Miracle-dz/UniFAR-FTUs huggingface dataset:
Gene expression deconvolution and co-expression methods

Gene expression analysis provides the link between genome information and phenotype, and is widely used in biomedical research. With the rapid advance of high-throughput technology, it is feasible to measure global mRNA expression in multiple samples at low cost. Over the past decade, many computational and statistical methods have been developed to interpret large-scale gene expression data. However, two questions still have not been thoroughly investigated: 1) how to study gene expression preservation across different tissues, like between brain and blood; and 2) how to analyze the gene expression data generated from heterogeneous tissues comprised of many cell types? Blood samples are an important surrogate to study neurological diseases due to the limited access of brain samples. My dissertation first investigated the gene expression preservation between brain and blood by cross-referencing three brain expression data sets (from cortex, cerebellum and caudate nucleus) with two large blood data sets. While previous studies have focused on the preservation of individual gene expression levels across the two tissues, I utilized a systems biology approach to study the preservation of gene co-expression modules. Since oligodendrocytes, astrocytes, and neurons are not present in blood, it is not surprised that only a handful of human brain modules showed evidence of preservation in human blood while global transcriptome organization is poorly preserved. These shared relationships characterized here may aid future efforts to identify blood biomarkers for neurological and neuropsychiatric diseases when brain tissue samples are unavailable. For the second question, several previous publications have proposed gene expression deconvolution methods, including estimating cell abundances or cell type-specific gene expression (CTSE) values, for admixed samples comprised of distinct cell types. These methods have not yet been widely adopted since comprehensive empirical evaluations are needed to assess their reliability. Here I evaluated different types of expression deconvolution methods in four empirical data sets, including a neuro-scientific application. Since cell type-specific estimation of the mean value for individual genes is sometimes problematic, we propose to consider sets of genes (as opposed to individual genes) and show that this can increase the accuracy of CTSE estimation. Furthermore, comprehensive simulation studies are used to evaluate the effect of mis-specifying cell types. Our simulations indicated that erroneously omitting cell types from the analysis only has an adverse effect on CTSE estimation if the omitted cell type has a high abundance. We also present two R functions, proportionsInAdmixture and populationMeansInAdmixture, which implement cell abundance estimation and CTSE estimation, respectively.
Putative Histone H2A Genes from a Red Alga, Griffithsia japonica

Histones are important proteins that interact with the DNA double helix to form nucleosome. Two putative histone genes, GjH2A-1 and GjH2A-2 were isolated from a red alga Griffithsia japonica. The putative open reading frame of GjH2A-1 and GjH2A-2 shared high similarity with the previously reported amino acid sequences of histone H2As. They have a motif consisting of seven amino acids A-G-L-Q-F-P-V, which matches the histone H2A motif [AC]-G-L-x-F-P-V. Phylogenetic trees were constructed from amino acid sequences of 38 histone H2As. The histone H2As were divided into two groups: major H2As and H2A.F/Z variants. The major histone H2A group consisted of animals, fungi, plants + green algae, and red algae H2A subgroups. The animal histone H2A subgroup was divided into vertebrates, echinoderms, nematodes, insects, and segmented worms H2As. The putative red algal histone genes, GjH2A-1 and GjH2A-2, constituted an independent lineage. This is the first report on red algal histone genes.
Critical role of interleukin-17 receptor signaling in the immunopathology of influenza infection

Interleukin-17 (IL-17) is a cytokine produced mainly by T cell lineages that plays a keyrole in regulation of neutrophil responses. Given the importance of neutrophils in the immune response directed against extracellular pathogens, it is no surprise that IL-17 is important in host defense against a multitude of pathogens. Importantly, however, neutrophils also have been shown to play a role in several immunopathological conditions, including acute lung injury. In this dissertation, we evaluate the role that IL-17 plays in the immunopathology of influenza infection. We show here that IL-17 is produced as early as day 2 following influenza challenge, and that this expression is sustained throughout the first week of infection. Further, we identify γδ T cells as at least one important source of IL-17 in response to influenza. We also demonstrate that loss of IL-17 receptor A (IL-17RA) signaling results in a profound decrease in neutrophil recruitment to the lung following influenza challenge. This decrease in neutrophils results in substantially less inflammation and lung injury, as well as higher survival rates. Additionally, there is only a moderate impact on viral clearance and T cell responses. Further, we detail similar findings in a non-infectious aspiration model of acute lung injury. Taken together, this data suggests that IL-17 signaling may be a key event, and intriguing therapeutic target, in the pathogenesis of acute lung injury.
Analisis Postur Kerja Menggunakan Metode PLIBEL Checklist dan Quick Exposure Check (QEC) Pada Perajin Batik Cap (Studi Kasus: UKM Batik Cap Supriyarso)

