]) and rs25487 (X-ray repair cross-complementing 1 [XRCC1]) with ovarian cancer in population of Jammu, India. Materials and Methods: The study conducted in the Shri Mata Vaishno Devi University is a 3-year study which included a total of 280 well-characterized samples (130 ovarian cancer cases and 150 healthy controls). hOGG1 and XRCC1 polymorphisms were determined by polymerase chain reaction-based restriction fragment length polymorphism, and these genotyping results were confirmed by Sanger sequencing. Hardy–Weinberg equilibrium for both single-nucleotide polymorphisms (SNPs) was assessed using the Chi-square test. The allele and genotype-specific risks were estimated by odds ratios with 95% confidence intervals. Results: In this preliminary study, SNP rs1052133 showed protection with ovarian cancer (P = 0.042). The SNP rs25487 was not found associated with ovarian cancer (P = 0.271). Conclusion: Our results indicate that the G allele of rs1052133 imparts protection to the population whereas variant rs25487 was not associated with ovarian cancer in population from the Jammu region, indicating that larger sample size is needed for further statistical validation. Further, association of other SNPs in these genes should also be carried out as their role cannot be ruled out.
Prospects for Durable Resistance Against an Old Soybean Enemy: A Four-Decade Journey from Rpp1 (Resistance to Phakopsora pachyrhizi) to Rpp7

Soybean rust (SBR), caused by Phakopsora spp. , is a major global concern for soybean producers. SBR causing fungi are polycyclic and obligate biotrophs, rendering the study of their biology particularly tedious. Over the past four decades, substantial progress has been made towards understanding the epidemiology of the disease, the identification of sources of resistance, and the mapping of soybean loci conferring resistance to P. pachyrhizi (Rpp genes), since this species is particularly well established and widespread in many soybean growing areas. Although host-plant resistance is generally considered as the most desirable solution from an environmental, economic, and social perspective, other disease control approaches such as agronomic practices and chemical application are also important, and influence rust epidemiology as well as the durability of host plant resistance. This review focusses primarily on genetic aspects of SBR management and summarizes the research in the following areas: SBR symptoms, aetiology, pathogenic variation and population structure of Phakopsora populations, expression of soybean resistance to Phakopsora infection, genetics and molecular diagnostics of host resistance to pathogen, and resistance gene deployment approaches. Finally, the role of multidisciplinary strategies is discussed for achieving higher durability of SBR resistance in soybean.
Oncoprotein GT198 Vaccination Delays Tumor Growth in MMTV-PyMT Mice

Different effects of anticancer drugs between mouse and human have caused increasing concerns. A better understanding of cancer initiation between the two species is needed. We have previously identified an oncoprotein GT198 (PSMC3IP) in human breast cancer. In this report, we investigated GT198 in MMTV-PyMT mouse mammary gland tumors and found a reconcilable mechanism in human and mouse. Specifically, distinct tumor initiating stimuli in human and mouse result in a common GT198-mediated tumorigenic pathway in both species. Here we show, similar to human breast cancer even before a tumor appears, GT198 has overexpressed in mouse tumor stroma including pericyte stem cells, descendent adipocytes, fibroblasts, and myoepithelial cells. Using recombinant GT198 protein as an antigen, we vaccinated MMTV-PyMT mice and found that the GT198 vaccine delayed mouse tumor growth and reduced lung metastasis. The antitumor effects in vaccinated mice were linearly correlated with serum titers of GT198 antibody, which can recognize cell surface GT198 protein on viable tumor cells confirmed by FACS. Furthermore, tumor cells isolated from MMTV-PyMT mice were re-implanted into normal FVB/N mice, GT198+ tumor cells induced faster tumor growths than GT198- tumor cells. Together, this first study of GT198 vaccine in mouse showed its effectiveness in antitumor and anti-metastasis. The finding may accelerate future development of GT198 immunotherapy in human cancer. Our finding also indicates that even though distinct cancer-initiation stimuli exist between mouse and human, a common tumorigenic pathway mediated by oncoprotein GT198 is shared in both species.
Statistical Analysis about Zero-failure Data of Electronic Products

The situation of zero-failure data may occur in the reliability life test of an electronic product when it has a high quality or the test time and fund are limited. In this case,when the prior distribution is Gamma distribution,the hierarchical Bayesian estimation for the failure rate is perfermed after introducing the failure information and calculation is carried out regarding to the practical problem.
Recent insight and future techniques to enhance rumen fermentation in dairy goats

