Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of biomarkers and pathways to identify novel therapeutic targets in Alzheimer’s disease: Insights from a systems biomedicine perspective

Alzheimer’s disease (AD) is a progressive neurodegenerative disease characterized by the accumulation of amyloid plaques and neurofibrillary tangles in the brain. However, there are no peripheral biomarkers available that can detect AD onset. This study aimed to identify such AD biomarkers through an integrative analysis of blood cell gene expression data. We used two microarray datasets (GSE4226 and GSE4229) comparing blood cell transcriptomes of AD patients and matched controls to identify differentially expressed genes (DEGs). Geneset and protein overrepresentation analysis, protein-protein interaction (PPI), DEGs-Transcription Factor interactions, DEGs-MicroRNAs interactions, protein-drug interactions, and protein subcellular localizations analyses were performed on DEGs common to the datasets. We identified 25 common DEGs between the two datasets. Integration of genome scale transcriptome datasets with biomolecular networks revealed hub genes (TUBB, ATF3, NOL6, UQCRC1, SND1, CASP2, BTF3, INPP5K, VCAM1, and CSTF1), common transcription factors (FOXC1, ZNF3, GEMIN7, and SMG9) and miRNAs (mir-20a-5p, mir-93-5p, mir-16-5p, let-7b-5p, mir-708-5p, mir-24-3p, mir-26b-5p, mir-17-5p, mir-4270, and mir-4441). These included 8 previously identified AD markers (BTF3, VCAM, FOXC1, mir-26b-5p, mir-20a-5p, mir-93-5p, let-7b-5p, mir-24-3p) and 13 novel AD biomarkers. Evaluation of histone modification revealed that hub genes and transcription factors possess several histone modification sites associated with AD. Protein-drug interactions revealed 10 compounds that affect the identified AD candidate markers, including anti-neoplastic agents (Vinorelbine, Vincristine, Vinblastine, Epothilone D, Epothilone B, CYT997, and ZEN-012), a dermatological (Podofilox) and an immunosuppressive agent (Colchicine). The subcellular localization of markers varied, including nuclear, plasma membrane and cytosolic proteins. This study identified blood-cell derived molecular biomarker signatures that might be useful as peripheral biomarkers in AD. This study also identified drug and epigenetic data associated with these molecules that may be useful in designing therapeutic approaches to ameliorate AD.
Order on disorder: Copper phthalocyanine thin films on technical substrates

We have studied the molecular orientation of the commonly used organic semiconductor copper phthalocyanine (CuPC) grown as thin films on the technically relevant substrates indium tin oxide, oxidized Si, and polycrystalline gold using polarization-dependent x-ray absorption spectroscopy, and compare the results with those obtained from single crystalline substrates [Au(110) and GeS(001)]. Surprisingly, the 20–50 nm thick CuPC films on the technical substrates are as highly ordered as on the single crystals. Importantly, however, the molecular orientation in the two cases is radically different: the CuPC molecules stand on the technical substrates and lie on the single crystalline substrates. The reasons for this and its consequences for our understanding of the behavior of CuPC films in devices are discussed.
Antecedents and outcomes of a City’s Global Image: the impact of a tourist staple

It is paramount to understand the impact of distinctive features in a city’s global image. This research was based on a questionnaire to tourists who visited Coimbra, Portugal (n=255), a city best known for its 727-year-old University. Results showed that the affective image and the personality of the University of Coimbra brand has a direct influence on the city’s global image as a tourist destination. Results also showed that the global destination image has a positive impact on satisfaction. Overall, there are impacts of memorable experience in affective image and of satisfaction in brand evangelism. A distinctive feature is forcedly an anchor for the city’s brand development; separate and unrelated brand strategies for a tourist staple and the city can be conflicting.
Smell Pittsburgh