This research was conducted on batik-making workers in UKM Batik Cap Supriyarso Kampoeng Batik Laweyan Surakarta. The process of batik and production in the batik industry is still done manually with a posture that is not ergonomic with repetitive movements that can cause musculoskeletal Disorders. Based on these problems, this study aims to determine the factors and the risk of skeletal muscle injury in batik stamp workers. This research uses PLIBEL checklist method and QEC method (Quick Exposure Check). The results showed that the calculations performed by PLIBEL Checklist revealed that the elbow, forearm and hands experienced the biggest musculoskeletal complaints that occurred in the process of pelorotan activity and poured the color blend with the value of 82% so that the work posture in both activities need to be repaired. While the calculation of of QEC using the score sheet states that the back and neck are at very high level that is on the process activity of pengecapan and the prosess pelorotan is in the range ≥70% so it needs to do research and change as soon. Comparison of both methods shows that on the activity of the process of pelorotan is a high-risk activity causing muscle injury or musculoskeletal disorders so that it needs to be made changes in posture work as soon. The results of the proposed improvement is expected to minimize the risk of muscle injury, especially skeletal muscle so that it can improve the work quality of the workers.
Sequence of Aβ‐Protein Deposition in the Human Medial Temporal Lobe

The deposition of Aβ-protein (Aβ) and the development of neurofibrillary changes are important histopathological hallmarks of Alzheimer disease (AD). In this study, the medial temporal lobe serves as a model for the changes in the anatomical distribution pattern of different types of Aβ-deposits occurring in the course of AD, as well as for the relationship between the development of Aβ-deposition and that of neurofibrillary pathology. In the first of 4 phases of β-amyloidosis, diffuse non-neuritic plaques are deposited in the basal temporal neocortex. The same plaque type appears in the second phase within the external entorhinal layers pre-β and pre-γ, and fleecy amyloid deposits occur in the internal entorhinal layers pri-α, pri-β, pri-γ, and in CA1. In the third phase, Aβ-deposits emerge in the molecular layer of the fascia dentata, and band-like Aβ-deposits occur in the subpial portion of the molecular layer of both the entorhinal region and the temporal neocortex. In addition, confluent lake-like Aβ-deposits appear in the parvopyramidal layer of the presubicular region. The fourth phase is characterized by diffuse and core-only plaques in CA4. Diffuse plaques evolve sporadically in the external entorhinal layer pre-α. Parallel to the evolution of β-amyloidosis as represented by the 4 phases, neuritic plaques gradually make their appearance in the temporal neocortex, entorhinal region, CA1, the molecular layer of the fascia dentata, and CA4. A prerequisite for their development is the presence of Aβ and the presence of neurofibrillary tangles in neurons targeting the regions where neuritic plaques evolve. Each of the different types of Aβ-deposits, including neuritic plaques, plays a specific role in the distinct developmental sequence as represented by the 4 phases so that the medial temporal lobe inexorably becomes involved to an ever greater extent. The step-for-step involvement of connected anatomical subfields highlights the importance of the entorhino-hippocampal pathways for the expansion of β-amyloidosis. The 4 phases in the evolution of β-amyloidosis correlate significantly with the stages of the neurofibrillary pathology proposed by Braak and Braak.
Floral Morphology in Relation to Pollination Ecology in Five Queensland Coastal Plants

Observations of pollination by birds in Acanthus ilicifolius and Lysiana subfalcata var. maritima, hawkmoths in Clerodendrum inerme and Sonneratia alba,, and bees in Sesuvium portulacastrum, are presented along with detailed descriptions of floral morphology and pollination efficiency using pollen/ovule ratios. Self fertilisation is restricted in Sesuvium, Acanthus and Clerodendrum by protandry, while the flowers of Lysiana, Sonneratia and Acanthus are morphologically incapable of automatic self-pollination. The high fruit set seen in flowers of these species suggests that these species are self-compatible. Self-compatibility in mangrove and mangrove-associated species will presumably allow some fruit set even in isolated, single plants after new habitat is colonised.
Época de suspender as irrigações da cultura do trigo