Recent development of novel techniques in systems biology have been used to improve and manipulate the rumen microbial ecosystem and gain a deeper understanding of its physiological and microbiological interactions and relationships. This provided a deeper insight and understanding of the relationship and interactions between the rumen microbiome and the host animal. New high-throughput techniques have revealed that the dominance of Proteobacteria in the neonatal gut might be derived from the maternal placenta through fetal swallowing of amniotic fluid in utero, which gradually decreases in the reticulum, omasum, and abomasum with increasing age after birth. Multi “omics” technologies have also enhanced rumen fermentation and production efficiency of dairy goats using dietary interventions through greater knowledge of the links between nutrition, metabolism, and the rumen microbiome and their effect in the environment. For example, supplementation of dietary lipid, such as linseed, affects rumen fermentation by favoring the accumulation of α-linolenic acid biohydrogenation with a high correlation to the relative abundance of Fibrobacteriaceae. This provides greater resolution of the interlinkages among nutritional strategies, rumen microbes, and metabolism of the host animal that can set the foundation for new advancements in ruminant nutrition using multi ‘omics’ technologies.
Genome Constitution of the Dryopteris atrata Complex (Dryopteridaceae)

Summary We analyzed molecular phylogenetically using two low-copy nuclear markers ( AK1 and Esterase ) and plastid ndhF DNA sequence in the Dryopteris atrata complex. According to nuclear allele constitution and plastid ndhF sequence, apogamous species of the D. atrata complex seemed to be of hybrid origin. The genome constitution of the D. atrata complex showed that apogamous fern species which produce regularly shaped spores can maintain genome constitution if it is of hybrid origin between apogamous species and sexual species. Otherwise, sterile hybrids will be going to hybrid collapse because they cannot prevent genetic segregation.
Understanding informal caregiver needs for coordinating care to support aging in place

In this poster, we present findings from a study focused on understanding the needs of informal family caregivers and gathering stakeholder perspectives on early concepts for an application designed to help family members coordinate the day-to-day care of their loved ones. The results of our formative study point to the need for solutions that can not only enhance the collaborative nature of caregiving but also support the family as the care recipient's journey and/or needs change.
Trial by phylogenetics - Evaluating the Multi-Species Coalescent for phylogenetic inference on taxa with high levels of paralogy (Gonyaulacales, Dinophyceae)

From publicly available next-gen sequencing datasets of non-model organisms, such as marine protists, arise opportunities to explore their evolutionary relationships. In this study we explored the effects that dataset and model selection have on the phylogenetic inference of the Gonyaulacales, single celled marine algae of the phylum Dinoflagellata with genomes that show extensive paralogy. We developed a method for identifying and extracting single copy genes from RNA-seq libraries and compared phylogenies inferred from these single copy genes with those inferred from commonly used genetic markers and phylogenetic methods. Comparison of two datasets and three different phylogenetic models showed that exclusive use of ribosomal DNA sequences, maximum likelihood and gene concatenation showed very different results to that obtained with the multi-species coalescent. The multi-species coalescent has recently been recognized as being robust to the inclusion of paralogs, including hidden paralogs present in single copy gene sets (pseudoorthologs). Comparisons of model fit strongly favored the multi-species coalescent for these data, over a concatenated alignment (single tree) model. Our findings suggest that the multi-species coalescent (inferred either via Maximum Likelihood or Bayesian Inference) should be considered for future phylogenetic studies of organisms where accurate selection of orthologs is difficult.
GROWTH AND PHYSIOLOGICAL RESPONSE OF COFFEE SEEDLINGS TREATED WITH FUNGICIDES

Research has shown that, in addition to the fungicidal action already known, strobilurins have positive physiological effects on the yield of some crops. Boscalid has also shown positive effects on plants, applied together or associated with strobilurin. The objective in this study was to evaluate the effect of fungicide application on growth and physiological behavior of coffee seedlings. The experimental design was in randomized blocks, with five replicates. There were five treatments: T1-Control, T2-Boscalid, T3-Pyraclostrobin, T4- Boscalid+ Pyraclostrobin and T5- Azoxystrobin applied in coffee seedlings. The application was at the “orelha de onça” stage (two round-shaped leaves), repeated every 15 days, counting 5 applications in total. Were evaluated shoot length, root length, stem diameter, shoot and root fresh matter, shoot and root dry matter, leaf photosynthesis, stomatal conductance, transpiration, intercellular CO2 concentration, water use efficiency and carboxylation efficiency. The application of fungicides promotes greater vegetative growth of coffee seedlings due to increased CO2 assimilation rate, reduced transpiration rates and increased water use efficiency, associated to the increased levels of auxin and cytokinins in leaves
Epichloë (formerly Neotyphodium) fungal endophytes increase adaptation of cool-season perennial grasses to environmental stresses