Urban air pollution has been linked to various human health concerns, including cardiopulmonary diseases. Communities who suffer from poor air quality often rely on experts to identify pollution sources due to the lack of accessible tools. Taking this into account, we developed Smell Pittsburgh, a system that enables community members to report odors and track where these odors are frequently concentrated. All smell report data are publicly accessible online. These reports are also sent to the local health department and visualized on a map along with air quality data from monitoring stations. This visualization provides a comprehensive overview of the local pollution landscape. Additionally, with these reports and air quality data, we developed a model to predict upcoming smell events and send push notifications to inform communities. We also applied regression analysis to identify statistically significant effects of push notifications on user engagement. Our evaluation of this system demonstrates that engaging residents in documenting their experiences with pollution odors can help identify local air pollution patterns and can empower communities to advocate for better air quality. All citizen-contributed smell data are publicly accessible and can be downloaded from https://smellpgh.org.
SLUDGE DEWATERING AND DRYING

ABSTRACT The production of wastewater treatment sludge, the basic characteristics of the sludge and the state of the water in the sludge are described in this paper. The methods for the determination of bound water content are discussed. The literature (including patents) on sludge dewatering and drying is reviewed, including vacuum filters, belt presses, centrifuges, direct dryers, indirect dryers and combined mode drying systems. The issues related to drying are briefly discussed. Photographs or schematics of typical dewatering and drying systems are also included.
Causality-based Feature Selection

Feature selection is a crucial preprocessing step in data analytics and machine learning. Classical feature selection algorithms select features based on the correlations between predictive features and the class variable and do not attempt to capture causal relationships between them. It has been shown that the knowledge about the causal relationships between features and the class variable has potential benefits for building interpretable and robust prediction models, since causal relationships imply the underlying mechanism of a system. Consequently, causality-based feature selection has gradually attracted greater attentions and many algorithms have been proposed. In this article, we present a comprehensive review of recent advances in causality-based feature selection. To facilitate the development of new algorithms in the research area and make it easy for the comparisons between new methods and existing ones, we develop the first open-source package, called CausalFS, which consists of most of the representative causality-based feature selection algorithms (available at https://github.com/kuiy/CausalFS). Using CausalFS, we conduct extensive experiments to compare the representative algorithms with both synthetic and real-world datasets. Finally, we discuss some challenging problems to be tackled in future research.
EVIDENCE FOR NONMICROBIAL OXIDATION OF MANGANESE IN SOIL

Bacteria, isolated from Vermont soil samples, oxidized Mn(II) on a yeast extractmineral salts agar medium. Oxidation was found only in the stationary phase of growth, usually after at least 1 week of incubation. None of these bacteria caused oxidation when inoculated into sterilized soil. Oxidation was found, however, when a small amount of fresh soil suspension was incubated with the sterile soil. Oxidation of Cr(III) to Cr(VI) by Mn oxides in soil samples was used as a sensitive indicator of changes in levels of oxidized Mn in the soils. Manganous sulfate, added to field-moist Nellis loam (Typic Eutrochrept) and Eldridge loamy fine sand (Aquic Udorthent) samples, rapidly oxidized. Streptomycin, chloramphenicol, cyclohexamide, HgCl2, and toluene had little or no effect on this rapid oxidation. Sodium azide inhibited the oxidation of added Mn(II). But sodium azide and chloroform each reduced Mn oxides in untreated soils, indicating that inhibition of Mn oxidation by these substances cannot serve as proof for microbial oxidation of Mn. Oxidation of added Mn(II) by 14 northeast soil samples was shown to be proportional to the level of existing reactive Mn oxides. Arrhenius plots of rates of oxidation in a Nellis loam of added Mn(II) between 1 and 35°C showed that oxidation had nonbiological characteristics. Higher temperatures caused reduction of existing Mn oxides. Generally, oxidation of added Mn(II) was initially rapid, with no lag period. Oxidation is theorized to be autocatalytic involving specific adsorption of Mn(II) on existing Mn oxide surfaces.
Glia mediated ionic balance in the stem cell niche is required for the proper proliferation of neurogenic tissues and wiring of neural circuits