O objetivo deste estudo foi avaliar o efeito do corte do suprimento de agua ao trigo (cv. BR- 12 Aruana) aos 69, 77, 85, 95, 102 e 115 dias apos o plantio, o que corresponde aos estadios de desenvolvimento de inicio da antese, cariopse aquosa, estado leitoso, estado de massa mole, estado de massa dura e cariopse dura, respectivamente, sobre o rendimento e seus componentes, e a qualidade dos graos. Todas as parcelas experimentais foram irrigadas sempre que a tensao de agua no solo, medida a 10 cm de profundidade, atingia valores de 48 kPa, ate o estadio de desenvolvimento, em que houve a suspensao das irrigacoes de cada tratamento. Verificou-se uma reducao significativa do rendimento de graos nos tratamentos em que as irrigacoes foram suspensas antes que os graos estivessem em estado de massa dura. Essa reducao do rendimento foi causada pela reducao do peso de 1.000 graos e do peso por hectolitro. A suspensao das irrigacoes na fase de graos em massa dura causou uma economia de 99 mm de agua em relacao ao tratamento irrigado ate a fase de cariopse dura. A fase de graos em estado de massa dura pode ser definida como aquela em que a maioria dos graos cedem a pressao da unha, sem, contudo, romper-se.
Development of Lentiviral Vectors Expressing siRNA

This chapter describes the use of lentiviral vectors to deliver small interfering RNA (siRNA)-mediated silencing cassettes. The combination of these two technologies allows for the development of a powerful tool to achieve long-term down-regulation of specific target genes both in vitro and in vivo. It combines the specificity of RNA interference with the versatility of lentiviral vectors to stably transduce a wide range of cell types.
Health-related Quality of Life and Muscle Functions among Pre-frail Elderly Outpatients: Stronger Correlation with Gait Speed than Handgrip Strength

Introduction: Frail elderly has an increased risk of having debilitating health outcomes that lead to poor health-related quality of life (HR-QoL). The central manifestation of frailty syndrome is the muscle functions. The aim of this study was to evaluate the correlation between muscle functions and HR-QoL among pre-frail elderly outpatients. Methods: This was a cross-sectional study using secondary data from a previous double blind RCT that investigated the effect of metformin on frailty syndrome among pre-frail elderly outpatients aged ≥ 60 years based on Cardiovascular Health Study and/or Frailty Index 40 items, recruited from March 2015 to June 2016 at Cipto Mangunkusumo Hospital. Muscle function was evaluated based on handgrip strength measured using hydraulic hand dynamometer and usual gait speed based on 15-feet walking test. HR-QoL was evaluated using Euro Quality of Life-5 Dimensions (EQ-5D) questionnaire. Spearman correlation test was used to analyze the correlation between HR-QoL and muscle function. Results: EQ-5D index score had significant moderate positive correlation with gait speed (r = 0.566; p < 0.05) and significant weak positive correlation with handgrip strength (r = 0.355; p < 0.05). Conclusion: The HR-QoL among pre-frail elderly outpatients had stronger correlation with gait speed than with handgrip strength.
User's guide for CodonRates 1.0

What is CodonRates ? CodonRates is a program to estimate divergence times and ‘absolute rates’ of synonymous and nonsynonymous substitution with protein-coding genes. The conventional programs, such as PAML (Yang 1997), HYPHY (Kosakovsky Pond and Muse 2000), are available for the estimation of the ‘amounts’ of nonsynonymous and synonymous substitution and their ratio. The evolutionary amount is confounded with time and rate, and CodonRates is designed to separate the evolutionary amount into time and synonymous and nonsynonymous rates under Bayesian framework without relying on molecular clock. Other information than sequence data, such as fossil constraints and prior distribution for the root time, are required. For the application of CodonRates, see Seo et al. (2004). For the more general things about Bayesian estimation of divergence times, see Thorne et al. (1998), Kishino et al. (2001) and Thorne and Kishino (2002). How to get and how to compile CodonRates You can get CodonRates from Tae-Kun Seo upon email request (seo@iu.a.u-tokyo.ac.jp). The web page for this program is being constructed. For Windows users, CodonRates software package includes an executable file (codonrates.exe), source files and a project file for Microsoft’s Visual Studio 6.0. For unix
Biogeographical Evidence for the Iberian Origins of R1b-L278 via Haplotype Aggregation

The status on the roots of haplogroup R1b remains split between an Iberian origin prior to the Last Glacial Maximum (LGM) and a West Asian origin coinciding with the Neolithic expansion. Existing methods generalize geographic patterns based on large population genetic frequency and diversity. Haplotype Aggregation delivers a coherent genetic record selection and Biogeographical Multilateration (BGM) illustrates directional flow as well as chronological and physical origins at the haplogroup level. The resulting phylogenetic relationships across multiple high level branches of R1b support an Iberian origin and a rapid Western Atlantic migration.
Parasitic Nematodes of Freshwater Fishes of Europe

Preface. Introduction. Methods of Study of Fish Nematodes. Morphology and Taxonomy of Fish Nematodes. Bionomy of Fish Nematodes. Pathogenicity of Nematodes Parasitizing Freshwater Fishes. Systematic Review of the Nematodes Parasitizing European Freshwater Fishes: Adult Nematodes Nematodes Parasitic in Fishes as Larvae. Host-Nematode Parasite List. References. Index.
Statistical genetic analysis of infectious disease (malaria) phenotypes from a longitudinal study in a population with significant familial relationships