Many cool-season grass species have evolved with asexual, nonsymptomatic fungal endophytes of the genus Epichloë (formerly Neotyphodium) of the family Clavicipitaceae. These associations range from parasitic to mutualistic and have dramatic effects on grass host chemistry, increasing resistance to abiotic (drought, soil mineral imbalance) and biotic (vertebrate and invertebrate herbivory, nematodes, plant pathogens, plant competition) stresses. Native endophyte strains produce a range of bioprotective alkaloid and other nonalkaloid secondary compounds, several of them known to have detrimental effects on grazing animals. In the past two decades, epichloid endophyte strains have been selected with marginal or no capacity of producing ergot and/or lolitrem alkaloids. These novel endophyte strains have been introduced to several grass cultivars with the idea to increase grass host resistance to abiotic stresses without hindering grazing livestock, and abiotic stresses to ensure high competitive ability of symbiotic grass cultivars. In this presentation, we discuss mechanisms underlying the competitiveness of epichloid endophyte/grass associations and consequences of endophyte infection for grassland ecosystem functions.
Dietary supplementation of Phoenix dactylifera L. seeds decreases pro-inflammatory mediators in CCl4-induced rats

Introduction: Low immunity causes the body to become more easily infected, resulting in inflammation. If the immune system is functioning properly, this inflammation will end in healing. The immune system has a protective role in the body, and its anti-inflammatory role is vital. During trauma, the initial immune response is marked by inflammation. The use of date-seed extract, although not steeped date seeds, has been studied as an anti-inflammatory agent. This study is aimed at demonstrating the anti-inflammatory effect of steeped date seeds (Phoenix dactylifera L.) in rats with CCl4-induced inflammation.Methods: This experiment included a pre- and post-test with control group design. Male Wistar rats (approximately 2–3 months of age, ranging in weight from 150 to 200 g) were assigned to the following groups: negative control (NC), positive control (PC), T1 treatment dose 1 g/kg, T3 treatment dose 3 g/kg, T5 treatment dose 5 g/kg, and healthy control (HC). Groups 1–5 were subjected to CCl4 induction at a single dose of 2 mL/kg before treatment. The levels of tumor necrosis factor (TNF-α), glutathione (GSH), and gamma interferon (IFN-γ) were compared in groups using one-way analysis of variance (ANOVA), followed by a least significant difference (LSD) post hoc test for comparisons between means.Results: Levels of tumor necrosis factor (TNF-α), GSH, and IFN-γ were significantly different among the HC and treatment groups after CCl4 induction. After 14 days of steeped date-seed treatment, TNF-α decreased, but GSH and IFN-γ levels increased significantly (P = 0.001). Conclusion: Administration of steeped date seeds at a dose of 5 g/kg can increase GSH and IFN-γ, and decrease TNF-α, the strongest inflammatory marker in CCl4-induced rats. The findings of this study indicate that date-seed supplementation can support body immunity by regulating pro-inflammatory mediators.
Key-Aggregate Cryptosystem based on Elliptic Curve Cryptography for Data Sharing in Cloud Storage

It is important to share data securely, efficiently and flexibly in cloud storage. We describe public-key encryption technique based on elliptic-curve theory which is used to create faster, smaller and more efficient cryptographic keys. This publickey cryptosystem produces constant size cipher texts and user can aggregate any set of secret keys and make them as compact as single and can decrypt any set of cipher texts by using that compact aggregate key but, files outside the set remain confidential. In this cryptosystem it is possible to efficiently assign decryption rights for the set of cipher texts to any users. The secret key holder can release a constant-size aggregate key for set of cipher texts and this compact aggregate key conveniently shared with others with very limited secure storage. In this paper, we study how to create a decryption key more powerful so that it can allows decryption of multiple cipher texts, without increasing key size.
Silencing PHOSPHOENOLPYRUVATE CARBOXYLASE1 in the Obligate Crassulacean Acid Metabolism Species Kalanchoë laxiflora causes Reversion to C3-like Metabolism and Amplifies Rhythmicity in a Subset of Core Circadian Clock Genes

Unlike C3 plants, Crassulacean acid metabolism (CAM) plants fix CO2 in the dark using phosphoenolpyruvate carboxylase (PPC; EC 4.1.1.31). PPC combines PEP with CO2 (as HCO3−), forming oxaloacetate that is rapidly converted to malate, leading to vacuolar malic acid accumulation that peaks phased to dawn. In the light period, malate decarboxylation concentrates CO2 around RuBisCO for secondary fixation. CAM mutants lacking PPC have not been described. Here, RNAi was employed to silence CAM isogene PPC1 in Kalanchoë laxiflora. Line rPPC1-B lacked PPC1 transcripts, PPC activity, dark period CO2 fixation, and nocturnal malate accumulation. Light period stomatal closure was also perturbed, and the plants displayed reduced but detectable dark period stomatal conductance, and arrhythmia of the CAM CO2 fixation circadian rhythm under constant light and temperature (LL) free-running conditions. By contrast, the rhythm of delayed fluorescence was enhanced in plants lacking PPC1. Furthermore, a subset of gene transcripts within the central circadian oscillator were up-regulated and oscillated robustly. The regulation guard cell genes involved controlling stomatal movements was also altered in rPPC1-B. This provided direct evidence that altered regulatory patterns of key guard cell signaling genes are linked with the characteristic inverse pattern of stomatal opening and closing during CAM.
A Single-Cell Immune Atlas of Triple Negative Breast Cancer Reveals Novel Immune Cell Subsets