The cellular niche that surrounds stem cells modulates their self-renewal and proliferative properties. In the nervous system glial cells form part of the neural stem cell niche and express a wide variety of ion channels. While the physiological roles of ion channels in glia have been mainly studied in the mature nervous system, the contribution of glial ion channel function in the niche to nervous system development is poorly understood. To gain insight we explored the function of the Drosophila ClC-a chloride channel since its human ortholog CLCN2 is expressed in glial cells and impairment of its function results in neurodevelopmental disorders. We found ClC-a expressed in the niche in cortex glia. These glial cells are in close association with neurogenic tissues and also wrap neuronal cell bodies as they mature away from the niche. Characterization of loss of function ClC-a mutants showed these animals had smaller brains and widespread axon guidance defects. Here we show that ClC-a is required in cortex glia for the proliferation of neuroepithelial cells and neuroblasts, as well as for neuronal survival. We could also relate the axon guidance defects observed in photoreceptors to impaired proliferation in a neuroblast lineage that generates guidepost glial cells essential for this process. Taken together, our results show that ion channels expressed in glia forming part of the neural stem cell niche can have a significant impact on nervous system development. We propose that ion channels can non-autonomously modulate the number of neural progenitors and the progeny of neuroblast lineages, consequently affecting the correct assembly of neural circuits.
Dual prognostic role for 2-oxoglutarate oxygenases in ten diverse cancer types: Implications for cell cycle regulation and cell adhesion maintenance

Objectives Tumor hypoxia is associated with metastasis and resistance to chemotherapy and radiotherapy. Genes involved in oxygen-sensing are clinically relevant and have significant implications on prognosis. Methods We identified of two signatures, signature 1 (good prognosis) and signature 2 (adverse prognosis), each consisting of 5 genes using three pancreatic cancer cohorts (n=681). We validated the signatures’ performance in predicting survival in ten cancers using Cox regression and receiver operating characteristic (ROC) analyses. Results Signature 1 and signature 2 were associated with good and poor overall survival respectively. Prognosis of signature 1 in 8 cohorts representing 6 cancers (n=2,627): bladder (hazard ratio [HR]=0.68, P=0.039), papillary renal cell (HR=0.35, P=0.013), liver (HR=0.64, P=0.033 and HR=0.49, P=0.025), lung (HR=0.66, P=0.014) and pancreatic (HR=0.42, P<0.001 and HR=0.64, P=0.04) and endometrial (HR=0.40, P<0.001). Prognosis of signature 2 in 12 cohorts representing 9 cancers (n=4,134): bladder (HR=1.46, P=0.039), cervical (HR=1.97, P=0.035), head and neck (HR=1.39, P=0.038), renal clear cell (HR=1.47, P=0.012), papillary renal cell (HR=3.89, P=0.0015), liver (HR=5.10, P<0.0001 and HR=2.26, P<0.001), lung (HR=1.54, P=0.011), pancreatic (HR=2.09, P=0.002, HR=1.46, P=0.018, and HR=1.99, P<0.0001) and stomach (HR=1.78, P=0.004). Multivariate Cox regression confirmed independent clinical relevance of signatures in these cancers. ROC analyses confirmed superior performance of signatures to current tumor staging benchmarks. KDM8 is a potential tumor suppressor downregulated in liver and pancreatic cancers and is an independent prognostic factor. KDM8 expression negatively correlated with cell cycle regulators. Low KDM8 in tumors was associated with loss of cell adhesion phenotype through HNF4A signaling. Conclusions Pan-cancer signatures of oxygen-sensing genes used for risk assessment in 10 cancers (n=6,761) could guide individualized treatment plans.
Epigenetic switching as a strategy for quick adaptation while constraining biochemical noise

Epigenetic switches are bistable, molecular systems built from self-reinforcing feedback loops that can spontaneously switch between heritable phenotypes in the absence of DNA mutation. It has been hypothesized that epigenetic switches ﬁrst evolved as a mechanism of bet-hedging and adaptation, but the evolutionary trajectories and conditions by which an epigenetic switch can outcompete adaptation through genetic mutation remain unknown. Here, we used computer simulations to evolve a mechanistic, biophysical model of a self-activating genetic circuit, which can both adapt genetically through mutation and exhibit epigenetic switching. We evolved these genetic circuits under a ﬂuctuating environment that alternatively selected for low and high protein expression levels. In all tested conditions, the population ﬁrst evolved by genetic mutation to regimes of high nonlinearity to decrease the genetic adaptation time after each environmental transition. Once at high nonlinearity, epigenetic switching became accessible and could start competing with genetic adaptation as a possible strategy. We show the existence of a trade-off between either minimizing the adaptation time or increasing the robustness of the phenotype to biochemical noise. Epigenetic switching was superior in a fast ﬂuctuating environment because it adapted faster than genetic mutation after an environmental transition. Conversely, genetic adaptation was favored in a slowly ﬂuctuating environment because it minimized the noise load during the constant environment between transitions. These simple trade-offs reliably predict the conditions and trajectories under which an epigenetic switch evolved to outcompete genetic adaptation, shedding light on possible mechanisms by which bet-hedging strategies might emerge and persist in natural populations.
THEME-RHEME ANALYSIS ON THE JAKARTA POST NEWSPAPER: INTERPOLATIONS, PREPOSED ATTRIBUTIVE, AND REPORTED CLAUSE