Long term longitudinal surveys have the advantage to enable several sampling of the studied phenomena and then, with the repeated measures obtained, find a confirmed tendency. However, these long term surveys generate large epidemiological datasets including more sources of noise than normal datasets (e.g. one single measure per observation unit) and potential correlation in the measured values. Here, we studied data from a long-term epidemiological and genetic survey of malaria disease in two family-based cohorts in Senegal, followed for 19 years (1990–2008) in Dielmo and for 16 years (1993–2008) in Ndiop. The main objectives of this work were to take into account familial relationships, repeated measures as well as effect of covariates to measure both environmental and host genetic (heritability) impacts on the outcome of infection with the malaria parasite Plasmodium falciparum, and then use findings from such analyses for linkage and association studies. The outcome of interest was the occurrence of a P. falciparum malaria attack during each trimester (PFA). The two villages were studied independently; epidemiological analyses, estimation of heritability and individual effects were then performed in each village separately. Linkage and association analyses used family-based methods (based on the original Transmission Disequilibrium Test) known to be immune from population stratification problems. Then to increase sample size for linkage and association analyses, data from the two villages were used together.
Latent variable models in statistical genetics

Understanding the complexities that are involved in the genetics of multifactorial diseases is still a monumental task. In addition to environmental factors that can influence the risk of disease, there is also a number of other complicating factors. Genetic variants associated with age of disease onset may be different from those variants associated with overall risk of disease, and variants may be located in positions that are not consistent with the traditional protein coding genetic paradigm. Latent Variable Models are well suited for the analysis of genetic data. A latent variable is one that we do not directly observe, but which is believed to exist or is included for computational or analytic convenience in a model. This thesis presents a mixture of methodological developments utilising latent variables, and results from case studies in genetic epidemiology and comparative genomics. Epidemiological studies have identified a number of environmental risk factors for appendicitis, but the disease aetiology of this oft thought useless vestige remains largely a mystery. The effects of smoking on other gastrointestinal disorders are well documented, and in light of this, the thesis investigates the association between smoking and appendicitis through the use of latent variables. By utilising data from a large Australian twin study questionnaire as both cohort and case-control, evidence is found for the association between tobacco smoking and appendicitis. Twin and family studies have also found evidence for the role of heredity in the risk of appendicitis. Results from previous studies are extended here to estimate the heritability of age-at-onset and account for the eect of smoking. This thesis presents a novel approach for performing a genome-wide variance components linkage analysis on transformed residuals from a Cox regression. This method finds evidence for a dierent subset of genes responsible for variation in age at onset than those associated with overall risk of appendicitis. Motivated by increasing evidence of functional activity in regions of the genome once thought of as evolutionary graveyards, this thesis develops a generalisation to the Bayesian multiple changepoint model on aligned DNA sequences for more than two species. This sensitive technique is applied to evaluating the distributions of evolutionary rates, with the finding that they are much more complex than previously apparent. We show strong evidence for at least 9 well-resolved evolutionary rate classes in an alignment of four Drosophila species and at least 7 classes in an alignment of four mammals, including human. A pattern of enrichment and depletion of genic regions in the profiled segments suggests they are functionally significant, and most likely consist of various functional classes. Furthermore, a method of incorporating alignment characteristics representative of function such as GC content and type of mutation into the segmentation model is developed within this thesis. Evidence of fine-structured segmental variation is presented.
Guardian of the Line of Control

: Border security is very risky work to maintain the peace in the country and to prevent the enemies from entering the country illegally by crossing the border. This paper elaborates the solution by which the border security strength can be increased and the lives of the soldiers can be saved. This robot is based on the Raspberry Pi with different sensors for detection purpose and the camera is mounted on the robot for capturing the image of the suspect. Based on the input sensor the robot will move in that direction and will capture the image. After capturing the image , it will be attached to the message which will alert the control room nearby.
Ca2+ and nucleotide dependent regulation of voltage dependent anion channels in the plasma membrane of guard cells.

Using the patch‐clamp technique we discovered that the voltage dependent anion channels in the plasma membrane of guard cells are activated by a rise in cytoplasmic Ca2+ in the presence of nucleotides. Upon activation, these anion channels catalyse anion currents 10‐20 times higher than in the inactivated state, thus shifting the plasma membrane from a K+ conducting state to an anion conducting state. Prolonged stimulation by depolarizing voltages results in the inactivation of the anion current (t1/2 = 10‐12 s). We suggest that activation of the anion channel by Ca2+ and nucleotides is a key event in the regulation of salt efflux from guard cells during stomatal closure.