Triple-negative breast cancer (TNBC) represents the most aggressive breast cancer subtype, which recently attracts great interest for immune therapeutic development. In this context, in-depth understanding of TNBC immune landscape is highly demanded. Here we report single-cell RNA sequencing results of 9683 tumor-infiltrated immune cells isolated from 14 treatment naïve TNBC tumors, where 22 immune cell subsets, including T cells, macrophages, B cells, and DCs have been characterized. We identify a new T cell subset, CD8+CXCL8+ naïve T cell, which associates with poor survival. A novel immune cell subset comprised of TCR+ macrophages, is found to be widely distributed in TNBC tumors. Further analyses reveal an up-regulation of molecules associated with TCR signaling and cytotoxicity in these immune cells, indicating TCR signaling activation. Altogether, our study provides a valuable resource to understand the immune ecosystem of TNBC. The novel immune cell subsets reported herein might be functionally important in cancer immunity. SIGNIFICANCE This work demonstrates a single-cell transcriptome atlas of immune cells in treatment naïve TNBC tumors, revealing novel immune cell subsets. This study provides a valuable resource to understand the immune ecosystem of TNBC, which will be helpful for the immunotherapeutic strategy design of TNBC.
Preparation, Characterization and Antibacterial Effect of Chitosan Nanoparticles against Food Spoilage Bacteria

Fresh cut fruits and vegetables spoiled by number of bacterial pathogens. In this experiment the low cost, nontoxic and pollution free chitosan nanoparticles were prepared in the laboratory level, characterized by FTIR, XRD and SEM and confirmed the presence of nanoparticles. Various concentrations of nanoparticles (10μg, 20μg, 50μg, 100μg and 150μg) were prepared and used to investigated the antibacterial activity against one positive (Bacillus sp) and one negative bacteria (pseudomonas sp) respectively. The results showed that zone of inhibition against Bacillus sp and Pseudomonas sp were noted at 50μg, 100μg and 150μg concentrations respectively. These results suggested that chitosan nanoparticles can be used as effective growth inhibitors for food spoilage microorganisms. It is confirmed that this pollution free low cost technology is suitable for arresting food spoilage bacteria effectively. Hence, the present study indicated that the non-toxic chitosan nanoparticles may be considered as a food preservative. Hence this preliminary study which will create further research in this new field.
Neuronal Responses in Posterior Parietal Cortex during Learning of Implied Serial Order

Monkeys are able to learn the implied ordering of pairs of images drawn from an ordered set, without ever seeing all of the images simultaneously, and without explicit spatial or temporal cues. Learning is evidenced by their ability to make transitive inferences (TI), which are judgments of serial order based on the transitive relation that A>B and B>C implies A>C. Because posterior parietal cortex has been shown to integrate spatial and numerical information, we recorded the activity of parietal neurons in rhesus macaques while they learned 5- and 7-item TI lists. Symbolic distance (but not ordinal position) strongly predicted decision accuracy, and learning was consistently faster as symbolic distance increased. Neurons exhibited selectivity for stimulus identity during learning, but not before or after. Furthermore, across the population of neurons, there was significant modulation of firing correlated with the relative rank of the two stimuli presented on each trial. The observed behavior during learning is best explained by a virtual workspace model, not by associative or reward mechanisms. The neural data support a role for posterior parietal cortex in representing several variables that contribute to serial learning, particularly information about the ordinal ranks of both stimuli presented during a given trial. Thus, parietal cortex can be considered as part of the neural substrate for learning and representing abstract relationships in a virtual workspace.
tACS entrains neural activity while somatosensory input is blocked

Recent results suggest that transcranial alternating current stimulation (tACS) can non-invasively change humans’ mental states, but the neural mechanisms behind these exciting results remain poorly understood. Although tACS is traditionally thought to produce electrical fields that directly affect neurons in the targeted area, much of the current never reaches the brain, and flows through the skin instead. Since the skin is packed with somatosensory afferents, this shunted current can produce tactile percepts that affect subjects’ behavior, even if the targeted brain area is otherwise unaffected. These sensations are widely recognized as a potential confound in tACS experiments, but a recent Nature Communications article by Asamoah, et al. 1 argues that somatosensory input is the principal mechanism underlying the neural effects of tACS. Here, we directly test that hypothesis with neural recordings from non-human primates. We find that tACS entrains hippocampal neurons even when somatosensation is blocked or strongly suppressed, suggesting that peripheral input is not required for tACS to affect the brain.