This research focused on Theme and Rheme analysis, interpolations in Theme, preposed attributive, and Theme in reported clause. Theme and Rheme are concerned with organization within the clauses in a text. Theme is the beginning point of message and the Rheme explains more about the message from the Theme of the clauses. The aim of this research was to determine the type of Theme and Rheme. This research used qualitative method. The unit of the analysis of this research will be focused on every clause in the editorial on The Jakarta Post newspaper May 12nd 2019 edition entitled “ Handmade Boyolali sarong an Idul Fitri Tradition ” . The steps in analyzing the data were; segmenting the sentences into clauses, identifying the Theme and Rheme for each clause, determining the type of Theme and Rheme for each clause, and drawing conclusion. The result analysis found that there were three types of theme that were used namely Ideational/Topical, Textual and Interpersonal. The most dominant Theme was Topical followed by Textual and Interpersonal Themes. Besides, the used of Interpolations in Theme, Preposed Attributive, and Theme in Reposted Clause was also found.
Pengaruh Dukungan Sosial dan Orientasi Masa Depan Terhadap Penyesuaian Diri

Penelitian ini bertujuan untuk mengetahui pengaruh dukungan sosial dan orientasi masa depan terhadap penyesuaian diri santri di Pondok Pesantren Al-Aziziah Samarinda. Penelitian ini menggunakan pendekatan kuantitatif. Subjek penelitian ini adalah 115 siswa yang dipilih dengan menggunakan teknik total sampling. Metode pengumpulan data yang digunakan adalah skala dukungan sosial teman sebaya dan orientasi masa depan terhadap penyesuaian. Teknik analisis data menggunakan uji analisis regresi berganda dan uji analisis regresi parsial. Hasil penelitian menunjukkan bahwa: (1) terdapat pengaruh yang signifikan antara dukungan sosial dan orientasi masa depan terhadap penyesuaian diri santri di pondok pesantren Samarinda al-Aziziah, dengan hasil pengujian hipotesis menggunakan uji analisis regresi model (Fhitung> F tabel) = 26.647> 3.08, sesuaikan R square (R2 = 0.322); dan p = (0,000 <0,050). (2) terdapat pengaruh variabel dukungan sosial teman sebaya terhadap penyesuaian diri santri di pondok al-aziziah dengan nilai beta = 0,455, t hitung = 5675> 1,981 dan p = 0,000> 0,050; (3) terdapat pengaruh variabel orientasi masa depan terhadap penyesuaian diri santri di pondok al-aziziah dengan nilai beta = 0,245, t hitung = 3,052> 1,981 dan p = 0,003> 0,050.
The genomic architecture of introgression among sibling species of bacteria

Gene transfer between bacterial species is an important mechanism for adaptation. For example, sets of genes that confer the ability to form nitrogen-fixing root nodules on host plants have frequently moved betweenRhizobiumspecies. It is not clear, though, whether such transfer is exceptional, or if frequent inter-species introgression is typical. To address this, we sequenced the genomes of 196 isolates of theRhizobium leguminosarumspecies complex obtained from root nodules of white clover (Trifolium repens). Core gene phylogeny placed the isolates into five distinct genospecies that show high intra-genospecies recombination rates and remarkably different demographic histories. Most gene phylogenies were largely concordant with the genospecies, indicating that recent gene transfer between genospecies was rare. In contrast, very similar symbiosis gene sequences were found in two or more genospecies, suggesting recent horizontal transfer. The replication and conjugative transfer genes of the plasmids carrying the symbiosis genes showed a similar pattern, implying that introgression occurred by conjugative plasmid transfer. The only other regions that showed strong phylogenetic discordance with the genospecies classification were two small chromosomal clusters, one neighbouring a conjugative transfer system. Phage-related sequences were observed in the genomes, but appeared to have very limited impact on introgression.Introgression among these closely-related species has been very limited, confined to the symbiosis plasmids and a few chromosomal islands. Both introgress through conjugative transfer, but have been subject to different types of selective forces.
Dose Tracking Accuracy of the Dose on the Treatment Day using Cone-beam Computed Tomography for Radiation Therapy of Prostate Cancer: Pilot Study

Background : The benefit of cone-beam computed tomography (CBCT) is not only for pretreatment setup verification, but also their potential in providing the three-dimensional anatomical information to present the organ deformation and daily actual dose distribution. Objective: This study aimed to investigate the dose tracking on the treatment day for 5 volumetric modulated arc therapy (VMAT) prostate cancer patients using CBCT-based dose calculation. Materials and methods: The CBCT HU to electron density calibration curve was firstly generated. Then, the accuracy of CBCT-based dose calculation (DCBCT) was verified by comparing with dose measurements on CIRS pelvic phantom using IC (0.13cc) and Gafchromic EBT3 film. Velocity 3.2. 0 deformable image registration (DIR) software was applied to map organ contours from planning CT (PCT) to the fractionated CBCT and modified by the radiation oncologist. Isodose distribution on CBCT images was calculated and variation of the organ volume as well as the dosimetric parameters following the QUANTEC-guideline for the planning target volume (PTV) and organ at risks were collected and analyzed. Results: Point dose and dose distribution difference in phantom, between the measurements and DCBCT, 2.28% and 87.7% (3%/3mm) gamma passing rate was presented. In clinical investigation, the volume ratio of CBCT/PCT for PTV, bladder and rectum were found to be 1.04, 1.11 and 0.91. DCBCT was found to be deviated from DPCT about -8.26% for D95% of PTV, 1.12% and 9.12% for Dmean and V70Gy of bladder, 6.60%, and 7.10%, for Dmean and V70Gy of rectum, respectively. Conclusion: Dose tracking on treatment day using CBCT-based dose calculation and DIR to guide organ contouring is found to be feasible and adequate to predict the actual dose delivery to the VMAT prostate cancer.
Improving Students' Understanding of Molecular Structure through Broad-Based Use of Computer Models in the Undergraduate Organic Chemistry Lecture

Several articles suggest how to incorporate computer models into the organic chemistry laboratory, but relatively few papers discuss how to incorporate these models broadly into the organic chemistry lecture. Previous research has suggested that manipulating physical or computer models enhances student understanding; this study demonstrates that by simply viewing the appropriate manipulations performed by an educator on a computer model during a recitation period, students in both semesters of introductory organic chemistry performed significantly better on a post-test measuring understanding of molecular structure than those who did not view the computer models (OCHEM 1, p = 0.005, d = 0.98; OCHEM 2, p = 0.035, d = 0.75). The post-test results were also analyzed by topic: the topics that displayed the most significant differences in student scores were bond angle (OCHEM 1, p = 0.0003, d = 1.28; OCHEM 2, p = 0.03, d = 0.77) and 3-D properties (OCHEM 1, p = 0.06, d = 0.64; OCHEM 2, p = 0.04, d = 0.72), suc.
THE MECHANISM OF COPOLYMER RETENTION IN INTERACTIVE POLYMER CHROMATOGRAPHY. II. GRADIENT SEPARATION

The molecular-statistical theory of polymer solutions in confined media is applied to the conventional chromatographic theory of gradient elution. This approach leads to the prediction of the special mode of interactive polymer chromatography: gradient elution at critical point of adsorption. We demonstrate theoretically and experimentally that under appropriate conditions elution of each compositionally homogeneous fraction of copolymer occurs at the critical mobile phase composition. This critical mobile phase composition depends only on the local structure of the copolymer chain and is independent of its molecular weight. As a consequence, gradient elution produces the chemical composition distribution of the copolymer. The theory provides the quantitative conditions for statistical copolymer chains to have a single transition point. Equations describing relationships between the critical eluent composition and the chemical composition and microstructure of macromolecules are developed. The experimenta.